(Ara Kirakosyan, Peter B. Kaufman) Recent Advances (BookFi) PDF

Recent Advances in Plant Biotechnology
Ara Kirakosyan · Peter B. Kaufman
Recent Advances in Plant

Biotechnology
123
Ara Kirakosyan Peter B. Kaufman
University of Michigan University of Michigan
1150 W. Medical Center Dr. 1150 W. Medical Center Dr.
Ann Arbor MI 48109-0646 Ann Arbor MI 48109-0646
USA USA
[email protected] [email protected]
ISBN 978-1-4419-0193-4 e-ISBN 978-1-4419-0194-1

DOI 10.1007/978-1-4419-0194-1
Springer Dordrecht Heidelberg London New York
Library of Congress Control Number: 2009928135
c Springer Science+Business Media, LLC 2009

All rights reserved. This work may not be translated or copied in whole or in part without the written
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Printed on acid-free paper
Springer is part of Springer Science+Business Media (www.springer.com)

We dedicate this book to the memory of Ara
Kirakosyan’ parents, Anna and Benik
Kirakosyan, and to the memory of Peter B.
Kaufman’s wife, Hazel Kaufman.
Preface
Plant biotechnology applies to three major areas of plants and their uses: (1) control
of plant growth and development; (2) protection of plants against biotic and abiotic
stresses; and (3) expansion of ways by which specialty foods, biochemicals, and
pharmaceuticals are produced. The topic of recent advances in plant biotechnology
is ripe for consideration because of the rapid developments in this field that have
revolutionized our concepts of sustainable food production, cost-effective alter-
native energy strategies, environmental bioremediation, and production of plant-
derived medicines through plant cell biotechnology. Many of the more traditional
approaches to plant biotechnology are woefully out of date and even obsolete. Fresh
approaches are therefore required. To this end, we have brought together a group of
contributors who address the most recent advances in plant biotechnology and what
they mean for human progress, and hopefully, a more sustainable future.
Achievements today in plant biotechnology have already surpassed all previous
expectations. These are based on promising accomplishments in the last several
decades and the fact that plant biotechnology has emerged as an exciting area of
research by creating unprecedented opportunities for the manipulation of biological
systems. In connection with its recent advances, plant biotechnology now allows for
the transfer of a greater variety of genetic information in a more precise, controlled
manner. The potential for improving plant productivity and its proper use in agricul-
ture relies largely on newly developed DNA biotechnology and molecular markers.
A number of methods have been developed and validated in association with the
use of genetically transferred cultures in order to understand the genetics of specific
plant traits. Such relevant methods can be used to determine the markers that are
retained in genetically manipulated organisms and to determine the elimination of
marker genes. As a result, a number of transgenic plants have been developed with
beneficial characteristics and significant long-term potential to contribute both to
biotechnology and to fundamental studies. These techniques enable the selection
of successful genotypes, better isolation and cloning of favorable traits, and the
creation of transgenic organisms of importance to agriculture and industry.
We start the book by tracing the roots of plant biotechnology from the basic
sciences to current applications in the biological and agricultural sciences, indus-
try, and medicine. These widespread applications signal the fact that plant biotech-
nology is increasingly gaining in importance. This is because it impinges on so
vii
viii Preface
many facets of our lives, particularly in connection with global warming, alternative
energy initiatives, food production, and medicine. Our book would not be complete
unless we also addressed the fact that some aspects of plant biotechnology may have
some risks. These are covered in the last section.
The individual chapters of the book are organized according to the following
format: chapter title and contributors, abstract, introduction to the chapter, chapter
topics and text, and references cited for further reading. This format is designed in
order to help the reader to grasp and understand the inherent complexity of plant
biotechnology better.
The topics covered in this book will be of interest to plant biologists, biochemists,
molecular biologists, pharmacologists, and pharmacists; agronomists, plant breed-
ers, and geneticists; ethnobotanists, ecologists, and conservationists; medical prac-
titioners and nutritionists; and research investigators in industry, federal labs, and
universities.
Ann Arbor, MI Peter B. Kaufman

Ann Arbor, MI Ara Kirakosyan
Contents
Part I Plant Biotechnology from Inception to the Present

1 Overview of Plant Biotechnology from Its Early Roots
to the Present . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Ara Kirakosyan, Peter B. Kaufman, and Leland J. Cseke
2 The Use of Plant Cell Biotechnology for the Production
of Phytochemicals . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Ara Kirakosyan, Leland J. Cseke, and Peter B. Kaufman
3 Molecular Farming of Antibodies in Plants . . . . . . . . . . . . . 35
Rainer Fischer, Stefan Schillberg, and Richard M. Twyman
4 Use of Cyanobacterial Proteins to Engineer New Crops . . . . . . 65
Matias D. Zurbriggen, Néstor Carrillo, and Mohammad-Reza
Hajirezaei
5 Molecular Biology of Secondary Metabolism: Case Study
for Glycyrrhiza Plants . . . . . . . . . . . . . . . . . . . . . . . . . 89
Hiroaki Hayashi
Part II Applications of Plant Biotechnology in Agriculture

and Industry
6 New Developments in Agricultural and Industrial Plant
Biotechnology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
7 Phytoremediation: The Wave of the Future . . . . . . . . . . . . . 119
Jerry S. Succuro, Steven S. McDonald, and Casey R. Lu
8 Biotechnology of the Rhizosphere . . . . . . . . . . . . . . . . . . 137
Beatriz Ramos Solano, Jorge Barriuso Maicas,
and Javier Gutierrez Mañero
ix
x Contents
9 Plants as Sources of Energy . . . . . . . . . . . . . . . . . . . . . 163

Leland J. Cseke, Gopi K. Podila, Ara Kirakosyan,
and Peter B. Kaufman
Part III Use of Plant Secondary Metabolites in Medicine

and Nutrition
10 Interactions of Bioactive Plant Metabolites: Synergism,
Antagonism, and Additivity . . . . . . . . . . . . . . . . . . . . . 213
John Boik, Ara Kirakosyan, Peter B. Kaufman, E. Mitchell
Seymour, and Kevin Spelman
11 The Use of Selected Medicinal Herbs for Chemoprevention
and Treatment of Cancer, Parkinson’s Disease, Heart
Disease, and Depression . . . . . . . . . . . . . . . . . . . . . . . . 231
Maureen McKenzie, Carl Li, Peter B. Kaufman, E. Mitchell
Seymour, and Ara Kirakosyan
12 Regulating Phytonutrient Levels in Plants – Toward
Modification of Plant Metabolism for Human Health . . . . . . . 289
Ilan Levin
Part IV Risks and Benefits Associated with Plant Biotechnology

13 Risks and Benefits Associated with Genetically Modified
(GM) Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
Peter B. Kaufman, Soo Chul Chang, and Ara Kirakosyan
14 Risks Involved in the Use of Herbal Products . . . . . . . . . . . . 347
Peter B. Kaufman, Maureen McKenzie, and Ara Kirakosyan
15 Risks Associated with Overcollection of Medicinal Plants
in Natural Habitats . . . . . . . . . . . . . . . . . . . . . . . . . . 363
Maureen McKenzie, Ara Kirakosyan, and Peter B. Kaufman
16 The Potential of Biofumigants as Alternatives to Methyl
Bromide for the Control of Pest Infestation in Grain and
Dry Food Products . . . . . . . . . . . . . . . . . . . . . . . . . . 389
Eli Shaaya and Moshe Kostyukovsky
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 405
About the Authors
Ara Kirakosyan, Ph.D., D.Sc. is an associate professor of biology at Yerevan

State University, Armenia, and is currently a research investigator at the Univer-
sity of Michigan Medical School and University of Michigan Integrative Medicine
Program (MIM). He received a Ph.D. in molecular biology in 1993 and Doctor
of Science degree in biochemistry and biotechnology in 2007, both from Yerevan
State University, Armenia. Dr. Kirakosyan’s research on natural products of medic-
inal value in plants focuses on the molecular mechanism of secondary metabolite
biosynthesis in selected medicinal plant models. His primary research interests
focus on the uses of plant cell biotechnology to produce enhanced levels of medic-
inally important, value-added secondary metabolites in intact plants, and plant cell
cultures. These studies involve metabolic engineering coupled with integration of
functional genomics, metabolomics, transcriptomics, and large-scale biochemistry.
He carried out postdoctoral research in the Department of Pharmacognosy at Gifu
Pharmaceutical University, Gifu, Japan, under the supervision of Prof. Kenichiro
Inoue. The primary research topic was molecular biology of biosynthesis of sev-
eral secondary metabolites in plants, particularly this was applied to the sweet
triterpene glycyrrhizin in cell cultures of Glycyrrhiza glabra and dianthrones in
Hypericum perforatum. In addition, he took part in several visiting research inves-
tigator positions in Germany. First, he was a visiting scientist under collaborative
grant project DLR in Heinrich-Heine-University, Düsseldorf (project leader Prof.
Dr. W.A. Alfermann). The research here concerned a lignan anticancer project,
i.e., the production of cytotoxic lignans from Linum (flax). The second involved
a carbohydrate-engineering project as a DAAD Fellow in the Institute of Plant
Genetics and Crop Plant Research (IPK), Gatersleben, under supervision of Prof.
Dr. Uwe Sonnewald. His collaboration with US scientists started with the USDA-
founded project on plant cell biotechnology for the production of dianthrones in
cell/shoot cultures of H. perforatum (St. John’s wort). This research has been carried
out with Dr. Donna Gibson at USDA Agricultural Research Service, Plant Protec-
tion Research Unit, US Plant, Soil, and Nutrition Laboratory, Ithaca, New York,
USA. In 2002, he was a Fulbright Visiting Research Fellow at the University of
Michigan, Department of Molecular, Cellular, and Developmental Biology in the
Laboratory of Prof. Peter B. Kaufman. Dr. Kirakosyan is principal author of over
50 peer-reviewed research papers in professional journals and several chapters in
xi
xii About the Authors
books dealing with plant biotechnology and molecular biology. He is second author
of the best-selling book, Natural Products from Plants, 2nd edition (2006). Ara
Kirakosyan is a full member of the Phytochemical Society of Europe and European
Federation of Biotechnology. He serves as an editorial board member in the Open
Bioactive Compounds Journal, Bentham Science Publishers, and as an editor as
part of the editorial board of 19 scientific domains journals, Global Science Books
(GSB), Isleworth, UK. He has received several awards, fellowships, and research
grants from the United States, Japan, and the European Union.
Peter B. Kaufman, Ph.D., is a professor of biology emeritus in the Department
of Molecular, Cellular, and Developmental Biology (MCDB) at the University
of Michigan and is currently senior scientist, University of Michigan Integrative
Medicine Program (UMIM). He received his B.Sc. in plant science from Cornell
University in Ithaca, New York, in 1949 and his Ph.D. in plant biology from the Uni-
versity of California, Davis, in 1954 under the direction of Prof. Katherine Esau. He
did post-doctoral research as a Muelhaupt Fellow at Ohio State University, Colum-
bus, Ohio. He has been a visiting research scholar at University of Calgary, Alberta,
Canada; University of Saskatoon, Saskatoon, Canada; University of Colorado, Boul-
der, Colorado; Purdue University, West Lafayette, Indiana; USDA Plant Hormone
Laboratory, BARC-West, Beltsville, Maryland; Nagoya University, Nagoya, Japan;
Lund University, Lund, Sweden; International Rice Research Institute (IRRI) at Los
Banos, Philippines; and Hawaiian Sugar Cane Planters’ Association, Aiea Heights,
Hawaii. Dr. Kaufman is a fellow of the American Association for the Advance-
ment of Science and received the Distinguished Service Award from the American
Society for Gravitational and Space Biology (ASGSB) in 1995. He served on the
editorial board of Plant Physiology for 10 years and is the author of more than
220 research papers. He has published eight professional books to date and taught
popular courses on plants, people, and the environment, plant biotechnology, and
practical botany at the University of Michigan. He has received research grants
from the National Science Foundation (NSF), the National Aeronautics and Space
Administration (NASA), the US Department of Agriculture (USDA) BARD Pro-
gram with Israel, National Institutes of Health (NIH), Xylomed Research, Inc, and
Pfizer Pharmaceutical Research. He produced with help of Alfred Slote and Marcia
Jablonski a 20-part TV series entitled, “House Botanist.” He was past chairman
of the Michigan Natural Areas Council (MNAC), past president of the Michigan
Botanical Club (MBC), and former secretary-treasurer of the American Society for
Gravitational and Space Biology (ASGSB). He is currently doing research on nat-
ural products of medicinal value in plants in the University of Michigan Medical
School in the laboratory of Steven F. Bolling, M.D. and serves on the research staff
of UMIM.
Contributors
John Boik Department of Statistics Clark, Room S.264, Stanford University,

Stanford, CA, USA, [email protected]
Néstor Carrillo Instituto de Biologı́a Molecular y Celular de Rosario (IBR,

UNR/CONICET), División Biologı́a Molecular, Facultad de Ciencias Bioquı́micas
y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK
Rosario, Argentina, [email protected]
Soo Chul Chang University College, Yonsei University, Seoul 120-749, Korea,
[email protected]
Leland J. Cseke Department of Biological Sciences, The University of Alabama

in Huntsville. Huntsville, AL 35899, USA, [email protected]
Rainer Fischer Fraunhofer Institute for Molecular Biology and

Applied Ecology (IME), Forckenbeckstrasse 6, 52074 Aachen, Germany,
[email protected]
Mohammad-Reza Hajirezaei Leibniz-Institute of Plant Genetics and

Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany,
[email protected]
Hiroaki Hayashi School of Pharmacy. Iwate Medical University. 2-1-1

Nishitokuta, Yahaba, Iwate 028-3603, Japan, [email protected]
Peter B. Kaufman University of Michigan, Ann Arbor MI 48109-0646, USA,

[email protected]
Ara Kirakosyan University of Michigan, Ann Arbor, MI 48109-0646, USA,

[email protected]
Moshe Kostyukovsky ARO, the Volcani Center, Department of Food Science, Bet
Dagan, 50250, Israel, [email protected]
Ilan Levin Department of Vegetable Research, Institute of Plant Sciences, The

Volcani Center, Bet Dagan, Israel 50250, [email protected]
xiii
xiv Contributors
Carl Li Department of Social and Preventive Medicine, State University of

New York at Buffalo, Buffalo, NY 14214, USA, [email protected]
Casey R. Lu Department of Biological Sciences, Humboldt State University,
Arcata, CA 95521, USA, [email protected]
Jorge Barriuso Maicas Department of Environmental Sciences and Natural
Resources, Faculty of Pharmacy, University San Pablo CEU, Boadilla del Monte,
Madrid 28668, Spain, [email protected]
Javier Gutierrez Mañero Department of Environmental Sciences and Natural
Steven S. McDonald Winzler & Kelly Consulting Engineers, Eureka, CA 95501,
USA, [email protected]
Maureen McKenzie Denali BioTechnologies, L.L.C., 35555 Spur Highway, PMB
321, Soldotna, Alaska 99669, USA, [email protected]
Gopi K. Podila Department of Biological Sciences, The University of Alabama in
Huntsville. Huntsville, AL 35899, USA, [email protected]
Stefan Schillberg Fraunhofer Institute for Molecular Biology and
Applied Ecology (IME), Forckenbeckstrasse 6, 52074 Aachen, Germany,
[email protected]
E. Mitchell Seymour Department of Cardiac Surgery, , B560 MSRB II, University
of Michigan, Ann Arbor, MI 48109-0686, USA, [email protected]
Eli Shaaya ARO, the Volcani Center, Department of Food Science, Bet Dagan
50250, Israel, [email protected]
Beatriz Ramos Solano Department of Environmental Sciences and Natural
Kevin Spelman Botanical Healing Department, Tai Sophia Institute, 7750
Montpelier Rd, Laurel, MD 20723, USA, [email protected]
Jerry S. Succuro Department of Biological Sciences, Humboldt State University,
Arcata, CA 95521, USA, [email protected]
Richard M. Twyman Department of Biology, University of York, Heslington,
York, YO10 5DD, UK, [email protected]
Matias D. Zurbriggen Instituto de Biologı́a Molecular y Celular de Rosario
(IBR, UNR/CONICET), División Biologı́a Molecular, Facultad de Ciencias
Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531,
S2002LRK Rosario, Argentina, [email protected]
Chapter 1
Overview of Plant Biotechnology from Its Early
Roots to the Present
Abstract In this chapter, we first define what is meant by plant biotechnology.

We then trace the history from its earliest beginnings rooted in traditional plant
biotechnology, followed by classical plant biotechnology, and, currently, modern
plant biotechnology. Plant biotechnology is now center stage in the fields of alter-
native energy involving biogas production, bioremediation that cleans up polluted
land sites, integrative medicine that involves the use of natural products for treatment
of human diseases, sustainable agriculture that involves practices of organic farm-
ing, and genetic engineering of crop plants that are more productive and effective
in dealing with biotic and abiotic stresses. The primary toolbox of biotechnology
utilizes the latest methods of molecular biology, including genomics, proteomics,
metabolomics, and systems biology. It aims to develop economically feasible pro-
duction of specifically designed plants that are grown in a safe environment and
brought forth for agricultural, medical, and industrial applications.
1.1 What Is Plant Biotechnology All About?
Today, when science and technology are progressing at ever increasing speeds and
humankind is experiencing both positive and negative feedback from this progress,
the presentation of an overview of modern plant biotechnology concepts is highly
germane. Inherently, plant biotechnology, along with animal biotechnology, phar-
maceutical biotechnology, and nanotechnology, constitutes a part of what we term
biotechnology. An unprecedented series of successes in plant science, chemistry,
and molecular biology has occurred and shifted plant biotechnology to new direc-
tions. This means that the newer aspects of plant biotechnology seen today are
vastly different from our understanding of what constitutes the earlier, more tra-
ditional aspects of this field. The earlier ventures in biotechnology (traditional
biotechnology) were concerned with all types of cell cultures, as they were sources
of important products used by humans. These ventures included the making of beer
A. Kirakosyan (B)
University of Michigan, Ann Arbor, MI 48109-0646, USA
e-mail: [email protected]
A. Kirakosyan, P.B. Kaufman, Recent Advances in Plant Biotechnology, 3

DOI 10.1007/978-1-4419-0194-1_1, C Springer Science+Business Media, LLC 2009
4 A. Kirakosyan et al.
and wine, the making of bread, cheese, yogurt, and other milk products, as well as
the production of antibiotics, pharmaceuticals, and vaccines.
What has radically changed since these earlier discoveries in plant biotechnol-
ogy? With the advent of recombinant DNA technology and new approaches that
utilize genomics, metabolomics, proteomics, and systems biology strategies (Cseke
et al., 2006), it may now be possible to re-examine plant cell cultures as a reasonable
candidate for commercial production of high-value plant metabolites. This is espe-
cially true if natural resources are limited, de novo chemical synthesis is too com-
plex or unfeasible, or agricultural production of the plant is not possible to carry out
year-round. Indeed, a study of the biochemistry of plant natural products has many
practical applications. Thus, specific processes have now been designed to meet the
requirements of plant cell cultures in bioreactors. In addition, plant cells constitute
an effective system for the biotransformation involving the addition of various sub-
strates to the culture media in order to induce the formation of new products. The
specific enzymes participating in such biotransformation processes can furthermore
be isolated and characterized from cells immobilized on various solid support matri-
ces, such as fiber-reinforced biocers (e.g., aqueous silica nanosols and commercial
alumina fibers) that are now used in bioreactors.
Modern plant biotechnology research uses a number of different approaches that
include high-throughput methodologies for functional analyses at the level of genes,
proteins, and metabolites. Other methods are designed for genome modification
through homologous and site-specific recombination. The potential for including
plant productivity or agricultural trials is directly dependent upon the use of the new
molecular markers or DNA construct technology. Therefore, plant biotechnology
now allows for the transfer of an incredible amount of useful genetic information
in a much more highly controlled and targeted manner. This is especially important
for the use of GM (genetically modified) organisms, in spite of risks and limita-
tions that have been voiced by individuals and organizations not in favor of this
technology. It is noteworthy that a number of transgenic plants are being developed
for long-term potential use in fundamental plant science studies (Sonnewald, 2003).
Some of these transgenic plants also have significant and beneficial characteristics
that allow for their safe use in industry and agriculture. Biotechnological approaches
can selectively increase the amounts of naturally produced pesticides and defense
compounds in crop plants and thus reduce the need for costly and highly toxic pes-
ticides. This applies also to nutritionally important constituents in crops. The new
techniques from the gene and metabolic engineering toolbox will bring forth many
viable strategies to produce phytochemicals of medicinal and industrial uses.
Plant biotechnology research is, by nature, multidisciplinary. Systematic botany
and organic chemistry, for example, aim to elucidate the systematic position and
the evolutionary differentiation of many plant families. For instance, accurate and
simple determination of chemotaxonomy can be attributed to the science of describ-
ing plants by their chemical nature. This interdisciplinary scientific field combines
molecular phylogenetic analysis with metabolic profiling. Furthermore, it helps to
investigate the molecular phylogeny and taxonomy of plants and to investigate the
structural diversity of unique secondary metabolites found only in endemic species.
1 Overview of Plant Biotechnology 5
Besides the evaluation of some compounds as chemotaxonomic markers, one can

also focus on the structural elucidation of these unique secondary metabolites,
applying modern techniques of analysis.
We then come to the conclusion as to what plant biotechnology is all about:
it aims to impart an understanding of plant metabolism and how plant metabo-
Agricultural Industrial
Agronomic plants
Pharmaceuticals
Plant Biotechnology
Applications
Food Flavors
quality and
fragrances
Ornamental Insecticides
plants
Reproduction Natural dyes
Plant defense Oils
Fig. 1.1 A schematic representation of plant biotechnology applications

lite biosynthesis is regulated by particular enzymes, transcription factors, substrate

availability and end-products and to apply this understanding to the economically
feasible production of specifically designed plants that are grown in a safe envi-
ronment and brought forth for agricultural, medical, and industrial applications
(Fig. 1.1).
1.2 Tracing the Evolution of Classical Plant Biotechnology

Early in the twentieth century, plant cell culture was introduced (White, 1943, 1963).
It had applications in plant pathology (Braun, 1974), plant morphogenesis, plant
micropropagation, cytogenetics, and plant breeding. Then, protoplast culture was
discovered (Cocking, 1960). It had applications in studies on cell wall biosynthesis,
somatic cell hybridization, and genome manipulation (Power et al., 1970). Paral-
lel studies led to the discovery that the ratio of auxin and cytokinin type hormones
in tissue culture media largely determined whether one obtained shoots, roots, or
undifferentiated callus tissue using tobacco (Nicotiana tabacum) as the model sys-
tem (Miller and Skoog, 1953; Murashige and Skoog, 1962). These three discoveries
in the plant sciences became the cornerstones of classical plant biotechnology.
The earliest roots of classical plant biotechnology emanate from studies by
agronomists, horticulturists, plant breeders, plant physiologists, biochemists, ento-
mologists, plant pathologists, botanists, and pharmacists. Their primary aim has
been to solve practical problems associated with (1) the use of classical meth-
ods of plant breeding to develop new cultivars of plants that are resistant to plant
pathogens, insect pests, and environmental stresses due to cold, drought, or flood-
ing; (2) field-crop yield improvement, especially as related to the development of
green revolution crop plants and of faster growing, higher yielding forest trees; (3)
improvements in the postharvest storage and handling of crops; (4) the use of plant
hormones to improve rooting responses of cuttings, enhancement of seed germina-
tion, breaking seed dormancy, prolongation of seed viability, and improvements in
seed storage technology; (5) the employment of plant propagation (e.g., micropropa-
gation via cell and tissue culture, grafting of new cultivars of plants); and (6) the use
of plant natural products for human needs. These problems have been resolved suc-
cessfully, primarily due to achievements in plant biology and crop science research.
In connection with point (6) above, these earlier studies focused mainly on a descrip-
tion of the different kinds of natural products produced by plants. The pursuit of this
direction became more popular in the past decades because many of the chemically
synthesized constituents showed adverse effects on human health. Furthermore, for
some constituents, chemical synthesis is either impossible or a very complicated
and costly process.
Collectively, plants make a vast array of small-molecular-weight compounds.
Most of these natural products are generally not essential for the basic metabolic
processes of the plant but are often critical to the proper functioning of the plant in
relation to its environment. With at least 100,000 so far identified, the total number
of such compounds in the plant kingdom is estimated to be much higher. Plants are
capable of producing a variety of pharmaceuticals, adhesives, and compounds used

for cosmetics and food preparation. Scientists working in this field have already
discovered impressive amounts of potentially useful constituents with antibiotic,
anti-inflammatory, antiviral, anticancer, cardiovascular, and other activities.
Natural products are believed to play vital roles in the physiology and ecol-
ogy of plants that produce them, particularly as defense elements against pests
and pathogens, or as attractants for beneficial organisms such as insect pollinators
(Cseke et al., 2006). Most metabolites produced never leave the plant, but occa-
sionally plant compounds, some of which attract and some of which repel, are the
basis for a complex type of communication between plants and animals. Because
of their biological activities, some plant natural products have long been exploited
by human beings as pharmaceuticals, stimulants, and poisons. Therefore, there is an
immense interest in isolating, characterizing, and utilizing these metabolites. While
plant natural products hold a great deal of potential use for many human ailments,
they are often made in only trace amounts within the specific plant species that
produce them. Furthermore, the biosynthesis of the various metabolites proceeds
along metabolic pathways that are highly complicated and located in one or more
cell compartment(s) (e.g., cell walls, membrane systems, the cytosol, and various
cellular organelles) within tissues that are often specialized for particular tasks. The
specific enzymes that catalyze the respective steps in each metabolic pathway are
encoded in nuclear, chloroplast, or mitochondrial genomes by specific genes.
Plant scientists enthusiastically endorsed the idea that plant cell and protoplast
culture would eventually lead to the production of natural products using in vitro
plant cell suspension cultures in bioreactors, similar to those produced by microbial
and fungal cells cultivated in bioreactors. However, this expectation, in large part,
failed to materialize, even in spite of ingenious strategies that were developed (Zenk
et al., 1977). Only a few compounds were able to be successfully produced in plant
cell cultures scaled-up in bioreactors for industrial applications (Verpoorte et al.,
1994; Cseke et al., 2006). The main limitations were attributed to relatively slow
growth rates of plant cells in shaker or bioreactor cultures, low rates of synthesis of
desired products, and synthesis of compounds not present in intact plants. In fact,
it was discovered in the course of these studies that biosynthesis of many types of
plant metabolites occurs only in organized shoots or roots, but not in cell cultures
per se. Thus, in vitro shoot or root cultures became an alternative strategy for the
production of desired metabolites (Kirakosyan et al., 2004).
Many scientists have now combined extensive research experience using plant
cell cultures in order to develop the best strategies for biotechnological application.
This is enabling us to follow-up in greater detail points of interest, both theoretical
and practical. Consequently, the development of an information base on a cellular
and molecular level has been considered as a cornerstone of plant cell biotechnol-
ogy. Using established cell cultures, it is now possible to define the rate-limiting
step in biosynthesis by determining accumulation of presumed intermediates, char-
acterizing the limiting enzyme activity, and probably relating it to the corresponding
gene for eventual genetic manipulation. Generally, this approach works for known
pathways. Therefore, step-by-step identification of all enzymatic activities that are
specifically involved in the pathway is more appropriate and has been carried out
successfully. It is also quite common that blockage of one pathway leads to diver-
sion of the substrate to alternative pathways. This would make it very difficult to
identify the rate-limiting step in synthesis of a particular metabolite. It may also be
that the pathway is subject to developmentally controlled flux at entry, as for exam-
ple, through the activity of transcription factors. This kind of research must, there-
fore, focus on metabolic regulation by first establishing the pathways at the level
of intermediates and enzymes that catalyze their formation. The subsequent step is
the selection of targets for further studies at the level of the genes. This knowledge
is also of interest in connection with studies on the role of secondary metabolism
for plants and may contribute to a better understanding of resistance of plants to
diseases and various herbivores. In addition, cell suspension cultures are used for
biotransformation of added substrates, in order to search for new compounds not
present in the intact plant, and finally to use plant cells for the isolation of enzymes
that are responsible for the important metabolic pathways and to use them in chemi-
cal synthesis of natural products (reviewed by Alfermann and Petersen, 1995). Such
complex studies that are based on molecular regulation of metabolite biosynthesis
and on the creation of a systems biology type of information base may eventu-
ally lead to transgenic plants or plant cell cultures with improved productivity of
the desired compounds (Fig. 1.2). Plant cell culture may therefore be a reasonable
candidate for commercial realization if the natural resources are limited, de novo
synthesis is complex, and the product has a high commercial value.
The biochemical capability of cultivated plant cells to transform exogenously
supplied compounds offers a broad potential and can make an interesting contri-
bution toward the modification of natural and synthetic chemicals as well. This
attribute of plant cells is designated as in vivo enzymatic bioconversion. In many
cases, the enzymes involved in this process can be identified, purified, and immo-
bilized, and this accomplished by what is termed in vitro bioconversion. Then, the
enzymatic potential of the plants can be employed for bioconversion purposes. The
bioconversion process thus involves enzyme-catalyzed modification of added pre-
cursors into more desired or valuable products, using plant cells or specific enzymes
isolated from plants. This type of metabolite modification is particularly accurate
and is not so labor intensive. The biocatalyst may be free in solution, immobilized
on a solid support, or entrapped in a matrix. Systems applied for bioconversion can
consist of freely suspended cells, where precursors are supplied directly to cultures;
immobilized plant cells, which are useful especially for secondary metabolite pro-
duction but still need development to elicit an increase in the half-life of the cells;
and finally enzyme preparation and further usage, which take into account prob-
lems connected with enzyme stability and sufficiency. In bioconversions elicited by
whole cells or extracts, a single or several enzymes may be required for an action to
occur.
In the same context, as described above, two biocatalytic systems can be
employed in biotechnology. First, the catalysis of specific foreign substances, either
chemically prepared or isolated from nature, can be carried out by enzymatic con-
version outside the organisms. Second, bioconversion of a particular product uses
Desired plant
Application of Functional genomics

Cell Line Selection
20e6
10e6
Plant Cell
0e6
5.0 7.5 Biotechnology
Transcriptiomics Proteomics Metabolomics
Metabolic and Gene Engineering
End Product
Blocking competitive pathway or Amplification of target gene
introducing new pathway OH O OH
A B
HO O
HO CH3
HO R
O O
OH O OH
Fig. 1.2 Plant cell biotechnology for the production of high-value metabolites. The general steps
presented involve the creation of an information base with the application of functional genomics,
genetic and metabolic engineering of plant cells, and cultivation of modified plant cell lines in
bioreactors for high-value secondary metabolite production
either plant cell cultures or whole plants. Improved metabolite production can be
achieved by the addition of precursors to the culture medium. The advantages
here are that the pharmaceutical, agricultural, and speciality chemical industries
are increasingly requiring molecules that have distinct left- or right-handed forms,
so-called chiral compounds. For example, the production of single left- or right-
handed forms is not easy, and it is apparent that no single approach is likely to
dominate. Scientists must continue to draw upon the entire range of chemical, enzy-
matic, and whole-organism tools that are available to produce chiral compounds.
Despite some duplication in activity amongst enzymes, there is a need to charac-
terize more of them in order to exploit their unique specificity and activity. In this
regard, plant enzymes are able to catalyze regio- and stereo-specific reactions and
therefore can be used for the production of desired substances. Stereospecificity con-
cerns high optical purity (100% of one stereoisomeric form) of biologically active
molecules being catalyzed by plant enzymes. Regiospecificity allows for more pre-
cise conversion of one or more specific functional groups into others or, in the case
of precursor molecules, selective introduction of functional groups on nonactivated
positions.
In studies with the above-described plant cell cultures and their applications, we
must, however, emphasize that not all aspects are clear and well-studied. Fundamen-
tal and practical researches are ongoing because problems related to monitoring the
production of secondary metabolites in cell cultures still exist.
1.3 Modern Plant Biotechnology
Present-day studies are progressing in several different directions. It is notewor-

thy that each new plant gene, protein, or metabolite discovery may proffer sev-
eral applications for agricultural, food, or pharmaceutical industries. These studies
not only focus on the above topics but also utilize (1) genetically modified organ-
isms (GMOs), (2) molecular farming techniques, (3) sustainable agriculture strate-
gies, (4) production of green energy crops, (5) development of biological control
strategies that can replace or reduce the use of toxic pesticides via integrated pest
management schemes, (6) development of life-support systems in space, and (7)
development of plant-derived products for use in medicine. These are topics that
constitute the basis for recent advances in plant biotechnology. The current state
of plant biotechnology research, using a number of different approaches, includes
high-throughput methodologies for functional analysis at the levels of transcripts,
proteins, and metabolites and methods for genome modification by both homolo-
gous and site-specific recombination.
Genetic and metabolic engineering are playing a substantial role in the develop-
ment of agricultural biotechnology. This sector is therefore starting to move forward
successfully, especially in the last several decades. The production and growth of
improved cereals, vegetables, and fruits have been priority initiatives for agricul-
tural biotechnology. Significant contributions have been made by plant biotechnol-
ogists to develop new crops involving the tools of gene and metabolic engineering.
For example, scientists have been working on tomatoes that can be vine-ripened
and shipped without bruising. Others have been trying to improve tomatoes that
are processed for catsup, soups, pastes, or sauces by genetically engineering them
to contain more solids, be thicker, and to contain more lycopene, β-carotene, and
flavonoids, which provide the red color and medicinal value (Rein et al., 2006); see
also Chapter 12 by Ilan Levin. The production of improved or “value-added” toma-
toes, however, requires a long-term program involving multiple efforts. It is worth
pointing out here that earlier, traditional plant breeding was also able to accomplish
much of this improvement in tomato “germplasm.” A good example is heirloom
tomatoes, which have been passed down for generations.
The priorities are given for processing tomatoes with improved viscosity (thick-
ness and texture, meaning fewer tomatoes for the same amount of catsup), higher
soluble solids, better taste, improved color, and higher vitamin content. It also may
include enhancing overall flavor, sweetness, color, and health attributes. Calgene
was the first company to introduce a genetically improved tomato that ripens on
the vine without softening and has improved taste and texture. Here, antisense gene
technology was introduced to inhibit the polygalacturonase enzyme, which degrades
pectin in the cell wall. The classical example here is the first genetically engineered
slow-ripening tomato plant. It was commercially developed by Calgene Corp. in
Davis, CA, and was called “FlavR Saver.” This tomato has two distinct advantages
over other tomato cultivars: first, it has a longer shelf life in storage, and second, the
fruit of this tomato could be left on the plant until optimally ripe. Because of these
attributes, FlavR Saver tomatoes are sold for premium prices.
Another successful marketing initiative was concerned with oilseed crops.
Canola-producing laurate is the world’s first oilseed crop that has been genetically
engineered to modify oil composition. Similarly, Calgene isolated the gene responsi-
ble for laurate production from the California laurel (Umbellularia californica) tree.
This gene was then engineered into canola (Brassica napus and B. rapa), resulting
in the production of oil containing approximately 40% laurate – a fatty acid that is
found in the seed oils of only a few plant species, mostly coconut and palm ker-
nel oil from tropical regions. Laurate possesses unique properties, which make it
desirable in edible and industrial products. Lauric oil is ideal for use in the soap and
detergent industries, as it is responsible for the cleansing and sudsing properties of
shampoos, soaps, and detergents.
Other examples of transgenic agricultural crops include many plants, such as
potatoes with more starch and less water to prevent damage when they are mechan-
ically harvested, crops with low saturated oils, sweet mini-peppers, modified lignin
in paper pulp trees, pesticide-resistant plants, and frost-resistant fruits.
One of the important directions in plant biotechnology is the introduction of
genetically engineered organisms (GMOs) to the market. This is based on a desire
by consumers for more tasty and more healthy foods. It is also based on a prefer-
ence for products grown without using pesticides or other soil additives. However,
the choice of companies to keep the public ignorant of these genetic changes led to
a great scare in the public once people found out what was going on. It would have
been better if companies had informed the public prior to releasing any GMOs. As
a consequence of these events, the regulatory requirements and safety assessment
studies are far greater, not only in the United States but also worldwide.
An improvement in the quality or the composition of animal products has also
been achieved through modern plant biotechnology. This has resulted in increased
feed utilization and growth rate, improved carcass composition, improved milk pro-
duction and/or composition, and increased disease resistance.
Modern plant biotechnology is also playing a role in “clean” manufacturing. Nev-
ertheless, various types of chemical manufacturing, metal plating, wood preserving,
and petroleum refining industries currently generate hazardous wastes, comprising
volatile organics, chlorinated and petroleum hydrocarbons, solvents, and heavy met-
als. No one single plant species can handle all contaminants in any given environ-
ment. Rather, unique species have been found that can deal with a single or a few
contaminants in a particular medium. For example, plants have been found that can
break down or degrade organic contaminants (similar to microbes), while others are
able to extract and stabilize toxic metal contaminants by acting as traps or filters.
The ramifications of these phenomena for environmental cleanup (i.e., phytoremedi-
ation) were quickly realized. In theory, by simply growing a crop of the appropriate
plant at a given polluted site, the contaminant concentration could be lowered to
environmentally acceptable levels. This may involve several rotations of the plants,
and indeed, it may even be possible to use a combination of plants (and microbes,
too) to treat sites polluted with both heavy metals and organics. Chapter 7 discusses
these several aspects of phytoremediation in detail.
These and other advances in plant biotechnology not only allow us to gain knowl-
edge to answer fundamental questions in plant science but also make it possible for
us to create new applications in response to threats of global warming, evolution of
new resistant pests, development of new crop and forest species/cultivars and their
products, and changes in market/consumer demands and needs.
For human health benefits, new technologies are required to introduce more nat-
urally produced pharmaceuticals and vaccines. These may be possible if all aspects
of plant natural product chemistry, including the biosynthetic pathways and pos-
sible biotransformation reactions, are included. This is true also for health issues
where in-depth knowledge of molecular immunology, pharmacology, or related dis-
ciplines is required. Thus, plant biotechnology has a huge contribution to make for
the world economy, largely through the introduction of DNA or RNA technologies
to the production of biopharmaceuticals.
In summary, plant biotechnology concentrates much attention on the complex-
ity and interrelatedness of plant biology, with such targets as agricultural and
pharmaceutical biotechnology. Needless to say, and subject to clarification of cer-
tain ethical and public acceptance issues, plant biotechnology is also set to make
an indelible contribution to human health and welfare well into the foreseeable
future.
References
Alfermann, A.W., Petersen, M. 1995. Natural product formation by plant cell biotechnology. Plant
Cell Tissue Organ Cult 43: 199–205.
Braun, A.C. 1974. The biology of cancer. Addison-Wesley Publishing Co., Reading, MA.
Cocking, E.C. 1960. A method for isolation of plant protoplasts and vacuoles. Nature 187:
927–929.
Cseke, L., Kirakosyan, A., Kaufman, P., Warber, S., Duke, J., Brielmann, H. 2006. Natural products
from plants, 2nd ed. Taylor-Francis, CRC Press, Boca Raton, FL.
Kirakosyan, A., Sirvent, T.M., Gibson, D.M., Kaufman P.B. 2004. The production of hyper-
icins and hyperforin by in vitro cultures of Hypericum perforatum (Review). Biotechnol Appl
Biochem 39: 71–81.
Miller, C.O., Skoog, F. 1953. Chemical control of bud formation in tobacco stem segments.
Am J Bot 40: 768–773.
Murashige, T., Skoog, F. 1962. A revised medium for rapid growth and bioassays with tobacco
tissue cultures. Physiol Plant 15: 473–497.
Power, J.B., Cummins, S.E., Cocking, E.C. 1970. Fusion of plant protoplasts. Nature 225:
1016–1018.
Rein, D., Schijlen, E., Kooistra, T., Herbers, K., Verschuren, L., Hall, R., Sonnewald, U., Bovy, A.,
Kleemann, R. 2006. Transgenic flavonoid tomato Intake reduces C-reactive protein in human
C-reactive protein transgenic mice more than wild-type tomato. J Nutr 136: 2331–2337.
Sonnewald, U. 2003. Plant biotechnology: from basic science to industrial application. J Plant
Physiol 160: 723–725
Verpoorte, R., van der Heijden, R., Hoge, J.H.C., ten Hoopen, H.J.G. 1994. Plant cell biotechnol-
ogy for the production of secondary metabolites. Pure Appl Chem 66: 2307–2310.
White, P.R. 1943. Handbook of plant tissue culture. The Ronald Press Co., New York.
White, P.R. 1963. The cultivation of animal and plant cells, 2nd ed. Ronald, New York, 228p.
Zenk, M.H., El-Shagi, H., Arens, H., Stockigt, J., Weiler, E.W., Deus, B. 1977. Formation of
indole alkaloids serpentine and ajmalicine in cell suspension cultures of Catharanthus roseus.
(Barz, W., Reinhard, E., Zenk M.H., editors). In Plant tissue culture and its biotechnological
application. Springer Verlag, Berlin, Germany, pp. 27–43.
Chapter 2
The Use of Plant Cell Biotechnology
for the Production of Phytochemicals
Ara Kirakosyan, Leland J. Cseke, and Peter B. Kaufman
Abstract In this chapter, we bring together up-to-date information concerning

plant cell biotechnology and its applications. Because plants contain many valuable
secondary metabolites that are useful as drug sources (pharmaceuticals), natural
fungicides and insecticides (agrochemicals), natural food flavorings and coloring
agents (nutrition), and natural fragrances and oils (cosmetics), the production of
these phytochemicals through plant cell factories is an alternative and concurrent
approach to chemical synthesis. It also provides an alternative to extraction of these
metabolites from overcollected plant species. While plant cell cultures provide a
viable system for the production of these compounds in laboratories, its applica-
tion in industry is still limited due to frequently low yields of the metabolites of
interest or the feasibility of the bioprocess. A number of factors may contribute
to the efficiency of plant cells to produce desired compounds. Genetic stability
of cell lines, optimization of culture condition, tissue-diverse vs. tissue-specific
site-specific localization and biosynthesis of metabolites, organelle targeting, and
inducible vs. constitutive expression of specific genes should all be taken into
consideration when designing a plant-based production system. The major aims
for engineering secondary metabolism in plant cells are to increase the content
of desired secondary compounds, to lower the levels of undesirable compounds,
and to introduce novel compound production into specific plants. Recent achieve-
ments have also been made in altering various metabolic pathways by use of spe-
cific genes encoding biosynthetic enzymes or genes that encode regulatory proteins.
Gene and metabolic engineering approaches are now being used to successfully
achieve highest possible levels of value-added natural products in plant cell cul-
tures. Applications through functional genomics and systems biology make plant
cell biotechnology much more straightforward and more attractive than through pre-
vious, more traditional approaches.
A. Kirakosyan (B)

2.1 Plant Cell Factories as a Source of High-Value Metabolites

The presence of valuable metabolites in plants has stimulated interest on the part
of industry in the fields of pharmaceuticals (as drug sources), agrochemicals (for
the supply of natural fungicides and insecticides), nutrition (for the acquisition of
natural substances used for flavoring and coloring foods), and cosmetics (natural
fragrances and oils). The bulk of the market products, such as secondary metabo-
lites from higher plants, are collected from plants growing in the wild or from field-
cultivated sources. In using a plant strategy, major issues are that these plants need a
seasonal period of growth before harvesting is possible. Other issues here include a
relatively short growing seasons in temperate regions, disease and insect predation,
and high costs for labor and machinery. On the other hand, total chemical synthesis
of several compounds is possible, but economically not feasible. Therefore, an alter-
native, economically viable, and environmentally sustainable production source for
desired secondary metabolites is of great interest. In this regard, plant cell cultures
can be an attractive alternative as a production system, as well as a model system,
to study the regulation of natural product biosynthesis in plants so as to ultimately
increase yields.
The commercial-scale use of plant cell cultures is now progressing rapidly
despite many drawbacks and limitations that scientists have acknowledged. Earlier,
Verpoorte et al. (1994) had shown that biotechnological application of plant cell
cultures on a large scale may become economically feasible. The limitation here,
however, concerns the high price of the final product. This is mainly attributed to
the slow growth of plant cell cultures, making the depreciation costs of the bioreac-
tor a major cost-determining factor in future attempts (Verpoorte et al., 1994).
The detailed monitoring of functional status of cells is now routinely per-
formed for plant cell cultures in order to permit accurate assessment of growth and
metabolite production rates. The availability of plant cells for quantitative measure-
ment parameters makes possible the accurate assessment of a culture’s status and
places the analysis of cell cultures on a par with the detailed monitoring that has
been successfully applied for commercial microbial fermentations. The collected
information may enable identification and clearer understanding of the biological
and chemical constraints within the process, as well as optimization of cell culture
production, planning, costs, and scheduling activities. All of these factors are now
considered in relation to scale, geometry, and configuration of the bioreactor. In
addition, in vitro plant cell cultures are currently carried out for a diverse range of
bioreactor designs, ranging from batch, airlift, and stirred tank to perfusion and con-
tinuous flow systems. For a small scale of operation, both the conventional and the
novel bioreactor designs are relatively easy to operate. In contrast, for a larger scale
of operation, problems of maintaining bioreactor sterility and providing an adequate
oxygen supply to the cells have yet to be resolved (Vogel and Tadaro, 1997).
While industrial applications of plant cell cultures are still in progress, recently,
some promising advances have already been achieved for the production of several
high-value secondary metabolites through cell cultivation in bioreactors. For exam-
ple the valuable progress has been achieved for paclitaxel (Taxol), where yields have
2 Use of Plant Cell Biotechnology 17
improved more than 100-fold using multifactorial screening strategy (Roberts and
Shuler, 1997). Such progress, however, is not universal and many trials with differ-
ent cell cultures initially failed to produce high levels of the desired products. The
failure to produce high levels of desired metabolites by cell factories is still due to
our insufficient knowledge as to how plants regulate metabolite biosynthesis.
Earlier, Zenk and coworkers (1997) suggested a strategy to improve the pro-
duction of secondary metabolites in cell cultures that is now being used by many
researchers. This strategy includes the following general steps: (1) plant screening
for secondary metabolite accumulation; (2) use of high producer plants for initia-
tion of callus cultures; (3) biochemical analysis of derived cultures for their vari-
ability and productivity; (4) establishment of cell suspension cultures; (5) analysis
of metabolite levels in cell suspension cultures; (6) selection of cell lines based on
single cells; (7) analysis of culture stability; and (8) further improvement of product
yields.
How does this strategy work and does it raise the bars of current modern plant
biotechnology? Here, we will trace in detail the main points of such a strategy in
order to show how these steps may work and what limitations may still occur when
they are employed in modern plant biotechnology. As a part of such strategy, the
primary effort has been devoted to the development of cultures from elite germplasm
so as to take advantage of the wide range of biosynthetic capacities within cultures.
This has been achieved either by selection or by screening germplasm for highly
productive cell lines, as for example, in production of Taxol from Taxus cell cultures
(Kim et al., 2005). On the other hand, several limiting factors can play crucial role
for successful use of plant cell cultures in biotechnology. These limiting factors can
include light intensity and quality; temperature; length of culture period, including
kinetics of production; concentration and source of major limiting nutrients such as
phosphate, carbon, and nitrogen; and concentration and source of micronutrients,
vitamins, and plant growth regulators.
The other point concerns optimization of cell culture conditions. This has been
carried out for a variety of media formulations and environmental conditions. The
Plackett and Burman technique was particularly useful in these cases. It allows
for testing of multiple variables within a single experiment (Plackett and Burman,
1946). This method relies on the following characteristics: (1) each variable is tested
at a high level in half of the test cultures, or at a low level or not at all in the other
half; (2) any two variables are tested in 25% of the test cultures; (3) both will be
excluded in 25%; and (4) only one variable is tested in the remaining 50% of the test
cultures. Since the production of secondary metabolites can be followed by HPLC
or GC, a medium can be selected that supports good cell growth and production
of secondary metabolites. The role of the cell cycle in plant secondary metabolite
production must also be considered.
Screening of cell cultures for metabolite high productivity is carried out on sev-
eral levels. In some cases, high-producing cell clones are obtained from single cells,
and subsequently, these are used for screening high-producing strains. For rapid
selection of high-producing cells, some simple techniques are applicable. A good
example is flow cytometry, which may be useful. This technique is based on the fact
that cells contain fluorescent products (e.g., thiophenes), and therefore, it is possible
to separate these (marked) cells from others. However, some problems may occur
with cell line stability, especially as a result of cell differentiation or morphogene-
sis. Therefore, such stability problems of cell lines have probably made researchers
reluctant to develop extensive screening programs, leaving this as the last step prior
to an industrial application (Verpoorte, 1996). The fluorescent proteins from a wide
variety of marine organisms have initiated a revolution in the study of cell behavior
by providing convenient markers for gene expression and protein targeting in living
cells and organisms. The most widely used of these fluorescent proteins, the green
fluorescent protein (GFP), first isolated from the jellyfish Aequorea victoria, can be
attached to virtually any protein of interest and still fold into a fluorescent molecule.
Fluorescent proteins are increasingly being employed as noninvasive probes in liv-
ing cells due to their ability to be genetically fused to proteins of interest for investi-
gations of localization, transport, and dynamics. Martin Chalfie, Osamu Shimomura,
and Roger Y. Tsien share the 2008 Nobel Prize in Chemistry for their discovery and
development of molecular probe uses of the green fluorescent protein. To date, many
plant cells, along with other organisms, have been selected using GFP as a marker
for gene expression.
Alternatively, selection of high-producing cell lines by culturing cells on media
containing certain additives, such as biosynthetic precursors or toxic analogues, also
may be applied (Verpoorte, 1996). In this case, some instability of many precursors
or toxic effects of some constituents on the cells is, however, possible. Therefore, it
is not possible to use a universal screening platform for plant cell cultures. Instead,
a specific screening for a particular plant cell culture must be employed in order to
produce specifically desired metabolites.
Whether with plant cell cultures or with intact plants, the key to success in dis-
covering naturally occurring phytochemicals rests on bioassay-guided fractionation
and purification procedures. Generally, screening of both natural products and syn-
thetic organic compounds has led to impressive advances in the identification of
active agents. High-throughput screens and sensitive instrumentation for structural
elucidation have greatly reduced the amount of time and the sample quantity that
are required for analysis.
Still, the main criterion for future biotechnological success is connected to the
biosynthetic capacity of cell factories. It is well known that the biosynthesis of
plant secondary metabolites could be up- or downregulated by biotic and abiotic
factors. In order to unravel the regulation of plant metabolism by such environmen-
tal stimuli, it is important to elucidate the factors that control the accumulation of
secondary metabolites in plants. Therefore, nowadays, scientists are carrying out
intensive research efforts to identify and apply limiting factors that can ultimately
increase plant cells’ biosynthetic capacities. With such research, attention has also
been given to the accumulation and storage of desired secondary metabolites in
plant cells. Secondary metabolites in plants, and perhaps in tissue cultures, are
usually stored intracellularly, as for example, in vacuoles or multicellular cavities.
Thus, transporters probably play an important role in the sequestration of secondary
metabolites (Kunze et al., 2002).
Biotic factors are among the environmental factors that affect to a large extent
the production of phytochemicals. Therefore, it is highly probable that there is a
relationship with defensive responses that is manifested either in phytoalexin pro-
duction or in the production of compounds produced along one of the signal trans-
duction pathways. An approach to characterize the biotic parameters that may elicit
the plant’s defensive mechanisms may be revealed by an analysis of the expression
of certain genes involved in the process and by correlation of gene induction with
particular metabolite levels.
In addition to the strategy described above, new approaches based on genetic
and metabolic engineering have been successfully introduced (Verpoorte and
Alfermann, 2000). Consequently, the development of an information base on
genetic, cellular, and molecular levels is now a prerequisite for the use of plants
or plant cell cultures for biotechnological applications for the following reasons.
First, a better understanding of the basic metabolic processes involved could provide
key information needed to produce high-value metabolites. Second, many biosyn-
thetic pathways in plants are extensive and complicated, requiring multiple enzy-
matic steps to produce the desired end-product. So, when engineering secondary
metabolism in plant cells, the primary aim should be to increase the content of
desired secondary compounds, to lower the levels of undesirable compounds, and
finally to introduce novel compound production into specific plants. This kind of
research must, therefore, focus on metabolic regulation by first establishing the path-
ways at the level of intermediates and enzymes that catalyze secondary metabolite
formation (metabolic pathways profiling). The subsequent step is the selection of
targets for further studies at the level of genes, enzymes, and compartments. Such
studies on regulation of metabolite biosynthesis might eventually lead to the deriva-
tion of transgenic plants or plant cell cultures with an improved productivity of
the desired compounds. Aside from practical applications with such organisms,
the knowledge gained will be of interest in connection with studies on the adap-
tive/functional roles of secondary metabolism in plants. These are covered in the
next section that deals with functional genomics.
2.2 Applications Through the Use of Functional Genomics

Interdisciplinary approaches that are based on molecular biology and biochemistry
led to rapid advances in the identification of biosynthetic genes, the elucidation of
specific biosynthetic enzymes, and the identification of end-products. The complete
genetic makeup of an organism has been generated in the plant sciences as well.
Because of the success of large-scale quantitative biology projects such as genome
sequencing (genomics), the suffix “omics” has been extended to other directions.
Proteomics is now well-established as a term that refers to a study of the pro-
teome. More recently, metabolomics has been introduced, which is now leading to
an incredible amount of research on all kinds of primary and secondary metabolites
(Cseke et al., 2006). Thus, quantitative and qualitative measurements of all kinds
of cellular metabolites, or metabolomics, yield a global view of the biochemical
phenotype or phytochemical database for a plant organism. This can be used to

differentiate phenotypes and genotypes at a metabolite level that may or may not
produce visible phenotypes. Due to the diversity of plant secondary metabolites, it
is generally accepted that there is no single analytical method employed that can
provide sufficient visualization of the entire metabolome. Multiple technologies are
therefore needed to measure the entire metabolome of a given plant sample. Most
metabolomic approaches seek to profile metabolites in a nontargeted way, i.e., to
reliably separate and detect as many metabolites as possible in a single analysis.
This is technically challenging due to the diverse chemical properties and large dif-
ferences in the abundance of the metabolites. In contrast, selective profiling of a
certain group of compounds, which is also called targeted metabolic profiling, is
relatively easy to perform.
One of the major applications of genome sequencing of plants is functional
genomics. In simple words, an understanding of the function of genes and other
parts of the genome is known as functional genomics. It is a field of molecular
biology that attempts to make use of the vast amount of data produced by genomic
projects (such as genome sequencing projects) to describe gene (and protein) func-
tions and their interactions. Unlike genomics and proteomics, functional genomics
focuses on the dynamic aspects, such as gene transcription, translation, and protein–
protein interactions, as opposed to the static aspects of the genomic information such
as DNA sequences or structures (Cseke et al., 2006). It aims to determine the bio-
logical function of every gene within a given genome. Functional genomics, then,
refers to the development and application of global (genome-wide or system-wide)
experimental approaches to assess gene function by making use of the informa-
tion and reagents provided by structural genomics. Functional genomics includes
function-related aspects of the genome itself, such as mutation and polymorphism
analysis, as well as measurement of molecular activities. Together, all measurement
modalities quantify the various biological processes and powers in order to enhance
our understanding of gene, protein, and metabolite functions and their interactions
(Fig. 2.1).
Functional genomics uses mostly modern techniques to characterize the abun-
dance of gene products such as mRNAs and proteins. It is characterized by high-
throughput or large-scale experimental methodologies combined with statistical or
computational analysis of the results. Some typical technology platforms are DNA
microarrays and SAGE (serial analysis of gene expression) for mRNA analysis, two-
dimensional gel electrophoresis and mass spectrometry (MS) for protein analysis,
and targeting and nontargeting mass spectrometry and nuclear magnetic resonance
(NMR) analysis in metabolomics. Because of the large quantity of data produced
by these techniques and the desire to find biologically meaningful patterns, bioin-
formatics is used here for this type of analysis of complex systems. Bioinformat-
ics refers to the extraction of biological information from genomic sequence and
the reconciliation of multiple data sets based on DNA and RNA microarrays. In
connection with the above, a DNA microarray (also called a DNA chip or gene
chip) is a piece of glass or plastic on which pieces of DNA have been affixed in a
microscopic array to screen a biological sample for the presence of many genetic
Fig. 2.1 Application of Genomics Proteomics Transcriptomics Metabolomics

functional genomics tools in
plant cell biotechnology
Using Omics Database for the Selection of Target Genes,

Proteins and Metabolites
Reconstruction experiment
Plant Cell Biotechnology Application
sequences simultaneously. The affixed DNA segments are known as probes. Thou-
sands of identical probe molecules are affixed at each point in the array in order to
make the chips effective detectors. Many microarrays use PCR products, genomic
DNAs, BACs (bacterial chromosomes), plasmids, or longer oligos (35–70 bases)
instead of short oligonucleotide probes of 25 bases or less. RNA microarrays are
used to detect the presence of mRNAs that may have been transcribed from dif-
ferent genes and that encode different proteins. The RNA is converted to cDNA or
cRNA. The copies may be amplified by RT-PCR (reverse transcriptase-polymerase
chain reaction). Fluorescent tags are enzymatically incorporated into the newly syn-
thesized strands or can be chemically attached to the new strands of DNA or RNA.
A cDNA or cRNA molecule that contains a sequence complementary to one of the
single-stranded probe sequences will hybridize, or stick, via base pairing (more so
for DNA) to the spot at which the complementary probes are affixed. The spot will
then fluoresce, or glow, when examined using a microarray scanner. The major com-
ponents, then, of a functional genomics approach include bioinformatics (the global
assessment of how the expression of all genes in the genome varies under chang-
ing conditions), proteomics (the study of the total protein complement expressed
by a particular cell under particular conditions), and reverse genetics (deducing the
function of novel genes by mutating them and studying mutant phenotypes).
Functional genomics, used as a means of assessing phenotypes, differs from more
classical approaches, primarily with respect to the scale and automation of biologi-
cal investigations. A classical investigation of gene expression might examine how
the expression of a single gene varies with the development of an organism in vivo.
Modern functional genomics approaches, however, can examine how 1,000–10,000
genes are expressed as a function of development.
The massive expansion of available genomic information in plants allows
researchers to push the limits as to what can be produced by a chosen organ-
ism. Such technology continues to hold great promise for the future of plant
biotechnology. We now may simultaneously analyze the expression or silencing

of thousands of genes in plants or in plant cell lines, screen for high- and low-
producer lines of the desired phytochemical(s), or determine the full spectra of
metabolites. With advances in proteomics, we should also be able to simultane-
ously quantify the levels of many individual proteins or to follow posttranslational
alterations that occur. What are now needed are analogous analytical methods for
cataloging the global effects of metabolic engineering on metabolites, enzyme activ-
ities, and metabolite fluxes.
So far as we are aware, many limitations or drawbacks occur when investiga-
tors try to engineer plant cells. The question here concerns: what cannot be genet-
ically engineered? Our imagination creates thousands of possible applications for
plant genetic engineering. It is easy to imagine, for example, that we will be able to
derive coffee beans with less caffeine and with hazelnut aroma. Theoretically, that
is possible. However, nothing can be successfully accomplished here without unrav-
eling relevant gene expression phenomena, proteins with multifunctional tasks, or
metabolic networks in particular plant organisms. Let us consider the fact that there
are many identical genes in plants, animals, microorganisms, and even in humans.
However, they all have so many differences in terms of their functions. For this
reason, complex traits involving multiple functions are still impossible to geneti-
cally engineer without the use of a systems biology approach. The systems biol-
ogy approach has four known steps in general. The first step consists of gathering
various high-throughput data sets in addition to legacy data sets. All of these data
are then used in the second step to reconstruct the biochemical reaction networks
that underlie the cellular function of interest. When such data are put into the for-
mat of a biochemically, genetically, and genomically structured database, they have
a mathematical format consistent with the underlying physicochemical processes.
This mathematically structured database can then be mathematically interrogated
(step 3). Constraint-based methods can be used to perform such interrogation at the
genome- and network-scale levels. The mathematical computations are then used to
perform new experiments. In plant cell biotechnology, extensive metabolic profil-
ing must be more systematic and involve considerable analysis in this case. Due to
the productivity issue we have mentioned previously, gene or metabolic engineering
must be based on a systems biology approach involving integrated metabolomics,
proteomics, and transcriptomics approaches (Carrari et al., 2003; Dixon, 2005).
Likewise, metabolic engineering (see below) is a potentially very powerful tool in
plant cell biotechnology for the regulation of secondary metabolism in transgenic
plants or plant cell cultures, with potential to have wide applications in the phyto-
chemical industry or in agriculture (Verpoorte and Alfermann, 2000).
2.3 Metabolic Engineering
Plant metabolic engineering treats the cell as a factory and adds or optimizes kinds
and amounts of metabolites within the cell for some specific design purpose. In
other words, metabolic engineering refers to a targeted metabolic pathway being
elucidated in plant or bacterial organisms with the purpose of unraveling and uti-
lizing this pathway for future modification of a plant’s end-products. It is generally
defined as the redirection of enzymatic reactions so as to improve the production of
high-value constituents, to produce new compounds in an organism, to mediate the
degradation of environmentally toxic compounds, or to create plants that become
resistant to environmental stress factors. In addition, metabolic engineering may
include not only the manipulation of endogenous metabolic pathways but also the
transfer of metabolic pathways into new host organisms.
The main goals of metabolic engineering in industry or agriculture are the stim-
ulation of the production of secondary metabolite end-products, biosynthetic pre-
cursors, polymers that have plant origin, and the derivation of new plant organisms
with high salt or drought resistance in agriculture. It is not surprising that metabolic
engineering applications in plant biotechnology in recent years have had incredible
achievements in agriculture, industry, and medicine.
This multidisciplinary field draws concepts and methodologies from molecular
biology, biochemistry, and genetics, as well as biochemical engineering. In addi-
tion, the extension of metabolic engineering to produce desired compounds in plant
organisms may answer many fundamental questions applied to plant development,
physiology, and biochemistry. For example, plant metabolic flux analysis in the pri-
mary carbon-based metabolic pathways presents fundamental information on the
application of plant metabolic engineering that is based on a thorough knowledge
of plant biochemistry and plant physiology. Plant metabolism itself concerns thou-
sands of interacting pathways and processes that are regulated by environmental
and genetic stimuli. Therefore, engineering even known metabolic pathways will
not always provide the expected results. Despite major advances in metabolic engi-
neering, still only a few secondary metabolic pathways have been enzymatically
characterized and the corresponding genes cloned. In this context, the biosynthetic
pathways for alkaloids, flavonoids, and terpenoids are presently the best character-
ized ones at the enzyme and gene levels. More successful cases of gene discovery
have also been considered for the lipid biosynthetic pathway, where most genes in
plants encoding enzymes for fatty acid biosynthesis have been cloned. This informa-
tion was applied for eventual manipulation through modification of many fatty acids
in transgenic plants by means of metabolic engineering. As for targeting metabolite
manipulation, DellaPenna advocated the conversion or chemical modification of an
existing compound(s), rather than attempting to increase flux through a metabolic
pathway. Another example, he cites, claims that modifications made in the end-
products or secondary metabolic pathways have been generally more successful
than in cases where manipulation of primary and/or intermediary metabolic path-
ways is attempted (DellaPenna, 2001). Recent achievements have been made in the
altering of various pathways by use of specific genes encoding biosynthetic enzymes
or genes encoding regulatory proteins (Verpoorte and Memelink, 2002; Maliga and
Graham, 2004). Most current metabolic engineering studies have focused on manip-
ulations of enzyme levels and the effect of amplification, addition, or blockage of
a particular pathway. A new area is the manipulation of cofactors, which play a
major role in plant biochemistry and physiology and in the fermentation process
of several end-products. Additionally cofactors are essential for many enzymatic

reactions.
Metabolic engineering is becoming a powerful technology for the successful
implementation of plant cell biotechnology in the future. This may be possible with
the advances we already have mentioned above and some other important issues and
key criteria that are cited as follows: (1) Metabolic flux analysis must be applied to
well-documented and elucidated metabolic pathways; (2) extension of metabolic
cross-talk between the desired metabolite pathway and other pathways for a possi-
ble direct impact on plant development and nutritional value must be considered;
(3) identification of further elements in the complex regulatory network (such as
transcription factors and their binding partners) needs to be examined; and (4) rig-
orous criteria must be developed for the assessment of the risk and benefit perfor-
mance of engineered plants. Comprehensive studies in several directions may help
to bring metabolic engineering out of the trial-and-error era and transform it into
industrial applications.
Metabolic engineering approaches can be defined according to several different
directions (Fig. 2.2). The first appropriate approach involves increases in the total
carbon flux toward the desired secondary metabolite. In addition, decreasing the
flux through competitive pathways is an alternative way to increase the biosynthe-
sis of desired metabolite. Other possible directions involve the introduction of an
antisense gene of the competing enzyme at the branch point, as well as overcoming
rate-limiting steps, or blocking competitive pathways.
2.3.1 Increasing Total Carbon Flux Through Metabolic Pathways

Metabolic flux analysis determines the rate of carbon flow for each metabolic reac-
tion in a biochemical pathway. A method to quantify flux through metabolite mea-
surements is necessary for the analysis of original and modified pathways. Flux of
carbon into a given metabolite pathway, diversion of metabolic flux at intermedi-
ate branches, and lack of final conversion at the end of a specific branch all may
affect secondary metabolite production in plants. Therefore, it is important to iden-
tify points of possible flux limitation to be able to pursue pathway steps for genetic
modification.
The biosynthesis of secondary metabolites in plants can be regulated by increas-
ing the metabolic flux within cells through reconstruction experiments. In vivo,
resource allocation is often accomplished by controlling the flux of branch point
intermediates in metabolic networks. For example, Kleeb with coworkers used this
approach to optimize an in vivo selection system for the conversion of prephenate
to phenylpyruvate, a key step in the production of the essential aromatic amino acid
phenylalanine (Kleeb et al., 2007). Careful control of prephenate concentration in a
bacterial host lacking prephenate dehydratase, achieved through the provision of a
regulable enzyme that diverts it down a parallel biosynthetic pathway, provides the
means to systematically increase selection pressure on replacements of the miss-
ing catalyst. Successful differentiation of dehydratases, whose activities vary over
1.
A B C
Branch point Increasing Desired

Total flux metabolite
Over-expression of
enzymes (or transporters)
Competitive
2. pathway
CoA S
O
CCH 3
4 HS CoA4 CO2
O
S CoA
O
O
S CoA
O
HO
2
O
S CoA
O
A
Acetyl-CoA
4 CoA-S-C
O-CH-COOH
2
Malonyl-CoA
O
OO +
NADPHNA DP
HO
OO O O
Introducing
3 Malon y -l Co A
3 HS CoA, 3CO 2
anti-sense gene
O O O O
O O O O
S CoA
5 ’.-A -G-U -C-A -C-U -U -U -G-C-A -A -C-G-.3 ’

O
OOO
D
OOO
OHOOH
3 H O, HS CoA, CO
2 2
OH O OH
••••••••••••
Chrysophanolanthrone
CH 3
OHOOH
[O]
3 ’ - C - A - G -T -G -A - A - A - C -G -T - T- 5 ’
HO CH3
Emodinanthrone
[O]
OHOH O
R=CH hypericin
3 HO R
R=CH OH pseudohypericin R=CH3 emodin
2
Desired
HO CH3 R=CH OH -hydroxyemodin
2
R=COOH e mod ci acid
OHOOH
R
O
OH
B C
metabolite
New pathway
3. introduced
CH 3 B
A Modification of
B product to C
OH
C
Precursor
D
4. Catabolic
Enzymes B
A
Blocking
Catabolism
Plant C
Vacuole
Fig. 2.2 Approaches in metabolic engineering: (1) increase in the total carbon flux at the branch
point; (2) decrease in the flux through competitive pathways or introduction of an antisense gene
of the competing enzyme; (3) regulation of desired metabolite yield either by competitive path-
way determination and targeting of rate-limiting steps or by introduction of a new pathway; and
(4) blocking catabolism either by increasing the transport of metabolites into the vacuole or by
downregulation of catabolic enzymes
a >50,000-fold range, and the isolation of mechanistically informative prephenate

dehydratase variants from large protein libraries illustrate the potential of the engi-
neered selection strain for characterizing and evolving enzymes (Kleeb et al., 2007).
This approach complements other common methods for adjusting selection pressure
and may be generally applicable to plant systems that are based on the conversion
of an endogenous metabolite. There are several examples that have been reported
for well-characterized rate-limiting enzymes of plants and their controversial role in
the regulation of pathway flux (for review, see DellaPenna, 2001).
Analysis of a wide range of secondary metabolites has significant advantages as
compared to a study of final product(s) accumulation. However, this approach may
require fairly comprehensive study, because it is based on complex mathematical
formulations for metabolite network analysis. The data are gathered from extracel-
lular measurements of biomass composition, quantification of secreted metabolites,
substrate utilization, and intracellular measurements of carbon partitioning. Such
flux analysis may have some limitations due to the complexity of mathematical
modeling.
A very interesting model that organizes the flux analysis by grouping metabolites
of similar biosynthetic origin has been proposed by Morgan and Shanks (2002).
They have quantified temporal profiles of metabolites from several branches of
the indole alkaloid pathway in Catharanthus roseus (L.) G. Don (Madagascar
pink) hairy root cultures and were able to examine the distribution of flux around
key branch points. As a result, this analysis provides crucial information, such as
an estimate of total flux for all the secondary metabolites produced in a multi-
branched pathway. Another good example is the regulation of metabolic flux to
cellulose, a major sink for carbon in plants, as reported by Delmer and Haigler
(2002). As for many pathways, it is still unclear where carbon flux is rate-limited
in the complex cellulose biosynthetic pathway. Cellulose is an important compo-
nent of the cell walls of higher plants. As a major sink for carbon on the earth,
possible means by which the quality or the quantity of cellulose deposited in
various plant parts might be manipulated by metabolic engineering techniques is
a worthwhile goal (Delmer and Haigler, 2002). Thus, putative mechanisms for
regulation-altered flux through this pathway, as well as multiple genes for cellulose
biosynthesis and their regulation, provide targets for metabolic manipulations. How-
ever, possible variation in flux control under environmental influences must also be
considered.
2.3.2 Introduction of an Antisense Gene of the Competing Enzyme

at the Branch Point
Metabolic engineering of a zeaxanthin-rich potato by antisense inactivation and

cosuppression of carotenoid epoxidation is a classical example for this approach
(Romer et al., 2002). In order to provide a better supply of zeaxanthin in a sta-
ple crop, two different potato (Solanum tuberosum L.) cultivars were genetically
modified. Sense and antisense constructs encoding zeaxanthin epoxidase have been
transformed into the potato plant. Subsequently, zeaxanthin conversion to violax-
anthin was inhibited. In this study, both approaches (antisense and cosuppres-
sion) yielded potato tubers with higher levels of zeaxanthin, up to 40 μg·g–1
dry weight. As a consequence of this metabolic engineering manipulation, the

amount of violaxanthin was diminished dramatically, and in some cases, the monoe-
poxy intermediate, antheraxanthin, accumulated (Romer et al., 2002). Most of
the transformants with higher zeaxanthin levels showed simultaneous increases in
total carotenoid content (up to 5.7-fold). The increase in total carotenoids sug-
gests that the genetic modification affects the regulation of the whole carotenoid
biosynthetic pathway in potato tubers, involving substantial higher phytoene syn-
thase and a slight increase of the β-carotene hydroxylase transcripts levels in
tubers.
Recent work has also led to the identification of a transcriptional regulator
that is possibly involved in the control of carotenogenesis (Welsch et al., 2007).
Another mechanism controlling carotenoid levels in plant tissues is their degrada-
tion (Ohmiya et al., 2006). The generality of such a mechanism remains to be tested,
but it could provide an additional approach for biotechnological improvement of
carotenoid synthesis. This is important because carotenoids are members of one
of the most diverse classes of natural compounds. Plant carotenoids are composed
of a C40 isoprenoid skeleton with or without epoxy, hydroxy, and keto groups. They
are high-value compounds in human nutrition as antioxidants and vitamin A precur-
sors. In previous years, several metabolic engineering efforts have been undertaken
in edible plants, again with the aim to improve their nutritional value (for review,
see Giuliano et al., 2008).
2.3.3 Overcoming Rate-Limiting Steps
The most important aspects in metabolic engineering are to identify enzymes that
may be involved in intermediate biosynthesis and subsequently to determine if
any of these may occur at regulatory steps, or as now named rate-limiting steps.
Such determinations may play a key role in future manipulation of secondary
metabolite biosynthesis, because rate-limiting steps can be considered as docking
targets.
For known metabolic pathways, the single-gene approach is an excellent way
to find out where a rate-limiting step occurs. However, if pathway architecture is
quite complicated, it raises the bar from the linear to a complex network. The anal-
ysis should therefore start with a step-by-step identification of all enzymatic activ-
ities that are specifically involved in the pathway. As we have mentioned, blockage
of one pathway may lead to diversion of the substrate to alternative pathways. In
such a situation, the identification of the rate-limiting step for biosynthesis of a par-
ticular metabolite may be difficult and become a “fishing expedition.” Therefore,
pathway architecture is one of the important factors that will allow one to deter-
mine the most suitable approach for engineering plant cells. It may also be that
the pathway is subject to developmentally controlled flux at entry, as for example,
through the activity of transcription factors. Several other factors, such as regula-
tory mechanisms or compartmentation, can also play a significant role. Thus, reg-
ulatory mechanisms such as feedback regulation may affect secondary metabolite
yield in plants. This is especially relevant with the single-gene approach. In con-
trast, with heterologous gene overexpression, a heterologous enzyme is shown to
be operative and, because of this, may have no feedback inhibition by downstream
products. Such an enzyme may be introduced from another source (Chartrain et al.,
2000). Compartmentation also plays a major role in the regulation of secondary
metabolite pathways because some important pathways occur in compartments
(Verpoorte et al., 1999). for example, the biosynthesis of terpenoid-type indole
alkaloids requires at least three compartments: the plastids for the terpenoid moi-
ety and tryptophan, the cytosol for decarboxylation of tryptophan, and the vacuole
for the coupling of tryptamine with secologanin (Verpoorte et al., 1999). Simi-
lar rules are shown for plant folate biosynthesis pathway, where it is split among
cytosol, mitochondria, and chloroplasts. For example, in pea leaves, folate is dis-
tributed among mitochondria (highest concentration), chloroplasts, and a fraction
consisting of the cytosol, nucleus, and vacuole (Gambonnet et al., 2001). Folates
and their biosynthetic intermediates must therefore move in and out of organelles,
thus requiring unraveling of its transport mechanisms. Since nothing is known about
folate or its precursor carrier, identifying and cloning some transporters have been
considered to be a priority for metabolic engineering of plant folate biosynthesis
(Basset et al., 2005). It may be based either on modification of folate transport
or on compartmentation. The engineering of folate transport, as reported by the
same authors, is also a potential strategy to prevent and stockpile folate within
an “inert” compartment like the vacuole. As the folate biosynthetic enzymes are
not present in the vacuole, it may be possible to accumulate folate without feed-
back inhibition of its synthesis by directing folate import into this organelle (Basset
et al., 2005).
Another example concerns plant polyketides and their biosynthesis. The plant
polyketide synthases, like most enzymes, display broad substrate specificity. Using
alternative substrates is the most straightforward and powerful approach to gener-
ate new polyketides in vitro. Initial efforts here also focus on how active site vari-
ation among enzymes making various molecules leads to product specificity. For
example, modification of the octaketide-producing polyketide synthase from Aloe
arborescens Mill. leads to a variety of octaketide products, which were produced by
certain bacteria polyketide synthases (for review, see Yu and Jez, 2008). Similarly,
three substitutions in chromone synthase, which make a pentaketide, triple the vol-
ume of the active site and result in synthesis of the nonaketide naphthopyrone from
nine malonyl CoA molecules (Yu and Jez, 2008).
Deletion of a key biosynthetic enzyme can severely affect metabolite flux within
a pathway. For example, the flow of precursors into the disrupted pathway often
results in the accumulation of one or more intermediates upstream of the blocked
step. This is because elevated concentrations of the substrate for the missing enzyme
boost nonenzymatic background reactions and favor the appearance of enzyme vari-
ants with low substrate affinity. Such problems can be minimized, or even elim-
inated, through metabolic engineering, where, for example, excess substrate can
be efficiently removed from cellular metabolism by providing a second enzyme to
channel it away from the blocked step (Kleeb et al., 2007).
2.3.4 Blocking Catabolism or Competitive Pathways

Generally, metabolic pathways contribute to catabolism – the oxidative degrada-
tion of molecules – and anabolism – the reductive synthesis of molecules. In this
regard, the catabolic or anabolic nature of the pathways must be revealed prior to
any reconstruction experiment. Since little is known about catabolism in secondary
metabolite pathways, there is an important question as to whether catabolism is an
important factor in secondary metabolite pathways for limiting product accumula-
tion. Interesting questions are also raised concerning the possible toxicity of some
compounds to plant cells and the role of catabolism in detoxification mechanisms.
In this context, naturally occurring storage compartments (e.g., vacuole(s) and plas-
tid(s) in plant cells) may play a key role in preventing secondary metabolites from
being catabolized. Catabolism thus may be an important factor in metabolic engi-
neering. A remarkable observation was made in plant cell cultures of C. roseusby
Dos Santos et al. (1994) concerning equality of the rate of catabolism with the rate
of de novo compound biosynthesis. The phenomenon of catabolism in secondary
metabolites has not been studied very extensively, and still few enzymes have been
characterized in catabolism of most secondary metabolites (Verpoorte et al., 2000).
Catabolism can be blocked by antisense genes or even by using some antibodies.
Blocking competitive pathways is also powerful tool to increase desired metabo-
lite yield. Isoflavone levels in Glycine max (L.) Merr. (soybean) have been increased
via metabolic engineering of the complex phenylpropanoid biosynthetic pathway
(Yu et al., 2003). Phenylpropanoid pathway genes were activated by the expres-
sion of the maize C1 and R transcription factors in soybean seeds, which decreased
genistein and increased the daidzein levels, with a small overall increase in total
isoflavone levels. Cosuppression of flavanone 3-hydroxylase to block the antho-
cyanin branch of the pathway, in conjunction with C1/R expression, resulted in
higher levels of isoflavones (Yu et al., 2003). The combination of transcription
factor-driven gene activation and suppression of a competing pathway provided a
successful means of enhancing accumulation of isoflavones in soybean seeds.
2.3.5 Inverse Metabolic Engineering

In contrast to classical metabolic engineering, where manipulation of known genes
affects metabolic pathways with possible systematic changes, inverse metabolic
engineering (IME) aims to identify and construct desired cell phenotypes of inter-
est so as to incorporate them into appropriate host organisms. The concept of
inverse metabolic engineering was first introduced by Bailey et al. (1996). The key
element of this concept is identification of the molecular basis of a desired pheno-
type and its subsequent transfer to an appropriate host organism. Generally the fol-
lowing approaches may be involved: (1) the identification of desired phenotype,
(2) determination of the influence of environmental or genetic factors on phenotype
sustainability, and (3) alteration of the phenotype of the selected host by genetic
manipulation.
IME is a powerful framework for engineering cellular phenotypes (Bailey et al.,

2002). Such cell phenotypes, for example, may be chosen based on the accumu-
lation of a desired metabolite. In order to discover cells with the most desirable
properties, the cells must be screened genetically to identify the genetic basis of
the relevant phenotype. It allows determination of particular genetic modifications
that could not be discovered with a more directed technique. Recent advances in
functional genomics, described in Section 2.2, have dramatically improved our
ability to relate changes in phenotype with associated changes in genotype. As a
result, inverse metabolic engineering can be a method for discovering new genes
to target with traditional metabolic engineering. Thus, the first step is to find
the genes that underlie the relevant phenotypes. Genetic selection or screenings,
together with conventional gene sequencing, may be used to identify such genes in
mutations.
While IME was initially designed for prokaryotes, nowadays its application
applies to plant or other eukaryotic organism’s cells also. The best example
described by Sauer and Schlattner (2004) concerns the ATP homeostasis exhibited
by animal cells. A variable ATP turnover in these cells is achieved through tempo-
ral and spatial energy buffering, where phosphagen kinase systems (consisting of
specific kinase and its cognate phosphagen) function as a large pool of high-energy
phosphates that are used to replenish ATP during periods of high energetic demand.
Thus, these authors suggest the use of recent advances and potentials of inverse
metabolic engineering of cell types that do not normally contain such systems (bac-
teria, yeast, and plants) in conjunction with creatine or arginine kinase systems
(Sauer and Schlattner, 2004). Beyond such applications in bioprocess engineering,
engineering of phosphagen kinase systems is potentially important for medical and
pharmaceutical applications. The advantage of inverse metabolic engineering may
be more applicable if we can rationally modify a given phenotype to engineer cell
behavior.
2.4 Development of Genetically Modified Plants That Express

Resistance to Different Kinds of Abiotic and Biotic Stresses
Environmental stresses (e.g., high salt levels, low water availability that leads to
drought, excess water that leads to flooding, or high- and low-temperature regimes)
can adversely affect plant growth and productivity. The genetic or epigenetic
responses of plants to these stresses are complex because they involve simultane-
ous expression of a number of genes or physiological reactions. Continuing efforts
of scientists have resulted in engineering of plants resistant to high temperatures,
low temperatures, and excess salinity. Some progress has also been achieved in gen-
erating plants resistant to water-deficit stress and to flooding. While such achieve-
ments are impressive, it is still a challenging task to understand complex functional
genetic resistance responses to such stresses. Here, metabolic engineering can play
an important role. The limiting factor in this aspect is the lack of information on
what are the “useful genes”, i.e., genes that would lead to better stress tolerance.
Metabolic engineering of rice leading to biosynthesis of glycine betaine and tol-

erance to salt and cold is one of the best examples in this field. Genetically engi-
neered rice (Oryza sativa L.) with the ability to synthesize glycine betaine was
established by introducing the codA gene for choline oxidase from the soil bac-
terium Arthrobacter globiformis (Sakamoto and Murata, 1998). This study indicates
that the subcellular compartmentalization of the biosynthesis of glycine betaine was
a critical element in the efficient enhancement of tolerance to salt and cold stresses
in the engineered rice plants.
Metabolic engineering to accumulate osmoprotectants in plants may increase
their drought and salinity tolerance. An effective mechanism to reduce damage
from these stresses is brought about by the accumulation of high intracellular lev-
els of osmoprotectant compounds including proline, ectoine, betaines, polyols, and
trehalose. Engineering osmoprotectant biosynthesis pathways is a potential way to
improve stress tolerance (Rontein et al., 2002). Several single genes for such osmo-
protectant pathways have been successfully introduced into several plants, including
rice (O. sativa L.), canola (Brassica napus L.), potato (S. tuberosum L.), tobacco
(Nicotiana tabacum L.), and Arabidopsis, to improve their stress tolerance.
Another possible mechanism by which plants could survive salt stress is achieved
by compartmentalization of sodium ions apart from the cytosol. Overexpression
of a vacuolar Na super(+)/H super(+) antiport from Arabidopsis thaliana (L.)
Heynh. in Arabidopsis plants promotes sustained growth and development in the
soil/water environment. This salinity tolerance was correlated with higher-than-
normal levels of AtNHX1 transcripts, protein, and vacuolar Na super(+)/H super(+)
(sodium/proton) antiport activity, as reported by Apse et al. (1999). These results
demonstrate the feasibility of metabolic engineering for salt tolerance in plants.
Improving plant drought, salt, and freezing tolerance by gene transfer of a single
stress-inducible transcription factor has also been reported to be successful (Kasuga
et al., 1999). Overexpression of the cDNA encoding this transcriptional factor in
transgenic plants activated the expression of many of these stress-tolerant genes
under normal growing conditions and resulted in improved tolerance to drought,
salt loading, and freezing.
Application of metabolic engineering to improve tolerance against UV radia-
tion, intensive high light intensities, and high temperatures has been reported for
Arabidopsis plants (Giuliano et al., 2008). Leaf carotenoids may have essential pho-
toprotective roles, because they scavenge reactive oxygen species (ROS), quench
dangerous triplet states of chlorophyll, and participate in thermal dissipation of
excess light energy. For example, zeaxanthin that is formed as a result of violaxan-
thin de-epoxidation under high irradiances enhances nonphotochemical quenching
(NPQ) of chlorophyll fluorescence and protects membrane lipids from peroxidation.
Thus, it is not surprising that genetically engineered Arabidopsis in which all leaf
xanthophylls have been substituted with zeaxanthin shows more resistance to pho-
tooxidative stress and lipid peroxidation (Giuliano et al., 2008). However, due to
genetic manipulations that may increase the levels of several β-xanthophylls simul-
taneously, each may have distinct photoprotective roles and therefore must be con-
sidered in future applications.
Improving resistance against pests or diseases also leads to improved yields. For
resistance against pathogenic microorganisms, metabolic engineering can program
for the expression of high levels of defense compounds, such as phytoalexins, or for
pest resistance, improve the production of endogenous defense compounds (e.g.,
pathogenesis-related proteins), or introduce genes that produce new toxic com-
pounds (e.g., the “B.T.” gene from Bacillus thuringiensis that produces a toxic crys-
talline protein that interrupts digestion in many types of feeding insect pests) into
plants to control insect predators.
References
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Bailey, J.E., Sburlati, A., Hatzimanikatis, V., Lee, K.H., Renner, W.A., Tsai, P.S. 1996. Inverse
metabolic engineering: a strategy for directed genetic engineering of useful phenotypes.
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Bailey, J.E., Sburlati, A., Hatzimanikatis, V., Lee, K., Renner, W.A., Tsai, P.S. 2002. Inverse
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Chapter 3
Molecular Farming of Antibodies in Plants
Rainer Fischer, Stefan Schillberg, and Richard M. Twyman
Abstract Biopharmaceuticals are produced predominantly in microbial or

mammalian bioreactor systems. Over the last few years, however, it has become
clear that plants have great potential for economical, large-scale biopharmaceutical
production. Following the commercial release of several maize-derived technical
proteins, the first plant-derived veterinary vaccine was approved in 2006. Plants
offer the prospect of inexpensive production without sacrificing product quality or
safety. The first therapeutic products for use in humans – mostly antibodies and vac-
cine candidates – are now at the clinical trials stage. In this chapter, we discuss the
different plant-based production systems that have been used to synthesize recombi-
nant antibodies and to evaluate the merits of plants compared with other platforms.
Despite the currently unclear regulatory framework, the benefits of plant-derived
systems are now bringing the prospect of inexpensive recombinant antibodies closer
than ever before.
3.1 Introduction
Antibodies are multisubunit glycoproteins produced by the vertebrate immune sys-

tem. They recognize and bind to their target antigens with great affinity and speci-
ficity, which allows them to be used for many applications, including the diagnosis,
prevention, and treatment of human and animal disease (Andersen and Krummen,
2003; Chadd and Chamow, 2001; Fischer and Emans, 2000). It is estimated that
approximately 1,000 therapeutic recombinant antibodies are under development,
up to one-quarter of which may already be undergoing clinical trials. A large pro-
portion of these antibodies recognize cancer antigens, but others have been devel-
oped for the diagnosis and treatment of infectious diseases, acquired disorders,
R. Fischer (B)
Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Forckenbeckstrasse 6,
52074 Aachen, Germany

36 R. Fischer et al.
and even transplant rejection (Gavilondo and Larrick, 2000). As well as having
biomedical applications, antibodies can also be exploited to prevent diseases in
plants (Schillberg et al., 2001), to detect and remove environmental contaminants,
and for various industrial processes such as affinity purification and molecular tar-
geting (Stoger et al., 2005b).
With such a diverse spectrum of uses, the potential market for antibodies is
extremely large and there is considerable interest in high-capacity production tech-
nologies that are robust, economical, and safe. Over the last 15 years, plants have
emerged as convenient, economical, and scalable alternatives to the mainstream
antibody production systems which are based on the large-scale culture of microbes
or animal cells (Chu and Robinson, 2001; Wurm, 2004). In this chapter, we dis-
cuss the advantages and disadvantages of plants for antibody production, the diverse
plant-based systems that are now available, and factors governing the success of
antibody production in plants. We begin, however, with a brief overview of recom-
binant antibody technology.
3.2 Recombinant Antibody Technology

The typical antibody format is the mammalian serum antibody, which comprises
two identical heavy chains and two identical light chains joined by disulfide bonds
(Fig. 3.1). Each heavy chain is folded into four domains, two on either side of a
flexible hinge region, which allows the multimeric protein to adopt its characteristic
shape. Each light chain is folded into two domains. The N-terminal domain of each
of the four chains is variable, i.e., it differs among individual B cells due to unique
Fig. 3.1 Structure of a typical mammalian serum antibody, comprising two identical heavy chains
(gray) and two identical light chains (pink). Solid black lines indicate continuation of the polypep-
tide backbone (simple lines indicate the constant parts of the antibody, curly lines indicate the
variable regions, and thick sectionsrepresent the hinge region). Antibody domains are indicated by
colored circles. Disulfide bonds are represented by gray bars
3 Molecular Farming of Antibodies in Plants 37
rearrangements of the germ-line immunoglobulin genes. This part of the molecule

is responsible for antigen recognition and binding. The remainder of the antibody
comprises a series of constant domains, which are involved in effector functions
such as immune cell recognition and complement fixation. Below the hinge, in what
is known as the Fc portion of the antibody, the constant domains are class-specific.
Mammals produce five classes of immunoglobulins (IgG, IgM, IgA, IgD, and IgE)
with different effector functions. The Fc region also contains a conserved asparagine
residue at position 297 to which N-glycan chains are added. The glycan chains play
an important role both in the folding of the protein and in the performance of effector
functions (Jefferis, 2001).
Antibodies are also found in mucosal secretions, and these secretory antibodies
have a more complex structure than serum antibodies. They are dimers of the serum-
type antibody, the two monomers being attached by an additional component called
the joining chain. There is also a further polypeptide called the secretory component,
which protects the antibodies from proteases (Fig. 3.2).
Antibodies obtained from immunized animals are polyclonal, i.e., derived from
many different B cells. The advantage of monoclonal antibodies, i.e., antibodies
derived from a single clone of B cells, is that their binding specificity does not
vary. The traditional source of monoclonal antibodies is murine B cells. To pro-
vide a constant source of the antibody, B cells of appropriate specificity are fused
to immortal myeloma cells to produce a hybridoma cell line. However, the use of
murine hybridoma-derived antibodies as therapeutics is limited because the murine
components of the antibodies are immunogenic in humans, resulting in a so-called
human antimouse antibody (HAMA) response. Therefore, numerous strategies
Fig. 3.2 Structure of a mammalian secretory antibody, comprising a dimer of the typical serum
antibody and including two additional components, the joining chain (blue disc) and the secretory
component (green disc). Heavy chains are shown in gray and light chains in pink. Solid black lines
indicate continuation of the polypeptide backbone (simple lines indicate the constant parts of the
antibody, curly lines indicate the variable regions, and thick sectionsrepresent the hinge region).
Antibody domains are indicated by colored circles. Disulfide bonds are represented by gray bars
have been developed to humanize murine monoclonal antibodies (Kipriyanov and

Little, 1999), culminating in the production of transgenic mice expressing the
human immunoglobulin genes (Green, 1999). An alternative approach is to use
phage display libraries based on the human immune repertoires. Phage display is
advantageous because high-affinity antibodies can be identified rapidly, novel com-
binations of heavy and light chains can be tested, and the DNA sequence encoding
the antibody is indirectly linked to the antibody itself (Griffiths and Duncan, 1998;
Sidhu, 2000). This avoids the laborious isolation of cDNA or genomic immunoglob-
ulin sequences from hybridoma cell lines.
The expression of serum-type or secretory-type antibodies as recombinant
molecules requires the preparation and expression of two and four different trans-
genes, respectively. However, this is often an unnecessary complication, because
in many cases, the effector functions conferred by the constant regions are nei-
ther required nor desired. The constant regions of native immunoglobulins are not
required for antigen binding, and the variable regions of the heavy and light chains
can interact perfectly well when joined on the same polypeptide molecule (Chadd
and Chamow, 2001; Fischer and Emans, 2000). Smaller antibody derivatives, which
still require two chains, include Fab and F(ab’)2 fragments (which contain only the
sequences distal to the hinge region) and minibodies (which contain only part of
the constant portion of the molecule). Other derivatives, such as large single chains,
single-chain Fv fragments (scFvs), and diabodies, contain the variable regions of
the heavy and light chains joined by a flexible peptide chain. Such derivatives are
often more effective as drugs than full-length immunoglobulins because they show
increased penetration of target tissues, reduced immunogenicity, and are cleared
from tissues more rapidly. Another variant is the camelid serum antibody, which is
unique in that it contains only heavy chains. A full-size camelid antibody can, there-
fore, be expressed from a single transgene. Further, more specialized derivatives
include bispecific scFvs, which contain the antigen recognition elements of two dif-
ferent immunoglobulins and can bind to two different antigens, and scFv fusions,
which are linked to proteins with additional functions. Examples of all these anti-
body derivatives are shown in Fig. 3.3.
3.2.1 Expression Systems for Recombinant Antibodies
Most of the recombinant full-length immunoglobulins being developed as pharma-

ceuticals are produced in mammalian cell cultures, a few in hybridoma lines, but
most in immortalized lines that have been cleared by the FDA (Food and Drug
Administration) and equivalent authorities in other countries. These lines include
Chinese hamster ovary (CHO) cells, the murine myeloma cell lines NS0 and SP2/0,
baby hamster kidney (BHK) and human embryonic kidney (HEK)-293 cells, and the
human retinal line PER-C6 (Chu and Robinson, 2001). The main reason for this is
the belief that mammalian cells yield authentic products, particularly in terms of gly-
cosylation patterns. However, there are minor differences in glycan chain structure
between rodent and human cells. For example, human antibodies contain only the
Antigen 1
Antigen 2
Minibody Fab fragment Single chain Fv Diabody Bispecific scFv Single

fragment (scFv) variable
domain
Camelid heavy chain Large single chain scFv-fusion
Fig. 3.3 Structure of recombinant antibody derivatives and atypical antibody formats, most of
which have been expressed in plants. Heavy-chain derivatives are shown in gray and light-chain
derivatives in pink. Solid black lines indicate continuation of the polypeptide backbone (simple
lines indicate the constant parts of the antibody, curly lines indicate the variable regions, and thick
sections represent the hinge region). Antibody domains are indicated by colored circles. Disulfide
bonds are represented by gray bars. The red disc indicates a new functional protein domain in the
scFv fusion protein
sialic acid residue N-acetylneuraminic acid (NANA), while rodents produce a mix-
ture of NANA and N-glycosylneuraminic acid (NGNA) (Raju et al., 2000). There
are many disadvantages to mammalian cell cultures, including the high setup and
running costs, the limited opportunities for scale-up, and the potential contamina-
tion of purified recombinant antibodies with human pathogens. Bacterial fermenta-
tion systems are more cost-effective than mammalian cell cultures and are therefore
preferred for the production of Fab fragments and scFvs, since these derivatives
are not glycosylated. Even so, the yields of such products in bacteria are generally
low because the proteins do not fold properly (Baneyx and Mujacic, 2004). The
main reason for sticking to these systems is that they are well characterized and
established and conform to the strict and extensive regulatory systems governing
biopharmaceutical production.
Several alternative production systems have been explored, some of which are
now well established while others are still experimental. In the former category,
yeast and filamentous fungi have the advantages of bacteria (economy and robust-
ness), but they do have the tendency to hyperglycosylate recombinant proteins
(Gerngross, 2004), while insect cells can be cultured in the same way as mam-
malian cells (although more cheaply) and also produce distinct glycan structures
(Ikonomou et al., 2003). A more recent development is the production of antibodies
in the milk of transgenic animals (Dyck et al., 2003). A disadvantage of animals, in
common with cultured mammalian cells, is the existence of safety concerns about
the transmission of pathogens or oncogenic DNA sequences. Finally, hen’s eggs
could also be used as a production system since they are protein-rich and already
synthesize endogenous antibodies, but they remain a relatively unexplored potential
expression system (Harvey et al., 2002). Plants offer a unique combination of advan-
tages for the production of pharmaceutical antibodies (Twyman et al., 2003, 2005;
Ma et al., 2003; Basaran and Rodriguez-Cerezo, 2008). Their main benefit is the
low production costs, reflecting the fact that traditional agricultural practices and
unskilled labor are sufficient for maintaining and harvesting antibody-expressing
crops. Also, large-scale processing infrastructure is already in place for most crops.
Scale-up is rapid and efficient, requiring only the cultivation of more land. There are
minimal risks of contamination with human pathogens.
The general eukaryotic protein synthesis pathway is conserved between
plants and animals. So plants can efficiently fold and assemble full-size serum
immunoglobulins (as first demonstrated by Hiatt et al., 1989) and secretory IgAs
(first shown by Ma et al., 1995). In the latter case, four different subunits need
to assemble in the same plant cell to produce a functional product, even though
two different cell types are required in mammals. The posttranslational modifica-
tions carried out by plants and animals are not identical to those in mammals, but
they are very similar (certainly more so than in fungal and insect systems). There
are minor differences in the structure of complex glycans, such as the presence in
plants of the residues α-1,3-fucose and β-1,2 xylose, which are absent from mam-
mals (Cabanes-Macheteau et al., 1999). These residues are immunogenic in sev-
eral mammals, including humans, but curiously not in mice and only after multiple
exposures in rats (Gomord et al., 2005; Faye et al., 2005). However, as discussed
in more detail below, there are now many studies that show how the glycan profile
of proteins produced in plants can be “humanized.” As well as full-size antibod-
ies, various functional antibody derivatives have also been produced successfully in
plants, including Fab fragments, scFvs, bispecific scFvs, single-domain antibodies,
and antibody fusion proteins (see Twyman et al., 2005).
3.2.2 Plant-Based Expression Platforms
The most widely used strategy for antibody production in plants is the nuclear trans-
genic system, in which the antibody transgenes are transferred to the plant nuclear
genome. The advantages of this approach when used in our major terrestrial crop
species include the following: (1) transformation is a fairly routine procedure in
many plant species and can be achieved by a range of methods, the two most com-
mon of which are Agrobacterium-mediated transformation and the delivery of DNA-
coated metal particles by microprojectile bombardment; (2) a stable transgenic line
can be used as a permanent genetic resource; (3) among the various plant systems, it
is the simplest to maintain (once the producer line of transgenics is available) and is
ultimately the most scalable; (4) it is possible to establish master seed banks. Disad-
vantages, compared to other plant systems, include the relatively long development
time required for transformation, regeneration, analysis of transgenics, selection and
bulking up of the producer line, the unpredictable impact of epigenetic events on
transgene expression (e.g., posttranscriptional gene silencing and position effects),
and the potential for transgene spread from some crops through outcrossing. A range
of different crops have been explored for antibody production, and the main cate-
gories are described below.
Leafy crops have two major benefits: they have a large biomass, which translates
to large product yields, and flowering can be prevented (e.g., genetically or by emas-
culation) to avoid the spread of transgenic pollen. On the other hand, leaf tissue is
very watery such that proteins are expressed and accumulate in an aqueous environ-
ment in which they are subject to degradation. This means that antibody-containing
leaves generally have to be processed soon after harvest or otherwise frozen or dried,
which can add significantly to production costs. Tobacco (Nicotiana tabacum L.)
has the longest history as a pharmaceutical production model crop system, having
been used to express the very first plant-derived antibodies and many of the others
since (Table 3.1). The major advantages of tobacco are the well-established technol-
ogy for gene transfer and expression, the high biomass yield (over 100,000 kg/h for
close cropped tobacco, since it can be harvested up to nine times a year), and the
existence of large-scale infrastructure for processing that does not come into con-
tact with the human or animal food chains. Particularly due to the yield potential
and safety features, tobacco could be a major source of plant-derived recombinant
antibodies in the future. Another leafy crop that has been evaluated for antibody
expression is alfalfa (Medicago sativa L.). This has been developed as a production
crop by the Canadian biotechnology company Medicago Inc., and they have secured
a robust IP portfolio covering the use of expression cassettes for biopharmaceutical
proteins in this species. Although not as prolific as tobacco, alfalfa nevertheless pro-
duces large amounts of leaf biomass and has a high leaf protein content. Alfalfa also
lacks the toxic metabolites produced in many tobacco cultivars, which are often
cited as a disadvantage, but instead it contains high levels of oxalic acid, which
can affect protein stability. Alfalfa is particularly useful because it is a perennial
plant that is easily propagated by stem cutting to yield clonal populations. Although
alfalfa has been put on the biosafety “hit list” by the regulators because it outcrosses
with wild relatives, this does not detract from the excellent properties of this species
for antibody production under containment, as in greenhouses or programmed plant
growth chambers. Alfalfa has been used for the production of a diagnostic IgG that
recognizes epitopes specific to the constant regions of human IgG (Khoudi et al.,
1999) and for several other antibodies in development by Medicago Inc.
The problem of protein instability in leafy tissue (see above) can be overcome
by expressing antibodies in the dry seeds of cereals and grain legumes. Several dif-
ferent species have been investigated for antibody production including four major
cereals (maize, rice, wheat, and barley) and two legumes (soybean and pea). The
42
Table 3.1 Recombinant therapeutic or diagnostic recombinant antibodies produced by molecular farming in plants and reported in the scientific litera-
ture (many antibodies in commercial development remain undisclosed until IP rights have been secured). Antibodies with alternative applications, such as
phytomodulation or the prevention of plant disease, are not listed
Antibody
Antigen format Production system Comments References
HIV gp120 (2F5) IgG Tobacco, maize, tobacco Maximum yield ∼75 μg/g seeds Floss et al. (2008), Sack
suspension cells et al. (2007)
HIV gp120 (2G12) IgG Tobacco, maize Maximum yield ∼100 μg/g seeds Rademacher et al. (2008),
Ramessar et al. (2008c)
B-cell lymphoma, murine scFv Virus vectors in tobacco Maximum yield 30.2 μg/g leaves McCormick et al. (1999)
38C13 leaves
Carcinoembryonic antigen scFv, IgG1 Tobacco agroinfiltration Directed to apoplast or ER. Maximum yields 5 μg scFv/g Vaquero et al. (1999)
dAb Tobacco, agroinfiltration leaves, 1 μg IgG/g leaves Vaquero et al. (2002)
and transgenic plants
scFv Rice, rice cell cultures Directed to apoplast or ER. Maximum yields 3.8 μg/g Torres et al. (1999), Stoger
callus, 29 μg/g leaves, 32 μg/g seed et al. (2000)
scFv Wheat Directed to apoplast or ER. Maximum yields 900 ng/g Stoger et al. (2000)
leaves, 1.5 μg/g seed
scFv Pea Directed to rER. Maximum yield 9 μg/g seed Perrin et al. (2000)
CD-40 scFv fusion Tobacco suspension Secreted into apoplast. Yield not reported Francisco et al. (1997)
cells
Colon cancer antigen IgG Virus vectors in tobacco Yield not reported Verch et al. (1998)
leaves
Epidermal growth factor IgG Tobacco Aglycosylated antibody was directed to the ER and binds Rodriguez et al. (2005)
receptor (EGFR) to EGFR expressed on the surface of human tumor cells
Human creatine kinase IgG1, Fab Tobacco and Accumulated in nucleolus or apoplast. Maximum yield De Neve et al. (1993), De
Arabidopsis leaves 1.3% TSP Wilde et al. (1998)
R. Fischer et al.
3
Table 3.1 (continued)
Antibody
scFv Tobacco leaves Directed to cytosol or apoplast. Maximum yield 0.01% Bruyns et al. (1996)
TSP
Rhesus D antigen IgG1 Arabidopsis leaves Reacted with RhD+ cells in antiglobulin technique and Bouquin et al. (2002)
elicited a respiratory burst in human peripheral blood
mononuclear cells
Ferritin scFv Tobacco leaves Semenyuk et al. (2002)
Hepatitis B virus surface IgG Tobacco leaves Up to 25 mg antibody per kilogram biomass Valdes et al. (2003ª,b)
antigen IgG Tobacco suspension Complement-dependent cytotoxicity demonstrated Yano et al. (2004)
cells
scFv Tobacco Four different targeting constructs used, ER targeting Ramírez et al. (2002)
Molecular Farming of Antibodies in Plants
achieved 0.22% TSP

Herpes simplex virus 2 IgG1 Soybean Secreted into apoplast. Yield not reported Zeitlin et al. (1998)
HIV antibodies in blood scFv fusion Tobacco leaves, barley Maximum yield 150 mg/g Schunmann et al. (2002)
grains, potato tubers
Human scFv, dAb, Tobacco leaves Secreted into apoplast. Maximum yield 40 mg/kg fresh Kathuria et al. (2002)
choriogonadotrophin IgG weight
IgG1, Tobacco and winter Directed to apoplast or ER. Glycan patterns were analyzed Sriraman et al. (2004)
diabody cherry leaves
Human IgG IgG1 Alfalfa Secreted into apoplast. Maximum yield 1% TSP Khoudi et al. (1999)
Interleukin-4 scFv Tobacco roots Maximum yield 0.18% TSP Ehsani et al. (2003)
Interleukin-6 scFv Tobacco roots Ehsani et al. (2003)
Protective antigen of IgG N. benthamiana Toxin activity was neutralized in vitro and in vivo Hull et al. (2005)
Bacillus anthracis
Rabies virus IgG Tobacco Directed to the ER. Activity of the rabies virus was Ko et al. (2003)
neutralized. Glycan patterns were analyzed
Salmonella enterica scFv Tobacco 41.7 μg purified scFv per gram leaf tissue Makvandi-Nejad et al.
lipopolysaccharide (2005)
43
44
Antibody
Streptococcal surface sIgA Tobacco leaves Secreted into apoplast. Maximum yield 500 μg/g fresh Ma et al. (1995)
antigen (I/II) weight
IgG1 Tobacco leaves Directed to plasma membrane. Maximum yield 1.1% TSP Vine et al. (2001)
in leaves
IgG1 Secretion from tobacco Up to 11.7 μg per gram dry root weight per day Drake et al. (2003)
roots
Substance P VH Tobacco leaves Secreted into apoplast. Maximum yield 1% TSP Benvenuto et al. (1991)
Tetanus toxin C IgG2a fused Tobacco Animals immunized with recombinant immune complex Chargelegue et al. (2005)
to tetanus without adjuvant were fully protected against lethal
toxin C challenge
Tumor-associated IgG Tobacco Secreted into the apoplast. Binding activity to colon cancer Ko et al. (2005)
antigen EpCAM cells and tumor inhibition activity in nude mice
R. Fischer et al.
idea is that such crops would be beneficial for production in developing countries,
where on-site processing would not be possible and a cold chain could not be main-
tained. The accumulation of recombinant antibodies in seeds allows for long-term
storage at ambient temperatures because the proteins accumulate in a stable form
(Ramessar et al., 2008a). Seeds have the appropriate molecular environment to pro-
mote protein accumulation, and they achieve this through the creation of specialized
storage compartments such as protein bodies and storage vacuoles that are derived
from the secretory pathway. Seeds are also desiccated, which reduces the level of
both nonenzymatic hydrolysis and protease degradation. It has been demonstrated
that antibodies expressed in seeds remain stable for at least 3 years at ambient tem-
peratures with no detectable loss of activity (Stoger et al., 2005a).
As well as their advantages in terms of product stability, seed expression might
also be beneficial in terms of downstream processing. This is because seeds have
a relatively simple proteome (therefore minimizing the likelihood that endogenous
proteins would be copurified) and lack the phenolic compounds abundant in leaves
that can interfere with affinity purification. The restriction of recombinant protein
accumulation in seeds also helps to avoid any potentially negative effects on the
growth and development of vegetative plant organs and on humans, animals, and
microorganisms that interact with the plant or feed on its leaves.
Disadvantages of seed crops include the lower overall yields that have been
obtained. The intrinsic yields are in a few cases higher than tobacco (e.g., on a
kilogram-per-kilogram basis of harvested material, rice grains can accumulate more
antibody than tobacco leaves; Stoger et al., 2002), but the vast abundance of har-
vested biomass per hectare from a tobacco crop far outweighs this. Also, seeds
are regarded as viable genetically modified organisms in their own right. So while
the transport of harvested transgenic tobacco leaves should not cause any problems,
the transport of seeds could fall afoul of national and international regulations on the
transport of GMOs (Sparrow et al., 2007; Spök et al., 2008); the seeds would have
to be crushed to flour beforehand and this might offset the advantage of increased
product longevity.
Maize (Zea mays L.) seeds have been investigated as an antibody production
vehicle by Prodigene Inc. following successful demonstrations of the economi-
cal production of other valuable proteins using this system, including avidin and
β-glucuronidase. Initial findings for the expression of a secretory IgA in maize
showed that the four chains were expressed, directed to the cell wall matrix, and
assembled correctly. The product accumulated to 0.3% of total soluble protein
in the T1 seeds, and based on previous results, significant improvements were
anticipated through selective breeding (Hood et al., 2002). An antibody deriva-
tive used for HIV diagnostics has been expressed in barley and has achieved a
yield of 150 μg/g. More recently, the HIV-neutralizing antibody, 2G12, was pro-
duced in maize seeds with a yield >100 μg/g for use as a potential microbicide
(Ramessar et al., 2008c).
Finally, antibodies have also been produced in soybean (Glycine max (L.) Merr.),
although in this particular case, it was expressed constitutively and isolated from the
leaves rather than from the seeds (Zeitlin et al., 1998). Soybean has been investigated
as a potential production crop by Prodigene and others because it is a self-fertilizing

crop with a high biomass yield, but product yields have been low and the system has
therefore been largely abandoned.
Recombinant antibodies have been produced in potato (Solanum tuberosum L.)
and tomato (Solanum lycopersicum L.), which also offer certain advantages over
other crops. Proteins accumulating in potato tubers are generally stable, because,
like the cereal seed endosperm, these are storage organs that are adapted for high-
level protein accumulation. The potential of potato tubers for antibody production
was first demonstrated by Artsaenko et al. (1998), who produced an scFv fragment
specific for the inflammatory agent oxazolone. Potatoes have since been developed
as a general production host for antibodies (De Wilde et al., 2002) as well as other
biopharmaceuticals based on antibodies (Schunmann et al., 2002). Fruit crops have
another potential advantage, i.e., antibody expression in organs that are consumed
raw allows the direct oral administration of recombinant antibodies designed for
passive immunotherapy, such as protection of the oral cavity against pathogens.
Stoger et al. (2002) describe preliminary experiments in which scFv84.66, recog-
nizing the carinoembryonic antigen (CEA), is expressed in tomato fruits, although
the accumulation levels are rather low (0.3 μg/g fresh weight). Other advantages
of tomato include the high biomass yields (about 68,000 kg/ha, approaching the
yields possible in tobacco) and the increased containment offered by growth in
greenhouses.
Instead of introducing transgenes into the nuclear genome, they can be targeted to
the chloroplast genome using particle bombardment or another physical DNA deliv-
ery technique and ensuring the transgene is embedded in a chloroplast DNA homol-
ogy region (Maliga, 2003, 2004; Bock, 2007). The main benefits of the chloroplast
system are that there are thousands of chloroplasts in a typical leaf cell, yet only
one nucleus; therefore, the number of transgene copies in the cell following plas-
tid transformation and the establishment of homoplasmy is much higher, promising
greater product yields. This is enhanced by the absence of epigenetic phenomena
such as transgene silencing in the chloroplast genome. Chloroplasts, derived from
ancient bacteria, also support operon-based transgenes, allowing the expression of
multiple proteins from a single transcript. Finally, and perhaps most importantly
from the regulatory perspective, chloroplasts are absent from the pollen of most of
our food crops, which limits the potential for outcrossing (Daniell et al., 2005a).
There are two disadvantages to the chloroplast system: first, chloroplast trans-
formation is not a standard procedure and is thus far limited to a relatively small
number of crops (e.g., tobacco, tomato, potato, cotton, soybean, lettuce, cauliflower,
and sugar beet; Daniell et al., 2005b; Lelivelt et al., 2005; Nugent et al., 2006;
De Marchis et al., 2009); second, since chloroplasts are derived from ancient bacte-
ria, they lack much of the eukaryote machinery for posttranslational modification,
i.e., they are unable to synthesize glycan chains. For this reason, they would be
suitable for the production of scFvs but not full-size immunoglobulins.
In the only published report thus far dealing with antibody expression in ter-
restrial plant chloroplasts, a camelid antibody fragment was expressed in tobacco
using an inducible T7-promoter system. Transcripts could be detected but no protein
(Magee et al., 2004). However, antibodies have been expressed successfully in algal
chloroplasts (see below).
Transient expression assays are generally used to evaluate the activity of expres-
sion constructs or to test the functionality of a recombinant protein before com-
mitting to the long-term goal of generating transgenic plants. However, transient
expression can also be used as a routine production method if enough protein can be
produced to make the system economically viable. The advantages of this approach
include the minimal setup costs and the rapid onset of protein expression, but
scaling-up is expensive and impractical. So this type of system is particularly useful
for the production of high-value proteins such as therapeutic antibodies, which have
specialized markets and are required in small amounts.
An example of a transient expression system is the agroinfiltration method, where
recombinant Agrobacterium tumefaciens is infiltrated into tobacco leaf tissue under
vacuum and milligram amounts of protein can be produced within a few weeks
(Kapila et al., 1997). This system has also been developed in alfalfa by Med-
icago researchers (D’Aoust et al., 2004) and is applicable in many other leafy
species. Although stable transformation occurs at very low efficiency, many cells
are initially transiently transformed, only for the exogenous DNA to get diluted
and degraded. However, before this happens, most cells contain the T-DNA and can
express any transgenes carried therein. As extrachromosomal constructs, these unin-
tegrated T-DNAs are free from position effects and epigenetic silencing phenomena
that often reduce or abolish the expression of integrated nuclear transgenes.
A number of different antibodies and their derivatives have been produced by
agroinfiltration, including the full-size IgG T84.66 along with its scFv and diabody
derivatives (Vaquero et al., 1999, 2002) and a chimeric full-size IgG known as PIPP
along with its scFv and diabody derivatives, which recognizes human chorionic
gonadotropin (Kathuria et al., 2002).
Plant viruses are advantageous for the production of antibodies because viral
genomes are easier to manipulate than plant genomes, and the infection of plants
with recombinant viruses is a very simple process compared to the regeneration of
transgenic plants (Yusibov et al., 2006; Yusibov and Rabindran, 2008). Potentially,
plants carrying recombinant viruses can be grown on the same scale as transgenic
plants, but with a much shorter development time. Viral infections are generally
systemic, so infected plants carry the virus in all cells and can produce the antibody
systemically, resulting in potentially very high yields. A further advantage of viruses
is that mixed infections are possible, making it a simple process to express, for
example, the multiple chains of a full-size immunoglobulin. Although the transgene
is carried on a viral genome rather than on the plant genome, the expressed protein
is processed in the same manner as it would be in transgenic plants, meaning that
appropriate folding, targeting, and modification of antibodies are possible. The viral
system is therefore uniquely simple, flexible, and efficient, and it has the potential
for protein manufacture in both contained and open facilities (Canizares et al., 2005;
Yusibov et al., 2006).
There are two types of expression systems based on plant viruses, one for full
polypeptides and one for peptide epitopes displayed on the virion surface. Both have
been used to express antibodies. In the polypeptide expression system, the antibody
is encoded by a discrete transgene and accumulates as a soluble protein within the
plant cell. In the epitope display system, a small antibody derivative such as an scFv
is expressed as a fusion with the viral coat protein in such a way that the antibody is
displayed on the surface of the virus particle.
Tobacco mosaic virus (TMV) has a monopartite RNA genome of 6.5 kb encoding
four proteins all of which are essential for systemic infection. The normal strategy
for polypeptide expression is to place the transgene under the control of an addi-
tional coat protein promoter, although not a perfect copy of the endogenous coat pro-
tein promoter, as this is an unstable configuration that leads to transgene elimination
(Donson et al., 1991). Many antibodies have now been expressed in TMV-infected
plants. McCormick et al. (1999) produced an scFv fragment based on the idiotype of
malignant B cells of the murine 38C13 B-lymphoma cell line. When administered
to mice, the scFv stimulated the production of anti-idiotype antibodies capable of
recognizing 38C13 cells, providing immunity against lethal challenge with the lym-
phoma. This has been developed into a personalized therapy for diseases such as
non-Hodgkin’s lymphoma, where antibodies capable of recognizing unique mark-
ers on the surface of any malignant B cells could be produced for each patient. Up
to 15 such antibodies were tested in phase I and phase II clinical trials by the US
biotechnology company Large Scale Biology Inc., before they went into liquidation.
Additionally, Verch et al. (1998) produced a full-length IgG in transgenic tobacco
plants by infecting them with two TMV vectors, one expressing the heavy chain and
one the light chain. This study showed that viral coexpression was compatible with
the correct assembly and processing of multimeric recombinant proteins.
Potato virus X (PVX), the type member of the Potexvirus family, has a 6.5-kb
monopartite RNA genome rather like that of TMV. Also, like TMV, PVX vectors
contain extra subgenomic promoters to drive transgene expression, but in this case,
the lack of a closely related alternative means that transgene elimination by homolo-
gous recombination is unavoidable. PVX vectors have been used for the expression
of several different antibodies, but none of medical relevance. Single-chain Fv anti-
bodies have been expressed, specific for proteins from potato virus V (Hendy et al.,
1999), tomato spotted wilt virus (Franconi et al., 1999) and against granule-bound
starch synthase I (Ziegler et al., 2000).
In addition to the use of complete viruses carrying additional foreign genes,
another strategy uses deconstructed viruses that cannot spread systemically in the
plant. The magnifection strategy, developed by Icon Genetics (now part of Bayer
CropSciences), renders the systemic spread of the virus unnecessary through the use
of A. tumefaciens as a delivery vehicle (Marillonnet et al., 2005; Gleba et al., 2005).
The bacterium delivers the viral genome to so many cells that local spreading is suf-
ficient for the entire plant to be infected. Like the infection stage, systemic spread
is a limiting function, often one of the primary determinants of host range. Taking
the systemic spreading function away from the virus and relying instead on the bac-
terium to deliver the viral genome to a large number of cells allow the same viral
vector to be used in a wide range of plants. The system has been used to express anti-
gens and antibodies at high levels in tobacco and other plants (Gleba et al., 2004).
The above systems all involve the use of whole plants as the expression plat-
form. Even if antibody production is limited to specific tissues, such as seeds
or leaves, these are harvested from the whole plant at the beginning of down-
stream processing. An alternative is to culture the specific organs or cells that pro-
duce the antibody and either isolate the antibody from these cells or tissues or
collect it from the culture medium. A number of different culture systems have
been developed, although most research has focused on cell suspension cultures.
In most cases where nuclear transgenic plants have been used for the production
of recombinant antibodies, the product has been extracted from plant tissues. An
alternative is to attach a signal peptide to the recombinant protein, thus direct-
ing it to the secretory pathway. In this way, the protein can be recovered from
the root exudates or leaf guttation fluid, processes known, respectively, as rhi-
zosecretion and phyllosecretion (Borisjuk et al., 1999; Komarnytsky et al., 2000).
Although not widely used, the secretion of recombinant antibodies into hydroponic
culture medium is advantageous because no cropping or harvesting is necessary.
The technology is being developed by the US biotechnology company Phytomedics
Inc. A monoclonal antibody was shown to be secreted into hydroponic culture
medium resulting in a yield of 11.7 μg antibody per gram of dry root mass per day
(Drake et al., 2003).
Other systems are based on the culture of plant organs. Hairy roots are neoplastic
structures that arise following transformation of a suitable plant host with Agrobac-
terium rhizogenes. If the plant is already transgenic, or if the transforming A. rhi-
zogenes strain is transgenic, and transfers the foreign gene to the host plant during
the process of transformation, then hairy root cultures can be initiated, which will
produce recombinant antibodies and secrete them into the growth medium (Sharp
and Doran, 2001b). Hairy roots grow rapidly and can be propagated indefinitely
in liquid medium. Thus far, hairy root cultures have been used to produce a rela-
tively small number of antibodies (Sharp and Doran, 2001a), mainly because of the
relative ease with which multisubunit proteins can be produced. The cultures can
be initiated from transgenic plants already carrying multiple transgenes, wild-type
plants can be infected with multiple A. rhizogenes strains, or established hairy root
cultures can be supertransformed with A. tumefaciens. A clonal root system based
on a similar principle has been developed as a commercial platform by the Fraun-
hofer Center for Molecular Biotechnology in Newark, Delaware. In this case, the
root system is combined with the use of viral-derived vectors for high-yield anti-
body expression in sealed vessels. A tissue culture system has been developed from
shooty teratomas, which are differentiated cell cultures produced by transformation
with certain strains of A. tumefaciens (Subroto et al., 1996). Thus far, there has been
only one report of pharmaceutical protein production in teratoma cultures, and the
levels of antibody were very low (Sharp and Doran, 2001a,b).
As stated above, most of the work in this area has focused on suspension cell cul-
tures, which are individual plant cells and small aggregates thereof growing in liquid
medium in a fermenter (Hellwig et al., 2004; Doran, 2006). Suspension cell cultures
are usually derived from callus tissue by the disaggregation of friable callus pieces in
shake bottles and are later scaled up for fermenter-based production. Recombinant
antibody production is achieved by using transgenic explants to derive the cultures,

or transforming the cells after disaggregation, usually by cocultivation with A.
tumefaciens. Suspension cultures have the same advantages as the simple plants,
i.e., controlled growth conditions, batch-to-batch reproducibility, containment, and
production under GMP procedures. Many foreign proteins have been expressed suc-
cessfully in suspension cells, including antibodies, enzymes, cytokines, and hor-
mones (reviewed by Hellwig et al., 2004; Fischer et al., 1999). Tobacco cultivar
“Bright Yellow 2” (BY-2) is the most popular source of suspension cells for molec-
ular farming, since these proliferate rapidly and are easy to transform. However, rice
(Oryza sativa L.) suspension cells have also been used to produce several antibodies
(e.g., Torres et al., 1999).
Recombinant antibodies expressed in plant cell suspension cultures may be
secreted into the culture supernatant or retained within the cells. Localization
depends on the expression construct design (see below) and the permeability of the
plant cell wall to the antibody. Targeting signals included in the expression construct
can be used to direct the protein to the apoplast or to retain it within intracellular
compartments. The fate of antibodies targeted for secretion depends to a large extent
on their size: molecules of 20–30 kDa (the size range of scFvs) will generally pass
through the plant cell wall and be secreted into the culture medium, whereas larger
proteins (such as IgGs) will be retarded in a size-proportional manner. The inclusion
of a C-terminal KDEL sequence results in higher levels of antibody accumulation
in cultured cells because the biochemical environment of the endoplasmic reticu-
lum favors stable protein folding and assembly while reducing the level of prote-
olytic degradation (see below). However, this also makes it necessary to disrupt the
cells in order to isolate the protein, which requires additional processing time and
causes the release of phenolic molecules that interfere with purification and reduce
production yield. Thus, the preferred approach is to secrete the target proteins and
capture them from the culture supernatant or release them from the cells by mild
enzymatic digestion.
Single-celled plants and aquatic plants can be maintained in bioreactors, offering
two advantages over terrestrial plants. First, the growth conditions can be controlled
precisely, which means that optimal growth conditions can be maintained, batch-
to-batch product consistency improved, and the growth cycle can conform to GMP.
Second, growth in bioreactors offers complete containment. Although more expen-
sive than agricultural molecular farming, the use of simple plants in bioreactors is
not as expensive as cultured animal cells because the media requirements are gener-
ally very simple. Added to this, the proteins can be secreted into the medium, which
reduces the downstream processing costs and allows the product to be collected in
a nondestructive manner. A final, major advantage is the speed of production. The
time from transformation to first product recovery is on the scale of days to weeks
because no regeneration is required, and stable producer lines can be established
in weeks rather than months to years because there is no need for crossing, seed
collection, and the testing of several filial generations to check transgene stability.
Three major bioreactor-based systems are currently under commercial development:
algae, moss, and duckweed (Lemna spp.).
Thus far, a single report discusses the production of monoclonal antibodies in

the chloroplast of the alga Chlamydomonas reinhardtii (Mayfield et al., 2003). Pro-
duction costs appear similar to those of recombinant proteins produced in terrestrial
plants, mainly due to the inexpensive media requirements. The medium does not
cost very much to start with and in any case can be recycled for algal cultures grown
in continuous cycles. Aside from the economy of producing recombinant proteins in
algae, there are further attributes that make algae ideal candidates for recombinant
protein production. First, transgenic algae can be generated quickly, requiring only a
few weeks between the generation of initial transformants and their scale-up to pro-
duction volumes. Second, both the chloroplast and the nuclear genome of algae can
be genetically transformed, providing scope for the production of several different
proteins simultaneously. In addition, algae have the ability to be grown on various
scales, ranging from a few milliliters to 500,000 l in a cost-effective manner. These
attributes, and the fact that green algae fall into the GRAS (generally regarded as
safe) category, make C. reinhardtii a particularly attractive alternative to other plants
for the expression of recombinant proteins. The production technology has been
reviewed recently (Franklin and Mayfield, 2005; Mayfield and Franklin, 2005).
The moss Physcomitrella patens is a haploid bryophyte, which can be grown
in bioreactors in the same way as algae, suspension cells, and aquatic plants. Like
these other systems, it has the advantages of controlled growth conditions, syn-
thetic growth media, and the ability to secrete recombinant proteins into the medium
(Decker and Reski, 2004). The unique feature of this organism, relative to all other
plants, is that it is amenable to homologous recombination (Schaefer, 2002). This
means that not only can it be transformed stably with new genetic information but
also that endogenous genes can be disrupted by gene targeting. The major applica-
tion of gene targeting in molecular farming is the modification of the glycosylation
pathway (by knocking out enzymes that add nonhuman glycan chains to proteins),
thus allowing for the production of humanized glycoproteins (Faye et al., 2005).
The P. patens system is being developed by the German biotechnology com-
pany Greenovation Biotech GmbH, which is based in Freiburg. The company has
developed transient expression systems that allow feasibility studies and stable pro-
duction strains that can be scaled up to several thousand liters. The Lemna System
is based on duckweed (Lemna minor) and has been developed by the US biotech-
nology company Biolex Inc. Lemna has a number of significant advantages for the
production of recombinant pharmaceutical proteins (Gasdaska et al., 2003). Unlike
transgenic terrestrial plants, this aquatic plant is cultured in sealed, aseptic ves-
sels under constant growth conditions (temperature, pH, and artificial light). Only
very simple nutrients are required (water, air, and completely synthetic inorganic
salts), and under these conditions, the plant proliferates vegetatively and doubles its
biomass every 36 h. This provides the optimal production environment for batch-
to-batch consistency. Duckweed constitutes about 30% dry weight of protein, and
recombinant proteins can either be extracted from wet plant biomass or secreted
into the growth medium. Biolex Inc. has reported the successful expression of tens
of proteins in this system, including several recombinant antibodies and enzymes
(Gasdaska et al., 2003).
3.3 Optimizing Antibody Production in Plants

The intrinsic production capacity of the chosen expression platform is a property
that cannot be modified easily, because it is dependent on the overall biomass yield
of the crop. However, the specific yield of recombinant protein per unit of plant
biomass can be influenced by the optimization of transgene expression, which is
achieved through expression construct design. Perhaps the most important compo-
nent of the expression construct is the promoter used to control transcription of
the transgene. For dicotyledonous species such as tobacco, potato, and tomato, the
strong and constitutive cauliflower mosaic virus 35S promoter (CaMV 35S) is often
chosen to drive transgene expression (Twyman et al., 2005). In cereals, the CaMV
35S promoter has a lower activity, and other promoters have been tested, such as the
maize ubiquitin-1 (ubi-1) promoter (Christensen and Quail, 1996). Some modified
dicot promoters do work rather well in cereals, an example being the pPLEX series
of constructs developed by Schunmann et al. (2003) adapted for use in monocots.
The original pPLEX vectors were based on regulatory elements from subterranean
clover stunt virus (SCSV). Modification was achieved by adding either the Ubi1 or
Act1 introns, as well as GC-rich enhancer sequences from banana bunchy top virus
(BBTV) or maize streak virus (MSV).
Regulated promoters can be used in preference to constitutive promoters to
improve practicality and biosafety in addition to yields. For example, although
constitutive promoters allow high-level accumulation of recombinant proteins in
seeds, the proteins are also expressed in leaves, pollen, and roots. The use of seed-
specific promoters largely restricts recombinant protein accumulation in the seeds,
so the vegetative organs do not accumulate detectable levels of the recombinant
protein. This increases the biosafety of the plants, since adventitious contact with
nontarget organisms is unlikely (Commandeur et al., 2003). Among the many dif-
ferent seed-specific promoters that have been used (reviewed by Christou et al.,
2004), the most impressive yields have been obtained with a novel seed-specific pro-
moter from the common bean (Phaseolus vulgaris L.), which was used to express
a single-chain antibody in Arabidopsis thaliana L. Heynh. In contrast to the CaMV
35S promoter, which resulted in antibody accumulation to 1% total soluble protein
(TSP), the bean arc5-I promoter resulted in antibody levels in excess of 36% TSP
in homozygous seeds, and the antibody retained its antigen-binding activity and
affinity (De Jaeger et al., 2002).
The use of inducible promoters (Padidam, 2003) is also advantageous because
recombinant protein synthesis can be delayed until just before harvest, or even
after harvest, as is the case for the tomato hydroxy-3-methylglutaryl CoA reduc-
tase 2 (HMGR2) promoter developed by the now defunct CropTech Inc. as the
MeGA promoter system (mechanical gene activation). The promoter used in this
system is wound inducible, and gene expression is activated when the harvested
tobacco leaves are shredded prior to protein extraction (Cramer et al., 1999). How-
ever, many endogenous inducible promoters show a degree of leakiness (background
expression) and, in some cases, a low induction ratio. Recombinant systems such as
those based on bacterial operons or animal hormones may be advantageous in these
circumstances.
After promoter choice, the next most important aspect of construct design is the
inclusion of sequences that control subcellular targeting of the protein. This is a
general method to increase the yield of recombinant proteins because the compart-
ment in which a recombinant protein accumulates influences its folding, assembly,
and posttranslational modification (Ma et al., 2003; Schillberg et al., 2003). Com-
parative targeting experiments with full-size immunoglobulins and single-chain Fv
fragments have shown that the secretory pathway is a more suitable compartment
for folding and assembly than the cytosol and is therefore advantageous for high-
level protein accumulation (Zimmermann et al., 1998; Schillberg et al., 1999). The
endoplasmic reticulum (ER) provides an oxidizing environment and an abundance
of molecular chaperones, while there are few proteases. Proteins are directed to
the secretory pathway using either a heterologous or an endogenous signal peptide,
located at the N-terminus of the native protein. Such proteins are cotranslationally
imported into the ER and are eventually secreted into the apoplast, a supracellu-
lar network of interlinked compartments underlying the cell wall. Depending on its
size, a protein can be retained in the cell wall matrix or can leach from the cell.
Although the majority of recombinant proteins are generally more stable in the
apoplast than the cytosol, they are even more stable in the ER lumen. Therefore,
antibody expression levels can be increased even further if the protein is confined
to the ER using an H/KDEL C-terminal tetrapeptide tag in addition to the signal
peptide (Conrad and Fiedler, 1998). Accumulation levels are generally two- to ten-
fold greater compared with an identical protein lacking the KDEL signal (Schillberg
et al., 2002). As an added benefit, antibodies retrieved in this manner are not mod-
ified in the Golgi apparatus, which means they possess high-mannose glycans but
not plant-specific xylose and fucose residues (Sriraman et al., 2003). Interestingly,
recent experiments with antibodies expressed as fusion proteins with elastin-like
peptides (ELPs) showed that the ELPs also had an impact on trafficking, albeit only
in seeds. Two HIV-neutralizing antibodies expressed in tobacco seeds, namely 2F5
(Floss et al., 2008) and 2G12 (Floss et al., unpublished), were secreted into the
apoplast when expressed as naked molecules bearing a KDEL tag, but initiated the
formation of novel protein bodies that budded directly from the ER when expressed
as ELP fusions. Aberrant antibody localization has also been reported in Arabidop-
sis seeds (Van Droogenbroeck et al., 2007).
Although the protein synthesis and folding pathways are highly conserved
between plants and animals, there are some differences in the capacity for posttrans-
lational modification. Plants do not, for example, hydroxylate proline residues in
recombinant collagen. There are also various differences in glycan structure: plant-
derived recombinant human glycoproteins tend to contain the carbohydrate groups
β(1→2) xylose and α(1→3) fucose, which are absent in mammals, but generally
lack the terminal galactose and sialic acid residues that are found on many native
human glycoproteins (Fig. 3.4). Since glycan structures can impact on the solu-
bility, stability, immunogenicity, and biological activity of recombinant proteins,
the “humanization” of glycan structures produced in plants has been an important
topic of research and debate in the scientific community. There has been consid-
erable interest in modifying the plant glycosylation pathway to humanize the gly-
can profile of recombinant proteins. Several changes in the pathway are required
A)
α(1−4)
β(1−2)
Mannose
α(1−6)
α
β(1−3) N-Acetylglucosamine
β(1−4) β(1−4)
α(1−3) Fucose
β(1−3) β(1−2) α(1−3)
β(1−2)
Xylose
α(1−4)
Galactose
B) β(1−2)
α(1−6)
β(1−4) β(1−4)
α(1−3)
β(1−2) α(1−3)
β(1−2)
Fig. 3.4 Two glycan structures produced in plants. (A) Galactose-extended complex glycan.
(B) Long-chain complex glycan. The xylose and α(1,3) fucose residues are not found in mam-
mals
to produce proteins with typical human glycan structures (Warner, 2000; Gomord
et al., 2005; Faye et al., 2005). Strategies used include the in vitro modification of
plant-derived recombinant proteins by purified human β(1,4)-galactosyltransferase
and sialyltansferase enzymes (Blixt et al., 2002) and the expression of human β(1,4)-
galactosyltransferase in transgenic plants to produce recombinant antibodies with
galactose-extended glycans (Bakker et al., 2001). In the latter case, 30% of the anti-
body was galactosylated, similar to the proportion found in hybridoma cells. In vivo
sialylation will be more difficult to achieve because plants lack the precursors and
metabolic capability to produce this carbohydrate group. A more recent report doc-
umenting sialylation in A. thaliana suspension cells has been challenged, although
the subject remains a matter of controversy (Shah et al., 2003, 2004; Seveno et al.,
2004). To remove the nonmammalian β(1→2) xylose and α(1→3) fucose residues,
some researchers have explored the possibility of inhibiting the enzymes responsi-
ble for synthesizing these groups, while in one case, this goal has been achieved in
whole A. thaliana plants by gene knockout techniques (Strasser et al., 2004). As dis-
cussed above, the moss P. patens can also be modified by gene targeting to eliminate
these enzymes (Decker and Reski, 2004). Another approach is to prevent the gly-
coproteins passing through the Golgi so that only high-mannose glycans are added.
This can be achieved simply by adding a KDEL C-terminal tag to the antibody, as
demonstrated by Sriraman et al. (2004) and Triguero et al. (2005). This issue has
been reviewed by Gomord et al. (2004).
3.3.1 Downstream Processing

Downstream processing, the isolation and purification of the recombinant product,
is an integral part of every biomanufacturing process. Whichever production system
is used, downstream processing represents up to 80% of overall production costs,
although this depends on the required level of purity and is highest for clinical-
grade materials (Drossard, 2003). In many cases, it is necessary to develop specific
processing steps for each product, although certain classes of product can be isolated
using a standardized approach (e.g., affinity chromatography to isolate recombinant
antibodies; Stoger et al., 2005b). Several aspects of downstream processing have to
be customized specifically for plant systems, including the removal of fibers, oils,
and other by-products from certain crops and process optimization for the treatment
of different plant species and tissues (Menkhaus et al., 2004; Nikolov and Woodard,
2004; Nikolov et al., 2009).
For the production of clinical-grade antibodies, downstream processing steps
need to meet the standards that have been set for other biopharmaceutical produc-
tion systems, including a strict regime of quality assurance and quality control to
achieve approval by regulatory agencies (Fahrner et al., 2001). The initial stages
of processing display the greatest variability and have to be optimized in a system-
specific manner. Disruption of cell walls and membranes is the first postharvesting
step, but different tissue types (leaves, seeds, fruits, etc.) require different forms of
treatments (grinding, milling, etc.). After cell disruption, clarification of the extract
is often carried out by dead-end or cross-flow filtration, sometimes preceded by bulk
cell mass removal using a decanter, plate separator, or centrifuge.
Several liquid chromatography steps are required in a full purification protocol,
and the initial chromatographic steps require the most specialization for plant-based
production (Platis et al., 2008). In industrial processing, robust and inexpensive
chromatography media are used in the initial steps, accepting that there will be some
loss of selectivity and resolution (Bai and Glatz, 2003; Menkhaus and Glatz, 2005).
However, important exceptions include the use of Protein A or Protein G affin-
ity chromatography for antibody purification and the use of affinity tags and their
respective capture agents (e.g., His6 and Ni-NTA resin), which are highly selective
initial capturing methods.
3.3.2 Regulatory Landscape

One of the greatest uncertainties surrounding the use of plants for the production of
pharmaceuticals is the regulatory landscape. While plants are grown in glasshouses
and in enclosed bioreactors, the production of pharmaceuticals is regulated in the
same way as for other production systems and comes under the authority of the FDA
and equivalent agencies in other parts of the world. The switch to open-field con-
ditions adds another layer of regulatory complexity, because the transgenic plants
then come under the authority of APHIS (Animal and Plant Health Inspection Ser-
vice, a part of the USDA) or their counterparts in Europe and other regions. The
involvement of multiple regulatory agencies makes the production process more

complex because the extent of each authority’s jurisdiction is not always clear, and
at the current time, only draft guidelines are available (FDA, 2002; CPMP, 2002,
2006). The impact of this is to suppress the market.
All recombinant pharmaceuticals, including those derived from plants, need to
comply with the national and international GMP (good manufacturing processes)
standards for product safety, quality, potency, and efficacy. However, it is not clear
at which stage GMP requirements should come into effect when plants are used
as the production system, since the strict rules governing defined growth condi-
tions are difficult to implement in the field, where variables such as the weather,
differences in soil quality, and the presence of other organisms need to be consid-
ered (Sparrow et al., 2007; Spök et al., 2008). This is increasingly important now
that European regulatory requirements regarding GMP compliance for the man-
ufacture of medicinal products have extended to the production of clinical trial
material (Directive 2001/20/EC). Another important issue is the different regulatory
structures for plant-derived pharmaceuticals and for genetically modified plants,
in general, prompting calls for the harmonization of regulations internationally
(Ramessar et al., 2008b).
3.4 Conclusions
The production of recombinant pharmaceuticals in plants is advantageous, theo-

retically offering unlimited production scales at unprecedented low manufacturing
costs. We are beginning to overcome the technical limitations, such as low yields,
instability, and nonauthentic glycan structures, that erect obstacles in the path toward
commercialization. But more needs to be done to convince industry that plants rep-
resent a true alternative to CHO (Chinese hamster ovary) cells and bacteria. Despite
the further limitations of a formative and, in some cases, restrictive regulatory frame-
work, the potential of molecular farming can be seen in the rich IP (intellectual prop-
erty) landscape and the multiple cross-licensing and collaborative ventures that are
possible between companies developing production platforms, extraction, and sep-
aration technologies and those with experience in the latter stages of drug develop-
ment and marketing. The welcome announcement of the first approved plant-derived
veterinary vaccine may open the way for antibodies, and in particular antibodies
with therapeutic and diagnostic potential, to follow.
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Chapter 4
Use of Cyanobacterial Proteins to Engineer New
Crops
Matias D. Zurbriggen, Néstor Carrillo, and Mohammad-Reza Hajirezaei
Abstract Cyanobacteria, the closest living relatives of the ancient endosymbiont

that gave rise to modern-day chloroplasts, offer a rich source of genes for
plant genetic engineering, due to both similarities with and differences from the
plant genetic systems. On the one hand, cyanobacteria share many metabolic path-
ways with plant cells, and especially with chloroplasts, which may be critical when
the transgenic product needs to interact with endogenous systems or substrates to
exert its function. On the other hand, most mechanisms involved in plant regula-
tion of gene expression have arisen after endosymbiosis, permitting a more rational
manipulation of the introduced trait, free from host regulatory networks. In addi-
tion, sequence divergence between plant genes and their cyanobacterial orthologues
prevents, in most cases, the unwanted consequences of gene silencing and cosup-
pression. Finally, a few cyanobacterial genes involved in tolerance to environmental
and/or nutritional stresses have disappeared from the plant genome during the evo-
lutionary pathway from cyanobacteria to vascular plants, raising the possibility of
recovering these adaptive advantages by introducing those lost genes into transgenic
plants. In spite of their obvious potential, the use of cyanobacterial genes to engineer
plants for increased productivity or stress tolerance has been relatively rare. In this
chapter, we review several examples in which this approach has been applied to plant
genetic engineering with considerable success. They include modification of central
metabolic pathways to improve carbon assimilation and allocation by expressing
unregulated cyanobacterial enzymes, development of chilling tolerance by increas-
ing desaturation of membrane-bound fatty acids, pigment manipulation, shifts in
light quality perception, production of biodegradable polymers, and synthesis of
ketocarotenoids not present in crops. Tolerance to adverse environments could be
achieved by the introduction of cyanobacterial genes lost from the plant genome
during evolution, such as flavodoxin. The results obtained illustrate the power of
gene and data mining in cyanobacterial genomes as a biotechnological tool for the
M.D. Zurbriggen (B)

División Biología Molecular, Facultad de Ciencias Bioquímicas y Farmacéuticas,
Instituto de Biología Molecular y Celular de Rosario (IBR, UNR/CONICET),
Universidad Nacional de Rosario, S2002LRK Rosario, Argentina

66 M.D. Zurbriggen et al.
design of transgenic plants with higher productivity, enhanced tolerance to environ-

mental stress, and potential for biofarming.
4.1 Introduction
Development of crops with higher productivity, nutritional value, or potential for
biofarming is a major goal of plant biotechnology. Direct transfer of plant genes
has resulted in new varieties with improved properties. However, this approach is
limited by the genetic stock of extant plant species. Therefore, the use of bacterial
genes to engineer crop and model plants has become commonplace, with expres-
sion of the Bt toxin of Bacillus thuringiensis (milky spore bacterium) being the
most conspicuous case of worldwide application to agriculture (for a recent review,
see Jube and Borthakur, 2007). There are also limitations to the use of heterolo-
gous genes in transgenic plants, with important implications for the effectiveness of
the desired manipulation. Several factors play a role in the success of this strategy,
including the expression level of the transgene in the alien environment, successful
interaction with suitable endogenous partners, availability of substrate if the trans-
gene product is an enzyme, compartmentalization, and codon usage. In this sense,
cyanobacteria offer special opportunities for crop improvement due to both impor-
tant similarities with and differences from the plant genetic system. With respect to
the former aspect, it is worth noting that many plant metabolic, regulatory, and dissi-
pative pathways, especially those concerning chloroplast physiology, were evolved
from cyanobacterial ancestors “enslaved” after the successful endosymbiosis that
gave origin to photosynthetic eukaryotes. Many of these routes have not diverged
much, thus allowing productive interactions of the transgenic products with the cor-
responding endogenous systems. At the same time, an unknown number of regu-
latory networks that complicate handling of transgene expression are newcomers
in plant development and are not present in cyanobacteria, permitting a more cus-
tomized manipulation of the engineered traits. The sequence divergence between
plant proteins and their cyanobacterial counterparts also prevents in most cases the
undesired consequences of gene silencing and cosuppression. Finally, a few genes
of cyanobacterial origin have disappeared from the plant genome or have been pro-
foundly modified. Their introduction into plants opens unpredictable possibilities to
regain some of the adaptive advantages that allowed cyanobacteria to flourish and
spread at the beginning of aerobic times on Earth.
The upcoming challenge for the scientists is to use specific genes from various
sources to achieve a broad tolerance of plants to rapidly changing environmental
conditions. In general, the final goal is to develop plants with higher yields or tol-
erant to unfavorable stress situations. It is also an important aim to generate plants
with high-quality food properties or capable of producing renewable products (bio-
farming) (Fig. 4.1). Despite the many potential advantages of cyanobacterial genes,
their use has still been relatively limited. We review herein the various existing
4 Use of Cyanobacterial Proteins 67
Fig. 4.1 Summary of current advances in plant biotechnology using cyanobacterial genes. Gene
mining on cyanobacteria offers a promising opportunity as a tool for biotechnological approaches
examples, highlighting the cases in which their employment was particularly suc-
cessful (Table 4.1).
4.2 Manipulation of CO2 Fixation and Sugar Metabolism
Photosynthetic carbon metabolism is believed to be one major determinant for plant

growth and final yield. To date, huge efforts have been made to use endogenous
genes in order to modify photosynthetic carbon assimilation and partitioning with
the aim to improve plant productivity (Morandini and Salamini, 2003; Geigen-
berger et al., 2004; Long et al., 2006). In most cases, these studies failed to provide
evidence for improvement of plant biomass production, since endogenous genes
derived from higher plants are likely to be prone to fine regulation in vivo. In this
connection, the main reasons could be found in the modulation of enzyme activity
by allosteric effects and covalent modification such as phosphorylation, or via inter-
mediates and effectors such as glucose 6-phosphate (G6P) (Krause et al., 1998),
suggesting that the use of cyanobacterial enzymes with different regulatory mech-
anisms could be a promising alternative. Attempts that have been made to manip-
ulate photoassimilate production, sucrose metabolism, and sugar utilization will be
discussed.
68
Table 4.1 A summary of recent publications related to the use of cyanobacterial proteins in plants to improve growth properties
Protein Donor organism Engineered plant Pathway/function Improvement/advantage References
FBP/SBPase Synechococcus Nicotiana tabacum, Carbon assimilation Avoidance of endogenous Miyagawa et al.
PCC 7942 Chloroplast-targeted (Section 4.2.1) regulation Bifunctional (2001)
(Calvin cycle) enzyme Increased
photosynthetic capacity
Synechococcus
ictB Arabidopsis thaliana Carbon assimilation Increased photosynthetic Lieman-Hurwitz
PCC 7942
Nicotiana tabacum (Section 4.2.1) capacity and growth et al. (2003)
(Calvin cycle)
SPS Synechocystis Nicotiana tabacum, Sucrose metabolism Avoidance of endogenous Curatti et al. (1998)
PCC6803 Solanum lycopersicum, (Section 4.2.2) regulation Increased sucrose
Oryza sativa (Sucrose synthesis) synthesis
PEPC Corynebacterium Vicia narbonensis Sugar utilization Avoidance of endogenous Rolletschek et al.
glutamicum Arabidopsis thaliana (Section 4.2.3) regulation Increased protein (2004)
Synechococcus (aminoacid content Chen et al. (2002)
vulcanus biosynthesis)
9 -desaturase Anacystis nidulans Nicotiana tabacum Lipid desaturation Novel desaturase. Cold Ishizaki-Nishizawa
Chloroplast-Targeted (Section 4.3) tolerance et al. (1996)
Acyl-lipid Synechococcus Nicotiana tabacum Lipid desaturation Cold tolerance Orlova et al. (2003)
9 -desaturase vulcanus (Section 4.3)
6 -desaturase Synechocystis Nicotiana tabacum Lipid desaturation Polyunsaturated fatty acid Reddy and Thomas
(Section 4.3) synthesis (1996)
(γ-linolenic acid
synthesis)
M.D. Zurbriggen et al.
4
Protein Donor organism Engineered plant Pathway/function Improvement/advantage References
CAO Prochlorothrix Arabidopsis thaliana Pigment manipulation Avoidance of endogenous Hirashima et al.
hollandica (Section 4.4) regulation (2006)
Change in pigment
composition
β-Carotene Synechocystis Solanum tuberosum, Pigment manipulation Novel compounds Gerjets and
ketolase Nicotiana glauca (Section 4.4) (astaxanthin) Sandmann (2006)
(ketocarotenoid Zhu et al. (2007)
synthesis)
Use of Cyanobacterial Proteins
Cyanophycin Thermosynechococcus Nicotiana tabacum, Production of Biofarming. Production of Neumann et al.

synthetase elongatus Solanum biodegradable cyanophycin (2005)
tuberosum (cytosol), polymers Hühns et al.
Nicotiana tabacum (Section 4.5) (2008)
(chloroplasts)
Fd-PCB Synechocystis Arabidopsis thaliana Phytochrome perception Shift in phytochrome Kami et al. (2004)
reductase PCC6803 (Section 4.6) reaction spectra
(synthesis of PCB)
Fld Anabaena PCC7119 Nicotiana tabacum Electron transport Multiple stress tolerance Tognetti et al.
(Section 4.7) (2006, 2007)
Zurbriggen et al.
(2008)
Cyt c 6 Porphyra yezoensis Arabidopsis thaliana Electron transport Improved metabolism Chida et al. (2007)
(Section 4.8)
DnaE intein Synechocystis Arabidopsis thaliana Protein splicing Novel biotechnological Yang et al. (2003)
PCC6803 (cytosol and (Section 4.8) tool Chin et al. (2003)
69
chloroplasts)
4.2.1 Carbon Assimilation

The Calvin cycle, which is the primary route for carbon assimilation in the chloro-
plasts of C3 plants (Sharkey, 1985), can be divided into three phases. The first one
involves carboxylation of the CO2 acceptor molecule, ribulose-1,5-bisphosphate
(RuBP) catalyzed by ribulose-1,5-bisphosphate-carboxylase/oxygenase (Rubisco),
generating 3-phosphoglycerate (3PGA). In the second phase, the reduction step,
3PGA, is converted to triose phosphate, and finally, the regeneration phase pro-
duces the acceptor molecule RuBP for CO2 assimilation (Fig. 4.2). The assimi-
lates formed are used either to synthesize transitory starch in the plastids or to
produce sucrose in the cytosol (Quick and Neuhaus, 1997). In order to main-
tain a balance between the photoassimilate export to the cytosol and the regen-
eration of the acceptor molecule, RuBP, an accurate regulation of the enzymes
involved in the Calvin cycle is necessary. Transgenic approaches, mainly through
downregulation of endogenous genes, have been performed to identify rate-limiting
steps of the CO2 fixation pathway. Decreases in the amounts of Rubisco acti-
vase, NADP+ -dependent glyceraldehyde-3-P dehydrogenase (GAPDH), plastidic
fructose-1,6-bisphosphatase (FBPase), and aldolase have been reported (for details,
see Frommer and Sonnewald, 1995). Based on the results obtained, the authors
conclude that a successful modulation of metabolite distribution can only be
achieved by using unregulated enzymes such as the plastidic aldolase. Follow-
ing this rationale, Miyagawa et al. (2001) isolated a bifunctional unique enzyme,
fructose-1,6-/sedoheptulose-1,7-bisphosphatase (FBP/SBPase), from Synechococ-
cus PCC 7942 and demonstrated that it could hydrolyze both FBP and SBP with
almost equal specific activities. The absence of homology between this enzyme and
higher plants’ FBPase and/or SBPase encouraged Miyagawa and coworkers to use
it for genetic engineering. Overexpression of the cyanobacterial gene in tobacco
plants (Nicotiana tabacum) under the control of the tomato rbscS promoter and
chloroplast-targeting sequence led to an increased photosynthetic capacity in source
leaves, carbohydrate accumulation, and accelerated growth rate (Miyagawa et al.,
2001). Recently, Tamoi et al. (2006) generated transgenic tobacco plants express-
ing either Synechococcus PCC 7942 FBPase-II or Chlamydomonas SBPase in the
chloroplasts to study the individual contribution of each enzyme. Interestingly, the
same increase (1.6- to 1.7-fold) in the activities of either SBPase or FBPase resulted
in different outcomes. While higher SBPase activity led to enhanced photosynthetic
rates, FBPase overexpression failed to improve photosynthesis. Using antisense
RNA technology, Kossmann et al. (1994) were able to show that photosynthesis and
growth rate were drastically inhibited in potato (Solanum tuberosum) plants only
when the FBPase activity was reduced below 14% of the wild-type (WT) levels.
In contrast, antisense inhibition of SBPase activity strongly affected the photosyn-
thetic pathway (Harrison et al., 1998, 2001). In plants with about 30% remaining
SBPase activity, photosynthetic rates were diminished by 36%. Collected data sug-
gest that SBPase is one of the primary limiting factors for RuBP regeneration in
the Calvin cycle and that an increase in its activity causes a shift toward FBPase as
a rate-limiting step of the photosynthetic carbon fixation. In conclusion, the use of
Fig. 4.2 Schematic presentation of the interaction between source and sink tissue
in plants. Some crucial regulatory steps are indicated in red. Abbreviations: 1,3diPGA,
1,3-diphosphoglycerate; Fru, fructose; Glc, glucose; G1P, glucose 1-phosphate; GAP, glyceralde-
hyde 3-phosphate; Ru5P, ribulose 5-phosphate; S7P, sedoheptulose 7-phosphate. Other abbrevia-
tions are given in the text
either the unique enzyme FBP/SBPase or the single gene SBPase not only allows
one to predict rate-limiting steps within the CO2 fixation pathway but also leads to
improvement of metabolic activity and thus to an increase in photosynthetic capac-
ity and biomass production of plants.
In a further attempt to improve photosynthetic performance, Lieman-Hurwitz
et al. (2003) expressed the ictB gene in Arabidopsis and tobacco plants. ictB is
supposed to be involved in HCO3 − accumulation within the cyanobacterium Syne-
chococcus sp. PCC 7942. Characterization of a mutant of this strain with high CO2
requirements revealed that the ictB gene is highly conserved among cyanobacteria
and is probably involved in inorganic carbon accumulation (Lieman-Hurwitz et al.,
2003). Transgenic Arabidopsis thaliana and tobacco plants expressing the ictB gene
showed enhanced photosynthesis and growth at limiting CO2 levels. The increased
photosynthetic rate is thought to be due to a higher Rubisco activity. Similar results
were also reported for the transgenic plants expressing the Synechococcus fructose-
1,6-/sedoheptulose-1,7-bisphosphatase (FBP/SBPase) in order to increase the level
of Ribulose-1,5bisP and thereby the photosynthetic rate (Miyagawa et al., 2001).
Taking this possibility into account, ictB was shown to be a potential useful tool
to enhance the yield of C3 plants, specially under specific conditions such as low
humidity in which stomatal closure may lead to CO2 limitation and thus to a retar-
dation of growth (Lieman-Hurwitz et al., 2003).
4.2.2 Sucrose Metabolism

Photosynthetically produced assimilates are exported to the cytosol and distributed
between various metabolic pathways such as glycolysis, amino acid metabolism,
and sucrose biosynthesis (Fig. 4.2). Since sucrose is the preferred transport form of
sugars toward sink organs in plants, its synthesis might be a rate-limiting step to
establish a balanced partitioning between sucrose and starch biosynthesis. Sucrose
is primarily formed from UDP-glucose (UDPGlc) and fructose-6-phosphate (F6P)
followed by dephosphorylation of the resulting sucrose-6-phosphate (S6P) to yield
sucrose. The first step of sucrose biosynthesis is catalyzed by sucrose-6-phosphate
synthase (SPS), an enzyme modulated by several mechanisms. On the one hand,
plant SPS is regulated by metabolites including G6P, which acts as an activator,
and inorganic phosphate, which has an inhibitory effect. On the other hand, SPS is
regulated by posttranslational modification via phosphorylation (Huber and Huber,
1992). Antisense RNA technology has been used to reduce the amount of SPS in
potato plants to investigate whether it exerts a control step in sucrose synthesis
(Krause et al., 1998). A 60–70% decrease in SPS activity led to a 40–50% inhi-
bition of sucrose synthesis and to a 34–43% stimulation of starch and amino acid
synthesis. Interestingly, the decrease in SPS amounts was partially compensated by
an increase in the activation state of the residual protein, being about 1.4-fold higher
in the best antisense plant as compared to nontransformed plants. Based on these
results, Krause et al. (1998) concluded that SPS plays a crucial role in controlling
sucrose synthesis, but it is not the only step of regulation between sucrose and
starch partitioning. All these observations led to the assumption that an increase
of SPS might result in an enhanced rate of sucrose biosynthesis and thus to a higher
final yield of plant productivity. Overexpression of maize SPS in transgenic tomato
(Solanum lycopersicum) resulted in a three- to sevenfold increase in SPS activity
(Galtier et al., 1993), while overexpression of spinach SPS led to a two- to three-
fold increase in SPS activity in transgenic tobacco and potato plants, respectively
(Krause, 1994). A detailed investigation of the transgenic plants revealed that only a
small stimulation of sucrose synthesis occurred in transgenic tobacco plants. Deter-
mination of the activation state showed that most of the excess SPS was deacti-
vated, presumably due to posttranslational modifications. On the other hand, Curatti
et al. (1998) identified and characterized a gene encoding SPS from Synechocys-
tis PCC6803, whose product was insensitive to G6P and only weakly inhibited
by phosphate. In addition, Synechocystis SPS lacks all the known phosphoryla-
tion sites found in plant SPS (Lunn et al., 1999). Expression of this nonregulated
SPS in tobacco, tomato, and rice (Oryza sativa) under the control of the constitutive
cauliflower mosaic virus 35S (CaMV 35S) promoter for tobacco and tomato, and the
constitutive maize Ubi1 promoter for rice, resulted in a two- to eightfold increase
in transcript levels (Lunn et al., 1999). In spite of these high expression levels, no
evidence could be found that the enzyme was active in leaf extracts (Lunn et al.,
2003). Interestingly, purified Synechocystis SPS from transgenic tobacco and rice
plants showed full catalytic activity. Based on these results, the authors proposed
that Synechocystis SPS expressed in plants is inherently active, but it is inhibited in
vivo by interacting with an endogenous plant protein. The nature of this protein, as
well as the mechanism of its interaction with SPS, has not yet been elucidated.
4.2.3 Sugar Utilization

Among various attempts to engineer plants with enhanced sink capacity (see
Frommer and Sonnewald, 1995), the use of genes playing a crucial role in assim-
ilate utilization might be useful to introduce a C4-like pathway to C3 plants by
genetic engineering. To this end, transgenic plants have been created using phospho-
enolpyruvate carboxylase (PEPC) from Corynebacterium glutamicum (Rolletschek
et al., 2004) or from the thermophilic cyanobacterium Synechococcus vulcanus
(svPEPC, Chen et al., 2004). PEPC catalyzes the addition of CO2 to PEP to pro-
duce oxalacetate, which is the direct precursor for the synthesis of amino acids such
as aspartate, asparagine, threonine, methionine, and lysine (Fig. 4.2). The obvious
advantage of the bacterial PEPC is that the enzyme is very stable, lacks a reg-
ulatory phosphorylation site, and does not require acetyl-coenzyme A (Ac-CoA),
which usually acts as an allosteric activator (Chen et al., 2002). Furthermore, bac-
terial PEPC is, in contrast to plant PEPC, insensitive to feedback inhibition by
malate (Chen et al., 2002; Chollet, 1996). When the PEPC gene from C. glutam-
icum was expressed in bean (Vicia narbonensis) plants, amino acid biosynthesis
was enhanced and an increase (ca. 20%) in protein content of dry seeds could be
achieved (Rolletschek et al., 2004).
In a similar study using svPEPC, Chen et al. (2004) generated three different
types of transgenic Arabidopsis plants: type-I was retarded in growth and leaf devel-
opment; type-II displayed reduced leaf growth; and type-III was apparently normal.
Biochemical analysis of the different plant types revealed that a switch in amino
acid metabolism and growth recovery was observed by the addition of aromatic
amino acids to the growth medium. Based on their results, the authors proposed
that svPEPC is able to efficiently exert its activity in the plant cell environment
(Chen et al., 2004).
Interestingly, cyanobacterial genes not only can be used to accelerate a specific
metabolic route but could also be used to answer relevant biological questions. In
this regard, Ryu et al. (2008) demonstrated that a cyanobacterial glucokinase, which
has both a catalytic and a sugar-sensing activity in Escherichia coli, yeast, and
mammals, can complement the glucose-sensing function of Arabidopsis hexoki-
nase1 (HXK1). The gene encoding cyanobacterial glucokinase was overexpressed in
the background of an Arabidopsis glucose-insensitive2 (gin2) mutant. This mutant
lacks the normal specific physiological function of hexokinase (HXK1) in the
plant glucose-signaling network. Noteworthy, the transgenic plants showed glucose-
sensitive phenotypes with glucose-induced decreases of chlorophyll and transcript
levels of the Rubisco small subunit (Ryu et al., 2008).
4.3 Lipid Desaturation and Cold Tolerance
Many plant species, including several important crops such as rice, maize (Zea
mays), and soybean (Glycine max), are injured or killed by exposure to low non-
freezing temperatures in the range of 0–15◦ C. Low-temperature photoinhibition is
one of the major factors that limits plant productivity. It has been shown that low
temperatures cause a decrease in the fluidity of biological membranes. The capabil-
ity of cells to acclimate to cold is largely determined by their ability to synthesize the
unsaturated fatty acids that fluidize the lipid bilayer and prevent lipids from undergo-
ing cold-induced phase separation (Orlova et al., 2003). Polar lipids containing only
saturated fatty acids display phase separations in the range of 30◦ C, but the pres-
ence of a single centrally positioned cis-double bond in the fatty acid decreases the
transition temperature to about 0◦ C, providing the membrane lipids with enhanced
molecular motions at low temperatures. Plant chloroplasts have a soluble desat-
urase that introduces double bonds at the 9 position of saturated fatty acids linked
to the acyl carrier protein (ACP) (Fukuchi-Mizutani et al., 1998; Orlova et al.,
2003). It is believed that desaturation occurs largely in the chloroplast stroma by
the acyl-ACP desaturase, limiting the cell’s ability to respond to temperature shifts
through desaturation of fatty acids already incorporated into membranes (Ishizaki-
Nishizawa et al., 1996). Transformation of tobacco plants with a 9 -desaturase gene
from Anacystis nidulans under the control of the CaMV 35S constitutive promoter
and a chloroplast-targeting sequence led to a significant increase in chilling toler-

ance (Ishizaki-Nishizawa et al., 1996). The cyanobacterial enzyme was nonspecific
with respect to substrate and could use both acyl-lipids and acyl-ACP, resulting in
higher levels of unsaturated fatty acids in most membrane lipids (Ishizaki-Nishizawa
et al., 1996). Similar results have been obtained in tobacco plants transformed with
an acyl-lipid desaturase gene from S. vulcanus (Orlova et al., 2003).
Lipid desaturation is also related to attempts to produce seed oils rich in essential
fatty acids, making them nutritionally superior (Reddy and Thomas, 1996). Triun-
saturated γ-linolenic acid (GLA), for instance, is important in human and animal
diets, and consumption of vegetable oils containing GLA is thought to alleviate
hypercholesterolemia and other related clinical disorders that correlate with sus-
ceptibility to coronary heart disease (Brenner, 1976). GLA does not accumulate in
oilseed crops and can only be found in a few plant species such as evening primrose
(Oenothera biennis), currant (Ribes spp.), and borage (Borago officinalis) (Reddy
and Thomas, 1996). Cyanobacteria, instead, have a 6 -desaturase that catalyzes the
synthesis of GLA from linoleic acid (Reddy et al., 1993). Transformation of tobacco
seedlings with the 6 -desaturase gene from Synechocystis under the control of the
CaMV 35S promoter generated transgenic plants with significant amounts of GLA
in their leaves, irrespective of whether the foreign enzyme was targeted to chloro-
plasts, to the cytosol, or to the endoplasmic reticulum (Reddy and Thomas, 1996).
Moreover, all lines produced even higher levels of octadecatetraenoic acid, a tetraun-
saturated fatty acid not present in plants that has numerous industrial uses, including
the production of oil films, special waxes, and plastics (Reddy and Thomas, 1996).
4.4 Pigment Manipulation
The organization of pigment molecules in photosystems is strictly determined. The

peripheral antenna complexes may contain chlorophyll a and b, and even other types
of pigments depending on the organism. But the core antennae of virtually all organ-
isms displaying oxygenic photosynthesis admit only chlorophyll a and β-carotene.
The diverse pigment composition of peripheral antennae is a beneficial feature that
enables plants to absorb multiple wavelengths from the broad range of the light spec-
trum that is available for photosynthesis (Fromme et al., 2001). In contrast, the pig-
ment and protein compositions of the core antennae do not change under any envi-
ronmental conditions that have been tested. The reasons for this strict discrimination
have been attributed to a regulatory domain of chlorophyllide a oxygenase (CAO),
the enzyme responsible for chlorophyll b synthesis, which modulates the levels of
this pigment. Cyanobacterial genes have been employed to evaluate this tenet by
transforming Arabidopsis plants with a CAO gene from Prochlorothrix hollandica,
which lacks the regulatory domain. About 40% of chlorophyll a in the core antenna
complexes of the transformants could be replaced by chlorophyll b with concomi-
tant changes in the photosynthetic action spectrum (Hirashima et al., 2006). Trans-
genic plants were able to grow like the wild type under low light intensity conditions
(80 μmol photons m−2 s−1 ) but underwent severe damage at the level of photosys-
tem II at higher irradiations ranging from 300 to 1,000 μmol photons m−2 s−1
(Hirashima et al., 2006).
Carotenoids constitute a vast group of lipophilic pigments synthesized by
microorganisms and plants, in which they participate in light capture and photo-
protection. Typical carotenoids contain 8 isoprenoid units (40 carbon atoms) and
an extended conjugated polyene system, which may carry hydroxyl, epoxy, or keto
groups. The ketocarotenoids, one type of carotenoids, are especially light stable
and display high antioxidant capacities (Guerin et al., 2003; Higuera-Ciapara et al.,
2006). They impart a distinct reddish color to tissues that accumulate them, such as
the flesh of salmon and crustaceans, and their antioxidant effects are of particular
interest in the food, nutraceutical, and aquaculture industries. Recent research has
demonstrated their anticancer and antibacterial properties, as well as potential bene-
fits in boosting the immune system and preventing cardiovascular disease, cataracts,
and tissue damage from ultraviolet radiation (Guerin et al., 2003; Higuera-Ciapara
et al., 2006).
Astaxanthin is one of the most important commercial ketocarotenoids derived
from β-carotene by 3-hydroxylation and 4-ketolation at both ionone end-groups
(Sandmann, 2001). Most of its demand is met by chemical synthesis; yet, natu-
ral sources are becoming more important (Guerin et al., 2003). The hydroxyla-
tion reaction is widespread in many organisms, but ketolation is restricted to a
few bacteria (including cyanobacteria), fungi, and unicellular green algae. Plants
are devoid of ketocarotenoids, but a cyanobacterial ketolase gene has been intro-
duced in both potato tubers (Gerjets and Sandmann, 2006) and tobacco (Nicotiana
glauca) flowers and leaves (Zhu et al., 2007). In the first case, plants were trans-
formed with a Synechocystis β-carotene ketolase gene, crtO, and ketocarotenoids
represented 10–12% of total carotenoids in leaves and tubers of the transformants
(Gerjets and Sandmann, 2006). In the second case, the same gene was introduced
in N. glauca, a species containing highly carotenogenic flowers, potentially repre-
senting new sources of ketocarotenoids. Upon transformation, high levels of keto-
carotenoids were found in all flower parts and leaves, with no concomitant decrease
in carotenoid contents accounting for an upregulation of total carotenoid quantities
(Zhu et al., 2007).
4.5 Production of Biodegradable Polymers
Plants are being widely used as bioreactors for the industrial production of bioactive
peptides, vaccines, hormones, antibodies, and other proteins (Fischer et al., 2004;
Gomord et al., 2005; Hellwig et al., 2004; Twyman et al., 2003). Biopharming is also
an environmentally acceptable and competitive way of producing several chemical
compounds used as raw material for the pharmaceutical and chemical industries.
An increasingly important challenge is the manufacture of biodegradable polymers
in transgenic plants, such as polyamino acids, to replace petrochemical compounds,
which tend to become expensive and scarce (Neumann et al., 2005). Among them,
polyaspartate is a soluble, nontoxic and biodegradable polycarboxylate widely used
in many industrial, agricultural, and medical applications (Oppermann-Sanio and
Steinbüchel, 2002). Polyaspartate is the backbone of the cyanobacterial carbon
and nitrogen storage material cyanophycin, a zwitterionic copolymer of L-aspartic
acid and L-arginine. It is produced via nonribosomal polypeptide biosynthesis by
the enzyme cyanophycin synthetase, encoded by the cphA gene, which is present
in many cyanobacterial and some noncyanobacterial eubacteria (Hühns et al., 2008;
Krehenbrink et al., 2002; Ziegler et al., 2002). Cyanobacterial cyanophycin is poly-
disperse (25–125 kDa), water insoluble, and stored in granules without membranes.
No organism produces polyaspartate; consequently, its industrial production has
relied either on chemical synthesis or on the hydrolysis of purified cyanophycin
obtained from cyanobacteria, after expensive and resource-consuming growth and
harvest of the microorganisms. Lately, a highly water-soluble polymer similar to
cyanophycin has been produced in E. coli cells expressing a cyanophycin synthetase
from Desulfitobacterium hafniense (Ziegler et al., 2002). Nevertheless, the need for
cost-intensive bioreactors reduces the cost-effectiveness of this production proce-
dure (Neumann et al., 2005).
Neumann et al. (2005) succeeded in producing cyanophycin in transgenic
N. tabacum plants expressing the coding region of the chpA gene of Thermosyne-
chococcus elongatus BP-1 in the cytosol under the control of the CaMV 35S pro-
moter. The transgenic tobacco plants were found to produce up to 1.1% dry weight
of both a water-soluble and a water-insoluble form of the polymer of size, com-
position, and structure very similar to those of the cyanobacterial cyanophycin.
Afterward, they used the same technology in order to develop transgenic potato
(S. tuberosum) plants with the aim of synthesizing cyanophycin in tubers. Har-
vesting of the polymer from the residues of starch isolation would conform to a
high yield and a cost-effective method. However, the authors obtained a decreased
content of cyanophycin in leaves (0.24% dry weight) in comparison to tobacco
and could only demonstrate the presence of cyanophycin in tubers by electron
microscopy. For both species, the resulting transgenic plants exhibited a deceler-
ated growth rate, variegated leaves, and changes in chloroplast morphology. These
undesired consequences could be related to exhaustion of the amino acid resources
of the plant due to cyanophycin production or to the presence of cyanophycin
aggregates in the cytoplasm, which could interfere with the normal metabolism of
this compartment (Neumann et al., 2005). To overcome these limitations, and at
the same time to increase polymer accumulation, Hühns et al. (2008) generated
tobacco transgenic plants in which the gene of the cyanophycin synthetase was
fused in-frame to a chloroplast-targeting sequence in order to direct the enzyme
to this organelle. The resulting plants were able to produce 6.8% dry weight
cyanophycin together with reduced stress symptoms. Achievement of higher poly-
mer accumulation in chloroplasts than in cytoplasm could be due to the similitude of
plastids with cyanobacteria, in which cyanophycin is synthesized naturally without
causing any deleterious effects. What is more, the building blocks of cyanophycin,
i.e., L-arginine and L-aspartate, are directly available in chloroplasts because
the synthesizing enzymes are located in this compartment (Hühns et al., 2008;
Chen et al., 2006). Transgenic plants expressing specific cyanobacterial enzymes
catalyzing new reactions could be utilized to produce renewable resources. In
this example, plant-produced cyanophycin could provide for a nonexpensive and
environment friendly production of polyaspartate, which could be a most likely
biodegradable substitute for polycarboxylates and polyacrylates for the industry.
4.6 Phytochrome Perception and Plant Development
Light quality, quantity, and duration influence nearly every stage of plant growth
and development. In vascular plants, red (R) and far-red (FR) lights are sensed pri-
marily by the phytochrome family of photoreceptors (Casal et al., 2003). The cova-
lently bound phytochromobilin (PB) prosthetic group is required for the diverse
activities of all members of the family. Mutant lines that are unable to produce PB
display aberrant photomorphogenesis with pleiotropic phenotypes that are most pro-
nounced under R and FR illumination. Interestingly, green algal and cyanobacterial
phytochromes employ the more reduced linear tetrapyrrole phycocyanobilin (PCB),
which displays a slightly different action spectrum (Frankenberg et al., 2001). The
difference is based on the existence of a distinct stock of enzymes in the two types
of organisms: a PB synthase in plants that converts biliverdin into PB and a
ferredoxin (Fd)-PCB reductase in algae and cyanobacteria that yields PCB as end-
product.
To determine if PCB could be assembled in plant phytochromes and as a
result to change the light quality responses of plants, Kami et al. (2004) intro-
duced the Fd-PCB reductase gene of Synechocystis PCC6803 into an Arabidopsis
mutant line that lacked PB synthase activity and was therefore unable to synthe-
size the normal phytochrome chromophore. The resulting transformants restored
phytochrome activities to WT levels, albeit with blue-shifted absorption maxima.
Expression of the cyanobacterial enzyme rescued phytochrome-mediated R and FR
responses, and only the high-irradiance FR response was shifted to shorter wave-
lengths (Kami et al., 2004). This result indicates that PCB can function in vascular
plants. It also allows dissection of functional features in the chromophore molecule.
4.7 The Case for the Lost Genes: Flavodoxin and Multiple
Stress Tolerance
Environmental adversities such as drought and extreme temperatures, exposure to
human-produced chemicals, and nutrient-poor soils usually affect plants growing in
natural habitats (Vij and Tyagi, 2007). Among nutritional deficits, iron deprivation
ranks at the top, as it is required for the function of a great number of metalloen-
zymes that are central to plant energetics and metabolism. Iron limitation is espe-
cially critical in the widespread alkaline calcareous soils where its bioavailability
is highly restricted (Guerinot, 2007; Kim and Guerinot, 2007). These factors place
major limits on plant growth and yield, and they account for much of the extensive
losses to agricultural production worldwide (Boyer, 1982). To overcome these lim-
itations and to improve production efficiency in the face of a world with increasing
food demands, more and better stress-tolerant crops must be developed.
Plant adaptation to environmental stresses is dependent upon the activation of
cascades of molecular networks involved in stress perception, signal transduc-
tion, and the expression of specific stress-related genes and metabolites. There-
fore, responses to abiotic stresses are multigenic and thus are difficult to control and
engineer (Vinocur and Altman, 2005). Past efforts to improve plant stress tolerance
through breeding and genetic engineering have had limited success precisely due to
this genetic complexity (Cushman and Bohnert, 2000). In addition, many projects
involving manipulation of endogenous plant genes faced intrinsic limitations such
as cosuppression and misregulatory phenomena. One approach that has not yet been
explored to any great extent is to take advantage of the tools available from plant
ancestors, namely the cyanobacteria.
Ferredoxin (Fd) is an iron–sulfur protein present in all photosynthetic organisms
ranging from cyanobacteria to plants. It is the final electron acceptor of the pho-
tosynthetic electron transport chain (PETC) and is essential for the distribution of
low-potential reducing equivalents to central metabolisms like CO2 fixation, nitro-
gen and sulfur assimilation, amino acid synthesis, fatty acid desaturation, as well
as many regulatory (e.g., thioredoxin (Trx) redox regulation system) and dissipa-
tory pathways (Fig. 4.3, see Hase et al., 2006). Fd levels experience a considerable
decrease in response to environmental stresses and other sources of reactive oxy-
gen species (ROS) production as a consequence of tight transcriptional and/or post-
transcriptional regulatory systems operating under these conditions (Singh et al.,
2004; Zimmermann et al., 2004). Likewise, iron deficiency also leads to dimin-
ished Fd levels. This affects central metabolisms as well as defense and regulatory
mechanisms, thus compromising cell survival (Fig. 4.3, see Thimm et al., 2001;
Erdner et al., 1999). Photosynthetic microorganisms like cyanobacteria and cer-
tain algae deploy an adaptive response meant to tackle Fd decrease upon stress by
synthesizing an isofunctional electron carrier, flavodoxin (Fld). Fld contains flavin
mononucleotide instead of iron as prosthetic group, is resistant to ROS inactiva-
tion, and is able to engage in most Fd reactions, albeit with somehow less effi-
ciency. Fd substitution results in the restoration of electron delivery to produc-
tive pathways, therefore preventing misrouting of reducing equivalents to O2 and
the concomitant ROS production. The net outcome is augmented tolerance toward
various sources of stress in algae and cyanobacteria (Erdner et al., 1999; Singh
et al., 2004; Palenik et al., 2006). As a matter of fact, Fld induction has been
used for many years as a reliable marker of iron deficiency in the oceans and
constitutes a key selective advantage for colonization of iron-poor waters by phyto-
plankton (Erdner et al., 1999). Fld is absent in the plant genomes; it was lost some-
where in the evolutionary transition from green algae to vascular plants, rendering
the latter unable to put into use such an efficient adaptive mechanism of defense
(Zurbriggen et al., 2007). Nevertheless, some plant enzymes, whose cyanobacterial
Fig. 4.3 Cyanobacterial Fld is able to substitute for chloroplast Fd functions. Chloroplast Fd
plays a central role in the distribution of reducing equivalents generated during photosynthesis.
Electrons originating in the PETC may be transferred via Fd to FNR for NADP+ photoreduc-
tion, generating the NADPH necessary for the Calvin cycle and other biosynthetic and protective
pathways. Reduced Fd is also the electron donor for nitrite and sulfite assimilation via nitrite and
sulfite reductases, for fatty acid desaturation by fatty acid desaturase, and for glutamate synthesis
mediated by glutamate–oxoglutarate aminotransferase (GS-GOGAT). Still other Fd molecules will
participate in Trx reduction via Fd–Trx reductase (FTR). Reduced Trx will then activate key tar-
get enzymes through reduction of their critical cysteines (–SH/–S–S– exchange), resulting in the
maintenance and/or stimulation of the Calvin cycle, the malate valve process, and other metabolic
routes. Dissipative systems requiring Fd include regeneration of active peroxiredoxins, the most
abundant peroxidase of chloroplasts, and of ascorbate. Fd also regulates the distribution of reduc-
ing equivalents between lineal and cyclic electron flow via Fd-ubiquinol reductase. Finally, it par-
ticipates in developmental processes through the synthesis of phytochromobilin, the chromophore
of the light sensor phytochrome, by donating electrons to two key enzymes of the pathway: heme
oxygenase and phytochromobilin synthase. On exposure to iron-deficit or adverse environments,
Fd levels are downregulated and the foreign Fld is proposed to take over electron distribution to
Fd redox partners in chloroplasts. Abbreviations: Ac-CoA, acetyl-coenzyme A; AGPase, ADP-
glucose pyrophosphorylase; DAHP, 3-deoxy-D-arabino-heptulosonate 7-phosphate; G6PDH, glu-
cose 6-phosphate dehydrogenase; GWD, α-glucan water dikinase; MDH, malate dehydrogenase;
MGDG, monogalactosyldiacylglycerol synthase; OPPP, oxidative pentose phosphate pathway;
PRK, phosphoribulokinase. Other abbreviations are given in the text. Adapted from Zurbriggen
et al. (2008)
counterparts used Fld as substrate (including Fd-NADP+ reductase (FNR) and Fd-
Trx reductase), are still able to engage with the flavoprotein in the electron transfer
reactions normally performed by Fd (Fig. 4.3) (Tognetti et al., 2008; Zurbriggen
et al., 2008). These observations triggered the obvious inquiry to evaluate if Fld
introduction into plants could improve tolerance to abiotic stress and iron defi-
ciency, as it occurs in microorganisms. Transgenic tobacco plants constitutively
expressing the Fld gene from Anabaena under the control of the CaMV 35S pro-
moter were thus engineered. A plastid-targeting sequence was fused in-frame to
the Fld gene to direct the protein to chloroplasts (pfld lines). Several indepen-
dent transformed lines were therefore obtained and selected for Fld expression lev-
els. It is worth noting that transgenic plants from the different lines grown under
normal conditions exhibited no significant phenotypic differences in relation to
WT individuals with respect to growth rate, flowering time, and seed production
(Tognetti et al., 2006).
Plants expressing 60 μM Fld (a level similar to endogenous Fd) were able to
survive and even to increase in height, fresh weight, and dry weight when subjected
to iron-deficiency protocols, whereas WT specimens exhibited the typical symp-
toms of this nutrient scarcity such as interveinal chlorosis, growth retardation, and
high lethality rates. The transgenic plants failed to improve iron uptake or accre-
tion and even developed a normal response to iron shortage, including induction of
different genes involved in metal uptake, mobilization, and storage (Tognetti et al.,
2007). Fld expression prevented the general decrease in CO2 fixation capacity and
downregulation of metabolic activities manifested by the nontransformed plants.
Moreover, it preserved the activation state of key plastidic enzymes that depend
on the Fd–Trx system like phosphoribulokinase (PRK) and FBPase. As a result,
the levels of many central metabolites belonging to the Calvin cycle, energy stor-
age, and anabolic routes, as well as the contents of most amino acids, were signifi-
cantly higher in the transformants (Tognetti et al., 2007). Taken together, the results
indicate that Fld expression could compensate for Fd decline occurring upon iron
deficiency by successfully engaging in at least some of the Fd-dependent pathways
of plant chloroplasts. It is tempting to consider that reallocation of available iron
to other demanding routes probably contributes to the general welfare of the iron-
starved pfld plants.
Plants expressing Fld in plastids were also able to withstand a remarkable range
of environmental stresses, including high temperature, chilling, drought, high light
intensities, UV radiation, and exposure to the redox-cycling herbicide methyl violo-
gen (MV), all having as a common feature ROS buildup and the establishment of an
oxidative stress condition (Tognetti et al., 2006). These stresses cause Fd downreg-
ulation independently of a general protein content breakdown, leading to potential
malfunction of the electron transport pathways and systems dependent on the iron–
sulfur protein. Tolerance was evidenced in the transformants by preservation of leaf
turgor, cellular and membrane integrity, and plastid ultrastructure. Fld expression
also preserved photosynthetic capacity, thus maintaining high levels of CO2 fix-
ation. Buildup of various ROS was impaired and there was little photooxidative
damage to PETC components. These observations have direct implications for the
antioxidant protection provided by Fld. Its involvement in NADP+ photoreduction

and Trx reduction helps to relieve the electron pressure imposed onto the PETC by
the stress condition. The latter function is crucial, as maintenance of high levels of
reduced Trx in the transgenic plants favors dissipative and scavenging pathways,
e.g., Prx-reductive regeneration to eliminate H2 O2 and organic peroxides produced
under stress, export of the excess of reducing power via the malate valve, and pro-
ductive consumption of the surplus of NADPH by the Calvin cycle. Finally, as is the
case with iron deficiency, the extent of protection conferred by the flavoprotein is
strictly dose dependent, with low-expressing lines displaying WT levels of tolerance
(Tognetti et al., 2006).
Fld expression thus restores electron transfer to productive routes, ameliorating
the damage suffered by stressed (or iron-starved) plants caused by faulty elec-
tron distribution within plastids and cells, leading to a healthy physiological con-
dition (Fig. 4.3, see Zurbriggen et al., 2008). It prevents an excessive reduction
of the PETC, which would result in ROS accumulation and impairment of key
metabolic, regulatory, and dissipatory pathways. Transfer of this technology to
crops is still at a preliminary stage, but increased tolerance to MV, water depri-
vation, and/or UV irradiation has already been observed in tomato, potato, Bras-
sica, barley, and maize lines, as reflected by lower damage to cells and tis-
sues, higher chlorophyll levels and growth rates, and in some cases, higher seed
yield (Zurbriggen et al., 2008). It is clear, then, that the expression of a single
gene from a photosynthetic prokaryote can be used as a general technology to
improve plant productivity and to utilize otherwise vast nonproductive agricultural
areas.
4.8 The Case for the Lost Genes: Cytochrome c6 , Intein
Photosynthetic organisms possess two membrane-embedded multiprotein com-

plexes, photosystems I and II, which mediate light energy conversion into elec-
trochemical energy in the form of low potential electrons. They are connected by
a series of electron carriers, namely plastoquinone, a cytochrome (Cyt) b6 f com-
plex, and a soluble metalloprotein. The last-mentioned component can be either
the heme-containing protein, Cyt c6 , and/or the copper protein, plastocyanin (PC),
depending on the organism. For instance, some cyanobacteria only contain the
Cyt c6 gene, whereas others (as well as some algae) are able to synthesize both,
depending on metal bioavailability. Plants, on the other hand, possess only PC
(De la Rosa et al., 2002). At the times when the first oxygen-evolving photosyn-
thetic organisms arose, the prevailing atmospheric conditions were highly reduc-
ing, favoring iron over copper bioavailability. Thus, in an evolutionary context,
it seems clear why an iron-containing electron carrier, Cyt c6 , evolved initially.
Later on, in the Precambrian, photosynthesis-derived oxygen started to accumu-
late slowly, turning the tables: now copper availability grew, whereas iron started
to be scarce. PC appeared as a substitute for Cyt c6 , providing microorganisms
with an adaptive response toward nutrient deficiency analogous to the Fld/Fd sys-
tem (see Section 4.7). The coexistence of both transporters in some cyanobacteria
and algae conveys metabolic adaptability to the extremely changing environments
they face living in seas, lakes, and rivers (De la Rosa et al., 2002). Plants lack
this adaptive versatility, as Cyt c6 was evolutionarily eliminated from their chloro-
plasts. However, the introduction in A. thaliana of a Cyt c6 gene from Porphyra
yezoensis, a red alga, fused to a luminal targeting sequence has led to the creation
of transgenic lines exhibiting enhanced growth (height, root, and leaf length) and
to an increase in the efficiency of photosynthetic electron transfer and CO2 fixa-
tion rates. In this connection, the amounts of some energy-related metabolites such
as NADPH, ATP, and storage sugars were higher in the transgenic plants than in
WT siblings, suggesting an explanation for the improved growth of these plants
(Chida et al., 2007).
Inteins are sequences within a protein that mediate posttranslational protein
splicing. The intein element in a protein precursor catalyzes a series of reactions
to remove itself from the precursor and ligate the flanking external protein frag-
ments (“exteins”) into a mature protein (Perler, 1998). The first and only natu-
rally split intein identified so far is the DnaE intein of Synechocystis PCC6803.
Many sequences potentially coding for inteins have been found in cyanobacteria,
but none in plants. Inteins can be split into an N-terminal part and a C-terminal
portion, which when fused to different polypeptides are able to perform a trans-
splicing reaction assembly of the two separate precursors into a mature hybrid
molecule, both in vivo (assayed on E. coli cells) and in vitro (Yang et al., 2003,
and references therein). Yang et al. (2003) used the DnaE intein to reassemble
the divided fragments (which would be the exteins) of β-glucuronidase (GUS) in
transgenic Arabidopsis plants. The trans-splicing reaction resulted in a full-length
GUS protein with catalytic activity, indicating accurate ligation and refolding of
the enzyme throughout the entire plant without leaving any footprint. Chin et al.
(2003) extended this approach to chloroplasts using the naturally split DnaE intein
in which both intein fragments were incorporated into the chloroplast genome
or separately in the chloroplast and nuclear genomes. As far as intein expres-
sion and excision in chloroplasts is concerned, the aadA gene and a soluble ver-
sion of modified GFP (gfp ) were ligated to sequences coding for the N- and
C-terminal residues of the DnaE intein, respectively, and a chimeric polypeptide
AAD-smGFP (soluble modified GFP) assembled. The strategy was further refined
with respect to transgene containment by splitting the herbicide resistance gene
5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) into two halves and inte-
grating them separately into nuclear and chloroplasts genomes after ligating to cod-
ing sequences for split inteins. The functional, full-size EPSPS gene product was
reconstituted either by crossing tobacco plants carrying split genes or by retrans-
forming nuclear-transformed plants with a chloroplast transformation construct
carrying C-terminal residues of both EPSPS gene and intein (Chin et al., 2003).
These findings demonstrated intein usage in plant organelles and also explored the
possibility of intein-mediated protein trans-splicing for limiting the environmental
impact of herbicide resistance, by separating parts of the gene in plastid and nuclear
genomes while assembling the mature gene product in the stroma of chloroplasts
(Khan et al., 2005).
This technology opens up important biotechnological applications. Thus, it might
be possible to construct intein–extein fusions under the control of chemically
inducible or tissue-specific promoters in order to perform the reconstitution of pro-
tein trans-splicing in plants. They could then be used as a molecular switch to
turn on a gene expression mechanism or a metabolic pathway through reassem-
bly of gene regulators or enzymes. In order to diminish the environmental impact
of some transgenic products, different traits can be stacked in parental plants and
brought together upon crossing. As explained before, it could also be possible to
take advantage of the potential for trans-splicing of transgenes using inteins in con-
junction with plastid engineering to provide for a more effective transgene con-
tainment strategy to yield transformed plants with greatly reduced risk of genetic
outcrossing.
4.9 Concluding Remarks
Cyanobacterial genes display both important similarities with and differences from
plant genes, and both could be exploited to improve plant productivity and stress tol-
erance by means of genetic engineering. Compared to other prokaryotes, many bio-
chemical and physiological pathways from cyanobacteria, especially those related to
chloroplast function, have been retained in plants. Therefore, transgenic cyanobac-
terial products could interact productively with plant routes and substrates, a con-
dition that may be critical in an important number of cases. On the other hand,
sequence divergence between cyanobacterial genes and their plant homologues pre-
cludes, in most situations, the unwanted consequences of silencing and cosuppres-
sion. Moreover, plants have evolved novel regulatory networks that are not present in
cyanobacteria. Expression of a cyanobacterial gene product instead of overexpres-
sion of a plant counterpart can circumvent these endogenous regulatory constrains,
thus allowing for a more customized manipulation of the introduced trait. Finally,
a few cyanobacterial genes related to adaptive value for survival in hostile environ-
ments have been lost somewhere in the evolution of vascular plants. The case of
Fld and Cyt c6 shows that reintroduction of these genes in the proper subcellular
compartment of model and crop plants restored some of the selective advantages
that allowed photosynthetic microorganisms to thrive in hostile habitats. The exam-
ples described in this chapter illustrate the potential of gene and data mining in
cyanobacterial genomes and physiology as a biotechnological tool for the genera-
tion of crops with increased yield and performance in the field, which are needed
to feed an increasing world population. In addition, it shows the contribution of this
strategy to the development of plants with biofarming potential in the frame of a high
demand of natural and ecologically accepted sources of renewable compounds and
materials.
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Chapter 5
Molecular Biology of Secondary Metabolism:
Case Study for Glycyrrhiza Plants
Hiroaki Hayashi
Abstract Licorice (roots and stolons of Glycyrrhiza plants) is one of the most
important crude drugs from ancient times, and its major constituent is an oleanane-
type triterpene saponin, glycyrrhizin, which is a well-known sweetener as well as
a pharmaceutical. We are using Glycyrrhiza glabra (common licorice) as a model
plant to elucidate the regulation of triterpene biosynthesis in higher plants. Cultured
cells of G.glabra do not produce glycyrrhizin but produce two structurally different
triterpenoid constituents, namely betulinic acid and soyasaponins. Glycyrrhizin is
localized exclusively in the woody parts of thickened roots, whereas soyasaponins
are localized mainly in the seeds and rootlets. Betulinic acid, a lupane-type triter-
pene, is localized in the cork layer of the thickened roots. The cultured licorice
cells converted exogenously administered glycyrrhetinic acid, the aglycone of gly-
cyrrhizin, into seven biotransformation products, but formation of glycyrrhizin was
not detected among the biotransformation products. To elucidate the regulation of
the triterpene biosyntheses in G.glabra, cDNAs of squalene synthase and three oxi-
dosqualene cyclaces were cloned and characterized. mRNA levels of these enzymes
were differently regulated in the cultured cells and intact plants of G.glabra. Exoge-
nously applied methyl jasmonate (MeJA) stimulated soyasaponin biosynthesis in
cultured cells, and mRNA levels of squalene synthase and β-amyrin synthase were
upregulated by MeJA.
5.1 Introduction
Roots and stolons of Glycyrrhiza plants (Licorice) are important crude drugs
from ancient times, and the name Glycyrrhiza comes from Greek words meaning
“sweet root” (Nieman, 1959; Gibson, 1978; Shibata, 2000). The sweet constituent
in licorice is an oleanane-type triterpene saponin, glycyrrhizin, which is used
in large quantities as a well-known natural sweetener as well as a pharmaceu-
H. Hayashi (B)
School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3603, Japan

90 H. Hayashi
tical. Commercial licorice is derived from three Glycyrrhiza species, G. glabra

L., G. uralensis, FISCH., and G. inflata BATAL. in the family Fabaceae, which
are indigenous to Asia and the Mediterranean region (Shibata, 2000). G. glabra
is found in South Europe, Turkey, Iran, Central Asia, and the northwestern part
of China, and G. uralensis is found in Central Asia, Mongolia, and northwestern
and northeastern parts of China. G. inflata is found only in the northeastern part of
China.
Higher plants produce diverse triterpenes and triterpene saponins, which are of
economical importance as drugs, detergents, and cosmetics. Although structural elu-
cidation of triterpenes and triterpene saponins has been extensively studied (Mahato
et al., 1988, 1992), our understanding about the regulation of their biosyntheses is
quite limited (Chappell, 1995; Haralampidis et al., 2002; Jenner et al., 2005). We
are using G. glabra (common licorice) as a model plant to elucidate the regulation
of triterpene biosynthesis in higher plants. In this review, biosynthesis of various
triterpene constituents in the intact plant and in cultured cells of Glycyrrhiza plants
will be discussed.
5.2 Triterpene Saponins Isolated from Glycyrrhiza Plants
The major sweet-tasting triterpene saponin in roots and stolons of Glycyrrhiza

plants is glycyrrhizin, which has the sweetness of about 200 times greater than
that of sucrose. Glycyrrhizin is a conjugate of two molecules of glucuronic acid
and glycyrrhetinic acid, an oleanane-type triterpene (Fig. 5.1). Glycyrrhizin is
used in sweet foods to enrich the sweet taste. In addition, glycyrrhizin is used in
salty foods to reduce the saline taste of foods, such as soy sauce and sausage,
in Japan. Glycyrrhizin is also an active ingredient of Glycyrrhiza radix (licorice),
which is the most frequently used component of the Chinese and Japanese tra-
ditional medicines (Shibata, 2000). Furthermore, glycyrrhizin is a pharmaceutical
used in treatments of liver diseases and allergic diseases as an injectable prepa-
ration (Stronger Neo-Minophagen) R as well as a tablet (Glycyron R
) in Japan,
China, Korea, Indonesia, India, and Mongolia(http://www.minophagen.co.jp/en/
index.html).
Chemical constituents of Glycyrrhiza plants have been extensively studied
to isolate not only glycyrrhizin but also many triterpene saponins (Kitagawa
et al., 1993a,b,c; Nomura and Fukai, 1998). Structures of these minor saponins,
licorice-saponin B2 (11-deoxoglycyrrhizin), licorice-saponin C2, licorice-saponin
E2, licorice-saponin G2, and licorice-saponin H2, isolated from licorice roots are
shown in Fig. 5.1. Contents of these saponins in licorice roots vary among various
Glycyrrhizaplants of different geographic origins (Kitagawa et al.,1998).
5 Molecular Biology of Secondary Metabolism 91
COOH COOH COOH
COOH COOH
O O COOH
O O O
O
OH OH
HO OH
HO HO
COOH COOH
O
O glycyrrhizin O
O licorice-saponin B2 COOH
O licorice-saponin C2
O
OH OH
HO OH
HO HO
OH OH OH
O
C
COOH HOOC
O
O
O O
COOH
O COOH COOH
O O O
O O
OH CH2OH
HO OH OH
HO HO
COOH
O
O
licorice-saponin E2 COOH
O
O licorice-saponin G2 COOH
O licorice-saponin H2
O
OH
HO OH OH
HO HO
OH
OH OH
Fig. 5.1 Structure of glycyrrhizin, licorice-saponin B2, licorice-saponin C2, licorice-saponin E2,
licorice-saponin G2, and licorice-saponin H2
5.2.1 Triterpenes and Triterpene Saponins Produced by Cultured

Licorice Cells
Callus and cell suspension cultures were established from various organs
of G.glabra, but they failed to produce detectable amounts of glycyrrhizin
(Hayashi et al., 1988). However, the cultured licorice cells produced two struc-
turally different triterpenoid constituents, namely soyasaponins (Hayashi et al.,
1990b) and betulinic acid (Hayashi et al., 1988). Soyasaponins were isolated from
various legumes, such as Glycine max (Kitagawa et al., 1974), Pisum sativum
(Yokota et al., 1982), Medicago sativa (Kitagawa et al., 1988), and Wisteria
brachybotrys (Konoshima et al., 1992), suggesting that soyasaponins are com-
mon saponins in leguminous plants. Soyasaponins are reported to possess antivirus
(Nakashima et al., 1989; Hayashi et al., 1997; Kinjo et al., 2000), hepatoprotective
(Ohminami et al., 1984: Kinjo et al., 1998), and antitumor-promoting (Konoshima
et al., 1992) activities. On the other hand, betulinic acid, a lupane-type triterpene, is
distributed widely in plant kingdom and was also isolated from licorice roots (Saitoh
and Shibata, 1969; Hattori et al., 1986). Derivatives of betulinic acid were reported
to be potent anti-HIV agents (Mayaux et al., 1994; Kashiwada et al., 1996), and one
of them, 3-O-(3 ,3 -dimethylsuccinyl)-betulinic acid (Bevirimat), is now undergoing
clinical trials in the United States(http://www.panacos.com/index.htm).
92 H. Hayashi
Biosynthetic pathways of these triterpenoid constituents are shown in Fig. 5.2.

Both glycyrrhizin and soyasaponins are oleanane-type triterpene saponins and share
β-amyrin as a common biosynthetic intermediate. Specific oxidations of β-amyrin at
C-11 and C-30 positions leading to glycyrrhizin are blocked in the cultured licorice
cells, and the cultured cells convert β-amyrin into soyasapogenol B, the aglycone of
soyasaponins I and II, via oxidations at the C-22 and C-24 positions. Betulinic acid
is biosynthesized via oxidations at the C-28 position of lupeol, a common biosyn-
thetic intermediate for lupane-type triterpenes. Gas chromatography (GC) analysis
showed that the contents of soyasaponins and betulinic acid widely vary with the dif-
ferent culture strains (Hayashi et al., 1990b), and there was no significant correlation
acetyl-CoA
mevalonic acid
sesquiterpene farnesyl diphosphate
2,3-oxidosqualene
HO
HO HO
β-amyrin lupeol cycloartenol
COOH
O OH
COOH
HO HO HO
CH2OH HO
glycyrrhetinic acid soyasapogenol B betulinic acid sitosterol
COOH
O OH
COOH COOH
OO OO CH2OH
OH OH
HO HO
COOH R
OO
OO glycyrrhizin HO
OH
R=CH2OH soyasaponin I
OH
HO
R=H soyasaponin II
OH HO O O
CH3
OH OH
Fig. 5.2 Biosynthetic pathways of triterpenes and triterpene saponins in G. glabra

between the contents of soyasaponins and betulinic acid. It is also noteworthy that
yeast extract promoted betulinic acid accumulation, whereas soyasaponin accumu-
lation was suppressed, indicating that the regulation of soyasaponin biosynthesis
was different from that of betulinic acid biosynthesis (Hayashi et al., 2005a).
5.2.2 Distribution of Triterpenoids in Different Organs

of G. glabra
The contents of glycyrrhizin, soyasaponins, and betulinic acid in various organs

of G. glabra were determined by HPLC (glycyrrhizin) and GC (soyasaponins and
betulinic acid) as shown in Table 5.1 (Hayashi et al., 1988, 1993a, 2004). Gly-
cyrrhizin was localized exclusively in the woody parts of thickened roots but not
in the aerial parts, rootlets, or root nodules. Soyasaponins were detected in all parts
of the plants examined, and the contents were higher in the seeds, rootlets, and root
nodules than in other parts. It is also noteworthy that an inverse relationship was
observed between the contents of soyasaponins and glycyrrhizin (Hayashi et al.,
1993a). The contents of soyasaponins were higher in younger parts of a growing
stolon, whereas those of glycyrrhizin tended to be higher in the older parts. Such
an inverse relationship between soyasaponins and glycyrrhizin was also observed
during the development of primary roots after germination. As the primary roots
grew and became thicker, the soyasaponin content tended to decrease, while the gly-
cyrrhizin content increased. On the other hand, betulinic acid was localized to the
rootlets, root nodules, and the cork layer of thickening roots (Hayashi et al., 1988,
2004). Since both soyasaponins and betulinic acid were produced in the rootlets,
root nodules, and cultured cells, the triterpenoid metabolism of the cultured licorice
cells was similar to that of the rootlets and root nodules.
Table 5.1 Contents of glycyrrhizin, soyasaponin, and betulinic acid in various organs of G. glabra
(Hayashi et al., 1988, 1993a, 2004)
Content (% of dry weight) of

Organ Glycyrrhizin Soyasaponins Betulinic acid
Leaf n.d. 0.001 n.d.

Stem n.d. 0.001 n.d.
Seed n.d. 0.35 n.d.
Old thickened root (diameter: 32 mm)
Woody part 2.2 0.004 n.d.
Cork layer 0.006 0.004 0.32
Young root (6 months old)
Thickened root (φ 4 mm) 0.23 0.28 0.14
Rootlet (φ < 1 mm) 0.002 0.82 0.1
Root nodule n.d. 0.98 0.06
94 H. Hayashi
5.3 Biotransformation of Glycyrrhetinic Acid by Cultured

Licorice Cells
The cultured licorice cells do not produce glycyrrhizin but do produce soyasaponins,
which are also oleanane-type triterpene glucuronides like glycyrrhizin. Thus, we
examined whether or not the cultured licorice cells can convert exogenously sup-
plied glycyrrhetinic acid, the aglycone of glycyrrhizin, into its glucuronide, gly-
cyrrhizin (Hayashi et al., 1990a, 1992). The structures of seven biotransformation
products derived from exogenous glycyrrhetinic acid administered to the cultured
licorice cells were determined and are shown in Fig. 5.3. However, formation of
glycyrrhizin was not detected among the biotransformation products.
glycyrrhetinic acid
O O
COOH COOH C O C O
O O O O
CH2OH CH2OH
O O
O O
HO CH2OH CH2OH OH OH
O O HO
O O HO HO
OH OH OH OH
HO HO
OH OH
O
COOH COOH COOH C O
O O O O
CH2OH
O
O
COOH COOH OH
HO O O HO
O O HO
CH2OH CH2OH CH2OH CH2OH
OH OH OH
HO HO
OH O
HO O
OH
OH
Fig. 5.3 Structures of biotransformation products derived from exogenous glycyrrhetinic acid
administered to cultured licorice cells
Studies on time course for the production of metabolites as well as the pattern of
chemical conversion of intermediate metabolites showed that hydroxylation of C-24
methyl group of glycyrrhetinic acid occurs at the first step of biotransformation,
which is followed by glucuronylation (Fig. 5.4). Furthermore, glycyrrhetinic acid
24-hydroxylase activity was detected in the microsomal fraction prepared from the
cultured licorice cells, and the participation of cytochrome P-450 in the reaction
was shown by inhibitor experiments (Hayashi et al., 1993b). The 24-hydroxylation
of glycyrrhetinic acid was prerequisite for glucuronylation in the cultured licorice
cells. The glucuronosyltransferase activities for 24-hydroxyglycyrrhietinic acid and
soyasapogenol B were also detected in the microsomal fraction of the cultured
licorice cells, whereas the glucuronosyltransferase activity for glycyrrhetinic acid
was not detected (Hayashi et al., 1993b, 1996). Since soyasapogenol B is the
aglycone of soyasaponins I and II, the glucuronosyltransferase activity for soyas-
apogenol B would be responsible for biosynthesis of soyasaponins in the cultured
COOH
COOH
COOH
O
O
X
O
COOH
O COOH
O O
HO O
OH
HO OH
HO
OH
glycyrrhetinic acid COOH
O
glycyrrhizin
O
OH
HO
OH
COOH COOH COOH
O O O
HO COOH COOH
O O
CH2OH O O
CH2OH CH2OH
OH OH
24hydroxy- HO HO
OH
glycyrrhetinic acid O
O
HO
OH
OH
Fig. 5.4 Metabolic pathway of glycyrrhetinic acid in cultured licorice cells
licorice cells. Although the glucuronosyltransferase for glycyrrhetinic acid was not
detected in the cultured cells, the glucuronosyltransferase for glycyrrhetinic acid
should be involved in the biosynthesis of glycyrrhizin, which is localized to the
thickened roots and stolons of Glycyrrhiza plants.
5.4 Saponin Variation in Seven Glycyrrhiza Species
It is of interest to elucidate the saponin variations among various Glycyrrhiza

species from the viewpoint of the evolution of glycyrrhizin biosynthesis. Thus, the
underground parts of seven Glycyrrhiza species, G. glabra, G. uralensis, G. inflata,
G. echinata L., G. macedonica Boiss. et Orph., G. pallidiflora Maxim., and G. lep-
idota (Nutt.) Pursh, were analyzed by HPLC to examine the saponin variations
in these species (Hayashi et al., 2000b, 2005b). Although the three Glycyrrhiza
species, G. glabra, G. uralensis, and G. inflata, produce glycyrrhizin as a major
saponin, the other three Glycyrrhiza species, G. echinata, G. macedonica, and
G. pallidiflora, do not produce glycyrrhizin but instead produce macedonoside C
as a major saponin (Shibano et al., 1999; Hayashi et al., 2000b). On the other hand,
G. lepidota, American licorice, produces licorice-saponin H2 and macedonoside
A as the two major saponins (Hayashi et al., 2005b). Licorice-saponin H2 is a
minor saponin isolated from the glycyrrhizin-producing species (Kitagawa et al.,
1993b), and macedonoside A is a minor saponin isolated from the macedonoside
96 H. Hayashi
COOH HOOC
OH
COOH COOH
O O
O O
OH OH
HO HO
COOH
glycyrrhizin COOH
macedonoside C
O O
O O
OH HOOC OH HOOC
HO HO
OH OH OH
O O
COOH COOH
O O
O O
OH OH
HO HO
COOH
O
licorice-saponin H2 COOH macedonoside A
O O
O
OH OH
HO HO
OH
G. glabra
OH
G. echinata
G. uralensis G. macedonica
G. inflata G. pallidiflora
G. lepidota
Fig. 5.5 Structures and distributions of glycyrrhizin, licorice-saponin H2, macedonoside C, and
macedonoside A in seven Glycyrrhiza species
C-producing species (Shibano et al., 1999). In addition, G. lepidota produces trace

amounts of glycyrrhizin and macednoside C. These results suggest that G. lepidota
is a chemotaxonomical intermediate of the glycyrrhizin-producing and macedono-
side C-producing species (Fig. 5.5).
To confirm the relationship of these Glycyrrhiza species, we determined the
nucleotide sequences of a chloroplast gene for the large subunit of ribulose-
1,5-bisphosphate carboxylase/oxygenase (rbcL). Based on the rbcL sequences, the
seven Glycyrrhiza species were divided into three groups: the three glycyrrhizin-
producing species (G. glabra, G. uralensis, and G. inflata), the three macedonoside
C-producing species (G. echinata, G. macedonica, and G. pallidiflora), and G. lep-
idota(Hayashi et al., 2000b, 2005b). This phylogenetic relationship by their rbcL
sequences is in accordance with their saponin compositions.
5.5 Molecular Cloning of Squalene Synthase and Oxidosqualene

Cyclase cDNAs from G. glabra
Since G. glabra produces various triterpenes and triterpene saponins, this plant is
an excellent model plant to study triterpenoid biosynthesis. Our next interest thus
focuses on the gene expression of enzymes involved in triterpenoid biosynthesis
(Fig. 5.6). Squalene synthase (SQS, EC 2.5.1.21) catalyzes the condensation of two
molecules of farnesyl diphosphate into squalene, a common precursor of sterols and
mevalonic acid farnesyl diphosphate
SQS
squalene
2,3-oxidosqualene
bAS CAS
LUS
HO HO
HO
β-amyrin lupeol cycloartenol
glycyrrhizin soyasaponin I betulinic acid sitosterol

soyasaponin II
Fig. 5.6 Squalene synthase and oxidosqualene cyclases involved in the biosynthesis of triter-
penoids in licorice. Squalene synthase (SQS), β-amyrin synthase (bAS), lupeol synthase (LUS),
and cycloartenol synthase (CAS)
triterpenoids. Although the SQS genes of yeast and human was reported to be single-
copy genes (Jennings et al., 1991; Robinson et al., 1993), two SQS genes are orga-
nized in a tandem array in the genome of Arabidopsis thaliana, a model plant used
for genomic studies (Kribii et al., 1997). Since plants accumulate not only sterols
but also various triterpenes and triterpene saponins, the regulation of the SQS gene
might be different from that of mammals. Thus, cDNA for SQS was screened from
a cDNA library of the cultured licorice cells to isolate two SQS cDNAs, designated
GgSQS1 and GgSQS2 (Hayashi et al., 1999). The deduced amino acid sequence
of GgSQS1 was 88% identical to that of GgSQS2. SQS activity was found in the
cell-free extracts of Escherichia coli transformed with the expression plasmids for
GgSQS1 and GgSQS2, indicating that the cultured cells of G. glabra produce two
functional isozymes for SQS, which may play an important role in the regulation
of biosynthesis of the different triterpenoids. Genomic Southern blot analysis sug-
gested that there are three SQS genes in the licorice genome.
Oxidosqualene cyclases catalyze the cyclization of 2,3-oxidosqualene, a
common intermediate of both sterols and triterpenes (Abe et al., 1993;
Haralampidis et al., 2002). To elucidate the regulation of the triterpenoid biosyn-
theses in G.glabra, cDNAs of the three oxidosqualene cyclases, β-amyrin synthase
98 H. Hayashi
(bAS), lupeol synthase (LUS) and cycloartenol synthase (CAS), which are situ-
ated at the branching step for biosynthesis of oleanane-type triterpene saponins
(glycyrrhizin and soyasaponins), lupane-type triterpene (betulinic acid) and phy-
tosterols, respectively (Fig. 5.6), were cloned and characterized (Hayashi et al.,
2000a, 2001, 2004). These three oxidosqualene cyclases cloned from G.glabra were
monofunctional triterpene synthases, each of which produces a sole major triter-
pene product. However, a multifunctional triterpene synthase, producing multitriter-
pene products, has been cloned from other leguminous plants (Morita et al., 2000;
Iturbe-Ormaetxe et al., 2003; Sawai et al., 2006).
5.6 Regulation of Triterpenoid Biosynthesis in the Cultured

Licorice Cells and in the Intact Licorice Plants
Since the oxidosqualene cyclases are situated at a crucial branching step for biosyn-
thesis of the respective triterpenes, molecular cloning of these cDNAs provides use-
ful tools for studying regulation of triterpenoid biosyntheses in cultured licorice
cells. Thus, the mRNA levels of two SQSs, bAS, LUS, and CAS were compared
by Northern blot analysis to elucidate the effects of various plant hormones on the
mRNA levels in cultured licorice cells (Hayashi et al., 2003, 2004). The mRNA lev-
els of two SQS and bAS were upregulated by jasmonate (JA) and methyl jasmonate
(MeJA), suggesting that jasmonates are positive regulators of soyasaponin biosyn-
thesis in G.glabra. In contrast, the mRNA level of LUS was downregulated by JA
and MeJA, whereas the mRNA level of CAS was relatively constant. On the other
hand, gibberellin A3 downregulated the mRNA level of bAS but not those of LUS
and CAS, suggesting that gibberellin may be a negative regulator of soyasaponin
biosynthesis in G.glabra (Hayashi et al., 2004).
Exogenously applied MeJA stimulated soyasaponin biosynthesis in cultured
licorice cells (Hayashi et al., 2003), and accumulations of bAS and SQS mRNAs
were not transient but lasted for 7 days after exposure to MeJA (Fig. 5.7), resulting in
Fig. 5.7 Time course of

accumulation of squalene
synthase (SQS1, SQS2),
β-amyrin synthase (bAS),
cycloartenol synthase (CAS),
and lupeol synthase (LUS)
mRNAs in cultured licorice
cells treated with MeJA
(Hayashi et al., 2003)
the high-level accumulation (more than 2% of dry weight) of soyasaponins (Hayashi

et al., 2003). Furthermore, enzyme activity of UDP-glucuronic acid: soyasapogenol
β-glucuronyltransferase, an enzyme involved in a later step of soyasaponin biosyn-
thesis, was also upregulated by MeJA, suggesting that the transcription of other
enzymes involved in the late steps of soyasaponin biosynthesis might be upregu-
lated by MeJA in cultured licorice cells.
Yeast extract was shown to induce isoflavone biosynthesis in cultured cells of
G. echinata (Ayabe et al., 1986; Nakamura et al., 1999). Thus, the effect of yeast
extract on the mRNA levels of cultured G. glabra cells was examined (Hayashi
et al., 2003). The mRNA level of polyketide reductase, an enzyme involved in the
biosynthesis of 5-deoxy-isoflavonoids in legumes, was transiently upregulated by
both yeast extract and MeJA in cultured G. glabra cells, whereas the mRNA levels
of two SQSs and bAS were coordinately downregulated by yeast extract in these
cells (Fig. 5.8). The opposite effects of MeJA and yeast extract on the levels of SQS
and bAS mRNA levels suggest that the signaling pathway leading to activation of
soyasaponin biosynthesis is different from that of the flavonoid biosynthesis.
Although the mRNA levels of bAS and LUS were highly regulated in cultured
cells of G.glabra, bAS and LUS also play an important role in the biosynthesis
of glycyrrhizin and betulinic acid, respectively, in intact licorice plants. Thus, the
mRNA levels of three OSCs in the intact plants were compared by Northern blot
analysis (Hayashi et al., 2003, 2004). A high level of bAS mRNA was observed
in the thickened main roots and root nodules. This finding was consistent with the
high-level accumulation of soyasaponins in the root nodules and that of glycyrrhizin
in the thickened main roots. The LUS mRNA was detected in the root nodules,
in which a relatively high level of betulinic acid was detected. The mRNA level
of CAS, responsible for sterol biosynthesis, was relatively constant in the various
organs of G.glabra. These results indicate that there is independent regulation of
three oxidosqualene cyclases in intact licorice plants. The levels of these mRNAs
correlate well with the accumulation of respective end-products, suggesting that the
transcription of oxidosqualene cyclases is an important regulatory step for triterpene
biosynthesis.
Fig. 5.8 Time course of

accumulation of squalene
synthase (SQS1, SQS2),
β-amyrin synthase (bAS),
cycloaretenol synthase
(CAS), lupeol synthase
(LUS), and polyketide
reductase (PKR) mRNAs in
cultured licorice cells treated
with yeast extract (Hayashi
et al., 2003)
100 H. Hayashi
Fig. 5.9 Seasonal variation of accumulation of β-amyrin synthase (bAS) and cycloaretenol syn-
thase (CAS) mRNAs in thickened main roots of licorice (Hayashi et al., 2005a). Reproduced with
permission from Biol. Pharm. Bull. 27(7) Copyright (2004), Pharmaceutical Society of Japan
The site of glycyrrhizin biosynthesis is localized in the thickened roots and

stolons of G.glabra (Fuggersberger-Heinz and Franz, 1984; Hayashi et al., 1998),
and seasonal variation for the incorporation of 14 C-mevalonic acid into the gly-
cyrrhizin fraction by the root segments was observed (Hayashi et al., 1998). The
incorporation rate was high in May, June, and September and low in August and
winter months. Seasonal variation of bAS mRNA level was also observed in the
thickened main roots (Hayashi et al., 2004). The level of bAS mRNA in thick-
ened main roots was high in May, June, July, and September when the aerial parts
were growing (Fig. 5.9). The level of bAS mRNA was low in August, when many
leaves had abscised due to the high temperature and high humidity in Japan, and in
the winter months, when the aerial parts were dormant. These results indicate that
the existence of the actively growing aerial parts is necessary for the expression of
bAS mRNA and glycyrrhizin biosynthesis in the thickened main roots. The level
of CAS mRNA was relatively constant, even during the winter months, suggesting
that CAS is a housekeeping enzyme. The level of LUS mRNA was not detectable in
the thickened roots.
5.7 Concluding Remarks
Glycyrrhizin, soyasaponins, and betulinic acid are localized in specific organs of

intact licorice plants, and biosyntheses of these constituents are differentially regu-
lated. Molecular cloning of SQS and oxidosqualene cyclase (bAS, LUS, and CAS)
cDNAs revealed that the transcription of these genes is also differently regulated
in the cultured cells as compared with intact plants of licorice. Upregulation of
bAS and SQS mRNAs by MeJA in cultured licorice cells suggests that transcripts
of other enzymes involved in the later steps of soyasaponin biosynthesis might be
upregulated by MeJA. Induction of bAS mRNA and saponin accumulation by MeJA
have also been reported in cultured cells of the model legume Medicago truncat-
ula (Suzuki et al., 2002, 2005), and MeJA-inducible triterpene glycosyltransferase
genes have been characterized from this plant (Achnine et al., 2005). Furthermore,
a cDNA of triterpene hydroxylase involved in soyasaponin biosynthesis was also

identified from elicitor-inducible soybean P450s (Shibuya et al., 2006). Further
experiments are underway to characterize the licorice genes involved in the later
steps of triterpene saponin biosynthesis.
Acknowledgments This research is supported in part by Grants-in-Aid for Scientific Research to

H. H. (07780500, 09771930, 13780470) from The Ministry of Education, Culture, Sports, Science
and Technology (MEXT), Japan.
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Chapter 6
New Developments in Agricultural
and Industrial Plant Biotechnology
Abstract New developments in agricultural and industrial plant biotechnology are

quite noteworthy and deserve special mention in this chapter.
In the agricultural sector, we have witnessed the advent of no tillage farming;
significant increases in the use of organic farming practices, including a decrease in
the use of toxic insecticides and herbicides; a quantum leap forward in the spread
of farmers’ markets and sale of locally grown food crops and products; an increase
in the use of seeds of heirloom cultivars of crop plants; an increase in crop species
diversity; an increase in the use of genetically modified food plants in America; a
slowly emerging trend toward urban agriculture; and increasing use of hydroponic
production systems to grow crops year-round in greenhouses.
In the industrial sector, we observe the advent of many new industrial-type prod-
ucts that are derived from plants. These include biodegradable plant-derived plas-
tics, paints and varnishes, adhesives, auto biofuels, de-icers, cleaners, vegetable oils,
essential oils, industrial solvents, pharmaceutical and industrial proteins; soy-based
inks; soy-based spray foam insulation; soy-based carpet backing and padding; and
soy-based wood-like composites used for floors, paneling, and table/countertops.
In this chapter, we present selected examples from each of these topics.
6.1 The Implementation of Organic Farming Practices:

The Reasons, Benefits, and Disadvantages
Organic farming refers to the use of sustainable, environmentally safe practices in

the growing of food crops for humans and domesticated animals. Organic farming
is a form of agriculture which excludes the use of synthetic fertilizers and pesti-
cides, plant growth regulators, livestock feed additives, and genetically modified
(GM) organisms. As far as possible, organic farmers rely on crop rotation, green
manure, compost, biological pest control, and mechanical cultivation to maintain
A. Kirakosyan (B)

soil productivity and control pests. Organic farming is often contrasted with con-
ventional, or mainstream, farming (Adeyemi, 2000). Advantages include high con-
sumer acceptance of organically grown products and willingness to pay a higher
price for such food items; enhanced soil fertility and water-holding capacity, espe-
cially long term; gradual purging of the soil of toxic pesticides that may have been
used previously after several years of instituting organic farming practices; organic
certification of the grower as a certified organic farmer once organic standards have
been met; enhanced value of the farmer’s land once it has qualified for organic
certification; fewer health-related problems for the organic grower because of the
practices he/she uses; lower incidence of crop insect pests because of increased
incidence of insect predators. Disadvantages include higher production costs and
greater problems with weeds; hence lower yields over the short term. Reasons for
implementation of organic farming practices include (1) consumer demand; (2)
loss of soil fertility; (3) health problems for the conventional/corporate farmer who
is exposed to a multitude of toxic chemical pesticides – herbicides, insecticides,
fungicides, nematicides, and fumigants; (4) increased profits for the farmer/grower
who grows certified organic crops; and (5) improved adherence to soil conservation
practices.
Regarding GM crops (see Chapter 13), the absolutist position taken by organic
farming adherents against any use of GM crops is currently meeting immense oppo-
sition worldwide from crop biotechnology proponents. The center of the contro-
versy lies in European Union (EU) countries. The latest test comes in the following:
The Public Research and Regulation Initiative (PRRI), a worldwide effort of public
sector scientists involved in research and development of biotechnology for the pub-
lic good, have sent an open letter to the members of the European Commission to
aid them in their orientation discussion on biotechnology. PRRI has expressed deep
concern about the effects of the political situation in Europe affecting genetically
modified (GM) foods and crops.
The initiative notes, that despite clear EU rules and The European Food Safety
Authority (EFSA) conclusions of GMOs not having adverse effect on human and
animal health or the environment, EFSA opinions continue to be ignored. As a result
of this situation, detrimental impacts have been felt both inside and outside the EU,
particularly in developing countries.
Plant pathologist, Pamela Ronald, from the University of California at Davis,
CA, believes that a combination of the two approaches – implementation of organic
farming protocols and inclusion of GM crops – will be important for the future of
global food production. Her view is that genetically modified seeds, when grown
by the use of organic agricultural methods, can significantly increase yields, and
at the same time, reduce the use of environmentally damaging chemicals. This
hypothesis is not dissimilar from the conclusion of the recently published IAASTD
(International Assessment of Agricultural Knowledge, Science and Technology for
Development) report. This 2-year intergovernmental project is designed to
investigate the role that agricultural science, knowledge, and technology can play
in world poverty. The report concludes that a complete agricultural revolution is
needed where agriculture is no longer thought of as production alone.
6 Agricultural and Industrial Plant Biotechnology 109
6.2 Recent Achievements in Improving Crop Diversity: What

Are the Driving Forces in Play Here?
As of 2003, in the United States, there were only 20 major agricultural products
(these are listed in a table along with amounts produced) in commercial production
(Table 6.1).
The only other crops to ever appear in the top 20 in the last 40 years were, com-
monly, tobacco, barley, and oats, and, rarely peanuts, almonds, and sunflower seeds
(in all, only 26 of the 188 crops the FAO tracks worldwide). Both alfalfa and hay
would be in the top 10 in 2003 if they were tracked by FAO.
This has resulted in a major loss in agricultural product diversity as compared
with that which existed in the 1800s. For example, concerning vegetable crop diver-
sity, according to the Rural Advancement Foundation (now called ETC Group),
75 types of vegetables, or approximately 97% of the varieties available in 1900,
are now extinct (Kimbrell, 2002). Accompanying this decrease in crop diversity of
vegetable and most other types of crops is the trend for small farms to disappear and
for existing farms to become much larger.
What are the attributes of this trend? Corporate agribusiness is the current model
and has ended up controlling farming practices. Linked to this is the fact that
monocultures have become most common. Furthermore, chemical agriculture is the
primary system in use. As a result, we have increased production costs. Fewer peo-
ple are engaged in farming. There is an increase in the incidence of crop pests. And,
there is a reduction in quality of the crop products produced. As a consequence of
these events, we might ask, is there any trend toward outsourcing crops from the
Table 6.1 The top 20

agricultural products of the Agricultural products Mass (tonnes)
United States by value as
1. Corn 256,904,992
reported by the Food and
2. Cattle meat 11,736,300
Agricultural Organization of
3. Cow’s,milk,whole,fresh 78,155,000
the United Nations (FAO) in
4. Chicken meat 15,006,000
2003 (Products are ranked by
5. Soybeans 65,795,300
their mass, multiplied by the
1999–2001 international 6. Pig meat 8,574,290
prices. Mass is in metric 7. Wheat 63,589,820
tonnes.) 8. Cotton lint 3,967,810
9. Hen eggs 5,141,000
10. Turkey meat 2,584,200
11. Tomatoes 12,275,000
12. Potatoes 20,821,930
13. Grapes 6,125,670
14. Oranges 10,473,450
15. Rice, paddy 9,033,610
16. Apples 4,241,810
17. Sorghum 10,445,900
18. Lettuce 4,490,000
19. Cottonseed 6,072,690
20. Sugar beets 27,764,390
United States to other countries? No, this is really not the case because we are sim-
ply now using more of crops, such as banana, papaya, mango, star fruit, and kiwi,
that are only grown in other countries.
With the advent of organic agriculture (see above), and because of consumer
demand, we are now witnessing a steady increase in crop diversity on American
farms. Consumers are demanding more nutritious products and foods that are health-
ier for them. This is driven, in part, by a parallel increase in the use of integrative
medicine and preventive medicine in our health system.
What are some of the less common edible crops, not included in the top
20 major crop species that account for this increase in crop diversity? They
include teff (Eragrostis tef (Zucc.) Trotter), quinoa (Chenopodium quinoa Willd.),
grain amaranth (Amaranthus cruentus L.), wild rice (Zizania aquatica L.),
canola/rapeseed (Brassica napus L.), sunflowers (Helianthus annuus L.), giant
pumpkins (Cucurbita pepo L.), culinary herbs, heirloom vegetables (see Seeds of
Change, www.seedsofchange.com), cassava, taro, kiwi, and many edible fruits that
include new cultivars of grapes (Vitis spp. L.), blueberries, (Vaccinium spp. L.),
sour cherries (Prunus cerasus L.), Goji berry/wolfberry (Lycium barbatum Thunb.),
elderberry (Sambucus canadensis L.), thornless blackberries (Rubus canadensis L.),
Cornelian cherry (Cornus mas L), chokeberry (Aronia arbutifolia (L.) Pers. and
A. melanocarpa (Michx.) Elliott), and hawthorn (Crataegus laevigata (Poir.) DC.
and C. monogyna Jacq.). Reasons why a wide spectrum of colored fruits and veg-
etables, like many of the above, are desirable for significantly improved health are
described in “The Color Code: A Revolutionary Eating Plan for Optimum Health”
by Joseph et al. (2002).
6.3 The Rise of Urban Agriculture
Grow gardens refer to collections of vegetables and flowers that are grown in rela-
tively small plots in urban environments. The increasing presence of grow gardens
in many cities in the United States, Europe, and Asia is one of the hallmarks of urban
agriculture at work. The impetus for this activity is to satisfy the need to obtain our
food locally rather than via world commerce, to save energy, to lower production
costs, to improve human health, and to obtain fresher produce. Grow gardens allow
urbanites to know where their food comes from, to be able to grow food crops
without the use of toxic pesticides, to learn how it is grown and harvested, to
get good exercise (and thus, to help fight a growing problem of obesity), to pro-
vide a greater diversity of foods in the diet, to promote human interactions, and to
reduce urban crime. Grow gardens have also helped to restore the work ethic among
urbanites. One other spin-off is that urban crops sequester carbon dioxide, and thus,
help to reduce global warming. They also mitigate high summer temperatures via
evaporative cooling from leaves of the crops grown (via the process of transpiration
or water evapo-transpiration from the leaves).
Many grow gardens are now being developed as “rooftop gardens” where grow-
ing space is limited. They are also being located at ground level near churches and
schools, in parks, botanical gardens, and arboreta, and in lots where old houses and
commercial buildings have been removed. It is essential that they should not be
located in brown fields where the soil is contaminated with toxic residual chemicals
and waste products.
6.4 The Use of Hydroponics Techniques for Commercial Food

Production
Hydroponics refers to the cultivation of plants in complete nutrient solutions in the

absence of soil. The first crops to be commercially grown with hydroponics included
tomatoes and peppers, but the techniques were soon successfully extended to other
crops such as lettuce, cucumbers, many kinds of culinary herbs, and cut flowers
(Sustainable Living Articles at http://www.articlegarden.com; Mason, 2000). Val-
ued at 2.4 billion dollars the hydroponic greenhouse vegetable industry has a growth
rate of 10% per year and accounts for nearly 95% of the greenhouse vegetables
produced in North America.
What are the advantages of hydroponics? Hydroponics, when used in green-
houses, allows for the cultivation of plants throughout the year. Other advantages
include nutritious, healthy, and clean produce; improved and consistent quality of
produce; and elimination of the use of toxic pesticides and herbicides. Notable, also,
is the fact that specialty crops like culinary herbs, or even the above-mentioned veg-
etable crops or florist crops, can be grown hydroponically in gutter troughs in 42-day
turn-around cycles (date of seed planting in biodegradable foam plugs to date of har-
vest) for most annual culinary herbs in greenhouses. The greenhouses can be heated
from natural gas (methane) derived from garbage-filled landfills or from geother-
mal systems and illuminated continuously with full spectrum lamps with electricity
generated by photovoltaic panels or wind generators.
Are there any disadvantages attributed to hydroponics? One entails high start-up
costs. Another is that the whole process is highly labor-intensive as compared with
field crop production, which, because of it being highly mechanized, involves much
less hand labor.
What about yield comparisons? Commercial hydroponics systems have proven
to be more productive than conventional systems of agriculture. Most commer-
cial hydroponics greenhouse facilities are built sufficiently large to take advan-
tage of economies of scale. Typically, these cover areas more than 10 acres, while
smaller ones measure around 2 acres. In commercial practice, the yield of hydro-
ponically grown tomatoes can be more than double that of soil-based systems due
to the reduced turnover time between crops, better nutrition, and crop management.
The dramatic increase in yields with hydroponics is best illustrated if we consider
the actual production figures of soil-grown and hydroponically grown produce. Field
grown tomatoes average yields ranging between 40,000 and 60,000 pounds per
acre; on the other hand top growing hydroponics facilities in the United States and
Canada report average yields of more than 650,000 pounds of tomatoes per acre.
Additionally, given the fact that only 10 years ago top hydroponics producers were
producing around 400,000 pounds per acre, the increase in yields with improve-
ments in growing practices has been truly phenomenal. Similar production figures
can be quoted for other agricultural produce like cucumbers with 10,000 pounds
per acre for field production and 200,000 pounds per acre for hydroponic green-
house yields. Hydroponic lettuce and pepper yields too average around four times
the corresponding yields of agricultural production.
In terms of global production, according to recent estimates, countries hav-
ing substantial commercial hydroponics production include Israel − 30,000 acres,
Netherlands − 10,000 acres, United Kingdom − 4,200 acres, and Australia and
New Zealand – around 8,000 acres between them. The fastest growing area for com-
mercial vegetable greenhouses is Mexico. There are several reasons for this. They
include free trade and favorable winter conditions that attract vegetable growers in
large numbers. Mexico has summers that are considered to be hot in the summer,
but with greenhouses located at the right altitudes, vegetables can be grown in the
hot summers as well as in the cold winters.
6.5 Examples of Food, Feed, and Industrial Products That Are

Derived from Soybeans (Glycine max (L.) Merr.)
Soybeans are a versatile crop with many uses (see Indiancommodity.com). But
before they can be used in food, feed, or industrial products, soybeans must be pro-
cessed. More than 95% of the soybeans are processed by solvent-extraction indus-
trial plants. When arriving at the processing plant, the soybeans are checked for
quality. The soybeans then are processed to extract the oil and meal. From 100
pounds of soybeans, the soybean-crushing process produces 18 pounds of soybean
oil and 80 pounds of soybean meal. There are several steps in the soybean-crushing
process: Dehulling – First, the soybeans are cracked and the hulls are removed.
Soaking – The soybeans then are flaked in special machines and moved to towers
or tanks where they are soaked in a chemical solution. This solvent removes about
99% of the pure, crude soybean oil from the flake. Refining– The crude soybean oil
may be refined further depending on how it is to be used. In the refining process,
crude oil can be degummed, bleached, deodorized, or hydrogenated with hydrogen
gas. In “degumming,” the fatty acid content of the oil is neutralized with a caustic
acid to produce some products like soap. The oil may also be “bleached” by treat-
ing it with an absorbent clay material before it is “deodorized” through a vacuum
steam-distillation process. Toasting and grinding – After the oil is removed, the soy-
bean flake then is cleaned, toasted, and ground to improve its nutritional value. This
produces the soybean meal, which consists of 48% protein.
Soybeans are found in hundreds of human foods, animal feeds, and industrial
products that are based on soybean oil and soybean meal. Some examples are as
follows: Soybean oil: About 97% of soybean oil is used in a wide range of products
for human use, such as cooking oils, salad dressings, sandwich spreads, margarine,
salad oils, coffee creamer, mayonnaise, shortenings, chocolate coatings, a flour

ingredient, and medicines. Soybean oil also is used in such industrial products as
printing inks, cosmetics, linoleum, vinyl plastics, paints, caulking compounds, pesti-
cides, epoxy glue, protective coatings, yeast soaps, shampoos, and detergents. Other
examples of industrial products that have been developed from soybeans include
candles, cleaners, composite materials, crayons, diesel additives, fabric condition-
ers, flooring, paint removers, pens, polish, solvents, tables/furniture, and waxes (see
information at soyworld.com). Soybean meal: About 98% of soybean meal is used
as a feed ingredient in mixed rations for poultry, hogs, and beef and dairy cattle.
The remainder is used for human food or industrial products. High-protein (48%)
soybean meal is used as a starter ration and high-performance feed. A lower-protein
soybean meal (44%) also may be produced by adding the high-fiber hulls for use in
bulky feeds, or as a carrier for molasses and other ingredients.
6.6 Production of Biodegradable Plastics from Plant-Derived

Starch
Biodegradable plastics derived from plant sources are now being developed in the
United States, Europe, and Asia from renewable resources such as corn, wheat,
and potato starches as substitutes for conventional and petroleum-based plastics.
Examples are provided in Table 6.2.
The term biodegradable means that a substance is able to be broken down into
simpler substances by the activities of living organisms, and therefore, is unlikely
to persist in the environment (Gross and Kalra, 2002). There are many different
standards used to measure biodegradability, with each country having its own stan-
dards. The requirements range from 90 to 60% decomposition of the product within
60–180 days of being placed in a standard composting environment.
The reason traditional plastics are not biodegradable is because their long poly-
mer molecules are too large and too tightly bonded together to be broken apart and
assimilated by natural decomposer organisms. However, plastics based on natural
plant polymers derived from wheat or corn starch have molecules that are readily
attacked and broken down by microorganisms (Fig. 6.1).
Table 6.2 Examples of

products using plant-based Plant-based plastics Producer companies
plastics and the companies
Plastic bags BioBag
that produce them
Water bottles Biota Water
Disposable forks and knives Cereplast
Wall carpets Interface
Cups for smoothies Mrs. Fields Brands
Electronics packaging and products Sony
Car floor mats Toyota
Produce packaging Wal-Mart
Deli containers Wild Oats
Plant-based plastics provide an alternative to conventional plastics, especially

for polyvinyl chloride (PVC) that relies heavily on extremely toxic feedstocks and
additives that have devastating impacts on our health and environment through their
production, use, and disposal. Many of the chemicals used in PVC production are
linked to cancer, birth defects, reproductive harm, and a host of other health prob-
lems. In contrast, bio-based plastics are generated from renewable materials, such
as corn starch into plastic. The production of bioplastics uses fewer fossil fuels com-
pared to petrochemical plastics, even after accounting for the fuel needed to plant
and harvest the corn or other feedstocks. Plant-based plastics are also compostable.
They can be effectively composted in a large-scale facility, where it will degrade
Plants as a Source of Biostarch, biocellulose,

Bioplastic Materials soy proteins, oils etc.
CO2, Photosynthesis
Synthesis of Bioplastics
Decomposition of plastic by
microorganisms
Bioplastics
Fig. 6.1 Natural, plant-based plastics and their decomposition

within 45 days. Conventional plastics, in contrast, can take over 100 years just to
begin the degradation process.
Starch is a natural storage polysaccharide-type polymer made up of α-(1,4)-
linked glucose (amylose or straight-chain starch) or α-(1,4) + α-(1,6)-linked glucose
(amylopectin or branch-chain starch) (see Cseke et al., 2006). It is a white, granu-
lar carbohydrate produced by plants during photosynthesis and it serves as one of
the plant’s energy stores. Grains of cereal plants and potato tubers normally con-
tain starch in large proportions. Starch can be processed directly into a bioplastic,
but because it is soluble in water, articles made from starch will swell and deform
when exposed to moisture, thus limiting its use. This problem can be overcome by
modifying the starch into a different polymer. First, starch is harvested from corn,
wheat, or potatoes, then microorganisms transform it into lactic acid, a monomer.
Finally, the lactic acid is chemically treated to cause the molecules of lactic acid to
link up into long chains or polymers, which bond together to form a plastic called
polylactide (PLA).
PLA has been commercially available since 1990. Certain blends have proved
to be successful in medical implants, sutures, and drug delivery systems because
of their capacity to dissolve away over time. However, because PLA is significantly
more expensive than conventional plastics, it has failed to win widespread consumer
acceptance.
Biodegradable plastic products currently available in the market are from 2 to 10
times more expensive than traditional petroleum-based plastics. Environmentalists
argue that the cheaper price of traditional plastics does not reflect their true cost
when their full impact is considered. A case in point is this: when we buy a plastic
bag, we do not pay for its collection and waste disposal after we use it. If we included
these kinds of associated costs, then traditional petroleum-based plastics would cost
more and biodegradable plastics might be more competitive.
Another way of making biodegradable polymers involves getting bacteria to pro-
duce granules of a plastic called polyhydroxyalkanoate (PHA) inside their cells.
Bacteria are simply grown in culture in bioreactors and the plastic is then harvested.
Going one step further, scientists have taken genes from this kind of bacterium and
transferred them into corn plants, which then manufacture the plastic in their own
cells.
Unfortunately, as with PLA, PHA is significantly more expensive to produce.
As yet, it is not having any success in replacing the widespread use of traditional
petrochemical-based plastics. Perhaps as the price of oil increases and supply dwin-
dles, biodegradable plastics will come into more favor benefit to our environment.
If cost is a major barrier to the acceptance of biodegradable starch-based plas-
tics, then the solution lies in investigating low-cost options to produce them. In
Australia, the Cooperative Research Centre (CRC) for International Food Manu-
facture and Packaging Science is examining ways of using basic starch, which is
cheaper to produce, in a variety of blends, with other more expensive biodegradable
polymers to produce a variety of flexible and rigid plastics. These are being made
into film-molded and injection-molded products, such as plastic wrapping, shop-
ping bags, bread bags, mulch films, and plant pots. Depending on the application,
scientists can alter polymer mixtures to enhance the degradative properties of the
final product. For example, an almost pure starch product will dissolve upon con-
tact with water and then biodegrade rapidly. But, by blending quantities of other
biodegradable plastics into starch, scientists can now make a waterproof product
that degrades within 4 weeks after it has been buried in the soil or composted
(Fig. 6.1).
In the United States, the primary company manufacturing bioplastics is Nature-
Works, owned by Cargill. They can produce 300 million pounds a year of a plastic
called PLA or poly lactic acid that is made from corn grown in Nebraska and Iowa.
Starch from the corn is extracted and converted into its basic monomer, D-glucose,
and then into lactic acid by fermentation. The lactic acid is further refined into pel-
lets that can be made into different end-products. This is actually a much better use
of non-feed corn than the production of ethanol. It gives more and is much more effi-
cient. Other companies manufacturing plant-based plastics include Dupont, BASF,
Eastman, Proctor & Gamble, and Cereplast. The end plastic products, indistinguish-
able from those derived from petrochemicals, are used to create food packaging, dis-
posable cups and forks, water bottles, auto parts, carpeting, compact disks, bedding
materials, and other consumer products.
In Europe, bioplastics are even more popular. Consumption doubled between
2001 and 2003. An Italian company called Novamont manufactures a plant-based
plastic called Mater-Bi that is used in many similar applications to PLA, including
food packaging and disposable food service items. Production is expanding across
the globe where capacity for bio-based plastics is around 800 million pounds and is
expected to top 1.3 billion pounds in 2008.
Despite numerous environmental and health benefits of plant-based plastics, sig-
nificant environmental challenges need to be addressed. These include the impacts
of industrial agricultural production, the use of harmful additives, and the impact
on recycling infrastructure and markets. Conventional corn production uses signifi-
cant amounts of toxic pesticides that can adversely impact groundwater and surface
water, leads to soil erosion, and impacts soil production and wildlife habitats. In
addition, much of the corn made into NatureWorks’ plastic is genetically modified.
Many environmental organizations are working to address the use of genetically
modified organisms (GMOs) in NatureWorks’ feedstock.
One concern raised by recyclers is the impact that bioplastics have on the recy-
cling of conventional plastics. Bio-based plastics, such as PLA, cannot be mixed
with conventional plastic such as PET/PETE (polyethylene terephthalate) because
these materials are not compatible for recycling purposes. PLA itself can be recy-
cled, but at present, the infrastructure to separate and recycle this material does not
exist in the United States. Until these problems are solved, the most sustainable dis-
posal option for bio-based plastics is composting. Clear labeling of bio-based plas-
tics is critical to ensuring that these materials are properly disposed of in composting
facilities. The technology is a step in the right direction in terms of responsible use
of plastics.
References
Adeyemi, A. 2000. Urban Agriculture: An Abbreviated List of References and Resource Guide
Alternative Farming Systems Information Center. National Agricultural Library, Agricultural
Research Service, US Department of Agriculture, 10301 Baltimore Avenue, Beltsville, MD
20705-2351.
Cseke, L., Kirakosyan, A., Kaufman, P., Warber, S., Duke, J., Brielmann, H. 2006. Natural products
from plants, 2nd ed. Taylor-Francis, CRC Press, Boca Raton, FL.
Gross, R.A., Kalra, B. 2002. Biodegradable polymers for the environment. Science 297:
5582–5583.
Joseph, J.A., Nadeau, D.A., Underwood, A. 2002. The Color Code: A Revolutionary Eating Plan
for Optimum Health. Hyperion, New York.
Kimbrell, A. 2002. Fatal Harvest: The Tragedy of Industrial Agriculture. Published by Foundation
for Deep Ecology, 1062 Fort Cronkhite, Sausalito, CA 94965.
Leveque, C., Mounolou, J. 2003. Biodiversity. John Wiley, New York.
Mason, J. 2000. Commercial Hydroponics. Simon & Schuster, Australia.
Resh, H.M. 2001. Hydroponic Food Production: A Definitive Guide of Soilless Food-Growing
Methods, 6th ed. Woodbridge Press Publishing Co., Beaverton, OR.
Ronald, P.C., Adamchak, R.W. 2008. Tomorrow’s Table. Organic Farming, Genetics, and the
Future of Food. Oxford University Press, Oxford, UK.
Chapter 7
Phytoremediation: The Wave of the Future
Jerry S. Succuro, Steven S. McDonald, and Casey R. Lu
Abstract As the industrial age developed, societies have allowed large amounts
of contaminants to enter the environment unchecked. As a result of this neglect,
the incidence of heavy-metal contaminated sites has been on the rise. These sites
are polluted with toxic hydrocarbons and radionuclides, as well as heavy met-
als, such as cadmium (Cd), chromium (Cr), copper (Cu), lead (Pb), and zinc
(Zn). The result is unsightly areas left untreated, undeveloped and are accurately
referred to as “Brown Fields.” Heavy metals in the soil can create a contaminated
and possibly toxic top layer ranging 2–5 cm deep in addition to the possibility
of entering the food chain. The typical and most common method of removing
contaminants is to excavate the soil by mechanical means and store it at off-site
locations.
Phytoremediation is an innovative, emerging technology that utilizes plant species
to remove contaminants from the environment using a distinct set of plant-based
technologies. Four types of remediation technologies have been employed: (1) phy-
tostabilization is the use of a plant’s root system to stabilize the metal-contaminated
soil thus preventing the spread of the contaminant; (2) phytodegradation is the pro-
cess of using plants to convert toxic contaminants into less toxic forms; (3) rhi-
zofiltration is the process of using plants to clean aquatic environments; and finally,
(4) phytoextraction is the practice of using plants to take up metals from the soil
and translocate them to the above-ground tissues which can then be harvested. By
utilizing phytoremediation techniques, the environmental disruption is minimized,
soil fertility is maintained, secondary air- and water-borne wastes are reduced, and
these techniques are well received by the public as in situ methods. This chapter will
discuss the use of multiple plant species in each of the listed remediation techniques
for the goal of rejuvenating Earth’s ecosystems.
J.S. Succuro (B)

Department of Biological Sciences, Humboldt State University, Arcata, CA 95521, USA

120 J.S. Succuro et al.
7.1 Introduction
During the industrial age, humans have allowed large amounts of contaminants to
enter the environment unchecked. As a result of this neglect, many toxins have been
permitted to accumulate in our soils and water systems. Since this neglect was
allowed to continue for so long, the incidence of heavy-metal contaminated sites
has been on the rise. The public is made aware of this issue through the media. In
most cases, the media have a tendency to paint a very grim picture of how these
contaminated sites will affect humans and animals alike (Environmental Protection
Agency, 2007). For the most part, their interpretation of the situation is correct. Con-
taminated sites do exist and are polluted with toxic hydrocarbons and radionuclides,
as well as heavy metals, such as cadmium (Cd), chromium (Cr), copper (Cu), lead
(Pb), and zinc (Zn) (Amaya-Chavez et al., 2006). This heavy-metal contamination
is a result of anthropogenic activities such as metal mining and smelting, agricul-
ture, sewage sludge, fossil fuel combustion, and chemical manufacturing (Alloway,
1995). In addition to manufacturing types of activities, recreational sports such
as the use of shooting ranges and improper storage techniques add to the list of
sources (Alloway, 1995; Ebbs and Kochian, 1997). Often these sites of contamina-
tion become unsightly reminders of the lackadaisical attitude people take toward the
environment.
These large, unsightly areas are often left untreated, undeveloped and are accu-
rately referred to as “Brown Fields.” Brown fields, or any other smaller toxic sites,
are subject to wind-blown dispersion if the soil is disturbed and the heavy metal
is set free. As the wind blows across the disturbed soil, soil particles and associ-
ated contaminants can be blown into the upper atmosphere and travel rather large
distances, thus contaminating locations, such as playgrounds, parks, and yards thou-
sands of miles from the original site (Xei et al., 1999). In addition to wind dispersal,
when a heavy metal such as lead contacts the soil, it becomes tightly adsorbed to the
soil particles. This can create a contaminated and possibly toxic top layer of soil that
ranges 2–5 cm deep (Sharma and Dubey, 2005), where, in playgrounds or backyards,
it becomes a threat to human health. Another concern for heavy-metal contaminated
sites is the possibility of it entering the food chain. Although animals, plants, and
microbes have no biological need for certain specific heavy metals, they can be
taken up and sequestered in the cells of living organisms. Furthermore, these heavy
metals can be moved from plants to animals as they graze on contaminated sites.
Once the heavy metal enters the food chain, secondary and tertiary predators can be
adversely affected by the quantities of metal present (Taylor and Crowder, 1983a).
As these organisms in the higher trophic levels continue to consume heavy-metal
contaminated foods, the toxic level within these organisms also increases (Taylor
and Crowder, 1983a,b). This process is known as bioaccumulation.
In response to public outcry, the US Environmental Protection Agency (EPA)
has spent billions of dollars on Superfund site cleanup projects across the nation
(Bouchier and Lu, 2002; USEPA, 1993). As public awareness increases, so have
the questions concerning how safe areas such as playgrounds, homes, and gardens,
are for plants and animals (including humans). The largest concern regarding the
7 Phytoremediation: The Wave of the Future 121
toxicity or accumulation of heavy metals, such as lead, is directed toward small

children. Their bodies and central nervous systems are developing rapidly and
any exposure to lead, even blood levels as low as 10 μg dL−1 , can cause long-
term health problems within many organ systems. Examples of affected systems
include, but are not limited to, gastrointestinal tract, cardiovascular system, ner-
vous system, kidneys, immune, reproductive, and mental and physical impairment
(www.epa.gov/iaq/lead.html, 2007; ATSDR, 2007; Pyatt and Gratten, 2001). Poten-
tial areas of concern for children are the ingestion of soil particles in playgrounds,
and most importantly, the consumption of small lead-based paint chips in homes
built before 1960, and the inhalation of lead dust from painted friction surfaces.
In an attempt to reduce exposure to heavy-metal contamination in soils, several
methods of disposal have been developed. The typical and most common method
is to excavate the soil by mechanical means using tractors and bulldozers, and then
to transport the soil to another location where it is stored (Memon et al., 2001;
Cunningham et al., 1995). Even though these storage facilities are lined with mate-
rial to prevent the spread of contamination, the sites themselves become areas that
are uninhabitable. In some cases, these sites become problems as heavy metals
escape the confines of the protective barriers such as native claystone soils (ATSDR,
2005) and leach into the surrounding area and possibly nearby sources of ground-
water. In addition to excavation of contaminated sites, some sites are remediated
by the process of covering the soil with large quantities of concrete, asphalt, and/or
clean, uncontaminated soil (Berti and Cunningham, 2000), which temporarily fixes
the problem right where it lays by covering it to reduce contact. When these types
of remediation techniques are used, they only satisfy an immediate and temporary
fix to a long-term problem. In addition, these options can be very costly. Depend-
ing on the type of management strategy, remediation of a site by traditional means
can cost between $10 and $3,000 m−3 per year (Cunningham et al., 1995). No one
really knows what the long-term ramifications will be if these types of manage-
ment techniques are allowed to continue. In light of this problem, a developing new
technology has begun to focus on utilizing plants to decontaminate areas of high
concentrations of heavy metals and organic contamination. This new technology is
termed phytoremediation.
7.2 What Is Phytoremediation?
Phytoremediation is an innovative, emerging technology that utilizes plant species

to remove contaminants from the environment (Tian et al., 2007; Amaya-Chavez
et al., 2006). Much research has been conducted in this field and is gaining global
acceptance because of the possibility of adapting this technology to many different
types of ecosystems in both developed and developing countries. The term phy-
toremediation stems from the words “phyto,” meaning plant, and the Latin suffix
“remedium,” meaning to clean or restore. Phytoremediation refers to a distinct set
of plant-based technologies utilizing naturally occurring and/or genetically mod-
ified plants to remove contaminants, such as metals and hydrocarbons from soil,
sediments, or water systems (Padmavathiamma and Li, 2007; Amaya-Chavez et al.,

2006). Plants accomplish this task by removal, transfer, stabilization, or decom-
position of these contaminants in the environments listed above (Hughes et al.,
1997). Heavy metals contaminate the major environmental systems of our planet:
air, water, and soil; therefore, biogeochemical cycles can be severely disrupted (Tian
et al., 2007). Heavy-metal pollution in soil differs from that of air- and water-based
systems because heavy metals have a tendency to remain in the soil for very long
periods of time. There are two major categories of contaminants that should be
considered, elemental pollutants and organic pollutants, each of which has its own
set of remediation strategies (Meagher, 2000). These will be discussed later in this
chapter. Based on the type of contaminant, site conditions, quantity of contami-
nant to be removed, and the species of plants to be used for the process, four types
of remediation technologies have been employed. They are classified based on the
containment of metals (phytostabilization and phytodegradation) or the extraction
of metals (phytofiltration and phytoextraction) (Padmavathiamma and Li, 2007). A
brief description of these processes is as follows: (1) phytostabilization is the use
of a plant’s root system to stabilize the metal-contaminated soil thus preventing the
spread of the contaminant; (2) phytodegradation is the process of using plants to
convert toxic contaminants into less toxic forms; (3) rhizofiltration is the process
of using plants to clean aquatic environments; and finally, (4) phytoextraction is the
practice of using plants to take up metals from the soil and translocate them to the
above-ground tissues which can then be harvested. In order for a plant to be listed
as a good candidate for phytoremediation, several factors should be met. A plant
must be tolerant to the environmental conditions of the contaminated site as well as
be fast-growing and produce high quantities of biomass in harvestable tissue (Yang
et al., 2005). With these conditions met, the phytoremediation process can begin.
7.2.1 Why Is Phytoremediation Important?
Taking into account the above-listed remediation techniques, the first thoughts
that come to mind are cost and how environmentally sound the phytoremediation
practices are at removing the contaminant from the environment. Traditionally,
contaminated sites are remediated by physical, chemical, or biological processes
(McEldowney et al., 1993). In the aftermath of the destructive treatments, irre-
versible effects may occur to soil properties. The destruction of biodiversity can
render soils useless for the growth of plants that could potentially remove remaining
contamination (Padmavathiamma and Li, 2007). By utilizing phytoremediation
techniques, the environmental disruption is minimized, soil fertility is maintained,
secondary air- and water-borne wastes are reduced, and these techniques are well
received by the public as in situ methods (Tian et al., 2007; Amaya-Chavez
et al., 2006; Padmavathiamma and Li, 2007). In some cases, phytoremediation
may be the only solution for reducing contaminated soil and water systems that
cover hundreds of thousands of square kilometers as a result of human activity
(Meagher, 2000). The harvesting of plants that have accumulated large quantities
of usable metals in their tissues, such as nickel, zinc, and copper, could be recy-
cled and used for other purposes, thus producing an economic incentive for using
phytoremediation (Ow, 1996). In addition to being environmentally friendly, the
phytoremediation process may also be cost-effective (Padmavathiamma and Li,
2007; Zhuang et al., 2007a,b; Yang et al., 2005). In the recent past, the cost to handle
contaminated waste was approximately $100 m−3 for incineration, $60–$300 m−3
for landfill, $200–$700 m−3 for special landfill requirements, and $1,000–$3,000
m−3 to dispose of radionuclides per year (Cunningham et al., 1995). Using the
techniques of phytoremediation, these costs are reduced remarkably to levels of
only $5–$40 t−1 and $0.02–$1.00 m−3 per year (Padmavathiamma and Li, 2007;
Cunningham et al., 1995).
7.2.2 Remediation of Organic Contaminants

Over many decades, humans have added large volumes of contaminants to the soil,
water, and atmosphere as a result of industrial manufacturing such as petroleum
and chemical operations and private independent operations such as dry-cleaning.
In addition to these processes, burning wood, coal, and fossil fuels, add a wide range
of organic chemicals to the environment, potentially causing negative health effects
for humans as well as wildlife. Further anthropogenic causes include car emissions,
waste incineration, service stations, solvent use, cigarette smoking, and the use of
pesticides.
Organic contaminants are carbon-containing compounds that are resistant to
environmental degradation through chemical, biological, and photolytic processes.
These compounds can be transported great distances, bioaccumulate in both human
and other animal tissues, as well as biomagnify in food chains. Health agencies have
identified several compounds as being extremely toxic to humans, wildlife, and the
environment. This list is by no means complete, but it includes aldrin, chlordane,
DDT, dieldrin, endrin, heptachlor, PCBs, and toxaphene (Fig. 7.1).
Some chemical properties of these organic toxins include decreased water solu-
bility, increased lipid solubility, semi-volatility, and higher molecular weights. With
their higher molecular weights and the addition of chlorine (Cl) substituents, the
compounds are increasingly difficult to break down and remain persistent in the
environment. Finally, their lipid solubility results in the ability of these molecules to
pass through biological phospholipid membranes and bioaccumulate in fatty tissues.
Humans may experience contamination through exposure from diet, environment,
and accidental discharges into the atmosphere or spills into the soil. Deleterious
health effects include damage to the endocrine system, the reproductive system,
the immune system, neurological disorders, cancer, and ultimately, death. In con-
trast, compounds with lower molecular weights, less than 236 g mol−1 , are usually
less toxic, thus reducing the health issues and environmental problems as a result
of being less persistent (http://en.wikipedia.org/wiki/persistent_organic_pollutant,
2007).
Aldrin Chlordane DDT
Dieldrin Endrin Heptachlor
Methyl parathion (MeP)
Fig. 7.1 Chemical structures of organic contaminates that are environmental risks to humans and
wildlife
Current research suggests that there are two different ways by which organic
contaminants can be removed from soil- and water-based systems, namely, phy-
todegradation and rhizofiltration. First we look at phytodegradation (Fig. 7.2), the
process that utilizes plants and their associated microflora to convert hydrocarbons
to non-toxic forms (Cunningham et al., 1995).
The conversion of contaminants by plants takes place in the following manner:
First the plant releases root exudates that include organic and inorganic substances
into the rhizosphere (soil–root–microorganism interface zone) during metabolism.
These root exudates act as substrates for soil microorganisms, thus enhancing the
uptake and degradation of toxic organic compounds by the plants. This principle
has been used to remediate crude oil, motor oil, and diesel fuel from soils (Chaineau
Fig. 7.2 Phytodegradation of organic contaminants. (Used with permission from Mueller et al.,
2001)
et al., 2000). In a field study conducted by Palmroth et al. (2006) over a 39-month
growth period, the initial soil concentration of contaminants was 11,400 mg kg−1
hydrocarbons in soil (dry weight). This soil contaminant component consisted of
two-thirds lubricating oil, and the remaining one-third, diesel fuel. The field area
was divided into four plots with two being fertilized with municipal biowaste,
one plot with NPK fertilizer (16.6:4:25.3), and in the remaining plot, no fertil-
izer was used. The target concentration of phytoremediation was set at a level of
1,500 mg kg−1 hydrocarbons in dry soil, which translates to a reduction of hydro-
carbons by 87% (Palmroth et al., 2006). Initially the hydrocarbon concentration did
not decrease significantly in non-amended soil; however, there was a 30% decrease
in the original concentration during the last 4 months of the experiment. In soil
amended with either NPK fertilizer or biowaste compost, 65 and 60% of the hydro-
carbons were removed, respectively, using a mixture of grasses (red fescue, Festuca
rubra; meadowgrass, Poa pratensis; and ryegrass, Lolium perenne), Dutch white
clover (Trifolium repens), Scots pine (Pinus sylvestris), and poplar seedlings (Pop-
ulus deltoides x Wettsteinii). Ultimately, 57% of the hydrocarbons were removed in
the plots amended with biowaste, clover, and grasses. Approximately 60% of the
hydrocarbons were removed in the plot with grasses, clover, and trees. For the plot
using NPK fertilizer, increased hydrocarbon removal was recorded compared to the
biowaste plots, but during the last 4 months of the study there was no significant
difference between the two amendments (Palmroth et al., 2006). This study shows
positive potential for phytodegradation with approximately 50% or more of the
hydrocarbons being removed by plants and associated microflora from contaminated
soil. The length of time for remediation can take several years to achieve treatment
goals. It should be noted that in this study, the goal of achieving the 1,500 mg kg−1
hydrocarbons in dry soil weight was not achieved. This, however, does not mean
that the process of phytodegradation is a non-viable technique; it does confirm the
need for further research into optimizing the phytoremediation process and possibly
using genetically modified (GM) plants.
7.3 Rhizofiltration
Rhizofiltration (Fig. 7.3) is the adsorption or precipitation of contaminants onto

plant roots or the absorption into the roots of contaminants that are in solution sur-
rounding the root zone due to biotic or abiotic processes.
The uptake, concentration, and translocation of contaminants by the plants may
occur and will depend on the contaminant and the type of plant. Exudates from the
plant roots may cause precipitation of some organics. Rhizofiltration first results in
decontamination, a process by which the contaminants are immobilized or accumu-
lated on or within the plant. Contaminants are then removed via plant harvesting
(www.gsd.harvard.edu/users/yauanian/phyto_processes_main.html). Work done by
Amaya-Chavez et al. (2006) has shown that cattails (Typha latifolia L.) have been
successful in removing methyl parathion (MeP) (Fig. 7.1), an organophosphorus
(OP) pesticide, from water systems and sediments. The cattails were subjected to
various levels of MeP in the following concentrations: 0, 25, 50, 100, 150, and
200 mg L−1 . Photosynthetic potential, based on chlorophyll a and chlorophyll b
concentration ratios, were used to determine the overall health of the plants. The
basal mean total chlorophyll content was determined to be 32.9 mg ml−1 and the
Fig. 7.3 Rhizofiltration of organic or inorganic contaminants. (Used with permission from Mueller
et al., 2001)
chlorophyll a/b ratio was 2.8. After 10 days of exposure to MeP, no significant dif-
ferences were shown in either total chlorophyll content or chlorophyll a/b ratio at the
different MeP exposure levels (Amaya-Chavez et al., 2006). As a result, T. latifolia
shows a low level of toxicity as a result of MeP uptake and a higher level of toler-
ance than other macrophytes tested to date. This higher tolerance could be due to
T. latifolia’s ability to produce higher biomass with its rhizomatous/fibrous root sys-
tem. As a result of these studies, T. latifolia has been determined to be quite efficient
at removing MeP from water and sediment systems. Glick (2003) surmises that this
efficiency could be due, in part, to a rhizosphere root/microorganism association
that aids in the organic contaminant degradation with T. latifolia’s extensive rhi-
zomatous/fibrous root system. Finally, given T. latifolia’s ability to tolerate a range
of MeP concentrations without any loss of removal efficiency and minimal toxic
effects to the plant, it should be seriously considered for remediation practices.
7.3.1 Remediation of Inorganic Contaminates

Inorganic contaminants (heavy metals or trace metals) compose much of the con-
tamination at sites throughout the world. These higher atomic weight elements and
some lower-weight elements can be called heavy metals as a group. Certain heavy
metals or trace metals are required for the metabolic processes in organisms. Some
of these trace metals, including iron, cobalt, copper, manganese, and zinc, however,
become toxic at elevated levels (Alloway, 1995). As discussed in the Introduction
section, some heavy metals have no biological use: these include mercury, lead, and
cadmium. The question arises, then, as to how we can safely and effectively remove
metals from our environment with as little destruction as possible, thus reducing or
removing the threat to environmental health? This is where the utilization of phy-
toremediation techniques becomes important, particularly since they can be more
cost-effective, less destructive, and at the same time, be more appealing to the pub-
lic. There are a number of different ways in which phytoremediation can work. As
discussed in the above section on rhizofiltration of organic types of contamination,
phytofiltration is used in this section as a means to remove heavy metals from an
aquatic environment. The processes are essentially the same.
Plants can also be used for phytoextraction (Fig. 7.4). This occurs when metal
contaminants in the soil are taken up by roots and translocated to the above-ground
tissues. The plants can then be removed from the site, or if removal of the entire
plant is not practical, then the above-ground tissues can be removed for continual
remediation of the soil. Removal of these tissues can occur multiple times during the
growing season, thus increasing the rate of contamination removal. The harvested
tissues can then be incinerated and the ash can be stored in a hazardous waste land-
fill. The volume of ash stored would be significantly less than excavating the soil
and storing it in the same hazardous waste landfill.
Since there is no single plant species that can remove all contaminants at one site,
several different species must be used for multiple contaminants. As these plants
grow, they can accumulate high quantities of heavy metals such as lead. The normal
Fig. 7.4 Phytoextraction of inorganic contaminants. (Used with permission from Mueller et al.,
2001)
range of lead a plant can accumulate is between 6.3 and 9.9 mg kg−1 (Outridge
and Noller, 1991). Lead becomes toxic to the plants at levels above 27 mg kg−1
(Beckett and Davis, 1978). In addition to lead uptake, some plants are tolerant to
increased levels of zinc, an essential mineral element. The mean level is 66 mg kg−1
and becomes toxic at levels of 230 mg kg−1 and higher (Borkert et al., 1998;
Long et al., 2003). In some cases, plants can be classified as hyperaccumulators
because of their ability to accumulate extremely high levels of the metal contami-
nant into their tissues. Hyperaccumulator status is achieved when a plant accumu-
lates more than 1,000 mg kg−1 or 0.1% of the metal by dry weight for lead and
10,000 mg kg−1 or 1.0% of the metal by dry weight for zinc (Brooks et al., 1977).
One example of a hyperaccumulator plant is Brassica juncea (L.) Czern. or Indian
Mustard. B. juncea has been known to accumulate 1.5% Pb (lead) by dry weight
with the addition of ethylenediaminetetraacetic acid (EDTA), a synthetic chelating
agent used to increase the solubility of lead when grown in media that had a large
quantity of lead available (Blaylock et al., 1997; Bouchier, 2003). Another plant
that receives much attention as a hyperaccumulator of zinc (Zn) and cadmium (Cd)
is Thlaspi caerulescens J. & C. Presl. or alpine penny cress. Research conducted
by Baker et al. (1994, as cited in Brown et al., 1994) has shown that field sam-
ples collected at sites contaminated with cadmium (Cd) and zinc (Zn) had shoot
concentrations as high as 164 and 21,000 mg kg−1 dry weight, respectively. Addi-
tionally, Brown et al. (1995) showed that when grown hydroponically in solutions
containing 650 mg L−1 Zn and 22 mg L−1 Cd, T. caerulescens could accumulate Zn
and Cd in shoots up to 33,600 and 1,140 mg kg−1 dry weight, respectively. These
heavy-metal concentrations far exceed the concentrations typically found in plant

tissues.
In addition to B. juncea and T. caerulescens achieving hyperaccumulator sta-
tus, Typha latifolia (the broadleaf cattail) is receiving attention due to its ability to
grow in many different types of semi-aquatic and aquatic environments and tolerate
high levels of contamination (Amaya-Chavez et al., 2006; Doucette et al., 2005).
A greenhouse study of 12 weeks duration conducted by McDonald (2006), con-
sisting of growing cattails in mason jars with lead levels of 0, 1,000, 2,000, and
4,000 mg kg−1 , has shown that there was no apparent reduction in growth caused
by the different lead levels. It should be noted that any reduction in growth was
attributed to the cattails being confined to a small growth area (McDonald, 2006). In
addition, the only visible signs of exposure to consistently increasing levels of lead
was the yellowing and burning of shoot tips subsequent to the addition of EDTA. To
determine if T. latifolia could achieve hyperaccumulator status, ethylenediaminete-
traacetic acid (EDTA) was added to the soil at the 10th week of the 12-week growth
period.
Over the 12-week period, the cattails that were exposed to the varying lev-
els of lead without the addition of EDTA revealed that the roots and rhizomes
of the 4,000 mg kg−1 exposed cattails accumulated large quantities of lead rather
than translocating lead to the above-ground tissues (McDonald, 2006). In this
particular case, the cattails accumulated 1,515.2 mg kg−1 in root/rhizome tis-
sue, showing that in the absence of a chelating agent, lead movement is sig-
nificantly confined to a greater extent to the rhizomes and roots. On the other
hand, with the addition of EDTA, the most promising results were obtained, as
large quantities of lead accumulated in the cattail shoots that were exposed to
the 4,000 mg kg−1 lead level. The roots were able to absorb 2,483.5 mg kg−1 , in
which 2,418.5 mg kg−1 was transported into the shoots (McDonald, 2006), indicat-
ing that the chelating agent facilitated the translocation of lead to aerial portions
of the plant. Based on these results, it was determined that T. latifolia can reach
hyperaccumulator status with the assistance of a chelating agent that allows for the
translocation of contaminates (lead in this case) from rhizomes and roots to the
shoots.
Plants can also be used for phytostabilization which refers to use of plants to
immobilize contaminants in the soil and/or ground water through absorption and
accumulation by roots, adsorption onto roots, or the precipitation of contaminants
within the rhizosphere (Fig. 7.5) (Phytoremediation Resource Guide, EPA, 1999;
Brookhaven National Laboratory, 2000).
Additionally, this technique reduces the mobility of the contaminant(s) and pre-
vents migration to groundwater, as well as reducing the bioavailability for entering
the food chain. Using plants that are metal-tolerant can restore vegetation on con-
taminated sites where the threat of contaminant migration from soil erosion is high
due to wind and water. Once a plant cover is established, the threat of direct con-
tact with humans and animals is significantly reduced. The vegetative cover can
provide a barrier between the contaminant(s) in the soil and the surrounding envi-
ronment. This technique works in the following way: a study of the nature of the
Fig. 7.5 Phytostabilization of inorganic or organic contaminants. (Used with permission from
Mueller et al., 2001)
soil contaminant(s) is determined; next, traditional fertilizers or specific amend-

ments are used to improve the soil conditions and render the contaminants immo-
bile. Once this is achieved, a plant species is selected based on the conditions of
the soil, the surrounding environment, the ability of the plant not to accumulate the
contaminants into above-ground tissues, and the plant’s tolerance to the specific site
contaminants.
This technique can be thought of as a two-step process. First, a suitable soil
amendment should be selected that is long-lasting if not permanent (Berti and
Cunningham, 2000). This selection should be based on the following considera-
tions: it must be inexpensive, easy to handle, safe for workers, be compatible and
non-toxic with the plants selected, be available for use, and finally, not cause the
environment further damage (Berti and Cunningham, 2000). In addition to the listed
considerations, some amendments may have secondary benefits to the growth of
plants by providing nutrients and by increasing soil water-holding capacity (i.e.,
phosphate fertilizers and organic materials). The most common amendments include
phosphate fertilizers (e.g., superphosphate), organic matter or biosolids such as
composts and manures, iron or manganese oxyhydroxides, clay minerals, or mix-
tures of these amendments (Cunningham and Berti, 2000; Berti and Cunningham,
2000). The second step is to determine a species of plant that is able to grow in
the harsh environment of the contaminated site. These plants will be responsible
for physically stabilizing the soil that they are growing on by having dense root
systems that prevent soil erosion by protecting the soil from human contact and
rain. In addition, the root systems should reduce the incidence of water percolation,
thus immobilizing the contaminant(s). Further considerations include these plants
being poor translocators of heavy metals to the above-ground tissues (to reduce risk
of entering the food chain via herbivory), their rapid growth rates, and their high
transpiration rates that allow for more effective removal of soil water (Berti and
Cunningham, 2000).
A study by Tang and Fang (2001) was conducted to determine the usefulness
of two perennial herbs from the Polygonaceae family, Polygonum microcephalum
D. Don (Red Dragon) and Rumex hastatus D. Don (Curly Dock), as plants that
could be used for phytostabilization. Plant and soil samples (from the root zone)
were taken from three different heavily contaminated copper mines of the Yunnan
Province in China for analysis. Results showed that P. microcephalum accumulated
high concentrations of copper in roots, stems, and shoots, averaging 491, 110, and
133 mg kg−1 , respectively. On the other hand, R. hastatus accumulated lower con-
centrations of copper in roots, stems, and shoots, averaging 33, 42, and 45 mg kg−1 ,
respectively. This, however, does show that both species can accumulate copper into
tissues when grown in a copper-contaminated soil (Tang and Fang, 2001). Since
P. microcephalum accumulated more copper in its tissues than R. hastatus, this
could indicate that P. microcephalum has a higher level of tolerance than R. hastatus.
When considering the higher levels of copper accumulated by P. microcephalum
and lower accumulation amounts in R. hastatus, one can infer from these data that
R. hastatus is excluding copper from the shoots. The result of the soil analysis
revealed that copper concentrations for P. microcephalum and R. hastatus, averaged
1,494 and 2,105 mg kg−1 dry weight, respectively, confirming that these species
can grow in highly contaminated soil. It should also be noted that there was a lack
of soil fertility as confirmed by low soil organic carbon (humus). In conclusion,
P. microcephalum appears to be more of an accumulator with respect to copper-type
contaminants, whereas R. hastatus is more of an excluder based on the compari-
son of shoot/root metal ratios (Tang and Fang, 2001). This evidence shows that two
species can grow side by side even though they have different uptake and trans-
port characteristics, thus providing the potential for phytostabilization (Tang and
Fang, 2001).
7.4 Case Study: Phytoremediation of Contaminated Air
There is also the concern today about how plants respond to air pollution and how
they might be used to help alleviate this problem. This occurs mainly in urban areas
as a result of industrialization and the burning of fossil fuels (Park et al., 2006).
A large contributor to this pollution is the automobile, causing roadside damage to
both plants and the underlying soil (Park et al., 2006). As fossil fuels are burned in
the engines of vehicles, many greenhouse gases are emitted, including sulfur dioxide
(SO2 ), carbon monoxide (CO), and particulate matter (Kulshreshtha et al., 2003).
Since plants provide a large leaf surface area that is in contact with the surrounding
environment, absorption, adsorption, and accumulation of these air pollutants can
occur, thus reducing pollution’s negative effect on the environment (Kulshreshtha
et al., 2003; Sharma et al., 2005). Research conducted by Kulshreshtha et al. (2003)
evaluated 30 species of plants to determine the tolerance to air pollution in a road-
side (heavily polluted) environment and a park/garden (non-polluted) environment.
In order to determine the tolerance of the plants, several factors were investigated.
These included chlorophyll and ascorbic acid contents, relative water content, and
leaf extract pH. These tolerance measures were then converted to an Air Pollution
Tolerance Index (APTI) (Kulshreshtha et al., 2003). Plants that had an APTI that
was high were considered to have a tolerance to pollutants, whereas plants with an
APTI that was low indicated plants were not as tolerant to the pollutants. Of the
30 plants that were investigated, species that had an APTI of 30 or greater included
Catharanthus roseus (L.) G. Don or Madagascar periwinkle (37), Ficus religiosa L.
or Sacred fig (35), Bougainvillea spectabilis Willd. or Bougainvillea (32), and Ficus
glomerata Roxb. or Bonsai tree (32), while plants that showed less tolerance (an
APTI of 5 or less) to air pollution included Delbergia sissoo Roxb., or Shisham
tree (3) and Cansa carendes (3). Further research with the plants that had high
APTI value should be considered for the reduction of roadside pollution in urban
areas.
Sharma et al. (2005) compared the use of bougainvillea plants as a means of
reducing air pollution along roadsides in both high- and low-traffic areas. Plants
of 11 cultivars grown in pots were subjected to a low-traffic-density area (LTDA)
represented by the NBRI Botanical Garden and a high-traffic-density area (HTDA)
represented by a median dividing roads in a high-traffic area (Sharma et al., 2005).
To determine the effectiveness of the bougainvilleas at removing pollutants from
the air, several different foliar aspects of health were studied. These parameters
included cuticle, stomata, subsidiary cells, and trichomes. In the LDTA the cuti-
cle was smooth, granular, or striate having inconspicuous wax at certain locations
while the stomata were globose and present at the same level as other cells. The
subsidiary cell walls were clear but slightly raised and the trichomes were non-
glandular, uniseriate, and multicellular with a bolbus base and globular tip (Sharma
et al., 2005). The HTDA foliage showed that the cuticle was wrinkled and stria-
tions were not present, while the stomata were raised from the surface of other cells
and present in larger numbers. Subsidiary cell walls had fused and were irregularly
shaped, while the number of trichomes increased, their overall length had decreased,
and the cuticle over the trichomes had become cracked (Sharma et al., 2005). It was
determined that because of morphological, anatomical, and physiological changes
within the foliage, absorption of toxic pollutants was confined to the cell sap which
neutralized these toxins, thus forming a stable complex within certain cellular com-
partments, thus allowing greater tolerance to pollutants. The conclusion reached was
that bougainvilleas with their relatively thick leaves of large surface area can trap
more dust and pollutants in the surrounding area of high traffic, reducing pollution,
while at the same time, presenting a pleasing environment since these plants provide
a wide array of flower colors (Sharma et al., 2005).
7.5 Conclusions
Since the beginning of time, humans have left their mark (in some cases, irre-
versibly) on the environment. During the industrial revolution, no one stopped to
think about the long-term ramifications of constantly polluting air, water, and soil.
The thinking during this period was that Earth’s environment is going to be around
forever and that it can clean itself. In addition to the industrial age releasing huge
amounts of contaminants into the environment, the consumption of fossil fuels also
increased as motor vehicles continued to grow in size and number. When humans
discovered that the oil used for the production of gasoline was in short supply, they
began to realize that our resources are limited. The same chain of events can be said
about the logging industry, fishing industry, and the mining industry, just to name
a few. As the realization became transparently clear, new ways to save our natural
resources and to help repair the environment began to be developed. One of the out-
comes of this greening revolution was the field or technology of phytoremediation,
whereby plants that are already here can be used to assist in the rejuvenation of
Earth’s ecosystems. Through phytoremediation techniques, the environment can be
“cleaned” in less destructive and most cost-effective ways by the virtue of the ability
of plants’ adaptation to many different types of contamination across many different
ecosystems. Although phytoremediation seems like it is the answer to many prob-
lems of pollution, it is subject to some limitations such as requiring supplemental
nutrients, having extended time requirements for remediation to occur, and only
removing contaminants within the root zone (rhizosphere). However, the picture is
not bleak because current research (from many different fields of study) is now com-
ing together as a multidisciplinary effort for the discovery of new ways to better the
phytoremediation processes. As long as there is a need for remediation (and there
may likely be from now on), scientists will continue to come together and to work
diligently to solve the problems of contamination in an attempt to make the world a
safer and more healthy place to live.
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Chapter 8
Biotechnology of the Rhizosphere
Beatriz Ramos Solano, Jorge Barriuso Maicas, and Javier Gutierrez Mañero
Abstract This chapter deals with the management of the rhizosphere as a living
system, paying special attention to one of the three partners that define the rhizo-
sphere: beneficial microorganisms (termed PGPR or the plant growth-promoting
rhizosphere bacteria) that inhabit it. After that, several biotechnological approaches
for management of the rhizosphere will be presented. These approaches relate to
environment friendly agricultural practices, the production of high-quality foods
with bioactive compounds (phytonutrients), and applications in the pharmaceutical
industry.
The rhizosphere refers to the soil region that is subject to the influence of plant
roots and their associated microorganisms. Among these microorganisms are plant
growth-promoting rhizobacteria which are beneficial for plant health in many ways:
by improving plant nutrition, protecting against other microorganisms, producing
plant growth regulators, or enhancing plant secondary metabolic pathways that are
directly related to a plant’s defense. In some plant species, these secondary metabo-
lites are useful to human health.
The biotechnology of the rhizosphere covers a wide array of applications that
deal with sustainable agriculture (intensive or extensive): lowering of chemical
inputs due to fertilizers and pesticides; improving crop productivity in saline and
non-fertile soils; improvement of plant fitness for reforestation of degraded soils;
and improvement in the bioactive levels of metabolites in medicinal plant species,
among others. In this connection, the identification of elicitors (molecules that stim-
ulate any of a number of defense responses in plants) appears to be an alternative to
PGPR for unraveling limiting steps of secondary metabolism pathways.
B.R. Solano (B)

Department of Environmental Sciences and Natural Resources, Faculty of Pharmacy,
University San Pablo CEU, Boadilla del Monte, Madrid 28668, Spain

138 B.R. Solano et al.
8.1 Introduction
The German agronomist Hiltner first defined the rhizosphere, at the end of the nine-
teenth century, as the “effect” of the roots of legumes on the surrounding soil, in
terms of higher microbial activity, due to the organic matter released by the roots
(Lynch, 1990). Until the end of the twentieth century, this “effect” was not consid-
ered to be an ecosystem in which the three components (plant, soil, and microor-
ganisms) define a unique environment (Barriuso et al., 2008a). This environment
changes depending on the conditions set up by the three components. Therefore, a
deep knowledge of the interactions between the plant, the soil, and the microor-
ganisms is vital to our understanding of how this complex rhizosphere system
operates.
In this context, a second concept that needs to be addressed here is what we shall
term biotechnology of the rhizosphere (Fig. 8.1).
Among the three components of the interaction shown in Fig. 8.1, microorgan-
isms appear as the easiest element to manipulate, since we will usually select the
plant of interest and the soil to work with. Microorganisms that inhabit the rhizo-
sphere play a key role in plant physiology by affecting either directly or indirectly
the plant’s metabolism. These bacteria may increase nutrient availability in the soil,
which will be reflected in better growth of the plant (indirect mechanisms), or may
affect the plant’s hormonal balance or its secondary metabolism (direct mecha-
nisms) (Ramos Solano et al., 2008a). When secondary metabolism is affected, the
plant’s defense against pathogen or insect attack may be improved for better fitness.
At the same time, in medicinal plant species, levels of phytopharmaceuticals are
altered. In this case, either known metabolites increase or even new molecules may
appear (Poulev et al., 2003). This role involves not only the direct effect of a sin-
gle bacterial strain but also that of the molecular dialogue established among soil
microorganisms and between microorganisms and the plant (Barriuso et al., 2008c).
PLANT
Fig. 8.1 Biotechnology of

the rhizosphere. The
rhizosphere is defined by the
interaction of three
components: plant, soil, and BIOTECHNOLOGY
microorganisms.
Biotechnology of the
rhizosphere refers to
management of any of the
MICROORGANISMS SOIL
three factors and/or their
interactions in order to obtain
a certain effect
8 Biotechnology of the Rhizosphere 139
A thorough understanding of the PGPR action mechanisms is fundamental to

manipulating the rhizosphere in order to maximize the processes within the system
that strongly influence plant productivity. Therefore, the first goal of this chapter
will be to examine rhizosphere microorganisms and then to explore their different
biotechnological applications.
8.2 Plant Growth-Promoting Rhizobacteria (PGPR)
A large number of macroscopic organisms and microorganisms such as bacteria,

fungi, protozoa, and algae coexist in the rhizosphere. The most abundant are bac-
teria. Plants release organic compounds via root exudates, which selectively attract
beneficial bacteria (Lynch, 1990), creating a very selective low-diversity environ-
ment (Marilley and Aragno, 1999; Lucas García et al., 2001; Barriuso et al., 2005).
Bacteria inhabiting the rhizosphere beneficial to plants are called PGPR (Plant
Growth-Promoting Rhizobacteria) (Kloepper et al., 1980a). The rhizosphere of wild
plant species appears to be the best source from which to isolate PGPR due to the
co-evolution processes that have taken place over time (Lucas García et al., 2001;
Gutiérrez Mañero et al., 2003; Barriuso et al., 2005; Ramos Solano et al., 2007).
PGPR have been reported as members of several genera including Azotobac-
ter, Acetobacter, Azospirillum, Burkholderia, Pseudomonas, and Bacillus (Arshad
and Frankenberger, 1998). The positive effect of PGPR occurs through various
mechanisms.
Mechanisms used by PGPR have traditionally been grouped into direct and indi-
rect mechanisms (for a recent review, see Ramos Solano et al., 2008a). Although the
difference between them is not always obvious, indirect mechanisms, as a general
rule, are those that happen outside the plant, while direct mechanismsare those that
occur within the plant and directly affect the plant’s metabolism. This means that the
latter require the participation of the plant’s defensive metabolic processes, which
transduce the signal sent from the bacteria influencing the plant. Accordingly, indi-
rect mechanisms are usually related to nutrient-related traits or defense against other
microorganisms outside the plant, while direct mechanisms include those that affect
the balance of plant growth regulators, either creating an outbound gradient from
the roots to the soil (Glick et al., 1998) or because the microorganisms themselves
release growth regulators that are integrated into the plant, leading to an improve-
ment in its adaptative capacity (Gutiérrez Mañero et al., 1996, 2001). Two important
phenomena are included in this group: systemic induction of secondary metabolism
related to defense against plant pathogens and protection against high-salinity con-
ditions (Barriuso et al., 2008b).
However, the existence of microorganisms able to prevent diseases from occur-
ring in plants without the plant’s direct participation is also known. This occurs by
systems such as niche exclusion or pathogen-inhibiting substance production. When
the physical contact of the pathogen and the protecting microorganism is required,
it is known as biocontrol (Bloomberg and Lugtenberg, 2001; Compant et al., 2005).
A short review of the most relevant mechanisms follows and will be integrated
into the subsequent case studies section later in this chapter.
8.2.1 PGPR That Utilize Indirect Mechanisms
The list of indirect mechanisms used by PGPR is substantial. A number of reports

in the literature illustrate these types of mechanisms, and some are quoted herewith.
Two groups can be devised, depending whether they are related to improvement
of plant nutrition or pertain to pathogen performance. The first group includes (1)
free nitrogen fixation, (2) siderophore production, and (3) phosphate solubilization.
The second group includes (1) hydrolysis of molecules released by pathogens (e.g.,
Toyoda and Utsumi, 1991 reported the ability of two strains, Pseudomonas cepa-
cia and Pseudomonas solanacearum, that are able to break down fusaric acid, a
compound responsible for root rot caused by the fungus Fusarium); (2) synthesis
of enzymes that are able to hydrolyze fungal cell walls (Lim et al., 1991); and (3)
synthesis of cyanhydric acid (Voisard et al., 1989).
In addition, improvement of symbiotic relationships with rhizobia and mycor-
rhizae has been reported (Duponnois and Plenchette, 2003; Founoune et al., 2002;
Garbaye, 1994; Marek-Kozackuk and Skorupska, 2001; Lucas García et al., 2004;
Barriuso et al., 2008d), although further research will demonstrate whether these are
direct or indirect.
Among indirect mechanisms, the most relevant for agricultural purposes are
those involving nutrient mobilization (e.g., free nitrogen fixation, siderophore
production, and phosphate solubilization). Such nutrient mobilization results in a
lowering of chemical inputs to the environment, since the amount of chemical fer-
tilizers necessary to achieve good crop yields would be lower. Interestingly, and for a
proper and successful handling of this type of PGPR, it should be taken into account
that there is increasing evidence that nutrient-related traits are inducible when the
environmental conditions require such a need (Rainey, 1999). Otherwise, it may be
the reason for the lack of success of some field inoculations (Ramos Solano et al.,
2007). Moreover, if used appropriately, especially in low-fertility soils, these could
be turned into better soils by increasing the culturable soil surface, which is one of
the limiting factors currently needed to palliate world famine.
A short description of nutrient-related traits follows.
8.2.1.1 Free Nitrogen Fixation

These types of nitrogen-fixing bacteria were the first PGPR assayed to improve
plant growth, especially crop productivity. The first report of these bacteria appeared
before World War II, when they were widely used on cereal fields in the Soviet
Union (Bashan and Levanony, 1990). They are free-living organisms able to fix
nitrogen that inhabit the rhizosphere but do not establish a symbiosis with the plant.
Although they do not penetrate the plant’s tissues, a very close relationship is estab-
lished; these bacteria live so close to the roots that the atmospheric nitrogen fixed
and not used by the bacteria is taken up by the plant, forming an extra supply of
nitrogen. This relationship is described as an unspecific and “loose” symbiosis. Bio-
logical nitrogen fixation is a high-cost process in terms of energy. Bacterial strains
able to perform this process do so to fulfill their needs, and thus, little nitrogen is
left for the plant’s use. However, difficulties may be overcome by biotechnological
approaches based on genetic manipulations and other strategies to improve colo-
nization capacities.
However, growth promotion caused by nitrogen-fixing PGPR was erroneously
attributed to nitrogen fixation for many years, until the use of nitrogen isotopes
occurred. This technique showed that the benefits of free nitrogen-fixing bacteria
are due more to the production of plant growth regulators than to nitrogen fixation
(Baldini, 1997). This kind of production of plant growth regulators is discussed later.
8.2.1.2 Production of Siderophores

Iron is an essential nutrient for plants. Iron deficiency is manifested in severe
metabolic alterations due to its role as a cofactor for a number of enzymes essential
to important physiological processes such as respiration, photosynthesis, and nitro-
gen fixation. Iron is quite abundant in soils, but it is frequently unavailable for the
plant or soil microorganisms, since the predominant chemical species is Fe3+ , the
oxidized form that reacts to form insoluble oxides and hydroxides, inaccessible to
plants or microorganisms.
Plants have developed two strategies for efficient iron absorption. The first one
consists of releasing organic compounds able to chelate iron, making it soluble; iron
diffuses toward the plant where it is reduced and absorbed by means of an enzymatic
system present in the cell membrane. The second strategy consists of absorbing the
complex formed by the organic compound and Fe2+ , where the iron is reduced inside
the plant and readily absorbed. Some rhizosphere bacteria are able to release iron-
chelating molecules to the rhizosphere and, hence, serve the same function as in
plants (Kloepper et al., 1980b).
Siderophores are low molecular weight compounds, usually below 1 kDa, which
contain functional groups capable of binding iron in a reversible way. The most
frequent groups are hydroximates and catechols, in which the distances among the
groups involved are optimal to bind iron. Siderophore concentration in soil is around
10–30 M.
Siderophore-producing bacteria usually belong to the genus Pseudomonas, the
most frequent being Pseudomonas fluorescens, which release the siderophores,
pyochelin and pyoverdine. Rhizosphere bacteria release these compounds to
increase their competitive potential, since these substances have antibiotic activity
and improve iron nutrition for the plant (Glick, 1995).
Siderophore-producing rhizobacteria improve plant health at various levels: they
improve iron nutrition, inhibit the growth of other microorganisms with their antibi-
otic molecules, and hinder the growth of pathogens by limiting the iron available
for the pathogen, generally fungi, which are unable to absorb the iron–siderophore
complex. Hence, siderophore-producing bacteria could be released to improve iron
nutrition at the same time that certain pathogens are controlled, resulting in lower
chemical inputs due to pesticides and fertilizers.
8.2.1.3 Phosphate Solubilization

After nitrogen, phosphorous is the most limiting nutrient for plants. However, phos-
phorous reserves, although abundant, are not available in forms suitable for plants.
Plants are only able to absorb the soluble forms, namely, monobasic and diba-
sic phosphates. Besides inorganic forms of phosphorous in soil, the phosphorous
present in organic matter is of considerable importance. The organic forms of phos-
phorous are estimated to be between 30 and 50% of the total phosphorous in the
soil. This reservoir can be mineralized by microorganisms, making it available to
the plant as soluble phosphates. There are many bacteria from different genera
that are able to solubilize phosphate. These include Pseudomonas, Bacillus, Rhi-
zobium, Burkholderia, Achromobacter, Agrobacterium, Micrococcus, Aerobacter,
Flavobacterium, Chryseobacterium, and Erwinia. Bacteria use two mechanisms to
solubilize phosphate: (1) releasing organic acids that mobilize phosphorous due to
ionic interactions with the cations of the phosphate salt and (2) releasing phos-
phatases responsible for releasing phosphate groups bound to organic matter. Most
of these bacteria are able to solubilize the Ca–P complex, and there are others which
operate in the Fe–P, Mn–P, and Al–P complexes. Generally, these mechanisms are
more efficient in basic soils.
Results with PGPR able to solubilize phosphate are sometimes erratic, probably
due to soil composition, given the inducibility of nutrient-related traits. In fact, in
order to have a good performance, they would have to be inoculated in soils with
a phosphorous deficit and stored in insoluble forms. Hence, inoculations of these
types of PGPR sometimes improve plant growth and sometimes they are completely
inefficient. Without doubt, knowledge of their mechanisms and ecology in the rhizo-
sphere will improve their use in sustainable agriculture (Gyaneshwar et al., 2002).
8.2.2 PGPR Using Direct Mechanisms
Direct mechanismsare those that occur inside the plant and directly affect the
plant’s metabolism (Ramos Solano et al., 2008a) by involving the plant’s defensive
metabolic processes, which transduce the signal sent from the bacteria that influence
the plant. Plant growth regulators can be considered as participants in the principal
PGPR mechanism, together with the induction of systemic resistance (ISR), which
has in recent years become an important issue. Both involve the existence of bac-
terial eliciting molecules, receptor binding, and further signal transduction. When
bacteria release a plant growth regulator, all three stages are known, because this
process is the same in plants and bacteria. However, this is not the case for induc-
tion of systemic resistance, in which the eliciting molecules, the receptor, and the
signal transduction mechanism, as a general rule, are still unknown.
8.2.2.1 PGPR That Modify Plant Growth Regulator Levels

Plant growth regulator production by bacteria was first described more than 40 years
ago. This was determined in the 1960s using the biological assays then available.
Nowadays, using modern techniques, it has been demonstrated that the production
of plant growth regulators such as auxins and ethylene by bacteria is a common trait
(Bent et al., 2001). Others, such as cytokinins, are less common, while gibberellins
in high concentrations have only been described for two strains of the genus Bacil-
lus, isolated in the rhizosphere of Alnus glutinosa (Gutiérrez Mañero et al., 2001),
the amounts being 1,000 times higher than those reported for Rhizobium that is
involved in forming the nodule.
Modification of a plant’s physiology by plant growth regulator production is a
very important mechanism, not only because it alters the principal mechanism of
growth regulation and cell differentiation in the plant but also because it is based
on the evolutionary development of common metabolic pathways in plants and bac-
teria. This implies interesting co-evolution aspects. Biosynthetic pathways of plant
growth regulators share many steps with the classical secondary metabolism path-
ways. This suggests a common ancestor, which in the course of evolution has pro-
duced either a large diversion in the function, conserving the genetic homology,
or the function has remained the same, but there has been a large genetic diver-
gence. This is evident in the phenolic compound biosynthesis pathway (shikimic
acid pathway), which is shared by both plants and microorganisms. It is essential
for synthesis of amino acids such as tryptophan, the precursor in auxin biosynthe-
sis. The same occurs in the biosynthetic pathway of terpenes, gibberellin precursors.
Therefore, the existence of common biosynthetic pathways and metabolic products
implies the possibility of creating a parallel evolutionary connection between plants
and microorganisms. Furthermore, it is striking that secondary metabolites synthe-
sized by plants for defense also target some human receptors that affect human
physiology, making the interest in these compounds even more interesting.
The production and release of plant growth regulators by bacteria cause an alter-
ation in the endogenous levels of plant growth regulators. This is dependent on sev-
eral factors, including (1) plant growth regulator concentration; (2) the proximity of
the bacteria to the root surface; (3) the ability of the growth regulator to diffuse in
soil and be transported across plant cell walls to the interior compartments of the
cells; and (4) the competitiveness of the bacteria to colonize and survive in areas
where there is high root exudation.
Based on the above discussion, we see that the effect of bacteria on the plant
growth regulators’ balance depends on many factors, and because of this, results
with these different types of PGPR may vary. Moreover, a PGPR producing more
than one type of plant growth regulator can cause a synergistic effect when their
action is coupled. The next logical points to consider here are the main physiological
functions of each growth regulator. A short description for each follows.
The production of hormones such as gibberellins or cytokinins has been reported
for a small number of bacteria able to produce these plant growth regulators
(Timmusk et al., 1999; de Salomone et al., 2001). Cytokinins are known to induce
cell division (Salisbury, 1994) and have recently been reported in free-living bac-
teria (Arkhipova et al., 2007). Concerning gibberellins, there is little information
regarding microorganisms that produce this type of plant growth regulator. How-
ever, it is known that symbiotic bacteria that form nodules in the plant to fix nitro-
gen (Rhizobia) are able to produce gibberellins, auxins, and cytokinins in very low
concentrations when the nodule is forming at the time of high cell duplication rate
(Atzorn et al., 1988). However, the production of gibberellins by PGPR is rare, with
only two described strains able to produce gibberellins in relevant concentrations:
Bacillus pumilus and Bacillus licheniformis (Gutiérrez Mañero et al., 2001).
Auxins are derived from tryptophan metabolism, and their effects depend on the
concentration, the organ affected, and the physiological status of the plant. Aux-
ins synthesized by the plant and the microorganisms only differ in the biosynthetic
pathway, depending on the plant and/or the microorganisms. More than 80% of soil
bacteria in the rhizosphere are capable of producing auxins. Thus, the potential of
these microorganisms to affect the endogenous levels of this regulator, and therefore
their effects on plant growth, is remarkable.
The reason there are so many bacteria in the rhizosphere that are able to produce
auxins is still unknown. Some authors suggest that these bacteria have a tryptophan-
related metabolism and that auxin biosynthesis represents a detoxification mecha-
nism (Bar and Okon, 1992). Other authors propose that auxins have some cellular
function because a clear relationship has been observed between auxin and cyclic
AMP (adenosine monophosphate) levels, which regulate many metabolic processes
(Katsy, 1997). However, the anthropomorphic view of this fact could be correct,
namely, that auxin synthesis improves plant growth that results in more exudation
and more nutrients for rhizobacteria. This hypothesis explains a mutualistic ben-
eficial association between rhizospheric microorganisms and the plant. The plant
controls the energy flux in the system because it has more genetic information and
contributes most of the organic matter to the rhizosphere.
Auxins released by rhizobacteria mainly affect the root system, increasing its
size and weight, branching number, and the surface area in contact with soil. All
of these changes lead to an increase in the ability of roots to extract nutrients from
the soil, therefore improving plant nutrition and growth capacity (Gutiérrez Mañero
et al., 1996). Another important result of inoculation with auxin-producing bacteria
is the formation of adventitious roots, which are derived from the stem. The auxins
induce dedifferentiation of the stem tissues to dedifferentiate as root tissue. All the
above effects can vary considerably depending on the auxin levels that reach the
root system, including an excess, which could be inhibitory. In order to explain
these inhibitory auxin effects, the relationship of auxin with ethylene has to be
considered.
Ethylene is another growth regulator whose levels alter PGPR, in turn affect-
ing physiological processes in the plant. It primarily functions in regulating plant
development processes, including seed germination, root growth, leaf abscission,
fruit development and ripening, as well as defense systems and stress responses.
Factors such as light, temperature, salinity, pathogen attack, and nutrition can cause
marked variations in ethylene levels. The influence of abiotic factors in ethylene
levels was deduced some time before biotic factors were discovered (Abeles et al.,
1992; Morgan and Drew, 1997).
As ethylene levels decrease, root systems increase their growth, with the benefits
already mentioned. Using PGPR to reduce ethylene levels in the plant could be an
interesting method to improve certain physiological processes in the plant. Ethy-
lene biosynthesis starts in the methionine cycle; one aminocyclopropanecarboxylic
acid molecule (ACC) results from each turn of the cycle. The enzyme responsi-
ble for ACC production is ACC synthase, whose expression level and activity are
regulated by a large number of signals such as auxin, ethylene, and environmental
factors. The ACC is the substrate for ACC oxidase, also called ethylene-forming
enzyme (EFE). This enzyme has been cloned from numerous species and belongs
to a multigenic family which produces different types of ACC oxidases depending
on the plant organ and development state.
The model proposed for ethylene regulation in the plant by PGPR is based on
the ability of some bacteria to degrade ACC, the direct precursor of ethylene (Glick
et al., 1994a). The degradation of this compound creates an ACC concentration gra-
dient outbound, favoring its exudation and, hence, a reduction of the ethylene level
inside. This, in combination with auxins that may be produced by the same microor-
ganism, has a considerable impact on important physiological processes, such as
root system development, since the bacterial ACC deaminase competes with the
plant’s ACC oxidase. This ACC deaminase enzyme has been isolated and identi-
fied in several bacterial and fungal genera, all having the ability to use ACC as the
sole nitrogen source. Curiously, no microorganism has yet been found that is able
to form ethylene from ACC (Glick et al., 1994b). Since ethylene and auxins are two
related types of growth regulators and since the balance between them is essential
for the formation of new roots, some effects attributed to auxin-producing bacteria
are actually due to ACC degradation.
PGPR that reduce ethylene levels in plants are also able to improve nodule forma-
tion in legumes and mycorrhizae formation in many other types of plants. A tem-
porary reduction of ethylene in the earlier stages of either of these processes is
beneficial.
Case study: The aim of this case study involving two separate studies (Gutiérrez
Mañero et al., 1996, 2001) is to highlight the synergistic effects of bacterial strains
producing two types of plant growth regulators.
These bacteria were isolated from the rhizosphere of A. glutinosa and produc-
tion of IAA-like compounds in the culture media was demonstrated by bioassay.
This bioassay was set up by adding bacteria cultures media free of bacteria to alder
seedlings in two different concentrations. When a bacterial strain tested positive
for enhancement of shoot and root growth, the results were plotted against data
for plants that were grown on media containing increasing concentrations of IAA
(Gutiérrez Mañero et al., 1996). However, addition of synthetic IAA to plants did
not reproduce exactly the same effects as obtained for compounds released by bacte-
ria, when their growth parameters were studied. Higher shoot surface suggested the
presence of gibberellin-type compounds. Hence, a second study was carried out to
detect these compounds. First, a bioassay was performed and second, identification
of putative compounds by HRGC-MS was employed. Bacterial culture media free

of bacteria were concentrated and added to the shoot tips of young, dwarf alder
seedlings; a control with GA3 was also used. The same bacterial medium that was
free of bacteria was used for HRGC-MS identification. These strains have shown
a capacity to produce large quantities of gibberellins (GA1 , GA3 , GA4 , and GA20 )
in vitro. The gibberellins were identified by HRGC-MS, and the amounts detected
reached 200 ng·mL–1 , GA1 being the most abundant (130–150 ng·mL–1 ). These
amounts were 1,000 times higher than for any other example of fungal or bacterial
gibberellin production reported. Furthermore, the combination of gibberellins pro-
duced caused a balanced physiological effect in the plant opposite to the effects of
GA3 alone. This resulted in excessively long stems with pale yellow leaves. The sug-
gested reason for the pronounced effect of gibberellins released by the PGPR present
in the rhizosphere is that these hormones can be translocated from the roots to the
aerial parts of the plant. The effects in the aerial part are notable, and even more so,
when the rhizobacteria also produce auxins that stimulate growth of the root system.
This enhances the nutrient supply to the sink generated in the aerial parts.
Based on these results, rhizobacteria able to release plant growth regulators can
be formulated in a biofertilizer, with its intended use being to strengthen plant
growth without any chemical input to the system.
8.2.2.2 PGPR That Induce Systemic Resistance (ISR)

At the beginning of the 1990s, Van Peer et al. (1991) and Wei et al. (1991) made
an important discovery about plant defense mechanisms and productivity. These
investigators found that certain non-pathogenic bacteria were able to prevent a
pathogen attack before the pathogen reached the plant. The difference with bio-
control is that the beneficial bacteria do not interact physically with the pathogen
but instead trigger a response in the plant which is effective against subsequent
attacks by a pathogen. This response is systemic; that is, the bacteria interact with
the plant in a restricted area, but the response extends to the whole plant. This
response is mediated by metabolic changes that are not evident at first glance. As
a matter of fact, priming or biopriming is the physiological state of a plant that
is systemically induced by non-pathogenic bacteria against subsequent pathogen
attack; but, the effect is not detected until pathogen challenge occurs (Conrath
et al., 2002). Since energetic metabolism is diverted to secondary metabolism, this
physiological state is usually coupled to lower growth rates as compared to non-
primed controls (van Hulten et al., 2006). For the protection to be effective, an
interval is necessary between the PGPR–plant contact and the pathogen attack in
order for the expression of the plant genes that are involved in the defense. This
mechanism was first known as “rhizobacteria-mediated induced systemic resis-
tance” (Liu et al., 1995), but it is now termed “induced systemic resistance” (ISR)
(van Loon et al., 1998). ISR was reported in the plant–pathogen-beneficial bac-
teria model, Arabidopsis thaliana–Pseudomonas syringae DC3000–P. fluorescens
WSC417r. Here, the defensive response induced by P. fluorescens WSC417r in
A. thaliana against P. syringae DC3000 is mediated by JA (jasmonic acid) and
ethylene. Since then, it has been described in many plant species, including bean,
tobacco, tomato, and radish, with different PGPR and pathogens, and an increasing
number of signal transduction pathways. This finding is fundamental because it pro-
poses an “immune” response in the plant, raising the possibility of “vaccination” for
the plant.
The plant can also acquire immunity after a pathogen attack. This response has
been described before the ISR. The acquisition of resistance by the plant after a
pathogen attack, causing little damage or localized necrosis in response to a fur-
ther pathogen attack, has been known for many years. The phenomenon is called
systemic acquired resistance (SAR) (Ryals et al., 1996). During a pathogen attack,
reactive oxygen species (ROS) are produced in necrotic areas, causing tissue death.
If the plant survives the challenge, it remains protected for life.
In A. thaliana, the SAR and ISR responses are regulated by distinctly different
pathways. SAR is associated with an increase in salicylic acid levels and the transla-
tion of an ankyrin-type protein called NPR1, located in the nucleus, which induces
the transcription of the pathogenetic-related (PR) genes. These genes codify the PR
proteins that are responsible for systemic resistance in the plant (Lawton et al., 1991;
Uknes et al., 1993). In the ISR response, salicylic acid levels are not altered, but
the response is mediated by other two growth regulators, namely, ethylene and jas-
monic acid, which act as signal transductors and not as stress hormones. In ISR, the
NPR1 protein is also involved. But here, it induces the expression of other proteins
different from PRs (Conrath et al., 2002). In addition to these pathways, research
with new beneficial agents and different pathways are being described, especially
since the ability of a PGPR to induce systemic resistance depends on the plant-
beneficial bacteria–pathogen system. There is evidence of certain PGPR that are
able to elicit systemic protection against P. syringae DC3000 in A. thaliana involv-
ing the SA-mediated pathway (Ramos Solano et al., 2008b).
SAR and ISR responses lead to plant protection against different pathogen
species, but there are species which overlap. However, both responses can coex-
ist in the same plant at the same time (van Wees et al., 2000). Thus, the use of
PGPR or PGPR mixes able to trigger both responses at same time would result in
an important advance in the improvement of pest defense systems.
The induction of defense metabolism, in fact, involves an induction of sec-
ondary metabolism developed by sessile organisms that are adapted to survive any
changes of a biotic and abiotic nature. Therefore, some PGPR may trigger secondary
metabolism against pathogens that at the same time may also be effective against
biotic stress, such as saline conditions in soils, a frequent situation in agriculture.
Furthermore, when a medicinal plant is used, phytopharmaceutical levels may also
be increased or even new molecules may appear. This topic will be discussed in
Section 8.4.
8.3 Application of PGPR for Agricultural Purposes
The use of PGPR in agriculture is one of the most interesting alternatives for improv-
ing sustainable agricultural practices, as well as for recovering degraded ecosys-
tems (Vessey, 2003). PGPR can be used for a wide range of purposes that include
biofertilizers, biocontrol agents, induction of systemic resistance, and elicitors of

secondary metabolic pathways that lead to products of nutritional and pharmaco-
logical interest and, therefore, of economic interest.
In view of the mechanisms described in Section 8.2, three case studies will be
discussed: (1) suitability of the PGPR for nutrient-related traits; (2) alteration of
plant metabolism mediated through plant hormonal balance; and (3) alteration of
soil communities and their relation to biological effects. They highlight important
aspects for successful application in agriculture.
Case study: A screening for PGPR to improve the growth of Cistus ladanifer
(Gum Rockrose) seedlings for reforestation of degraded Mediterranean ecosystems
was carried out by Ramos Solano et al. (2007). This screening for PGPR was car-
ried out in the rhizosphere of wild populations of C. ladanifer, with the aim being
to identify putative strains that are able to enhance the mycorrhization ability of
Cistus with its spontaneous mycorrhizal fungus, Amanita ponderosa. The aim of
identifying these strains was two-fold: one due to the great economic interest in the
edible fruiting body of Amanita and, the second objective, helping the mycorrhiza-
tion for soil recovery. Two hundred and seventy bacteria were isolated, purified,
and grouped by morphological criteria. Fifty percent of the isolates were selected
and tested for aminocyclopropanecarboxylic acid (ACC) degradation, auxin and
siderophore production, and phosphate solubilization. Fifty eight percent of the
isolates showed at least one of the evaluated activities, with phosphate solubiliza-
tion and siderophore production being the most abundant traits. This is consistent
with the chemical composition of the soil sampled, since usually the areas where
C. ladanifer grows consist of a degraded soil or one that is in a regeneration stage
following strong perturbation. A genetic analysis was performed with all strains
that showed at least one positive trait. After PCR-RAPDs (randomly amplified
polymorphic DNA) analysis, 11 groups appeared with 85% similarity, revealing
the low diversity in the system. One strain of each group was tested in a biolog-
ical assay, and those that enhanced Cistus growth were identified by 16S rDNA
sequencing.
Although 7 of the 11 assayed strains were phosphate solubilizers and able to
produce siderophores, only one was really effective in increasing all biometric
parameters in C. ladanifer seedlings. This suggests that other mechanisms apart
from nutrient mobilization might be involved in growth promotion by this strain.
The lack of effect of the other six strains was probably due to the rich substrate used
(peat) that diminishes the putative beneficial effect of the bacterium. Since this trait
is not useful for this condition, genes are not expressed. However, the low diversity,
together with the high redundancy detected by PCR-RAPDs and the predominance
of strains able to mobilize nutrients in the rhizosphere of Cistus, reveals that the
plant selects for bacteria that can help to supply scarce nutrients. These types of
plant growth-promoting rhizobacteria (PGPR) strains should be successful in refor-
estation practices or in agricultural soils where phosphate or iron is present but not
available for plants. This occurs under extreme conditions, where the PGPR repre-
sent a selective advantage for the plant.
The above case study shows that nutrient-related traits are not always useful for
growth promotion (indirect mechanisms). Inoculation of nutrient-mobilizing bacte-
ria will only result in positive results where nutrients are scarce. Therefore, bacte-
rial strains showing nutrient-related traits should be used to increase productivity
in areas with low yields due to lack of nutrients, not in rich cropping soils where
chemical fertilizers are used and would result in “silencing” of the bacterial effect.
In these latter soils, they should be used to lower the input of chemical fertilizers
into the system.
However, the same PGPR strain may act by several mechanisms or may use
different ones. The following case study illustrates another aspect of agriculture
where plant nutrition cannot be further improved and the bacterial strain is able to
improve yield under intensive greenhouse conditions. This strain is able to produce
plant growth regulators using direct mechanisms.
Case study: The aim of this case study is to show how the inoculation of one
PGPR strain is able to produce plant growth regulators (gibberellin and auxin types),
using intensive culture, that improve productivity and protect the plant. It is within
the aim of this study to show that inoculation of such biologic agents can be useful
and feasible in current agricultural practices.
The effects of inoculation with a strain of B. licheniformis on the growth of
pepper and tomato were investigated in three experiments. Before field trials, the
survival of the strain against pesticides used in greenhouse production was tested
to discard any possibility of failure due to pesticides; the bacterium was tolerant
to most of them, leaving a possibility to be a part of integrated pest management
(IPM). Of the three experiments, one was carried out under seedbed conditions and
two under greenhouse production conditions. In the first experiment, the bacterium
significantly increased the height of the plants and the leaf area in both species
and in both cultivars. This is interesting for the production of plantlets with bet-
ter adaptative capacities that will have better performance when transplanted to
production greenhouses. Effects were more marked on pepper than on tomato,
revealing certain specificity between the strain and the plant species. In the sec-
ond experiment, seedlings growing in sand and in hydroponic culture were stud-
ied. The number and diameter of tomato fruits produced in sand and in hydroponic
medium were increased significantly by PGPR inoculation, revealing the effects of
gibberellins released by the PGPR. Given the physiological effects of this PGPR
on flowering, it is interesting that flowering took place 15 days earlier in inocu-
lated plants. This would result in the fruit reaching the market 2 weeks before the
expected time. Hence, one can see the putative benefits for producers using these
types of inoculants. In addition, PGPR-treated plants showed a lower incidence of
disease than non-treated plants (no pesticides were used in either block), reveal-
ing a systemic induction of defensive metabolism by the PGPR. The effect could
also be attributed to the simple colonization that could be impeding soil pathogen
colonization (termed niche exclusion). In the third experiment, the total weight
of pepper fruits harvested from PGPR-inoculated plants increased significantly as
compared with non-inoculated controls. In light of the considerable colonization
and competitive ability of this PGPR strain and its effects on growth and plant phys-
iology, it could be used as a biofertilizer or biocontrol agent without altering nor-
mal management in greenhouses. This would allow for lower chemical inputs for
pathogen control.
However, the effects reported for greenhouse production have been validated
only for those conditions per se (that is, extreme nutrient control and hydroponic
or sand support). When this same bacterial strain is inoculated into soil contain-
ing its natural communities, the effect can be different. As a matter of fact, among
the number of studies conducted on this topic, two will specifically be addressed
in the third case study. But the general rule is that a strong alteration of native soil
communities results in a lack of effect on plant growth, while a slight alteration
of soil communities after PGPR inoculation is coupled with good results for plant
growth.
Case study: This study is concerned with the influence of an indigenous European
alder (A. glutinosa L. Gaertn) rhizobacterium (B. pumilus) on the growth of alder
and its rhizosphere microbial community structure in two soils (Ramos et al., 2003).
The aim of this study is to show that alteration of native communities of soils is neg-
atively related to biological effects. European alder seedlings were inoculated with a
suspension of the putative plant growth-promoting rhizobacteria (PGPR) B. pumilus
(CECT 5105), or left non-inoculated (controls) in two different soils, and grown
under controlled conditions. Soil A showed a coarse texture, was slightly acidic,
and possessed a high nitrogen content, while soil B showed a fine texture, was basic
in pH, and possessed a lower nitrogen content. The bacterium was isolated from
soil A. At each sampling time, over an 8-week period, shoot and root systems of
the plants were measured, determining shoot and root length and surface area; the
number of nodules produced were counted. In addition, changes in the microbial
rhizosphere structure were evaluated by the phospholipid fatty acid (PLFA) profile
after extracting directly from the rhizosphere soil.
The increases detected in shoot surface were significant only in soil A, while the
root system was affected in both soils, revealing the ability to produce auxin-like
compounds of this strain that elicited better growth of the root system. However,
while in soil A inoculation with B. pumilus caused a perturbation that subsequently
disappeared, the rhizosphere community structure was seriously altered in soil B.
This effect is based on the different profiles of phospholipids/fatty acids that indi-
rectly reveal changes in the composition of microbiota. All biometric parameters
were enhanced to a greater extent in soil A, in which the PGPR inoculum did not
alter the existing rhizosphere communities, and nutrient availability was better. This
is consistent with the previous hypothesis that release of auxin-type plant growth
regulators by inoculated PGPR will result in better growth of the root system, which
improves plant nutrient absorption potential. If this is coupled to enhanced nutrient
availability, plants will show an increase in their growth parameters. Also, results
were worst in soil B, in which case the PGPR strain had been isolated from soil
A. In addition to the problems that inoculation caused in rhizosphere communities,
there might be a nutrient dependence from the original soil that could condition the
synthesis of growth regulators or any other factors that could affect growth.
As a concluding remark from this case study, it is clear that the influence of
the soil cannot be discarded as a factor that has a negative influence on the benefi-
cial effects of PGPR. Thus, it should be considered so as to increase success when
releasing inoculants in soils. Although this case study was developed for a tree, not
an agronomic or vegetable crop, this concluding remark applies to any crop species
where the soil nature may condition the success of an added biofertilizer.
8.4 PGPR Affects Secondary Metabolism
Because plants have evolved secondary metabolism strategies to survive chang-

ing biotic and abiotic conditions encountered during their existence, this has also
allowed them to colonize most habitats. Given the number of possibilities of chang-
ing conditions, both for biotic and abiotic factors, the array of secondary metabolites
designed for each situation is enormous. Secondary metabolites can be studied from
different points of view, such as the above examples for agriculture, the evaluation of
their role in a plant’s defense against pathogens, and their effects on human health.
The following examples have been selected to illustrate each of them.
8.4.1 Lowering Chemical Inputs by Enhancing a Plant’s

Defensive Responses
When secondary metabolism is studied from the plant’s defense point of view, the
main goal is to meet requirements for sustainable development so as to achieve
the highest yields. The mechanisms involved can be direct or indirect. If the bac-
terium used triggers the plant’s defensive metabolism, it is a direct mechanism; if
the bacterium is not able to trigger the plant’s metabolism, but is able to interact with
other microorganisms (biocontrol), it is an indirect mechanism. Moreover, they can
happen simultaneously, achieving even better results than if they rely on a single
microorganism, or rely on different ones that may show complementary beneficial
traits, as for example, those related to nutrient mobilization.
The case study presented here pertains to rice: (Oryza sativa L.) production in
Southern Spain (Seville) (unpublished data) and brings together two aspects of
induction of secondary metabolism: (1) protection against pathogens and (2) pro-
tection against salinity inherent to rice cropping in this area.
The study was set up in Seville by the Guadalquivir River. Two PGPR strains
were tested in experimental plots in the area, namely, Chryseobacterium balustinum
and P. fluorescens. Both of them have demonstrated their ability to induce systemic
resistance in A. thaliana (L.) Heynh. against P. fluorescens DC3000, C. balustinum
being more effective (Ramos Solano et al., 2008), and has also shown biocontrol
activity against Rhizoctonia (Doménech et al., 2006). C. balustinum has, in addition,
demonstrated its ability to induce protection against saline conditions in A. thaliana
(L.) Heynh. (Barriuso et al., 2008b). With these two candidates, five treatments were
set up: each of the strains alone, the two combined, and two controls, one under
regular phytochemical treatments and the other without any addition of chemicals.
Interestingly, the addition of bacterial treatments, once in the seed and then fol-
lowed by several aerial inoculations during the growing season, resulted in a small
increase in yield, but in addition, caused a large decrease in disease incidence under
natural conditions. It is striking that the combination of the two strains achieved
the best results. In light of these results, a combined strategy is going to be pro-
posed for their use in integrated pest management. In this case, chemical pesticides
can be applied if disease incidence runs out of control when the biological agent
is used.
8.4.2 Increase in Secondary Metabolites

of Pharmaceutical Interest
Special interest has been paid to plant species of medicinal interest due to their
role in human health. Ever since plants have been used for healing, plant collectors
have selected those with a better effect on health. These differences, in effect, are
attributable to either higher levels of phytopharmaceuticals or differences in their
relative contents, which most of the time are affected by environmental conditions
when harvested from the field. A third possibility to explain this is that, for a known
medicinal plant species, new molecules with pharmacological interest may appear
when it is grown under a new set of environmental conditions or with a stress fac-
tor. Therefore, this would account for the improvement in its beneficial effects for
human health.
The variability of secondary metabolism is a problem for the pharmaceutical
industry since field production is uncertain and may condition availability of final
products. Sometimes, the problem may be solved by chemical synthesis, but it is not
always possible or at least it usually lacks economic feasibility. Another alternative
is cell culture, but for some plant species, it is not feasible, or yields achieved are
too low because secondary metabolism is not necessary under such controlled and
undifferentiated conditions. Therefore, one of the main goals in industry now is to
obtain reproducible extracts of plants grown in field production or, even more chal-
lenging, grown in plant cell cultures. For this purpose, the use of elicitors appears
to be an encouraging alternative (Radman et al., 2003). In support of this last state-
ment, a recent study by Poulev et al. (2003) has reported the potential of elicitation
to discover new molecules with pharmacological interest. But this study not only
reports the presence of new molecules but also the use of elicitors has been able
to duplicate the presence of these molecules and to increase the concentration of
known compounds. Hence, unraveling the nature of elicitors and the elicited path-
ways remains an exciting challenge for the pharmaceutical industry.
Among these putative elicitors, PGPR appear as good candidates for upregulating
secondary metabolism. The following case study (Gutiérrez Mañero et al., 2003)
illustrates how PGPR strains isolated from the rhizosphere of wild populations of
Digitalis are able to enhance levels of cardenolides in high-yielding varieties of
Digitalis lanata Ehrh., grown either in field production or as in vitro cell cultures.
Case study: The 480 isolates from a bacterial screening assay carried out in the
rhizosphere of two Digitalis species in two physiological stages were characterized
at the generic level. Bacillus was the dominant genus in all cases. Fifty percent of the
Bacillus strains isolated from each species were analyzed by PCR-RAPDs. At 85%
similarity, 12 groups separated out for D. thapsi L. and 18 for D. parviflora Jacq.
One strain of each group was selected for biological assay on high-yield selected
varieties of D. lanata Ehrh., kindly provided by Boehringer Mannheim (Spain).
The evaluated parameters were growth promotion and cardenolide content in leaves.
Inoculation was performed in the root system so as to obtain a systemic induction
of secondary metabolism. Only 17 strains caused significant increases in at least
one of the parameters evaluated. The most striking result was that some strains pro-
moted growth and increased cardenolide content at the same time. This effect was
detected in leaves, while inoculation was carried out in roots. Interestingly, these
two parameters are not enhanced simultaneously under regular conditions of pot
culture or in tissue cultures. This result shows that the biotic agent employed was
able to upregulate the plant’s metabolism. Moreover, it was striking that bacterial
strains selected from wild species were able to upregulate secondary metabolism in
selected varieties, especially for terpenes and cardenolides. The implication of this
study is that identification of eliciting agents may now make it possible to enhance
secondary metabolism in undifferentiated tissue cultures. This could be of major
economic importance for the pharmaceutical industry because it would make possi-
ble either field production with higher yields or biotechnological production in vitro
with good yields.
8.4.3 Modification of Secondary Metabolite Profiles

of Pharmaceutical Interest
The effects of secondary metabolites on human health may vary depending on

several factors. One of them is how they are delivered and incorporated into the
human body, either in a pharmaceutical formulation, as food supplements, or in
the diet. A pharmaceutical formulation will provide known concentrations of well-
characterized and identified compounds, while a food supplement will provide an
extract of the plant that possesses variable concentrations of known and unknown
compounds. The most variable input is seen through the diet. Some edible plants,
such as soybeans or berries, contain bioactive compounds that provide more benefits
than is attributed to their simple nutritional value. Levels of bioactive compounds
do change depending on environmental conditions; hence, the lack of an effect on
health may be due to a lack of reproducibility of the bioactive content. This lack
of reproducibility may be overcome by elicitation with biotic agents. However, the
effect of elicitation needs to be evaluated because variation in relative concentrations
of bioactive compounds may change their effects on human health when delivered
in the diet. Besides changing the relative profiles, some interesting metabolites can
be increased. This may be a very interesting tool for pharmaceutical companies as a
means to prepare normalized extracts of food supplements.
Case study: Biotechnological elicitation of isoflavones in Glycine max with

PGPR. Diploma de estudios avanzados (DEA) Elena Algar Parejo. Universidad
San Pablo CEU (unpublished results).The rationale for this study was to evaluate
the ability of PGPR to elicit soybean growth and secondary metabolism in terms of
isoflavone production .
In a study on biotechnological elicitation of isoflavone production in soybeans
(Glycine max (L.) Merr.) with PGPR by Elena Algar Parejo at the Universidad
San Pablo CEU (unpublished results), a battery of nine PGPR with diverse bene-
ficial capacities on different plant species were evaluated. None of them increased
significantly the concentration of isoflavones according to the isoflavone standards
that were evaluated (daidzein, daidzin, malonyl daidzin, genistein, genistin, malonyl
genistin). However, when considering daidzein and genistein, five PGPR caused a
decrease in their concentration, especially for genistein; one strain increased lev-
els of both isoflavones; and two increased daidzein and decreased genistein levels.
Decreases in levels of isoflavones may be coupled to increases in levels of protec-
tive compounds such as pterocarpanes. Although isoflavones have been traditionally
related to defense against pathogens, it seems that pterocarpanes, a family of com-
pounds derived from daidzein, are the compounds responsible for effective defense.
Another putative reason for this decrease may be that isoflavones are released from
the roots to the surrounding soil, creating an outbound gradient. The rationale for
this is that they are involved in establishment of the symbiosis with nitrogen-fixing
Rhizobia bacteria. Irrespective of the reasons underlying the different behaviors of
each PGPR, the fact is that there is a difference depending on the strain and that it is
a reproducible effect. It remains to be seen if these changes are relevant for human
health through the diet. If this were the case, this opens a new window for the food
supply industry.
8.5 Bacterial Cell Wall Lipopolysaccharides Are Able to Mimick

PGPR-Mediated Induction of Defense Metabolism
Communication between plants and microorganisms is a well-known fact consistent

with the many reports in the literature. Relations between plants and microorgan-
isms may be beneficial or harmful. Irrespective of their nature, there is a common
“language” used by both partners which is now starting to be elucidated. Some
plant secondary metabolites such as isoflavones are understandable signals for spe-
cific microorganisms, namely, rhizobia. Some plant growth regulators are released
by soil microorganisms that affect the plant’s metabolites by targeting the plant’s
receptor (see above). But still, there are other molecules, mainly bacterial or fungal
surface molecules, that are able to induce some receptors in plant tissues to start a
particular signaling pathway. The term “elicitor” includes all of those molecules of
different chemical nature, either constitutive of the microorganism or released, that
are able to upregulate a plant’s defense metabolic pathways (SAR and ISR path-
ways). This is especially relevant in plants with medicinal applications.
Biotic elicitors are classified into several groups that include proteins, polysac-
charides, lipopolysaccharides, and volatile compounds. Polysaccharides are the
most frequent elicitors described. Identification of these elicitors is essential for
the practical application of defense responses both for agricultural and industrial
purposes, since some of the defensive compounds are molecules with pharmacolog-
ical activity. Furthermore, they can be used to elicit plant tissues in vitro, opening a
promising window for biotechnological production of phytopharmaceuticals.
Case study: Ramos Solano et al. (2008b) have recently reported on systemic
disease protection elicited by plant growth-promoting rhizobacteria (PGPR) strains
in order to examine the relationship between metabolic responses, systemic disease
protection, and biotic elicitors. They were able to demonstrate that a fraction of the
bacterial cell wall is able to reproduce the defensive effect of the whole bacteria
inoculated on plant roots.
The rationale of this study was first to evaluate the ability of three PGPR to
elicit defensive metabolism in the model plant A. thaliana Col 0 against P. syringae
pv. tomato DC3000, focusing on the putative induction pathway by biochemical
and molecular markers. Second, it was carried out in order to demonstrate that
bacterial cell wall surface molecules were able to reproduce the effect of the bac-
terial strain. The PGPR employed included C. balustinum (AUR9), Azospirillum
brasilensis, and P. fluorescens (AUR6). All three strains decreased disease severity
when applied to A. thaliana prior to pathogen challenge. At a biochemical level,
each of the three strains induced ethylene (ET) biosynthesis when incubated with
1-amino-cyclopropane-1-carboxylic acid (ACC) as well as salicylic acid produc-
tion in the plant. Plants treated with each of the three strains showed lower levels
of salicylic acid after pathogen challenge compared to untreated controls, reveal-
ing a previous contact with an eliciting agent, as described for plants that have
survived a pathogen attack (SAR). This effect was more marked in plants treated
with C. balustinum AUR9, the strain most effective in decreasing disease sever-
ity. When this response was evaluated at the molecular level, the expression level
of PR1, a transcriptional marker of the SA-dependent pathway, in C. balustinum
AUR9-treated plants is four-fold that of controls, while the expression of PDF1.2,
a transcriptional marker for the SA-independent pathway, is not induced. This sug-
gests that this PGPR strain is inducing the plant defensive pathway that is dependent
on SA and one that has traditionally been associated with pathogenic microorgan-
isms. Once this systemic protective effect was demonstrated in vivo, inoculating the
bacterial strain C. balustinum on roots and evaluating disease incidence on leaves,
cell wall lipopolysaccharides were tested as putative bacterial elicitor molecules
on axenic cultures of A. thaliana (L.) Heynh. Putative elicitors were dissolved in
the culture media and were able to reproduce this systemic induction effect at low
doses (5 μg·mL–1 ), but failed to reproduce the effect at higher doses (50 μg·mL–1 ).
From these observations, we can hypothesize that certain PGPR strains are capa-
ble of stimulating different systemic responses in host plants. With C. balustinum
AUR9, the SA-dependent pathway is stimulated first, as indicated by increases in SA
levels and PR1 expression, followed by induction of the SA-independent pathway,
as indicated by the increases in ET concentrations. The effects on both pathways
combined, with respect to disease suppression, appear to be additive. Irrespective

of the defensive pathway involved, the ability of LPS to elicit the defensive path-
way has been demonstrated. This provides a challenging alternative for elicitation
of secondary metabolism pathways in medicinal plants.
8.6 Quorum Sensing Is Involved in PGPR-Mediated Systemic

Resistance Against Abiotic Stress
Quorum sensing (QS) is a widespread, rapid means for bacterial communities to

coordinately change genome expression patterns in response to environmental cues
and population density. The term quorum sensing was first used in a review by Fuqua
and Winans (1994), which essentially concerned the minimum threshold level of
individual cell masses required to initiate a concerted population response. Bacteria
that use QS produce and secrete certain signaling compounds called autoinducers,
or normally, N-acyl-homoserine lactone (AHL). The bacteria also have a receptor
that can specifically detect the inducer. When the inducer binds to the receptor, it
activates transcription of certain genes, including those for autoinducer synthesis.
When only a few other bacteria of the same kind are in the vicinity, diffusion reduces
the concentration of the inducer in the surrounding medium to almost zero. So, as a
result, the bacteria produce only small amounts of the inducer. When a large number
of bacteria of the same kind are in the vicinity, the inducer concentration crosses a
threshold, whereupon greater amounts of the inducer are synthesized. This forms
a positive feedback loop in which the receptor becomes fully activated (Whitehead
et al., 2001).
Many gram-negative bacteria utilize AHL in order to coordinate expressions
of virulence in response to the density of the surrounding bacterial population.
Several bacterial phenotypes essential for the successful establishment of symbi-
otic, pathogenic, or commensal relationships with eukaryotic hosts utilize motility,
exopolysaccharide production, biofilm formation, and toxin production to show reg-
ulation by QS (Gonzalez and Keshavan, 2006). It has been demonstrated that bac-
terial AHLs are released into the rhizosphere, where they reach biologically active
concentrations (Barriuso et al., 2008d). This study shows how QS is involved in
disease incidence, where several pathogenic microorganisms such as Xanthomonas
campestris, Erwinia carotovora, Pseudomonas corrugata, or Burkholderia sp.
strains are the causal agents (Ahmad et al., 2008).
Interestingly, the production of quorum-sensing interfering (QSI) compounds by
eukaryotic microorganisms has aroused immense interest among researchers, espe-
cially since such compounds can influence the bacterial signaling network positively
or negatively. Hence, strategies addressing disruption of QS among bacterial strains
appear to be an encouraging and novel strategy for plant health protection, especially
when supported by the fact that some plant species do release AHL-like compounds
to modulate bacterial communication in the rhizosphere (Teplistsky et al., 2000).
On the contrary, synthesis of structural homologues to various QS signal molecules
has resulted in the development of additional QSI compounds that could be used
to control pathogenic bacteria. Furthermore, the creation of transgenic plants that
express bacterial QS genes is yet another strategy that could be utilized to interfere
with bacterial behavior (Fray, 2002).
Case study: In a study on transgenic tomato plants that alter quorum sensing in
plant growth-promoting rhizobacteria (PGPR), Barriuso et al. (2008d) showed that
growth promotion and salt resistance are mediated by QS. This, then, extends the
roles of QS and reinforces the concept of disruption of QS to control plant pathogen
attack or to induce protection effects against different kinds of stresses. Details on
this study are provided in the following account.
Two gram-negative plant growth-promoting rhizobacteria (PGPR), designated as
M12 and M14, affiliated with Burkholderia graminis, could produce a variety of
N-acyl-homoserine lactone (AHL) signaling molecules. The involvement of these
molecules in plant growth promotion and induction of protection against salt stress
was examined. AHL production was evaluated in vitro by thin-layer chromatogra-
phy and bioindicator detection as well as by LC-MS/MS. In situ production of AHLs
in the rhizosphere of A. thaliana (L.) Heynh. plants was detected by GFP (green flu-
orescent protein) biosensor constructs and confocal laser scanning microscopy. To
determine if plant growth promotion and protection against salt stress were mediated
by quorum sensing (QS), these PGPR were assayed on wild-type (wt) tomato plants
as well as their corresponding transgenics expressing YenI (short-chain AHL pro-
ducers) and LasI (long-chain AHL producers). In wt tomato plants, only M12 pro-
moted plant growth, and this effect disappeared in both transgenic lines. In contrast,
the strain M14 did not promote growth in wt tomatoes, but did in LasI. Resistance
to salt stress was induced by strain M14 in wt tomato, but this effect disappeared
in both transgenic lines. Strain M12, however, did not induce salt resistance in wt
tomato, whereas it did in LasI tomato plants. These results reveal that QS AHL sig-
nal molecules mediate the ability of both PGPR strains, M12 and M14, to promote
plant growth and to induce protection against salt stress.
8.7 Metagenomics: The Rhizosphere as a Source of Genes

with Biotechnological Applications
A relative new perspective in the biotechnology of the rhizosphere is the metage-

nomic approach (Rolf, 2005). This approach is defined as the field of molecular
biology whose purpose is to study the genome of entire communities of microor-
ganisms instead of individual species. Also known as “communities genomics”,
this discipline examines the genetic material recovered from environmental sam-
ples derived from entire communities of microorganisms. Classical microbiology
and genetics, in trying to isolate genes with new and valuable functions, basically
are based on the isolation of single microorganisms and the sequencing of their
genomes. Metagenomics allows the study of non-culturable, or difficult-to-culture,
microorganisms. This approach gives a new estimation of microbial communities
independent of their culture in the laboratory (Rolf, 2005).
Rhizosphere metagenomics examines the total DNA extraction from the rhizo-
sphere, the preparation of a clonal library with this DNA, and the screening of the
clones to select the genes of interest among the vast genetic reservoir derived from
soil microbial communities.
The metagenomic approach has already been used for the identification of new
biomolecules based on the finding of genes codifying proteins with new activities.
This strategy has been validated by the isolation of novel genes that encode degrada-
tive enzymes (Henne et al., 1999), antibiotic resistance (Riesenfeld et al., 2004), and
antibiotic production (Wang et al., 2000). However, association of a certain gene
with its activity is quite difficult, and sometimes, the limiting factor is that the genes
in question may not be expressed at detectable levels. Despite the tedious and long
process of gene isolation and identification, rhizosphere metagenomics appears to
be a very promising field to find new genes with novel activities and high biotech-
nological value, but also implicit are its own technical limitations that have to be
overcome to assure new technical advances in the future.
8.8 Metabolic Engineering
The relevance of this perspective is fully described in Chapters 2 and 12. Neverthe-
less, a short discussion is needed here to examine the role of bacterial elicitors in
metabolic engineering. Despite the efforts devoted to increase and diversify bioac-
tive compounds in plants, it is still a challenge as to how to increase their content in
vivo and, as mentioned before, how to obtain reproducibility of bioactives under
field production conditions. These efforts rely on transgenic and non-transgenic
approaches which involve complex regulation mechanisms that are required for
increasing the levels of functional metabolites in plants. Bacterial elicitors may be
used to determine the key genes limiting a metabolic pathway once the limiting
step is identified. Transgenic approaches may allow us to overcome the low levels
of target compounds produced. Finally, and this is a very attractive and encouraging
challenge, upon elicitation, new molecules may appear after the activation of a given
metabolic pathway.
8.9 Future Perspectives
The future of PGPR research should involve all aspects that are highlighted in this
chapter. One of them is the selection of PGPR or PGPR mixes to help solve current
agricultural problems, including limiting the use of highly contaminating pesticides
and fertilizers and allowing for crop cultivation in low-fertility soils.
Although sustainable agriculture is directly related to human health, the use of
PGPR to enhance levels of secondary metabolites that directly affect health through
the diet may lead to the creation of functional foods, that is, foods having a benefi-
cial effect on human health, that are superior to the benefits ascribed to their simple
nutritional value.
Finally, identification of specific elicitors of bacterial origin may be used, either

in agriculture, in the production of phytopharmaceuticals in vitro under controlled
conditions, or at a physiological/molecular level, to study plant metabolism that
allows us to unravel the limiting steps of metabolic pathways.
Acknowledgements The authors wish to acknowledge all students that have participated in these
studies that are cited in this chapter and also University San Pablo CEU, Ministerio de Ciencia y
Tecnologia, Comunidad Autónoma de Madrid, and the EU for funding this research.
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Chapter 9
Plants as Sources of Energy
Leland J. Cseke, Gopi K. Podila, Ara Kirakosyan, and Peter B. Kaufman
Abstract This chapter is concerned with biotechnological applications involving

the use of plants as sources of energy. Plants contain stored carbon captured from
light-catalyzed carbon dioxide fixation via photosynthesis. This stored carbon from
plants is available in oil and coal deposits that can be used as energy sources known
as petrofuels. Living plants or plant residues can be used to generate biofuels such
as methane from methane generators, wood fuel from wood chips, and alcohol from
plant-based starch or cellulose in fermentation reactions. Topics that illustrate these
applications include plant-based biofuels for engines – biodiesel and bioethanol;
energy from woodchips (woodchip combustion, gazogen, or wood gasification); and
methane (CH4 ) or natural gas – methane gas production from landfills, methane gas
produced in biodigesters using plant materials as substrate. We discuss the pros and
cons of these applications with plant-derived fuels as well as the different types
of value-added crops, including algae, that are currently being used to produce
biofuels.
9.1 Introduction
Through the process of photosynthesis, plants have the capacity to capture and uti-
lize energy, derived from the Sun, along with carbon from the Earth’s atmosphere
and nutrients from our soils to generate biomass. This biomass, in the form of roots,
stems, leaves, fruits and seeds, is also consumed by animals and microorganisms,
which in turn, generate their own forms of biomass. Manure, leaf litter, wood, gar-
den waste, and crop residues are all common examples of biomass. Consequently,
one definition of biomassis any organic/biological material which contains stored
sunlight in the form of chemical energy. Typically, humans release this energy by
burning the material, and humans have used biomass as an energy source in the form
of solid biofuels for heating and cooking since the discovery of fire.
L.J. Cseke (B)

Department of Biological Sciences, The University of Alabama in Huntsville,
Huntsville, AL 35899, USA

164 L.J. Cseke et al.
Bioenergy is energy made available from organic materials and is often used as
a synonym to biofuel. However, an important distinction between bioenergy and
biofuel is that biomass is the fuel/biofuel and bioenergy is the energy contained
in that fuel (Anderson, 2003; Agarwal, 2007; Drapcho et al., 2008). Biofuel can
be broadly defined as any solid, liquid, or gas fuel derived from recently dead
organic/biological material. This distinguishes it from fossil fuels such as coal, oil,
and natural gas, which are derived from long dead, subterranean deposits of biolog-
ical material. Unlike fossil fuel resources, which have an inevitable finite supply,
biofuels are largely renewable energy sources based on a balance within the Earth’s
carbon cycle. As the human population continues to expand, and the demand for
fossil fuels exceeds its supplies, pressure is mounting to find efficient and effective
methods to produce renewable biofuels. Various plants and plant-derived materials
are currently used for biofuel manufacturing, and biofuel industries are expanding
in Europe, Asia, and the Americas. Agriculturally produced biomass fuels, such
as biodiesel, bioethanol, and bagasse (often a by-product of sugarcane cultivation)
can be burned in internal combustion engines and cooking stoves (Agarwal, 2007).
However, there are many criticisms and concerns surrounding current practices for
the production of biofuels. Consequently, research into more sustainable methods of
generating biofuels will depend largely on the creation of environmentally respon-
sible policies in farming, processing, and transporting of biofuels.
This chapter examines some of the pros and cons in the current methods used for
generating various types of bioenergy, namely, energy derived from solid biomass,
bioalcohol, biodiesel, biogas, and presents a critical look at how biotechnology can
help to solve the world’s current and future energy needs.
9.2 Energy Crisis and the Balance of Carbon
Biofuels were the first form of fuel used by human cultures around the world. Even
up to the discovery of electricity and the start of the industrial revolution, fuels such
as wood, whale oil, manure, and even alcohol were the primary sources of energy
for heating, cooking, and lighting. However, the discovery and use of fossil fuels,
including coal, oil, and natural gas dramatically reduced the emphasis on biomass
fuel in the developed world (Peters and Thielmann, 2008). In the United States, for
example, large supplies of crude oil were discovered in Pennsylvania and Texas in
the mid- and late 1800s. This allowed petroleum-based fuels to become inexpensive.
Because of these low costs, fossil fuels were widely used to promote the growing
industrial age, especially for the production of power used to run factories and auto-
mobiles.
Despite the huge increase in the use of fossil fuels, most of the world continued
to depend upon and make use of biofuels. Even in the United States, during the high-
energy demand seen during wartime periods of World War II, biofuels were valued
as a strategic alternative to imported oil. However, during the peacetime postwar
period, inexpensive oil from the Middle East helped to trigger a worldwide shift
away from biofuels. Since then, there have been a number of “energy crises” around
9 Plants as Sources of Energy 165
the world, caused by a variety of social and political factors. An energy crisisis any
large-scale bottleneck (including price rises) in the supply of energy resources to an
economy. Two of the best known ones occurred in 1973 and 1979, when geopolit-
ical conflicts in the Middle East caused OPEC (Organization of Petroleum Export-
ing Countries) to cut exports. Consequently, non-OPEC nations experienced a very
large decrease in their oil supply. This crisis resulted in severe shortages and a sharp
increase in the prices of high-demand oil-based products, most notably gasoline.
Throughout history, the fluctuations of supply and demand, energy policy, military
conflict, and environmental impacts have all contributed to a highly complex and
volatile market for energy and fuel. On the other hand, such problems always resur-
rect the principles of green energy and sustainable living. This has led to an increas-
ing interest in alternate power/fuel research such as bioethanol, biodiesel, biogas,
fuel cell technology, hydrogen fuel, solar/photovoltaic energy, geothermal energy,
tidal energy, wave power, wind energy, and fusion power. Heretofore, only hydro-
electricity and nuclear power have been significant alternatives to fossil fuels, which
still dominate as energy sources (Fig. 9.1).
Although technology has made oil extraction more efficient, the world is having
to struggle to provide oil by using increasingly costly and less productive methods,
such as deep sea drilling and developing environmentally sensitive areas such as the
Arctic National Wildlife Refuge. In addition, the world’s population continues to
grow at a rate of ∼250,000 people/day, and while a small part of the world’s popu-
lation consumes most of the resources, the people of developing nations continue to
Coal, 23%
Natural gas, 24%
Biomass, 47%
Renewable energy,
6% Hydroelectric, 45%
Nuclear, 8%
Geothermal, 5%
Wind, 2%
Solar, 1%
Petroleum, 39%
Biomass Consumption Million dry tons/year

Forest products industry
Wood residues 44
Pulping liquors 52
Urban wood and food & other process residues 35
Fuelwood (residential/commercial & electric utilities) 35
Biofuels 18
Bioproducts 6
Total 190
Fig. 9.1 Estimated world energy use from different sources. From the state energy conservation
office web site (http://www.seco.cpa.state.tx.us/re_biomass-crops.htm). Source: The US Depart-
ment of Energy’s (DOE) Energy Information Agency (EIA), used with their permission
adopt more energy-intensive lifestyles. Currently, the United States, with its popula-
tion of 300 million people, consumes far more oil than China, with its population of
1.3 billion people. But, this is also beginning to change, leading to an ever increasing
demand for energy around the world. Many energy experts have concluded that the
world is heading toward an unprecedented large and potentially devastating global
energy crisis due to a decline in the availability of cheap oil and other fossil fuels
and a progressive decline in extractable energy reserves.
To add to this problem, carbon emissions, including greenhouse gasses like carbon
dioxide (CO2 ), have been increasing ever since the industrial revolution. It is well
documented that atmospheric CO2 concentrations have risen by ∼30% in the last
250 years. Data from monitoring stations, together with historical records extracted
from ice cores, show that atmospheric CO2 is now at a level higher than at any
time in the last 650,000 years (Meehl et al., 2007). Such increases in CO2 appear
to be driven, in part, by the addition of 6–8 Pg (one Pg [petagram] = 1 billion met-
ric tonnes = 1,000 × 1 billion kg) of carbon/year from human-derived sources,
especially the burning of various fossil fuels which power our electricity and auto-
mobiles. Atmospheric CO2 is predicted to continue to rise an additional 50% by
2050 (Meehl et al., 2007), and such rising levels of CO2 are at the heart of the
concerns over global warming and many of the associated environmental problems.
Biofuels and other forms of renewable energy aim to be carbon neutral or even
carbon negative. Carbon neutral means that the carbon released during the use of
the fuel is reabsorbed and balanced by the carbon absorbed by new plant growth
during photosynthesis (Fig. 9.2). The plant biomass is then harvested to make the
next batch of fuel, thus perpetuating the cycle of carbon in the Earth’s atmosphere
without adding to the problem. The Intergovernmental Panel on Climate Change
(IPCC) estimates that between 46 and 56% of terrestrial carbon is found in for-
est biomes and that actions to preserve and enhance this carbon sink would likely
increase the global terrestrial carbon by 60–87 Pg C by 2050, thereby offsetting
ca. 15% of the anthropogenic emissions predicted for the same period (Saundry
and Vranes, 2008). Using biomass to produce energy can reduce the use of fos-
sil fuels, reduce greenhouse gas emissions, and reduce pollution and waste man-
agement problems (Agarwal, 2007). Therefore, carbon-neutral fuels, in theory, can
lead to no net increases in human contributions to atmospheric CO2 levels, thereby
reducing the potential human contributions to global warming.
In addition to these arguments for biofuels, one of the strongest political drivers
for the adoption of biofuel is “energy security.” This means that a nation’s depen-
dence on oil is reduced and substituted with use of locally available sources, such
as coal, gas, or renewable bioenergy sources. While the extent to which bioenergy
can contribute to energy security and carbon balance will remain in active debate, it
is clear that the dependence on oil is reduced. The US NREL (National Renewable
Energy Laboratory) says that energy security is the number one driving force behind
the US biofuels program (Bain, 2007) and the White House “Energy Security for
the 21st Century” makes clear that energy security is a major reason for promoting
bioenergy. Whether the driving forces behind a need for bioenergy is energy secu-
rity, rising oil prices, concerns over the potential oil peak, greenhouse gas emissions
Fig. 9.2 The carbon cycle. Gigatons of carbon (GtC)/year, stored at various sites along the cycle.
Illustration courtesy of NASA Earth Science Enterprise, available at Wikipedia public domain
(causing global warming and climate change), rural development interests, or insta-
bility in places such as the Middle East, it is clear that at some point, our global
society is going to have to embrace the use of biofuels as a more stable, sustainable
means of meeting our energy needs.
9.3 Disadvantages of Biofuels
While there are many potentially positive aspects to bioenergy and biofuels, there
is growing international criticism because many biofuel energy applications take up
large amounts of land, actually create environmental problems, or are incapable of
generating adequate amounts of energy. While the plants that produce the biofuels
do not produce pollution directly, the materials, farming practices, and industrial
processes used to create this fuel may generate waste and pollution. Large-scale
farming is necessary to produce agricultural biofuels, and this requires substantial
amounts of cultivated land, which could be used for other purposes such as grow-
ing food, or left as undeveloped land for wildlife habitat stability. The farming of
these lands often involves a decline in soil fertility. This is due to a reduction of
organic matter, a decrease in water availability and quality due to intensive use of
crops, and an increase in the use of pesticides and fertilizers (typically derived from
petroleum). The need for more energy crop land has been cited to cause deforesta-
tion, soil erosion, huge impacts on water resources and is implicated in the disloca-
tion of local communities. Proponents of biofuels, however, point out that while the
production of biofuels does require space, it may also reduce the need for harvesting
non-renewable energy sources, such as vast strip-mined areas and slag mountains
for coal, safety zones around nuclear plants, and hundreds of square miles being
strip-mined for oil/tar sands.
As an example of such issues, the current alcohol-from-corn (maize) production
model in the United States has come under intense scrutiny. When one considers
the total energy consumed by farm equipment, soil cultivation, planting, fertiliz-
ers, pesticides, herbicides, and fungicides made from petroleum, irrigation systems,
harvesting, transport of feedstock to processing plants, fermentation, distillation,
drying, transport to fuel terminals and retail pumps, and lower ethanol fuel energy
content, the net benefit does little to reduce unsustainable imported oil and fossil
fuels required to produce the ethanol in the first place. The June 17, 2006, edito-
rial in the Wall Street Journal stated, “The most widely cited research on this sub-
ject comes from Cornell University’s David Pimental and University of Californa,
Berkeley’s Ted Patzek. They’ve found that it takes more than a gallon of fossil fuel
to make one gallon of ethanol from corn – 29% more. That’s because it takes enor-
mous amounts of fossil-fuel energy to grow corn (using fertilizer and irrigation), to
transport the crops and then to turn that corn into ethanol.” Ethanol is also corro-
sive and cannot be transported in current petroleum pipelines; so, more expensive
over-the-road stainless-steel tank trucks need to be used. This not only uses fuel but
increases the cost to the customer at the pump. In addition, the subsidies paid to fuel
blenders and ethanol refineries have often been cited as the reason for driving up
the price of corn, in farmers planting more corn, and the conversion of considerable
land to corn production, which generally consumes more fertilizers and pesticides
than many other land uses and also leads to serious environmental consequences
such as dead zones in the Gulf of Mexico (Ahring and Westermann, 2007).
There are many concerns that, as demand for biofuels increases, food crops are
replaced by fuel crops, driving food supplies downward and food prices upward.
This is especially true for biofuels derived from food crops such as corn and soy-
bean, which impacts food security and food prices, especially in poorer countries
where the inhabitants have barely enough money to purchase their food let alone
any fuel for cars or even stoves they cannot afford. There are those, such as the
National Corn Growers Association, who say biofuel is not the main cause of food
price increases and, instead, point to government actions to support biofuels as the
cause. Others say increases are just due to oil price increases.
Some have called for a freeze on biofuels. Others have called for more fund-
ing for second generation biofuels which should not compete with food production.
Alternatives such as cellulosic ethanol or biogas production may alleviate land use
conflicts between food needs and fuel needs. Instead of utilizing only the starch
by-products from grinding corn, wheat, and other crops, cellulosic ethanol and/or
biogas production maximizes the use of all plant materials. Critics and proponents
both agree that there is a need for sustainable biofuels, using feedstocks that min-
imize competition for prime croplands. These include farm, forest, and municipal
waste streams; energy crops engineered to require less water, fertilizers, and pes-
ticides; plants bred to grow on marginal lands; and aquatic systems such as algae
used to produce alcohol, oil, and hydrogen gas (Ahring and Westermann, 2007). In
short, biofuels, produced and utilized irresponsibly, could make our environmen-
tal/climate problems worse, while biofuels, done sustainably, could play a leading
role in solving the energy supply/demand challenges ahead.
9.4 What Are the Major Types of Biofuels

(Solid, Liquid, and Gas)?
There are several common strategies of producing biofuels. Each strategy is derived
from growing an “energy crop.” This is a type of plant grown at low cost and low
maintenance that is converted into solid, liquid, or gas biofuels. Where the energy
crop will be burned directly to exploit its energy content, woody crops such as Mis-
canthus, Salix, or Populus are widely used. Liquid biofuels can be generated from
energy crops that are high in sugars (sugarcane, sugar beet, and sweet sorghum)
or starch (corn/maize) by using yeast (Saccharomyces) alcoholic fermentation to
produce ethyl alcohol (ethanol). It is also possible to make cellulosic ethanol from
non-edible plants (switchgrass, hemp, and timber) and plant parts (rice husks, corn
stalks, or grass clippings). Other liquid biofuels are derived from plants that con-
tain high amounts of vegetable oil, such as oil palm, soybean, Jatropha or even
algae. When these oils are heated, their viscosity is reduced, and they can be burned
directly in diesel engines or they can be chemically processed to produce fuels such
as biodiesel (Agarwal, 2007). In fact, the diesel engine was originally designed to
run on vegetable oil rather than fossil fuel. Finally, biogas (methane, CH4 ) has been
produced for hundreds of years from waste materials including manure and crop
residues. If high carbohydrate content is desired for the production of biogas, whole-
crops such as maize, sudan grass, millet, white sweet-clover, wood, and many others
can be made into silage and also be converted into biogas.
Depending on geographic location in the world, the type of energy crop grown
often varies. These include corn, switchgrass, and soybeans, primarily grown in the
United States; rapeseed, wheat, and sugar beet primarily grown in Europe; sugar-
cane in Brazil; palm oil and Miscanthus grown in Southeast Asia; sorghum and
cassava in China; and Jatropha in India. In many locations, biodegradable outputs
from industry, agriculture, forestry, and households can also be used for biofuel
production, either by the use of anaerobic digestion to produce biogas or by the
use of second generation biofuels to make use of straw, timber, manure, rice husks,
sewage, and food waste. It is unfortunate that most governments appear fixated on
the liquid fuel paradigm. Refocusing and balancing policies and communications
to support the development of other technologies, including biogas and methods to
extract the most energy out of plant and waste material would be very prudent. How
to use biotechnology to better access this stored energy is a hot topic in science
these days.
9.4.1 Solid Biomass

As mentioned above, humans have used solid biomass as a fuel for cooking and heat-
ing since the discovery of fire. The most obvious examples are wood and grasses,
which have been used in campfires for centuries. Many native cultures around the
world have also used the burning of solid biofuels, not only to release stored energy
in the form of heat but also to release stored nutrients used to fertilize fields for bet-
ter plant growth. The Aborigines in Australia, for example, have routinely burned
the native Spinifex grass (Spinifex sericeus R. Br.) to elicit better plant growth in the
desert and to aid in hunting animals by driving them in a known direction. Other,
more agricultural societies use burning to fertilize crop lands to this day. Cattle farm-
ers in the United States still use fire to trigger the growth of new grasses for their
cattle, not to mention their traditional uses of cow manure for fertilizer, heating, and
cooking. In fact, cow manure is estimated to still contain two-thirds of the original
energy consumed by the cow. Wood was the main source of energy in the United
States and the rest of the world until the mid-1800s, and biomass continues to be a
major source of energy in much of the developing world.
In modern societies, solid biomass continues to be used directly as a combustible
fuel, producing 10–20 MJ·kg−1 of heat. Its forms and sources include wood, the
biogenic portion of municipal solid waste, or the unused portions of field crops.
In the United States wood and wood waste (bark, sawdust, wood chips, and wood
scrap) provide only about 2% of the energy we use today. About 84% of the wood
and wood waste fuel used in the United States is consumed by the forest industry,
electric power producers, and commercial businesses. The rest is used in homes for
heating and cooking.
In addition to wood as a fuel, field crops may be used as fuel sources. For exam-
ple, not only the field crops be grown intentionally as an energy crop but also the
remaining plant by-products be used as a solid fuel. Sugarcane residue (also called
bagasse), wheat chaff, corncobs, rice hulls, and other plant matter can be, and are
burned quite successfully. Processes to harvest biomass from short-rotation poplars
(Populus spp.) and willows (Salix spp.), and perennial grasses such as switchgrass
(Panicum virgatum L.), Phalaris, and Miscanthus, require less frequent cultivation
and less nitrogen than from typical annual crops. Pelletizing Miscanthus and burn-
ing it to generate electricity is being studied and may be economically viable.
Heating by wood is a more attractive option these days because technological
improvements have made wood burning safer, more efficient, and cleaner. Options
range from traditional wood stoves to pellet- and wood chipburning systems. While
pellet fuel is manufactured by compressing ground wood and biomass waste into
small, cylindrical pellets; woodchip fuel requires very little processing. In a typi-
cal woodchip heating system, a motor-driven conveyor system moves the chip fuel
slowly and steadily from a chip hopper into a very efficient combustion chamber
where the chips are burned (Fig. 9.3). As the chips burn, a fan blows hot air into a
heat exchange boiler where water-filled tubes are heated. The hot water then circu-
lates in pipes to provide heat to homes. In some commercial operations, steam can
also be produced to power turbines that generate electricity. Many manufacturing
Fig. 9.3 An example of a modern woodchip heating system
plants in the wood and paper products industry use wood waste to produce their
own steam and electricity. This saves these companies money because they do not
have to dispose of their waste products and they do not have to purchase as much
electricity.
Another advantage of solid biofuels is that the net carbon dioxide emissions that
are added to the atmosphere by the burning process are only derived from the fos-
sil fuels that were used to plant, fertilize, harvest, and transport the solid biomass.
Likewise, chip combustion contributes less pollution and is a renewable resource.
Modern woodchip combustion also gives the opportunity to use mill waste and lower
grade wood from thinning operations. Wood chip fuel produced from such residues
is cheaper than cordwood and pellet fuels. While the capital costs of wood chip
heating systems are higher than oil-based systems, the operating costs are lower.
9.4.1.1 Combustion of Coal as a Biomass Energy Source: Pros and Cons

Coal is a solid fossil fuel formed in ecosystems where plant remains were preserved
by water and mud during oxidization and biodegradation, thus sequestering atmo-
spheric carbon present thousands or even millions of years ago. It is composed
primarily of carbon and hydrogen along with small quantities of other elements,
notably sulfur. Such elements are the primary source of pollution when the coal is
finally burned. Since coal is the largest source of fuel for the generation of electric-
ity worldwide, as well as the largest worldwide source of carbon dioxide emissions,
its contribution to climate change and global warming is immense. In terms of car-
bon dioxide emissions, coal is slightly ahead of petroleum and about double that of
natural gas. In addition, coal is extracted from the ground by coal mining, either
by underground mining or by open pit mining (surface/strip mining). The prac-

tices of mining coal are deleterious to the local environment as seen in mountain
top removal with strip mining, pollution of streams and rivers, and destruction of
ecosystems.
In recent years, there has been talk about “clean coal”. This is an umbrella term
used in the promotion of the use of coal as an energy source by emphasizing methods
being developed to reduce its environmental impact. These efforts include chemi-
cally washing minerals and impurities from the coal, gasification (see also IGCC),
treating the flue gases with steam to remove sulfur dioxide, and carbon capture and
storage technologies to capture the carbon dioxide from the flue gas. These methods
and the technology used are described as clean coal technology, and such technol-
ogy is a popular conversational topic for politicians. Clean coal can certainly be
beneficial to the energy security of a country, but it is unlikely that coal will ever
be truly clean. The same is true for most solid biofuels. Over 2 billion people cur-
rently cook every day and heat their homes by burning biomass, and this process
is not “clean.” In the nineteenth century, for example, wood-fired steam engines
were common and contributed significantly to unhealthy air pollution seen during
the industrial revolution. Today, the black soot that is being carried from Asia to
polar ice caps appears to be causing them to melt faster in the summer.
9.4.1.2 Does Wood as a Solid Biofuel Offer Any Benefits

as a Transportation Fuel?
With current technology, solid biofuels are not ideally suited for use as a trans-
portation fuel. Most transportation vehicles require power sources with high-energy
density, such as that provided by internal combustion engines. These engines gener-
ally require clean burning fuels, which are in liquid form, and to a lesser extent,
compressed gases. Liquid biofuels are more portable, and they can be pumped,
which makes handling much easier. This is why most transportation fuels are liq-
uids. Non-transportation applications such as boilers, heaters, and stoves can usually
tolerate the low-energy density contained in solid fuels, but technologies are being
developed to make better use of solid fuels. Wood and its by-products can now be
converted through process such as gasification into biofuels such as wood gas (syn-
thesis gas), biogas, methanol, or ethanol fuel; however, further development may be
required to make these methods affordable and practical.
Because solid fuels have inherent problems of relatively high costs, air pollution
on combustion, and production inefficiency, one has to look at other, less polluting,
more efficient, lower cost fuel sources. These include bioalcohol and biogas, which
are covered in the next two sections. In contrast to the above, energy harvesting via
bioreactors (methane generators) is a cost-effective solution, as for example, when
applied to the animal solid waste product (manure) disposal issues faced by the dairy
farmer. They can produce enough biogas/natural gas (methane, CH4 ) to run a farm
and work quite well in internal combustion engines (see Section 9.4.4)
9.4.2 Bioalcohol
The most abundant source of ethanol is the hydration of ethylene (CH2 =CH2 )
derived from petroleum and other fossil fuels. While bioalcohols (especially
bioethanol) have been in use for hundreds of years, it is only relatively recently that
ethanol from biological sources has become more substantial. Ethanol fuel is now
the most common biofuel worldwide, particularly in Brazil and the United States.
Alcohol fuels are produced by fermentation of sugars derived from energy crops,
such as corn, sugarcane, sugar beets, sorghum, wheat, or any sugar or starch that
alcoholic beverages can be made from, including potatoes and fruit waste. Creation
of ethanol starts with the energy of the Sun, carbon dioxide from the atmosphere
and nutrients from soil, which allow the feedstocks to grow. Plants produce sug-
ars such as glucose through the process of photosynthesis (6CO2 + 6H2 O + light
→ C6 H12 O6 + 6O2 ). During ethanol fermentation, performed primarily by yeast
(Saccharomyces spp.), glucose is decomposed into ethanol and carbon dioxide
(C6 H12 O6 → 2C2 H6 O + 2CO2 + heat). During combustion, ethanol reacts with oxy-
gen to produce carbon dioxide, water, and heat (C2 H6 O + 3O2 → 2CO2 + 3H2 O +
heat). Since two molecules of ethanol are produced for each glucose molecule, there
are equal numbers of each type of molecule on each side of the equation, and the
net reaction for the overall production and consumption of ethanol is simply (light
→ heat). The heat of the combustion of ethanol can be used to drive the piston
of an internal combustion engine (Agarwal, 2007). Ethanol is considered “renew-
able” because it is primarily the result of conversion of the Sun’s energy into usable
energy.
The most common steps in the production of bioalcohols are as follows:
(1) enzymatic digestion (to release sugars from stored starches); (2) fermentation
of the sugars through the action of microorganisms (yeasts that generate alcohol in
the process); (3) distillation (to concentrate the alcohol); and (4) drying (to remove
residual water that can prevent the liquid from being used as a fuel). The distillation
process, in particular, requires significant energy input as heat (often using natural
gas from fossil fuels). Likewise, we have already discussed some of the concerns
over the amount of land needed to produce ethanol fuel crops and how land used
for this purpose seems to be adversely impacting usable land for food resources (see
Sections 9.2 and 9.3).
More recently, attention has focused on making use of non-food crops or the
waste biomass leftover from other crops. Plant biomass high in cellulose (including
wood and paper waste) can also be tapped for its stored sugar content. Once the
cellulose is broken down through the action of enzymes and microorganisms (e.g.,
cellulose-decomposing fungi), it can be used as a starting material for fermenta-
tion and alcohol production. However, since cellulose is extremely stable, it is very
difficult to break apart. In addition, it is commonly linked to lignin (another support
molecule found in the cell walls of plants), and the resulting “lignocellulose” is one
of the toughest plant materials to decompose. One good example of a plant high in
both sugars and cellulosic biomass is sugarcane. The cane can be pressed to extract
its juice which has high levels of sugar. The leftover bagasse, the waste left after
sugarcane is pressed, can also be dried and used as a solid biomass to provide heat
for the distillation process after fermentation.
Ethanol can be used in automobile engines as a replacement for gasoline
(Agarwal, 2007). It can be mixed with gasoline to any percentage; however, most
existing automobile gasoline engines can only run on blends up to 15% bioethanol
with petroleum/gasoline. Gasoline with ethanol added has a higher octane, which
means that the engine can typically burn hotter, more efficiently, and more cleanly.
In high-altitude (thin air) locations, some states mandate a mix of gasoline and
ethanol as a winter oxidizer to reduce atmospheric pollution emissions (Agarwal,
2007). The top five producers of ethanol for fuel are the United States, Brazil,
China, India, and France. Brazil and the United States accounted for ∼70% of
all ethanol production, with total world production of 13.5 billion US gallons (40
million tonnes).
9.4.2.1 History of Bioalcohol Use

Throughout the history of its use as a fuel, bioethanol has been at the crux of supply,
demand, and often subtle price variations between ethanol and other liquid fuels.
Since ancient times, ethanol has been used for lamp oil and cooking, along with
plant and animal oils. Before the US Civil War, many US farmers had alcohol stills
that could turn crop waste into virtually free lamp and stove fuel. In 1826, Samuel
Morey, experimented with a prototype internal combustion engine that used ethanol
(combined with turpentine and ambient air then vaporized) as fuel. At that time, his
discovery was overlooked, mostly due to the success of steam power. And while
ethanol was known of for decades, it received little attention as a fuel until 1860,
when Nicholas Otto began experimenting with internal combustion engines. Such a
use would have meshed well with the farmers’ alcohol stills. However, the Indus-
trial Age caused many farmers to move to city jobs, leaving their farms and ethanol
fuel stills behind. Despite this, alcohol remained popular for lighting, cooking, and
industrial purposes. In 1862, and again in 1864, a tax on alcohol was passed in
the United States to help pay for the Civil War. This increased the price of ethanol
dramatically, causing farmers not to be able to sell their ethanol due to reduced
demand. Consequently, farmers used the ethanol themselves. Later in the 1890s,
alcohol-fueled engines were used in farm machinery, train locomotives, and even-
tually cars in the United States and Europe. Henry Ford’s first car, the Quadracycle,
was released in 1896 and ran on 100% ethanol. Thus ethanol was the first fuel used
by American cars before gasoline.
The early 1900s were an important time in the history of how gasoline eventu-
ally overtook alcohol fuels as the fuel of choice for automobiles. In 1902, the Paris
alcohol fuel exposition exhibited alcohol-powered cars, farm machinery, lamps,
stoves, heaters, laundry irons, hair curlers, coffee roasters, and many household
appliances that were powered by alcohol. A few years later, the United States
repealed the alcohol tax while under Theodore Roosevelt, who was strongly against
fossil fuels like oil. This allowed the price of ethanol (∼14 cents/US gallon) to
fall below the price of gasoline (∼22 cents/US gallon). Unfortunately, in 1907,
the discovery of new oil fields in Texas caused the price of gasoline to drop to
between 18 and 22 cents/US gallon, and at the same time, alcohol fuel prices
rose to around 25–30 cents/US gallon. Because of the struggle between the mar-
kets for alcohol and gasoline, Henry Ford introduced his Ford Model T in 1908.
It had an engine that could run on either ethanol or gasoline or a mix of both.
Ford continued to be an advocate for ethanol as a fuel, even during the prohibi-
tion. But in 1919, the prohibition police destroyed virtually all corn-alcohol stills,
putting what appeared to be an end to the use of alcohol as a fuel in the United
States.
It is interesting to note that in many other parts of the world, people believed that
ethanol would be the fuel that would eventually replace petroleum. Experiments on
the use of alcohol as fuel continued in these other parts of the world because there
continued to be a battle between the prices of ethanol and gasoline. For example, in
1923, the price of alcohol from molasses was less than 20 cents/US gallon, while
retail gasoline prices had reached an all-time high of 28 cents/gal. At about the same
time, Standard Oil Co. experimented with a 10% alcohol/90% gasoline blend to
increase octane and stop engine knocking. By the mid-1920s, ethanol blended with
gasoline was standard in every industrialized nation except the United States. By
1925, France, Germany, Brazil, and other countries had already passed “mandatory
blending” laws. During this time, Ford Motor Co. was building cars that could be
changed slightly to run on gasoline, alcohol, or kerosene. It is noteworthy that the
situation changed in the United States. In 2007, Portland, Oregon, became the first
city in the United States to require all gasoline sold within city limits to contain
at least 10% ethanol. As of January 2008, three states – Missouri, Minnesota, and
Hawaii – require ethanol to be blended with gasoline motor fuel. Many cities are
also required to use an ethanol blend due to non-attainment of federal air quality
goals.
In 1933, faced with the 25% unemployment rate of the Great Depression, the
US government considered tax advantages that would help ethanol production to
increase employment among farmers. The “farm chemurgy” movement, supported
by farmers, Republicans, and Henry Ford, searched for new crop-based products
from farms (such as soybean-derived plastics) and supported alcohol fuel. From
1933 to 1939, The American Petroleum Institute argued that such government help
would hurt the oil industry, reduce state treasuries, and cause an unhealthy criminal
“bootlegger” atmosphere around fueling stations. They claimed alcohol fuel was
in every way inferior to gasoline, and eventually, the government did not pass any
alcohol fuel incentives. Pressure from the oil companies has also been blamed for the
demise of various ethanol fuel companies. For example, in 1937, Agrol, an ethanol-
gasoline blend, was sold at 2,000 service stations in the United States. Agrol plant
managers complained of sabotage and bitter infighting elicited by the oil industry
that resulted in cheaper gasoline prices. At this time, alcohol was 25 cents/gal, while
gasoline was 17–19 cents/gal. In 1939, Agrol production shut down because of a
lack of a viable market, and by 1940, the US Midwestern alcohol fuel movement
had disintegrated.
Fuel pressures that arose during World War II resulted in yet another revival
of alcohol as fuel, and new technologies were developed to make use of such a
fuel. For example, on October 14, 1947, legendary test pilot Chuck Yeager became
the first man to fly faster than Mach 1, the speed of sound. He was piloting the
Bell X-1, a bullet-shaped rocket plane (powered by liquid oxygen and alcohol
fuel) that was the first in a series of secret high-speed research aircraft that were
flown out of California’s Edwards Air Force Base in the late 1940s and 1950s.
Another boost for ethanol came in 1973, when a worldwide energy crisis began.
This caused ethanol to once again become cheaper than gasoline. Gasoline contain-
ing up to 10% ethanol has been increasing in use in the United States since the
late 1970s. By the mid-1980s, over 100 new corn-alcohol production plants had
been built, and over a billion US gallons of ethanol were sold for fuel each year.
However, the tide would turn against ethanol again when, in the late 1980s and
1990s, new oil wells were discovered and the price of gasoline once again became
much cheaper than alcohol fuel. This time, however, ethanol plants were able to get
subsidies from the US government to support farmers who were growing energy
crops.
Between 1997 and 2002, three million US cars and light trucks were produced
which could run on E85, a blend of 85% ethanol with 15% gasoline (Agarwal,
2007). Ford, DaimlerChrysler, and GM are among the automobile companies that
sell “flexible fuel” cars, trucks, and minivans that can use gasoline and ethanol
blends that range from pure gasoline up to 85% ethanol (E85). Such flex-fuel vehi-
cles are now having a significant impact on an attempted alcohol fuel transition
because they allow drivers to choose different fuels based on price and availabil-
ity. The primary problem, however, is that there are almost no gas stations that
sell E85 fuel, and the ones that do are mostly located in the Midwest part of the-
United States. During this time, the invasion of Iraq, and the subsequent turmoil it
caused, allowed Americans to become aware of their dependence on foreign oil. In
addition, the demand for ethanol fuel produced from field corn was spurred by the
discovery that methyl tertiary butyl ether (MBTE) was contaminating groundwater.
MBTE was the most common fuel oxygenate additive used to reduce carbon monox-
ide emissions. The groundwater contamination issue eventually led to MTBE being
banned in almost 20 states by 2006. In 2003, California was the first state to start
replacing MTBE with ethanol, and other states start switching soon afterward. This
switch thus opened a new market for ethanol fuel, the primary substitute for MBTE.
This event, coupled with worry over climate change, caused the leading alternative
energy sources, including bioalcohol, solar and wind power, to expand ∼20–30%
each year (Agarwal, 2007). At a time when corn prices were around US $2 a bushel,
corn growers recognized the potential of this new market and delivered accordingly.
Since 2003, crude oil prices have risen by as much as 80%, and gasoline and
US diesel fuel prices have risen by as much as 50%, only to fall again in highly
volatile markets. These rises are caused by hurricane damage to oil rigs in the Gulf
of Mexico, attacks on Iraqi oil pipelines, disruptions elsewhere, and rising demand
for gasoline in Asia, particularly as Asians buy more cars. Gasoline prices rise as
ethanol prices stay the same, due to rapidly a growing ethanol supply and federal
tax subsidies for ethanol production. In 2008, the United Nations urged that there be
a cessation in the provision of subsidies for food-based biofuels, including ethanol,
due to rising controversies over fuel price fluctuations, production costs, and sup-
ply/demand variables.
9.4.2.2 Advantages and Disadvantages of Bioalcohol: Can Corn Do the Job?

As mentioned above, one advantage of bioalcohol is that it can be produced
from a variety of feedstocks, including sugarcane, bagasse, miscanthus, sugar beet,
sorghum, grain sorghum, switchgrass, barley, hemp, kenaf, potatoes, sweet potatoes,
cassava, sunflower, fruit, molasses, corn, stover, grain, wheat, straw, cotton, biomass
in general as well as many types of cellulose waste and harvestings. As discussed
in Section 9.2, the primary advantage of biofuels such as bioalcohol is that they are
relatively “renewable” or carbon neutral as compared to fossil fuels. Carbon diox-
ide, a greenhouse gas, is emitted during fermentation and combustion. However, this
by-product is canceled out by the greater uptake of carbon dioxide by the plants as
they grow to produce the input material for the alcohol. The replacement of MTBE
(an environmental toxin) with ethanol as an oxygenate in gasoline has also reduced
carbon monoxide emissions (Agarwal, 2007). However, ethanol is not a completely
clean burning fuel. When burned in the atmosphere, harmful nitrous oxide gases are
produced, including nitrogen dioxide which contributes to the formation of “brown
smog.” Acetaldehyde and other aldehydes are also produced when alcohols are oxi-
dized. When only a 10% mixture of ethanol is added to gasoline (as is common in
E10 gasohol), aldehyde emissions increase by as much as 40%, and these compo-
nents are not regulated in emissions laws.
The use of alcohol in various mixes with gasoline is also cited as the reason for
reducing prices. According to a 2008 analysis by Iowa State University, the growth
in US ethanol production has caused retail gasoline prices to be 29–40 cents/gal
lower than would otherwise have been the case. However, because alcohol mixes
with both gasoline and with water, ethanol fuels are often diluted after the dry-
ing process by absorbing environmental moisture from the atmosphere. Water in
alcohol-mix fuels reduces efficiency, makes engines harder to start, causes intermit-
tent operation (sputtering), and oxidizes aluminum and steel components (Agarwal,
2007). Ethanol itself is also corrosive to standard fuel systems, rubber hoses and
gaskets, aluminum, and combustion chambers. It also corrodes fiberglass fuel tanks
such as those used in marine engines. For higher ethanol percentage blends, and
100% ethanol vehicles, engine modifications are required. In addition, corrosive
ethanol cannot be transported in gasoline pipelines, so more expensive stainless-
steel tank trucks are required to deliver ethanol to customers. Perhaps even more
problematic, ethanol fuel has less BTU energy content, which means it takes more
fuel to produce the same amount of work. Even dry ethanol has roughly one-third
lower energy content per unit of volume compared to gasoline.
Current interest in ethanol fuel in the United States mainly lies in bioethanol,
produced from corn, but there has been considerable debate about how useful
bioethanol will be in replacing fossil fuels in vehicles. As described in Section
9.3, concerns relate to the large amount of arable land required for energy crops
as well as energy and pollution balance of the whole cycle of ethanol production.
Large-scale farming is necessary to produce agricultural alcohol and this requires

substantial amounts of cultivated land. Farming may also involve a decline in soil
fertility due to reduction of organic matter, a decrease in water availability and qual-
ity, an increase in the use of pesticides and fertilizers, deforestation, and potential
dislocation of local communities. Likewise, “food vs. fuel” is the dilemma regard-
ing the risk of diverting farmland away from food crops and toward the production
of biofuels. The “food vs. fuel” debate is internationally controversial, with good
arguments on all sides. Recent developments with cellulosic ethanol production and
commercialization may allay some of these concerns.
One rationale given for extensive ethanol production in the United States is its
benefit to energy security by shifting the need for some foreign-produced oil to
domestically produced energy sources. In the United States, the number of ethanol
factories has almost tripled from 50 in 2000 to about 140 in 2008. A further 60 or
so are under construction, and many more are planned. The debates surrounding
bioalcohol production are needed to prevent too many resources being placed into
a technology that could have too many problems to make energy issues any better.
Such projects are being challenged by residents at courts in Missouri (where water
is drawn from the Ozark Aquifer), Iowa, Nebraska, Kansas (all of which draw water
from the non-renewable Ogallala Aquifer), central Illinois (where water is drawn
from the Mahomet Aquifer) and Minnesota. With large current unsustainable, non-
scalable subsidies, ethanol fuel still costs much more per distance traveled than cur-
rent high gasoline prices in the United States.
The United States produces and consumes more ethanol fuel than any other coun-
try in the world. This is partly due to energy crisis issues and price battles between
ethanol and gasoline as explained in Section 9.4.2.1. However, one of the main
incentives has been legislation that has been passed. A senior member of the House
Energy and Commerce Committee, Congressman Fred Upton, introduced the leg-
islation to use at least E10 fuel by 2012 in all cars in the United States. Likewise,
the US Energy Independence and Security Act of 2007 requires American “fuel
producers” to use at least 36 billion gallons of biofuel in 2022. This is nearly a five-
fold increase over current levels. Such legislation is at the heart of the push to use
corn as fuel and causing a significant shift of resources away from food production.
Essentially all ethanol fuels in the United States are now produced from corn. As
described above, the amount of land used to generate such large amounts of corn
ethanol is a central concern behind the food vs. fuel debate and other environmental
issues. Unfortunately, corn is a very energy-intensive crop. In the current alcohol-
from-corn production model in the United States, considering the total energy con-
sumed by farm equipment, cultivation, planting, fertilizers, pesticides, herbicides,
and fungicides made from petroleum, irrigation systems, harvesting, transport of
feedstock to processing plants, fermentation, distillation, drying, transport to fuel
terminals and retail pumps, and lower ethanol fuel energy content, the net energy
content value added and delivered to consumers is very small. And, the net benefit
(all things considered) does little to reduce unsustainable imported oil and fossil
fuels required to produce the ethanol.
The problem here is that current processes for the production of ethanol from
corn use only a small part of the corn plant. The corn kernels are taken from the
corn plant and only the starch is transformed into ethanol. Corn is typically 66%
starch and the remaining 33% is not fermented. This unfermented component is
called distillers grain, which is high in fats and proteins, and makes good animal
feed. US corn-derived ethanol costs 30% more because the corn starch must first be
converted to sugar before being fermented into alcohol. Here enzymes are required
to first liquefy the starch. A second enzyme converts the liquefied starch to sugars,
which are fermented by yeast into ethanol and carbon dioxide. The released CO2 can
also be captured and sold for use in carbonating beverages and in the manufacture of
dry ice; however, this is not always done. Despite the cost differentials in production,
in contrast to Japan and Sweden, the United States does not import much Brazilian
ethanol because of US trade barriers corresponding to a tariff of 54-cent/gal – a
levy designed to offset the 51-cent/gal blender’s federal tax credit that is applied to
ethanol no matter its country of origin.
9.4.2.3 Ethanol Derived from Sugarcane

Sugarcane or sugar cane (Saccharum) is a genus of 6–37 species (depending on tax-
onomic interpretation) of 2–6 m tall perennial grasses (family Poaceae, tribe Andro-
pogoneae). They are native to warm temperate to tropical regions of the world, hav-
ing stout, jointed, fibrous stalks that are very rich in sugar. Sugarcane is one of the
most efficient photosynthesizers in the plant kingdom. It is able to convert up to 2%
of incident solar energy into biomass. All of the sugarcane species interbreed, and
all of the major commercial cultivars are complex hybrids. Sugarcane originated
from tropical South and Southeast Asia. Different species likely originated in dif-
ferent locations with S. barberi originating in India and S. edule and S. officinarum
from New Guinea. The thick stalk stores energy as sucrose in the sap. This sap can
be extracted by pressing, and sugar is extracted by evaporating the water from the
resulting juice. The use of crystallized sugar has been reported for over 5,000 years
in India. The methods of growing sugarcane and processing sugar were transferred
to China from India in the seventh century, and around the eighth century C.E.,
Arabs introduced sugar to the Mediterranean, Mesopotamia, Egypt, North Africa,
and Spain. By the tenth century, there was virtually no village in Mesopotamia that
did not grow sugarcane, and sugarcane was among the early crops brought to the
Americas by the Spaniards.
Currently, about 200 countries grow sugarcane to produce ∼1,325 million tons
of sugary biomass. As of 2005, the world’s largest producer of sugarcane by far is
Brazil, followed by India. Uses of sugarcane include the production of sugar, Faler-
num, molasses, rum, soda, cachaça (the national spirit of Brazil), and ethanol for
fuel. Ethanol is produced most typically by yeast (Saccharomyces species) fermen-
tation of the sugar extracted from the cane. The bagasse that remains after crushing
the sugarcane may also be burned to provide heat both for distillation processes and
for the production of electricity. Because of its high cellulose content, it may also
be used as raw material for paper and cardboard, as a starting material for cellulosic
ethanol, and is branded as “environmentally friendly” because it is a renewable by-

product of sugar production.
Brazil has the largest and most successful sugarcane biofuel programs in the
world, and it is considered to have the world’s first sustainable biofuels economy.
In 2006, Brazilian ethanol provided ∼18% of the country’s transportation fuel, and
by April 2008, more than 50% of the fuel used as a replacement to gasoline was
derived from sugarcane. As a result of the increasing use of ethanol, together with
the exploitation of domestic deep water oil sources, Brazil reached complete self-
sufficiency in oil supply in 2006, whereas years ago, the country had to import a
large share of the petroleum needed for domestic consumption. Since 1977, the gov-
ernment made it mandatory to blend 20% of ethanol (E20) with gasoline, requiring
just minor adjustments on standard gasoline engines (Agarwal, 2007). Today, the
mandatory blend is allowed to vary nationwide between 20 and 25% ethanol (E25),
and it is used by all normal gasoline vehicles. In addition, three million Brazilian
cars run on 100% anhydrous ethanol and six million flexible fuel vehicles are now
active in Brazil. Introduced to the market in 2003, these flex-fuel vehicles became
a commercial success, representing around 23% of Brazil’s standard motor vehi-
cles. The ethanol-powered and flex vehicles have also been manufactured to tol-
erate even hydrated ethanol, an azeotrope comprised of 95.6% ethanol and 4.4%
water.
Together, Brazil and the United States lead the industrial world in global ethanol
production, accounting for ∼70% of the world’s total production and nearly 90%
of the ethanol used for fuel. However, Brazil’s sugarcane-based industry is far more
efficient than the US corn-based industry. Brazilian distillers are able to produce
ethanol for less than 22 cents/l, compared with the 30 cents/l for corn-based ethanol.
Sugarcane plantations cover 3.6 million ha of land for ethanol production, represent-
ing only 1% of Brazil’s arable land, with a productivity of 7,500 l of ethanol/ha, as
compared with the US maize ethanol productivity of 3,000 l/ha. However, as with
corn in the United States, significant areas of land are likely to be dedicated to sug-
arcane in future years, as demand for ethanol increases worldwide. The expansion
of sugarcane plantations is already placing pressure on environmentally sensitive
native ecosystems, including rainforests in South America, where deforestation is
contributing to the elevation of greenhouse gases, loss of habitat, and a reduction in
biodiversity.
In some respects, it is good that sugarcane cultivation requires a tropical or sub-
tropical climate, with a minimum of 24 in. of annual rainfall. This has limited its
use in North America and has forced the development of technologies that are bet-
ter suited to North America. However, sugarcane production in the United States
is occurring in Florida, Louisiana, Hawaii, and Texas, and the first three ethanol
plants to produce sugarcane-based ethanol are expected to go online in Louisiana
by mid-2009.
9.4.2.4 Ethanol Derived from Biomass

Plant biomass is the most abundant renewable resource on Earth and is also a poten-
tial source of fermentable sugars for the production of bioalcohol. As in the pro-
duction of other bioalcohols, fermentation of sugars derived from biomass can be
accomplished through the action of microorganisms that generate alcohol, which
then needs to be distilled and dried to remove residual water. However, conver-
sion of plant biomass to fermentable sugars typically requires manual and/or chem-
ical pretreatment and the hydrolysis of lignocellulose, a structural material that
comprises most of the plant biomass. Lignocellulose is composed primarily of
cellulose (a β-1,4-linked glucose polymer), hemicellulose (with various types of
5- and 6-carbon sugar polymers), and lignin (a polymer of phenolic compounds)
(Table 9.1). Unfortunately, the use of lignocellulose as a fuel has been curtailed by
its highly rigid structure. Consequently, an effective pretreatment is needed to liber-
ate the cellulose from the crystalline structure of lignin so as to render it accessible
for subsequent hydrolysis (also called cellulolysis).
In contrast to ethanol produced from corn and sugarcane starches and sugars,
cellulose is contained in nearly every natural, free-growing plant, tree, and shrub, in
every meadow, forest, and field all over the world. Since the components of lignocel-
lulose cannot be digested by humans, the production of cellulosic ethanol does not
have to compete with the production of food, and if marginal lands are used to grow
cellulose-rich crops, it does not have to compete with the land used to grow food
crops. According to US Department of Energy studies conducted by the Argonne
National Laboratories and the University of Chicago, the major benefit of cellulosic
ethanol is that it can reduce greenhouse gas emissions by as much as 85% over
reformulated gasoline. By contrast, starch ethanol from corn most frequently uses
natural gas to provide energy for processing and may not reduce greenhouse gas
emissions at all, depending on how the starch-based feedstock is produced. In addi-
tion, cellulosic crops require fewer inputs, such as fertilizer, herbicides, and other
Table 9.1 Composition of various types of cellulosic biomass material (% dry weight)
Material Cellulose Hemicellulose Lignin Ash Extractives
Softwood barks 18–38 15–33 30–60 0.8–1.0 4–6

Hardwood barks 22–40 20–38 30–55 0.8–1.0 6–8
Soft woods 42–44 27–29 28–31 0.5–0.6 3–5
Newspapers 40–55 25–40 18–30 – –
Hard woods 45–47 30–35 20–24 0.6–0.8 5–8
Grasses 25–40 25–50 10–30 – –
Wheat straw 37–41 27–32 13–15 11–14 7–9
Chemical pulps 60–80 20–30 2–10 – –
Cornstalks 39–47 26–31 3–5 12–16 1–3
Cotton and flax 80–95 5–20 – – –
Algae 20–40 20–50 – – –
Modified from Demirbas et al. (2005).

chemicals that can pose risks to wildlife. Their extensive roots improve soil quality,
reduce erosion, and increase nutrient capture. Herbaceous energy crops reduce soil
erosion by greater than 90%, when compared to conventional food crop production.
This can translate into improved water quality for rural communities. Additionally,
cellulosic energy crops add organic material to depleted soils and can increase soil
carbon as long as the land being used is not totally stripped of plant material. In addi-
tion, the price per ton of the raw cellulose material is much cheaper than for grains
or fruits, and since cellulose is the main component of plants, the whole plant can
be harvested. This results in much better yields per acre, up to 10 t, instead of 4 or 5
t for the best crops of grain. Thus, production of ethanol from lignocellulose has the
advantage of having abundant and diverse resources that do not require agricultural
effort or costs for growth; however, it does require a greater amount of processing
to make the sugar monomers available to the microorganisms that produce ethanol
during fermentation.
The first attempt at commercializing a process for ethanol from wood was under-
taken in Germany in 1898. It involved the use of dilute acid to hydrolyze the cel-
lulose to glucose and was able to produce 7.6 l of ethanol/100 kg of wood waste
(18 gal/t). The Germans soon developed an industrial process optimized for yields
of around 50 gal/t of biomass. This process soon found its way to the United States,
where two commercial plants were put into operation in the southeast during World
War I. These plants used what was called “the American Process,” a one-stage dilute
sulfuric acid hydrolysis of wood products and waste. Although the yields were half
that of the original German process (25 vs. 50 gal of ethanol/ton), the output of the
American process was much higher. However, a drop in lumber production forced
these ethanol plants to close shortly after the end of World War I. In the meantime, a
small, but steady amount of research on dilute acid hydrolysis has continued at the
USDA’s Forest Products Laboratory in Madison, WI.
Currently, corn stover (leaves and stalks of maize left in the field after harvest),
switchgrass, miscanthus, and woodchips are some of the more popular cellulosic
materials for ethanol production. For example, switchgrass (Panicum virgatum L.) is
a native prairie grass, known for its hardiness, rapid growth (from 2 to 6 ft tall), and
high cellulose content. It can be grown in most parts of the United States, including
swamplands, plains, streams, and along the shores and interstate highways. Since
switchgrass yields twice as much ethanol per acre than corn, less land is needed
for production, helping to prevent habitat fragmentation. It is unfortunate, how-
ever, that typical municipal practices discard the majority of cellulosic biomass. It
is estimated that over 320 million tons of cellulose-containing raw materials, which
could be used to generate ethanol, are thrown away each year. According to the
International Energy Agency, this includes 36.8 million dry tons of urban wood
wastes, 90.5 million dry tons of primary mill residues, 45 million dry tons of for-
est residues, and 150.7 million dry tons of corn stover and wheat straw. Likewise,
organic waste makes up 71.5% of all landfill wastes deposited each day, consisting
of large amounts of wood, envelopes, newsprint, grass, leaves, food scraps, office
paper, corrugated cardboard, and agricultural composites as well as small amounts
of manures, glossy paper, and paper ledger. All of these materials can be converted
into fuels, and transforming such leftovers into ethanol can actually reduce solid
waste disposal costs and provide as much as 30% of the current fuel consumption in
the United States. Thus, the raw material to produce cellulosic ethanol is basically
free, and it may actually have a negative cost, where ethanol producers can get paid
to take it away.
To date, the available pretreatment techniques include acid hydrolysis, steam
explosion, alkaline wet oxidation, ozone pretreatment, and ammonia fiber expan-
sion. Besides effective cellulose liberation, an ideal pretreatment has to minimize
the formation of degradation products because of their inhibitory effects on sub-
sequent hydrolysis and fermentation processes. The presence of inhibitors will
not only complicate ethanol production, but also, increase the cost of produc-
tion by adding detoxification steps. Even though pretreatment by acid hydrolysis
is probably the oldest and most studied pretreatment technique, it produces sev-
eral potent inhibitors including furfural and hydroxymethyl furfural (HMF) which
are toxic compounds present in lignocellulosic hydrolysate. Ammonia fiber expan-
sion (AFEX) is currently the only pretreatment which features promising efficiency
with no inhibitory effect in resulting hydrolysate, although experiments using fun-
gal organisms that naturally breakdown the biomass are showing some promise
for the release of cellulose polymer from lignocellulose. In the hydrolysis process,
these polymers are broken down to free the sugar before it is fermented for alcohol
production.
There are two primary approaches to cellulose hydrolysis (cellulolysis): a chem-
ical approach using acids, or an enzymatic approach. In the traditional method,
hydrolysis is performed by attacking the cellulose with an acid. Dilute acid may
be used under high heat and high pressure or more concentrated acid can be used at
lower temperatures and atmospheric pressure. The product from this hydrolysis is
then neutralized and yeast fermentation is used to produce ethanol. As mentioned,
a significant obstacle to the dilute acid process is that the hydrolysis is so harsh
that toxic degradation products can be produced that can interfere with fermenta-
tion. In enzymatic hydrolysis, cellulose can be broken into glucose molecules by
cellulase enzymes. Such enzymes are commonly found in the digestive systems
of ruminants, such as cows, sheep, and termites, where a collection of enzymes
are produced by bacteria. They are also found in naturally occurring fungi and
soil bacteria that are part of the global carbon cycle. Using a similar enzymatic
system, lignocellulosic materials can be enzymatically hydrolyzed under relatively
mild conditions (50◦ C and pH = 5), thus enabling effective cellulose breakdown
without the formation of by-products that would otherwise inhibit enzyme activ-
ity. To be viable for large-scale fuel production, all major pretreatment methods,
including dilute acid pretreatment, require some type of enzymatic hydrolysis step
to achieve the high sugar yields required for ethanol fermentation. Various enzyme
companies have already contributed significant technological breakthroughs in cel-
lulosic ethanol production through the mass production of various cellulase enzymes
at competitive prices. Iogen Corporation, for example, is a Canadian producer
of enzymes for an enzymatic hydrolysis process that uses “specially engineered
enzymes.”
Traditionally, baker’s yeast (Saccharomyces cerevisiae) has long been used in the
brewery industry to produce ethanol from hexoses (6-carbon sugars). Yeast cells are
especially attractive for cellulosic ethanol processes because they have been used in
biotechnology for hundreds of years. They are tolerant to high ethanol and inhibitor
concentrations, and they can grow at low pH values, which avoids bacterial contam-
ination. Due to the complex nature of the carbohydrates present in lignocellulosic
biomass, a significant amount of xylose and arabinose (5-carbon sugars derived from
the hemicellulose portion of the lignocellulose) is also present in the hydrolysate.
For example, in the hydrolysate of corn stover, approximately 30% of the total fer-
mentable sugars are xylose. Thus, the ability of the fermenting microorganisms to
utilize the whole range of sugars available from the hydrolysate is vital to increase
the economic competitiveness of cellulosic ethanol.
In recent years, metabolic engineering for microorganisms used in bioethanol
production has shown significant progress. Besides Saccharomyces, bacteria such
as Zymomonas mobilis and Escherichia coli have been targeted for metabolic engi-
neering to improve their fermentation abilities, and thus, improve cellulosic ethanol
production. Likewise, genetically engineered yeasts have been described that effi-
ciently ferment xylose and arabinose sugars. Some species of bacteria have also
been determined to be capable of the direct conversion of cellulose into ethanol.
One example is Clostridium thermocellum, which utilizes a complex cellulosome to
breakdown cellulose and synthesize ethanol. However, C. thermocellum also pro-
duces contaminating by-products during cellulose metabolism, including acetate
and lactate, in addition to ethanol. While this lowers the efficiency of the process,
further research into the ethanol-producing pathways of such organisms holds great
potential for future improvements in the generation of bioalcohol. Enzymes from
thermophilic organisms are also particularly well suited for industrial applications
because they are typically thermostable and relatively tolerant of other stresses such
as pH extremes. Genes for a variety of thermostable cellulase enzymes from both
bacteria and fungi are currently being assessed for their ability to improve cellulosic
ethanol efficiency.
Similarly, much effort has been devoted to developing transgenic plants as biore-
actors to produce heterologous proteins, including industrial cellulase enzymes
(Park et al., 2003). Such plants, expressing genes from other species, are typ-
ically fertile and grow normally, and they supply easy access to the enzymes
needed when cellulose is to be broken into sugars. Manufacturing heterologous cel-
lulases in crop plant bioreactors could significantly reduce costs associated with
enzyme production and could offer a potentially high-volume alternative to tradi-
tional enzyme production methods. Other plant biotechnology approaches aim to
improve the lignocellulose characteristics of the biomass crops themselves. This has
been done in switchgrass, where alteration of gene expression in the lignin biosyn-
thesis pathway has both increased and reduced the amount of lignin within the plant
(Fig. 9.4A). The reduction of lignin in plant tissues allows easier access to the cellu-
lose; however, the amount of reduction has to be carefully tailored so as not to cause
the growing plant to collapse due to lack of support structure. Other approaches to
improved cellulosic crops include more traditional breeding programs that identify
Fig. 9.4 Examples of improvements in cellulosic biomass. (A) Modifications in gene expression
can result in both increased and decreased deposition of lignin in switch grass. (B) Genetic-based
breeding programs can improve biomass in switch grass. Modified from Vermerris (2008) Genetic
Improvement of Bioenergy Crops, Springer
useful traits to help develop superior varieties, including those that have enhanced
biomass production (Fig. 9.4B).
It should be noted here that, while most efforts have focused on acid pretreat-
ment and enzymatic hydrolysis of lignocellulose, gasification of the lignocellulosic
raw material into gaseous carbon monoxide and hydrogen is also useful for ethanol
production (Ahring and Westermann, 2007). The gasification process does not rely
on chemical decomposition of the cellulose chain (cellulolysis). Instead of breaking
the cellulose into sugar molecules, the carbon in the raw material is converted into
wood gas (also called synthesis gas), using what amounts to partial combustion.
The resulting carbon monoxide, carbon dioxide, and hydrogen may then be fed into
a special kind of fermenter. Instead of sugar fermentation with yeast or bacteria,
this process uses a bacterium named Clostridium ljungdahlii. C. ljungdahlii will
ingest (eat) carbon monoxide, carbon dioxide, and hydrogen and produce ethanol
and water. The ethanol can then be distilled and dried as usual. More recently, C.
thermocellum (a thermophilic bacterium) has been found to be twice as efficient in
making ethanol from carbon monoxide as C. ljungdahlii. Alternatively, the synthe-
sis gas from gasification may be fed to a catalytic reactor where the synthesis gas is
used to produce ethanol and other higher alcohols through a thermochemical pro-
cess. Such technology development and the use of biotechnology will likely be key
to the development of truly sustainable fuel sources in the future.
9.4.2.5 Biobutane as an Alternative Fuel

Biobutanol (also called biogasoline) has a longer hydrocarbon chain than ethanol.
This causes it to be fairly non-polar, making it more similar to gasoline than ethanol.
It is often claimed to provide a direct replacement for gasoline, because it can be
used directly in internal combustion engines without modification. Butanol better
tolerates water contamination and is less corrosive than ethanol, making it more
suitable for distribution through existing pipelines for gasoline. In blends with diesel
or gasoline, butanol is less likely to separate from the fuel than ethanol if the fuel
is contaminated with water. There is also a vapor pressure co-blend synergy with
butanol and gasoline containing ethanol. This better facilitates ethanol blending,
thus allowing better storage and distribution of blended fuels. Butanol also has a
high octane rating (over 100) and high energy content, is only about 10% lower than
gasoline, and subsequently is about 50% more energy dense than ethanol (100%
more so than methanol). Butanol’s only major disadvantages are its high flashpoint
(95◦ F or 35◦ C), potential toxicity (but not necessarily more than gasoline), and the
fact that the distillation process requires a large energy input.
The feedstocks for biobutanol are the same as for bioethanol, including energy
crops such as sugar beets, sugarcane, corn grain, wheat, and cassava as well as
agricultural by-products such as straw, corn stalks, and various other biomass.
Biobutanol is formed by acetone/butanol/ethanol fermentation (ABE fermentation)
through the activity of the bacterium, Clostridium acetobutylicum, also known as the
Weizmann organism. This process was first delineated by Chaim Weizmann in 1916
for the production of acetone from starch for making cordite, a smokeless gunpow-
der. At the time, the butanol was a by-product of this fermentation, forming twice as
much butanol as acetone. The process also creates a recoverable amount of hydro-
gen gas and a number of other by-products, including acetic, lactic and propionic
acids, acetone, and isopropanol.
Experimental modifications of the process have shown potentially high net
energy gains with biobutanol as the only liquid product. However, the key research
challenge that must be resolved is that butanol production inhibits microbial growth
even at low concentrations. The Weizmann organism can only tolerate butanol lev-
els up to 2%, compared to 14% for ethanol from yeast. Thus, the overwhelming
constituent of the fermentation broth is water; so, an energy-intensive distillation
step is required for purification. This may be acceptable if the goal is to produce
butanol for use as a solvent, but if butanol is to gain traction as a fuel, energy inputs
need to be minimal. Currently, biobutanol is far to expensive (∼$4/US gallon) to be
viable as a fuel. However, a number of companies are working on the problem. For
example, DuPont and British Petroleum (BP) are working together to help develop
biobutanol as a fuel source. According to DuPont, existing bioethanol plants can
cost-effectively be retrofitted to produce biobutanol. Similarly, a Swiss company,
Butalco GmbH, uses a special technology to modify yeasts in order to produce
butanol instead of ethanol. Yeasts as production organisms for butanol production
have decisive advantages compared to bacteria because they are much more tolerant
to alcohol and contaminants that may inhibit fermentation.
9.4.2.6 Future Perspectives for Bioalcohol

In the United States, crops grown for biofuels are the most land- and water inten-
sive of the renewable energy sources. In 2005, about 12% of the nation’s corn crop
(covering 11 million acres (45,000 km2 ) of farmland) was used to produce 4 billion
gallons of ethanol, which equates to about 2% of annual US gasoline consumption.
For biofuels to make a much larger contribution to the energy economy, the industry
will have to accelerate the development of new feedstocks, agricultural practices,
and technologies that are more land- and water-efficient. The 200-page scientific
roadmap cites recent advances in biotechnology that have made cost-effective pro-
duction of ethanol from cellulose, or inedible plant fiber, an attainable goal, with fed-
eral loan guarantees for new cellulosic biorefineries. The report outlines a detailed
research plan for developing new technologies to transform cellulosic ethanol– a
renewable, cleaner burning, and carbon-neutral alternative to gasoline – into an
economically viable transportation fuel. The US Department of Energy (DOE) has
invested in research on enzymatic, thermochemical, acid hydrolysis, hybrid hydrol-
ysis/enzymatic, and a variety of other technologies that are aimed toward achieving
success in discovering an efficient and low-cost method of converting cellulose to
ethanol. Already, the efficiency of biofuels production has increased significantly,
and there are new methods being developed to boost biofuel production through
the use of genetic engineering of both microorganisms and the plant feedstocks
themselves (see Section 9.5). Many analysts suggest that, whichever ethanol fuel-
production strategy is used, conservation efforts are also needed to make a large
impact on reducing fossil fuel use, and biotechnology will likely play a central role
in such conservation efforts by improving our ability to generate alternative fuels
while also reducing energy inputs.
9.4.3 Biodiesel
Biodieselis another type of liquid biofuel, commonly produced by the trans-
esterification of the vegetable oil or animal fat feedstocks. This biofuel can be used
directly in modern diesel engines. However, it is common to use various percentages
of biodiesel blended with petroleum diesel (also called petrodiesel) so that modifica-
tions to the diesel engines can be avoided. Much of the world uses a system known
as the “B” factor to state the amount of biodiesel in any fuel mix. Fuel containing
20% biodiesel is labeled B20, while pure biodiesel is referred to as B100. Blends of
20% biodiesel with 80% petrodiesel (B20) are generally used in unmodified diesel
engines. Biodiesel can also be used in its pure form (B100), but may require cer-
tain engine modifications to avoid maintenance and performance problems. In many
European countries, a 5% biodiesel blend is widely used and is available at thou-
sands of gas stations (Agarwal, 2007).
A variety of plant oils can be used to produce biodiesel. Currently, rapeseed
or canola (Brassica napus L.) and soybean (Glycine max L.) oils are most com-
monly used, where soybean oil alone accounts for about 90% of all biodiesel in
the United States. Other plant crops can also be used, including oil palm (Elaeis
guineensis Jacq. and Elaeis oleifera Jacq.), sunflower (Helianthus annus L.), flax
(Linum usitatissimum L.), mustard (Brassicaspp.), mahua (Madhuca longifolia) (J.
Konig, J.F. Macbr.), Jatropha, cotton (Gossypium spp.), hemp (Cannabis sativa L.),
field pennycress (Thlaspi arvense L.). Waste vegetable oil is also a useful start-
ing material for biodiesel, as are animal fats including tallow, lard, yellow grease,
chicken fat, and the by-products derived from the production of omega-3 fatty acids
from fish oil. Each of these oils can, in theory, be used as fuel; however, to ensure
that the fuel injectors atomize the fuel in the correct pattern for efficient combus-
tion, vegetable oils must be heated to reduce its viscosity to that of diesel (Agarwal,
2007). This typically is done with electric coils or heat exchangers.
The trans-esterification step used to produce biodiesel generates a lower vis-
cosity fuel that has combustion properties very similar to those of petroleum
diesel. Chemically, trans-esterified biodiesel is a mix of mono-alkyl esters of long
chain fatty acids. Thus, its chemical name is fatty acid methyl (or ethyl) ester
(FAME). There are several methods for carrying out the trans-esterification reaction
(Lachenmaier-Koelch and Meyer-Pittroff, 2005). These include the common batch
process, supercritical processes, ultrasonic methods, and even microwave meth-
ods. In the most commonly used method, oils are mixed with sodium hydroxide
and methanol (or ethanol), and the resulting trans-esterification reaction produces
biodiesel and glycerol. Methanol (converted to sodium methoxide in the reaction)
is normally used to produce methyl esters, as it is the cheapest alcohol available.
However, ethanol can be used to produce ethyl ester biodiesel, and higher alcohols
such as isopropanol and butanol have also been used. In addition, one part glycerol
is produced for every 10 parts biodiesel, and this by-product can be used as a starting
material for other processes. The glycerol by-product can be used as a humectant
(hygroscopic moistening agent), solvent, sweetener, and food preservative and as a
starting material in the production of nitroglycerin.
Biodiesel can also be used as a heating fuel in domestic and commercial boil-
ers, where it is sometimes known as bioheat. In countries such as the United States,
where more than 80% of commercial trucks and city buses run on diesel, biodiesel
offers a promising alternative to petroleum-derived diesel. Since the feedstocks con-
tain very little sulfur, biodiesel is a cleaner burning fuel than petrodiesel. Likewise,
the solvent characteristics of biodiesel tend to keep engine deposits from forming,
thus maintaining cleaner operation.
9.4.3.1 History of Biodiesel vs. Petrodiesel Production

Trans-esterification of a vegetable oil was conducted as early as 1853 by scientists
E. Duffy and J. Patrick, many years before the first diesel engine became functional.
It was not until 40 years later when Rudolf Diesel’s invention, a single 10 ft (3 m)
iron cylinder with a flywheel at its base, ran on its own power for the first time
in Augsburg, Germany, on August 10, 1893. A few years later, Mr. Diesel also
demonstrated his diesel engine. This engine was engineered to run on peanut oil
(at the request of the French government) and built by the French Otto Company. It
was shown at the World Fair in Paris, France, in 1900, where it received the Grand
Prix (highest prize). This engine stood as an example of Diesel’s vision because it
was powered by peanut oil – a biofuel. While peanut oil is not trans-esterified to a
true diesel fuel, Rudolf Diesel believed that the utilization of biomass fuel was the
real future of his engine. In a 1912 speech, Diesel said, “the use of vegetable oils for
engine fuels may seem insignificant today but such oils may become, in the course
of time, as important as petroleum and the coal-tar products of the present time.”
During the 1920s, diesel engine manufacturers altered their engines to utilize the
lower viscosity of petrodiesel, a fossil fuel, rather than vegetable oil, a biomass
fuel. The petroleum industries were able to penetrate the fuel markets because
their fuel was much cheaper to produce than the biomass alternatives at the time.
The result, for many years, was a near elimination of the biomass fuel production.
Only recently, environmental impact concerns and decreasing price differences have
made vegetable oils an appealing alternative. Despite the widespread use of fossil
petroleum-derived diesel fuels, interest in vegetable oils as fuels in internal combus-
tion engines is reported in several countries during the 1920s and 1930s.
Later, during World War II, Belgium, France, Italy, the United Kingdom, Portu-
gal, Germany, Brazil, Argentina, Japan, and China have been reported to have tested
and used vegetable oils as fuels. As mentioned above, operational problems were
reported due to the high viscosity of vegetable oils as compared to petroleum diesel
fuel, which resulted in poor atomization of the fuel in the fuel spray and often leads
to deposits and coking of the injectors, combustion chamber, and valves. Attempts
to overcome these problems included heating of the vegetable oil, blending it with
petroleum-derived diesel fuel or ethanol, pyrolysis, and catalytic cracking of the oils
(Agarwal, 2007).
On August 31, 1937, G. Chavanne of the University of Brussels in Belgium was
granted a patent for a “Procedure for the transformation of vegetable oils for their
uses as fuels” (fr. ‘Procédé de Transformation d’Huiles Végétales en Vue de Leur
Utilisation comme Carburants’ Belgian Patent 422,877). This patent described the
trans-esterification of vegetable oils using methanol and ethanol in order to separate
the fatty acids from the glycerol by replacing the glycerol by short linear chain
alcohols. This appears to be the first account of the production of what is known
as “biodiesel” today. More recently, in 1977, Brazilian scientist Expedito Parente
produced biodiesel using trans-esterification with ethanol and filed a patent for the
same process. Research into the use of trans-esterified sunflower oil, and refining
it to low viscosity diesel fuel standards, was initiated in South Africa in 1979. By
1983, the process for producing fuel-quality, engine-tested biodiesel was completed
and published internationally.
Since then, the benefits of the technology have been spreading. An Austrian com-
pany, Gaskoks, obtained the technology from the South African Agricultural Engi-
neers. This company erected the first biodiesel pilot plant in November 1987 and
the first industrial-scale plant in April 1989 (with a capacity of 30,000 t of rape-
seed/year). Throughout the 1990s, biodiesel plants were opened in many European
countries, including the Czech Republic, Germany, and Sweden. France launched
local production of biodiesel fuel (referred to as diester) derived from rapeseed oil,
which is mixed into regular diesel fuel at a level of 5%, and into the diesel fuel used
by some public transportation at a level of 30% (Agarwal, 2007). During the same
period, nations in other parts of the world also saw local production of biodiesel
starting up, and by 2000, over 21 countries had commercial biodiesel projects.
In September 2005 Minnesota became the first US state to mandate that all
diesel fuel sold in the state contain part biodiesel, requiring a content of at least
2% biodiesel. The world’s first biofuel-powered commercial aircraft took off from
London’s Heathrow Airport on February 24, 2008, and touched down in Amsterdam
on a demonstration flight, hailed as a first step toward “cleaner” flying. The “BioJet”
fuel for this flight was produced by Seattle-based Imperium Renewables, Inc.
In summary, Biodiesel is a clean burning fuel for diesel engines made from
domestically produced, renewable fats and oils such as soybean oil. Biodiesel has
no sulfur or aromatic compounds and already meets the new Environmental Protec-
tion Agency (EPA) ultra-low sulfur diesel fuel mandated for introduction in 2006.
Biodiesel can be used in existing diesel engines without modification. Biodiesel
burns substantially cleaner than petroleum-based diesel fuel. It is a powerful option
for improving our environment while reducing dependence on foreign oil, stretching
our fossil fuel reserves, and providing value-added markets for agricultural products.
9.4.3.2 Sources of Plant Oils

European production of biodiesel from energy crops has grown steadily in the last
decade, principally focused on rapeseed used for oil and energy. In North Amer-
ica rapeseed was renamed Canada Oil or Canola. Production of oil/biodiesel from
rapeseed covers more than 1.2 million ha in Germany alone and has doubled in the
past 15 years. Typical yield of oil as pure biodiesel may be as much as 1,000 l/ha or
more. This makes biodiesel crops economically attractive. They also provide sus-
tainable crop rotations that are nutrient balanced and preventative of the spread of
disease.
Soybeans are by far the main source of vegetable oil production in the United
States and likewise biodiesel production. While US biodiesel is being produced
from a diverse array of feedstocks, soybean oil is still used for up to 80% of US
biodiesel production. Based on US Bioenergy program requirements, the Renew-
able fuel Standards (RFS) for biomass-based diesel is 500 million gallons in 2009
and ramps up to 1 billion gallons by 2012. Some experts estimate that if the biodiesel
industry keeps its current momentum, over 10% of US soybean oil could be used
for biodiesel production in the next few years. Biodiesel yield of soybeans is signif-
icantly lower than that of rape, as can be seen in Table 9.2.
Since none of the current crop plants produce enough oil to completely replace
fossil fuel usage, there is ongoing research into finding more suitable crops and
improving oil yields. For example, it is estimated that it would require twice the
land area of the United States to be devoted to soybean production, or two-thirds to
be devoted to rapeseed production, to meet current US heating and transportation
needs. The use of alternative crops that do not make use of prime cropland may be
one way to curb problems associated with crops that overlap with food demands.
Table 9.2 Amount (%) of oil in various crop plants
Crop plant Scientific name % Extractable oil
Copra Cocos nucifera 62

Castor bean Ricinus communis 50
Sesame Sesamum indicum 50
Groundnut kernel Arachis hypogaea 42
Jatropha Jatrophaspp. 40
Rapeseed Brassica napus 37
Palm kernel Elaeisspp. 36
Mustard seed Brassicaspp. 35
Sunflower Helianthus communis 32
Palm fruit Elaeisspp. 20
Soybean Glycine max 14
Cotton seed Gossypium hirsutum 13
Non-food crops, such as mustard, Camelina, and Jatropha, are used for biodiesel
and can thrive on marginal agricultural land where many trees and crops will not
grow, or would produce only slow growth yields. Specially bred mustard varieties
can produce reasonably high oil yields and are very useful in crop rotations with
cereals. Mustards have the added benefit that the meal leftover after oil has been
extracted can act as an effective and biodegradable pesticide. Camelina (Camelina
sativa L. Crantz) is virtually 100% efficient. It can be harvested and crushed for oil
and the remaining parts can be used to produce high-quality omega-3-rich animal
feed, fiberboard, and glycerin. Most camelina is grown in areas that were previ-
ously not utilized for farming. For example, camelina can be grown in areas that
receive limited rainfall that cannot sustain corn or soybeans without the addition of
irrigation.
Jatropha is a genus of approximately 175 succulent plants, shrubs, and trees
(some are deciduous, like Jatropha curcas L.) from the spurge family, Euphor-
biaceae. The name is derived from (Greek iatros = physician and trophe = nutri-
tion), hence the common name physic nut. These plants are drought resistant and
can share space with other cash crops such as coffee, sugar, fruits, and vegetables.
It is well suited to semi-arid lands and can contribute to slowdown desertification,
according to its advocates. The hardy Jatropha produces seeds containing up to 40%
oil. When the seeds are crushed and processed, the resulting oil can be used in stan-
dard diesel engines, while the residue can also be processed into biomass to power
electricity plants (Agarwal, 2007). However, estimates of Jatropha biodiesel yield
vary, primarily due to a lack of research data, genetic diversity of different species,
the range of environments in which the plants are grown, and Jatropha’s perennial
life cycle. Seed yields under cultivation can range from 1,500 to 2,000 kg/ha, corre-
sponding to extractable oil yields of 540–680 l/ha (58–73 US gallons/acre).
Jatropha is native to Central America and has become naturalized in many trop-
ical and subtropical areas, including India, Africa, and North America. Originating
in the Caribbean, Jatropha was disseminated as a valuable hedge plant to Africa
and Asia by Portuguese traders. Cultivation and fruit picking by hand is labor inten-
sive and needs ca. 1 person/ha. So, in parts of rural India and Africa, this provides
much-needed jobs. About 200,000 people worldwide now find employment through
the production of Jatropha. Moreover, villagers often find that they can grow other
crops in the shade of Jatropha trees. Currently, the oil from Jatropha curcas seeds is
used to make biodiesel in the Philippines, as promoted by a law authored by Philip-
pine senators Miriam Defensor-Santiago and Miguel Zubiri. Likewise, Jatropha oil
is being promoted as a biofuel crop in hundreds of projects throughout India and
other developing countries. One good example of its ability to grow on marginal
lands is its use along the railway lines between Mumbai and Delhi in India, where
the train itself runs on 15–20% biodiesel. In Africa, cultivation of Jatropha is also
being promoted and it is grown successfully in countries such as Mali.
Since food crops are not efficient sources for oil-based fuels, often having less
oil content and requiring more input energy for growth, energy crops that can be
grown on marginal lands may have higher oil content and thus be a much better
choice.
9.4.3.3 Advantages and Disadvantages of Biodiesel

One of the primary advantages of biodiesel comes from feedstocks used to create
it. Fossil fuels, including petrodiesel, contain minor contaminants, such as salts and
sulfur compounds that end up in the refined diesel. When the fuel is burned, these
compounds build up in the atmosphere, where they have been causing environmental
problems for years. Since the feedstocks used to make biodiesel contain virtually no
sulfur, biodiesel is a cleaner-burning fuel than petrodiesel. Pure biodiesel (B100) is
by far the lowest emission diesel fuel, and it is often used as an additive to ultra-low
sulfur diesel (ULSD) fuel (Agarwal, 2007). However, while B100 biodiesel has a
viscosity similar to petrodiesel, it may become more viscous at lower temperatures,
depending on the feedstock used, thus requiring vehicles to have fuel line heaters.
Biodiesel is also an oxygenated fuel, meaning that it contains a reduced amount
of carbon and higher hydrogen and oxygen contents than fossil diesel. This improves
the combustion of fossil diesel and reduces the particulate emissions from unburnt
carbon (Agarwal, 2007; Armas et al., 2008). Similarly, biodiesel has better lubri-
cating properties than other diesel fuels. Thus, the addition of biodiesel to vari-
ous blends of petrodiesel fuels reduces engine wear, increases the life of the fuel
injection systems, and effectively cleans the engine combustion chamber of carbon
deposits, helping to maintain efficiency.
On the other hand, while biofuels are generally considered to improve emissions
and engine efficiency, biodiesel still produces local air pollution, including nitro-
gen oxides, the principal cause of smog. Since biodiesel is an effective solvent and
cleans residues deposited by fossil diesel, engine filters may need to be replaced
more often, as the biofuel dissolves old deposits in the fuel tank and pipes. Like-
wise, while older furnaces can burn biodiesel without any required conversion, the
biodiesel may cause problems because rubber parts are adversely affected by the
solvent properties of this fuel.
Perhaps the most profound problem with biodiesel is that worldwide production
of vegetable oil and animal fat is not yet of sufficient magnitude to replace liquid
fossil fuel use. As described in Section 9.3, some people object to the vast amount
of farming required for such crop-based biofuels and the resulting fertilization, pes-
ticide use, and land use conversion that would be needed to produce the additional
vegetable oil. Transitioning fully to biodiesel would require immense tracts of land
if traditional food crops (such as rapeseed (canola) or soybean) are used. The prob-
lem would be especially severe for nations with large economies, where energy con-
sumption is proportional to economic output. If using only traditional food plants,
most of such nations do not have sufficient arable land to produce biofuel for the
nation’s vehicles. Nations with smaller economies (hence, less energy consumption)
and more arable land may be in better situations. However, many regions cannot
afford to divert agricultural land away from food production.
In some regions of the world, a combination of increasing demand for food,
and increasing demand for biofuel, is causing deforestation and threats to biodiver-
sity. The best reported example of this is the expansion of oil palm plantations in
Malaysia and Indonesia, where rainforest is being destroyed at alarming rates to
establish new oil palm plantations to keep up with growing biodiesel demand in
Europe and other markets. It is an important fact that 90% of the palm oil pro-
duced in Malaysia is also used by the food industry in a wide variety of food
products; therefore, biofuels cannot be held solely responsible for this deforesta-
tion. Palm oil is also used in the manufacture of detergents and in electricity and
heat generation both in Asia and around the world. So, there is a pressing need
for sustainable palm oil production for both the food and fuel industries. Fortu-
nately, many organizations, such as the Roundtable on Sustainable Biofuels, are
working to define criteria, standards, and processes to promote sustainably produced
biofuels.
Many biodiesel advocates suggest that waste vegetable oil and animal fats are
the best sources of oil to produce biodiesel, but since the available supply of these
oils is drastically less than the amount of petroleum-based fuel that is burned for
transportation and home heating in the world, this local solution can only account
for a very small percentage of petrodiesel usage. It is likely that biodiesel sources
that make use of marginal lands (where food crops cannot be grown) would make
much more sense as a solution to land use issues (e.g., palm oil nuts grown along
roads or Jatrophagrown along rail lines, see Section 9.4.3.2).
9.4.4 Biogas
Unlike natural gas derived from fossil fuels, biogas is a renewable “natural gas” that
is produced from organic/biological materials as they decay. There are two primary
types of biogas. The most common biogas is produced by anaerobic digestion or
fermentation of organic/biological materials such as manure or sewage, municipal
waste, and energy crops through the action of anaerobic bacteria. The resulting bio-
gas is comprised primarily of methane (also called biomethane) and carbon dioxide.
Methane bacteria are responsible for such biological sources of methane, including
symbiotic relationships within other life forms such as termites, ruminants, and cul-
tivated crops. Another type of biogas is wood gas (also called synthesis gas), created
by the gasification of wood, wood chips, or other carbon-rich biomass. This type of
biogas requires a gasifier or wood gas generator. This biogas is comprised primarily
of nitrogen, hydrogen, and carbon monoxide, with trace amounts of methane. These
gasses can be combusted with oxygen present in the atmosphere to release energy,
thus allowing wood gas to be used as a fuel.
Both types of biogas can be utilized for cooking, space heating, and water heat-
ing. They can also be utilized in modern waste management facilities to run heat
engines that generate either mechanical or electrical power (Fig. 9.5). If compressed,
they can replace compressed natural gas for use in vehicles, where they can fuel
internal combustion engines or fuel cells. Biogas can be produced easily and cost-
effectively from current waste streams, such as paper production, sugar production,
sewage, and animal waste. It is most commonly produced using agricultural waste,
such as plants and manure. The gas can also be produced by separating organic
materials from waste that otherwise goes to landfills. Using materials that would
otherwise generate no income, or even cost money to dispose of, improves the prof-
itability and energy balance of biogas production. Similarly, the solid by-product
or digestate derived from the biogas process can typically be used as a biofuel or
LIGHT
PHOTOSYNTHESIS
CO2
O2
VEGETABLE
BIOMASS
H2O
ANIMAL MANURE
FERTILISER
BIOGAS
ORGANIC WASTES
ANAEROBIC DIGESTION ELECTRICITY AND HEAT
Fig. 9.5 A schematic of biogas formation. From www.makinemekanik.com

natural fertilizer. It is important to point out; however, that both carbon monoxide
and methane are potent greenhouse gasses. Methane in particular is 21 times more
reactive as a greenhouse gas than carbon dioxide (CO2 ), and it is normally released
into the atmosphere at most waste treatment facilities and landfills. Modern methods
of biogas production have the advantage of keeping such gasses contained, avoid-
ing potential environmental issues. Thus, biogas is considered to be one of the most
climate-friendly sources of fuel.
9.4.4.1 History of the Use of Biogas

Some types of biogas, such as that derived from manure, have been used as a low-
cost fuel for heating and cooking for hundreds of years. Anecdotal evidence indi-
cates that biogas was used for heating bath water in Assyria during the tenth century
BCE and in Persia during the sixteenth century CE. Some ancient Chinese litera-
ture also suggests that biogas was generated from sewage 2,000 to 3,000 years ago.
However, Jan Baptita Van Helmont, in the seventeenth century, was credited as the
first to determine that flammable gases could evolve from decaying organic matter.
Likewise, Count Alessandro Volta concluded in 1776 that there was a direct corre-
lation between the amount of decaying organic matter and the amount of flammable
gas produced. In 1808, Sir Humphrey Davy determined that methane was present in
the gases produced during the anaerobic decomposition of cattle manure.
It was not until the mid-1800s that the first biogas digesters were built. India has
a quite long history of biogas development. The first unit usually referred to in lit-
erature is a biogas unit at the Mantunga Homeless Lepers Asylum near Mumbai in
1859. However, methane was first recognized as having practical and commercial
value in England, where a specially designed septic tank was first used to gener-
ate gas for the purpose of lighting in the 1890s (Cheremisinoff et al., 1980). One
other important development came from the development of microbiology as a sci-
ence. This led to research by Buswell and others in the 1930s to identify anaero-
bic methane bacteria and the conditions that promote methane production by these
organisms. Once the process became fairly well understood, the stage was set for
the expansion of the use of biogas around the world. Such trends continue to this
day, where India remains one of the biggest investors in biogas, making use of small
biogas digester units installed in millions of homes.
9.4.4.2 Biogas Derived from Biodigesters

In India, biogas produced from the anaerobic digestion of manure in small-scale
digestion facilities is called gober gas. This biogas is predominantly composed of
methane and carbon dioxide. It is generated in more than 2 million household facili-
ties. A typical gober gas digester consists of an airtight circular pit made of concrete
with a pipe connection. The manure is directed to the pit, usually directly from a
cattle shed, and the pit is then filled with a required quantity of wastewater. In this
milieu, anaerobic bacteria create an oxygen-free environment in which they effi-
ciently degrade the organic material and generate gas. The gas pipe can then be
connected to a kitchen fireplace through control valves, and the flammable methane
gas generated out of this apparatus is largely odorless and smokeless. The residue
left after the extraction of the gas is commonly used as fertilizer for crop plants.
Owing to its simplicity in implementation and use of cheap raw materials in the
villages, it is often quoted as one of the most environmentally sound energy sources
for rural needs.
Similar biogas digesters are now used extensively in rural regions around the
world, including China, Costa Rica, Nepal, and Vietnam. The Government of
Pakistan provides 50% of funds needed for the construction of moveable gas cham-
ber biogas plants. Farmers around the world are making use of such small-scale
units to convert plant and animal wastes into a useful combustible gas like methane.
In Colombia, experiments with diesel engine generators partially fuelled by bio-
gas demonstrate that biogas can reduce electricity costs by 40% as compared with
purchase from regional utilities.
Although based on the same principles as employed in the simple digesters
above, larger municipal plants generate biogas in more advanced anaerobic digesters
that recover the recyclable elements of household waste, sewage sludge, food
wastes, farm wastes, or energy crops (such as maize silage) and process the
biodegradable fraction in the anaerobic digesters. The methane contained in the
resulting biogas can be concentrated to the same quality standards as fossil natu-
ral gas (typically called biomethane). If the local gas utility network grants permis-
sion, the producer of the biogas may then be able to utilize the local gas distri-
bution networks to deliver the gas to consumers. Such biomethane, however, must
be very clean and be of the correct composition to reach pipeline standards. Car-
bon dioxide, water, hydrogen sulfide, and particulates must therefore be removed
if present. Biomethane can also be concentrated and compressed for use in vehicle
transportation. Compressed biogas is becoming widely used in Sweden, Switzer-
land, and Germany as a renewable fuel source.
Sweden is cited as a particularly good example of a global leader in converting
biowaste (largely agricultural material and residues) into usable biomethane. Facing
oil shortages, waste management problems, and lacking any natural gas reserves of
its own, Sweden was motivated to develop its biomethane industry under the Kyoto
Accords. The resulting biogas is now used to generate electricity, residential heating,
and transportation fuel. According to the Swedish Gas Association, more than 50%
of the methane used to power Sweden’s natural gas vehicles now comes from bio-
logical sources. More than 8,000 vehicles in Sweden are powered by a combination
of natural gas and biomethane. The vehicles include transit buses, refuse trucks, and
more than 10 different models of passenger cars. There are more than 25 biomethane
production facilities in Sweden and 65 filling stations. A biogas-powered train has
even been in service since 2005.
9.4.4.3 Biogas Derived from Landfills

Biogas is also produced in landfills from organic waste decomposing under anaero-
bic conditions. When a clay cap is placed atop the compacted waste materials within
the landfill, this prevents oxygen from penetrating the waste. As a consequence,
anaerobic microorganisms like methane bacteria thrive under such conditions. One
problem with such clay-capped landfills is that the resulting biogas builds up and is
slowly released into the atmosphere. This gas contains a large portion of methane,
which is 21 times more potent as a greenhouse gas as carbon dioxide. Therefore,
uncontained landfill gas which escapes into the atmosphere may significantly con-
tribute to the effects of global warming. In addition, volatile organic compounds
(VOCs) contained within landfill gas contribute to the formation of unhealthy pho-
tochemical smog. However, if engineered properly, landfill sites can be made to
capture such gases via pipes inserted into the clay cap that deliver the gases to gas
clean-up and combustion facilities.
The European Union presently has some of the strictest legislation regarding
waste management at landfill sites called the Landfill Directive. The United States
legislates against landfill gas as it contains these VOCs. The US Clean Air Act
and Title 40 of the Code of Federal Regulations (CFR) require landfill owners to
estimate the quantity of non-methane organic compounds (NMOCs) emitted. If the
estimated NMOC emissions exceeds 50 t/year, the landfill owner is required to col-
lect the landfill gas and treat it to remove the NMOCs, which is usually done though
combustion.
The composition of biogas varies depending upon the origin of the anaerobic
digestion process. There are literally thousands of different types of anaerobic bac-
teria living in landfills. Their differing interactions, types of available waste, and
resulting products generate different amounts of usable gas. Landfill gas typically
has methane concentrations around 50%; however, advanced waste treatment tech-
nologies can produce biogas with 55–75% methane. This gas can be used to heat
on-site buildings or to power engines for the generation of electricity, which can,
in turn, be sold back to electricity utility companies for renewable energy sub-
sidies. However, because of the remoteness of landfill sites, it is sometimes not
economically feasible to produce electricity from this biogas. Still, it is estimated
that a 3 MW landfill power plant can power 1,900 homes and at the same time
prevent 6,000 t/year of methane from entering the environment. This is equiva-
lent to eliminating 18,000 t/year of CO2 derived from fossil fuel use or removing
25,000 cars from the road, planting 36,000 acres (146 km2 ) of forest, or not using
305,000 barrels (48,500 m3 ) of oil/year.
9.4.4.4 Wood Gas Derived from Carbon-Rich Biomass

Wood gas (or synthesis gas) is another form of biogas produced by thermal gasifi-
cation of woody biomass or other carbon-rich materials in a gasifier or wood gas
generator. Usable materials include wood chips, sawdust, charcoal, coal, rubber, or
similar materials which are burned incompletely in a fire box that produces wood
gas, tars, solid ash, and soot. The latter three by-products have to be removed peri-
odically from the gasifier. In this case, the wood gas is filtered from tars and soot/ash
particles, then cooled and directed to an engine or fuel cell to produce mechanical
or electrical power. The gas is the result of two high-temperature reactions (above
700◦ C or 1,292◦ F): an exothermic reaction, where carbon burns to CO2 ; and an
endothermic reaction, where carbon reacts with steam to produce carbon monoxide
(CO), hydrogen (H2 ), and carbon dioxide (CO2 ). Wood gas is flammable mainly
because of the carbon monoxide and hydrogen content, but it also contains nitrogen
and small amounts of methane, which is also flammable (Ahring and Westermann,
2007).
The first wood gasifier was apparently built by Bischof in 1839, and as a result,
gasification became an important and familiar nineteenth and early twentieth cen-
tury technology. “Town gas,” produced by centralized gasifiers, was once quite pop-
ular and used primarily for lighting purposes. By the time World War II arrived in
United States, large numbers of such generators were constructed and commercial
generators were in production both before and after the war. The applicability of
wood gas to the internal combustion engine was well understood from its earliest
days of development, and the first vehicle powered by wood gas was built by Parker
in 1901. Internal combustion engines were initially fueled by town gas during the
nineteenth century; however, wood and wood chips can also be used to power cars
with ordinary internal combustion engines if a wood gasifier is attached. This was
actually quite popular during World War II in several European and Asian countries
because the war prevented easy and cost-effective access to oil. Many of these early
gas generators had the problem of generating soot and tar, which would in turn clog
the engines if not first removed from the gas. This problem has only recently been
solved through the use of modern heat-resistant filters that can separate practically
all the particles, allowing easy disposal of clean, dry ash.
Modern gasifiers, especially those used to power gas turbines or fuel cells for
the production of electricity, are quite efficient. The gasification process in modern
designs is usually preceded by pyrolysis, where the biomass or coal is initially con-
verted to char, releasing methane (CH4 ) and tar rich in polycyclic aromatic hydro-
carbons (PAH). This pyrolyzed char is then fed into another gasifier to generate
the gasses described above. Such staged gasifiers, where pyrolysis and gasification
occur separately, can also be engineered to produce essentially tar-free gas (less than
1 mg·m−3 ), while single reactor fluid-bed gasifiers may exceed 50,000 mg·m−3 tar.
Contrary to general belief, exhaust gas emission levels of internal combustion
engines are significantly lower for wood gas than for gasoline. The efficiency rate
of the gasifier system is relatively high: it converts about 75% of fuel energy content
into combustible gas that can be used directly as fuel for the engine. Based on long-
term studies, comparing otherwise unmodified vehicles during real transportation
and under similar driving conditions, the energy consumption for wood gas has
been determined to be 1.54 times greater as compared to the energy demand of the
same car powered by gasoline (not including the energy needed to extract, transport,
and refine the oil from which gasoline is derived).
The primary disadvantages of wood gas generators are their typically large size
and relatively slow starting speeds. In addition, while the carbon monoxide is an
intentional fuel-product that is subsequently burned to safer carbon dioxide in the
engine, it is poisonous to humans, even in small to moderate concentrations. How-
ever, if the system is well maintained, the chance of exposure to CO is extremely
low. Wood gas generators have several key advantages over other sources of fuel.
They are relatively easy and inexpensive to build and can be used directly to run
internal combustion engines using wood and other forms of carbon-rich biomass.
This can reduce dependency on fossil natural gas, gasoline, and oil. Such generators
have a closed carbon cycle. This means that the carbon released from the gener-
ator, in the form of CO2 , is absorbed by plants that via photosynthesis convert it
to biomass. Gasifiers are also far cleaner burning than equivalent burning processes,
such as a wood fire or even a gasoline-powered engine (without emissions controls).
In more recent times, wood gas has been suggested as a clean, cheap, and effi-
cient method to heat and cook in developing countries or even to produce electricity
when used in internal combustion engines, gas turbines, or fuel cells for maximal
efficiency. Gasifiers have been built for remote Asian communities using rice hulls,
which in many cases has no other use except for being utilized as a strengthener
type additive in concrete. One installation in Burma uses an 80 kW modified diesel
engine to supply power for about 500 people who are otherwise without power. The
ash is also used as an efficient fertilizer.
So, in summary, it is clear that wood gas generators represent a promising tech-
nology based on its utilization of renewable biomass. Once improvements in this
technology result in improved efficiency, their uses are expected to expand greatly.
9.4.4.5 Future Perspectives for Biogas

Whatever its source, biogas presents us with viable renewable energy opportuni-
ties for the following reasons: Anaerobic digesters allow us to sequester a poten-
tially dangerous and environmentally unfriendly waste (biomethane) by using it as
major biofuel. Of all the greenhouse gas emissions, biomethane is 21 times more
harmful to the atmosphere than carbon dioxide. It is generated during natural pro-
cesses of decay; so it is essentially free. Biogas is closer to carbon-neutral than any
other source of fuel, making it a near perfect fuel. As biogas technologies such as
anaerobic digesters and biomass gasification development increases and becomes
more common, one of the fundamental questions is, what is the size of the potential
biomass resource supply in the United States?
In April 2005, the US Department of Energy (DOE) and the US Department
of Agriculture (USDA) co-published a report assessing the potential of the land
resources in the United States for producing sustainable biomass entitled, “Biomass
as Feedstock for a Bioenergy and Bioproducts Industry: The Technical Feasibility of
a Billion-Ton Annual Supply.” Looking at forest land and agricultural land, the two
largest potential biomass sources, this study estimated that the United States can sus-
tainably produce up to 1.3 billion tons of biomass feedstock by mid-century (2050).
This would be enough feedstock to produce 60 billion gallons of B100 biodiesel and
E100 ethanol with existing technologies. This is an impressive number. However,
the study does not address the opportunities for biogas production from biomass
feedstock or biomass gasification technologies. Some recent estimates indicate that
biogas could replace up to 50% of present natural gas consumption in the United
States. In some countries, such as Iceland, biogas already provides 100% of the
natural gas resources. Sweden currently obtains 51% of its methane from biogas,
and Switzerland, 37%. Countries such as France, Norway, Germany, and Austria
use smaller amounts for vehicles. China, India, Korea, the Ukraine, Spain, and Italy
are other examples of countries now initiating projects where biogas will be used as
a vehicle fuel.
When viewed in a broader perspective, biogas has an outstanding potential
to help solve current environmental problems, including urban and agricultural
waste management, water purification, and the need for cleaner air. By converting
biomass waste, such as municipal solid waste, sewage sludge, crop residues, energy
crops, and manure, into biogas, governments can address energy and environmen-
tal problems in a sustainable manner (Ahring and Westermann, 2007). However,
most governments, including the United States, are perhaps too focused on liquid
fuels to support the development of a biogas infrastructure. It is very unlikely that
any one technology will come close to solving global energy needs. A combina-
tion of all technologies will therefore be required to address such problems, and
the development of new technologies will clearly play an important role in this
approach.
9.5 Future Technologies in Biofuels: Algae for Energy

The idea of using algae as a source of fuel is not new, but it is now becoming a
promising technology because of the escalating price of petroleum and, more sig-
nificantly, the emerging concern that burning fossil fuels is contributing to global
warming (Chisti, 2007; Briggs, 2004). Like plant tissues, algae can provide several
different types of renewable biofuels. These include methane produced by anaerobic
digestion of the algal biomass; bioethanol fermented from algal cell walls; biodiesel
derived from algal oil; and photobiologically produced biohydrogen. Unlike other
plant energy crops, algae species can grow extremely rapidly and many are exceed-
ingly rich in oil. Microalgae (single-celled algae) commonly double their biomass
within 24 h, and biomass doubling times during exponential growth are commonly
as short as 3.5 h. Thus, algae can develop huge amounts of biomass usable as start-
ing material for both bioethanol and biogas production. An added benefit here is
that algae do not produce lignin (Table 9.1); however, the amount of cellulose and
hemicellulose is relatively low compared to other plants.
It is not yet feasible to collect algal biomass from natural sources. However, the
US Department of Energy’s Aquatic Species Program has experimented with “race-
way ponds” for the cultivation of algae. These artificial, shallow ponds are divided
into a rectangular grid, with each rectangle containing one channel in the shape of an
oval, like an automotive raceway circuit. Each rectangle contains a paddle wheel to
make the water flow continuously around the circuit. Under such conditions, nutri-
ents can be delivered to algae crops, and biomass doubling rates can be optimized.
Another promising technology for algae growth involves photobioreactors.
Unlike open raceways, photobioreactors permit essentially single-species culture of
algae for prolonged durations, and they have been successfully used for producing
large quantities of microalgal biomass. A tubular photobioreactor consists of an
array of straight transparent tubes that are usually made of plastic or glass. This
tubular array, or the solar collector, is where algal broth is circulated from a reser-
voir and where sunlight is captured. Such reactors can be constructed in areas that
are not suitable for plant growth (such as deserts), and they hold great promise for
the large-scale production of algae oil and biohydrogen.
9.5.1 Biodiesel and Biopetroleum from Algae
Oil content in some algae species can exceed 80% by weight of dry biomass. Since
many common algae (e.g., Chlorella vulgaris) have a natural oil content greater
than 50%, they have a high potential to be low-input, high-yield feedstocks useable
for biofuel production (Chisti, 2007). Oil-based algae fuel, also called oilgae or
sometimes third generation biofuel, is a biofuel derived from oil content of algal
biomass. A self-published article by Michael Briggs, at the UNH Biodiesel Group,
offers estimates for the realistic replacement of all vehicular fuel with biodiesel by
utilizing algae, which Briggs suggests can be grown on algae ponds at wastewater
and sewage treatment plants. These oil-rich algae can then be extracted from the
system and processed into biodiesel, with the dried remainder further reprocessed
to create ethanol.
Algae fuel yields have not yet been accurately determined; however, the US
Department of Energy is reported as saying that algae yield 30 times more energy
per acre than land crops such as soybeans. The DOE estimates that if algae fuel
replaced all of the petroleum fuel in the United States, it would require only 15,000
square miles (38,849 square km), which is roughly the size of Maryland. These esti-
mates are very promising; however, algal oil is difficult to extract, and more research
needs to focus on the development of efficient extraction protocols.
Many companies are pursuing algae bioreactors for various purposes, including
high-yield oil production that can scale biodiesel production up to commercial lev-
els. Alternative fuel companies such as Solazyme (South San Francisco, CA) and
Solix Biofuels (Fort Collins, CO) are using algae to produce biodiesel (Fig. 9.6).
While the cultivation of algae to harvest oil for biodiesel has not yet been undertaken
on a commercial scale, one of the most appealing aspects of alga-culture is that –
unlike crop-based biofuels – it does not entail a decrease in food production, since
it requires neither farmland nor fresh water. Unfortunately, like ethanol, biodiesel
(including that extracted from algae) attracts water and thus cannot be shipped in
existing pipelines. Both ethanol and biodiesel also have lower energy density than
traditional gasoline and diesel fuels.
Some companies, such as Sapphire Energy (formally launched in May of 2007)
have developed molecular platforms that converts sunlight and CO2 into renewable,
carbon-neutral alternatives to conventional fossil fuels without the numerous down-
sides of current biofuel efforts. The end product is not ethanol – and not biodiesel.
The end product is “green crude,” which is chemically identical to molecules in
Fig. 9.6 Colorado’s Solix Biofuels tackles the difficult task of harvesting algae for oil with a field
of bioreactors that take a kind of painter’s drop cloth (inset) to bubble CO through its system.
From Popular Mechanics online article “Pond-Powered Biofuels: Turning Algae into America’s
New Energy” 2007 (http://www.popularmechanics.com/science/earth/4213775.html)
crude oil, making the products entirely compatible with the current energy infras-
tructure. Such green crude is said to have the same energy density as gasoline and
can be shipped in existing pipelines and refined the same way gasoline and diesel
are. Such technologies are at the forefront of an entirely new industry with the poten-
tial to profoundly change America’s energy and petrochemical landscape. However,
the use of such technology will be dependent on the enactment of government poli-
cies that pressure oil companies to turn their attention away from foreign oil.
9.5.2 Biohydrogen
Hydrogen is regarded as the fuel of the future, being easy to handle and extremely
clean burning. The efficiency of conversion of hydrogen to useable energy is espe-
cially high in fuel cells for the production of electricity, with water being the sole
end product. Presently, hydrogen is produced from fossil reserves with the con-
comitant release of anthropogenic carbon dioxide. Therefore, new hydrogen pro-
duction technologies, making use of renewable resources such as the production
of biohydrogen from biomass through the action of microorganisms, are being
pursued.
In 1939, a German researcher named Hans Gaffron, while working at the
University of Chicago, observed that the algae he was studying, Chlamydomonas
reinhardtii (a green alga), would sometimes switch from the normal production of
oxygen to the production of hydrogen. Gaffron never discovered the cause for this
change and for many years other scientists failed in their attempts at its discovery.
However, in the late 1990s professor Anastasios Melis, a researcher at the University
of California at Berkeley, discovered that if the algae culture medium is deprived
of sulfur it will switch from the production of oxygen (normal photosynthesis) to
the production of hydrogen. He found that the enzyme responsible for this reac-
tion is hydrogenase, but that the hydrogenase is not functional in the presence of
oxygen.
As a result of these findings, photobioreactors, harboring various algae species,
are currently being used for biological hydrogen production (Rupprecht et al., 2006).
Initially, the yields were not very high; however in 2006, researchers from the
University of Bielefeld and the University of Queensland used genetic modifica-
tions to changed C. reinhardtii in such a way that it produces an especially large
amount of hydrogen, producing five times the volume made by the wild form of the
algae with up to 2.0% energy efficiency. Later in 2007 while studying mutants of
C. reinhardtii, Anastasios Melis achieved 15% energy efficiency, demonstrating that
truncated chlorophyll antenna size would minimize wasteful dissipation of sunlight
by individual cells. Such results hold great promise for alternative fuels, but other
areas of research need to be address, including the development of oxygen-tolerant
hydrogenases and increasing hydrogen production rates through improved electron
transfer.
Biohydrogen can and is also produced in bioreactors that utilize feedstocks other
than algae, the most common feedstock being waste streams. The hydrogen is
produced by bacterial species such as Rhodobacter sphaeroides and Enterobacter
cloacae through dark fermentation either by mixed cultures of hydrogen-producing
sludge or pure cultures of anaerobic bacteria, such as Clostridium butyricum. This
process involves allowing the bacteria to feed on hydrocarbons under anoxic condi-
tions so that they release hydrogen and CO2 . Under natural conditions, this hydro-
gen is usually consumed as soon as it is being produced by methanogenic bacteria,
releasing methane as the end product. However, under bioreactor conditions, the
CO2 can be sequestered successfully by several methods, and the methanogens can
be omitted from the system, allowing hydrogen gas to be captured. A prototype
hydrogen bioreactor using waste as a feedstock is in operation at Welch’s grape
juice factory in North East, Pennsylvania.
By uncoupling methane production from hydrogen production, more hydrogen
can be harvested. In such systems, hydrogen and acetic acid are first produced from
biomass by thermophilic bacteria. Then in a second stage, the acetic acid in the
effluent is converted to hydrogen by purple non-sulfur bacteria (Zheng et al., 2008).
Biohydrogen can also be produced from glucose in upflow biofilm reactors with
plastic carriers under extreme thermophilic conditions (>70◦ C). Biological hydro-
gen production derived from these systems is also promising but needs to address
the following issues: (1) conversion of biomass from an energy crop or an organic
waste stream to fermentable feedstock; (2) selection of thermophilic and/or photo-
heterotrophic microorganisms and design of optimal growth and production condi-
tions; (3) design of an integrated bioprocess; and (4) development of recovery and
purification methods for upgrading the gas to fuel cell specifications.
9.6 How Can Plant Biotechnology Contribute to Bioenergy?

Technology tends to change in cycles that last approximately 50 years. The Russian
economist Nikolai Kondratiev (1892–1938) was the first to bring this observation
international attention in his book The Major Economic Cycles (1925), and others
have expanded upon his observations (Fig. 9.7). Starting with the industrial age,
when the expansion of steam power changed the world, this source of power
(fueled by biomass) led to the era of the railroads. Railroads in turn promoted the
development of petrochemicals (including coal and oil), which gave ample energy
required to develop information technology. Currently, the information age is in
full swing, and without this technology, modern biology and biotechnology would
not be possible. Computers play an essential role in the generation and analysis of
the gene sequences used in most modern biotechnological applications. With the
invention of new processes for large-scale gene sequencing (e.g., pyrosequencing
approaches) and even faster computer technology, it appears that we have only
scratched the surface of the potential held within a new biological age. This
new age will likely be driven by the human need for food and energy, and plant
biotechnology will play an essential role in meeting these human needs while
finding ways to address land and water usage issues and potential environmental
problems including global carbon balance.
The use of biotechnology for improving plant-derived materials for bioenergy
production can be achieved at different levels. At the front end of potential improve-
ments are improvements to the plant feedstocks themselves. High-energy yield can
Fig. 9.7 Progressive cycles of technology: 1780–2080 CE based on the work of Nikolai Dim-
itriyevitch Kontratyev (CE refers to “common era” that replaces “AD”)
be realized through plant breeding programs designed to identify genetic markers

for beneficial traits and to enhance these traits in existing energy crops, especially
sugarcane, sorghum, switchgrass, and non-traditional oil crops having especially
high levels of oil (e.g., Camelina, mustard, and Jatropha). Genetic modification of
biosynthetic pathways (metabolic engineering) and the application of biotechnol-
ogy will likely play the biggest role because of the promise of significant and rapid
improvements. Plants will very likely be manipulated to create greater yields of
oils and biomass; show greater resistance to abiotic and biotic stresses; require less
water and grow in harsher environments; and reduce associated costs of growth and
processing. Some such modifications have already been accomplished, such as the
reduction of lignin biosynthesis, allowing easier extraction of cellulose and hemicel-
lulose polymers in preparation for processing (see Section 9.4.2.4) or altering plant
oil profiles so that specific types of plant oils are produced.
Improvements in bioenergy can also be achieved at the level of processing plant
materials. This can include (1) improvements to extraction and pretreatment stages
of plant oil and ethanol production; (2) improvements to chemical and enzymatic
processes used to extract stored energy (including mass production of tailor-made
cellulase enzymes that are more efficient or by genetically engineering plants and
fungi to produce desired cellulase, xylanase, and/or other hydrolase enzymes that
can help degrade plant polymers); or (3) improvements to the efficiency of collect-
ing and transporting the plant oil tissues or cellulosic biomass to the biofuel refinery.
Efforts are also being directed toward improving the efficiency of the biosynthetic
pathways of the microorganisms (yeast and bacteria) that perform ethanol fermen-
tation or ABE fermentation (see Section 9.4.2.4), as well as methanogen processes
that generate biogas.
Improvements can also be made at the tail end of bioenergy production. This may
include improvements to distillation efficiency by engineering microorganisms to be
more resistant to bioalcohol (allowing higher concentrations of ethanol or butanol)
or by simply improving the ability of the biofuels to be used in existing networks of
pipes for delivery to the consumer (see Section 9.5.1). The point here is that there is
room for biological improvement at virtually every stage of bioenergy production.
Almost all of these improvements, however, are dependent on an in-depth under-
standing of the biological processes and biosynthetic pathways that control each of
these stages.
Sorghum (Sorghum spp.), which is related to corn and sugarcane, provides a
good example because it has a number of characteristics that make it an attractive
biomass crop for ethanol production. Sorghum requires little water and little fer-
tilizer compared to traditional bioenergy crops. It is tolerant to heat and drought,
has high biomass yield, and bioalcohol can be produced from sugars stored in the
stems, starch from the grain as well as the lignocellulose from the leftover stalks.
Two traits of particular interest are the “sweet sorghum trait,” which results in the
accumulation of fermentable sugars in the juice of the stems (similar to sugarcane),
and the “brown midrib trait,” which changes the chemical composition (and hence
color) of the vascular tissue resulting in higher yields of fermentable sugars obtained
after enzymatic processing of the lignocellulosic biomass. The genetic basis of these
traits, however, is poorly understood and impedes the full exploitation of sorghum
for bioenergy production.
Consequently, research is being directed toward identification of regions of the
genome (through quantitative trait loci [QTL] and genomics) that contain genes
associated with the sweet sorghum trait and other traits of interest for bioenergy
production. In addition, identification of the genes that are responsible for the accu-
mulation of sugars in the stem (through genetic mapping, cloning, and elucidation
of biochemical functions) will aid in the understanding of the brown midrib trait.
Without an understanding of the biochemical and molecular mechanisms behind
such traits, improvements to subsequent ethanol production are limited.
Perhaps the most major improvements can be made at the front end of bioenergy
production, i.e., improvement of cellulosic biomass/cell wall production in herba-
ceous grasses such as sorghum, sugarcane, and switchgrass. Likewise, improve-
ments to woody biomass may include the manipulation of wood productivity and
carbon sequestration as well as improved cellulose biosynthesis in poplar trees (Pop-
ulus species) for use as energy crops (Joshi and Mansfield, 2007). Attention to front
end production is especially important because it can benefit multiple types of bio-
fuels at the same time, including the production of solid biomass, bioalcohol and
biogas.
There are a number of traits that are especially beneficial for the biological
improvement of bioenergy. An ideal energy crop plant would have a combination
of (1) a high yield of biomass resulting from a high rate of growth and high pho-
tosynthetic capacity; (2) a higher fuel to mass ratio resulting from efficient nutrient
uptake from the soil and high levels of stored sugars or oils; (3) reduced need for
soil nutrients and soil moisture resulting from the growth of deep roots; (4) resis-
tance to pests, disease, and the extremes of cold and hot temperatures; (5) tolerance
to salt, high and low pH, and heavy metal contaminants in the soil; (6) a peren-
nial grow habit to allow collection of biomass each year without fresh planting; and
(7) the silencing of flowering to help avoid the spread of foreign genes to native
populations (Fig. 9.8). Many of these traits have already been studied in model
plant species such as Arabidopsis, rice, soybean and poplar trees, and some of the
genes that are orchestrating molecular events behind such traits have been identified
(Fig. 9.9). Therefore, the stage is already set for the use of plant biotechnology to
genetically engineer plants.
While genetic modification of algae has received little attention until just
recently, metabolic engineering will also likely have an impact on improving the
economics of biomass, oil production, and biohydrogen formation from algae
species. Molecular level engineering can be used to potentially (1) increase the pho-
tosynthetic efficiency to enable increased biomass yield and rate of production; (2)
improve temperature tolerance to reduce the expense of cooling within photobiore-
actors; (3) eliminate the light saturation phenomenon so that growth continues to
increase in response to increasing light level; (4) reduce photoinhibition that actu-
ally reduces growth rate at midday light intensities; and (5) reduce the suscepti-
bility to photooxidation that can damage the cells; and (6) increase oil content in
biomass.
High biomass: increased

growth rate, photosynthetic Rapid and
efficiency, delayed flowering cost-effective propagation
Improved composition & Stand establishment: cold

structure: higher fuel germination, cold growth
yield per ton
Disease and pest resistance Perennial: multi-year crop,

efficient nutrient use, high
fossil energy ratio
Optimized architecture:
dense planting, no lodging,
easier harvest
Deep roots: drought
tolerance, nutrient uptake,
carbon sequestration
Salt, pH and Aluminum
tolerance
Fig. 9.8 Traits of the perfect energy crop. Modified from Ceres Technologies “The Promise of
Dedicated Energy Crops” 2008
Drought tolerance Increased yield Heat tolerance
Drought recovery Nutrient utilization Root growth Cold germination Increased biomass
Shade tolerance Flowering time Stature control Salt tolerance
Fig. 9.9 Traits for which genes have been identified that offer improvements in biofuel production.
Modified from Ceres Technologies “The Promise of Dedicated Energy Crops” 2008
As far as plant oil is concerned, development of knowledge-based approaches

to generate high-yielding oil crop species is key to manipulating oil biosynthe-
sis through plant biotechnological methods (Abbadi et al., 2004; Dyer et al.,
2008). Based on our current understanding of seed oil production, improvements
can be made for increasing oil content and composition in oil crops. For exam-
ple, triacylglycerol (TAG) is the plant oil product that is chemically most simi-
lar to fossil oil and therefore has the most potential to replace petroleum-based
oil (Agarwal, 2007). Thus, manipulation of the biosynthetic pathways leading to
TAG is a useful endeavor. In addition, the study of high-yield oil crops that can
be grown on marginal lands, such as Camelina, mustard, and Jatropha, will also
be important (Table 9.2). These crops offer benefits to small-scale farmers, espe-
cially those in under-developed countries, by providing new sources of income
using land that they would otherwise not have developed. Since oil biosynthesis
pathways and genes that can be manipulated to improve oil yield and composi-
tion have been tested in model crops such as soybean and castor bean, the applica-
tion of altered oil biosynthesis can now be implement in new marginal land energy
crops.
While there are still limitations on the widespread application of plant biotech-
nology for bioenergy production, expanding information on the genes involved in
plant biosynthetic pathways, compartmentation of intermediates within plant cells,
and the genomics of bioenergy-producing plant species are helping to design new
approaches for improving yields and composition in a variety of plant species (Allen
et al., 2007). It remains to be seen if such a push can be accomplished. However,
it is clear that the world is moving in the direction of bio-based energy, focus-
ing on renewability and efficiency in energy consumption. Genetic improvements
of energy crops require knowledge of desired quality attributes; the relative eco-
nomic value of the quality parameters in relation to yield, genetic variation for
the desired traits, or for molecular breeding; knowledge of genes to suppress or
add; and knowledge of any associated negative consequences of biomass quality
manipulation. Finding the optimal direction forward in the new biological age will
Fig. 9.10 A multidisciplinary approach to improvements in bioenergy. DOE’s Bioenergy

Roadmap for Biomass. From the DOE Genome Program (http://doegenomes.org)
certainly require a multidisciplinary approach that combines and spans many differ-
ent fields of research (Fig. 9.10). Because plant bioenergy technology is still under
development, desirable plant feedstock characteristics have not yet been completely
delineated, but there is no question that plant biotechnology and modern biological
techniques (such as genomics, proteomics, metabolomics, and fluxomics) will be at
the heart of the improvements to bioenergy.
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Chapter 10
Interactions of Bioactive Plant Metabolites:
Synergism, Antagonism, and Additivity
John Boik, Ara Kirakosyan, Peter B. Kaufman, E. Mitchell Seymour,

and Kevin Spelman
Abstract Drugs are commonly used in mixtures, also called cocktails, to treat dis-
ease, particularly cancer and viral infections. Any two or more drugs, or for that
matter, two or more bioactive plant compounds, will either interact in some way
or fail to interact. If an interaction produces an effect greater than that expected
for each individual drug, the interaction is termed synergistic. If the effect is less
than expected, it is termed antagonistic. If the effect is equal to the expected effect
(i.e., there is no interaction), the interaction is termed additive (see Greco et al.,
1995; Spelman, 2007, in Cseke et al., 2006). In most therapeutic situations, the hope
is that mixtures will produce a synergistic effect, but additivity can also be useful
and should not be neglected.
Our focus in this chapter is on interactions between bioactive plant compounds
used in food and medicine. In particular, we are interested in plant compounds that
have potential therapeutic effects, but also exhibit low systemic toxicity, and thus
do not pose a high risk of producing adverse effects. Thousands of such compounds
are known to exist, and more are being discovered each year. Even a single plant
can contain dozens of bioactive compounds. With such a large pool to draw from,
there is nearly an unlimited number of ways in which compounds can be combined,
either with each other or with market-approved drugs. Clearly many opportunities
exist to find mixtures that exhibit synergism or additivity.
In the following sections we explore physical models of drug interaction, discuss
a mathematical model that can be used to assess interactions, and provide a number
of examples of plant compounds that have been shown to interact in a synergis-
tic fashion. In particular, we look at ways by which mixtures of plant compounds
may bind to proteins and affect signaling pathways, as well as ways by which plant
compounds could alter receptors indirectly by affecting the plasma membrane. The
mathematical model discussed provides an accurate method to estimate interaction
indices as well as to construct confidence intervals of the indices. An interaction
index is of little use if it is not accompanied by confidence intervals. Technical
J. Boik (B)
Department of Statistics Clark, Room S.264, Stanford University, Stanford, CA, USA

214 J. Boik et al.
aspects of the model are presented in order to provide a full description, but publi-
cally available software for the model can be used without a complete understanding
of the mathematics involved.
10.1 Introduction
We start this chapter by noting that most drugs approved for the market were not
developed with synergism in mind. The conventional regulatory process requires
that the safety and efficacy of a drug be based on the merits of the drug used alone. It
is only after market approval that assessment of synergistic interactions with other
approved drugs begins in earnest. The current guiding philosophy in drug devel-
opment is one of targeted therapy, whereby a single drug is designed to affect a
single protein target. This target could be a cell surface receptor or an intracellular
protein. The goal is to develop drugs that bind with high affinity to a target, but
have little affinity for off-target proteins. In this way, some adverse effects can be
avoided.
When developing bioactive plant compounds as drug mixtures, nutraceuticals, or
medicinal foods, an alternative philosophy is needed. The development process for
a mixture of plant bioactive compounds must necessarily be different from that for a
single-target drug. At least four primary differences between the two types of prod-
ucts stand out. First, rather than a single active constituent, there could be several or
even many dozens of active constituents in a plant extract. Indeed, a given meal rich
in plant compounds could contain hundreds of bioactive compounds, albeit in small
doses. Second, within the class of (reasonably) nontoxic plant compounds that are
the focus of this chapter, the binding affinity for known drug targets is often modest
to low. Rather than using a low dose of a single high-affinity compound, the opti-
mal clinical effect for many of these plant compounds might be seen when either a
relatively high dose of a single compound is administered or, as preferred, modest
doses of numerous compounds are given in a complex mixture that takes advantage
of additive and synergistic effects. Third, many plant compounds are promiscuous,
in that they bind with multiple targets, which may exist in different signaling path-
ways within the cell (Frantz, 2005; Aggarwal and Harikumar, 2009). Fourth, many
bioactive plant compounds, such as flavonoids and curcuminoids, are not soluble in
water, are metabolized to less-active conjugates or other products after oral adminis-
tration, or in some other way exhibit nonideal absorption, distribution, metabolism,
or excretion (ADME) characteristics. The fact that many bioactive plant compounds
bind with relatively low or modest affinity to known targets, bind with multiple tar-
gets, and/or exhibit poor pharmacokinetics rules them out as useful drugs according
to the conventional mode of thinking.
However, this does not mean that bioactive plant compounds do not and could
not play a highly useful role in health and medicine. Indeed, in spite of the fact that
most do not resemble a “silver bullet” drug, it is likely that such compounds are
responsible for much of the disease-prevention effects seen in human populations
that consume a diet rich in plant compounds (Liu, 2003). To understand how their
10 Interactions of Bioactive Plant Metabolites 215
beneficial properties can best be exploited, we must redefine, or at least expand, our
definition of a model drug.
Within the class of nontoxic bioactive plant compounds, the characteristics that
appear to limit their use in medicine also provide us with opportunities. The fact
that a plant extract or mixture of extracts may have a large number of bioactive
constituents means that there are abundant opportunities for additivity and syner-
gism. It should be emphasized that although synergistic interactions tend to receive
the most research attention, additive interactions are more common, and in large
mixtures they may play an even more important role than synergism. For example,
in a cytotoxicity study on doxorubicin and nine natural compounds against human
lung cancer cells, Boik and Newman (2008) found that synergism in smaller mix-
tures could allow a tenfold reduction in the concentration of doxorubicin needed to
produce a given effect level. Importantly, larger mixtures that exhibited less syn-
ergism (and more additivity) allowed a similar degree of reduction in doxorubicin
concentrations. In the larger mixtures, each drug was used at a lower concentration.
Additivity and synergism arise in mixtures through their ability to affect multi-
ple targets. The importance of affecting multiple targets cannot be overemphasized
when dealing with complex diseases such as cancer, chronic inflammatory diseases,
chronic viral infection, and many others. In these diseases, numerous macro home-
ostatic systems may be affected, as well as numerous intracellular and intercellular
signaling pathways. A large number of proteins can be involved, and each may be
considered as a potential target. For complex diseases, acceptance is growing in the
pharmaceutical industry for the design of mixtures or drugs capable of affecting
multiple targets (Tortora et al., 2004; Roth et al., 2004; Frantz, 2005; Zimmermann
et al., 2007).
Taking common solid tumors as an example, multiple signaling pathways can
be critically under- or overregulated (Chandran et al., 2007; Chan et al., 2008). As
tumors progress, the genetic machinery of tumor cells tends to become increasingly
unstable. When this occurs, more proteins can become involved and the tumor pop-
ulation becomes better able to adapt to drug therapy, immune attack, or other obsta-
cles to growth. It would seem unlikely that any single drug, particularly a drug that
affects a single target, would have a lasting effect on such a flexible cell population.
If the drug does not kill 100% of cells, there is a reasonable chance that the surviv-
ing cells will reestablish a population resistant not only to the applied drug but also
to other drugs. This characteristic is termed multidrug resistance. Cells may become
resistant through gene amplification and overproduction of the target protein, pro-
duction of proteins that pump the drug out of the cell, underproduction of proteins
that allow the drug to enter the cell, improved repair of drug-induced DNA damage,
production of proteins that inactivate the drug, and/or production of proteins that
serve the same function as the target protein but that are not affected by the drug.
Literally, hundreds of proteins could be involved in the progression of cancer and
developed resistance to drugs.
While plants may offer a rich source of bioactive compounds for use in mixtures,
do these compounds need to bind to their targets with high affinity in order to be
effective? Csermely et al. (2005) have proposed that in some cases, partial inhibition
216 J. Boik et al.
of multiple signaling pathways may be more efficient than complete inhibition of a

single pathway (see also Ágoston et al., 2005). This suggests that compounds that
exhibit modest binding affinity could still be useful.
Could administration of multiple compounds lead to adverse effects? Of course,
adverse effects are possible with any pharmacologic therapy. Thus, mixtures will
need to be designed carefully. But the risk of adverse effects can be minimized
through the use of relatively nontoxic compounds. In addition, keeping doses as
low as possible can reduce risks. Because of additivity and synergism in a well-
designed mixture, relatively low doses of individual compounds may still be capable
of producing a desired effect without excessive risk of toxicity.
Pharmacokinetic issues are also important when considering the medical and
health effects of plant compounds. While many otherwise interesting compounds
exhibit poor ADME characteristics, a good number of these could still be useful.
For example, the vehicle used to deliver the compounds could be altered to improve
the pharmacokinetics. In some cases, enteric-coated tablets, emulsifiers, complex-
ing agents, or lipid-based formulations might be useful. In addition to manipula-
tions based on physical pharmacy, the act of using mixtures of compounds can
in some cases affect ADME characteristics. For example, the ability of grapefruit
juice to affect drug metabolism is now well established. This is discussed more in
Chapter 14 in relation to adverse drug interactions. But beneficial effects on ADME
characteristics are also possible. For example, hypericin, thought to be one of the
active constituents of Hypericum perforatum (St. John’s wort), is nearly insoluble
in water. Jürgenliemk and Nahrstedt (2003) showed that some phenolic constituents
typical for Hypericum extracts increased the concentration of hypericin in the water
phase by up to 400-fold. Butterweck et al. (2003) showed that the oral bioavailability
of hypericin was increased if administered with hyperoside, also found in Hyper-
icum extracts. In another example, Gawande et al. (2008) found that oral adminis-
tration of a black grape extract along with (–)-epigallocatechin gallate (EGCG), a
green tea component, increased the systemic availability of EGCG in humans.
We see then that interactions in a mixture may be due to pharmacodynamic or
pharmacokinetic events (Spinella, 2002). In the former, the effects are due to two
or more drugs acting on single or multiple regulatory proteins. Such interactions
are often directly related to the binding affinity or membrane-altering ability of the
drugs. In contrast, pharmacokinetic interactions are due to influences of a compound
on another’s ADME characteristics.
10.2 Physical Models of Drug Interaction – Protein Binding

and the Plasma Membrane
As discussed above, drugs in a mixture may interact by binding to target proteins.

For convenience, we use the term drug here and in the remaining portions of this
chapter to refer to both approved drugs and bioactive plant compounds. The binding
of a drug to a protein may affect the function of that protein through a number of
mechanisms. For example, if the protein were an enzyme that binds substrate S, the
drug could bind near the active site of the enzyme, thereby sterically inhibiting the
binding of S. If the enzyme contains an allosteric binding site, distant from the active
site, the drug may bind to the allosteric site and thereby affect the conformation of
the active site and its ability to bind S. When multiple drugs affect a single protein,
the complexity of binding patterns and the mechanical alteration of protein function
will influence the type of interaction produced: additive, synergistic, or antagonistic.
If multiple proteins are involved, the complexity of the (signaling) network in which
the target proteins exist will also influence the type of interaction produced.
As a simple example, targets could be two intracellular enzymes serially con-
nected in a signaling pathway. In this case, inhibition of an enzyme by each drug
in a binary mixture might produce additive effects. In more complex cases, drugs
may affect multiple proteins in a signaling pathway that contains positive and/or
negative feedback loops or drugs may affect proteins that are involved in distinct
but connected signaling pathways. As the number of bound proteins and the com-
plexity of the signaling pathways increase, there are increasing opportunities for
antagonistic or synergistic interactions.
In addition to intracellular proteins, drugs may also bind to protein targets on the
plasma membrane. In particular, they may bind to transmembrane receptors embed-
ded in the lipid bilayer. Many signals that originate outside of the cell enter the cell
via cell surface receptors. Growth factors, such as epidermal growth factor (EGF),
are an example of an extracellular signal. Extracellular EGF binds to EGF receptors
(EGFR) on the plasma membrane, and the resulting signal is propagated into the
cell, eventually reaching the nucleus and causing proliferation.
Drugs can directly bind to receptor proteins on the plasma membrane, in some
cases stimulating signal transduction and in other cases inhibiting it. For exam-
ple, plant compounds that bind weakly with estrogenic receptors may physically
block the binding of more potent ligands, thereby producing an antiestrogenic effect.
Genistein, from soybean, is reported to act in part by this mechanism in some experi-
mental models (Kogiso et al., 2006). If multiple therapeutic compounds are used and
multiple receptor types are affected, downstream signaling pathways may interact
in additive, antagonistic, or synergistic ways.
The interaction of drugs can be influenced by the properties of the plasma mem-
brane that contains the receptors. Although the membrane has been described as a
system driven by thermodynamic equilibrium (Aon et al., 1996), it is more accu-
rately seen as an emergent structure consisting of highly asymmetrical structures
and undergoing dynamic transitions (Perillo, 2002). Typically, mammalian cellular
plasma membranes consist of about eight major classes of lipids (Simons and Vaz,
2004) and also include a variety of proteins embedded in the bilipid structure. The
plasma membrane serves a number of purposes, including protection, endocytosis,
signaling, and mechanical stability. It must be rigid enough to protect the cell and
offer stability, but at the same time, it must be dynamic and pliable enough to allow
cell deformation and promote adaptation to diverse environmental messages. Either
directly or indirectly, the characteristics of the lipid membrane affect nearly every
activity that occurs in a cell.
218 J. Boik et al.
One way that the membrane affects signaling is by supporting the dynamic cre-
ation and movement of lipid rafts (also known as membrane rafts), which are clus-
ters of proteins that horizontally “float” in the membrane. One report has identified
as many as 250 proteins that exist in lipid rafts (Patra, 2008). A good number of these
proteins, including ras (ras is a signal transduction protein that belongs to a large
superfamily of low-molecular-weight G proteins) and EGFR, are cell surface recep-
tors. Several authors have postulated or shown that receptors in a raft can cooperate
to affect each other’s conformation, thereby coordinating the overall response to a
ligand (Duke and Bray, 1999; Graham and Duke, 2005; Fuxe et al., 2008; Sourjik,
2004). For example, consider a receptor that switches probabilistically between two
conformations, active and inactive, and binding of a ligand stabilizes the active state.
Certain cellular responses, such as chemotaxis, in response to a chemoattractant, are
most useful if they are binary. For example, it might be beneficial if a cell moves
toward a weak stimulus with the same force that it moves toward a stronger stimu-
lus. This requires that as a group, the receptors act like an on/off switch. One way to
accomplish this is by allowing adjacent receptors in a raft to influence the confor-
mation, active or inactive, of one another. Above a critical but low ligand concentra-
tion, a small percentage of receptors are bound, but these cause unbound receptors
to switch to the active conformation. In a more complicated scenario, receptors may
simultaneously bind two ligands, and in this case, receptor–receptor interactions
may produce the equivalent of AND/OR logic gates. For example, if a cell senses
both poison and chemoattractant in the same location, it is beneficial if the cell does
not move toward the chemoattractant.
The switching characteristics mentioned above are dependent on receptor–
receptor interactions, which in turn are dependent upon the characteristics of lipid
rafts. The notion that membrane characteristics may influence the type of drug inter-
action (additive, antagonistic, or synergistic) begs the question of whether some
drugs may act directly on the plasma membrane itself, in addition to or in con-
trast to protein binding. Indeed, this seems to occur for a good number of drugs
and bioactive plant compounds. It is well known that hydrophobic drugs tend to
interact with biological membranes (Schreier et al., 2000). At high concentrations,
they can act like detergents and disrupt membranes, while at low concentrations,
they tend to stabilize membranes, such as protecting red blood cells from hemol-
ysis. Many bioactive plant products are also hydrophobic and can be expected to
interact with membranes. For example, some flavonoids have been shown to affect
lipid viscosity. In addition, flavonoids preferentially located in the hydrophobic por-
tion of the bilayer have been shown to initiate the formation of raft-like domains,
whereas those located in the polar interface region can fluidize membranes and have
a raft-breaking effect (Tarahovsky et al., 2008). In a study on human colon cancer
cells, the flavonoid quercetin was shown to induce the accumulation of cell death
receptors in lipid rafts and thereby facilitate apoptosis (programmed cell death) in
response to death-inducing signals (Psahoulia et al., 2007). Adachi et al. (2007)
reported that EGCG from green tea inhibited the binding of EGF to EGFR and the
subsequent activation of EGFR by altering membrane organization related to lipid
rafts. As a last example, omega-3 fatty acids (EPA, eicosapentaenoic acid, and DHA,
docosahexaenoic acid) have been shown to inhibit the proliferation of human breast
cancer cells in vitro, in part by reducing EGFR levels in lipid rafts (Schley et al.,
2007).
In summary, the type of interaction produced by a drug mixture is influenced
by the complexity of protein binding patterns, the complexity of the network in
which the bound proteins interact, the degree of receptor–receptor interactions, and
the effects of drugs on the plasma membrane, particularly on the formation and
composition of lipid rafts. In the interest of brevity, other mechanisms by which a
drug can affect cellular function have not been discussed. For example, some drugs
can bind directly to DNA molecules. Many of these drugs, however, tend to exhibit
high systemic toxicity. Drugs can also affect cellular function by acting as pro- or
antioxidants.
10.3 Quantifying Synergism Using Nonlinear

Mixed-Effects Modeling
In the following discussion on mathematical models of drug interaction, we shift

to a more technical tone. In particular, the reader is given a complete mathematical
description of the MixLow method for assessing interaction indices developed by
Boik et al. (2008). An implementation of the MixLow method is currently available
in the R language (package mixlow) and can be downloaded from the CRAN web
site (http://cran.r-project.org/). Although details of the model are presented here,
the R package can be used without a complete understanding of the mathematics
involved. For those readers who are not biostatisticians, the details given here should
provide a general insight into the many issues involved in estimating an interaction
index, and for those who do become users of the mixlow package or other software,
the details should provide useful reference material.
10.3.1 Background
Over the last few decades, several mathematical methods have been proposed to
assess synergism between drugs in a mixture.1 All of these are based on some index
of additivity (or null interaction). There has been disagreement on a strict math-
ematical definition of additivity and reviews have been published discussing the
various proposals (Berenbaum, 1989; Greco et al., 1995; Merlin, 1994; Tallarida,
2001). Two indices that have gained widespread acceptance are those for Loewe
1 Where convenient and not confusing, the continuum of antagonism/additivity/synergism is

referred to as degrees of synergism. The term method is used to refer to the combination of a
model to estimate concentration–response curve parameters, an interaction index, and a procedure
to calculate confidence intervals. The term confidence interval is used to refer to the nominal 95%
confidence interval of the Loewe index or other interaction indices.
220 J. Boik et al.
additivity and Bliss independence (Greco et al., 1992). The Loewe additivity index
forms the basis for the present work, as well as the basis for isobolograms (Poch,
1990), which are graphical assessments of additivity. In contrast to other indices,
particularly that of Bliss independence, the Loewe index produces the intuitively
reasonable result that a sham mixture, a mixture of a drug with itself, is additive.
In the MixLow method, developed by Boik et al. (2008), estimation of the Loewe
index is a three-step process: (1) estimate parameter values that define the shape of
concentration–response curves for the mixture and its component drugs; (2) use the
estimated parameters in calculating the Loewe index; and (3) generate confidence
intervals of the index.
Methods to assess synergism can be distinguished not only by the interaction
index used but also by the experimental design used to obtain data, the model used
to estimate parameters of the concentration–response curves, and the dimensions
of the resulting interaction index plot (two- or three-dimensional). Experimental
designs are usually either factorial, where concentrations of each drug are crossed
(or partially crossed) with concentrations of other drugs, or fixed-ratio, where con-
centrations of all drugs are fixed at a constant ratio. If fixed-ratio concentrations in a
two-drug mixture are graphed, where each axis represents the concentration of one
drug, then the plotted points fall on a straight line, or ray, extending out from the
origin. With the fixed-ratio design, synergism can be assessed either along one ray
or along a three-dimensional response surface based on a series of rays. The current
MixLow method assesses data from a single ray.
The factorial design is used primarily when a three-dimensional response surface
(additivity surface) is desired. An example of a factorial design is given by Martinez-
Irujo et al. (1996). Examples of response surface methods for multiray data include
those by White et al. (2003, 2004), Minto et al. (2000), and Fidler and Kern (2006).
While response surface methods do provide more information than can be obtained
from the analysis of single-ray experiments, they require that more data be collected.
For this reason, single-ray experiments remain common.
The de facto standard for assessing synergism in single-ray experiments is
the median-effect method of Chou and Talalay (1984). This method estimates
concentration–response curve parameters by using log linearization and ordinary
least squares. The method presented here, dubbed the MixLow (Mixed-effects
Loewe) method for convenient reference, is similar to the median-effect method
in that it assesses data from single-ray experiments, presents results in graphical
form (as a plot of fraction affected versus combination index; see below), and uses
the Loewe index to define additivity. Unlike the median-effect method, however, it
employs a mixed-effects model to estimate parameters of concentration–response
curves. This approach allows more accurate estimation of concentration–response
curve parameters and can also produce confidence intervals with improved cover-
age. Coverage is the probability that a confidence interval method captures the true
parameter. If the coverage differs markedly from the nominal confidence coefficient
(typically 0.95), then the confidence intervals are of questionable value. Confidence
intervals for the interaction index, as well as accurate parameter estimators, are vital
to fully assess whether drugs in a mixture interact synergistically, antagonistically,
or additively. By extension, knowledge of the coverage of these intervals is also

vital. As reported in Boik et al. (2008), in a series of simulations, the MixLow
method produced confidence intervals with excellent coverage properties.
The approach described here is applicable to the common situation where within-
unit and between-unit measurements are available, responses follow a sigmoidal
pattern,2 and ratios between drugs in a mixture are fixed (that is, various dilutions
of the mixture and its component drugs are tested). While such data could be gen-
erated in many types of experiments, the discussions here focus on data obtained
from in vitro cytotoxicity experiments, where cancer cells are exposed to a drug for
a specified length of time (typically 72 hours) and then cell viability is indirectly
measured, usually via fluorescence readings after addition of a suitable dye. Such
cytotoxicity assays use multiwell incubation trays, where each tray receives one
drug or mixture, each column of the tray typically receives a different drug concen-
tration, and replicate trays are tested for each drug and mixture. The experimental
unit in this situation is the incubation tray.
Regardless of the drugs tested and assay employed, cytotoxicity responses
occur in a nonlinear relationship with drug concentration. If a parametric model
is employed, either the relationship can be linearized prior to estimation of
concentration–response curve parameters, as is done in the median-effect method,
or parameters can be estimated using a nonlinear model, as is done in the MixLow
method. Furthermore, when using a nonlinear (or linear) model, effects can be either
fixed or random. A mixed-effects model contains both fixed and random effects.
Random effects are commonly associated with observations sharing the same level
of a classification factor. In this paper, that factor is incubation tray. Nonlinear
mixed-effects models are widely used in medicine, particularly to assess pharma-
cokinetic data. Their use is rare, however, with cytotoxicity data.
In the median-effect method, raw data must be preprocessed. This is accom-
plished by (1) scaling data by control-well means – responses are averaged across
in-tray replicates and divided by average responses of in-tray control wells – and
(2) taking the log of a function of the scaled data. Each of these steps can have detri-
mental effects on the precision of parameter estimators, and the MixLow method
does not require any preprocessing.
10.3.2 MixLow Method
Let the random variable Fa signify the fraction of cells affected by a drug concen-
tration. Define φ = E [Fa], where E [•] is the expected value. In some contexts, φ
is estimated based on concentration–response data, and in other contexts, a concen-
tration is estimated that results in a fixed value of φ. Denote by ψd,φ the φ-effective
log concentration of drug d. This is the log concentration that produces a fraction
2A sigmoidal pattern is relatively flat at high and low concentrations, with a smooth transition
linking the two. The overall shape is that of an elongated S.
222 J. Boik et al.
affected equal to a fixed φ. For example, the log concentration of drug d that inhibits
proliferation of a cell population by 10% relative to controls is denoted by ψd,0.1 . By
convention, exp (ψd,0.1 ) is referred to as the IC10 (10% inhibitory concentration).
The MixLow method fits a sigmoid curve to concentration–response data and
uses the resulting parameter estimates to estimate an interaction index. The sig-
moidal curve is parameterized by two constants, ψd,0.5 and a shape parameter
denoted by γd . The shape parameter indexes the steepnessof the concentration–
response curve. At the IC50, the slope of the curve is 0.25γd exp (ψ d,0.5 ).
The Loewe index, which is used by both the median-effect and the MixLow meth-
ods, provides a measure of drug interaction. For two drugs, the Loewe index and its
estimator3 are

2
exp (md,φ )
2
exp (m̂d,φ )
Lφ = and L̂φ = , (10.1)
d=1
exp (ψd,φ )
d=1
exp (ψ̂d,φ )
respectively, where md,φ is an unknown constant signifying the log concentration

of drug d in the mixture when the mixture is at its φ-effective log concentration
and ψd,φ is the unknown φ-effective log concentration of drug d alone. The mixture
is antagonistic, additive, or synergistic at φ depending on whether the value of the
Loewe index is greater than 1, equal to 1, or less than 1, respectively. Chou and
Talalay (1984) were apparently the first to use plots of L̂φ versus φ as a summary of
drug interactions.
10.3.3 Basic MixLow Model

For clarity of presentation, the basic MixLow model is introduced first. Later, a
modified model is discussed. The MixLow model uses a nonlinear mixed-effects
framework to represent the concentration–response curve. As a skeleton description,
responses are modeled as the expected mean of control wells times a sigmoidal
function, plus an error term. Sigmoidalmodels of this type are sometimes referred
to as Hill models. Formally, responses, Yd,t,w , obtained from unprocessed data are
modeled as a sigmoidal function of the concentration:

Yd,t,w = exp (μ + bt ) 1 − φd,t,w + εd,t,w , (10.2)
where
1
φd,t,w = 1 − , (10.3)
exp (cd,t,w ) γd
1+ exp (ψd,0.5 )
3 Throughout this discussion the hat notation is used to denote parameter estimators and estimates.
and the subscripts d, t, w refer to the dth drug, tth tray, and wth well, respectively.4
Here, drug d could refer to a single drug or a mixture, and cd,t,w refers to the log of
the drug concentration for the dth, tth, and wth observation, a known constant. The
expected value of exp (μ + bt ) refers to the expected mean of control wells from all
trays, where bt is a random deviate specific to tray t. Values {bt } are independently
distributed as bt ∼ N(0, σb2 ). The error terms in Model (10.2) are independently

distributed as εd,t,w ∼ N 0, f (σ 2 , E Yd,t,w |bt ) , where f(•) is a function discussed
later.
Differences in control-well means across trays occur for a variety of reasons. For
example, if one tray in a group of replicates is seeded with a higher density of cells,
the responses in the tray will tend to be higher than those of the other trays. Dif-
ferences can also occur because of differential handling of trays, differential growth
conditions (e.g., incubating trays on different days), differential assay procedures
(e.g., allowing one tray to incubate for a slightly longer time before reading results),
and/or random biologic variations in cell proliferation.
Having explained the model, the procedures for calculating the Loewe index and
its confidence intervals are described. An n-drug generalization of the Loewe index
in (10.1) is given by

n

n

Lφ = exp md,φ − ψd,φ = τd exp ψm,φ − ψd,φ , (10.4)
d=1 d=1
where ψd,φ is the φ-effective log concentration of drug d alone, ψm,φ is the
φ-effective log concentration of the mixture, and τd is the fraction of the mixture
that is composed of drug d. Note that md,φ = log (τd ) + ψm,φ .
If cd,t,w in (10.3) is equated to the φ-effective log concentration, ψd,φ , then φd,t,w
becomes φ. That is,
1
φ =1− . (10.5)
exp (ψd,φ ) γd
1+ exp (ψd,0.5 )
To write the Loewe index as an explicit function of ψd,φ , first solve (10.5) for
ψd,φ to obtain
1
φ γd
ψd,φ = log + ψd,0.5 . (10.6)
1−φ
Second, substitute the expression for ψd,φ in (10.6) into (10.4) to obtain
4 Thenotation (1 – φ) is used to denote the expected fraction unaffected, rather than introducing a
new symbol for the latter. The exponent term in Model (10.2) is used to ensure that the expected
response in control wells is always positive.
224 J. Boik et al.
n
L̂φ = τd exp ψ̂m,φ − ψ̂d,φ
d=1
1 1 , (10.7)

n
φ γ̂m φ γ̂d
= τd exp log 1−φ + ψ̂m,0.5 − log 1−φ − ψ̂d,0.5
d=1
which is written here as the estimator of the index, where

1
φ γ̂d
ψ̂d,φ = log + ψ̂d,0.5 . (10.8)
1−φ
Confidence intervals
of L φ can be based on the standard error of L̂φ or its log
transformation SE log (L̂φ ) . The latter approach ensures that confidence interval
limits are positive and this is the approach used here. The standard error of the
transformed index is obtained using the Delta method as follows:
⎛⎛ ⎞T ⎛ ⎞⎞ 1/2
∂ log (L̂φ ) ∂ log (L̂φ )
⎜
SE log(L̂φ ) ≈ ⎝⎝ ∂ log
∂ˆ ⎠ vâr ψ̂ ⎝ ∂ ˆ ⎠⎟
∂ log (L̂φ ) ⎠
, (10.9)
(L̂φ ) γ̂
∂ γ̂ ∂ γ̂

where the superscript T refers to transpose. The term vâr ψ̂γ̂ is obtained from the
observed information matrix, which is produced when Model (10.2) is fit by maxi-
mizing the likelihood function. The confidence interval for the Loewe index at φ is
calculated as

exp log (L̂φ ) ± tdf ,1−α/2 SE log (L̂φ ) , (10.10)
where tdf ,1−α/2 . is a multiplier obtained from the t-distribution with df degrees of
freedom and α significance level.
Within-group
errors for
cytotoxicity data tend to be heteroscedastic, with smaller
errors at low E Yd,t,w |bt values and larger errors at high ones. To allow for

this, the
error term in Model (10.2), εd,t,w , can be modeled as a function of σ and E Yd,t,w |bt .
Table 10.1 lists four error functions, e1–e4, which are useful for cytotoxicity data.
Note that all functions listed belong to a single family of functions. For example, e4
and e3 are identical when βd is equal to 1.0 for all drugs. The error functions listed
Table 10.1 Error functions

Error function Formula εd,t,w ∼ N 0,σd,t,w
2 , where σd,t,w equals
e1 σ
e2 σ αd
, where the scaling parameter αd is drug dependent
e3 σ E Yd,t,w |bt

β
e4 σ E Yd,t,w |bt d , where the power parameter βd is drug dependent
in Table 10.1 stem from straightforward application of variance options for the nlme
function in R (http://cran.r-project.org/).
10.3.4 Modified MixLow Model

The MixLow model can be modified to allow for a “double” sigmoid response pat-
tern. The extension is similar in spirit to modification of a single Hill model to a
“double” one. A double-sigmoid response pattern has been observed for a number
of drugs in various cell lines (Levasseur et al., 1998; Yeung et al., 1999). The modi-
fication to the basic MixLow model is straightforward. Model (10.2) is modified to
represent a weighted sum of two sigmoidal curves, which is as follows:

Yd,t,w = (1 − λd ) exp (μ + bt ) (1 − φd,t,w ) + λd exp (μ + bt ) (1 − φd,t,w ) + εd,t,w ,
(10.11)
where
1 1
φd,t,w =1− γ , φd,t,w = 1 − γ , (10.12)
d d
exp (cd,t,w ) exp (cd,t,w )
1+
exp (ψd,0.5 )
1+ )
exp (ψd,0.5
and 0 ≤ λd ≤ 0.5 is a drug-dependent weight.

As illustrated in Fig. 10.1, each of the component curves and their weighted
sum converge to zero as the drug concentration increases. The term φd,t,w refers to
the expected fraction
affected
for the first weighted curve; the corresponding IC50

is denoted by exp ψd,0.5 and the slope by γd . Parameters for the second curve
are
defined analogously.
The maximal expected response of the weighted sum is
E exp (μ + bt ) . The maximal

expected
responses

for the first
and second weighted
curves are (1 − λd ) E exp (μ + bt ) and λd E exp (μ + bt ) , respectively. If λd is
equal to zero, then Model (10.11) collapses to Model (10.2).
Denote the fraction affected according to Model (10.11) by φ. That is,

E Yd,t,w
1 − φd,t,w =
= (1 − λd ) (1 − φd,t,w ) + λd (1 − φd,t,w ). (10.13)
E Y0,t,w
If cd,t,w in (10.12) is equated to the φ-effective log concentration ψd,φ , then φd,t,w
becomes φ and
(1 − λd ) λd
(1 − φ) = γ + γ . (10.14)
d d
exp (ψd,φ ) exp (ψd,φ )
1+
exp (ψd,0.5 )
1+ )
exp (ψd,0.5
The solution to (10.14) for ψd,φ is the root of the polynomial

(1 − φ) exp (ψd,φ )γd +γd + a exp (ψd,φ )γd + b exp (ψd,φ )γd + c = 0, (10.15)
226 J. Boik et al.
3500
(1–λd) curve 1
3000 λd curve 2
(1–λd) curve 1 + λd curve 2

2500 E[exp(μ + bt)]
Fluorescence
2000
1500
1000
500 λd E[exp(μ + bt)]
0
10–8 10–6 10–4 10–2 100 102 104
Log concentration
Fig. 10.1 Example of double-sigmoid curve

)γd , b = (λ − φ) exp (ψ
where a = (1 − φ − λd ) exp (ψd,0.5 γd
d d,0.5 ) , and

)γd exp (ψ
c = − exp (ψd,0.5 γ
d,0.5 ) d φ. Equation (10.15) has at most one real
root because the weighted sum of curves is monotonic decreasing by con-
struction.
To obtain an estimator
of ψd,φ , namely
ψ̂d,φ , substitute estima-

tors λ̂d ,γ̂d ,γ̂d ,ψ̂d,0.5
,ψ̂
,ψ̂d,0.5
d,φ for parameters λd ,γd ,γd ,ψ d,0.5,ψd,0.5 ,ψd,φ in
(10.15) and label the root of (10.15) as ψ̂d,φ .

The estimator ψ̂d,φ is substituted into (10.4) to obtain the Loewe index as a func-
tion of φ. Although the estimator is not in closed form, the implicit function theorem
can be used to obtain derivatives for computing confidence intervals using equations
similar to (10.9) and (10.10).
In practice, drug solubility or other issues can limit the concentration at which a
drug can be tested. If the drug produces a double-sigmoid response, but high enough

concentrations were not tested to see the full curve, then ψd,0.5 is higher than the
highest concentration tested and it can appear as if the drug produces a nonzero
asymptotic response. This situation is not uncommon in practice. It presents a prob-
lem in that ψd,φ cannot be estimated for φ > 1 − max (λ̂d ). When φ is greater than
d
1 − max (λ̂d ), the data only tell us that ψ̂d,φ is not lower than the largest concen-
d

tration tested. To account for this, ψd,0.5 can be fixed at infinity and Model (10.11)
changed to

Yd,t,w = (1 − λd ) exp (μ + bt ) (1 − φd,t,w ) + λd exp (μ + bt ) + εd,t,w , (10.16)
where the Loewe index and its confidence intervals are computed only for φ <
1 − max (λ̂d ). An equation analogous to (10.15) is used to obtain an expression for
d
ψ̂d,φ .
10.3.5 Use of the MixLow Method
While the equations given above may appear complex to some readers, the use of
the MixLow method is relatively straightforward. The R package mixlow can be
downloaded from the CRAN website, and a paper describing the package and its
use has been submitted (Boik and Narasimhan, 2008). In brief, the following six
steps are performed in sequence:
1. Design the experiment, collect the data, and prepare the data file. An example
data file is included with the R package.
2. Read the data file using the function readDataFile.
3. Prepare and subset the data using the function prepareData.
4. Obtain starting values for the fixed-effects parameters of the nonlinear mixed-
effects (NLME) model by using nonlinear least squares (NLS) analysis. This is
done using the function doNls.
A
3.5
estimated Loewe index
cont. interval
reference
3.0
Estimated Loewe index
2.5
2.0
1.5
1.0
0.5
0.0
0.0 0.2 0.4 0.6 0.8 1.0
Fraction afftected
Fig. 10.2 Example of Loewe index versus fraction affected

228 J. Boik et al.
5. Use the estimated NLS parameters as starting values for the NLME model. The
mixed-effects model is estimated using the function doNlme.
6. Use the estimated NLME parameters to estimate the Loewe index. This is done
using the function doLoewe.
In summary, the process is: read data → prepare data → NLS → NLME →
Loewe. Figure 10.2 shows the Loewe index versus fraction-affected values for an
example data set. Confidence intervals of the index are shown by dotted lines. In
the figure, statistically significant synergism is occurring between fraction-affected
values of about 0.1–0.85 (the upper confidence interval is less than 1.0).
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Chapter 11
The Use of Selected Medicinal Herbs
for Chemoprevention and Treatment of Cancer,
Parkinson’s Disease, Heart Disease,
and Depression
Maureen McKenzie, Carl Li, Peter B. Kaufman, E. Mitchell Seymour,

and Ara Kirakosyan
Abstract In this chapter, we present recent advances on the use of several different
kinds of medicinal herbs to treat cancer, Parkinson’s disease (PD), heart disease,
and depression. These include recent studies on the use of Vaccinium spp. (blue-
berries and relatives) for cancer treatment and prevention; blueberries in the diet to
improve motor skills and cognitive ability in patients with PD; digitalis (foxglove)
to treat patients with heart disease; and St. John’s wort that is used to treat patients
with mild-to-moderate depression. The basic conclusion from these studies is that
rigorous, well-designed clinical trials are needed to validate the safe use of these
and other medicinal herbs for treatment of these and other diseases.
11.1 Introduction
In the last few years, medicinal plants with promise to impact human health have
undergone extensive laboratory and clinical testing. Many scientific methods of
analysis have been developed for the investigation of the constituents and bio-
logical activities of these constituents of plants. Various chromatographic, spec-
troscopic, and biological (e.g., anticancer, anti-inflammatory, immunostimulant,
antioxidant, antiprotozoal, and antimicrobial) techniques are being used for medic-
inal plant research (Cseke et al., 2006). Advances in scientific methodology have
been made that contribute to our understanding of the mechanisms of action of
herbal constituents (see Chapter 10). Examples of active constituents of different
medicinal plants and their known activities are listed in Table 11.1 and can also be
found in Duke, J.A. Phytochemical and Ethnobotanical Database; http://www.ars-
grin.gov/duke/.
Although medicinal plants have been known for thousands of years and have
been used for a variety of medicinal purposes, understanding of the activity and
M. McKenzie (B)
Denali BioTechnologies, L.L.C., 35555 Spur Highway, PMB 321, Soldotna, Alaska 99669, USA

232 M. McKenzie et al.
Table 11.1 Examples of constituents and their activities from different medicinal plants
Constituents Activity
Dianthrone derivatives: hypericin, Photodynamic, anti-depressive (MAO inhibitor),

pseudohypericin, frangula-emodin antiviral
anthranol
Phloroglucinols derivatives: hyperforin, Anti-depressant and antibacterial
secohyperforin
Flavanols: (+)-catechin (+polymers: Astringent, anti-inflammatory, styptic, antiviral,
condensed tannins), (–)-epicatechin, heart disease
proanthocyanidins
Flavonoids: hyperoside (hyperin), quercetin, Capillary-strengthening, diuretic, antidiarrheal,
isoquercetin, rutin, methyhespericin, cholagogic, dilated coronary,
iso-quercitrin, quercitrin, anti-inflammatory, arteries, sedative, tumor
I-3/II-8-biapigenin, kaempferol, myricetin inhibition, antitumor, blood glucose lowering
Anthocyanins: cyanidin, delphinidin, Antioxidants and anti-inflammatory
malvidin, pelargonidin, petunidin, and
peonidin
Isoflavones: genistein, genistin, daidzein, Antiosteoporosis, phytoestrogen, anti-
daidzin and puerarin alcoholism, anti-colon cancer
Lignans: podophyllotoxin, α- and β-peltatin Anti-cancer, antioxidants, phytoestrogen
Xanthones: xanthonolignoid compound Generally, xanthones exhibit anti-depressant,
antitubercular, choleretic, diuretic,
antimicrobial, antiviral, and cardiotonic activity
Coumarins: umbelliferone, scopoletin
Phenolic carboxylic acids: caffeic acid, Antioxidants
chlorogenic acid, genistic acid, ferulic acid
Phloroglucinol derivatives: hyperforin Anti-bacterial (Staphylococcus aureus)
Essential oil components: monoterpenes Antifungal, disinfectant, deodorant, pain reliever,
α-pinene, β-pinene, myreene, limonene counterirritant, anesthetic, expectorant, and
camphor, borneol, menthol, geraniol, and antipruritic
terpineol
Sesquiterpenes: caryophyllene, humulene
Terpens: Sesquiterpenes; farnesol, artemisinin Anti-cancer, anti-malaria
Diterpenes: examples of diterpenes are They are known to be antimicrobial and
cafestol, kahweol, cembrene, and taxadiene anti-inflammatory. The herb Sideritis contains
(precursor of taxol). Diterpenes also form diterpenes
the basis for biologically important
compounds such as retinol, retinal, and Anti-inflammatory, anti-hypertensive
phytol
Triterpenes: lanosterol, cycloartenol, and Antioxidants
soyasaponins
Tetraterpenes: Biologically important
tetraterpenes include the acyclic lycopene,
the monocyclic gamma-carotene, and the
bicyclic α- and β-carotenes
n-Alkanols: 0.42% of total dried herb: Health products including octacosanol are sold in
1-tetracosanol (9.7%), 1-hexacosanol Japan and the United States as “metabolic
(27.4%), 1-octacosanol (39.4%), stimulants” (Japanese studies show it stimulates
1-triacontanol (23.4%) feeding of silkworm larvae; studies with
neurological disorders (Parkinson’s, ALS, MS)
show mixed results)
11 Use of Selected Medicinal Herbs for Chemoprevention 233
Constituents Activity
Carotenoids: epoxyxanthophylls, lutein, Available oxygen in xanthophylls may explain

zeaxanthin, lycopene, β-carotene burn-healing activity, eye pigment protection
from blue light, prostate health, pro-vitamin A
activity
Phytosterols: β-sitosterol Anticancer, hearing loss, benign prostatic
hypertrophy, hypercholesterolemia
mechanisms of action of their bioactive constituents is relatively new and not well
understood, particularly in connection with applications for human health benefits.
11.2 Cancer
A body of now firmly established research and epidemiological evidence has shown
overwhelmingly that dietary intake of berry fruits has a positive and profound
impact on human health, performance, and disease (Seeram, 2008a). Evidence from
tissue culture, animal models, and human studies suggests that flavonoid-rich fruits,
in particular, deeply colored berries, have promise to limit the development and
severity of diseases based on inflammatory processes including atherosclerosis and
ischemic stroke, neurodegenerative diseases of aging, and certain cancers. The first
report of the anticancer properties of “anthocyan” flavonoids from fruits and veg-
etables was published over 40 years ago and cited their significance as cell respira-
tory activators for cancer prophylaxis and therapy (Seeger, 1967). Early studies also
proposed enzymatic modulatory and anti-inflammatory activities and related pro-
cesses, including inhibition of prostaglandin biosynthesis, platelet-activating factor
(PAF)-induced exocytosis, and inflammatory cyclooxygenase activities, as well as
numerous therapeutic benefits of berry “anthocyanosides” and other flavonoids in
traditional medicine and the clinic (Cluzel et al., 1970; Amouretti, 1972; Lietti et
al., 1976; Jonadet et al., 1983; Tunon et al., 1995; Middleton et al., 2000).
11.2.1 Case Study on and Cancer
The anticancer effects of berries are hypothesized to be mediated through many

mechanisms mostly associated with their flavonoid content (Seeram, 2008b).
Although berries from numerous families and included genera provide an array of
flavonoid compounds that could contribute to cancer chemoprevention and therapy,
species from the family Ericaceae, and especially the genus Vaccinium, are widely
favored for their anticancer attributes. A number of informative reviews published
in the literature cover this subject, as well as the cancer chemopreventive proper-
ties of specific Vaccinium components and metabolites (Prior and Wu, 2006; Neto,
2007a,b; Neto et al., 2008; Seeram, 2008b).
The principal Vaccinium species discussed in this chapter include Vaccinium

corymbosum L. (cultivated blueberry), Vaccinium ashei Reade (southern rabbiteye
blueberry), Vaccinium angustifolium Ait. (lowbush blueberry), Vaccinium myrtillus
L. (European bilberry), Vaccinium uliginosum L. (bog bilberry or whortleberry),
Vaccinium macrocarpon Ait. (North American cranberry), Vaccinium oxycoccus L.
(European cranberry), and Vaccinium vitis-idaea L. (lingonberry).
All species in the genus Vaccinium are replete with flavonoids such as antho-
cyanins (flavylium ion moieties that contribute the blue, purple, and red colors
to fruits and flowers which are primarily glycosylated derivatives of the antho-
cyanidins, cyanidin, delphinidin, peonidin, malvidin, and petunidin), proantho-
cyanidins, tannins, catechin (and epicatechin, gallocatechin and epigallocatechin
units), flavonols (myricetin, quercetin, and kaempferol), phenolic acids (gallic acid,
p-hydroxybenzoic acid, caffeic acid, ferulic acid, and ellagic acid), substituted cin-
namic acids, and stilbenes such as resveratrol, pterostilbene, and piceatannol, and
triterpenoids such as ursolic acid and its esters, oleanic acid, alpha-amyrin and beta-
amyrin, steroidal, and iridoid glycoside compounds. Extensive work has focused
on phytochemical and chemotaxonomic investigations with the goal of isolating
and identifying constituents of not only fruits but also flowers, leaves, stems, and
roots that have been used for food and traditional medicinal purposes (Ramstad,
1954; Thieme et al., 1969; Schonert and Friedrich, 1970; Friedrich and Schonert,
1973; Nees et al., 1973; Sticher et al., 1979; Dombrowicz et al., 1991; Fraisse
et al., 1996; Sun et al., 1997; Prior et al., 2001; Dugo et al., 2001; Nyman and
Kumpulainen, 2001; Gu et al., 2002; Jensen et al., 2002; Kandil et al., 2002; Du
et al.,2004; Ichiyanagi et al., 2004c, 2004d; Rimando et al., 2004; Vvedenskaya
et al., 2004; Migas et al., 2005; Zadernowski et al., 2005; Ek et al., 2006; Seeram
et al., 2006; Burdulis et al., 2007; Harris et al., 2007; Pyka et al., 2007; Szakiel
and Mroczek, 2007). The data that emerged from these investigations demon-
strated strong similarities in the chemical composition of species within the genus
Vaccinium.
Nonetheless, clear differences could be observed in the relative and absolute
amounts of flavonoids, in particular anthocyanins, and in their species-dependent,
unique “fingerprints”. By comparison, the main phenolics found in widely con-
sumed fruits from the family Rosaceae were ellagitannins, phenolic acids, and
anthocyanins. Many Vaccinium fruits contain 15–25 distinct anthocyanins (based
on the anthocyanidins, delphinidin, cyanidin, petunidin, peonidin, and malvidin) in
conjunction with abundant proanthocyanidins and a diverse array of polyphenolic
compounds. Both V. myrtillus and V. ashei contained 15 identical anthocyanins with
different distribution patterns, as elucidated by high-performance liquid chromatog-
raphy (HPLC) coupled with photodiode array detection and electrospray ionization
– mass spectrometry (LC/PDA/ESI-MS) (Nakajima et al., 2004). Distinctive simi-
larities in the distribution of conjugated forms of phenolic compounds among berry
species of the same family were confirmed, but differences in chromatographic
profiles of conjugates and compositions of aglycones were also observed, espe-
cially in the case of anthocyanins (Määttä-Riihinen et al., 2004). One report delin-
eated anthocyanins as the main phenolic constituents in V. myrtillus, V. uliginosum,
and V. macrocarpon, but in V. vitis-idaea, belonging also to the family Ericaceae

genus Vaccinium, flavanols and proanthocyanidins predominate in the composition
(Kähkönen et al., 2001). Proanthocyanidins of various degrees of polymerization
(DP) have been identified in many types of foods, but Vacciniumspecies contain
oligomeric (DP ≤ 10) and polymeric proanthocyanidins (DP > 10), in both A- and
B-type linkages (Gu et al., 2003). Later experiments employing advanced analyt-
ical techniques, including liquid chromatography-time-of-flight mass spectrome-
try (LC-TOFMS), liquid chromatography-tandem mass spectrometry (LC-MS/MS),
and nuclear magnetic responance spectrometry (NMR) to identify V. vitis-idaea
polyphenolics revealed a total of 28 flavonols, anthocyanidins, catechins and their
glycosides, and different caffeoyl and ferulic acid conjugates (Ek et al., 2006). This
appears to be the first report of coumaroyl-hexose-hydroxyphenol, caffeoyl-hexose-
hydroxyphenol, quercetin-3-O-alpha-arabinofuranoside, kaempferol-pentoside, and
kaempferol-deoxyhexoside, and the flavonol acylglycosides quercetin-3-O-[4
-(3-hydroxy-3-methylglutaroyl)]-alpha-rhamnose and kaempferol-3-O-[4 -(3-
hydroxy-3-methylglutaroyl)]-alpha-rhamnose. Compounds from parts of Vaccinium

plants, other than fruit flesh, including essential fatty acids from seeds and seed oils,
and fibers, such as microcrystalline cellulose, pectins, lignins, cutin-like polymers,
and condensed tannins, have been suggested to have potential health benefits and
cancer chemopreventive attributes (Parry et al., 2006; Wawer et al., 2006).
Although little direct data uniquely link berry consumption with lower cancer
risk, evidence is mounting that berry extracts and berry phytochemicals modulate
biomarkers of DNA damage and indicators of malignant transformation in vitro and
in vivo (Hou, 2003; Duthie, 2007; Seeram, 2008b). The anticancer effects on macro-
molecules, in particular DNA, and cells, tissues, and organ systems involve (1) pro-
tection from genotoxicity; (2) regulation of carcinogen and xenobiotic metabolizing
enzymes; (3) ability to prevent and mitigate damage resulting from oxidative stress;
(4) inhibition of cancer cell proliferation and induction of apoptosis; (5) regulation
of subcellular signaling pathways and modulation of transcription factors; and (6)
inhibition of growth factors and inflammatory cytokines linked to tumor angiogen-
esis and invasiveness. In addition, berry phytochemicals may induce sensitivity of
tumor cells to chemotherapeutic agents by inhibiting pathways that lead to drug
resistance and ameliorate therapy-associated toxicities.
11.2.1.1 Protection from Genotoxicity

The initial step in the transformation of a normal, somatic cell to a malignant
one is damage to the genome resulting in a mutation. Mutagenic agents may be
chemical, radioactive, or biological (e.g., viruses) in nature. Chemical mutagens
cause DNA modifications through base pair substitutions, frameshifts, and strand
breaks. Carcinogens are mutagens that have been documented to cause progres-
sion to a cancerous state. Carcinogens are typically classified as (1) direct acting
and possess a chemical structure that is sufficient to cause DNA damage or (2)
require metabolic activation to convert a prescursor to an active form. Mutation of
a particular oncogene or a tumor-suppressor gene may enhance susceptibility to

development of specific types of cancer.
There is evidence that Vaccinium preparations may preserve DNA integrity or
promote repair of DNA damage. Juice of V. corymbosum suppressed mutagenic-
ity of the polycyclic aromatic hydrocarbons 2-amino-3-methyl[4,5-f]-quinoline
and, in part, of 2-amino-3,4-dimethylimidazo-[4,5-f]quinoline or 2-amino-3,8-
dimethylimidazo[4,5-f]quinoxaline in Ames tester strains Salmonella typhimurium
TA98 and TA100 (Edenharder et al., 1994). Ethanol extracts of V. ashei (cv. Premier)
significantly inhibited mutagenesis by both direct-acting and metabolically activated
carcinogens (Wedge et al., 2001). Similar results were obtained with juices from
V. ashei (cv. Tifblue and cv. Premier), shown to inhibit the production of mutations
by the direct-acting mutagen, methyl methanesulfonate, and the metabolically acti-
vated carcinogen, benzo[a]pyrene (Hope Smith et al., 2004). Moreover, a V. asheis
extract reduced oxidative DNA damage in mouse brain tissue in vitro (Barros et al.,
2006).
11.2.1.2 Regulation of Carcinogen and Xenobiotic Metabolizing Enzymes

The metabolism of carcinogens (and other xenobiotics defined as “foreign” chemi-
cal substances) by the body is often divided into three phases: (1) modification; (2)
conjugation; and (3) excretion. These reactions act in concert to detoxify and remove
them from cells. In Phase I, a variety of enzymes and isozymes in the cytochrome
P-450-dependent mixed-function oxidase system (CYP450) act to introduce reac-
tive and polar groups into their carcinogen or xenobiotic substrates. These enzyme
complexes incorporate an atom of oxygen into non-activated hydrocarbons, which
can result in either the introduction of hydroxyl groups or oxygen (O-), nitrogen
(N-), and sulfur (S-)mediated dealkylation of substrates. A typical reaction mech-
anism of the CYP450 oxidases proceeds through the reduction of cytochrome-
bound oxygen and the generation of an oxyferryl species, according to the general
scheme:
NADPH + H+ + RH → NADP+ + H2 O + ROH
In ensuing Phase II reactions, these activated metabolites are conjugated with

charged species such as glutathione (GSH), sulfate, glycine, or glucuronic acid. A
large group of broad-specificity transferases catalyze these reactions which, in com-
bination, can metabolize almost any hydrophobic compound that contains nucle-
ophilic or electrophilic groups. The principal of these are glutathione S-transferases
(GSTs) and are responsible for the addition of large anionic groups (such as GSH)
to detoxify reactive electrophiles and produce more polar metabolites that cannot
diffuse across membranes and may, therefore, be actively transported by specialized
systems for their removal. During Phase III, conjugates may be further metabo-
lized prior to excretion. A common example is the processing of glutathione conju-
gates to acetylcysteine (mercapturic acid) conjugates in which the gamma-glutamate
and glycine residues in the glutathione molecule are removed by gamma-glutamyl

transpeptidase and dipeptidases. In the final step, the cystine residue in the conjugate
is acetylated. Through another Phase II mechanism, conjugates and their metabo-
lites can be excreted from cells as a result of the anionic groups acting as “affin-
ity tags” for membrane-associated transporters of the multidrug resistance protein
(MRP) family. These proteins are members of the larger family of ATP-binding
cassette transporters that catalyze the ATP-dependent transport of a huge variety of
hydrophobic anions across cell membranes. Thus, further metabolism may result in
removal or excretion of Phase II products across the plasmalemma to the extracel-
lular medium.
Many polyphenols, including phenolic acids, anthocyanins, stilbenes, catechins,
and other flavonoids, which constitute a large fraction of phytochemicals in all
Vaccinium species, modulate components of the detoxification systems and cellu-
lar levels of endogenous antioxidants, such as glutathione (Rodeiro et al., 2008).
Experiments with Chinese hamster lung fibroblasts, genetically engineered for the
expression of rat CYP450 (also known as cytochrome P450-dependent monooxyge-
nase) and rat sulfotransferase 1C1 (V79-rCYP1A2-rSULT1C1 cells), were designed
to seek possible protective effects of berries and other fruits, vegetables, spices,
and plant-derived beverages against genotoxicity induced by 2-acetylaminofluorene
(AAF) or 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) (Edenharder
et al., 2002). Applying alkaline single-cell gel electrophoresis (comet assay),
which detects DNA strand breaks and abasic sites, the genotoxicity of PhIP
could be demonstrated only in the presence of hydroxyurea and 1-[beta-D-
arabinofuranosyl]cytosine, known inhibitors of DNA repair synthesis. AAF and
PhIP predictably were unable to induce any genotoxic effects in the parent V79
cells. Genotoxic activity of PhIP was strongly reduced in a dose-related manner by
V. myrtillus and many other plant preparations to a lesser extent, but Vaccinium did
not inhibit the genotoxicity of N-OH-PhIP metabolite or of another benzo[a]pyrene,
benzo[a]pyrene-7,8-dihydrodiol (BaP-7,8-OH), whereas the genotoxicity of AAF
was strongly reduced by other fruits. Through presentation of N-OH-PhIP and
benzo[a]pyrene-7,8-dihydrodiol (BaP-7,8-OH) as substrates for enzymes of the
rSULT 1C1 and CYP450-1A family, respectively, these results demonstrate enzyme
inhibition as the mechanism against genotoxicity of heterocyclic aromatic amines.
This inhibition may take place within metabolically competent mammalian cells and
under the conditions of the Salmonella/reversion assay, as demonstrated previously
by some of these workers.
A number of genes important for expression of detoxification and antioxidant
defense enzymes, proteins, and endogenous cofactors induced by environmen-
tal stress may provide health benefits by deployment of such defense responses.
One Phase II detoxification enzyme, NAD(P)H:(quinone-acceptor) oxidoreductase
(QR), belongs to the flavoprotein clan in the human genome and is encoded by two
genes, NQO1and NQO2 (Vasiliou et al., 2006). QR functions to inactivate elec-
trophilic forms of carcinogens, particularly quinones, providing a mechanism for
the inhibition of carcinogenesis. QR catalyzes the beneficial two-electron reduc-
tion of quinones to hydroquinones, thereby preventing the unwanted one-electron
reduction of quinones by other quinone reductases. One-electron reduction results

in the formation of reactive oxygen species (ROS), generated by redox cycling of
semiquinones in the presence of molecular oxygen. Both mammalian NQO1 and
NQO2 genes are upregulated as a part of the oxidative stress response and are inex-
plicably overexpressed in particular types of tumors. In early investigations, extracts
of fruit from four Vaccinium species, V. angustifolium, V. myrtillus, V. macrocarpon,
and V. vitis-idaea, and a hydrophobic subfraction of V. myrtillus were tested for
their ability to induce QR in vitro in Hepa 1c1c7 human liver cells and to serve as
possible dietary anticarcinogens (Bomser et al., 1995; 1996). The crude extracts,
as well as anthocyanin and proanthocyanidin fractions, were not highly active or
were inactive in QR induction, whereas the ethyl acetate extracts were potent QR
inducers. The concentrations required to double QR activity (designated CDqr) for
the ethyl acetate extracts of V. angustifolium, V. macrocarpon, V. vitis-idaea, and
V. myrtillus were 4.2, 3.7, 1.3, and 1.0 μg tannic acid equivalents (TAE), respec-
tively. The V. myrtillus ethyl acetate extract was processed into a hexane/chloroform
subfraction, a step that revealed the majority of inducer potency (Cdqr =
0.3–70 ng TAE). Analysis of this subfraction of the V. myrtillus ethyl acetate
extract was required to elucidate the compounds responsible for the induction
of QR.
Anthocyanins from Vaccinium have been shown to inhibit oxidative stress and
unregulated cell proliferation, although regulation of apoptosis and Phase II detoxi-
fying enzymes QR and glutathione-S-transferase (GST) are other potential mech-
anisms through which anthocyanins and other flavonoids may prevent cancer.
V. myrtillus anthocyanins and other phenolics have been shown to upregulate mRNA
transcripts of the oxidative stress defense enzymes, heme oxygenase 1 (HO-1) and
glutathione-S-transferase-pi (GST-pi), in cultured human retinal epithelial cells.
This suggests that they stimulate signal transduction pathways influencing genes
controlled by the antioxidant response element, at least in this tissue type in vitro
(Milbury et al., 2007). Interestingly, anthocyanins from preparations of all four
V. ashei cultivars (cv. Tifblue, cv. Powderblue, cv. Brightblue, and cv. Brightwell)
significantly lowered QR activity in treated cells as compared to untreated control
cells (Srivastava et al. 2007). The activity decreased gradually when treated with
increasing concentrations of anthocyanin fractions (50–150 μg·mL–1 ) from cv. “Tif-
blue” and cv. “Powderblue”. Similarly, GST activity was lower in cells treated with
anthocyanin fractions from all of the cultivars and at all tested concentrations as
compared to untreated controls; however, in HT-29 colon cancer cells, apoptosis
was induced by treatment with anthocyanins from all V. ashei cultivars but, at the
same concentrations, Phase II QR and GST activities decreased rather than demon-
strating induction in this cell line. Polyphenolic flavonoids and other plant phy-
tochemicals are thought to transactivate detoxification and genes containing elec-
trophile response elements (EpREs) within their promoters. A product of one of
these genes, gamma-glutamylcysteine synthetase, has previously been shown to be
positively regulated by quercetin, a flavonoid found in high concentrations V. myr-
tillus, diverse Vaccinium species, and other foods, through EpRE transactivation
(Myhrstad et al., 2006).
11.2.1.3 Prevention of Damage from Oxidative Stress

According to the “free-radical theory of aging”, oxidative damage intiated by reac-
tive oxygen species (ROS) is a major contributor to the functional decline that is
characteristic of senescence and chronic disease. ROS form as by-products of the
normal metabolism of oxygen (e.g., food metabolism and respiration) and have
important roles in cell signaling and immune function; however, the presence of
unpaired valence shell electrons causes high reactivity so these same free radicals
can participate in unwanted side reactions resulting in cumulative cell damage. In
addition to endogenously generated sources in the body, ROS are also generated
by exposure to exogenous sources such as ionizing radiation (e.g., ultraviolet light
exposure leading to sunburn among other environmental exposures, cigarette smoke,
radon gas, to name a few). During times of environmental stress, ROS levels can
increase dramatically and result in significant damage to cell structures. Harmful
effects of reactive oxygen species on the cell are most often observed as (1) dam-
age of DNA; (2) oxidations of unsaturated fatty acids in lipids; (3) oxidations of
amino acids in proteins; and (4) inactivation of specific enzymes through oxidation
of catalytic cofactors. Many forms of cancer are thought to be the result of reactions
between oxygen-free radicals and DNA, resulting in mutations that can adversely
affect the cell cycle and other growth regulatory mechanisms that potentially lead to
malignancy.
ROS associated with cell damage include superoxide (O2 ∗– ) (a term used inter-
changeably with superoxide anion), hydrogen peroxide (H2 O2 ), singlet oxygen
(1 O2 ), peroxyl (ROO∗ ) and hydroxyl (OH∗ ) radicals, and peroxynitrite (ONOO− ),
formed in vivo through reaction of the free-radical superoxide with the free radi-
cal, nitric oxide, that are derived from molecular oxygen under reducing conditions.
Because free radicals are necessary for life, the body has a number of mechanisms to
minimize free radical-induced damage and to repair damage which does occur, such
as through the action of the enzymes, superoxide dismutase, catalase, glutathione
peroxidase, and glutathione reductase. In addition, antioxidants, such as vitamin A,
vitamin C, and vitamin E, play a key role in these defense mechanisms. For years,
the antioxidant power of fruits was thought to be attributable to conventional vitamin
content, but far more complexity is now attributed to total reactive oxygen scaveng-
ing capacity. Studies on antioxidant capacities of flavonoids revealed that they could
scavenge free radicals, chelate metals, bind specific proteins, and act through other
mechanisms that involve inhibition of oxidative enzymes.
11.2.1.4 In Vitro Antioxidant Protection

Fruits – especially berries – have been examined extensively in vitro for antioxi-
dant capacity with Vaccinium species being no exception (Vinson et al., 2001; Neto,
2007a; Vinson et al., 2008; Seeram, 2008a). Some of these experiments revealed
extracts of Vaccinium protect against oxidation of lipids (methyl linoleate) and
protein tryptophan (Trp) residues (Kähkönen et al., 2001; Viljanen et al., 2004;
Salminen and Heinonen, 2008). Mechanisms of antioxidative action of phenolic
compounds from Vaccinium and fruits from other genera toward the oxidation of
biomolecules were distinct, as the pattern of oxidation products varied with different
phenolic compounds. The extent of protein oxidation was measured by determining
the loss of tryptophan fluorescence and formation of protein carbonyl compounds,
and that of lipid oxidation, by conjugated diene hydroperoxides and hexanal anal-
yses. V. myrtillus phenolics possessed some of the best overall antioxidant activ-
ity toward protein oxidation. Anthocyanins found in V. myrtillus contributed most
to the antioxidant effect by inhibiting the formation of both hexanal and protein
carbonyls. V. macrocarpon proanthocyanidins were also found to provide potent
antioxidant protection toward oxidation of Trp residues. The antioxidant protec-
tion toward lipid oxidation was best provided by V. vitis-idaeaand V. myrtillus phe-
nolics, whereas proanthocyanidins, especially the dimeric and trimeric molecules,
from V. vitis-idaea, were among the most active phenolic constituents toward both
lipid and protein oxidation.
Crude extracts of Vaccinium were shown to be potent scavengers of chemi-
cally generated O2 ∗– and possessed inhibitory activity toward the enzyme xanthine
oxidase (Constantino et al., 1992). Tannins isolated from V. vitis-idaea exhibited
O2 ∗− scavenging and multiple antioxidant activities (Ho et al., 1999). Cinnam-
tannin B1 displayed the strongest anti-lipid peroxidation activity, proanthocyanidin
A-1 displayed the strongest superoxide scavenging activity, and epicatechin-(4beta
→ 6)-epicatechin-(4beta → 8, 2beta → O → 7)-catechin had the strongest anti-
superoxide formation effect. Subsequent work marked distinctions among various
antioxidants in their abilities to scavenge different reactive oxygen species (Wang
and Jiao, 2000). Juice from different cultivars of V. corymbosum, V. angustifolium,
and V. macrocarpon, as well as from various species in the family Rosaceae, was
assessed for antioxidant activities against O2 ∗− , H2 O2 , ‘O2 , and OH∗ radicals.
Vaccinium cultivars had high antioxidant capacity against all four reactive oxygen
moieties but, in general, were lower in antioxidant capacity inhibition of scavenging
activity than Rosaceae juices. V. macrocarpon had the lowest inhibition of hydrogen
peroxide moieties, while V. corymbosum had the lowest antioxidant capacity against
OH∗ and O2 .
The reactivities of 12 major anthocyanins identified in V. myrtillus extracts
toward nitric oxide (NO) and ONOO− were studied in vitro using capillary zone
electrophoresis (Ichiyanagi et al., 2004b). With the exception of delphinidin gly-
cosides, the reactivities of anthocyanins toward NO. were weaker than that of (+)-
catechin as a reference antioxidant under anaerobic conditions. Aglycon structure
or type of sugar moiety did not significantly affect the reactivities of other antho-
cyanins. Conversely, all anthocyanins and catechin showed significant enhancement
of reactivity under aerobic conditions, indicating that they reacted with other reac-
tive species secondarily generated from NO. Delphinidin glycosides showed rather
comparatively high reactivity toward ONOO− compared to other anthocyanins,
which also showed approximately two times lower reactivity than catechin. These
results were corroborated, in part, by others (Rahman et al., 2006). This group found
that antioxidant activities of 15 purified V. myrtillus anthocyanins, together with
pelargonidin 3-O-beta-D-glucopyranoside and 4 -O-methyl delphinidin 3-O-beta-D-
glucopyranoside, the major metabolite of delphinidin 3-O-beta-D-glucopyranoside,

were evaluated in order to study the structure-antioxidant activity relationship
and any synergism between them in the mixture. Both the aglycone structure
and the attached sugar moiety affected the superoxide radical- and peroxynitirite-
scavenging activities, although the effect of the attached sugar moiety was smaller
than that of the aglycone structure. The potency of activity toward the superoxide
radical was in the following order: delphinidin > petunidin > malvidin = approx-
imately cyanidin > (+)-catechin > peonidin > pelargonidin. The activity toward
ONOO− was in the following order: delphinidin > cyanidin = approximately petu-
nidin > malvidin = approximately (+)-catechin > peonidin > pelargonidin. It was
confirmed that methylation of 4 -OH markedly reduced the antioxidant activity of
anthocyanin. Further, it was revealed that synergism occurred in both O2∗− and
ONOO− scavenging activities among the anthocyanins in the mixture.
Kinetic parameters of 12 major anthocyanins identified in V. myrtillus extracts
toward 2,2 -azobis (2-amidinopropane) (AAPH) radicals, tert-butylhydroperoxides
(t-BuOOH), and H2 O2 were studied in vitro using capillary zone electrophoresis
(Ichiyanagi et al., 2004a). The reactivity of anthocyanins toward H2 O2 was not sig-
nificantly affected by aglycon structure or by the type of sugar moiety, with no
marked difference observed in reaction rates among various anthocyanins. Reac-
tivity toward t-BuOOH was essentially the same as toward H2 O2 , although the
reaction rate was several times smaller. Also, the reaction rate of anthocyanin
toward H2 O2, compared to that of (+)-catechin, was relatively high (approximately
30 times larger) when measured as a reference antioxidant. Conversely, reactivity
toward AAPH radicals was determined principally by the aglycon structure instead
of the type of sugar moiety. Delphinidins carrying three-hydroxyl groups on the
B-ring were most reactive followed by cyanidins, with two-hydroxyl groups. Fur-
ther, methylation of the hydroxyl groups reduced reactivity toward AAPH radi-
cals. The reactivities of anthocyanins and (+)-catechin toward AAPH radicals were
similar.
Over the past decades, more specific antioxidant assays were developed and
numerous reports on the radical-scavenging capacity of Vaccinium were added to the
literature. Some of the most widely used were (1) oxygen radical absorbing capac-
ity (ORAC) (otherwise known as Trolox-equivalent antioxidant capacity (TEAC))
based on fluorescence decay of Trolox R
(6-Hydroxy-2,5,7,8-tetramethylchroman-
2-carboxylic acid), a water soluble analogue of vitamin E sensitive to peroxyl
(ROO∗ ) radicals; (2) total oxyradical-scavenging capacity (TOSC), which measures
the decrease in ethylene production caused by antioxidants; (3) scavenging capacity
against the artificial free-radical 1,1-diphenyl-2-picrylhydrazyl (DPPH∗ ); and (4)
ferric-reducing/antioxidant power (FRAP), also known as ferric-reducing antioxi-
dant of plasma (Klouwen, 1962; Cao et al., 1993; Winston et al., 1998; Regoli and
Winston, 1999; Lichtenthäler and Marx, 2005; Tomer et al., 2007).
In a TOSC assay, V. vitis-idaea extracts were shown to scavenge efficiently
three ROS, peroxyl and hydroxyl radicals, and peroxynitrite (Lichtenthäler and
Marx, 2005). Others confirmed that fruit of V. vitis-idaea contains high antioxi-
dant activity and potent-free radical-scavenging activities for DPPH∗ , ROO∗ , OH∗ ,
and O2 ∗− , despite the fact that soluble solids, titratable acids, antioxidant capacity,
and anthocyanin and phenolic contents varied between cultivars (Wang et al., 2005).
Among ethanol extracts of 10 edible berries, that from V. myrtillus fruit contained
the largest amounts of phenolic compounds, including anthocyanins, and showed the
greatest DPPH∗ -scavenging activity (Katsube et al., 2003). Cold-pressed V. corym-
bosum seed oil, along with seed oils from Rosaceae genera, was evaluated for its
fatty acid composition, carotenoid content, tocopherol profile, total phenolic content
(TPC) as gallic acid equivalents per gram, oxidative stability index (OSI), peroxide
value, and antioxidant properties (Parry et al., 2005). All tested seed oils contained
significant levels of alpha-linolenic acid, ranging from 19.6 to 32.4 g per 100 g of oil,
along with a low ratio of n–6/n–3 fatty acids (1.64/3.99). The total carotenoid con-
tent ranged from 12.5 to 30.0 μmoles·kg−1 oil. Zeaxanthin was the major carotenoid
compound in all tested berry seed oils, along with beta-carotene, lutein, and cryp-
toxanthin. Total tocopherol was 260.6–2276.9 μmoles·kg−1 oil, including alpha-,
gamma-, and delta-tocopherols. The lowest OSI was attributed to V. corymbosum
oil, and the highest TPC and ORAC values were achieved by various Rosaceae seed
oils. All tested berry seed oils directly reacted with and quenched DPPH∗ in a dose-
and time-dependent manner. These data suggest that the cold-pressed berry seed oils
may serve as potential dietary sources of tocopherols, carotenoids, and other natural
antioxidants. Seed flours from V. macrocarpon and other fruits were also examined
for their total fat content, fatty acid composition, total phenolic content (TPC), and
total anthocyanin content (TAC), against the peroxyl (ORAC) and stable DPPH rad-
icals, and chelating capacity against Fe2+ (Parry et al., 2006). Significant levels of
fat were detected in the fruit seed flours, and their fatty acid profiles may differ from
those of the respective seed oils. V. macrocarpon seed flour, compared to that from
other fruits, had the highest level of alpha-linolenic acid (30.9 g/100 g fat) and the
lowest ratio of n–6/n–3 fatty acids (1.2/1). The fruit seed flours also differed in their
TAC values and Fe2+ -chelating capacities; ORAC, which correlated significantly to
TPC values in this report, was not the highest in the flour of V. macrocarpon seed
flour.
A number of novel compounds, such as ortho-benzoyloxyphenyl acetic acid
ester, also called vaccihein A, isolated from the fruit of V. ashei, rare A-type
proanthocyanidin dimers and trimers from V. vitis-idaea, V.oxycoccus, V. myrtillus,
V. macrocarpon, and V. uliginosum, and uncommon anthocyanin derivatives, such
as anthocyanin-pyruvic acid adducts and vinylpyranoanthocyanin-catechins (por-
tisins) from V. myrtillus, have been identified and contribute to antioxidant capac-
ity, as measured in DPPH∗ scavenging and FRAP assays (Gu et al., 2003; Ono
et al., 2002; Faria et al., 2005; Määttä-Riihinen et al., 2005). The A-type proan-
thocyanidins inhibited the oxidation of methyl linoleate emulsion and human LDL,
whereas anthocyanin derivatives were able to inhibit lipid peroxidation induced by
2,2 -azobis (2-methyl-propanimidamide) dihydrochloride, in a liposomal membrane
system.
The radical-scavenging activity of a V. macrocarpon extract, composed primarily
of flavonol glycosides, was the greatest compared to those with other compo-
nents derived from the whole fruit (Yan et al., 2002). Seven flavonol glycosides
were isolated and purified from whole fruit for further evaluation; the anthocyanin
cyanidin 3-galactoside was also purified for comparison with the flavonoids.
Three flavonol monoglycosides were newly identified by 13 C NMR as quercetin
3-xyloside, 3-methoxyquercetin 3-beta-galactoside (isorhamnetin), and myricetin
3-alpha-arabinofuranoside; the other four isolated were the previously identi-
fied quercetin 3-beta-galactoside, quercetin 3-alpha-arabinofuranoside, quercetin 3-
alpha-rhamnopyranoside, and myricetin 3-beta-galactoside. These compounds were
evaluated in vitro for DPPH∗ -scavenging activity. Most of the flavonol glycosides
showed antioxidant activity comparable or superior to that of vitamin E; cyanidin
3-galactoside showed activity superior to that of the flavonoids as well as vitamin E
or Trolox (the reference compound for the ORAC assay) in both antioxidant assays.
The antioxidative activities of proanthocyanidins from V. macrocarpon were found
to be much stronger than vitamin C or vitamin E in aqueous systems; the mech-
anisms for their antioxidative actions were shown to involve radical scavenging,
quenching, and enzyme-inhibiting actions (Ariga, 2004). Other authors identified
20 compounds in V. macrocarpon fruit, but those with potent antioxidant activity
in the μmolar range were quercetin, 3,5,7,3 ,4 -pentahydroxyflavonol-3-O-beta-D-
glucopyranoside, 3,5,7,3 ,4 -pentahydroxyflavonol-3-O-beta-D-galactopyranosi-de,
and 3,5,7,3 ,4 -pentahydroxyflavonol-3-O-alpha-l-arabinofuranoside (He and Liu,
2006).
Although anthocyanins were the main components, specific compounds such
as chlorogenic acid in V. corymbosum (cv. Sierra), and quercetin glycosides in
V. macrocarpon (cv. Ben Lear) and V. vitis-idaea (cv. Amberland) were found to
be present in relatively high concentrations (Zheng and Wang, 2003). Chlorogenic
acid, peonidin 3-galactoside, and cyanidin 3-galactoside were the most important
antioxidants in V. corymbosum, V. macrocarpon, and V. vitis-idaea, respectively.
The point has been made that the major metabolite of cyanidin, protocatechuic acid,
is largely responsible for its antioxidant and other effects in humans (Galvano et al.,
2007; Vitaglione et al., 2007). The total antioxidant capacity was generally depen-
dent on the structure of individual phenolics and content in the berries, and variabil-
ity was considerable. Important phenolics from Vaccinium, such as quercetin and
cyanidin, with 3 ,4 -dihydroxy substituents in the B-ring and conjugation between
the A- and B-rings, had highly effective radical-scavenging structures. Furthermore,
strong iron-binding properties have been confirmed for polyphenolic compounds,
but especially for those containing the “iron-binding motifs” identified in their struc-
tures (Guo et al., 2007). A build-up of iron in biological systems is believed to result
in the production of free radicals, leading to oxidative stress, cellular damage and
eventual cellular death via apoptotic signaling (apoptosis is a process also known
as “programmed cell death”). Quercetin, both at μmolar levels, and in the presence
of major cellular iron chelators like ATP or citrate, could suppress completely Fen-
ton chemistry, described as (1) Fe2+ + H2 O2 → Fe3+ + OH· + OH− and (2) Fe3+
+ H2 O2 → Fe2+ + OOH· + H+ , where ferrous iron (II) is oxidized by hydrogen
peroxide to ferric iron (III), a hydroxyl radical, and a hydroxyl anion. Iron (III) is
then reduced back to iron (II), a peroxide radical, and a proton by the same hydrogen
peroxide (disproportionation). However, the radical-scavenging activity of quercetin
provides only partial protection against Fenton chemistry-mediated damage, while

iron chelation by quercetin can completely inhibit Fenton chemistry, indicating that
the chelation may be the key to its antioxidant activity.
A cellular antioxidant activity (CAA) for quantifying antioxidant activity in cell
culture was developed recently to meet the need for a more biologically representa-
tive method than the popular chemistry antioxidant capacity measurements (Wolfe
and Liu, 2007). CAA accounts for some aspects of uptake, metabolism, and loca-
tion of antioxidant compounds within cells. This method measures the ability of test
compounds to prevent 2,2 -azobis (2-amidinopropane) dihydrochloride (ABAP)-
generated peroxyl radicals from forming oxidized, fluorescent dichlorofluorescein
(DCF) from its non-fluorescent precursor in human hepatocarcinoma cells (HepG2).
The decrease in cellular fluorescence generated from the precursor dichlorofluores-
cein probe, when compared to the control cells, indicates the antioxidant capacity
of the compounds. V. angustifolium and V. corymbosum had some of the highest
CAA values, followed by V. macrocarpon, among 25 commonly consumed fruits
(Wolfe et al., 2008). Of the pure tester compounds, quercetin had the highest CAA
value, followed by kaempferol, epigallocatechin gallate (EGCG), myricetin, and
luteolin (expressed in μmoles of quercetin equivalents). These authors also point
out that flavonoid structures with the most antioxidant activity in the CAA assay
possessed a 3 ,4 -O-dihydroxyl group in the B-ring, a 2,3-double bond combined
with a 4-keto group in the C-ring, and a 3-hydroxyl group (Wolfe and Liu, 2008).
Flavanols with a galloyl moiety had higher antioxidant activity than those with-
out, and a B-ring 3 ,4 ,5 -trihydroxyl group further improved their efficacy. On the
other hand, isoflavones had no cellular antioxidant activity. Interestingly, chemically
based ORAC values for flavonoids were not related to their CAA values.
The primary conclusion reached in these in vitro studies was that a high cor-
relation exists between antioxidant potency and flavonoids, in particular polyphe-
nolics, anthocyanins, and proanthocyanidins (Moyer et al., 2002; Sellappan et al.,
2002; Sanchez-Moreno et al., 2003; Ehala et al., 2005; Seeram, 2008b). One group
pointed out the importance of careful chemical analysis of these compounds, since
they occur in many derivative forms (Sun et al., 2002). Their report describes, as
an example, the underestimation of total phenolics because bound forms were not
quantified with soluble forms in many analyses. Similarly, bioactive anthocyanins
and derivatives must be differentiated from inactive anthocyanidins in assessments
of composition and antioxidant potency. A further critical consideration for evalu-
ating the potential health benefits of any Vaccinium antioxidants is their capacity to
function in vivo as ROS scavengers. In vitro antioxidant potency does not prove in
vivo biological activity, although there is clinical evidence of antioxidant potency for
the most potent beverages (e.g., red wine) correlating with positive health benefits.
11.2.1.5 In Vivo Antioxidant Protection

A body of literature indeed documents effects of consumption of Vaccinium on post-
prandial antioxidant status in animal models, including orchidectomized rats and
strains with hereditary defects in oxidative metabolism, as well as exercising dogs
(Shabalina et al., 2001; Ariga, 2004; Dunlap et al., 2006; Kolosova et al., 2006;
Sinitsyna et al., 2006; Deyhim et al., 2007; Villarreal et al., 2007).
Mouse models have been employed to measure restraint-stress oxidation in liver
tissue (Bao et al., 2008b). Restraint stress may induce serious liver damage, with an
increase in plasma alanine aminotransferase (ALT) level. A concomitant increase
in malondialdehyde (MDA) levels and lowered ORAC values in plasma and liver
were observed in restraint mice compared with starved mice. Oral administra-
tion of a V. myrtillus extract containing ∼42% anthocyanins remarkably decreased
plasma ALT level and, thus, alleviated stress-induced liver damage. In addition, the
extracts increased glutathione GSH and vitamin C levels and significantly decreased
MDA and nitric oxide (NO) levels in the liver tissues. These results suggest that
V. myrtillus extract plays an important role in protecting against restraint-stress-
induced liver damage by both free radical-scavenging activity and a lipid per-
oxidation inhibitory effect. This group also examined chemically induced organ
damage of the kidney by potassium bromate (KBRO3 ), an oxidizing agent used
as a food additive (Bao et al., 2008a). The mechanism of potent nephrotoxicity
has been hypothesized to occur through the generation of oxygen free radicals.
A single intraperitoneal administration to mice could induce serious kidney dam-
age, with an increase in serum blood urea nitrogen (BUN) and creatinine levels.
Intervention with V. myrtillus extract resulted in a reversal in serum BUN and crea-
tinine to normal levels and decreased kidney MDA, NO, and the enzyme, xanthine
oxidase, levels. Also, the extract improved ORAC levels in kidney tissue, which
showed that it reduced the degree of oxidative stress and kidney damage induced by
KBrO3 .
Sophisticated methods have been designed for analysis of ORAC and total
antioxidant status (TAS) values in plasma. In humans, in a single-blinded crossover
study performed with a group of eight middle-aged male subjects (38–54 years),
ingestion of freeze-dried V. angustifolium resulted in a significant increase in
ORAC and TAS (Kay and Holub, 2002). Post-prandial plasma antioxidant capac-
ity changes differed depending on the food consumed, and Vaccinium was shown
to influence hydrophilic and hydrophobic ORAC values in human plasma (Prior
et al., 2003; 2007). Conversely, consumption of an energy source of macronutri-
ents containing no antioxidants was associated with a decline in plasma antioxidant
capacity.
In other investigations, Vaccinium species increased vitamin C and quercetin con-
centrations in human plasma, and some revealed correlation with FRAP, electron
spin resonance (ESR) values, and suppression of serum levels of advanced oxida-
tion protein and lipoprotein products (Erlund et al., 2003; 2006; Ruel et al., 2005;
Duthie et al., 2006; Valentova et al., 2007). Nonetheless, a comprehensive study in
healthy female human subjects compared the total phenol, anthocyanin, and cate-
chin content of V. macrocarpon supplements prior to ingestion and in the plasma
following ingestion, as well as the total antioxidant ability determined by ESR
spectrometry and by the FRAP assay (Duthie et al., 2006). Vitamin C, homocys-
teine (tHcy), and reduced glutathione (GSH) were measured by HPLC. Glutathione
peroxidase (GSH-Px), catalase (CAT), and superoxide dismutase (SOD) activities
were measured in erythrocytes. Urine was collected for analysis of malondialdehyde

(MDA) by HPLC and 8-oxo-deoxyguanosine (8-oxo-dG) by ELISA. Endogenous
and induced DNA damage were measured by single-cell gel electrophoresis in
lymphocytes. Also measured were plasma total cholesterol, high-density lipopro-
tein (HDL), and low-density lipoprotein (LDL) cholesterol and triglycerides (TG).
V. macrocarpon juice, as compared with the placebo, contained higher vitamin C,
total phenol, catechin, and anthocyanin concentrations. Vitamin C increased signif-
icantly in volunteers consuming juice, but no anthocyanins (plasma) or catechins
(plasma or urine) were detectable and plasma total phenols were unaffected. The
antioxidant potential of the plasma, GSH-Px, CAT and SOD activities, and MDA
were similar for both groups and changes were not noted in tHcy, TC, TG, HDL,
or LDL. Supplementation with cranberry juice did not affect endogenous or H2 O2 -
induced DNA damage in lymphocytes or appearance of 8-oxo-dG in urine. Thus,
the authors concluded that juice consumption, compared to placebo, did not affect
plasma or cellular antioxidant status and had no effect on basal or induced oxidative
DNA damage, or several biomarkers of lipid status. Although these results seem to
be inconsistent with those of others, they highlight the importance of distinguishing
between in vitro and in vivo antioxidant and other bioactivities of dietary antho-
cyanins in relation to human health.
11.2.1.6 Inhibition of Cancer Cell Proliferation and Induction of Apoptosis

Unlike normal cells, cancer cells proliferate rapidly and fail to respond to growth
inhibitory signals. In the latter, apoptosis does not occur in a regulated manner. The
polyphenolic extracts and flavonols, proanthocyanidin oligomers, and triterpenoids
isolated from Vaccinium inhibit the growth and proliferation of several types of
tumor cells lines in vitro and may act in a complementary fashion to limit this aspect
of the carcinogenic process (Neto, 2007a,b).
Studies in tumor cell lines. In early work, fruit extracts of four Vaccinium species
(V. angustifolium, V. myrtillus, V. macrocarpon, and V. vitis-idaea) were screened in
vitro for anticarcinogenic compounds by a combination of fractionation and ability
to inhibit the induction of ornithine decarboxylase (ODC), the rate-limiting enzyme
in polyamine synthesis, by the tumor promoter, phorbol 12-myristate 13-acetate
(also known as 12-O-tetradecanoyl phorbol-13-acetate (TPA)) (Bomser et al., 1996).
In contrast to their effects on the enzyme quinone reductase (QR), crude extracts of
V. angustifolium, V. macrocarpon, and V. vitis-idaea were active inhibitors of ODC
activity. The IC50 values were 8.0, 7.0, and 9.0 μg TAE, respectively. The great-
est activity in these extracts appeared to be contained in the polymeric proantho-
cyanidin fractions of these fruits (IC50 = 3.0, 6.0, and 5.0 μg TAE, respectively).
A proanthocyanidin fraction from these fruits inhibited ODC and suppressed the
formation of polyamines typically enhanced in rapidly proliferating cells charac-
teristic of cancer. The anthocyanidin and ethyl acetate extracts of the four Vac-
cinium species were either inactive or relatively weak inhibitors of ODC activity.
Different authors also reported significant chemopreventive activity, as measured
in a TPA tumor promoter-induced ODC assay (as well as antioxidant activity in
a wide range of fractions generated from a crude extract) that localized to one
particular proanthocyanidin-rich fraction from V. macrocarpon (Kandil et al., 2002).
The active anticarcinogenic fraction was found to contain the following compo-
nents: a series of oligomeric proanthocyanidins, seven flavonoids, mainly quercetin,
myricetin, the corresponding 3-O-glycosides, (–)-epicatechin, (+)-catechin, and
dimers of both gallocatechin and epigallocatechin types.
In further investigations, a proanthocyanidin-rich extract of V. angustifolium was
separated into fractions and was characterized by mass spectrometry and NMR
spectroscopy. One fraction, with an average degree of polymerization (DP) of 5.65,
had significant antiproliferation activity against human prostate and mouse liver
cancer cell lines (Schmidt et al., 2004). A significant positive correlation was estab-
lished between proanthocyanidin content of different fractions and biological activ-
ity. Proanthocyanidin-rich fractions from Vaccinium fruits demonstrated differential
inhibitory effects on the proliferation of LNCaP, an androgen-sensitive prostate can-
cer cell line, and DU145, a more aggressive androgen-insensitive prostate cancer
cell line. Two similar proanthocyanidin-rich fractions from V. corymbosum sig-
nificantly inhibited LNCaP growth in the mg·mL−1 range (Schmidt et al., 2006).
Only one fraction modestly inhibited the growth of DU145 cells. Differences in
cell growth inhibition of LNCaP and DU145 cell lines by V. corymbosum fractions
rich in proanthocyanidins indicate that its proanthocyanidins exert an effect through
mechanisms characteristic of androgen-dependent growth in prostate cancer cells.
An extract of V. myrtillus was effective at inhibiting the growth of HL60 human
leukemia cells and HCT116 human colon carcinoma cells in vitro (Katsube et al.,
2003). The extract induced apoptotic cell bodies in both, but to a far lesser extent
in HCT116 than HL60 cells, and caused nucleosomal DNA fragmentation only in
HL60 cells. Likewise, pure delphinidin and malvidin induced apoptosis in HL60
cells, as did related glycosides isolated from the extract. Only pure delphinidin and
its glycoside isolated from the V. myrtillus extract, but not malvidin and its glyco-
side, inhibited the growth of HCT116 cells.
Polyphenol-rich V. vitis-idaea extracts were screened for their antiproliferative
effectiveness in human cervical cancer (HeLa) cells (McDougall et al., 2008). In
this system, V. vitis-idaea and other berry extracts were effective with EC50 val-
ues in the range of 25–40 μg·mL−1 relative to phenol content. These extracts
were also effective against the human colon cancer cell line, Caco-2, which was
generally more sensitive at low concentrations, but conversely, less sensitive at
higher concentrations. Although some of the extracts share common polyphe-
nol constituents, especially the ellagitannins, shown to be effective antiprolifer-
ative agents, the bioactive components of V. vitis-idaea extracts are not known.
Although anthocyanin-enriched fractions were considerably less effective than the
crude extract, antiproliferative activity was retained in the tannin-rich fraction com-
posed almost entirely of proanthocyanidins of type A and B linkages. Others found,
through statistical analyses, that anthocyanin chemical structure affected chemopro-
tection, with non-acylated monoglycosylated anthocyanins having greater inhibitory
effect on proliferation of another colon cancer cell line, HT-29, whereas antho-
cyanins with pelargonidin, triglycoside, and/or acylation with cinnamic acid exerted
the least effect (Jing et al., 2008). They concluded that anthocyanins played a major
role in chemoprotection and exerted an additive interaction with the other phenolics
present.
Freeze-dried preparations of two V. ashei cultivars (cv. Tifblue and cv. Premier)
were sequentially extracted with solvents of various polarities and shown to pos-
sess in vitro antiproliferative activity against CaSki and SiHa cervical cancer cell
lines and MCF-7 and T47-D breast cancer cell lines (Wedge et al., 2001). Prolifer-
ation inhibitory and apoptosis-inducing effects of polyphenolic compounds from
V. ashei (cv. Briteblue, cv. Tifblue, and cv. Powderblue) were also assessed in
a systematic study of Caco-2 and HT-29 (Yi et al., 2005). Extracts were further
separated into phenolic acid, tannin, flavonol, and anthocyanin-enriched fractions,
and some individual phenolic acids and flavonoids were identified by HPLC with
>90% purity in anthocyanin fractions. The dried extracts and fractions were tested
for antiproliferation activities and induction of apoptosis by addition to the cell
culture medium. Flavonol and tannin fractions resulted in 50% inhibition of cell
proliferation, whereas the phenolic acid fraction showed relatively lower bioactiv-
ities with 50% inhibition at higher concentrations of test preparations in both cell
lines. The greatest antiproliferation effect among all four fractions was from the
anthocyanin fractions, which significantly inhibited cell growth by >50% at con-
centrations in the μg·mL−1 range. Anthocyanin fractions also induced apoptosis
resulting in —two to seven times increase in DNA fragmentation. Anthocyanin frac-
tions from V. ashei cultivars, principally containing delphinidin, cyanidin, peonidin,
petunidin, and malvidin, increased apoptosis as determined by DNA fragmenta-
tion and cysteine–aspartic acid protease, caspase-3, activity assays (Srivastava et al.
2007). DNA fragmentation increased at anthocyanin concentrations from 50 to 150
μg·mL−1 with cv. Tifblue and cv. Powderblue, but a prominent ladder was apparent
in cells treated with 50–100 μg·mL−1 of the anthocyanin fraction of cv. Bright-
blue and cv. Brightwell as compared to cells treated with 150 μg·mL−1 . Apoptosis
related caspase-3 activity in the control cells and the cells treated with anthocyanins
from all four cultivars demonstrated a significant positive difference.
Extracts of six popularly consumed berries, including V. corymbosum,
V. macrocarpon, as well as Rubus and Fragaria species, were analyzed for their
phenolic constituents using high-performance liquid chromatography with ultra-
violet detection (HPLC-UV) and electrospray ionization mass spectrometry (LC-
ESI-MS) detection, and evaluated ability to inhibit the growth of human oral (KB,
CAL-27), breast (MCF-7), colon (HT-29, HCT116), and prostate (LNCaP) tumor
cell lines (Seeram et al., 2006). At concentrations in the μg·mL−1 range, increasing
concentration of berry extract was shown to increase inhibition of cell proliferation
in all of the cell lines tested, but with different degrees of potency between cell
lines. All berry extracts were also evaluated for their ability to stimulate apoptosis
of the inflammatory cyclooxygenase (specifically, COX-2) expressing HT-29 cells,
but Rubus and Fragaria were most effective. V. corymbosum (cv. Bluecrop) leaf
extract was highly inhibitory in vitro against a drug-sensitive promyelocytic HL60
human cell line, although it was much less effective against multi-drug resistant
sublines exhibiting two different MDR phenotypes: HL60/VINC (overexpressing
P-glycoprotein) and HL60/DOX (overexpressing multi-drug resistance protein,

MRP1) (Skupien et al., 2006).
Antiproliferation assays in vitro with HepG2 human liver cancer cells showed a
high inhibitory effect of V. macrocarpon, followed by many other types of popular
fruits (Sun et al., 2002). Extracts of whole V. macrocarpon fruit were assayed for
radical-scavenging activity and tumor growth inhibition using seven tumor cell lines
(Yan et al., 2002). Selective inhibition of K562 human leukemia cells and HT-29
colon cancer cells was observed from a methanolic extract. In a further of inves-
tigation of tumor cell inhibitory components of Vaccinium, a total V. macrocarpon
extract (TCE) was analyzed, quantified, and separated into fractions enriched with
respect to sugars (39.4%), organic acids (30.0%), total polyphenols (10.6%), proan-
thocyanidins (5.5%), and anthocyanins (1.2%) (Seeram et al., 2004). The antipro-
liferative effects of the TCE (200 μg·mL−1 ) versus all fractions were evaluated
against human oral (KB, CAL27), colon (HT-29, HCT116, SW480, SW620), and
prostate (RWPE-1, RWPE-2, 22Rv1) cancer cell lines using a luminescent ATP cell
viability assay. The total polyphenols fraction was the most active fraction against
all cell lines with 95 and 96.1% inhibition of CAL27 and KB oral cancer cells,
respectively. For the colon cancer cell lines, the antiproliferative activity of TCE
was greater against HCT116 (92.1%) than against HT-29 (61.1%), SW480 (60%),
and SW620 (63%). TCE and all fractions showed ≥50% antiproliferative activity
against prostate cancer cells, but total polyphenols was the most inhibitory fraction,
with efficacy against RWPE-1 (95%), RWPE-2 (95%), and 22Rv1 (99.6%). Con-
versely, the sugars’ fraction did not inhibit the proliferation of any cancer cell lines.
The authors concluded that enhanced antiproliferative activity of total polyphenols
compared to TCE, and its individual phytochemicals (and with a compositional
majority of sugars and organic acids), suggests synergistic or additive antiprolif-
erative interactions of the anthocyanins, proanthocyanidins, and flavonol glycosides
within the extract.
A V. macrocarpon proanthocyanidin-rich extract (PAC) was evaluated for chemo-
prevention of esophageal adenocarcinoma (recognized through its precursor lesion,
Barrett’s esophagus) in model SEG-1 human esophageal adenocarcinoma cells
(Kresty et al., 2008). PAC pretreatment significantly inhibited the viability and pro-
liferation of SEG-1 cells in a time- and dose-dependent manner. Moreover, PAC
significantly inhibited acid-induced cell proliferation of SEG-1 cells and induced
cell cycle arrest at the G1 checkpoint with a significant reduction in the percentage
of SEG-1 cells in S-phase following 24 and 48 h of exposure. PAC treatment also
resulted in significant induction of apoptosis. The authors propose that PAC mod-
ulates cell cycle regulation, aberrant proliferation, and apoptosis, all key biological
processes altered during progression to esophageal adenocarcinoma.
Extracts of V. macrocarpon significantly inhibited MCF-7 cell proliferation at
doses of 5–30 mg·mL−1 (Sun and Hai Liu, 2006). Doses from 10 to 50 mg·mL−1
arrested MCF-7 cells at G0 /G1 phase, and a constant increasing pattern of the G1 /S
index was observed in the treatment group, whereas the G1 /S ratio of the control
group decreased concomitantly between 10 and 24 h of treatment. Following 24 h
exposure to extracts, the G1 /S index of MCF-7 cells was approximately six times
higher than that of the control group. Induction of apoptosis in MCF-7 cells was
observed in a dose-dependent manner after exposure to extracts for 4 h. A dose of
50 mg·mL−1 resulted in a 25% higher ratio of apoptotic cells to total cells as com-
pared to the control groups. These results suggest that extracts of V. macrocarpon
possess the ability to suppress the proliferation of MCF-7 cells, which can be
attributed, at least in part, to both the initiation of apoptosis and the G1 phase arrest.
Novel purified triterpene cinnamates from V. macrocarpon, identified as
cis (1) and trans (2) isomers of 3-O-p-hydroxycinnamoyl ursolic acid, were
bioassayed in human tumor cell lines in vitro (Murphy et al., 2003). The
cis isomer showed slightly greater activity than the trans moiety in most
cell lines, with a GI50 of approximately 20 μM in MCF-7, ME180 human
cervical epithelial, and PC3 androgen-independent human prostate tumor cell
lines. The GI50 value is a redefinition of the IC50 value, the concentration
that causes 50% growth inhibition, corrected for the cell count at time zero
(http://dtp.nci.nih.gov/docs/compare/compare_methodology.html). Quercetin was
slightly less active than cis-3-O-p-hydroxycinnamoyl ursolic acid, while cyanidin-
3-galactoside exhibited much lower cytotoxicity, with greater than 250 μM in
all cell lines. Antiproliferative activities of isolated V. macrocarpon compounds
against MCF-7 and HepG2 human liver cancer cells were also evaluated through
bioactivity-guided fractionation (He and Liu, 2006). Among the compounds iso-
lated, ursolic acid, quercetin, and 3,5,7,3 ,4 -pentahydroxyflavonol-3-O-beta-D-
glucopyranoside showed potent inhibitory activity toward the proliferation of
MCF-7 cells, with EC50 values of 11.7 ± 0.1, 137.5 ± 2.6, and 23.9 ± 3.9
μM, respectively. Ursolic acid, quercetin, and 3,5,7,3 ,4 -pentahydroxyflavonol-3-
O-beta-D-glucopyranoside showed potent antiproliferative activities against HepG2
cell growth, with EC50 values of 87.4 ± 2.7, 40.9 ± 1.1, and 49.2 ± 4.9 μM,
respectively.
In hormone-dependent tumor cell lines, an extract of V. macrocarpon presscake
(material remaining after squeezing juice from the berries) containing flavonoids
inhibited proliferation of eight human tumor cell lines of multiple origins (Ferguson
et al., 2004). The androgen-dependent prostate cell line LNCaP was the most sen-
sitive of those tested, but other human tumor lines originating from breast (MCF-
7), skin (SK-MEL-5), colon (HT-29), lung (DMS114), and brain (U87) were less
sensitive. An estrogen-independent breast line (MDA-MB-435) and an androgen-
independent prostate line (DU145) were the least sensitive and required compar-
atively high doses of extract to inhibit proliferation. Nonetheless, the extract was
able to block cell cycle progression in MDA-MB-435 cells and induce cells to
undergo apoptosis in a dose-dependent manner as demonstrated by using flow cyto-
metric analyses of DNA distribution (cell cycle) and annexin V-positivity (apop-
tosis marker). These authors also reported that V. macrocarpon presscake was
shown to decrease the growth and metastasis of tumors in mice bearing human
breast tumor MDA-MB-435 cells. Subsequently, explants of human tumor cell
lines glioblastoma multiforme (U87), colon carcinoma (HT-29), and androgen-
independent prostate carcinoma (DU145) were shown to be sensitive to a flavonoid-
rich fraction and a more purified proanthocyanidin-rich fraction of V. macrocarpon
(Ferguson et al., 2006). Both significantly slowed the growth of explant tumors of
U87 in vivo, but the proanthocyanidin-rich fraction inhibited growth of HT-29 and
DU145 explants, inducing complete regression of two DU145 tumor explants. Flow
cytometric analyses of in vitro-treated U87 cells indicated that both fractions also
could arrest cells in G1 phase of the cell cycle and induce cell death within 24–48 h
of exposure, consistent with in vivo results. V. macrocarpon seed flour extracts were
found also to significantly inhibit HT-29 cell proliferation, although specific com-
pounds were not cited for this effect (Parry et al., 2006).
Studies in animal models. The chemopreventive efficacy of V. macrocarpon juice
concentrate in an experimental in vivo model of urinary bladder cancer was evalu-
ated using female Fischer-344 rats (Prasain et al., 2008). The animals received N-
butyl-N-(4-hydroxybutyl)-nitrosamine (OH-BBN) and, following treatment, a dose-
dependent preventive effect of juice concentrate was observed, with a reduced
number of urinary bladder cancers (38%) versus those observed in the control
group. Serum and urine were collected after the administration of the juice con-
centrate, and quercetin, as well as its methylated derivative, was detected in the
urine samples. As a consequence of poor bioavailability, no quercetin was detected
in the serum samples. Although quercetin moieties were detected predominantly,
the authors conclude that many components of V. macrocarpon juice concentrate
may be responsible for some of the observations.
Experiments designed to study the inhibitory effect against the formation of
colonic aberrant crypt foci (ACF) pre-neoplastic lesions of pterostilbene, an impor-
tant compound in Vaccinium fruits, were conducted in Fisher 344 male rats (Suh
et al., 2007). Animals were treated with the colon carcinogen, azoxymethane
(AOM), and were fed experimental diets with or without pterostilbene. At sacrifice,
colons were evaluated for ACF formation, for inhibition of inducible nitric oxide
synthase (iNOS) and proliferating cell nuclear antigen, and for effects on mucin gly-
coprotein (MUC2). Administration of pterostilbene significantly suppressed AOM-
induced formation of ACF and multiple clusters of aberrant crypts. Importantly,
dietary pterostilbene also suppressed AOM-induced colonic cell proliferation and
iNOS expression, with the latter effect being confirmed in cultured human colon
cancer cells. To test directly the chemopreventive potential of fruit rich in pterostil-
bene, another study examined the possible effects of V. corymbosum and V. macro-
carpon juice, as well as other fruit preparations, on AOM-induced ACF in Fisher
344 male rats (Boateng et al., 2007). The rats received subcutaneous injections of
AOM and, upon sacrifice, total ACF numbers assessed in the rats fed control diet,
V. corymbosum, and V. macrocarpon were, respectively, 171.67 ± 5.6, 11.33 ± 2.85,
and 39.0 ± 15.31, with numbers from other types of flavonoid-rich fruits ranging
from 15.67 ± 1.86 to 33.67 ± 0.89. Total glutathione-S-transferase (GST) activ-
ity in the liver of the rats fed fruit preparations was significantly higher as compared
with the control. Although juice from V. macrocarpon was effective, among all fruits
and fruit juices, V. corymbosum juice induced the most significant reductions in the
formation of AOM-induced ACF.
The chemoprotective activity of anthocyanin-rich extracts (AREs) from
V. myrtillus and other fruits was assessed with multiple biomarkers of colon cancer
in male rats treated with AOM (Lala et al., 2006). Fischer 344 male rats were fed
the AIN-93 diet (control) or AIN-93 diet supplemented with AREs for 14 weeks.
Biomarkers that were evaluated included the number and multiplicity of colonic
aberrant crypt foci (ACF), colonic cell proliferation, urinary levels of oxidative
DNA damage, and expression of COX-2 genes. To assess the bioavailability, lev-
els of anthocyanins in serum, urine, and feces were evaluated; total ACF were
reduced in all treatment groups compared with the control group. The number
of large ACF, colonic cellular proliferation, and COX-2 mRNA expression was
decreased by V. myrtillus in ARE-fed rats. High levels of fecal anthocyanins and
increased fecal mass and fecal moisture occurred in ARE-fed rats. There was also
a significant reduction in fecal bile acids in ARE-fed rats. The levels of urinary
8-hydroxyguanosine were similar among rats fed different diets. These results are
consistent with other studies and suggest a protective role of AREs in colon car-
cinogenesis through multiple mechanisms of action. Collectively, these observations
provide insights into pivotal mechanisms of anthocyanin- and stilbene-mediated
antitumor effects and support recommending consumption of fruits and prepara-
tions rich in these for colon cancer chemoprevention and, potentially, for treatment
of human gastrointestinal tract cancer.
Prevention studies in the estrogen-sensitive female ACI rat model allowed iden-
tification of agents that are effective against estrogen-induced mammary tumorige-
nesis (Aiyer et al., 2008). Compared with the control group, V. corymbosum powder
showed a 40% reduction in tumor volume, whereas pure ellagic acid reduced tumor
volume by 75% and tumor multiplicity by 44%. This is the first report showing
the significant efficacy of both ellagic acid and berries in the prevention of solely
estrogen-induced mammary tumors.
11.2.1.7 Regulation of Subcellular Signaling Pathways and Modulation

of Transcription Factors
Studies in tumor cell lines. Commercially prepared anthocyanin-rich extracts were
shown to inhibit proliferation of colon cancer-derived HT-29 cells at low concentra-
tions that did not affect non-tumorigenic colonic NCM460 cells (Zhao et al., 2004).
The effects of berry extracts containing different phenolic profiles on cell viabil-
ity and expression of markers of cell proliferation and apoptosis were studied in
HT-29 cells by another group (Wu et al., 2007). Anthocyanins were the predomi-
nant phenolic compounds in V. myrtillus and other extracts (including those from
V. vitis-idaea). Among these, V. myrtillus extract was the most potent. An increase
in the expression of p21WAF1, an inhibitor of cell proliferation and a member of the
cyclin kinase inhibitors, was seen in cells exposed to all extracts. The pro-apoptosis
marker, Bax, was increased 1.3-fold in V. myrtillus-treated cells, whereas the pro-
survival marker, Bcl-2, was detected only in control cells. The results demonstrate
that berry extracts inhibit cancer cell proliferation mainly via the p21WAF1 path-
way. As other berries with comparatively very low anthocyanin content were potent
inhibitors of cell proliferation, it was concluded that, in addition to anthocyanins
found in V. myrtillus and other deeply pigmented fruits, an array of phenolic or non-
phenolic phytochemicals is responsible for the antiproliferative activity of berries.
The juice of 14 different berries, including four Vaccinium species, was evalu-
ated for antioxidant capacity, antiproliferative activity, induction of apoptosis and
cell cycle arrest, and anti-inflammatory activity (Boivin et al., 2007). The growth
of various cancer cell lines, including those of stomach, prostate, intestine, and
breast, was strongly inhibited by V. angustifolium, V. myrtilloides, and V. macro-
carpon juices, but not (or only slightly) by V. corymbosum juice. No correlation was
found between the antioxidant capacity and antiproliferative activity of the juice.
The inhibition of cancer cell proliferation appeared to involve cell cycle arrest, not
caspase-dependent apoptosis, as evidenced by downregulation of the expression of
calmolulin-dependent kinases, cdk4 and cdk6, cyclin D1 and cyclin D3. Approx-
imately half of the berries evaluated, including those of Vaccinium, significantly
inhibited the tumor necrosis factor (TNF)-induced activation of COX-2 expres-
sion and activation of NF-kappaB. Interestingly, berry juices have a pronounced
distinction in their potential chemopreventive activity, and thus, consumption of a
variety of berries may prove useful for preventing or delaying the onset of tumor
development.
V. vitis-idaea extracts produced a dose-dependent inhibition of transcription acti-
vator protein-1 (AP-1) and NF-kappaB induced by either TPA tumor promoter
or ultraviolet-B (UVB) radiation in JB6 P+ mouse epidermal cells (Wang et al.,
2005). Both proteins play an important mechanistic role in ultraviolet (UV)-induced
skin carcinogenesis in mice. Pretreatment of cells with extracts blocked UVB-
induced phosphorylation of the mitogen-activated protein kinase (MAPK)-signaling
members, extracellular kinase signal-regulated kinases (ERK1 and ERK2), stress-
activated protein kinase (p38), and extracellular signal-regulated ERK kinase
(MEK1/2), but not c-Jun N-terminal kinase (JNK). The c-Jun protein is synonymous
with AP-1 and is an important regulator of cell cycle progression and apoptosis. The
extract also prevented TPA-induced phosphorylation of ERK1, ERK2, and MEK1/2
and TPA-induced neoplastic transformation of JB6 P(+) cells was also suppressed in
a dose-dependent manner in soft agar assays. In addition, extracts promoted apop-
tosis of human leukemia HL-60 cells in a dose-independent manner. These results
suggest that ERK1, ERK2, and MEK1/2 may be the primary targets of V. vitis-idaea
extracts that result in suppression of AP-1, NF-kappaB, and neoplastic transforma-
tion in JB6 P(+) cells and that cancer cell death is caused by an apoptotic mechanism
in human leukemia HL-60 cells. In other mouse epidermal cells, methanol extracts
of Vaccinium were unable to inhibit AP-1 and NF-kappaB activation by UVB and
short UV radiation, UV-C (Huang et al., 2007). Different berry extracts were able
to exert this inhibitory effect. These results suggest that berries differ in their com-
position, and hence, ability to influence signaling pathways leading to activation of
NF-kappaB and AP-1 when using UV light as the inducer. Another group inves-
tigated whether V. myrtillus and quercetin, notably abundant in this fruit, have the
ability to induce transcription of Fos-related antigen 1 (Fra-1), which contains two
EpREs in its promoter (Myhrstad et al., 2006). Fra-1 is a member of the AP-1 fam-
ily of transcription factors and, due to the lack of transactivation domain Fra-1, can
suppress activation of AP-1. Their work demonstrated that V. myrtillus preparations

and pure quercetin were able to induce the Fra-1 promoter as well as the cellular
content of Fra-1 mRNA, and suggested that induction is mediated through EpREs.
Naturally occurring stilbenes, resveratrol, pterostilbene, and piceatannol, occur
in Vaccinium and are known to be strong antioxidants and anti-inflammatory agents
with cancer chemopreventive activities (Rimando et al., 2004). Pterostilbene was
able to inhibit cell proliferation and induce apoptosis of human gastric carcinoma
AGS cell line (Pan et al., 2007). Pterostilbene-induced cell death was characterized
with changes in nuclear morphology, DNA fragmentation, and cell morphology.
The results showed that caspase-2, -3, -8, and -9 are all activated by pterostilbene,
together with cleavage of the downstream caspase-3 target DNA fragmentation
factor (DFF-45) and poly(ADP-ribose) polymerase. Moreover, activation of the cas-
pase cascade, the Bcl-family of proteins, and the mitochondrial pathway is respon-
sible for pterostilbene-induced apoptosis. Pterostilbene markedly enhanced the
expression of growth arrest of DNA damage-inducible gene 45 and 153 (GADD45
and GADD153), blocked cell cycle progression at G1 phase, increased the p53,
p21, p27, and p16 proteins, and decreased levels of cyclin A, cyclin E, cyclin-
dependent kinases Cdk2, Cdk4, and Cdk6, but the expression of cyclin D1 was not
affected. Also, the degree of phosphorylation of retinoblastoma protein (Rb) was
decreased. Collectively, pterostilbene induced apoptosis in AGS cells through acti-
vating the caspase cascade via the mitochondrial and Fas/FasL pathway, GADD
expression, and by modifying cell cycle progress and changes in several cycle-
regulating proteins.
Studies in animal models. Mirtoselect, a 36% anthocyanin mixture from
V. myrtillus (available from Indena, S.p.A., http://www.mirtoselect.info) or isolated
cyanidin-3-glucoside (C3G), the most abundant anthocyanin in the diet, was eval-
uated for intestinal adenoma formation in the Apc-mutated multiple intestinal neo-
plasia (Min/+) mouse, a genetic model of human familial adenomatous polyposis
(Cooke et al., 2006). Min/+ mice ingested Mirtoselect or C3G at <0.3% of the
diet, and intestinal adenomas were counted at sacrifice. Plasma, urine, and intestinal
mucosa were analyzed for presence of anthocyanins by high-pressure liquid chro-
matography (HPLC) with detection by UV spectrophotometry (520 nm) or tandem
mass spectrometry (multiple reaction monitoring). Total anthocyanin levels in mice
on C3G or Mirtoselect were 43 ng and 8.1 μg·g−1 tissue, respectively, in the intesti-
nal mucosa, and 7.2 and 12.3 μg·g−1 in the urine. Anthocyanins were found at the
analytical detection limit in the plasma and at quantifiable levels in the intestinal
mucosa; glucuronide and methyl metabolites were identified in intestine and urine.
Ingestion of either C3G or Mirtoselect reduced adenoma load dose dependently. At
the highest doses of C3G and Mirtoselect, adenoma numbers were decreased signif-
icantly by 45 or 30%, respectively, compared to controls.
Subsequently, V. myrtillus and V. vitis-idaea, along with other berry prepara-
tions, natural ellagitannins, and pure ellagic acid were evaluated for their effects on
adenoma formation in the intestinal tract of Min/+ mice (Misikangas et al., 2007;
Mutanen et al., 2008). The mice were fed high-fat AIN93-G diets containing test
substances for 10 weeks. All of the berries significantly reduced tumor number
(15–30%), but V. vitis-idaeaalso reduced tumour size by over 60% and, as compared
to the control, resulted in a larger proportion of small adenomas with a smaller pro-
portion of large adenomas. On the molecular level, beta-catenin and cyclin D1 pro-
tein levels in the adenomas and in the normal-appearing mucosa were determined
by Western blotting and immunohistochemistry. Early changes in gene expres-
sion in the normal-appearing mucosa were analyzed by Affymetrix microarrays.
V. vitis-idaea increased the level of cyclin D1 in the large adenomas. Affymetrix
microarrays revealed changes in genes implicated in colon carcinogenesis, includ-
ing the decreased expression of the adenosine deaminase, ecto-5f-nucleotidase and
prostaglandin receptor PGE2 subtype EP4. Ellagic acid had no effect on the number
or size of adenomas in the distal or total small intestine, but it increased adenoma
size in the duodenum when compared with the control diet. The ellagitannins did not
have any effect on the adenoma formation. Taken together, the results of these three
groups, the efficacy of berry preparations, Mirtoselect from V. myrtillus, and C3G
in the Min/+ mouse, warrant the further development of anthocyanins as potential
human colorectal cancer chemopreventive agents.
11.2.1.8 Inhibition of Growth Factor-Dependent Processes, Inflammation,

and Tumor Angiogenesis and Metastasis
Inflammatory processes mediated by COX-2 and associated growth factors have
been implicated in the invasiveness of various types of tumors. COX-2 inhibitors,
such as nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit carcinogenesis,
reduce blood flow through the tumor tissue and, thereby, inhibit angiogenic activity
within the tumor. A crude hydroalcoholic extract from V. corymbosum was assessed
in anti-inflammatory and antinociceptive models (Torri et al., 2007). Inflamma-
tion was reduced significantly in the carrageenan test (rat paw edema), histamine
assay, and myeloperoxidase (MPO) assay after injection of carrageenan. For the
abdominal constriction test, inhibition observed for the extract was almost as
potent as that for indometacin. In the formalin test, the V. corymbosum extract
and indometacin similarly inhibited only the second phase. With the granulomatous
tissue assay, the steroidal anti-inflammatory, dexamethasone, displayed significant
activity, whereas the test extract was inactive. Consumption of V. corymbosum dis-
played anti-inflammatory, as well as antinociceptive activity, and it may be helpful
for the treatment of inflammatory disorders, some of which participate in the etiol-
ogy of cancer.
However, V. corymbosum and V. macrocarpon preparations were found to
be inactive against the COX enzyme system (Seeram et al., 2001). A possible
explanation is the absence in Vaccinium species of compounds (i.e., cyanidin-
3-glucosylrutinoside and cyanidin-3-rutinoside) to which cyclooxygenase inhibi-
tion was attributed in these experiments. Subsequently, commercial extracts of
V. angustifolium (VitaBlueTM ) were shown to selectively inhibit COX-2 in vitro
and to inhibit proliferation of an unspecified human prostate tumor cell line (VDF
FutureCeuticals, www.futureceuticals.com). Potent in vitro inhibition of COX-2
was observed, with no effect of the extract on the related enzyme, COX-1. The
importance of this finding relates to the overexpression of COX-2 in neoplasias, and

that increased activity of COX-2 promotes tumor vascularization and angiogenesis.
In later investigations, the effect of anthocyanidins on expression of COX-2 was
investigated in lipopolysaccharide (LPS)-activated murine macrophage RAW264
cells. Delphinidin and cyanidin aglycones inhibited LPS-induced COX-2 expres-
sion, but pelargonidin, peonidin and malvidin were ineffective (Hou et al., 2005).
Delphinidin was the most potent inhibitor and possesses an ortho-dihydroxyphenyl
structure on the B-ring. A dose-dependent inhibition by delphinidin of COX-2
expression at both mRNA and protein levels was observed. Suppression of degrada-
tion of an inhibitor of the nuclear transcription factor NF-kappaB (IkappaB-alpha),
nuclear translocation of a subunit of NF-kappaB (p65) and CCAAT/enhancer-
binding protein (C/EBP) delta, and phosphorylation of c-Jun, but not CRE-binding
protein (CREB), was demonstrated by Western blotting. Moreover, delphinidin sup-
pressed the activations of MAPK including JNK, ERK, and p38 kinase. MAPK
inhibitors (U0126 for MEK1/2, SB203580 for p38 kinase and SP600125 for JNK)
specifically blocked LPS-induced COX-2 expression. Thus, it appears LPS-induced
COX-2 expression by activating MAPK pathways, and delphinidin suppressed
COX-2 by blocking MAPK-mediated pathways with the attendant activation of NF-
kappaB, AP-1, and C/EBPdelta. These authors provide the first molecular basis that
anthocyanidins with ortho-dihydroxyphenyl structure may have anti-inflammatory
properties through the inhibition of MAPK-mediated COX-2 expression.
Various Vaccinium extracts and a commercial mixed berry powder (Optiberry R
)
exhibited a high ORAC value, low cytotoxicity, and superior anti-angiogenic
properties (Atalay et al., 2003; Bagchi et al., 2004; InterHealth Nutraceuticals,
http://www.interhealthusa.com). Anti-angiogenic approaches to treat cancer rep-
resent a priority area in vascular tumor biology, as invasive tumors develop new
blood vessels to fuel their rapid proliferation by a process known as angiogene-
sis. The mixed berry powder, as well as that derived from V. angustifolium, signif-
icantly inhibited expression of both H2 O2 and TNF-α-induced vascular endothe-
lial growth factor (VEGF), a key regulator of tumor angiogenesis, in human
keratinocytes. Optiberry significantly inhibited inducible monocyte chemotactic
protein 1 (MCP-1) and NFkappaB transcription associated with angiogenesis in
endothelioma cells. When pre-treated with berry powders, endothelioma cells
showed diminished hemangioma formation, a powerful model to study in vivo
angiogenesis, and markedly decreased tumor growth by more than 50%. Matrigel
assay, using human microvascular endothelial cells, showed that OptiBerry impaired
angiogenesis. Histological analysis demonstrated substantially decreased infiltra-
tion of macrophages in hemangioma of treated mice compared to placebo-treated
controls. These studies provided the first in vivo evidence to substantiate the anti-
angiogenic property of edible berries.
Cancer cells invade normal tissue with matrix-metalloproteinase enzymes. Reg-
ulation of these matrix-metalloproteinases (MMPs), the major mediators of extra-
cellular matrix (ECM) degradation, is crucial to regulate ECM proteolysis, which
is important in metastasis. In a study of three flavonoid-enriched fractions pre-
pared from V. angustifolium, a crude fraction, an anthocyanin-enriched fraction,
and a proanthocyanidin-enriched fraction were compared for inhibitory effects on

MMP activity in DU145 human prostate cancer cells in vitro (Matchett et al.,
2005). All fractions elicited a downregulation of MMP-2 and MMP-9, but the
proanthocyanidin-enriched fraction was found to be the most effective. No induc-
tion of either apoptotic or necrotic cell death was noted in response to treatment of
DU145 cells. The activity of the endogenous tissue inhibitors of metalloproteinases
(TIMPs) from these cells was also evaluated (Matchett et al., 2006). Increases in
TIMP-1 and TIMP-2 activity were observed in response to these fractions. The pos-
sible involvement of protein kinase C (PKC) and mitogen-activated protein (MAP)
kinase pathways in the flavonoid-mediated decreases in MMP activity was observed.
These findings indicate that Vaccinium flavonoids may employ multiple mechanisms
for downregulation of MMP activity in these cells, which may decrease overall
ECM degradation. These effects may be important in controlling tumor metastatic
processes.
V. myrtillus extracts were tested for effects on angiogenesis in vitro and in
vivo (Matsunaga et al., 2007). The extracts, at low μg·mL−1 concentration and
GM6001, a MMP inhibitor (0.1–100 μM), inhibited in a dose-dependent man-
ner both tube formation and migration of human umbilical vein endothelial cells
(HUVECs) induced by vascular endothelial growth factor-A (VEGF-A). Further-
more, the extracts inhibited VEGF-A-induced proliferation of HUVECs and VEGF-
A-induced phosphorylations of extracellular signal-regulated kinase 1/2 (ERK 1/2)
and serine/threonine protein kinase family protein kinase B (Akt). Phosphoryla-
tion of phospholipase Cgamma was not affected by treatment. In an in vivo assay,
intravitreal administration of extracts inhibited the formation of neovascular tufts
during oxygen-induced retinopathy in mice. Thus, inhibition of phosphorylations
of ERK 1/2 and Akt by extracts may be responsible, at least in part, for inhibition
of angiogenesis both in vitro and in vivo. In order to evaluate further the molec-
ular basis of anti-inflammatory function and underlying genes targeted by V. myr-
tillus, gene expression profiling through DNA microarray was performed on extract-
treated macrophages (Chen et al., 2008). Utilizing “Panther” group analysis, 308
genes affected by the extract with ≥1.5-fold change were classified into 43 cate-
gories relating to signaling pathways (26), biological processes (97), and molec-
ular functions (186). The genes categorized as “defense, inflammatory response,
cytokines activities, and receptor activities” were further identified, and some of
them were confirmed by real-time polymerase chain reaction. These findings indi-
cate that V. myrtillus may be effective against diseases involving angiogenesis, such
as cancer, although investigations will be needed to clarify the major angiogenesis-
modulating constituent(s) in the extracts.
A point that must be considered in the vigorous pursuit of dietary com-
pounds as chemopreventives, particularly based on the success of therapeutic anti-
inflammatory compounds to inhibit, delay, and reverse colon carcinogenesis, is the
metabolic transformation of these food-derived compounds in the gut that may
affect their bioactivity (Russell et al., 2007). An example was made of esterified
ferulic acid and its 5-5 -linked dimer, one of many commonly consumed dietary phe-
nolics which have the potential to undergo predominant microbial transformations
(de-esterification, hydrogenation, demethylation, dehydroxylation, and dimer cleav-

age). Following incubation with human intestinal flora, potential anti-inflammatory
properties were compared by measuring the ability of the parent compounds and
their metabolites to modulate inflammatory prostanoid production in a responsive
cell line following a cytokine-induced insult. Various metabolites demonstrated
highly different effects, suggesting that microbial transformation of dietary com-
pounds will have important anti-inflammatory implications in chemoprevention,
especially with respect to colon cancer.
11.2.1.9 Protection from Toxicity of Chemotherapeutic Agents

The overall protective properties of Vaccinium preparations and compositions have
led to proposals of their potential protective effects from cancer chemotherapeutic
agents (Seeram, 2008b). In C57BL/6 mice, anthocyanin-rich preparations demon-
strated protective effects from myelotoxicity caused by a single dose of the cancer
chemotherapeutic agent, 5-fluorouracil (5-FU), expressed as induced severe periph-
eral erythrocytopenia, thrombocytopenia, and leucopenia as well as hypocellularity
of the spleen and bone marrow (Choi et al., 2007). Furthermore, treatment with a
monomeric anthocyanin did not interfere with, but rather, enhanced the chemother-
apeutic efficacy of 5-FU in vitro. These results suggest that V. myrtillus components
may have protective potential against 5-FU-induced myelotoxicity and/or the ability
to enhance the chemotherapeutic effectiveness of 5-FU.
Anecdotal evidence from chemotherapy patients in a clinic providing transfu-
sions for thrombocytopenia was suggestive of a potent effect on platelet recov-
ery of a commercial Vaccinium preparation, AuroraBlue R
(Denali BioTech-
nologies, www.denalibiotech.com). AuroraBlue is a proprietary blend of whole,
wild Alaska Vaccinium ovalifolium Sm. (Alaska early blueberry), V. alaskaense
How. (Alaska black huckleberry), V. uliginosum L. subsp. alpinum (Bigel.)
Hult. (Alpine blueberry), and V. uliginosum L. subsp. microphyllum Lange
(Bog Bilberry), dried by Refractance Window R
technology (MCD Technologies,
http://www.mcdtechnologiesinc.com). These berries are comparable or higher in
levels of flavonoids reported for V. myrtillus on a fresh weight basis, and those com-
pounds are preserved during the gentle drying process. Patients who voluntarily con-
sumed recommended daily doses of AuroraBlue received fewer transfusions over a
6-week period than in a former comparable preceding period without intervention.
In preliminary studies, AuroraBlue was also observed to have significant inhibitory
effects on HUVECs, in particular on MCP-1 and epithelial cell-derived neutrophil-
activating peptide-78 (ENA-78/CXCL5), consistent with some of the observations
of others. Interestingly, such pro-inflammatory and angiogenic chemokines are
potential factors that contribute to the aggressive biology of many malignancies.
Furthermore, a natural product preparation containing, in part, Vaccinium phyto-
chemicals, has been shown to protect against oxidative stress in hematopoietic and
stem cell lines (Shytle et al., 2007). Collectively, these observations clearly merit
further investigation in controlled clinical trials.
11.2.1.10 Studies on Novel and Wild Vaccinium Species

Only a small part of the wild plant flora has been tested for any kind of bioactiv-
ity. Yet, many of these plants have been essential to humans as food and medicine
throughout the ages. More than 400 species in the genus Vaccinium have played
an important role in human cultures worldwide. Wild and novel Vaccinium species
have been shown to possess similar health-promoting compositions as the com-
mercially important species (Sakakibara et al., 1973; Sticher et al., 1979; Shang
and Chen, 1992; Tu et al.,1997; Chkhikvishvili and Kharebava, 2001; Meyer et al.,
2002; Lee et al., 2004; Taruscio et al., 2004; Ayaz et al., 2005; Chukarina et al.,
2007; Hosseinian and Beta, 2007; Nicoue et al., 2007; Wei et al., 2007; Latti
et al., 2008; Rieger et al., 2008; Zhao et al., 2008). Despite variability between cul-
tivars of commercially important species, comparisons of conventionally cultivated
versus organically grown crops consistently show organic fruits to contain the higher
levels of flavonoids. In conventionally cultured fruit, the average values for the
ORAC, total anthocyanin, and total phenol content were 30.8 μmol of TE (Trolox
equivalents)·g−1 of fwt, 82.4 mg·100 g−1 of fwt, and 190.3 mg·100 g−1 of fwt,
respectively. In organically cultured fruit, the average values for ORAC, total antho-
cyanins, and total phenolic content were 46.14 μmol of TE (Trolox equivalents)·g−1
of fresh weight (fwt), 131.2 mg·100 g−1 of fwt, and 319.3 mg·100 g−1 of fwt,
respectively. The organic culture also produced fruit with higher contents of
myricetin 3-arabinoside, quercetin 3-glucoside, delphinidin 3-galactoside, delphini-
din 3-glucoside, delphinidin 3-arabinoside, petunidin 3-galactoside, petunidin 3-
glucoside, and malvidin 3-arabinoside than conventional culture. Notably, the levels
of flavonoids in wild species are, on average, two- to ten-times higher than those of
cultivated and organic relatives (Kalt et al., 2001; Wang and Stretch, 2002; Taruscio
et al., 2004; Brambilla et al., 2008; Wang et al., 2008).
Investigations of wild Vaccinium species revealed exceptional compositions and
antioxidant properties (Taruscio et al., 2004). Of particular note were V. ovatum
Pursh (Evergreen Huckleberry) and V. ovalifolium Sm. In another study, two west-
ern North American species, V. ovatum and V. membranaceum Douglas ex Torr.
(Thinleaf Huckleberry), were evaluated for their total, and individual, anthocyanin
and polyphenolic compositions (Lee et al. 2004). Total anthocyanins (ACY), total
phenolics (TP), ORAC and FRAP were greater in V. ovatum than in V. mem-
branaceum. Anthocyanin fractions of each species had the highest amount of
ACY, TP, and antioxidant activity. Similar to V. myrtillus, each species contained
15 anthocyanins (galactoside, glucoside, and arabinoside of delphinidin, cyanidin,
petunidin, peonidin, and malvidin) but in different proportions. Polyphenolic pro-
files differed but, in both species, were composed mainly of cinnamic acid deriva-
tives and flavonol glycosides. The major polyphenolic compound in V. ovatum was
chlorogenic acid, but in V. membranaceum, was neochlorogenic acid. An ethanol
extract of Vaccinium parvifolium Sm. (Red Huckleberry) was tested in the DPPH∗
assay and compared to nine other North American edible plant extracts, although
the results from this work on V. parvifolium were unremarkable (Acuña et al.,
2002).
Compared to juices derived from 43 small fruits, Vaccinium smallii A.

Gray strongly inhibited the proliferation of multiple cancer cell lines exam-
ined; and yet, all of these juices were substantially less cytotoxic toward nor-
mal human cell lines (Yoshizawa et al., 2000a). Furthermore, V. smallii clearly
induced, in a concentration-dependent manner, differentiation of HL-60 cells
to monocyte/macrophage characteristics, as indicated by histochemical and bio-
chemical examinations (Yoshizawa et al., 2000b). In a later study, fruit of Vac-
cinium stamineum L. (Deerberry) was evaluated for antioxidant capacity and
anticancer properties in JB6 P (+) mouse epidermal cells, human lung, and
leukemia cells (Wang et al., 2007). AP-1 and NF-kappaB induced by either 12-O-
tetradecanoylphorbol 13-acetate (TPA) or UVB were inhibited by pretreatment of
JB6 P (+) mouse epidermal cells with fruit extracts. The extracts also blocked TPA-
or UVB-induced phosphorylation of ERKs and MEK 1/2, two upstream regulators
of AP-1. Furthermore, the extracts inhibited proliferation of human leukemia HL-60
cancer cells and human lung epithelial cancer A549 cells and induced apoptosis in
HL-60 cells. These results suggest ERKs and MEK 1/2 signal pathway mediate inhi-
bition of TPA- or UVB-induced AP-1 and NFkappaB activity, inhibit proliferation
by HL-60 cells and cancer A549 cells, but promote apoptosis in human leukemia
HL-60 cancer cells.
11.2.2 Intervention Studies in Humans
Data from numerous cell culture and animal models indicate that Vaccinium
flavonoids are potent anticarcinogenic agents and are protective at several sites
in the carcinogenic development pathway. In the majority of in vitro and in vivo
studies, the concentration of extract or phytochemical employed is non-nutritional
(Duthie, 2007). Precisely which berry constituents are cancer chemopreventive
remains uncertain, and evidence for an anticarcinogenic effect in human studies
also remains weak, albeit promising for future work.
Intervention studies in healthy human subjects with V. corymbosum/blended fruit
juice compared to one of their principal components, quercetin, have demonstrated
protection in vitro and ex vivo against induction of oxidative DNA damage from
hydrogen peroxide (H2 O2) and formation of bulky DNA adducts of benzo(a)pyrene
(B(a)P) formed through its diol-epoxide metabolite (BPDE) (Wilms et al., 2005).
Human lymphocytes were pre-incubated with various concentrations of quercetin,
followed by incubation with hydrogen peroxide, and protection against oxidative
DNA damage was evaluated by the use of the single-cell gel electrophoresis (Comet)
assay. Quercetin-treated human lymphocytes were challenged by treatment with
B(a)P, and adduct formation was measured by 32 P-post-labeling. In these assays,
a significant dose-dependent protection by quercetin was observed against both the
formation of oxidative DNA damage and of BPDE–DNA adducts. Also, lympho-
cytes from female volunteers who consumed a quercetin-rich juice mixture for 4
weeks were treated ex vivo with an effective dose of H2 O2 and B(a)P, respectively,
before the intervention. Juice intervention led to a significant increase in the total
antioxidant capacity of plasma, as reflected by the increase of the Trolox equivalent

TEAC value and an increase in plasma quercetin content. After intervention, the
level of oxidative damage upon exposure to H2 O2 and BPDE–DNA adduct level
induced ex vivo was not significantly decreased; nonetheless, taken together with
the quercetin results, the authors suggest a protective role of dietary fruit against
destructive DNA modifications.
In a subsequent human intervention study, these authors assessed the antiox-
idative and possible anti-genotoxic properties of fruit-borne antioxidants in indi-
viduals bearing genetic polymorphisms for genes related to quercetin metabolism,
B(a)P metabolism, oxidative stress, and DNA repair, and evaluated differences in
their response to DNA protective effects of increased antioxidant intake (Wilms
et al., 2007). Healthy volunteers consumed juice containing, in part, V. corymbo-
sum, that provided known quantities of quercetin and ascorbic acid each day. After
an intervention period, plasma concentrations of quercetin and ascorbic acid and
TEAC were significantly increased. Further, a significant decrease was noted in ex
vivo H2 O2 -provoked oxidative DNA damage, measured by comet assay. Notably,
the level of ex vivo-induced BPDE–DNA adducts significantly increased upon
intervention. Statistical analysis of 34 biologically relevant genetic polymorphisms
revealed that six significantly influenced the outcome of the intervention. Lym-
phocytes from individuals bearing variant genotype for cytochrome P-450 isoform
1B1 5 (Cyp1B1 5) seemed to benefit more than wild types from DNA damage-
protecting effects upon intervention. Variants for catechol-O-methyltransferase
(COMT) tended to benefit less, or even experienced detrimental effects, from inter-
vention. With respect to glutathione S-transferase theta 1 (GSTT1), the effect is
ambiguous; variants respond better in terms of intervention-related increase in
TEAC, but wild types benefit more from its protecting effects against oxidative DNA
damage. These results support the possibility that genotyping for relevant polymor-
phisms may enable the selection of subgroups among the general population that
benefit more from DNA damage-modulating effects of micronutrients and opens
many interesting opportunities in nutrigenomic research.
Another intervention study was performed with an anthocyanin/polyphenolic
rich, mixed berry juice with a high TEAC value, and a corresponding polyphenol-
depleted juice (polyphenols largely removed, low TEAC value) serving as a control
(Weisel et al., 2006). The study design includes a run-in period, an intervention
period, followed by a washout in healthy male humans. Samples were collected to
analyze DNA damage (Comet assay), lipid peroxidation (plasma malondialdehyde:
HPLC/fluorescence; urinary isoprostanes: gas chromatography–mass spectrome-
try), blood glutathione (photometrically), DNA-binding activity of NF-kappaB
(enzyme-linked immunosorbent assay) and plasma carotenoid/alpha-tocopherol lev-
els (HPLC-diode array detection). During intervention with the fruit juice, but not
control juice, a significant decrease in oxidative DNA damage and an increase of
reduced glutathione and of glutathione status were observed, which returned to the
run-in levels in the subsequent washout phase. The other biomarkers were not sig-
nificantly modulated by the juice supplement. These authors concluded that the fruit
juice clearly reduces oxidative cell damage in healthy probands.
11.2.2.1 Conclusions
Compiled results show promise for the cancer chemopreventive and possible ther-
apeutic applications of Vaccinium preparations and derived phenolic acids, antho-
cyanins, catechins, stilbenes, and several other flavonoids. Although promising, the
differences in occurrence and amounts of flavonoids between species make appro-
priate selection of preparations difficult for a given application. Likewise, effects on
cancer, both positive and negative, and the various proposed mechanisms through
which the chemicals exert their effects, may obfuscate future directions for research,
health-care professional recommendations for use of Vaccinium-based products, and
public confidence in their benefits. Although most of the work done to date indicates
a chemopreventive activity of these compounds, there are some studies that show
cancer-inducing or no effects. Perhaps the most fundamental of these concerns is
the ability to distinguish between the in vitro and the in vivo antioxidant activities
of dietary anthocyanins in relation to human health. But, despite outstanding ques-
tions regarding the relevance of in vitro antioxidant capacity to in vivo antioxidant
protection from deleterious ROS and health consequences, Vaccinium flavonoids
have demonstrated other mechanisms for anti-aging and anticancer potential (Wil-
son et al., 2006; Neto, 2007). These include effects on proliferation, apoptosis, cel-
lular differentiation, and effects on proteins and enzymes that are involved in these
processes at a molecular level, and other various effects through altered immune
function and chemical metabolism (Nichenametla et al., 2006). Several common
mechanisms by which these chemicals exert their effects appear to be conducive
to additive, synergistic, or antagonistic interactions. Further long-term clinical trials
will be required to translate these experimental observations and resulting hypothe-
ses into a potential decreased risk of aging, chronic disease, or cancer chemopre-
vention and treatment in the general population.
11.3 Parkinson’s Disease
Parkinson’s disease (also known as Parkinson disease or PD) is a degenerative dis-

order of the central nervous system that often impairs the sufferer’s motor skills
and speech. Parkinson’s disease belongs to a group of conditions called movement
disorders. It is characterized by muscle rigidity, tremor, a slowing of physical move-
ment (bradykinesia) and, in extreme cases, a loss of physical movement (akinesia).
The primary symptoms are the results of decreased stimulation of the motor cortex
by the basal ganglia, normally caused by the insufficient formation and action of
dopamine, which is produced in the dopaminergic neurons of the brain. Secondary
symptoms may include high-level cognitive dysfunction and subtle language prob-
lems. PD is both chronic and progressive. Parkinson’s disease (PD) affects over 1.2
million Americans.
So far, there have been no known human clinical trials conducted that attempt
to unambiguously answer the question: Do blueberries in the diet have any posi-
tive benefits for patients afflicted with early stages of Parkinson’s disease? This is
remarkable in light of the fact that manifold studies conducted by Dr. James Joseph
USDA, Agricultural Research Service Research Physiologist at the Neuroscience
Laboratory at the Jean Mayer USDA Human Nutrition Research Center on Ageing
at Tufts University, Boston, MA and colleagues, using a rat model system, have
shown how a blueberry-rich diet, in comparison with placebo, elicits significant
improvement in motor skills and cognitive ability in rats induced to manifest PD
symptoms (Lau et al., 2006; Emborg, 2004). Similar results have been reported by
Strömberg et al. 2005 following injury of the rat nigrostriatal dopamine system.
What is the basis for blueberries having beneficial effects for PD, aside from
their nutritional value? Blueberries contain an array of anthocyanins and polyphe-
nols which have high antioxidant activity and anti-inflammatory activity. It is pos-
sible that these kinds of constituents act synergistically at target sites of action
(Cseke et al., 2006) as we have shown recently for sour cherry products. However,
no one yet knows how blueberries act at target sites in the human brain to ameliorate
the severe deleterious effects of PD on cognitive ability and motor skills. A well-
designed human-based clinical trial using blueberries (as whole berries or blueberry
juice) versus placebo is certainly needed to help answer this question.
V. myrtillus preparations are documented for their anthocyanin content and
improvement of cerebral functions, neurotransmitter levels, emotional stress, and
progression of neurodegenerative conditions such as Parkinson’s and Alzheimer’s
diseases (Rahman et al., 2008).
11.4 Heart Disease
11.4.1 Case Study with Digitoxin from Digitalis purpurea

L. ‘Used as a Heart Stimulant
Digoxin is one of the most commonly prescribed cardiac glycosides by physicians,
a closely related group of drugs that can affect the myocardium or heart muscle
(Carey et al., 1998; Sanborn, 2007). The term “digitalis” is used to describe the
entire group of cardiac glycosides (Sanborn, 2007). Digitalis is more commonly
prescribed as digoxin, tradename LanoxinTM , an extract from the leaves of Digitalis
lanata Ehrh. (Sanborn 2007), or sometimes as digitoxin, from foxglove or the leaves
of Digitalis purpurea L. (Wilkins et al., 1985).
11.4.1.1 History
For centuries, cardiac glycosides have been used to treat congestive heart failure,
since it has the ability to increase the power of contraction of the failing heart (Norn
and Kruse, 2004). However, ancient Romans and Syrians might have used squill
or sea onion, a seashore plant, to treat their patients with edema, or water in their
tissues (Norn and Kruse, 2004).
For many centuries, foxglove had been used for various purposes, but had fallen
out of use by 1745 due to inappropriate use (Wilkins et al., 1985). Dr. William
Withering introduced foxglove back to the medical profession in An Account of the
Foxglove and Some of Its Medical Uses: With Practical Remarks on Dropsy, and
Other Diseases in 1785. In this book, he took the first steps in transforming digitalis
into a modern drug with his observation that foxglove, Digitalis purpurea L., was
the active ingredient chosen from more than 20 substances that could treat many
diseases, including dropsy, or congestive heart failure (Drury, 1984; Hauptman and
Kelly, 1999; Breckenridge, 2006). Unaware of its effect on heart failure, he believed
that digitalis was a diuretic (Eichhorn and Gheorghiade, 2002a).
Early in the 20th century, digitalis was found to be useful for treating patients
with heart failure and normal cardiac rhythm (Eichhorn and Gheorghiade, 2002a,b).
The pharmaceutical activity of foxglove was found to be influenced by when the
leaves were harvested and how the plant was grown (Goldman, 2001). In 1906,
the potencies of 16 commercial digitalis preparations were found to vary over a
fourfold range (Goldman, 2001). In the 1927, animal and human studies demon-
strated the hemodynamic effects of digitalis on failing myocardium (Eichhorn and
Gheorghiade 2002a,b). Ultimately, digoxin was found to be the preferred form of
digitalis for treating heart problems in humans (Goldman, 2001).
During the 1970s, the effects of digoxin on heart failure were further elucidated
(Eichhorn and Gheorghiade, 2002b). However, three challenges to digoxin therapy
were discovered: an increase among patients with digoxin intoxication due to ele-
vated serum levels, the development of newer drugs to treat heart failure, and a
perceived increase in mortality due to the use of digoxin. During the 1980s, inter-
est in using digoxin was renewed with a decrease in cases of digoxin intoxication,
newer heart failure drugs demonstrating poorer survival rates, and the discovery that
digoxin might benefit patients with heart failure and normal cardiac rhythm (Eich-
horn and Gheorghiade 2002a). During the late 1980s, digoxin was discovered to
have, in addition to its hemodynamic effects, neurohormonal modulating effects.
However, the utility of digoxin was questioned because of the development of new
neurohormonal modulators for heart failure and the lack of mortality data on digoxin
(Eichhorn and Gheorghiade 2002b).
In the late 1980s and early 1990s, several randomized placebo-controlled trials
demonstrated the utility of digoxin in patients with heart failure and normal cardiac
sinus rhythm (Eichhorn and Gheorghiade 2002a). By 1990, one of the first system-
atic reviews of seven large-scale randomized controlled trials concluded that digoxin
prevented clinical deterioration in patients with heart failure (Hood et al., 2004). In
1997, a large clinical trial showed digoxin had no effect on mortality but it decreased
hospitalizations for heart failure (Eichhorn and Gheorghiade, 2002b). By the 1990s,
digoxin became the most commonly prescribed cardiac glycoside by physicians
for both heart failure and atrial fibrillation due its flexible routes of administra-
tion, the ability to measure its serum levels, and an intermediate duration of action
(Hauptman and Kelly, 1999). Because digoxin is inexpensive and well tolerated,
it may result in considerable medical cost savings (Eichhorn and Gheorghiade,
2002a).
11.4.1.2 Heart Failure

With heart failure more common in the elderly, heart failure represents a major
public health problem in industrialized nations since the prevalence of heart failure
is likely to increase dramatically as the population continues to age (Fauci, 1998).
Heart failure is becoming an increasingly common condition associated with high
morbidity and mortality (Carey et al., 1998). In the United States, heart failure is
responsible for almost one million hospital admissions and 40,000 deaths per year
(Fauci, 1998).
Heart failure is the pathophysiologic state in which an abnormality of cardiac
muscle function results in the failure of the heart to pump blood out to the body at
a rate commensurate with its metabolic requirements (Fauci, 1998). As a result, the
heart is unable to maintain a cardiac output of blood adequate to meet the metabolic
demand of the body (Carey et al., 1998). Cardiac output is defined as a function
of the heart rate and stroke volume. Hypertension, i.e., high blood pressure, and
coronary artery disease are the most frequent causes of heart failure (Carey et al.,
1998). Often, heart failure is caused by a defect in myocardial contraction (Fauci,
1998). Heart failure manifests itself as organ hypoperfusion and tissue hypoxemia,
i.e., inadequate delivery of oxygen to the tissues, as a result of low cardiac out-
put leading to decreased cardiac reserve and pulmonary and systemic whole body
venous congestion (Carey et al., 1998).
11.4.1.3 The Evidence for Heart Failure

Digoxin is widely used to treat mild-to-moderate heart failure in normal sinus
rhythm, i.e., normal heart beat (Sanborn, 2007). In one of the more comprehensive
systematic reviews of the literature, the results of 13 randomized placebo-controlled
double-blinded trials of digitalis for treating individuals with heart failure who
are in normal cardiac rhythm were analyzed (Hood et al., 2004). Patients treated
with digitalis compared to placebo had an odds ratio (OR) for mortality of 0.98
with a 95% confidence interval (CI) from 0.89 to 1.09, for hospitalization of 0.68
(95% CI 0.61–0.75), and for clinical deterioration of 0.31 (95% CI 0.21–0.43). This
means that digitalis had 31% probability of resulting in clinical deterioration, or it
decreased the probability of clinical deterioration by 69%, preventing deterioration
in the clinical status of the patient. Confidence intervals measure the robustness and
stability of the estimate of the odds ratio, and if the confidence interval excludes 1.0,
then there is a statistically significant association. This means that digitalis had no
effect on long-term death rates, significantly decreased the need for hospitalization
for worsening heart failure, and significantly improved clinical cardiac symptoms
(Hood et al., 2004).
From one of the more definitive clinical studies of digoxin, it was reported that
digoxin when used in patients with heart failure and normal sinus rhythm decreased
the number of heart failure-related hospitalizations and emergency care visits, while
having no effect on mortality, i.e., death due to heart failure (The Digitalis Inves-
tigation Group, 1997; Sanborn, 2007). This means that digoxin most likely affects
the frequency of hospitalizations rather than survival for patients with heart failure
in normal rhythm (The Digitalis Investigation Group, 1997).
11.4.1.4 Atrial Fibrillation

Atrial fibrillation, a type of heart arrhythmia defined as an irregular heart beat or
loss of rhythm is a common heart arrhythmia that can occur with or without heart
failure. Atrial fibrillation, often describing the heart as a bag of worms, begins as
a loss of atrial contraction, irregular rhythm, and increased heart rate leading to a
decreased cardiac output.
Digoxin is effective for treating heart failure accompanied by chronic atrial fib-
rillation with a rapid ventricular rate, because digoxin slows the ventricular rate
and results in a positive inotropic effect (Carey et al., 1998; Fauci, 1998). Digoxin
decreases the rate of beating of the heart ventricles, the chambers of the heart that
push blood out to the body, in most patients with atrial fibrillation (Eichhorn and
Gheorghiade, 2002b). Because digoxin is taken once a day simplifying manage-
ment, is well tolerated by the patient, is inexpensive, and can be measured in the
blood if intoxication is suspected, it remains a useful drug for heart rate control in the
management of atrial fibrillation (Eichhorn and Gheorghiade, 2002a). But because
digoxin does not appear to restore normal cardiac rhythm in patients with atrial fib-
rillation without heart failure (Eichhorn and Gheorghiade, 2002b), it is likely that in
patients that have atrial fibrillation with a rapid ventricular response, digoxin should
be combined with beta-blockers (Eichhorn and Gheorghiade, 2002b). Digoxin may
also be prescribed in combination with other heart drugs, such as calcium-channel
blockers or beta-adrenergic antagonists, as adjunctive therapy for heart rate con-
trol of chronic atrial fibrillation without heart failure or left ventricular dysfunction
(Sarter and Marchlinski, 1992; Carey et al., 1998).
For many years, digitalis was the only drug available for rate control in patients
with atrial fibrillation resulting in much of the clinical experience with rate control
being based on the sole use of this drug (Bjerregaard et al., 2004). As a result, current
clinical treatment guidelines for ventricular rate control in patients with atrial fib-
rillation are based primarily on the clinical experience with digitalis rather than the
results of clinical trials (Bjerregaard et al., 2004).
11.4.1.5 Mechanism
The underlying physiologic mechanism for digoxin is that it provides positive
inotropic support, meaning it increases the contractility of heart muscle by prevent-
ing the movement of sodium and potassium across the cellular membrane by inhibit-
ing sodium-potassium adenosine triphosphatase (ATPase), a cell surface transport
enzyme that regulates the quantity of sodium and potassium inside cells (Carey
et al., 1998; Fauci, 1998; Sanborn, 2007). Inhibition of this enzyme leads to an
increase in the intracellular concentration of sodium and then an increase in the
intracellular concentration of calcium (Sanborn, 2007). The increased myocardial
uptake of calcium during excitation of the myocardial cells invokes a positive

inotropic response (Fauci, 1998).
At the cellular and organ level, digoxin has direct mechanical action on cardiac
muscle and indirect electrophysiologic action on the cardiovascular system medi-
ated through the autonomic nervous system, its neurohormonal effect (Sanborn,
2007). The pharmacologic consequences of these actions on the myocardium are
an increase in the force and velocity of myocardial contraction (positive inotropic
action), a decrease in the activation of the adrenergic sympathetic nervous system
mediated through norepinephrine and the renin-angiotensin system originating in
the kidneys (both neurohormonal deactivating effects), and the slowing of the heart
rate and decreased nerve impulse conduction velocity through the atrio-ventricular
(AV) node (vagomimetic effect) in the heart (Sanborn, 2007). The effects of digoxin
on heart failure are related to the positive inotropic and neurohormonal deactivat-
ing effects. The effect of digoxin on atrial arrhythmias, such as atrial fibrillation, is
related to its vagomimetic actions (Sanborn, 2007).
Ultimately, digoxin’s inotropic action increases the amount of blood pushed out
the heart, the left ventricular ejection fraction, improving ventricular emptying and
increasing cardiac output. The increased cardiac output improves the clinical symp-
toms resulting from heart failure as evidenced by increased exercise capacity on a
treadmill (DiBianco et al., 1989).
11.4.1.6 Current Status

Current controversies include the determination of the most efficacious and least
toxic serum level for digoxin (Hauptman and Kelly, 1999; Hood et al., 2004) and
the concern over interaction of digoxin with other prescribed drugs (Eichhorn and
Gheorghiade, 2002a,b). Because current clinical treatment guidelines for rate con-
trol in patients with atrial fibrillation is based primarily on clinical experience with
digitalis, more studies are needed to demonstrate the clinical significance of var-
ious treatment strategies, including newer drugs like beta-receptor blockers, for
rate control in patients with chronic atrial fibrillation (Bjerregaard et al., 2004).
Further, as new therapies for heart failure are developed, such as angiotensin-
converting enzyme (ACE) inhibitors, beta receptor-blocking agents, aldosterone
inhibitor spironolactoneTM or angiotensin-receptor blockers like valsartanTM (Hood
et al., 2004), it is not known whether digoxin will remain as the standard therapy for
heart failure (Hauptman and Kelly, 1999).
In the future, there might be other uses for digitoxin. There is evidence that dig-
itoxin might have utility in cancer therapy. Recent reports suggest that digitoxin
might inhibit the growth or promote apoptosis, or cell death, of cancer cells. The
inhibition of glycolysis has been proposed as the mechanism for digitoxin’s anti-
cancer effect (Lopez-Lazaro, 2007). Other mechanisms include regulating angio-
genesis, or the creation of blood vessels, promoting factors, like fibroblast growth
factor-2, or inhibiting the activation of a transcription factor, such as NF-kappaB
(Winnicka et al., 2006). More studies are needed to further evaluate the anti-
neoplastic effects of digitoxin.
After some 200 years of use, digoxin still appears to have utility in treating
heart failure and atrial fibrillation (Eichhorn and Gheorghiade, 2002a,b). In the mid-
1990s, the results of several studies prompted the Food and Drug Administration to
approve the current regulations for physicians to prescribe digoxin for the treatment
of heart failure (Eichhorn and Gheorghiade, 2002a), which is in agreement with a
recent American College of Cardiology/American Health Association (ACC/AHA)
Guidelines for Chronic Heart Failure (Young, 2005). Physicians prescribe digoxin
for patients with symptomatic heart failure despite the availability of angiotensin-
converting enzyme (ACE) inhibitors or diuretics, or for patients with atrial fibril-
lation with or without heart failure for rate control (Eichhorn and Gheorghiade,
2002b).
11.5 Depression
11.5.1 Case Study with Polyketides (Hypericin, Pseudohypericin,

Hyperforin) in St. John’s Wort (Hypericum perforatum L.)
Hypericum, an extract of the flower of St. John’s wort, has been used for the treat-
ment of depression for centuries (Mischoulon, 2007). St. John’s wort is the common
name for the flowering plant, Hypericum perforatum L. (Gaster and Holroyd, 2000),
a member of the Hypericaceae family. Its yellow flower has been gathered for the
feast of St. John the Baptist and the word “wort” is the Old English word for plant
(Gaster and Holroyd, 2000).
11.5.1.1 History
The use of St. John’s wort has risen dramatically in the United States (Gaster
and Holroyd, 2000) as well as worldwide (Mischoulon, 2007). European physi-
cians have used hypericum to treat mild-to-moderate depression for some time
(Mischoulon, 2007). In the United States, St. John’s wort accounts for about 10% of
all herbal medicine sales (Williams et al., 2000) and currently is one of the largest
selling “natural” remedies (Mischoulon, 2007). The three top-selling herbal prod-
ucts in the United States are Ginkgo biloba L., St. John’s wort, and ginseng (Ernst,
2002).
11.5.1.2 Depression
Depression is an international public health issue that will continue to grow in
importance. According to the World Health Organization (WHO), the prevalence
of major depressive disorder is increasing internationally, with an estimated 120
million persons experiencing a depressive episode in a year (Sarris, 2007). The
American Psychiatric Association defines major depressive disorder, or unipolar
depression, as depressed mood or reduced interest or pleasure accompanied by at
least four other additional symptoms such as weight or appetite change, fatigue,
psychomotor agitation, insomnia or hypersomnia, i.e., excess sleep, lack of concen-
tration, suicidal ideation, feelings of worthlessness or guilt, and low libido (Sarris,
2007). However, major depression has also been defined as a clinical syndrome with
at least 2 weeks of depressed mood and at least five additional symptoms, such as
depressed mood most of the day, nearly everyday; loss of interest in nearly all activi-
ties most of the day; significant weight loss or gain or appetite disturbance; insomnia
or hypersomnia; psychomotor agitation or retardation; inappropriate guilt; difficulty
in concentrating or making decisions; or recurring thoughts of death, including sui-
cidal ideation (Snow et al., 2000).
The use of complementary medicines by patients with psychiatric disorders has
been estimated to range from 8 to 57%, with use most frequently reported for those
with depression or anxiety (Werneke et al., 2006). In one study from the United
States, seven percent of respondents reported severe depression with 54% of these
individuals using complementary medicines (Kessler et al., 2001).
11.5.1.3 The Evidence

The use of extracts from the plant H. perforatum L., commonly called St. John’s
wort, to treat clinical depression has been reviewed by The Cochrane Collaboration,
authoritative specialists in systematic reviews (Linde et al., 2005a).
The major objective of the review was to ascertain the effectiveness of St. John
wort for treating depressive disorders. Cochrane reviewers searched for results from
clinical trials in computerized databases and from projects conducted by manufac-
turers and researchers. Clinical trials were included if they met the following inclu-
sion criteria: (1) if they were double-blinded randomized controlled clinical trials;
(2) if they included adults with mild, moderate, or major depression; (3) if they com-
pared extracts of St. John’s wort with controls, including placebo or antidepressant
drugs; and (4) if they measured outcomes with questionnaires assessing depressive
symptoms, such as the Hamilton Depression Scale (HAMD) and the Clinical Global
Impression Index (CGI).
Of 68 potential studies found, 37 clinical trials met inclusion criteria and demon-
strated heterogeneous results with 26 trial results compared to placebo and 14 com-
pared to prescribed antidepressants. In the larger more precise trials restricted to
major depression, the response rate ratio was 1.15 with a 95% confidence interval
(CI) of 1.02–1.29, signifying minimal effect. A response rate ratio was defined as the
ratio of the number of patients classified as responders to treatment divided by the
number of patients randomized to the respective group. Response rate ratios greater
than 1.0 demonstrated a better response to St. John’s wort (Linde et al., 2005a,b).
Confidence intervals measure the robustness and stability of the estimate of the
response rate ratio, and if the confidence interval excludes 1.0, then there is a statisti-
cally significant association. In the larger more precise clinical trials not restricted to
major depression, the response rate ratio was 1.71 (95% CI 1.40–2.09), signifying a
higher level of effectiveness (Linde et al. 2005a; Linde et al., 2005b). In clinical tri-
als comparing St. John’s wort to older antidepressants, such as amitriptylineTM and
imipramineTM , the rate ratio was 1.03 (95% CI 0.93–1.14), signifying no difference
in effect. In clinical trials comparing St. John’s wort to selective serotonin reuptake
inhibitors (SSRIs), such as sertralineTM and fluoxetineTM , the rate ratio was 0.98
(95% CI 0.85–1.12), signifying no difference in effect (Linde et al., 2005a).
One major limitation of this systematic review is that publication bias could not
be excluded (Linde et al., 2005a). Publication bias is the likelihood that published
studies, likely to have positive results, might in aggregate have different results from
unpublished studies, which are likely to have negative results. It is possible that the
published studies included in the systematic review might overestimate the effect
of St. John’s wort. However, a search of unpublished trials revealed few additional
relevant trials (Linde et al., 2005b).
The results of the systematic review suggest non-uniform findings because of
the “inconsistent and confusing” data (Linde et al., 2005a). When clinical trials
did not use a strict diagnosis of major depression, St. John’s wort demonstrated
greater effectiveness when compared to placebo (Mischoulon, 2007). Clinical tri-
als that closely adhered to the Diagnostic and Statistical Manual of Mental Dis-
orders, 4th edition (DSM-IV) criteria for depression demonstrated less robust
findings (Mischoulon, 2007). Extracts of St. John’s wort had minimal effects on
treating major depression, a more severe form of depression, when compared
to placebo and likely no benefit among patients with chronic depression (Linde
et al., 2005a). However, extracts of St. John’s wort had similar effectiveness as
standard anti-depressants, such as selective serotonin reuptake inhibitors (SSRIs)
and tri- or tetracyclic antidepressants, but were more effective than placebo for
treating mild-to-moderate depression in adults (Linde et al., 2005a; Linde et al.,
2005b).
The Cochrane reviews are an internationally known highly regarded source
of evidence about the effects of health-care interventions. Since 1996, system-
atic reviews prepared and maintained by the Cochrane Collaboration have been
published in The Cochrane Library. The Cochrane Collaboration, a loose-knit
organization of experts in conducting systematic reviews who voluntarily con-
tribute to the Collaboration, is an international attempt to develop evidence-based
research guidelines about different treatment modalities. The Cochrane Library,
also called The Cochrane Database of Systematic Reviews (Starr, 2003), contains
more than 5,000 randomized controlled clinical trials (RCTs) and more than 60
systematic reviews of complementary and alternative medicine (CAM) therapies
(Hughes, 2001). The Cochrane Database of Systematic Reviews, available at the
web site http://www.update-software.com/cochrane, provides high-quality informa-
tion to health-care providers and patients and those in research, teaching, funding,
and administration.
The randomized controlled clinical trial (RCT) has become the objective sci-
entific standard for evaluating the efficacy of therapeutic procedures in humans
(Talalay, 2001). The ultimate source of evidence is the double-blinded randomized
placebo-controlled clinical trial (RCT) since the research subjects are randomly allo-
cated into the treatment group and a control group that receives placebo. Appropri-
ate randomization should result in the treatment and control groups being uniform
with respect to the distribution of known and unknown characteristics, including

known and unknown biases (systematic errors) and confounders (extraneous vari-
ables that can confuse any association between treatment exposure and disease out-
come), except for the treatment exposure. If neither the investigators nor the study
subjects know who was allocated into the treatment group or the control group, then
the RCT was “double-blinded.” Neither investigator nor study subject can influ-
ence, or bias, the assessment of the effect of the treatment on disease outcome. RCT
study design features of particular importance include the following: an appropriate
and large enough sample size to detect small effects of the treatment, uniform entry
criteria for study subjects allocated to the treatment or control groups, objective
measurable clinical disease endpoints, inclusion of placebo-controlled or standard-
of-care controlled groups, reproducible administration of the treatment interven-
tions, and compliance by the study subjects preventing “crossing over” by patients
in the placebo study arm into the treatment arm by surreptitiously taking the study
supplement (Berman and Straus, 2004). The RCT is considered the “gold standard”
because it provides high-quality data that have a high degree of validity and include
a minimum of bias and confounding.
Systematic reviews summarize the existing evidence from groups of RCTs.
Assessing the methodologic quality of primary studies refers to aspects of study
design, performance, and analysis, with a focus on randomization of the study sub-
jects, blinding of the investigators and study subjects, and the handling of dropouts
and withdrawal of study subjects (Linde et al., 2001). Herbal therapies have been
submitted to systematic reviews more frequently than any other complementary or
alternative medicine therapy (Ernst, 2003).
In another systematic review of 14 clinical treatment trials for adults with depres-
sion, 8 studies compared St. John’s wort to placebo and six studies compared
the results to first-generation tricyclic antidepressants, such as amitriptylineTM ,
desipramineTM , and imipramineTM . Mild-to-moderate depression was defined as
fewer symptoms standardized to the 17-time Hamilton Depression Rating scale
(Williams et al., 2000). St. John’s wort was found to be more effective than placebo
for mild–to-moderate depression with a risk ratio (RR) of 1.9, meaning that the
probability of an improvement in symptoms with treatment increased by 90%, with
a 95% confidence interval (CI) from 1.2 to 2.8, using confidence intervals as a mea-
sure of robustness and stability of the estimate of the risk ratio. However, extracts of
St. John’s wort were as effective as the older tricyclic antidepressants (RR = 1.2, CI
1.0–1.4, with a risk ratio of 1.0 implying no statistical significance) (Williams et al.,
2000). Tests for publication bias were statistically significant, meaning that publi-
cation bias might have spuriously overestimated the treatment benefits (Williams
et al., 2000). The authors conclude that extracts of St. John’s wort appear to be
more effective than placebo for short-term treatment of mild-to-moderate depres-
sion, though they state that more research on clinical efficacy still needs to be con-
ducted (Williams et al., 2000).
In contrast, in another systematic review of eight studies examining tricyclic
antidepressants of moderately high methodologic quality, St. John’s wort was found
to be more effective than placebo in treating mild-to-moderate depression (Gaster
and Holroyd, 2000). The response rate to St. John’s wort ranged from 23 to
55% higher than placebo, but compared to imipramineTM and amitriptylineTM , the
response rate ranged from 6 to 18% lower than the response rate to these tricyclic
antidepressants (Gaster and Holroyd, 2000). This means that St. John’s wort was
more effective than placebo, but less effective than the tricyclic antidepressants for
treating mild-to-moderate depression (Gaster and Holroyd, 2000).
In a review of systematic reviews and randomized controlled clinical trials, the
evidence suggests that St. John’s wort is superior to placebo for the short-term treat-
ment of mild-to-moderate depression (De Smet, 2002). One of the studies demon-
strated that St. John’s wort was significantly more efficacious than placebo and as
effective as imipramineTM , an antidepressant, for treating moderate depression (De
Smet, 2002). However, in studies of major depression, two methodologically rigor-
ous randomized controlled trials of an 8-week treatment with St. John’s wort did not
demonstrate statistically significant differences when compared to placebo for out-
patients with major depression of moderate severity (De Smet, 2002). Limitations
of this review included the methodologic quality of the randomized controlled clin-
ical trials under review and potential publication bias (De Smet, 2002). In addition,
most trials excluded severely depressed patients (Goldman, 2001). This researcher
concluded that based on the evidence cited, St. John’s wort should not be substituted
for a conventional antidepressant in patients with moderately severe or severe major
depression (De Smet, 2002).
In the most recent review of systematic reviews and randomized controlled
clinical trials in 2007, the evidence suggests that St. John’s wort has greater effi-
cacy than placebo and equal efficacy to low-dose tricyclic antidepressants, such as
imipramineTM , in most trials for treating mild-to-moderate depression (Mischoulon,
2007). In the last 5–6 years, about 10 randomized controlled double-blinded stud-
ies compared St. John’s wort to the newer antidepressants, the selective serotonin
reuptake inhibitors (SSRIs), as well as placebo. St. John’s wort demonstrated equal
efficacy compared to SSRIs and placebo in more recent studies, but this is likely
because more severely and/or chronically depressed patients were recruited to
the more recent studies (Mischoulon, 2007). Several other studies indicated that
St. John’s wort was as effective as selective serotonin reuptake inhibitors (SSRIs)
for treating depression (Jorm et al., 2002).
In summary, most of the evidence suggests that St. John’s wort was more effec-
tive than placebo, but as effective as standard antidepressants, for treating mild-to-
moderate depression (Werneke et al., 2006; Sarris, 2007). The evidence for major
depression is less well defined.
11.5.1.4 Mechanism
The mechanism of action for St. John’s wort is still under investigation (De Smet,
2002; Mischoulon, 2007). Constituents of extracts of St. John’s wort under inves-
tigation as the effective pharmacologic agents include hypericins, hyperforin (De
Smet, 2002), polycyclic phenols, and pseudohypericin (Mischoulon, 2007). Some
studies indicate that the antidepressant activity of St. John’s wort might be related
to hyperforin (Goldman, 2001; Werneke et al., 2006; Mischoulon, 2007). It has been
proposed that hyperforin inhibits the synaptic reuptake of several neurotransmitters,
including serotonin, dopamine, and norepinephrine (Mischoulon, 2007). Hypericin
has not been confirmed as the active ingredient for St. John’s wort (Goldman,
2001). Hypericin might decrease the production of cortisol or inhibit reuptake of
neurotransmitters, such as serotonin, norepinephrine, and dopamine (Mischoulon,
2007).
11.5.1.5 Safety and Tolerability

Uncommon and mild adverse events reported with use of St. John’s wort as
monotherapy include gastrointestinal symptoms such as constipation, dizziness or
confusion, fatigue, dry mouth, restlessness, headache, allergic skin reactions, sex-
ual dysfunction, frequent urination, swelling, and photosensitivity (De Smet, 2002;
Mischoulon, 2007). Other possible adverse effects have also been reported, includ-
ing serotonin syndrome or serotonin overload (De Smet, 2002), mania, or hypoma-
nia (Mischoulon, 2007).
In the past few years, adverse events between St. John’s wort and other drugs have
been increasingly reported in the literature (Mischoulon, 2007). St. John’s wort has
been found to interact with a number of conventional drugs, such as amitriptylineTM
(an antidepressant), paroxetineTM (a selective serotonin reuptake inhibitor [SSRI]
antidepressant) leading to serotonin syndrome, and simvastatinTM (an anticholes-
terol drug) (Goldman, 2001; De Smet, 2002; Eggertsen et al., 2007). St. John’s wort
has been reported to decrease the activity of several drugs including warfarinTM (an
anticoagulant used to prevent blood clotting), oral contraceptives, theophyllineTM
(a drug to treat chronic obstructive pulmonary disease [COPD]), digoxin (a drug for
the heart) (Mischoulon, 2007), and HIV protease inhibitors (drugs to treat human
immunodeficiency virus [HIV] disease).
The Cochrane Library, Embase and phytobase databases, case reports, case
series, clinical trials, or other types of human investigations relating to herbal
supplement and prescription medication interactions were included in a litera-
ture review using Medline (an electronic scientific literature database) (Izzo and
Ernst, 2001). The results indicated that St John’s wort lowers blood concentrations
of cyclosporine (an immunosuppressive drug used to prevent rejection of trans-
planted organs), amitriptylineTM , digoxinTM (a cardiovascular drug), warfarinTM ,
and theophyllineTM ; and causes menstrual bleeding, delirium, or mild serotonin
(a neurotransmitter) syndrome when used concomitantly with oral contraceptives,
loperamideTM (an antidiarrheal drug), or selective serotonin-reuptake inhibitors
(sertralineTM , paroxetineTM , nefazodoneTM , all are anti-depression drugs), respec-
tively (Izzo and Ernst, 2001).
In a recent study, when healthy volunteers added St. John’s wort to a regimen of
the HIV protease inhibitor indinavirTM , the serum level of indinavirTM decreased
below the therapeutic concentration necessary for antiviral activity leading to
potential HIV treatment failure (Piscitelli et al., 2000). Following this report, the
Food and Drug Administration (FDA) issued a public health advisory warning
that St. John’s wort appeared to induce cytochrome P-450 enzymes, liver enzymes
responsible for the metabolism of many prescription medications including those
used to treat heart disease, depression, seizures, and cancers, or to prevent trans-
plant rejection or pregnancy (oral contraceptives). These prescription medications
lose their therapeutic effects when given with St. John’s wort (Talalay, 2001).
In an authoritative systematic review of 35 randomized controlled double-blinded
studies, part of an update of a meta-analysis by the authoritative Cochrane Col-
laboration, experts on systematic reviews, on the use of hypericum extracts for
depression, the rate of dropouts and adverse effects for patients receiving hyper-
icum extracts was similar to placebo, less than that for older antidepressants
such as amitriptylineTM and imipramineTM , and similar to selective serotonin-
reuptake inhibitors (Knuppel and Linde, 2004). Data from published case reports
and national drug surveillance agencies suggest that the most relevant adverse
effects of hypericum extracts were related to drug interactions and dermatologic
reactions (Knuppel and Linde, 2004). Hypericum extracts had documented interac-
tions with cyclosporineTM in transplant patients, warfarinTM (an anti-clotting drug),
and selective serotonin reuptake inhibitors (SSRIs) resulting in serotonin syndrome
(Knuppel and Linde, 2004). A potential mechanism for this drug interaction is the
induction of a hepatic enzyme through the activation of the P450 cytochrome system
which metabolizes drugs (Ernst, 2002) and the induction of P-glycoprotein which
results in increased drug excretion (Knuppel and Linde, 2004). This mechanism
could lead to decreased plasma levels of the drugs. The majority of other adverse
effects were related to skin and allergic reactions, such as erythema (redness), der-
matitis, urticaria (hives or itching edematous wheals), hyperesthesia (abnormally
acute sensitivity to sensation such as touch or pain), and neuropathy (Knuppel and
Linde, 2004). The authors conclude that hypericum extracts are well tolerated and
safe if they are taken under the supervision of a physician who is aware of its poten-
tial risks. Further, the authors suggest that self-medication by patients might be
acceptable for those with very mild depressive symptoms and who are not taking
any other medication (Knuppel and Linde, 2004).
11.5.1.6 Current Status and Recommendations

In 2000, the American College of Physicians-American Society of Internal
Medicine published a guideline stating that St. John’s wort might be considered
for short-term treatment of mild acute depression, though patients should be warned
that this treatment is neither approved nor regulated by the Food and Drug Admin-
istration (FDA) and that the constituents in the extracts of St. John’s wort may vary
substantially from those tested in the randomized trials (Snow et al., 2000). Fur-
thermore, the quality of the extract might be considerably different. Because the
composition of St. John’s wort extracts might vary among preparations that are
produced and sold, the results of the systematic reviews apply only to those prepara-
tions analyzed in the studies that were reviewed. Because the FDA does not regulate
St. John’s wort, unlike all medications prescribed by physicians, St. John’s wort is
not subject to randomized clinical trial testing for efficacy. Unlike prescription med-
ications, no animal investigations, clinical trials, or post-marketing surveillance are
required before herbal treatments are marketed to the public. Dietary supplements
can be sold to the public without Food and Drug Administration approval.
With the high potential for adverse effects and drug interactions, clinicians should
treat patients in a safe, evidence-based fashion. Because extracts of St. John wort
might have adverse interactions with other drugs, individuals taking other drugs
should consult their physician before using St. John wort (Linde et al., 2005a,b;
Mischoulon, 2007). With nearly 70% of patients who use alternative therapies not
informing their health-care providers about their use of herbal products (Eisenberg
et al., 1993) it is imperative that health-care providers inquire into their patients’ use
of herbal treatments.
Health-care providers and their patients should proactively discuss the use or
avoidance of complementary and alternative medicine (CAM) therapies. They
should formally discuss patient’s preferences and expectations, and in order to mon-
itor for toxicity of CAM therapies; they should ask patients to maintain a symp-
tom diary and see patients in follow-up visits (Eisenberg, 1997). Both patients and
health-care providers must acknowledge that data on CAM therapy efficacy and tox-
icity remain incomplete and that recommendations remain a matter of best judgment
and not fact.
Health-care providers should be vigilant about potential interactions between
herbal products and prescription medications. Health-care provider can report
potential interactions by calling FDA’s MedWatch hotline at 1-800-FDA-1088 or
using the web site http://www.fda.gov/medwatch/report/hcp.htm. The MedWatch
program allows health-care providers to report problems possibly caused by FDA-
regulated products such as drugs, medical devices, and medical foods in addition
to dietary supplements. The identity of the patient is kept confidential. Patients
may also report an adverse event or illness they believe to be related to the
use of a dietary supplement by calling the FDA at 1-800-FDA-1088 or using
the web site http://www.fda.gov/medwatch/report/consumer/consumer.htm. Health-
care providers should recognize and report suspected interactions between herbal
therapies and prescription medications since this leads to increasing knowledge
and awareness of herbal treatment and medication interactions and ultimately, to
improvement in the quality of patient care.
Future well-designed controlled studies of St. John’s wort should address fur-
ther clinical issues such as standardization of dosing and extracts of St. John’s wort
(Werneke et al., 2006), more specific reporting of adverse effects (Werneke et al.,
2006), comparison with other antidepressant agents, including other selective sero-
tonin reuptake inhibitors (Snow et al., 2000), effects of acute short-term and long-
term therapy, effects on measures of functional status and quality of life (Gaster
and Holroyd, 2000), efficacy in treating severe depression (Gaster and Holroyd,
2000), and efficacy in treating adolescents (Sarris, 2007) and minority populations.
More studies are needed to test the efficacy of St. John’s wort for treating major
depression and its efficacy compared to other antidepressants (Gaster and Holroyd,
2000). Future well-designed controlled studies of St. John’s wort should address
epidemiologic methods issues such as using an improved definition of depression
as an inclusion criteria (Werneke et al., 2006), strict use of the diagnostic criteria
for defining major depression using DSM-IV criteria (Mischoulon, 2007), having
longer observation periods, and further elucidating mechanisms of action.
In summary, studies of St. John’s wort show promise as a potential treatment for
mild-to-moderate depression (De Smet, 2002; Werneke et al., 2006; Mischoulon,
2007). However, St. John’s wort might be less effective for treating severe depres-
sion or chronic depression though more research should be conducted (Mischoulon,
2007). The current lack of regulation by the Food and Drug Administration and lack
of standardization of commercially available preparations remain a major barrier to
implementing recommendations for physicians to prescribe St. John’s wort to treat
patients with depression (Gaster and Holroyd, 2000).
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Chapter 12
Regulating Phytonutrient Levels in Plants –
Toward Modification of Plant Metabolism for
Human Health
Ilan Levin
Abstract Plants constitute a major component of our diet, providing pigments and
additional phytonutrients that are thought to be essential for maintenance of human
health and are therefore also referred to as functional metabolites. Several fruit and
vegetable species already contain high levels of several of these ingredients, while
others do not. Nevertheless, efforts have been devoted to increasing and diversifying
the content of phytonutrients, such as carotenoids, flavonoids, and vitamins, even
in plants that normally produce high levels of such nutritional components. These
efforts rely on transgenic and non-transgenic approaches which have exposed com-
plex regulation mechanisms required for increasing the levels of functional metabo-
lites in plants. The study of these regulatory mechanisms is essential to expedite
improvement of levels of these metabolites in fruits, vegetables, cereals, legumes,
and starchy roots or tubers. Such improvement is important for the following rea-
sons: (1) to increase the efficiency of the industrial extraction of these compounds
that are later being used as natural food supplements or fortifiers and as a source of
natural colors to replace the chemical alternatives; (2) to improve and diversify the
diet in populations of developing countries, where malnutrition may occur through
lack of variety in the diet; (3) to provide fresh agricultural products such as fruits
and vegetables highly enriched with certain phytonutrients to possibly substitute the
chemically synthesized food supplements and vitamins; and (4) to provide an array
of new and attractive colors to our diet.
Three basic approaches to modifying a biosynthetic pathway to increase amounts
of desirable phytonutrients are available: (1) manipulation of pathway flux, includ-
ing increasing, preventing, or redirecting flux into or within the pathway; (2)
introduction of novel biosynthetic activities from other organisms via genetic
engineering; and (3) manipulation of metabolic sink to efficiently sequester the end-
products of particular metabolic pathways. These approaches have been effectively
demonstrated in relation to the flavonoid and carotenoid biosynthetic pathways in
I. Levin (B)
Department of Vegetable Research, Institute of Plant Sciences, The Volcani Center,
Bet Dagan, Israel 50250

290 I. Levin
tomato (Solanum lycopersicum). This chapter is therefore focused on carotenoids

and flavonoids, their importance to human nutrition, and approaches used to induce,
regulate, and diversify their content in tomato fruits. In addition, several examples
of outstanding approaches employed to modulate carotenoid content in other plant
species will also be given.
12.1 Introduction
Plants synthesize and accumulate an excess of 200,000 natural products (Fiehn,

2002). Plants also constitute a major component of our diet, providing fiber
(i.e., cellulose, hemicellulose, and starch), carotenoids, flavonoids, vitamins,
minerals, and additional pigmented and non-pigmented metabolites thought to
promote or at least maintain good health (Willcox et al., 2003; Fraser and
Bramley, 2004, Davies, 2007). These metabolites are referred to as phytonutri-
ents, functional metabolites, phytochemicals, and lately also nutraceuticals (Davies,
2007), defined as certain organic components of plants that are thought to pro-
mote human health (The American National Cancer Institute drug dictionary
at http://www.cancer.gov/drugdictionary/). Major examples of phytonutrient-rich
plant foods and the principle phytonutrients which they accumulate are listed in
Table 12.1.
Phytochemicals have been used, even as drugs, for centuries (Yonekura-
Sakakibara and Saito, 2006). For example, Hippocrates (ca. 460–370 BC) used
to prescribe willow tree leaves to abate fever. The active ingredient, salicin, with
potent anti-inflammatory and pain-relieving properties was later extracted from the
White Willow Tree (Salix alba) and eventually synthetically produced to become
the staple over-the-counter drug called Aspirin. Noteworthy, the initial conceptual
link between food and human health is also related to Hippocrates, who has been
referred to as the “father of modern medicine”. He stated, “Let thy food be thy
medicine and thy medicine be thy food”.
The recent completion of the human genome sequence and the advances made in
high-throughput technologies brought about the area of nutragenomics that is pre-
dicted to uncover more precisely the possible relationship between human genetic
makeup and nutrients, including phytonutrients. Meanwhile, efforts have been
invested in increasing and diversifying the content of nutrients, such as carotenoids,
flavonoids, tocopherols, minerals, fatty acids, phytosterols, and vitamins in both
model and agricultural plant species (extensively reviewed with selected exam-
ples by Galili et al., 2002; Levin et al., 2006; Davies, 2007). While it is not at
all clear whether these efforts would necessarily lead to agricultural products with
better functional properties for human health benefits, they have exposed regula-
tion mechanisms important for increasing and maintaining high levels of functional
metabolites in plant products. The study of these regulatory mechanisms will have
an important role in delivering functional attributes through foods, once better rela-
tionships between these ingredients and human health will be unraveled.
12 Regulating Phytonutrient Levels in Plants 291
Table 12.1 Examples of phytonutrient-rich plant foods and the principle phytonutrients they
accumulate
Plant food Phytonutrients
Soybean Protease inhibitors, β-sitosterol, saponins,

phytic acid, isoflavones
Red apples, grapes, blackberries, Anthocyanins
blueberries, raspberries, red wine
Tomato Lycopene, β-carotene, vitamin C
Broccoli Vitamin C, 3,3 -diindolylmethane,
sulforaphane, lignans, selenium
Garlic Thiosulfonates, limonene, quercitin
Flax seeds Lignans
Citrus fruits Monoterpenes, coumarin, cryptoxanthin,
vitamin C, ferulic acid, oxalic acid, flavanones
Corn, watercress, spinach, parsley, Lutein, zeaxanthin
avocado, honeydew melon
Broccoli, Brussels sprouts, kale Glucosinolates, indoles
Garlic, onions, leeks, chives Allyl sulfides
Blueberries Tannic acid, lignans, anthocyanins
Sweet potatoes, carrots, mangos, apricots, α-Carotene, β-carotene
pumpkin, winter squash
Chilli peppers Capsaicin
Cantaloupe, peaches, tangerines, papaya, b-Cryptoxanthin, flavonoids
oranges
Celery Flavones
Tea, apple, cocoa Flavanols
Beans, peas, lentils Omega fatty acids, saponins, catechins,
quercitin, lutein, lignans
Several plant foods already contain high levels of certain phytonutrients, while
others do not (Davies, 2007). Nevertheless, efforts have been invested in increas-
ing and diversifying the content of phytonutrients, such as carotenoids, flavonoids,
and vitamins in several plant species, even in those that already contain high levels
of one or several of these ingredients. The tomato fruit, for instance, is consid-
ered to be a good source of lycopene, vitamin C, β-carotene, folate, and potassium
(Davies and Hobson 1981; Willcox et al., 2003). The tomato could also potentially
be a good source for flavonoids as well (Jones et al., 2003; Willits et al., 2005;
van Tuinen et al., 2006; Sapir et al., 2008). Nevertheless, efforts have been invested
in increasing the content and diversifying phytonutrients, such as carotenoids and
flavonoids, in the tomato fruit (Verhoeyen et al., 2002; Fraser and Bramley, 2004;
Levin et al., 2004).
Increasing the levels of phytonutrients, such as lycopene in the tomato fruit,
is highly justified from the perspective of the extraction industry due to cost-
effectiveness reasons (Levin et al., 2006). Further enriching phytonutrients in plant
species that already contain high levels of such ingredients is also directed to possi-
bly substitute the chemically synthesized food supplements and vitamins in human
populations that normally consume such supplements (Sloan, 2000; Levin et al.,
292 I. Levin
2006). Diversifying phytonutrients, including those that contribute to fruit color,

can provide an array of new and attractive colors to our diet and also harness syner-
gistic effects among phytonutrients which are important to human health. Increas-
ing the levels of phytonutrients in plant species that normally do not contain high
levels of these ingredients, including cereals, some legumes, and starchy roots or
tubers/tuberous roots, is important in order to improve the diet in populations of
people in developing countries, where nutrition is not diversified enough to provide
all of the essential metabolites, primarily vitamins and minerals needed to main-
tain proper health (Davies, 2007). Due to these reasons, there is now a growing
interest in the development of food crops with enhanced levels of phytonutrients.
The tomato is an excellent candidate for the following reasons: (1) it is a major
crop; (2) it is already a good source of several phytonutrients such as lycopene
and vitamin C; (3) it contains many accessions with modulated levels of essential
metabolites; (4) it can be easily modified by both classical genetic and transgenic
means; and (5) it has been a subject of many studies aimed at increasing and diver-
sifying the content of fruit phytonutrients, mainly carotenoids and flavonoids. Also,
excellent analytical and genomics tools have been developed for tomatoes which
can facilitate the molecular analysis of a certain gene modification. This chapter
will therefore focus on factors that induce, regulate, and diversify carotenoids and
flavonoids in tomato (Solanum lycopersicum) and their importance to human nutri-
tion. A few outstanding examples of similar factors in other plant species will be also
given.
Strategies to increase and diversify the content of either carotenoids or
flavonoids in tomato fruits are reviewed here. These efforts rely on transgenic and
non-transgenic approaches (i.e., use of spontaneous or induced mutations and/or
quantitative trait loci affecting levels of these phytonutrients). The tomato light-
responsive high-pigment (hp) mutations are an outstanding example of the latter
alternative (Levin et al., 2003; 2004) and will therefore be presented in more detail.
Due to their impact on fruit lycopene content, these hp mutations were already intro-
gressed into elite tomato germplasm (Levin et al., 2003; 2006). Introgression of one
of these hp mutations, hp-2dg , into elite processing cultivars, characterized by an
average fruit lycopene concentration of 80–90 μg·g−1 FW, resulted in cultivars with
an average fruit lycopene concentration of up to 280 μg·g−1 FW, representing an
up to 3.5-fold increase in fruit lycopene content. Most notably, recent studies also
reinforce earlier ones suggesting that plants carrying these mutations are also char-
acterized by higher levels of other health-promoting metabolites, such as flavonoids
and vitamins (Bino et al., 2005). Further, and more recently, it was shown that cross-
hybridizing light-responsive hp mutant plants with plants carrying either the Antho-
cyanin fruit (Aft) or the atroviolacium (atv) mutations, known to cause anthocyanin
expression in tomato fruits, displayed a significant more-than-additive effect on the
production of fruit anthocyanidins and flavonols (van Tuinen et al., 2006; Sapir et
al., 2008). This effect was manifested and quantitatively documented as a remark-
able ∼5-, 19-, and 33-fold increase of petunidin, malvidin, and delphinidin, respec-
tively, in the hp-1/hp-1 Aft/Aft double mutants compared to the cumulative levels
of their parental lines (Sapir et al., 2008). These results underlie the importance of
light-responsive hp mutations in modulating phytonutrient content in plants, either

on their own or in combination with other gene mutations.
Up to date, five light-responsive hp mutations have been discovered (Lieberman
et al., 2004; Galpaz et al., 2008). These mutations, i.e., hp-1, hp-1w , hp-2, hp-2j ,
and hp-2dg , were initially marked as lesions in structural genes of the carotenoid
biosynthetic pathway (Stevens and Rick, 1986). However, more recent studies have
demonstrated that they represent mutations in two evolutionary conserved regula-
tory genes active in light signal transduction, known also as photomorphogenesis
(Mustilli et al., 1999; Levin et al., 2003; Lieberman et al., 2004). The identification
of the genes that encode these hp mutant phenotypes has therefore created a con-
ceptual link between photomorphogenesis and biosynthesis of fruit phytonutrients
and suggests that manipulation of light signal transduction machinery may be very
effective toward the practical manipulation of an array of fruit phytonutrients (Levin
et al., 2003; 2006; Liu et al., 2004). Recent studies focusing on the manipulation of
light signaling genes in tomato plants, cited in this chapter, support this approach.
12.2 Carotenoids
Carotenoids are orange, yellow, and red pigments that exert a variety of critical
functions in plants. They comprise a class of lipid-soluble compounds within the
isoprenoid family, which is one of the largest classes of natural products in the plant
kingdom with over 22,000 known constituents (Connolly and Hill, 1992; Britton,
1998).
The isoprenoid family also includes gibberellins, phytosterols, saponins, toco-
pherols, and phylloquinones. Chlorophylls also contain an isoprenoic component,
formed from the same precursor of the carotenoid metabolism, geranylgeranyl
diphosphate (GGDP) (Fig. 12.1). In addition to their many functional roles in pho-
tosynthetic organisms, carotenoids have many industrial applications as food and
feed additives and colorants, in cosmetics and pharmaceuticals, and as nutritional
supplements (Galili et al., 2002). Carotenoids are C40 hydrocarbons with polyene
chains that contain 3–15 conjugated double bonds. These double bonds are respon-
sible for the absorption spectrum, and therefore the color of the carotenoid, and for
the photochemical properties of the molecule (Britton, 1995).
The carotenoid backbone is either linear or contains one or more cyclic β-ionone
or ε-ionone rings or, less frequently, the unusual cyclopentane ring of capsan-
thin and capsorubin that impart the distinct red color to peppers. Non-oxygenated
carotenoids are referred to as carotenes, whereas their oxygenated derivatives are
designated as xanthophylls. The most commonly occurring carotenes are β-carotene
in chloroplasts and lycopene as well as β-carotene in chromoplasts of some flow-
ers and fruits, e.g., tomatoes. The most abundant xanthophylls in photosynthetic
plant tissues (lutein, violaxanthin, and neoxanthin) are key components of the light-
harvesting complexes.
Carotenoids are synthesized in the membranes of nearly all types of the plant
plastids and accumulate to high levels in chromoplasts of many flowers, fruits,
294 I. Levin
Fig. 12.1 A schematic

presentation of the
carotenoid biosynthetic
pathway and its structural
genes. Gene abbreviations:
CRTISO = carotenoid
isomerase, βLCY =
β-lycopene cyclase, εLCY =
ε-lycopene cyclase, NXS =
neoxanthin synthase, βOHase
= β-carotene hydroxylase,
PDS = phytoene desaturase,
PSY = phytoene synthase,
ZDS = ζ -carotene desaturase,
ZE = zeaxanthin epoxidase;
Metabolite abbreviations:
GGDP, geranylgeranyl
diphosphate; IPP, isopentenyl
diphosphate
and roots (Howitt and Pogson, 2006). They are involved in photosystem assem-
bly, light harvesting and photoprotection, photomorphogenesis, non-photochemical
quenching, lipid peroxidation, and affect the size and function of the light-harvesting
antenna and seed set (Pogson et al., 1998; Havaux and Niyogi, 1999; Niyogi,
1999; Davison et al., 2002; Kulheim et al., 2002; Lokstein et al., 2002; Holt
et al., 2004, 2005; Cuttriss and Pogson, 2006; Wang et al., 2008). In chromoplasts,
carotenoids serve as pigments that furnish fruits and flowers with distinct colors in
order to attract insects and animals for pollination and seed dispersal (Fraser and
Bramley, 2004).
Animals as well as humans are unable to synthesize carotenoids de novo and
rely upon the diet as a source of these compounds. Over recent years there has
been considerable interest in dietary carotenoids with respect to their potential in
alleviating age-related diseases in humans, propelling a market with an estimated
yield of 100 million tons and a value of about US $935 million per annum (Fraser
and Bramley, 2004). Although key carotenoids can be chemically synthesized, there
is an increasing demand for the natural alternatives mainly those which are being
extracted or consumed from plants (Sloan, 2000). This attention has been mir-
rored by significant advances in cloning most of the carotenoid genes and in the
genetic manipulation of crop plants with the intention of increasing their levels in
the diet.
12.2.1 The Carotenoid Biosynthetic Pathway
During the past decade, a near-complete set of genes required for the synthesis of
carotenoids in photosynthetic tissues has been identified, primarily as a result of
molecular genetic- and biochemical genomics-based approaches in the model organ-
isms such as Arabidopsis (Arabidopsis thaliana) and several agricultural crops such
as the tomato. Mutant analysis and transgenic studies in these and other systems
have provided important insights into the regulation, activities, integration, and evo-
lution of individual enzymes and are already providing a knowledge base for breed-
ing and transgenic approaches to modify the types and levels of these important
compounds in agricultural crops (Dellapenna and Pogson, 2006).
In higher plants, carotenoids are synthesized from the plastidic isoprenoid
biosynthetic pathway (Lichtenthaler, 1999; Fraser and Bramley, 2004, DellaPenna
and Pogson, 2006). They are biosynthetically linked to other isoprenoids such
as gibberellins, tocopherols, chlorophylls, and phylloquinones via the five-carbon
compound isopetenyl pyrophosphate (IPP). Two distinct pathways exist for IPP
production: the cytosolic mevalonic acid pathway and the plastidic mevalonate-
independent methylerythritol 4-phosphate (MEP) pathway. The methylerythritol
4-phosphate pathway combines glyceraldehyde-3-phosphate and pyruvate to form
deoxy-D-xylulose 5-phosphate, and a number of steps are then required to form IPP
and dimethylallylpyrophosphate (DMAPP) (Lichtenthaler, 1999). IPP is subject to
a sequential series of condensation reactions to form geranylgeranyl diphosphate
(GGDP), a key intermediate in the synthesis of carotenoids, tocopherols, and many
other plastidic isoprenoids (Fig. 12.1).
The initial steps of plant carotenoid synthesis and their chemical properties
have been thoroughly discussed in several prior reviews (Cunningham and Gantt
1998; Hirschberg, 2001; Cunningham, 2002; Fraser and Bramley, 2004; Cuttriss
and Pogson, 2006). Briefly, the first committed step in plant carotenoid synthesis
is the condensation of two molecules of GGDP to produce phytoene (Fig. 12.1)
by the enzyme phytoene synthase (PSY). Phytoene is produced as a 15-cis isomer,
which is subsequently converted to all-trans isomer derivatives. Two plant desat-
urases, phytoene desaturase (PDS) and ζ -carotene desaturase (ZDS), catalyze sim-
ilar dehydrogenation reactions by introducing four double bonds to form lycopene.
Desaturation requires a plastid terminal oxidase and plastoquinone in photosynthetic
tissues (Beyer, 1989; Norris et al., 1995; Carol et al., 1999). Bacterial desatura-
tion differs from plants in that a single enzyme, crtI (phytoene desaturase), intro-
duces four double bonds into phytoene to yield all-trans-lycopene (Cunningham
and Gantt, 1998). This bacterial enzyme was therefore used as a target to increase
lycopene and other carotenoids content in plant species as will be further outlined.
296 I. Levin
Until recently, the higher plant desaturases were assumed sufficient for the pro-
duction of all-trans-lycopene. This conclusion was reached despite the accumula-
tion of tetra-cis-lycopene in tangerine (t) tomato and algal mutants (Tomes et al.,
1953; Cunningham and Schiff, 1985) and biochemical evidence to the contrary from
daffodil (Beyer et al., 1991). Recently, the carotenoid isomerase gene, CRTISO, was
identified in Arabidopsis and tomato, which catalyzes cis–trans isomerizations and
resulting in all-trans-lycopene (Isaacson et al., 2002; Park et al., 2002).
In plants, the carotenoid biosynthetic pathway diverges into two main branches
after lycopene, distinguished by different cyclic end-groups. Two beta rings lead
to the β,β branch (β-carotene and its derivatives: zeaxanthin, violaxanthin, anther-
axanthin, and neoxanthin), whereas one beta and one epsilon ring define the β,ε
branch (α-carotene and its derivatives). These initial reactions are carried out by two
enzymes: β-lycopene cyclase (βLCY) and ε-lycopene cyclase (εLCY) (Fig. 12.1).
βLCY converts lycopene into β-carotene which is later converted to zeaxanthin by
β-carotene hydroxylase (βOHase). An epoxide group is introduced into both rings of
zeaxanthin by zeaxanthin epoxidase (ZE) to form violaxanthin. Conversion of vio-
laxanthin to neoxanthin is performed by the enzyme neoxanthin synthase (NXS).
Both the β- and ε-lycopene cyclase enzymes (βLCY and εLCY, respectively) are
initially required to form α-carotene (Cunningham and Gantt, 1998; Pogson et al.,
1996), which is being converted to lutein, via zeinoxanthin, by β-carotene hydroxy-
lase (βOHase) and ε-carotene hydroxylase (εOHase) (Fig. 12.1).
Unlike the flavonoid pathway (see herein below), the regulation of carotenoid
biosynthesis at the gene and enzyme level is poorly understood. No regulatory
genes involved in carotenoid formation have been isolated thus far. It was rea-
soned that a heavily branched pathway such as that of carotenoids formation from
isoprenoid precursors is unlikely to be controlled by a sole regulatory process
(Fig. 12.1). Instead, it was suggested that control points, yet to be identified, are
likely to exist at each branch point which probably involve both transcriptional
and post-transcriptional regulation events (Fraser and Bramley, 2004). Despite this
apparent complexity, several examples exist which resulted in an exceptional up-
regulation of the carotenoid biosynthetic pathway by transgenic (“golden” rice)
and non-transgenic approaches (the Or gene identified in cauliflower and the light-
responsive hp mutations identified in tomato). These examples underlie the great
potential of current knowledge to modulate levels of these important phytonutrients
for the benefit of human health and will, therefore, be separately discussed in a later
part of this chapter.
12.3 Flavonoids
Flavonoids comprise a group of plant polyphenols that provide much of the flavor
and color to fruits and vegetables (Ross and Kasum, 2002). They are a large fam-
ily of low-molecular-weight secondary metabolite compounds that are widespread
throughout the plant kingdom, ranging from mosses to angiosperms (Koes et al.,
1994). Their basic chemical structure, a C6 −C3 −C6 configuration, consists of two
aromatic rings joined by a three-carbon link. This makes the flavonoids good hydro-
gen and electron donors. Based on their core structure, the aglycone, the flavonoids
can be grouped into different classes, such as flavones (e.g., apigenin, luteolin),
flavonols (e.g., quercetin, myricetin), flavanones (e.g., naringenin, hesperidin), cat-
echins or flavanols (e.g., epicatechin, gallocatechin), anthocyanidins (e.g., cyanidin,
pelargonidin), and isoflavones (e.g., genistein, daidzein) (Ross and Kasum, 2002).
Within each group, single or combinatorial modifications of the aglycones, such as
glycosylation, methylation and acylation, contribute to the formation of individual
compounds.
Flavonoids are mainly responsible for the blue to purple, red, and yellowish col-
ors in plants. Proanthocyanidins and their monomer units, catechins (Fig. 12.2),
are the natural substrates of polyphenol oxidases and are, therefore, involved in the
browning phenomenon of fruits.
To date, more than 6,000 flavonoids have been described and the number is still
increasing. Notably, most of them are conjugated to sugar molecules and are com-
monly located in the upper epidermal layers of leaves and fruits as well as in seed
coats (Stewart et al., 2000, Willits et al., 2005). In plants, flavonoids are involved in
many aspects of growth and development, including pathogen resistance, pigmen-
Fig. 12.2 A schematic presentation of the flavonoid biosynthetic pathway and its struc-
tural genes. Gene abbreviations: ANR = anthocyanidin reductase, ANS/LDOX = anthocyani-
din synthase, C4H = cinnamate 4-hydroxylase, 4CL = 4-coumarate-COA ligase, CHS =
chalcone synthase, CHI = chalcone isomerase, DFR = dihydroflavonol 4-reductase, F3H =
flavanone 3-hydroxylase, FLS = flavonol synthase, 3GT (UFGT) = UDPG-flavonoid-3-O-
glucosyltransferase, LAR = leucoanthocyanidin reductase, LDOX = leucoanthocyanidin dioxy-
genase, PAL = phenylalanine ammonia lyase, 3RT = anthocyanidin-3-glucoside rhamnosyl trans-
ferase
298 I. Levin
tation, and therefore attraction of pollinating insects, UV light protection, pollen

tube growth, plant defense against pathogenic micro-organisms, plant fertility and
germination of pollen, seed coat development, and in signaling for the initiation of
symbiotic relationships (Harborne, 1986; Dooner et al., 1991; Koes et al., 1994;
Dixon and Paiva, 1995; Parr and Bolwell, 2000; Schijlen et al., 2004).
Historically, flavonoids have been an attractive research subject mainly because
of the colorful anthocyanins. These eye-catching pigments have been very useful
in performing genetic experiments, including Gregor Mendel’s study on the inheri-
tance of genes responsible for pea seed coat color and the discovery of transposable
elements interrupting maize pigment biosynthetic genes (McClintock, 1967; Lloyd
et al., 1992; Koes et al., 1994).
The composition of flavonoids in different fruit species varies greatly (Macheix
et al., 1990, Robards and Antolovich, 1997). The main anthocyanins in fruits are
glycosides of six anthocyanidins that are widespread and commonly contribute to
the pigmentation of fruits. Cyanidin is the most common anthocyanidin, the others
being delphinidin, peonidin, pelargonidin, petunidin, and malvidin. Of the flavonols,
quercetin, kaempferol, myricetin, and isorhamnetin are common in fruits, quercetin
being the predominant flavonol. A third predominant flavonoid group in fruits is
proanthocyanidins and their monomer units, catechins (procyanidin) or gallocate-
chins (prodelphinidins).
Delphinidin-derived anthocyanins are known to be responsible for the bluish col-
ors, whereas cyanidin- and pelargonidin-derived anthocyanins are found in mauve
and reddish tissues, respectively. Anthocyanins tend to form complexes with so-
called co-pigments that can intensify and modify the initial color given by the
pigment. Apparently, almost all polyphenols, as well as other molecules, such as
purines, alkaloids, and metallic cations, have the ability to function as co-pigments.
The final color of anthocyanins can also be affected by the temperature and pH of
the vacuolar solution where they reside (Brouillard and Dangles, 1994; Brouillard
et al., 1997; Mol et al., 1998; Cseke et al., 2006).
Because flavonoids impart much of the color and flavor of fruits, vegetables,
nuts, and seeds, they form an integral part of the human diet (Parr and Bolwell,
2000). Rich dietary sources of flavonoids include soybean (isoflavones); citrus (fla-
vanones); tea, apple, and cocoa (flavanols); celery (flavones); onion (flavonols); and
berries (anthocyanins) (Table 12.1; Rice-Evans et al., 1996; Ross and Kasum, 2002;
Le Gall et al., 2003).
12.3.1 The Flavonoid Biosynthetic Pathway
The flavonoid biosynthetic pathway has been almost completely elucidated and
comprehensively reviewed (e.g., by Dooner et al., 1991; Koes et al., 1994; Holton
and Cornish, 1995; Mol et al., 1998; Weisshaar and Jenkins, 1998; Winkel-Shirley,
2001). Many of the genes controlling this pathway have been cloned from several
model plants including maize (Zea mays), snapdragon (Antirrhinum majus), petunia
(Petunia hybrida), gerbera (Gerbera hybrida), and more recently, Arabidopsis (van
der Krol et al., 1988; Goff et al., 1990; Taylor and Briggs, 1990; Martin et al., 1991;
Tonelli et al., 1991; Shirley et al., 1995; Elomaa et al., 1993, Helariutta et al., 1993,
1995; Holton and Cornish, 1995). These genes can be divided into two classes: (1)
structural genes which encode enzymes that directly participate in the formation
of flavonoids and (2) regulatory genes that control the expression of the structural
genes.
An overview of the flavonoid pathway is presented in Fig. 12.2. Flavonoids
are synthesized via the phenylpropanoid pathway, generating organic compounds
that are biosynthesized from the amino acid phenylalanine. Phenylalanine ammo-
nia lyase (PAL) catalyzes the conversion of phenylalanine to cinnamate. PAL also
shows activity by converting tyrosine to p-coumarate, albeit with a lower efficiency.
The cinnamate 4-hydroxylase (C4H) catalyzes the synthesis of p-hydroxycinnamate
from cinnamate, and 4-coumarate:CoA ligase (4CL) converts p-coumarate to its
coenzyme-A ester, activating it for reaction with malonyl-CoA. The flavonoid
biosynthetic pathway starts with the condensation of one molecule of 4-coumaroyl-
CoA and three molecules of malonyl-CoA, resulting in the yellow-colored narin-
genin chalcone. This reaction is carried out by the enzyme, chalcone synthase
(CHS), the key enzyme for flavonoid biosynthesis. In most plants chalcones are not
the end-product, as the pathway proceeds with additional enzymatic steps to gen-
erate other classes of flavonoids, such as flavanones, dihydroflavonols, and finally,
anthocyanins, the major water-soluble pigments in flowers and fruits and root crops
like beets. Other flavonoid classes, i.e., isoflavones, aurones, flavones, proantho-
cyanidins, and flavonols, represent side branches of the flavonoid pathway and are
derived from intermediates in anthocyanin formation (Fig. 12.2).
Naringenin chalcone is isomerized to the flavanone naringenin by the enzyme
chalcone isomerase (CHI). Even in the absence of CHI, naringenin chalcone may
spontaneously isomerize to form naringenin (Holton and Cornish, 1995). From these
central intermediates, the pathway diverges into several side branches, each result-
ing in a different class of flavonoids. Flavanone 3-hydroxylase (F3H) catalyzes the
stereospecific 3β-hydroxylation of flavanones to dihydroflavonols. For the biosyn-
thesis of anthocyanins, dihydroflavonol reductase (DFR) catalyzes the reduction of
dihydroflavonols to flavan-3,4-diols (leucoanthocyanins), which are converted to
anthocyanidins by anthocyanidin synthase (ANS). The formation of glucosides is
catalyzed by UDP glucose-flavonoid 3-O-glucosyl transferase (UFGT), which sta-
bilizes the anthocyanidins by 3-O-glucosylation (Harborne, 1994; Bohm, 1998).
12.4 Health Benefits of Carotenoids and Flavonoids
Diet is believed to play an important role in the development of chronic human dis-
eases (Willcox et al., 2003; Lila, 2007). It is now becoming recognized that certain
fruits and vegetables can help prevent or treat chronic human diseases (Heber and
Bowerman, 2001; Sloan, 2000; Lila, 2007). However, this recognition is primarily
supported by in vitro and epidemiological studies, but by only a limited number of
in vivo studies (Willcox et al., 2003). Nonetheless, it is currently believed that not
300 I. Levin
single components in plant-derived foods but rather complex mixtures of interact-

ing natural chemicals are producing health-protective effects. These phytochemicals
accumulate simultaneously in a plant, and they provide a multifaceted defensive
strategy for both the plant and the human consumer (Heber and Bowerman, 2001;
Lila, 2007).
Many phytochemicals are colorful, providing an easy way to communicate
increased diversity of fruits and vegetables to the public (Joseph et al., 2003).
These colors have provided various recommended color codes for plant-derived diet,
advising consumers to ingest one serving of each color groups daily. For instance, a
seven-color code was suggested by Heber and Bowerman (2001) which includes (1)
red foods that contain lycopene, the pigment in tomatoes, which becomes localized
in the prostate gland and may be involved in maintaining prostate health; (2) yellow-
green vegetables, such as corn and leafy greens, that contain lutein and zeaxan-
thin, which become localized in the retina where age-related macular degeneration
occurs; (3) red-purple foods containing anthocyanins, which are powerful antiox-
idants found in red apples, grapes, berries, and wine; (4) orange foods, includ-
ing carrots, sweet potatoes, yams, mangos, apricots, pumpkin, and winter squash,
which contain β-carotene; (5) orange-yellow foods, including oranges, tangerines,
and lemons, which contain citrus flavonoids; (6) green foods, including broccoli,
Brussels sprouts, and kale, which contain glucosinolates; and (7) white-green foods
in the onion family that contain allyl sulfides. Interestingly five of the above color
groups can be assigned to the carotenoid or flavonoid families of phytonutrients,
underlying their importance for human nutrition.
Some members of the carotenoid family of compounds, such as β-carotene, are
precursors (provitamins) of vitamin A. Following ingestion by humans and animals,
β-carotene is being converted into vitamin A. Low dietary intake of fruits, vegeta-
bles, and preformed sources of vitamin A consumed from animals, can often lead
to vitamin A deficiency that causes acute health disorders. Vitamin A deficiency is
an endemic nutrition problem throughout much of the developing world, especially
affecting the health and survival of infants, young children, and pregnant and lactat-
ing women. One of the earliest manifestations of vitamin A deficiency is impaired
vision, particularly in reduced light (night blindness). Other health consequences
of vitamin A deficiency include impaired immunity, xerophthalmia, keratomalacia,
growth and developmental problems among children, and increased risk of mortality
(Mayne, 1996; West, 2003; Wintergerst et al., 2007). Noteworthy, excessive intake
of vitamin A, manifested as hypervitaminosis A, can also lead to health disorders
such as birth defects, liver problems, and reduced bone mineral density. However,
these toxicities are usually related to overconsumption of the preformed sources of
vitamin A (i.e., retinyl esters from animal foods, fortified foods, and pharmaceutical
supplements). Carotenoid forms, such as β-carotene as found in fruits and vegeta-
bles, usually give no such symptoms (Penniston and Tanumihardjo, 2006).
Studies carried out since 1970 displayed a correlation between high intake of
carotenoids and health benefits. These studies have suggested that diets high in
carotenoids reduce the risk of chronic diseases such as lung, breast, prostate, and
colorectal cancers; cataract and macular degeneration; light-induced erythema; and
cardiovascular diseases (recently reviewed by Fraser and Bramley, 2004; Levin

et al., 2006).
Recent studies have suggested that the consumption of tomatoes and tomato-
based products reduces the risk of chronic diseases such as cancer and cardiovas-
cular diseases. This protective effect has been associated with carotenoids, which
are one of the major classes of phytochemicals in this fruit. The most abundant
carotenoid in ripe-red tomato is lycopene, followed by phytoene, phytofluene,
ζ-carotene, γ-carotene, β-carotene, neurosporene, and lutein (Khachik et al., 2002).
Although the proposed health benefits of tomato and tomato-based products are
usually related to lycopene, the possibility that other phytochemicals in the tomato
fruit also contribute to these protective properties should not be ignored. A recent
study, in which the effect of tomato lycopene on low-density lipoprotein (LDL) oxi-
dation in vitro was compared with the effect of oleoresin (a lipid extract of tomato
containing 6% lycopene, 0.1% β-carotene, and 1% vitamin E), provides evidence
for a concerted and/or synergistic activity of phytochemicals. The tomato oleoresin
exhibited higher capacity to inhibit LDL oxidation in comparison to pure lycopene,
by up to fivefold. In addition, lycopene was shown to have a synergistic effect on
LDL oxidation with vitamin E and, to a lesser extent, with β-carotene (Fuhrman
et al., 2000). From a nutritional point of view, these findings reinforce the advan-
tage of consuming tomato oleoresin rather than pure synthetic lycopene as a dietary
supplement.
Lycopene, lutein, and zeaxanthin are the major carotenoids found in human blood
and tissues and may be protective in degenerative eye diseases because they absorb
damaging blue light. These carotenoids may also protect the skin from light-induced
damage (Johnson, 2002; Sies and Stahl, 2003).
Carotenoids and flavonoids have been shown to play a role in preventing car-
diovascular diseases due to their antioxidative property. These compounds may
function individually, or in concert, to protect lipoproteins and vascular cells
from oxidation, which is widely hypothesized to be one of the major causes
of atherosclerosis. This hypothesis has been supported by studies that associate
reduced cardiovascular risk with consumption of antioxidant-rich foods. Other car-
dioprotective functions provided by plant phytonutrients may include the reduc-
tion of LDL, homocysteine, platelet aggregation, and blood pressure (Willcox et
al. 2003). Oxidation of the circulating LDL (LDLox ) may play a key role in the
pathogenesis of atherosclerosis and coronary heart disease. It is suggested that
macrophages inside the arterial wall take up the LDLox and initiate the process
of plaque formation. Dietary antioxidants such as vitamin E and β-carotene have
been shown to prevent the formation of LDLox and their uptake by microphages
in vitro (Rao, 2002). Healthy human subjects ingesting lycopene, in the form of
tomato juice, tomato sauce, and oleoresin soft gel capsules, for 1 week had signif-
icantly lower levels of LDL compared with controls (Rao and Agarwal, 1998). At
present, however, the role of lycopene in the prevention of coronary heart disease is
strongly suggestive. Although the antioxidant property of lycopene may be one of
the principal mechanisms for its effect, other mechanisms may also be involved.
Lycopene was shown to inhibit the activity of an essential enzyme involved in
302 I. Levin
cholesterol synthesis both in vitro and in a small clinical study suggesting a hypoc-
holesterolemic effect. Other possible mechanisms include enhanced LDL degra-
dation, effect on LDL particle size and composition, plaque rupture, and altered
endothelial functions (Rao, 2002).
Several studies focusing on dietary assessment suggest that the intake of toma-
toes and tomato products may also be associated with a lower risk of prostate cancer.
It is possible that lycopene is one of the compounds in raw and processed tomato
products that may contribute to the lower risk of that type of cancer. However, this
hypothesis remains to be further investigated. A recent study has also found an asso-
ciation between higher plasma lycopene concentrations and lower risk of prostate
cancer, among older participants (>65 years of age) without a family history of
prostate cancer (Wu et al., 2004). Several carotenoids have also been shown to have
an effect on the immune response: β-carotene, lutein, canthaxanthin, lycopene, and
astaxanthin are active in enhancing cell-mediated and humoral immune responses
in animals and humans (Chew and Park, 2004).
There is an increasing evidence suggesting that flavonoids, in particular those
belonging to the class of flavonols (such as kaempferol and quercetin), are poten-
tially health-protecting components in the human diet as a result of their high antiox-
idant capacity (Rice-Evans et al., 1997; Lean et al., 1999; Sugihara et al., 1999;
Dugas et al., 2000; Duthie and Crozier, 2000; Ng et al., 2000; Proteggente et al.,
2002) and their ability, in vitro, to induce human protective enzyme systems (Cook
and Samman, 1996; Manach et al., 1996; Janssen et al., 1998; Choi et al., 1999;
Frankel, 1999; Hollman and Katan, 1999; Shih et al., 2000). Based on these find-
ings, it was postulated that flavonoids may offer protection against major diseases
such as coronary heart diseases and cancer (Hertog and Hollman, 1996; Steinmetz
and Potter, 1996; Trevisanato and Kim, 2000; Singh and Agarwal, 2006). In addi-
tion, several epidemiological studies have suggested a direct relationship between
cardioprotection and consumption of flavonols from dietary sources such as onion,
apple, and tea (Hertog et al., 1993; Keli et al., 1996). In this respect, anthocyanins
have received particular attention because of their very strong antioxidant activity
as measured by the oxygen radical absorbing capacity (ORAC) assay. Antioxidants
such as carotenoids and flavonoids are potentially useful agents in the management
of human neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s dis-
ease, and schizophrenia because one of the factors increasing the incidence of those
diseases is accumulation of oxidative damage in neurons (Levin et al., 2006).
The antioxidant activity of flavonoids is thought to slow the aging of cells and to
protect against lipid peroxidation. In vitro studies have also shown that flavonoids
can inhibit, and sometimes induce, enzymatic systems. They are thought to reduce
the proliferation of certain types of tumor cells (Zava and Duwe, 1997; Kawaii et al.,
1999) and to be involved in the apoptosis of HL-60 leukemia cells (Ogata et al.,
2000).
The flavonoid quercetin, also present in the tomato fruit, was shown to have
a strong inhibitory action against cholesterol oxidation, a process leading to
the formation of oxysterols, a potentially cytotoxic, mutagenic, atherogenic, and
possibly carcinogenic compound found in many commonly processed foods. A
supplementation with quercetin was shown to have a blood pressure lowering effect
on spontaneously hypertensive rats (Duarte et al., 2001).
As outlined above, flavonoids comprise a group of plant polyphenols. Polyphe-
nols are in general related to human health and were recently related to the
French paradox. The French paradox refers to the observation that the French
suffer relatively low incidence of coronary heart disease, despite having a diet
relatively rich in saturated fats (Ferrières, 2004). This low incidence of coro-
nary heart diseases was ascribed to consumption of red wine and was ini-
tially attributed to resveratrol, a non-flavonoid polyphenol naturally present
in red wine. However, a recent study has identified a particular group of
flavonoid polyphenols, known as oligomeric proanthocyanidins (condensed tan-
nins) (Fig. 12.2), which are believed to offer the greatest degree of protection
to human blood vessel cells and, therefore, to reduced coronary heart diseases
(Corder et al., 2006).
In contrast to their suggestive positive effects, potential risks have been asso-
ciated with excessive intake of carotenoids and flavonoids as supplements. For
instance, harmful properties were found for β-carotene (provitamin A) in partic-
ular when given to smokers or to individuals exposed to environmental carcino-
gens. It was hypothesized that under these circumstances β-carotene was acting as
a pro-oxidant rather than an antioxidant (Omenn, 1998). Flavonoids, at high doses,
may also act as mutagens, pro-oxidants that generate free radicals, and as inhibitors
of key enzymes involved in hormone metabolism. For example, although the pro-
tective effect of the flavonoid, quercetin, from oxidative stress has been strongly
implied, its excessive intake is suggested to have an adverse effect on the body
(Formica and Regelson, 1995; Skibola and Smith, 2000; Galati and O’Brien, 2004;
Bando et al., 2007). It was further found that catechol-type compounds, includ-
ing quercetin, are able to act as pro-oxidants by generating reactive oxygen species
(ROS) and semiquinone radicals during the autocatalytic oxidation process (Guohua
et al., 1997; Metodiewa et al., 1999; Kawanishi et al., 2005). Thus, the effect of
dietary supplement of phytochemicals on human health should be further investi-
gated, taking into account genetic and environmental factors, as well as specific
sub-populations such as smokers. Nevertheless, a diet rich in fruits and vegetables as
a natural source for those health-promoting phytochemicals is recommended (Heber
and Bowerman, 2001; Riboli and Norat, 2003; Key et al., 2004; Srinath and Katan,
2004; Lila, 2007).
12.5 Approaches for Modification of Metabolite Biosynthesis
Strategies to increase and diversify the content of a certain metabolite in plants

focused initially on (1) transgenic modulation of structural genes involved in
its biosynthesis, (2) transgenic modulation of genes encoding transcription fac-
tors or other regulatory genes affecting its metabolic pathway, and (3) mutations
(spontaneous or induced) in structural or regulatory genes and/or quantitative
trait loci with pronounced effects on such metabolite levels. Recently, manipula-
304 I. Levin
tions of metabolic sink to efficiently sequester the end-products of the carotenoid

biosynthetic pathway were also shown to be very effective in the accumulation of
carotenoid compounds in fruits and vegetables (Lu et al., 2006; Diretto et al., 2007;
Kolotilin, et al., 2007; Li and Van Eck, 2007; Simkin et al., 2007).
Modifying a biosynthetic pathway to increase the amount of a desirable com-
pound may be further divided into (Davies, 2007) manipulation of its pathway flux
within an organism or introduction of its biosynthetic genes from other organisms.
The methods for increasing, preventing, or redirecting flux into or within the path-
way include increasing levels of a rate-limiting biosynthetic enzyme, inhibition
of the activity of a gene that competes for a limited substrate supply, and up- or
down-regulation of the pathway using regulatory factors. For reducing production
of undesirable compounds, the well-proven approach is to inhibit gene activity
for one of the biosynthetic enzymes. RNA interference (RNAi) is an effective and
reliable approach for preventing enzyme production, with examples of better per-
formance than using antisense or sense-suppression constructs (Nakamura et al.,
2006).
Successful genetic engineering of biosynthetic pathways requires knowledge
of the production and accumulation of the metabolites of interest, the availability
of DNA sequences encoding appropriate biosynthetic enzymes or regulatory fac-
tors, and gene transfer methods for the target species. Given a sufficient knowl-
edge of the target system, predictive metabolic engineering approaches may be
applied, in which data from metabolomics, transcriptomics, and proteomics are
used to identify key targets, such as flux control points or regulatory proteins
(Dixon, 2005). However, at present, the required information and tools are avail-
able only for a few pathways and crops. For most pathways, there is incom-
plete knowledge of the genes involved, key flux points, regulatory factors, and
the impact of cellular compartmentalization or metabolic channeling. Thus, in
many cases, a reiterative “trial and error” approach has usually been used to
achieve a successful genetic engineering of biosynthetic pathways (Davies, 2007).
A detailed checklist of tools and prior considerations needed to obtain a suc-
cessful metabolic engineering of plant secondary metabolism has been lately pre-
sented which properly illustrates the complexity of this issue (Dixon 2005). This
checklist includes understanding the target pathway, taking into account knowl-
edge of pathway intermediates and the enzymes/genes associated with it, avail-
ability of precursors for an introduced pathway, the choice of the right gene to
engineer in the case of multigene families, understanding of related competing
pathways, prediction of spillover pathways, understanding the tissue or cell speci-
ficity of the pathway, availability of tissue-specific promoters, knowledge of the
inter- and intra-cellular transport mechanisms for intermediates and end-products of
the pathway, and knowledge of transcriptional regulators of the pathway and their
targets.
Mutations (spontaneous or induced) in structural or regulatory genes of biosyn-
thetic pathways as well as quantitative trait loci with pronounced effects on
such phytonutrient levels have proven to be an excellent tool for both pathway
engineering and gene identification (Table 12.2). Of particular interest are the
tomato light-responsive high-pigment (hp) mutations: hp-1, hp-1w , hp-2, hp-2j ,

and hp-2dg . The identification of genes that cause these mutations has created
a conceptual link between genes-related light signaling and overproduction of
an array of fruit phytonutrients (Mustilli et al., 1999; Levin et al., 2003; 2004;
2006; Lieberman et al., 2004; Sapir et al., 2008). Due to their importance, these
mutations and the transgenic modulation of light signaling genes to increase
the functional properties of the tomato fruit will be separately discussed in this
chapter.
Table 12.2 Gene identification and map location for selected mutants that increase or modulate
carotenoid content in ripe tomato fruits
Mutation Description Gene Map location Reference
R Yellow color of ripe PSY1 Chromosome 3 Fray and

fruit flesh Grierson, 1993
B Orange color of fruits, βLCY Chromosome 6 Ronen et al., 2000
fruit β-carotene
highly increased
og, ogc Corolla tawny orange, βLCY Chromosome 6 Ronen et al., 2000
fruit β-carotene
highly reduced,
∼15–20% increase in
fruit lycopene
content
DEL Fruit color orange due εLCY Chromosome 12 Ronen et al., 1999
to the accumulation
of δ-carotene at the
expense of lycopene
T Fruit flesh and stamens CARTISO Chromosome 10 Isaacson et al.,
orange colored. 2002
Fruits accumulate
prolycopene
(7Z,9Z,7 Z,9 Z-tetra-
cis-lycopene) instead
of the
all-trans-lycopene
hp-1, Fruit carotenoids, DDB1 Chromosome 2 Lieberman et al.,
hp-1w including lycopene, 2004; Liu et al.,
highly increased 2004
hp-2, Fruit carotenoids, DET1 Chromosome 1 Mustilli et al.,
hp-2j , including lycopene, 1999; Levin
hp-2dg highly increased et al., 2003
hp-3 Fruits accumulate 30% ZE Chromosome 2 Galpaz et al.,
more carotenoids 2007
gh Fruits milky white, PTOX Chromosome 11 Josse et al., 2000;
fruit phytoene Mackinney
increased et al., 956
306 I. Levin
12.5.1 Non-transgenic Approaches of Modulating the Carotenoid

Biosynthetic Pathway in the Tomato Fruit
Fruit quality has been a major focus of most classical tomato breeding programs
during the past century (recently reviewed by Foolad, 2007). Color and nutri-
tional quality are among the major tomato fruit quality characteristics of interest.
The attention to tomato fruit color has recently increased as the health benefits of
lycopene, the major carotenoid in tomato that is responsible for the red fruit color,
have become more obvious (Di Mascio et al., 1989; Levy et al., 1995; Stahl and
Sies, 1996; Gerster, 1997; Kohlmeier et al., 1997). Several major genes with sig-
nificant contribution to high contents of fruit lycopene (e.g., the genes encoding
the hp and ogc mutant phenotypes) and other carotenoids (e.g., beta-carotene, B)
were previously phenotypically identified and mapped onto the classical linkage
map of tomato (Wann et al., 1985; Stevens and Rick, 1986). In addition, during
the past two decades, numerous QTLs (quantitative trait loci) and candidate genes
with significant effects on fruit color and/or lycopene content were identified in
tomato wild accessions such as S. pimpinellifolium, S. peruvianum, S. habrochaites,
S. chmielewskii, and S. pennellii and mapped onto tomato chromosomes along with
the previously identified genes (Foolad, 2007). While some of the identified QTLs
mapped to the chromosomal locations of many of the known genes of the carotenoid
biosynthesis pathway, many mapped to other locations (Liu et al., 2003). It was
therefore suggested that there might be more genes affecting fruit color in tomato
than those known to affect the carotenoid biosynthesis pathway (Liu et al., 2003).
Tomato mutant accessions with divergent color phenotypes in their fruits were
the subject of molecular genetic studies, leading to the identification of genes
responsible for such phenotypes. A selection of such mutants, their gene identifi-
cation, and map location are presented in Table 12.2, while their characteristic color
is shown in Fig. 12.3. The sequence of these genes can now serve as recombination-
free DNA markers to expedite breeding toward altering pigmentation and enhanc-
ing nutritional value of plant foods. Of particular interest are the light-responsive hp
mutations that will be dealt with herein below. Another mutant that is becoming of
special interest is t (tangerine), which produces orange-colored fruits accumulating
prolycopene (7Z,9Z,7’Z,9’Z-tetra-cis-lycopene) instead of the all-trans-lycopene
that accumulates in regular red-fruited tomatoes (Fig. 12.3; Isaacson et al., 2002).
cis isomers of lycopene, thought to be powerful antioxidants, have been shown
to be more bioavailable than the trans isomer, indicating that they are more effi-
ciently absorbed and, therefore, deliver lycopene into the plasma more effectively.
This might be interpreted to mean that cis isomers of lycopene are more beneficial
and, therefore, more valuable to human health than the trans isomer (Ishida et al.,
2007). Results recently published support the hypothesis that lycopene cis isomers
are highly bioavailable and suggest that special tomato varieties can be utilized
to increase both the intake and the bioavailability of health-beneficial carotenoids
(Unlu et al., 2007). Because light-responsive hp mutants are characterized by higher
total fruit carotenoids, hp-1/hp-1 t/t double mutant fruits share almost double the
content of cis isomers of lycopene, in comparison to non-hp, +/+ t/t, mutant fruits,
Fig. 12.3 Tomato fruit color mutants related to carotenoids biosynthesis. Abbreviations are
as follows: at = apricot, yellow-pink color of fruit flesh; B = beta-carotene, high β-carotene,
low lycopene in ripe fruit; DEL = delta, Reddish-orange mature fruit color, due to inhibition of
lycopene, and increase of delta-carotene; hp-1 = high pigmen-1, chlorophyll, carotenoids, ascorbic
acid content of fruit intensified; og = old gold, increased fruit lycopene content; r = yellow flesh,
yellow color of ripe fruit flesh; sh = sherry, fruit flesh yellow with reddish tinge; t = tangerine;
fruit flesh and stamens orange colored
demonstrating the power of classical breeding to both modulate the profile and
increase the content of selected carotenoids in the tomato fruit (Levin I, personal
communication).
12.5.2 Non-transgenic Approaches of Modulating the Flavonoid

Biosynthetic Pathway in the Tomato Fruit
Despite the relative success obtained in increasing flavonoid content in tomato fruits
by transgenic modifications, there is an ongoing interest in breeding a high flavonoid
tomato without genetic engineering (Willits et al. 2005). This interest is motivated
by customers’ reluctance to consume transgenic fruits and vegetables.
As recently summarized (Jones et al. 2003; Sapir et al., 2008), fruits of several
tomato accessions, as well as species which are closely related to the cultivated
308 I. Levin
tomato, contain significantly higher amounts of anthocyanins (Giorgiev 1972; Rick

1964; Rick et al. 1994; Fig. 12.4). The Anthocyanin fruit (Aft, formerly Af) from
S. chilense, Aubergine (ABG) from S. lycopersicoides, and the recessive atrovio-
lacium (atv) mutation from Lycopersicon cheesmaniae cause anthocyanin expres-
sion in tomato fruit. We have also managed to introgress the trait of fruit antho-
cyanin expression from S. peruvianum accessions (Fig. 12.4), and recently, the wild
species S. pennellii var. puberulum was shown to be a source for enriching tomato
fruits with functional flavonoids (Willits et al., 2005).
Another approach to increase fruit flavonoids is through the introgression of the
high-pigment (hp) mutations hp-1, hp-1w , hp-2, hp-2j , and hp-2dg . These mutations
are best known for their positive effect on carotenoid levels in ripe-red fruits (Levin
et al., 2003; Mochizuki and Kamimura, 1984; van Tuinen et al., 2006; Wann et al.,
1985). In addition, mature fruits of plants carrying the hp-1 mutation were also
found to exhibit a 13-fold increase of the flavonol quercetin in tomato fruit pericarp
relative to their isogenic counterparts (Yen et al., 1997). We have also shown similar
increases in quercetin levels in fruits of the hp-2dg mutant and in fruit skin of hp-2
and hp-2j mutants (Bino et al., 2005; Levin et al., 2006).
Fig. 12.4 Tomato fruit color phenotypes related to flavonoid biosynthesis. (A) Anthocyanin
fruit (Aft) from S. chilense, (B) Aubergine (ABG) from S. lycopersicoides, (C) S. peruvianum (PI
128650), (D) Purple Smudge introgressed from S. peruvianum, (E) fruits of a double homozygous
AFT/AFT hp-1/hp-1 plant, (F) fruit skin from a tomato y mutant, and (G) fruit skin from regular
tomato
Results recently presented in a textbook manuscript (van Tuinen et al., 2006),

indicated that several phenolic compounds with high antioxidant capacity are new
or increased in fruits of double mutant Aft/Aft hp-1w /hp-1w , as compared to fruits of
single mutant parents. One of these compounds was identified as the flavonoid, rutin
(van Tuinen et al., 2006). The hp-1w mutation is as an extreme mutation (Lieber-
man et al., 2004), yielding plants with poor horticultural performances in compar-
ison to its allelic hp-1 mutation. Thus, it has been of practical importance to also
analyze the interaction between Aft and hp-1 mutants. We have recently shown
that (Sapir et al., 2008) (1) Aft fruits are also characterized by significantly higher
levels of the flavonols, quercetin and kaempferol, thus enhancing their functional
value; (2) the tomato ANT1 gene, encoding a MYB transcription factor, displayed
nucleotide and amino acid polymorphisms between the Aft genotype, originating
from S. chilense, and cultivated genotypes; (3) a DNA marker based on ANT1
showed that the Aft trait is encoded by a single locus on chromosome 10 fully asso-
ciated with ANT1; and (4) double homozygotes Aft/Aft hp-1/hp-1 plants displayed
a more-than-additive (synergistic) effect on the production of fruit anthocyani-
dins and flavonols. This effect was manifested by ∼5-, 19-, and 33-fold increases
of petunidin, malvidin, and delphinidin, respectively, in the double mutants com-
pared to the cumulative levels of their parental lines (demonstrated visually
in Fig. 12.4).
Another important mutant related to the flavonoid biosynthetic pathway is the
y mutant (Fig. 12.4). Fruits of this mutant are typified by colorless fruit epidermis,
resulting in pinkish fruits that are preferred by consumers in most Asian countries.
It is highly likely that the phenotype of the y mutant is attributed to major changes in
the flavonoid pathway leading to the formation of naringenin chalcone, the yellow
pigment accumulating in tomato fruit cuticle.
12.5.3 Metabolic Engineering of the Carotenoid Biosynthetic

Pathway in Tomato
The economic value and health-promoting properties related to the tomato fruit
make it an important target for increasing nutritional content either by traditional
breeding or genetic manipulation. In view of the health-promoting properties of
carotenoids and flavonoids, many attempts have been made to genetically modify
the tomato fruit into overproduction of these phytochemicals. In most cases, this
was achieved by modulating the expression of structural genes encoding biosyn-
thetic enzymes of the dedicated pathway. In the carotenoid biosynthesis path-
way, phytoene synthase (PSY), the enzyme that catalyzes the first committed step
(Fig. 12.1), has been a preferred target for gene manipulation of the carotenoid
biosynthetic pathway (Fraser and Bramley, 2004). The choice in PSY as such a tar-
get gene was also due to the fact that it exhibits the highest flux control coefficient
among enzymes of the pathway, suggesting that it possess the greatest control
over flux through the pathway (Fraser et al., 2002). Constitutive expression of
310 I. Levin
PSY in tomato plants resulted in earlier production of lycopene in the fruits of

these transgenic plants, but the final concentration of lycopene was lower in these
plants compared to their azygous controls. In addition, that manipulation has led
to dwarfism, which is presumably caused by redirecting geranylgeranyl diphos-
phate (GGDP) from the gibberellin pathway into carotenoid synthesis (Fray et al.,
1995; Fig. 12.1). In a later study, transformation of tomato plants with an additional
PSY from Erwinia uredovora in a fruit-specific manner has led to a two to fourfold
increase in total fruit carotenoids, whereas phytoene, lycopene, and β-carotene lev-
els were increased 2.4-, 1.8-, and 2.2-fold, respectively. The transgene had no effect
on the levels of related isoprenoids (tocopherols, plastoquinone, and ubiquinone),
and the activities of other enzymes in the pathway were not significantly altered
(Fraser et al., 2002).
Interestingly, increase in lycopene levels was also achieved by manipulation of
the polyamines biosynthesis pathway. A two to threefold increase in lycopene was
observed in tomato fruits expressing the yeast S-adenosylmethionine decarboxylase
gene fused to a ripening-inducible E8 promoter (Mehta et al., 2002).
Increase of β-carotene in tomato fruits has been achieved by various genetic
manipulations. Constitutive expression of the bacterial phytoene desaturase (PDS)
gene, which converts phytoene into lycopene, doubled the concentration of
β-carotene in the fruit but halved the total carotenoid content. Interestingly, sev-
eral endogenous carotenoid genes were up-regulated, except for PSY, which was
repressed. These findings, coupled with the decrease observed in total carotenoids
and the increase in β-carotene levels, suggest feedback inhibition within the pathway
(Romer et al., 2000). Transgenic overexpression of the native lycopene β-cyclase
gene in tomato fruit resulted in a 3.8-fold increase in the concentration of β-carotene,
while the total carotene concentration was unchanged or slightly elevated. Transfor-
mation of an antisense construct of this same gene inhibited the enzyme expres-
sion by 50% and resulted in a slight increase in lycopene content (Rosati et al.,
2000). Transgenic overexpression of the alternative lycopene β-cyclase has led to
a greater increase in β-carotene concentration. That increase was accompanied by
lower lycopene content in a manner that resembles the situation in the B mutant of
tomato (Ronen et al., 2000). Recently, transgenic tomato lines containing a bacte-
rial 1-deoxy-D-xylulose-5-phosphate synthase gene targeted to the plastid with the
tomato DXS transit sequence resulted in increased carotenoid content (1.6-fold).
Phytoene and β-carotene exhibited the greatest increases (2.4- and 2.2-fold, respec-
tively). Extra-plastidic isoprenoids were unaffected in these lines (Enfissi et al.,
2005).
Xanthophylls are an important class of target compounds, because of their antiox-
idant properties, their chemical stability, and the difficulties associated with their
chemical synthesis. Metabolic engineering of xanthophyll content in tomato fruit
was successfully achieved by overexpressing the Arabidopsis lycopene β-cyclase
and the pepper β-carotene hydroxylase genes in a fruit-specific manner. This manip-
ulation resulted in about tenfold increase in β-carotene level and accumulation of
β-cryptoxanthin and zeaxanthin, two xanthophylls that were not detectable in the
Moneymaker parental line (Dharmapuri et al., 2002).
12.5.4 Metabolic Engineering of the Flavonoid Biosynthetic

Pathway in Tomato
There is a growing interest in producing food plants with increased amounts

of flavonoids because of their potential health benefits. With several exceptions
(Fig. 12.4), many tomato accessions contain only small amounts of flavonoids,
which are usually produced in the peel of the fruit (Willits et al., 2005). Transforma-
tion of tomato plants with the chalcone isomerase (CHI) gene from P. hybrida, under
the control of cauliflower mosaic virus (CaMV) 35S promoter, resulted in a dramatic
increase in peel flavonoid levels. An up to 78-fold increase in flavonoids content was
observed in transformed ripe-red fruits compared with the control, mainly due to an
accumulation of rutin (Muir et al., 2001). In a different study, a significant accumu-
lation of isoquercitrin, the immediate precursor to rutin, was achieved by ectopic
expression of CHI (Olthof et al., 2000). Isoquercitrin is thought to be more bioavail-
able than rutin, the quercetin glycoside found in wild-type tomato peel and, thus,
is considered to have a higher nutritional value. These studies show that ectopic
expression of one gene, i.e., P. hybrida CHI, is sufficient to increase flavonol accu-
mulation in tomato peel. However, no increase in flavonol levels were observed in
leaves and in green, breaker, and turning tomato flesh from high flavonol transgenic
plants, although relatively high levels of CHI transcripts were detected in these
tissues. This indicates that, in tomato, flavonoid biosynthesis is subject to tissue-
specific regulation and that in order to achieve a significant increase in flavonol
accumulation in tomato flesh, a different approach is required (Willits et al., 2005).
Indeed, flavonoid accumulation in tomato flesh, and hence an overall increase in
flavonoid levels in tomato fruit, was achieved by simultaneous overexpression of the
maize genes encoding the transcription factors LC and C1. LC and C1 are members
of MYC- and MYB-type transcription factors families, respectively, that control
the expression of several structural genes in the pathway leading to anthocyanins
in maize (Dooner et al., 1991). Fruit-specific expression of both LC and C1 genes
had caused an up to 60-fold increase in kaempferol glycosides in tomato flesh tis-
sue and an overall increase in total fruit flavonols of up to 20-fold (Bovy et al.,
2002). In an alternative approach, genes encoding four key biosynthetic enzymes
from P. hybrida leading to flavonols, chalcone synthase (CHS), CHI, flavanone-3-
hydroxylase (F3H), and flavonol synthase (FLS), were ectopically and simultane-
ously expressed in tomato plants. About 75% of the primary transformants con-
taining all four transgenes accumulated very high levels of quercetin glycosides
in the peel and more modest but significantly increased levels of kaempferol- and
naringenin-glycosides in columella tissue (Verhoeyen et al., 2002). That study has
also shown that CHS and FLS appear to be the key genes leading to flavonol biosyn-
thesis in tomato flesh (pericarp and columella) tissue. While ectopic expression of
CHS alone resulted in increased levels of naringenin-glycosides, but no increase in
flavonols, and the FLS transgene showed no significant effect by itself, expression
of both CHS and FLS had a synergistic effect resulting in a significant accumula-
tion of both naringenin glycosides and kaempferol glycosides (flavonols) in tomato
flesh. Apparently, CHI is the key enzyme for flavonol accumulation in tomato peel,
312 I. Levin
while CHS and FLS enzymes are required for the production of flavonols in flesh
tissue. Therefore, it was reasoned that, in order to achieve increased flavonol accu-
mulation throughout the tomato fruit, ectopic expression of three genes encoding
the biosynthetic enzymes CHS, CHI, and FLS would be needed. Indeed, cross har-
boring these three genes accumulates increased levels of quercetin glycosides in
peel and kaempferol glycosides in flesh (Colliver, unpublished results). It is also
noteworthy that a similar phenotype can be achieved by crossing tomatoes contain-
ing LC and C1 transgenes with tomatoes containing the CHI transgene – the only
structural gene for the production of kaempferol-type flavonols and pelargonidin-
type anthocyanins that was not strongly induced by the LC/C1 transcription factors
(Muir, unpublished results).
Further, T-DNA activation-tagging experiments in tomato identified a MYB tran-
scriptional regulator of anthocyanin biosynthesis, termed ANT1, which shares high
homology with Petunia AN2 (Mathews et al., 2003). These ant1 mutant tomato
Fig. 12.5 Phenotypes obtained by overexpression of the ANT1gene in tomato and tobacco.
(A) Transgenic tomato fruits (upper two fruits) in comparison to a non-transgenic fruit (lower fruit),
(B) transgenic tomato seedlings (left) in comparison to their non-transgenic counterparts (right),
(C) transgenic tomato seeds (left) in comparison to their non-transgenic counterparts (right), (D) a
transgenic tobacco fruit (left) in comparison to its non-transgenic counterpart (right), (E) a trans-
genic tobacco flower (left) in comparison to its non-transgenic counterpart (right), (F) a transgenic
tomato flower (left) in comparison to its non-transgenic counterpart (right), and (G) a transgenic
tobacco seedling (upper) in comparison to its non-transgenic counterpart (lower)
plants yielded fruits with purple spotting on the fruit epidermis and anthocyanin-
pigmented leaves and flowers. Overexpression of ANT1, controlled by the cassava
vein mosaic promoter, generated similar phenotypes in Micro-Tom tomato plants
and anthocyanin-pigmented leaves in tobacco plants. We have recently transformed
the ANT1 gene under the control of 35S promoter and obtained much stronger
phenotypes in transformed Moneymaker tomato plants and similar phenotypes in
tobacco plants. These results, which are presented in Fig. 12.5, visually demon-
strate the immense potential of up-regulating the flavonoid biosynthetic pathway by
transcription factors.
Recently, transgenic tomato plants accumulating new flavonoid compounds in
their fruit peel were engineered using structural flavonoid genes from different
plant sources (Schijlen et al., 2006). In this study, structural flavonoid genes (encod-
ing stilbene synthase, chalcone synthase, chalcone reductase, chalcone isomerase,
and flavone synthase) from different plant sources were used to produce transgenic
tomatoes accumulating new phytochemicals. Biochemical analysis showed that the
fruit peel contained high levels of stilbenes (resveratrol and piceid), deoxychalcones
(butein and isoliquiritigenin), flavones (luteolin-7-glucoside and luteolin aglycon),
and flavonols (quercetin glycosides and kaempferol glycosides). Using an online
high-performance liquid chromatography (HPLC) antioxidant detection system, it
was possible to demonstrate that, due to the presence of the novel flavonoids, the
transgenic tomato fruits displayed altered antioxidant profiles. In addition, total
antioxidant capacity of tomato fruit peel with high levels of flavones and flavonols
increased more than threefold.
12.6 The Tomato Photomorphogenic Light-Responsive hp

Mutants
Plants respond to light intensity, direction, duration, and spectral quality by modu-
lating their developmental processes in an array of interactions that are referred to
as photomorphogenesis. Photomorphogenic mutants have proven to be an excellent
tool in the study of the complex interactions between light and plant development,
and some of them have also been harnessed in several breeding programs of agricul-
tural crops. Photomorphogenic mutants have been reported in a number of species,
including Arabidopsis, Sorghum, Brassica, tobacco, tomato, and pea. In general,
these mutants may be classified either as defective in photoreceptors or altered in
some element of the light signal transduction pathway (Chory, 1993).
Several photomorphogenic mutants have been described in tomato (van Tuinen
et al., 1997). Among these, mutants carrying the monogenic recessive high-pigment
(hp-1, hp-1w , hp-2, hp-2j , and hp-2dg ) mutations are characterized by their exagger-
ated light responsiveness. These mutants display higher anthocyanin levels, shorter
hypocotyls, darker foliage, and higher fruit pigmentation than their isogenic nor-
mal counterparts (Mochizuki and Kamimura, 1984; Wann et al., 1985, Peters et al.,
1989, Mustilli et al., 1999; Levin et al., 2003). The high pigmentation of fruits of
these mutants is due to significantly elevated levels of chlorophylls at most of their
314 I. Levin
pre-mature developmental stages. The mature ripe-red fruits of these mutants are
characterized by an intense red color which is mainly due to increased levels of
carotenoids, primarily lycopene. Because of their effect on fruit color, attributed to
enhanced lycopene content, hp mutations have been introgressed into several com-
mercial processing and fresh-market tomato cultivars that are currently marketed
as lycopene-rich tomatoes (LRT) (Wann, 1997; Levin et al., 2006). The process-
ing tomato varieties are primarily cultivated for the purpose of lycopene extrac-
tion, which is further used as food additive, food supplement, and food colorant
in many processed products (http://www.lycored.com/). Current processing tomato
cultivars harboring such mutations can reach a remarkable up to 3.5-fold increase
in fruit lycopene content (from 80 to 280 μg·g−1 FW). Interestingly, this increase
is higher than that reported thus far using the genetically modified alternatives dis-
cussed herein above.
The origins of hp-1, hp-1w , hp-2, hp-2j , and hp-2dg mutations have been lately
extensively summarized (Lieberman et al., 2004; Levin et al., 2006). Further, the
hp-2, hp-2j , and hp-2dg mutations were mapped to the gene encoding the nuclear
protein DEETIOLATED1 (DET1), a central negative regulator of photomorphogen-
esis (Mustilli et al., 1999, Levin et al., 2003). The gene encoding the hp-1 and hp-1w
mutant phenotypes has also been recently identified (Lieberman et al., 2004) and
later independently confirmed by an additional laboratory (Liu et al., 2004). Results
show that hp-1 and hp-1w are alternative alleles at the tomato gene encoding UV
DAMAGED DNA BINDING protein 1 (DDB1), recently shown to interact both
biochemically and genetically with the DET1 protein (Schroeder et al., 2002, Liu et
al., 2004). DDB1 is a protein evolutionally conserved from fission yeast to humans.
It was initially identified, together with DDB2, as a subunit of a heterodimeric pro-
tein complex that recognizes the UV-induced DNA lesions in the nucleotide exci-
sion repair pathway. Mounting evidence has now established a major role of DDB1
as a substrate-recruiting subunit of the Cullin 4(CUL4)-based E3 ubiquitin ligase
complexes that also contain RBX1 (also named ROC1), DET1 and, in the case of
Arabidopsis, COP10 as well (Wertz et al., 2004; Hu et al., 2004; Bernhardt et al.,
2006; Chen et al., 2006).
Tomato hp mutations (hp-1, hp-1w , hp-2, hp-2j , and hp-2dg ) are best known for
their positive effect on carotenoid (lycopene and carotenes) levels in ripe-red fruits
(Mochizuki and Kamimura, 1984; Wann et al., 1985, Levin et al., 2003). Interest-
ingly, however, mature fruits of plants carrying the hp-1 mutation were also found to
exhibit a 13-fold increase of the flavonoid, quercetin, in tomato fruit pericarp (Yen
et al., 1997) and also some increase in ascorbic acid (vitamin C) (Mochizuki and
Kamimura, 1984). In a study carried out during a summer season, similar increases
were identified in quercetin levels in the fruit peel of the tomato mutants hp-2 and
hp-2j compared to their isogenic normal counterparts (Levin et al., 2006). These
results suggest that other metabolites may be increased in tomato hp mutants. To
validate this hypothesis, the overall metabolic modifications between hp-2dg tomato
mutant fruits and their isogenic non-mutant counterparts were compared (Bino et al.,
2005). Targeted metabolite analyses, as well as large-scale non-targeted mass spec-
trometry (MS)-based metabolite profiling, were used to phenotype the differences
in fruit metabolite composition. Targeted high-performance liquid chromatography

with photodiode array detection (HPLC–PDA) metabolite analyses showed higher
levels of isoprenoids and phenolic compounds, as well as vitamin C, in hp-2dg
fruits. A selected list of such metabolites including their average levels in ripe-
red fruits and their fold increase in hp-2dg were presented in Levin et al. (2006).
Non-targeted GC–MS profiling of red fruits produced 25 volatile compounds that
showed a 1.5-fold difference between the genotypes (Bino et al., 2005). Analyses
of red fruits using HPLC coupled to high-resolution quadruple time-of-flight mass
spectrometry (LC–QTOF–MS) in both ESI-positive and ESI-negative modes gen-
erated, respectively, 6168 and 5401 mass signals, of which 142 and 303 showed a
twofold difference between the genotypes. Of this total of 443 mass signals, 383
(∼86%) were up-regulated in the hp-2dg genotype, while only 62 (∼14%) were
found down-regulated in that mutant (Bino et al., 2005). Overall, these results show
that the hp-2dg fruits are more active metabolically and are characterized by over-
production of many metabolites, several of which are known for their antioxidant or
photo-protective activities. It was hypothesized that these metabolites may serve as
resources recruited by plants to respond to and manage light stress. Because hp-2dg
is highly iso-phenotypic to other tomato hp mutants, similar metabolic responses
are also expected in these other mutants.
A transcriptional profiling study was also carried out on fruits harvested from
hp-2dg mutant plants in comparison to their isogenic counterparts using microar-
ray technology (Kolotilin et al., 2007). Results show that a large portion of the
genes that are affected by hp-2dg mutation display a tendency for up- rather than
down-regulation, indicating that this genotype is more active transcriptionally as
well. Ontology assignment of these differentially regulated transcripts revealed a
consistent up-regulation of transcripts related to chloroplast/chromoplast biogen-
esis and photosynthesis in hp-2dg mutants throughout fruit ripening. A tendency
of up-regulation was also observed in structural genes involved in phytonutrient
biosynthesis. However, this up-regulation was not as consistent, positioning plas-
tid biogenesis as a more important determinant of phytonutrient overproduction in
hp-2dg and possibly other hp mutant fruits. These results were linked to microscopic
observations that revealed a highly significant increase in chloroplast/chromoplast
size and number in pericarp cells of mature-green hp-2dg /hp-2dg and hp-2j /hp-2j
fruits in comparison to their normal counterparts.
As noted herein, the identification of genes responsible for the light-responsive
hp mutant phenotypes has created a conceptual link between light cues and over-
production of fruit phytonutrients, primarily those that accumulate in the plastids. It
was further shown that in these mutants plastid biogenesis is the major determinant
of the drive that increases these phytonutrients (Kolotilin et al., 2007). Interestingly,
these concepts were also lately documented in the characterization of tomato plants
mutated at the zeaxanthin epoxidase (ZE) gene (Galpaz et al., 2007) and its overex-
pression in an additional study (Wang et al., 2008). Fruits harvested from the mutant,
termed hp-3, displayed 30% more carotenoids in the mature fruit compared to their
isogenic normal counterparts. This increase in fruit carotenoids content was accom-
panied by at least a twofold increase in plastid compartment size (Galpaz et al.,
316 I. Levin
2007). In addition, constitutive overexpression of ZE in tomato plants characterized

in a later study was found to display enhanced sensitivity of the tomato plants to
photo-inhibition caused by high light stress (Wang et al., 2008).
12.6.1 Light Signal Transduction as a Target for Nutritional

Enhancement
As indicated above, tomato hp mutants plants are characterized by overproduction of

many metabolites, some of which possess antioxidant or photo-protective activities.
The genes responsible for these mutations have been cloned and represent tomato
homologs of light signal transduction regulatory genes, previously described in Ara-
bidopsis. Therefore, targeting the light signaling pathway might be an effective
approach to engineer fruit nutritional quality. Although carotenoid accumulation
in edible plant tissues has been manipulated by altering corresponding biosynthetic
enzymes (e.g., “golden” rice, Beyer et al., 2002), the outcome of such approaches
has at times fallen short of expectations, as summarized above. This is probably
because of a lack of understanding regarding endogenous mechanisms of regula-
tion and accumulation of carotenoids and/or undesirable side effects on non-target
metabolites derived from the altered pathway (Fray et al., 1995; Beyer et al., 2002;
Liu et al., 2004). Engineering of an existing signal transduction network already
capable of regulating flux through the carotenoid synthesis pathway in a biologically
viable manner might represent an alternative to optimizing the carotenoid-associated
nutritional benefit in plant tissues such as fruit (Liu et al., 2004). Indeed, recently
it has been shown that manipulating tomato light signal transduction genes homol-
ogous to HY5 and COP1 from Arabidopsis can result in modified fruit carotenoid
accumulation in tomatoes (Liu et al., 2004). Down-regulated LeHY5 plants exhibit
defects in light responses, including inhibited seedling photomorphogenesis, loss of
thylakoid organization, and reduced carotenoid accumulation. In contrast, repres-
sion of LeCOP1like expression results in plants with exaggerated photomorpho-
genesis, dark green leaves, and elevated fruit carotenoid levels. Manipulation of
DET1 expression in tomato resulted in photomorphogenic phenotypes caused by
post-transcriptional gene silencing and fruits with increased carotenoids (Davuluri
et al., 2004). These results were later supplemented by fruit-specific RNAi-mediated
suppression of DET1, resulting in increased fruit flavonoid content in addition to
carotenoids (Davuluri et al., 2005).
Antisense tomato plants carrying the C-terminal portion of the tomato cryp-
tochrome 1 (TCRY1) gene have also been characterized (Ninu et al., 1999). Syn-
thesis of anthocyanins under blue light was reduced in antisense seedlings. In
contrast, carotenoid and chlorophyll levels were essentially unaltered. Tomato
cryptochrome 2 overexpression, on the other hand, resulted in a high-pigment phe-
notype, with overproduction of anthocyanins and chlorophyll in leaves and of
flavonoids and lycopene in fruits. The accumulation of lycopene in fruits was
accompanied by the decreased expression of lycopene β-cyclase genes (Giliberto
et al., 2005). These results finally confirm the hypothesis that genes encoding
components of the light signal transduction machinery also influence fruit pigmen-
tation and thus represent powerful tools for the manipulation of tomato fruit nutri-
tional quality. Because light signaling genes are evolutionarily highly conserved, it
seems reasonable that they may have an impact on the nutritional quality in plant
species other than the tomato, including species that are distantly related to the
tomato.
12.7 Outstanding Examples of Engineering Metabolic Pathways

in Other Plant Species
Metabolic engineering of the carotenoid, flavonoid, and other metabolic pathways

in the tomato and other species has been recently extensively reviewed (Galili
et al., 2002; Fraser and Bramley, 2004; DellaPenna and Pogson, 2006; Yonekura-
Sakakibara and Saito, 2006; Davies, 2007; Li and Van Eck, 2007). In addition to the
tomato, efforts to up-regulate synthesis of carotenoids were also invested in agricul-
tural species such as the potato (Solanum tuberosum) and rice (Oryza sativa), while
synthesis of flavonoids was successfully up-regulated in potato and corn (Z. mays).
In addition, major metabolic engineering efforts were carried out to modulate lev-
els of other phytonutrients such as tocopherols, vitamin C, iron, selenium, and zinc
(Davies, 2007; DellaPenna and Pogson, 2006; Li and Van Eck, 2007). Outstanding
in this regard are the “golden” rice (Fig. 12.6), achieved by a transgenic approach,
and the Orange (Or) gene mutation identified in cauliflower (Brassica oleracea,
Fig. 12.6). In both cases, accumulation of high levels of β-carotene was conferred
in tissues that are normally devoid or contain very low levels of carotenoids.
The apparent lack of high levels of carotenoid accumulation in low-pigmented
tissues of crops such as rice endosperm and cauliflower curds could be due to
(1) low metabolic flux into the carotenoid biosynthetic pathway, (2) high metabolic
flux out of the carotenoid biosynthetic pathway into branching points and/or toward
non-carotenoid end-products, (3) inactivation and absence of key genes in the
biosynthetic pathway, and (4) lack of a deposition sink to efficiently sequester the
end-products of the carotenoid biosynthetic pathway. While modulating metabolic
flux by structural or regulatory genes of metabolic pathways was demonstrated
above, and recently elsewhere (Davies, 2007; DellaPenna and Pogson, 2006), the
“golden” rice and the Or gene mutation exemplify, respectively, the latter two
possibilities.
The “golden” rice was named for its bright yellow endosperm due to the pro-
duction and accumulation of β-carotene, a precursor of vitamin A, which is nor-
mally not produced in regular rice (Fig. 12.6). Engineering “golden” rice was
designed to combat vitamin A deficiency in third-world Southeast Asian countries in
which rice is a major nutritional commodity. The “golden” rice was first engineered
with the insertion of the PSY gene from daffodil (Narcissus pseudonarcissus) and
the bacterial phytoene desaturase (CrtI) gene from E. uredovora, which can cat-
alyze three enzymatic steps from phytoene to all-trans-lycopene (Ye et al., 2000).
The PSY gene was inserted under the control of an endosperm-specific glutelin
318 I. Levin
Fig. 12.6 Phenotypes of the Ormutant and the “golden” rice. (A) Regular cauliflower, (B) Or
mutant cauliflower, (C) regular rice, and (D) “golden” rice
promoter, and in order to localize the gene product to the plastids (site of carotenoid
biosynthesis), CrtI was designed as a fusion with the transit peptide of RUBISCO
(ribulose-1,5-bisphosphate carboxylase/oxygenase) small subunit under the control
of 35S promoter. An alternative construct was made by co-transformation with con-
structs carrying the PSY/CrtI gene, as described above, and the LCY gene under
the control of a glutelin promoter. By the latter approach, the carotenoid content of
edible rice endosperm was about 1.6 μg·g−1 dry weight (Ye et al., 2000).
In 2005, “golden” rice 2 was developed and the β-carotene content was increased
up to 23-fold (about 37 μg·g−1 dry weight) compared to the original “golden” rice,
a level adequate to provide the recommended dietary allowance of provitamin A for
children in an average daily consumption of rice. The higher β-carotene content was
achieved by choosing the maize PSY gene rather than the PSY genes from Arabidop-
sis, daffodil or the carotenoid-accumulating vegetables such as tomato, bell pepper,
and carrot (Paine et al., 2005).
Recently, a similar approach has been employed to successfully produce
“golden” potato tubers (Diretto et al., 2007). Earlier, seed-specific overexpression
of a bacterial phytoene synthase gene (crtB) in a seed-specific manner produced
“golden” canola (Brassica napus) seeds containing up to 50-fold higher total

carotenoids (Shewmaker et al., 1999).
Another novel alternative approach to increasing metabolites in plant tissues
emerged from the recent work on isolation and functional characterization of the
carotenoid gene mutation, denoted Or, in cauliflower (Fig.12.6; Lu et al., 2006). Or
is a spontaneous semi-dominant mutation that confers the accumulation of high lev-
els of β-carotene in various tissues normally devoid of carotenoids (Li and Van Eck,
2007).
The Or gene was found to encode a DnaJ cysteine-rich domain-containing pro-
tein. Rather than directly regulating carotenoid biosynthesis, the Or gene appears to
mediate the differentiation of proplastids and/or non-colored plastids (leucoplasts)
in apical shoot and inflorescence meristematic tissues of the curds into chromo-
plasts for the associated carotenoid accumulation (Lu et al., 2006; Li and Van Eck,
2007). Transformation of the Or gene into wild-type cauliflower converts the white
color of curd tissue into distinct orange color with increased levels of β-carotene
(Fig. 12.6). Examination of the cytological effects of the Or transgene revealed that
expression of the Or transgene leads to the formation of large membranous chro-
moplasts in the cauliflower curd cells of the Or transformants (Lu et al., 2006).
Interestingly, when the Or gene, under the control of a potato granule-bound starch
synthase promoter, was introduced into potato, it resulted in the production of tubers
with orange-yellow flesh (parenchymatous tissue). The total carotenoid levels in the
Or transgenic potato lines were up to sixfold higher than in the non-transformed
controls. Further examination of the cellular contents of these transgenic tubers by
light microscopy showed that while the tubers in the controls contain exclusively
various sizes of starch grains in amyloplasts, the Or transgenic tubers have addi-
tional orange bodies. These orange bodies include intact chromoplasts and a large
number of more sharply outlined orange structures of helical sheets and fragments
released from chromoplasts. These results and those of others have led to the con-
clusion that Or gene-associated carotenoid accumulation in these transgenic tubers
is most likely due to the formation of carotenoid sequestering structures in chromo-
plasts, which provide a metabolic sink to facilitate accumulation of carotenoids. It
was thus demonstrated that successful metabolic engineering of carotenoid accumu-
lation can be also achieved by creating a metabolic sink (Li and Van Eck, 2007).
This conceptual approach was also recently tested in tomatoes following over-
expression of fibrillin (Simkin et al., 2007). Fibrillin is involved in the formation
of lipoprotein structures, such as plastoglobules and fibrils in certain chromoplast
types, which have been implicated in the overproduction of pigments due to a sink
effect. In order to examine its effect in differentiating chromoplasts of a non-fibrillar
type, the pepper fibrillin gene was expressed in tomato fruits. Both the transcript and
protein were found to accumulate during tomato fruit ripening from an early mature-
green stage. However, formation of carotenoid deposition structures in tomato chro-
moplasts, such as fibrils, was not observed. Nevertheless, a twofold increase in
carotenoid content and associated carotenoid-derived flavor volatiles (6-methyl-5-
hepten-2-one, geranylacetone, β-ionone, and β-cyclocitral) was observed. The trans-
genic fruit displayed delayed loss of thylakoids in differentiating chromoplasts,
320 I. Levin
leading to the transient formation of plastids exhibiting a typical chromoplastic zone

adjacent to a protected chloroplastic zone with preserved thylakoids. These results
therefore suggest that fibrillin may protect plastids against degradation, thus extend-
ing their carotenoid production life span and leading to greater carotenoid accumu-
lation. In this respect, the recent transcriptional profiling carried out on hp-2dg fruits
has underlined plastid number as the main contributor to plastid-accumulating phy-
tonutrients (Kolotilin et al., 2007). This study has further shown that in mature-
green fruits harvested from hp-2dg mutant plants, the plastid compartment size is
8.4-fold higher as compared to its normal counterpart, suggesting a similar poten-
tial to increase fruit carotenoid content. However, upon ripening, a sharp decrease
was observed in plastid compartment size in fruits of hp-2dg , primarily attributed to
a sharp decrease in plastid number, which was much more attenuated in their nor-
mal counterparts. Ripe-red fruits of the hp-2dg mutant were characterized by only
∼2.8-fold increase in chromoplast compartment compared to their normal counter-
part. This increase corresponds to the 2.3-fold increase usually observed in total
carotenoids between these genotypes at this ripening stage. These results cumula-
tively suggest that prevention of the enhanced plastid degradation observed upon
ripening in hp-2dg mutant fruits could potentially be a target to increase carotenoid
accumulation in these mutant fruits. Such prevention of plastid degradation could be
possibly achieved via overexpression of fibrillin in hp-2dg mutant plants. An alter-
native approach to achieve higher carotenoid accumulation in hp-2dg mutant plants
could be via overexpression of DnaJ to create an alternative metabolic sink.
12.8 Concluding Remarks and Perspectives

It is now becoming recognized that consumption of fruits and vegetables can pre-
vent or even be used to treat chronic human diseases. However, this recognition
is mainly supported by in vitro and by epidemiological studies that seem to vary
between sub-populations. There is therefore a need for more clinical in vivo tri-
als to substantiate these effects on a whole organism basis and in different human
sub-populations. There is also a need to formulate appropriate directives for recom-
mended daily allowance for each metabolite in each sub-population.
It is predicated that the recent completion of the human genome sequence,
the advances made in high-throughput technologies, and the emerging area of
nutragenomics will uncover more precisely the possible relationship between human
genetic makeup and the type and quantity of phytonutrients needed to maintain
proper health. This may position phytonutrient consumption behavior in humans
more at the level of pharma- rather than nutraceuticals with recommendations for
a critical dosage rather than a daily allowance. In other words, food may become
medicine and vice versa, in accordance with Hippocrates statement, “Let thy food
be thy medicine and thy medicine be thy food”.
Meanwhile, transgenic genetic modifications (GMO) have already been
exploited and found to be useful in enriching and diversifying the content of phy-
tonutrient metabolites in a variety of plant species. As outlined in this chapter, these
modifications can be justified, but it is not entirely clear whether consumption of

plant foods highly enriched with a certain phytonuterients will indeed contribute to
maintenance of proper health and/or to treat chronic human diseases.
Despite the relative success obtained in increasing the phytonutrient content of
plant foods by GMO modifications, consumers, in particular those that share higher
health awareness, are reluctant to consume transgenic plant foods. Luckily, several
genetic resources such as the tomato light-responsive hp mutants and the Or gene
mutation identified in cauliflower show that there are efficient non-GMO alterna-
tives to increase phytonutrient content in plant foods. Of particular interest are the
tomato hp mutants characterized by higher levels of both carotenoids and flavonoids
in the fruits. Moreover, ripe-red fruits, harvested from these mutants, also display
increased levels of several other metabolites, including vitamins C and E. Thus, con-
sumption of fruits of this type may maximize positive synergistic health effects that
were already documented among several of these phytonutrients.
The genes that cause hp mutant phenotypes were cloned and identified as two
evolutionarily conserved genes active in light signal transduction, known also as
photomorphogenesis. The identification of the genes that encode the hp mutant
phenotypes has therefore created a conceptual link between photomorphogenesis
and biosynthesis of fruit phytonutrients and thus point to modulation of light sig-
nal transduction machinery as an effective approach toward practical manipulation
of the kinds and amounts of fruit phytonutrients. The high-evolutionary conserva-
tion of these genes also suggests that similar effects may be obtained by manip-
ulating these genes in plant species other than the tomato either by transgenic or
non-transgenic methodologies.
Acknowledgments The author would like to thank Dr. Yaakov Tadmor from the Institute of Plant
Sciences, the Volcani Center, Israel, for his contribution of tomato fruit photos to this chapter. The
author also thanks Dr. Li Li from the USDA-ARS, Plant, Soil and Nutrition Laboratory, Cornell
University, Ithaca, NY 14853, USA, for his contribution of cauliflower curd photos.
The purple smudge photo was kindly provided by Jim Myers and Peter Boches, Department of
Horticulture, Oregon State University, USA.
The transgenic tomato and tobacco plants presented herein were generated as part of the M.Sc.
theses of Miss Maya Sapir and Mr. Amir Butbool, under the guidance of the author, Dr. Michal
Oren-Shamir and Dr. Moshe Reuveni and with the assistance of Dr. Dalia Evenor.
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Chapter 13
Risks and Benefits Associated with Genetically
Modified (GM) Plants
Peter B. Kaufman, Soo Chul Chang, and Ara Kirakosyan
Abstract Genetically modified (GM) plants are those whose genomes have been
modified by the introduction of foreign DNA constructs derived from bacteria,
fungi, viruses, or animals. The most common genetically modified plants include
soybeans, maize/corn, rapeseed mustard, potatoes, cotton, sugarcane, tomato, rice,
and aspen/Populus.
In this chapter, we list 16 goals of genetic engineers in developing GM plants.
These are plants that manifest frost hardiness; insect and herbicide tolerance; virus
resistance; altered starch, cellulose, and lignin production; altered levels and kinds
of oils and proteins in seed crops; higher levels of antioxidants in edible fruits,
synthesis of new metabolites like beta-carotene in rice grains and vaccines in non-
edible plants; and sequestration of hazardous wastes from polluted (“brown field”)
areas.
The next section of this chapter includes a discussion of the purported benefits and
risks of GM plants. Our goal here is to present this information in as balanced a
fashion as possible.
Lastly, we address important questions and answers concerning GM plants and
food products.
13.1 Genetically Modified Plants: What Are They and Goals

for Their Production
Genetically modified (GM) plants are those whose genomes have been modi-
fied by the introduction of foreign DNA constructs derived from bacteria, fungi,
viruses, or animals. The most common genetically modified plants include soy-
beans, maize/corn, rapeseed mustard, potatoes, cotton, sugarcane, tomato, rice, and
aspen/Populus. It is important to emphasize here that the generation of transgenic
plants can modify natural selection-induced evolution of plants.
P.B. Kaufman (B)

University of Michigan, Ann Arbor MI 48109-0646, USA

334 P.B. Kaufman et al.
The goals of genetic engineers in developing genetically modified plants include

the following:
• To develop herbicide-resistant crop plants such as “Roundup Ready”/glyphosate-

resistant soybeans with a gene derived from bacteria.
• To develop insect-resistant crop plants such Bt (Bacillus thuringinensis or
milky spore bacterium) cotton (to kill the cotton boll weevil), potatoes (to
kill the Colorado potato beetle), and corn/maize (to kill the corn ear worm).
Bt-containing plants can cause emergence of Bt-resistant insects. In “Botany
of Desire” by Machael Pollan, he reports that Monsanto Company designed a
method to avoid this. They suggest that farmers allot a part of a field for wild-
type plants, while most of the field is used for Bt-containing transgenic plants.
This strategy can cause wild-type insects to outcompete Bt-resistant mutant
insects.
• To develop viral disease-resistant plants such as papaya and squash that have
virus coat protein gene inserted into their genomes. The virus coat protein gene
that is inserted into these plants prevents the virus from reproducing because it
cannot make coat protein. The mechanism here is called co-suppression.
• To develop plants with enhanced levels of an essential vitamin such as “golden
rice” that produces significant amounts of B-carotene/vitamin A in the grains
based on the introduction of two foreign genes from daffodil and one from a
bacterium. “Golden rice” – enrichment with carotenoids (provitamin A): This
project produced a rice cultivar with enhanced levels of beta-carotene and other
carotenoids, which are metabolic precursors of vitamin A. Vitamin A can be
absorbed with fat by the human body. Because rice naturally contains only
a negligible amount of beta-carotene, vitamin A deficiency is widespread in
regions of the world where rice is a staple food. “Golden rice” was devel-
oped for people of underdeveloped countries. However, the primary drawback
here is that people who live in underdeveloped countries do not have chance
to have such well-nourished foods such as “golden rice” primarily due to its
high cost.
• To develop plants with enhanced frost resistance, GM-frost resistance has been
achieved by research scientists (Professor German Spangenberg and Dr Ulrik
John of the Victorian AgriBiosciences Centre at La Trobe University) in Vic-
toria, Australia, through the use of a gene sequence from Antarctic hairgrass
(Deschampsia antarctica, Poaceae, tribe Aveneae (Oats)). The same degree of
frost tolerance is achieved in cereals and grasses. Frost tolerance is activated by
a protective protein that is activated once the temperature drops below 5◦ C, and
the plant then has the ability to inhibit ice crystal growth which gives the plant its
freezing tolerance.
• To develop plants with altered composition of sugars or starch. GM potato
plants (EH 92-527-1) have been engineered to have tubers with a higher ratio
of branched starch (amylopectin) to straight-chain starch (amylose). These plants
have not been approved for human consumption and were developed primarily
13 Risks and Benefits Associated with GM Plants 335
for production of starch for industrial purposes. Overexpression of the sucrose-

6-phosphate synthase (SPS) gene from maize in tomato, and the same gene from
spinach in tobacco and potato, led to significant increases in sucrose biosynthesis
in the transgenic plants (see Chapter 4).
• To develop tree crops with altered composition of lignin and cellulose in their
wood (xylem) tissues through alterations in lignin biosynthesis (e.g., reduction,
augmentation and/or structural changes) and cellulose biosynthesis (e.g., aug-
mentation, reduction, and/or quality including high degree of polymerization and
crystallinity).
• To develop crop plants whose fruits have longer shelf life due to decreased
action of cell wall hydrolases such as cellulases and polygalacturonases (pecti-
nases). The FlavrSavr tomato is the most famous example. These tomatoes
were the first GM fruit sold in the United States and were sold as tomato purée
in the UK. Apples, raspberries, and melons with delayed ripening have also been
developed.
• To develop seeds with “Terminator” or other sterilizing traits in crops and orna-
mentals so as to prevent collection of seeds of these plants and thus protect the
interests of the owners of patents for such seeds.
• To develop plants with modified oil content and composition (e.g., polyunsat-
urated fatty acids such as linoleic acid and laureic acid) for maize, soybeans,
rapeseed, and other oil crops: These modified crops could be important in the
fight against cardiovascular disease, obesity, and certain forms of cancer.
• To develop plants with higher content of protein or amino acids, or modified
amino acid composition for enhanced nutritional value: For example, a GM
potato was developed in India containing more than one-third of protein includ-
ing essential, high-quality nutrients. The novel gene came from the protein-rich
grain amaranth plant. Another example is LY038, a maize line with enhanced
lysine content for improved animal feed quality. It is now awaiting authorization
in the EU.
• To develop gluten-free wheat: Celiac sprue patients cannot tolerate the protein
gluten (something similar to an allergy).
• To develop higher levels of beneficial antioxidant compounds (e.g., lycopene,
flavinols found in tomato) to prevent cardiovascular diseases and certain forms
of cancer.
• To eliminate or reduce undesirable substances like allergens or toxic substances
(e.g., caffeine, nicotine).
• To develop transgenic “amylopectin potato” that contains almost exclusively
amylopectin (an increase from 75 to 98%) rather than a mix of different starches
(amylose and amylopectin). This starch will be used for paper, textiles, and
adhesives.
• To develop GM rapeseed oil with high erucic acid content. This oil is used in
plastics and in high-grade industrial lubricants.
• To develop plants with higher carbon fixation rates via photosynthesis.
• To introduce into C-3 plants C-4 photosynthesis capabilities.
13.2 Benefits and Risks of Genetically Modified Plants

A number of positive and negative issues are associated with plant biotechnology
and its applications (Ellstrand, 2000; Gadgil, 2000). The positive issues concern
the major benefits that plant biotechnology may contribute to industry, agriculture,
and the environment. One of the significant issues is concerned with economically
feasible production of crops, pharmaceuticals, and other industrial products (Arber,
2009). We are able to grow more tolerant crops with new traits or produce important
vaccines using plant cell factories. Other positive impacts on the environment may
involve clearance of contaminated soil by means of phytoremediation as described
in Chapter 7. Plants have been found to break down or degrade organic contami-
nants (similar to microbes), while others are able to extract and stabilize toxic metal
contaminants by acting as traps or filters.
Scientists engaged in plant biotechnology should follow all regulatory mandates
as well as socially and ethically acceptable targets (Boulter, 1995). Thus, the risks
must be evaluated in connection with workplace safety, environmental contamina-
tion, and public exposure. In conducting risk assessments, it is important to consider
all normal and foreseeable abnormal operations, maintenance, cleaning, and secu-
rity. Following completion of a risk assessment and risk characterization, devel-
opment of effective risk management programs, such as implementation through
training and selection of risk management tools, is needed.
The criteria for risk assessment are based on both genetically modified and orig-
inal unmodified plants, their potential environmental interactions, as well as the
possible effects of plants or their products on the human health (Magaña-Gómez
and de la Barca, 2009). Characterization of the novel trait plays a central role in
the assessment process and overlaps the assessment of the modified plant. The main
criteria assigned pertain to information about the genetic construct (inserted genes,
regulatory mechanisms, marker genes, and donors or recipients), the gene func-
tions, complementary and breakdown products, affected metabolic pathways, and
potential toxic and allergic effects of the plant product(s). Thus, the negative issues
relative to plant biotechnology include potential harm to non-target organisms or
potential introduction of regulatory molecules (such as transcriptional factors or hor-
mones) into the same organism with subsequent effects on other genes. The main
issue associated with gene biotechnology is that the foreign genes could escape into
nature and this process could be uncontrolled. This can lead to loss of biodiversity
or to the derivation of new plant organisms with unpredicted properties. The other
most serious concern is that pollen from genetically engineered plants could con-
taminate natural populations due to pollination. In order to escape such difficulties,
foreign gene(s) may be transferred to the special organelles, such as chloroplasts
or mitochondria, for gene function and possible application, and therefore, the risk
assessment with pollination is kept to the minimum.
With the entry of genetically modified (GM) crops into our food chain, con-
sumers are demanding both satisfactory information and choice about GM crops
(Parker and Kareiva, 1996; Krebs, 2000; Pimentel et al., 2000). To satisfy this
demand, many countries are introducing legislation to control the circulation of GM
crops or to trace the use of approved GM crops. GM plants must go through a rigor-
ous stepwise screening process involving both confined and unconfined field trails.
In general, plants with novel traits are regulated on the basis of the characteristics
of the product, not the specific process by which the product is made. More specif-
ically, when the next novel plant is assessed, emphasis is placed on the insertion of
the novel gene(s) into the plant genome; the number of sites of integration (loci); the
copy numbers; presence of rearrangements; the stability; the expression; alterations
of metabolic pathways; the activity of an inserted gene product in the plant; and the
activity of the gene product in the environment. Potential altered interactions of the
novel plants involve identifying changes to the relative phenotype with respect to
stress adaptation, composition, toxins, and agronomic characteristics.
A list of potential ecological benefits (Daily, 1999; Dyson, 1999) and risks of
selected GM crops is presented in Table 13.1. It provides a framework that makes
Table 13.1 Examples of the potential ecological benefits and risks of selected GM crops
GM modification Benefits Risks
Herbicide resistance in Reduced herbicide use Increased herbicide use

crops Increased opportunities for Reduced in-field biodiversity
reduced tillage systems that may reduce the ecological
services provided by
agricultural ecosystems
Crops with Bt toxin Reduced pesticide use Promotes development of Bt
Kills fewer non-target resistance, which will eliminate
organisms than alternatives Bt as a relatively safe pesticide
such as broad-spectrum Kills non-target caterpillars and
pesticides butterflies such as monarchs
(Pimentel 2000)
Virus resistance in Reduced insecticide use to Facilitates the creation of new
small grains due to control insect dispersers of viruses (Hails 2000)
coat proteins pathogens (Hails 2000) Moves genes into
nonagricultural ecosystems
where the subsequent increase
in fitness of weedy species could
eliminate endangered species
Terminator or other Prevents the movement of traits Prevents farmers from developing
sterilizing traits in to non-target species their own seed supplies adapted
crops and Prevents the movement of to local conditions (Conway
ornamentals introduced species to other 2000)
ecosystems (Walker and
Lonsdale 2000)
Synthesis of vitamin A Improves nutrition of people Disrupts local ecosystems if an
or other nutrients who depend heavily on rice ecologically limiting nutrient or
(Conway 2000) protein is produced
Nitrogen fixation by Reduces energy used in Adds to excess nitrogen leaching
non-legumes fertilizer production and from agricultural activities,
application (Pimentel 2000) degrading human health and
reducing biodiversity
it easier to screen for the possible combinations of technology, crop, and ecological
contexts that are likely to be relatively benign or hazardous. However, constructing
such lists is only the first step in a risk assessment. These risks need to be quantita-
tively assessed for specific organisms in different contexts on a case-by-case basis.
Various groups of ecologists have developed a methodology for evaluating the use of
GM crops (Tiedje et al., 1989, Scientists’ Working Group on Biosafety, 1998). They
recommend an incremental, tiered approach to risk assessment that moves from the
laboratory to greenhouse and field trials, and finally, to gradually increased, moni-
tored use.
While field trials are a necessary step in evaluating GM crops on their own,
they are insufficient. A more comprehensive analysis is required that includes an
assessment of the relative benefits and risks of GM crops for other ecosystems and
for people. To illustrate this approach, we provide a partial list of the questions
for assessment in Table 13.2. Comprehensive risk assessments could allow people
to reap substantial benefits from GM crops while avoiding or mitigating serious
risks (Arber, 2009).
Table 13.2 Questions to assess the relative benefits and risks of a GM crop
Impacts Benefit-related questions Risk-related questions
Agricultural and Are alternatives available that Are risks minimized through good
industrial provide greater agronomic, design; e.g., Is it certain that genes
economic, social, and ecological inserted into chloroplast
benefits? DNA cannot escape through
Does the GM crop prevent some pollen?
specific harm to humans or to Has the organism been examined in
ecosystems; e.g., Does it reduce order to determine whether genetic
pesticide use? modifications to produce a desired
trait have not also inadvertently
produced risky changes?
Ecological Does the GM crop help to solve an Does the modified trait have the
existing environmental problem; potential to increase the fitness
e.g., Does it produce sterile feral ofthe organism outside of the
animals to control pests (Walker managed environment; e.g.,
and Lonsdale 2000)? Does it impart herbivore
resistance or increase the
reproductive rate?
In the locale of release, can the trait
spread to other species; i.e., Can the
species hybridize with other species
nearby?
Social Will the benefits of this GM Is a mechanism in place for
organism be widely shared? surveying possible negative
Does the GM crop provide some effects after widespread release
specific benefit to humans or of the GM crop has occurred?
ecosystems; e.g., Does it Do institutions exist that could
enhance human nutrition or help mitigate the potential harmful
to restore degraded land? impacts of GM crops?
13.3 Purported Advantages of GM Food Plants

The world population has now reached six billion people and is predicted to double
in the next 50 years. Ensuring an adequate food supply for this booming population
is going to be a major challenge in the years to come. GM foods have the potential
to meet this need in a number of ways.
Insect Pest Resistance: Crop losses from insect pests can be immense, result-
ing in substantial financial loss for farmers and starvation of people in develop-
ing countries. Farmers typically use many millions of kilos of chemical pesticides
annually. Consumers do not wish to eat food that has been treated with pesticides
because of potential health hazards and because runoff of agricultural wastes from
excessive use of pesticides and fertilizers can poison the water supply and cause
harm to the environment. Growing GM foods such as Bt corn can help to eliminate
the application of chemical pesticides and to reduce the cost of bringing a crop to
market.
Herbicide Tolerance: For some crops, it is not cost-effective to remove weeds
by physical means such as by tillage. So farmers will often spray large quantities
of different herbicides to destroy weeds. This is a time-consuming and expensive
process that requires care so that the herbicide does not harm the crop plant or the
environment. Crop plants genetically engineered to be resistant to one very power-
ful herbicide could help prevent environmental damage by reducing the amount of
herbicide needed. For example, Monsanto has created a strain of soybeans geneti-
cally modified to be not affected by their herbicide product Roundup . A farmer
grows these soybeans which then only require one application of herbicide instead
of multiple applications, thus reducing production costs and limiting the dangers of
agricultural waste runoff.
Disease Resistance: There are many viruses, fungi, and bacteria that cause plant
diseases. Plant biologists are working to create plants with genetically engineered
resistance to these diseases.
Frost Resistance: Unexpected frost can destroy sensitive crop seedlings. An anti-
freeze gene from cold water fish has been introduced into plants such as tobacco and
potato. With this anti-freeze gene, these plants are able to tolerate cold temperatures
that normally would kill genetically unmodified seedlings.
Drought Tolerance/Salinity Tolerance: As the world population grows and more
land is utilized for housing instead of food production, farmers will need to grow
crops in locations previously poorly suited for plant cultivation. Consequently, cre-
ating plants that can withstand long periods of drought or high salt content in the
soil and groundwater will help people to grow crops in formerly inhospitable places.
Human Nutrition: Malnutrition is common in African countries which face
hunger and poverty where impoverished people rely on a single crop such as rice for
the main staple of their diet. However, rice does not contain adequate amounts of all
necessary nutrients to prevent malnutrition. If rice could be genetically engineered
to contain additional vitamins and minerals, nutrient deficiencies could be allevi-
ated. For example, blindness due to vitamin A deficiency is a common problem in
third-world countries. Researchers at the Institute for Plant Sciences, Swiss Federal
Institute of Technology, have created a genetically modified strain of “golden” rice

containing an unusually high content of beta-carotene (vitamin A).
Phytoremediation: Not all GM plants are grown as crops. Soil and groundwater
pollution continues to be a problem in all parts of the world. Plants such as poplar
trees have been genetically engineered in order to clean up heavy metal pollution
from contaminated soil (see also Chapter 7).
13.4 Genetically Modified (GM) Plants and Foods Derived from

GM Plants: Questions and Answers
The questions and answers cited below have been prepared by the World Health
Organization (WHO) in response to questions and concerns by a number of (WHO)
Member State Governments with regard to the nature and safety of genetically mod-
ified food. They have been modified substantially for presentation here.
Q1. What are genetically modified (GM) organisms and GM foods?

Genetically modified organisms (GMOs) can be defined as organisms in which
the genetic material (DNA) has been altered in a way that does not occur natu-
rally. The technology is often called “modern biotechnology” or “gene technology”,
sometimes also “recombinant DNA technology” or “genetic engineering”. It allows
selected individual genes to be transferred from one organism into another, and also,
between non-related species.
Such methods are used to create GM plants – which are then used to grow GM
food crops.
Q2. Why are GM foods produced?

GM foods are developed – and marketed – because there is some perceived advan-
tage either to the producer or consumer of these foods. This is meant to translate
into a product with a lower price, greater benefit (in terms of durability or nutri-
tional value), or both. Initially GM seed developers wanted their products to be
accepted by producers so have concentrated on innovations that farmers (and the
food industry more generally) would appreciate.
The initial objective for developing plants based on GM organisms was to
improve crop protection. The GM crops currently on the market are mainly aimed at
an increased level of crop protection through the introduction of resistance against
plant diseases caused by insects or viruses or through increased tolerance toward
herbicides.
Insect resistance is achieved by incorporating into the food plant the gene for
toxin production from the milky spore bacterium, Bacillus thuringiensis (Bt). This
toxin is currently used as a conventional insecticide in agriculture and is safe for
human consumption. GM crops that permanently produce this toxin have been
shown to require lower quantities of insecticides in specific situations, e.g., where
pest pressure is high.
Herbicide tolerance is achieved through the introduction of a gene from a bac-

terium conveying resistance to some herbicides. In situations where weed pressure
is high, the use of such crops has resulted in a reduction in the quantity of the her-
bicides used.
In some cases, biotechnology can be used to make virus-resistant crops. The
most common way of doing this is by giving a plant a viral gene encoding the virus
coat protein. The plant can then produce this viral protein before the virus infects
the plant. If the virus arrives, it is not able to reproduce. The explanation for this is
called co-suppression. The plant has ways of knowing when the viral coat protein
should not be produced, and it has ways of eventually shutting down the protein’s
expression. When the virus tries to infect the plant, the production of its essential
coat protein is already blocked. All genetically modified virus-resistant plants on
the market (e.g., papayas and squash) have coat protein-mediated resistance. It may
also be possible to confer resistance by taking a resistance gene naturally found in
one plant and then transferring it to an important crop.
Q3. Are GM foods assessed differently from traditional foods?

Generally consumers consider that traditional foods (that have often been eaten for
thousands of years) are safe. When new foods are developed by natural methods,
some of the existing characteristics of foods can be altered, either in a positive or a
negative way. National food authorities may be called upon to examine traditional
foods, but this is not always the case. Indeed, new plants developed through tradi-
tional breeding techniques may not be evaluated rigorously using risk assessment
techniques.
With GM foods most national authorities consider that specific assessments are
necessary. Specific systems have been set up for the rigorous evaluation of GM
organisms and GM foods relative to both human health and the environment. Sim-
ilar evaluations are generally not performed for traditional foods. Hence, there is
a significant difference in the evaluation process prior to marketing for these two
groups of foods.
One of the objectives of the WHO Food Safety Programme is to assist national
authorities in the identification of foods that should be subject to risk assessment,
including GM foods, and to recommend the correct assessments.
Q4. How are the potential risks to human health determined?

The safety assessment of GM foods generally investigates (a) direct health effects
(toxicity); (b) tendencies to provoke allergic reaction (allergenicity); (c) specific
components thought to have nutritional or toxic properties; (d) the stability of the
inserted gene; (e) nutritional effects associated with genetic modification; and (f)
any unintended effects which could result from the gene insertion.
Q5. What are the main issues of concern for human health?
While theoretical discussions have covered a broad range of aspects, the three main
issues debated are tendencies to provoke allergic reaction (allergenicity), gene trans-
fer, and outcrossing.
Allergenicity. As a matter of principle, the transfer of genes from commonly

allergenic foods is discouraged unless it can be demonstrated that the protein prod-
uct of the transferred gene is not allergenic. While traditionally developed foods are
not generally tested for allergenicity, protocols for tests for GM foods have been
evaluated by the Food and Agriculture Organization of the United Nations (FAO)
and WHO. No allergic effects have been found relative to GM foods currently on
the market.
Gene transfer. Gene transfer from GM foods to cells of the body or to bacteria
in the gastrointestinal tract would cause concern if the transferred genetic mate-
rial adversely affects human health. This would be particularly relevant if antibiotic
resistance genes, used in creating GMOs, were to be transferred. Although the prob-
ability of transfer is low, the use of technology without antibiotic resistance genes
has been encouraged by a recent FAO/WHO expert panel.
Outcrossing. The movement of genes from GM plants into conventional crops
or related species in the wild (referred to as “outcrossing”), as well as the mixing
of crops derived from conventional seeds with those grown using GM crops, may
have an indirect effect on food safety and food security. This risk is real, as was
shown when traces of a maize type which was only approved for feed use appeared
in maize products for human consumption in the United States. Several countries
have adopted strategies to reduce mixing, including a clear separation of the fields
within which GM crops and conventional crops are grown.
Feasibility and methods for post-marketing monitoring of GM food products, for
the continued surveillance of the safety of GM food products, are under discussion.
Q6. How is a risk assessment for the environment performed?

Environmental risk assessments cover both the GMO concerned and the potential
receiving environment. The assessment process includes evaluation of the charac-
teristics of the GMO and its effect and stability in the environment, combined with
ecological characteristics of the environment in which the introduction will take
place. The assessment also includes unintended effects which could result from the
insertion of the new gene.
Q7. What are the issues of concern for the environment?

Issues of concern include the capability of the GMO to escape and potentially intro-
duce the engineered genes into wild populations; the persistence of the gene after
the GMO has been harvested; the susceptibility of non-target organisms (e.g., insects
which are not pests) to the gene product; the stability of the gene; the reduction in the
spectrum of other plants including loss of biodiversity; and increased use of chemi-
cals in agriculture. The environmental safety aspects of GM crops vary considerably
according to local conditions.
Current investigations focus on the potentially detrimental effect on beneficial
insects or a faster induction of resistant insects; the potential generation of new
plant pathogens; the potential detrimental consequences for plant biodiversity and
wildlife; a decreased use of the important practice of crop rotation in certain local
situations; and the movement of herbicide resistance genes to other plants.
Q8. Are GM foods safe?

Different GM organisms include different genes inserted in different ways. This
means that individual GM foods and their safety should be assessed on a case-by-
case basis and that it is not possible to make general statements on the safety of all
GM foods.
GM foods currently available on the international market have passed risk assess-
ments and are not likely to present risks for human health. In addition, no effects on
human health have been shown as a result of the consumption of such foods by the
general population in the countries where they have been approved. Continuous use
of risk assessments based on the Codex principles and, where appropriate, includ-
ing post market monitoring, should form the basis for evaluating the safety of GM
foods.
Q9. How are GM foods regulated nationally?

The way governments have regulated GM foods varies. In some countries GM foods
are not yet regulated. Countries which have legislation in place focus primarily on
assessment of risks for consumer health. Countries which have provisions for GM
foods usually also regulate GMOs in general, taking into account health and envi-
ronmental risks, as well as control- and trade-related issues (such as potential testing
and labeling regimes). In view of the dynamics of the debate on GM foods, legisla-
tion is likely to continue to evolve.
Q10. What kind of GM foods are on the market internationally?

All GM crops available on the international market today have been designed using
one of three basic traits: resistance to insect damage; resistance to viral infections;
and tolerance toward certain herbicides. All the genes used to modify crops are
derived from microorganisms.
Q11. What happens when GM foods are traded internationally?

No specific international regulatory systems are currently in place. However, several
international organizations are involved in developing protocols for GMOs.
The Codex Alimentarius Commission (Codex) is the joint FAO/WHO body
responsible for compiling the standards, codes of practice, guidelines, and recom-
mendations that constitute the Codex Alimentarius: the international food code.
Codex is developing principles for the human health risk analysis of GM foods. The
premise of these principles dictates a premarket assessment, performed on a case-
by-case basis and including an evaluation of both direct effects (from the inserted
gene) and unintended effects (that may arise as a consequence of insertion of the
new gene). Codex principles do not have a binding effect on national legislation,
but are referred to specifically in the Sanitary and Phytosanitary Agreement of the
World Trade Organization (SPS Agreement), and can be used as a reference in case
of trade disputes.
The Cartagena Protocol on Biosafety (CPB), an environmental treaty legally
binding for its parties, regulates transboundary movements of living modified organ-
isms (LMOs). GM foods are within the scope of the protocol only if they contain
LMOs that are capable of transferring or replicating genetic material. The corner-
stone of the CPB is a requirement that exporters seek consent from importers before
the first shipment of LMOs intended for release into the environment.
Q12. Have GM products on the international market passed a risk

assessment?
The GM products that are currently on the international market have all passed
risk assessments conducted by national authorities. These different assessments in
general follow the same basic principles, including an assessment of environmental
and human health risk. These assessments are thorough; they have not indicated any
risk to human health.
Q13. Are there implications for the rights of farmers to own their crops?
Yes, intellectual property rights are likely to be an element in the debate on GM
foods, with an impact on the rights of farmers. Intellectual property rights (IPRs),
especially patenting obligations of the TRIPS Agreement (an agreement under the
World Trade Organization concerning trade-related aspects of intellectual property
rights), have been discussed in the light of their consequences on the further avail-
ability of a diversity of crops. In the context of the related subject of the use of gene
technology in medicine, WHO has reviewed the conflict between IPRs and an equal
access to genetic resources and the sharing of benefits. The review has considered
potential problems of monopolization and doubts about new patent regulations in
the field of genetic sequences in human medicine. Such considerations are likely to
also affect the debate on GM foods.
Q14. What further developments can be expected in the area of GMOs?

Future GM organisms are likely to include plants with improved disease or drought
resistance, crops with increased nutrient levels, fish species with enhanced growth
characteristics, and plants or animals producing pharmaceutically important pro-
teins such as vaccines. At the international level, the response to new develop-
ments can be found in the expert consultations organized by FAO and WHO in
2000 and 2001, and the subsequent work of the Codex ad hoc Task Force on
Foods Derived from Biotechnology. This work has resulted in an improved and
harmonized framework for the risk assessment of GM foods in general. Specific
questions, such as the evaluation of allergenicity of GM foods or the safety of
foods derived from GM microorganisms, have been covered and an expert consul-
tation organized by FAO and WHO will focus on foods derived from GM animals
in 2003.
Q15. What is WHO doing to improve the evaluation of GM foods?

WHO will take an active role in relation to GM foods, primarily for two reasons:
(1) on the grounds that public health could benefit enormously from the potential
of biotechnology, for example, from an increase in the nutrient content of foods,
decreased allergenicity, and more efficient food production and (2) based on the
need to examine the potential negative effects on human health of the consump-
tion of food produced through genetic modification, also at the global level. It is
clear that modern technologies must be thoroughly evaluated if they are to consti-
tute a true improvement in the way food is produced. Such evaluations must be
holistic and all-inclusive and cannot stop at the previously separated, non-coherent
systems of evaluation focusing solely on human health or environmental effects in
isolation.
Work is therefore under way in WHO to present a broader view of the evaluation
of GM foods in order to enable the consideration of other important factors. This
more holistic evaluation of GM organisms and GM products will consider not only
safety but also food security, social and ethical aspects, access, and capacity build-
ing. International work in this new direction presupposes the involvement of other
key international organizations in this area.
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Chapter 14
Risks Involved in the Use of Herbal Products
Peter B. Kaufman, Maureen McKenzie, and Ara Kirakosyan
Abstract The use of different herbal products can involve several kinds of risks
that include improper labeling or failure to provide the correct constituents; inad-
equate testing of the herbal product in clinical trials; failure to provide the stated
amounts of active constituents; contraindications between known herbs and syn-
thetic prescription drugs used to treat the same disease; overdosing or underdos-
ing; contamination of herbal preparations with pathogens, pesticides, and heavy
metals; expired shelf life; and problems with formulations that render them inef-
fective (e.g., ineffective dried preps in capsules versus effective formulations
taken as tinctures). In this chapter, we shall address many of these issues. They
are basically issues of quality control that involve the latest advances in plant
biotechnology.
14.1 Compromised Quality in the Preparation

of Herbal Medicines
Herbs to be grown for the preparation of herbal medicines can be compromised in

their quality for the following reasons:
• Herbs obtained from different sources (countries, regions, and growers) are
mixed in order to make commercial preparations.
• Herbs are not grown under uniform field or greenhouse conditions from year to
year.
• Herbs are not collected at the optimum stage of development.
• Herbs collected are adulterated with other herbs, some of which may be toxic or
devoid of the same biological activity.
P.B. Kaufman (B)

University of Michigan, Ann Arbor MI 48109-0646, USA

• Processing of herbs after collection (e.g., drying or freeze-drying) is not uni-

form. Herbs are often sun-dried in the field and, as a result, lose much of their
potency.
• Processed herbs are not packaged or stored properly before commercial sale.
• Herbs are adulterated with other constituents (e.g., preservatives and fillers) when
packaged for commercial sale.
In order to mitigate these problems, growers and processors need to use standard
conditions and guidelines for growing, harvesting, formulating, and packaging of
herbal preparations. Good sources for this kind of information are found in Ody
(1993) and Moore (1995).
14.2 Inadequate Testing of Herbal Medicine Products
Many medicinal herbs have not yet been subjected to testing in human clinical trials.
Instead, they are promulgated for use based on animal (nonhuman) models or based
on oral tradition or practices of shamans.
Even if human clinical trials are conducted, they can suffer from improper design.
For example, this can include the following:
• Failure to use a double-blind, placebo-controlled, randomized clinical trial pro-
tocol.
• Failure to include greater than a single biologically active dose. The best judg-
ment here is to include half optimum, optimum, and twice optimum levels/doses
of the herb.
• Failure to include a sufficient number of time points to do good kinetics or to
obtain meaningful data.
• Failure to carry out the study for a sufficient length of time. This is especially crit-
ical for many herbal preparations, which often tend to be slow acting or require
administration of prescribed doses over an extended period of time (not hours or
days, but weeks).
14.3 Risks in the Use of Medicinal Herbs
The use of medicinal herbs to treat specific human disease can involve risks,
especially when used in combination with different kinds of synthetically pro-
duced prescription drugs. Patients taking herbal medicines as well as prescrip-
tion drugs to treat a specific ailment must consult their doctor before using such
combinations.
Examples (cited in The Merck Manual of Medical Information, second home edi-
tion, 2004, by Mark H. Beers) of such adverse interactions are given in Table 14.1.
14 Risks Involved in the Use of Herbal Products 349
Table 14.1 Some possible medicinal herb–drug interactions
Medicinal herb Affected drugs Interaction
Chamomile Anticoagulants (such as warfarin) Chamomile taken with

anticoagulants may increase the
risk of bleeding
Barbiturates (such as Chamomile may intensify or
phenobarbital) and other prolong the effects of sedatives
sedatives
Iron Chamomile may reduce iron
absorption
Echinacea Drugs that can damage the liver Echinacea taken for more than 8
(such as anabolic steroids, weeks may damage the liver.
amiodarone, methotrexate, and When echinacea is taken with
ketoconazole) another drug that can damage
the liver, the risk of liver
damage may be increased
Immunosuppressants (such as By stimulating the immune system,
corticosteroids and echinacea may negate the effects
cyclosporine) of immunosuppressants
Feverfew Anticoagulants (such as warfarin) Feverfew taken with
anticoagulants may increase the
risk of bleeding
Iron Feverfew may reduce iron
absorption
Drugs used to manage migraine Feverfew may increase heart rate
headaches (such as ergotamine) and blood pressure when it is
taken with drugs used to manage
migraine headaches
Nonsteroidal anti-inflammatory NSAIDs reduce the effectiveness
drugs (NSAIDs) of feverfew in preventing and
managing migraine headaches
Garlic Anticoagulants (such as warfarin) Garlic taken with anticoagulants
may increase the risk of
bleeding
Drugs that decrease blood sugar Garlic may intensify the effects of
levels (hypoglycemic drugs such these drugs, causing an
as insulin and glipizide) excessive decrease in blood
sugar levels (hypoglycemia)
Saquinavir (used to treat HIV Garlic decreases blood levels of
infection) saquinavir, making it less
effective
Ginger Anticoagulants (such as warfarin) Ginger taken with anticoagulants
bleeding
Ginkgo Anticoagulants (such as warfarin), Ginkgo taken with anticoagulants
aspirin, and other NSAIDs or with aspirin or other NSAIDs
bleeding
Anticonvulsants (such as Ginkgo may reduce the
phenytoin) effectiveness of anticonvulsants
in preventing seizures
Monoamine oxidase Ginkgo may intensify the effects of

inhibitors (MAOIs, a type these drugs and increase the risk of
of antidepressant) side effects, such as headache,
tremors, and manic episodes
Ginseng Anticoagulants (such as Ginseng taken with anticoagulants or
warfarin), aspirin, and with aspirin or other NSAIDs may
other NSAIDs increase the risk of bleeding
Drugs that decrease blood Ginseng may intensify the effects of
sugar levels these drugs, causing an excessive
(hypoglycemic drugs) decrease in blood sugar levels
(hypoglycemia)
Corticosteroids Ginseng may intensify the side effects
of corticosteroids
Digoxin Ginseng may increase digoxin levels
Estrogen replacement Ginseng may intensify the side effects
therapy of estrogen
MAOIs Ginseng can cause headache, tremors,
and manic episodes when it is
taken with MAOIs
Opioids (narcotics) Ginseng may reduce the effectiveness
of opioids
Goldenseal Anticoagulants (such as Goldenseal may oppose the effects of
warfarin) anticoagulants and may increase
the risk of blood clots
Licorice Antihypertensives Licorice may increase salt and water
retention and increase blood
pressure, making antihypertensives
less effective
Antiarrhythmics Licorice may increase the risk of an
abnormal heart rhythm, making
antiarrhythmic therapy less
effective
Digoxin Because licorice increases urine
formation, it can result in low levels
of potassium, which is excreted in
urine. When licorice is taken with
digoxin, the low potassium levels
increase the risk of digoxin toxicity
Diuretics Licorice may intensify the effects of
most diuretics, causing increased,
rapid loss of potassium. Licorice
may interfere with the effectiveness
of potassium-sparing diuretics,
such as spironolactone, making
these diuretics less effective
MAOIs Licorice may intensify the effects of
these drugs and increase the risk of
side effects, such as headache,
tremors, and manic episodes
Milk thistle Drugs that decrease blood sugar Milk thistle may intensify the
levels (hypoglycemic drugs) effects of these drugs, causing
an excessive decrease in blood
sugar levels
Saquinavir Milk thistle decreases blood levels
of saquinavir, making it less
effective
Saw palmetto Estrogen replacement therapy and Saw palmetto may intensify the
oral contraceptives effects of these drugs
St. John’s wort Benzodiazepines St. John’s wort may reduce the
effectiveness of these drugs in
reducing anxiety and may
increase drowsiness and the risk
of side effects such as
drowsiness
Cyclosporine St. John’s wort may reduce blood
levels of cyclosporine, making it
less effective, with potentially
dangerous results (such as
rejection of an organ transplant)
Digoxin St. John’s wort may reduce blood
levels of digoxin, making it less
effective, with potentially
dangerous results
Indinavir (a drug used to treat St. John’s wort may reduce blood
AIDS) levels of indinavir, making it
less effective
Iron St. John’s wort may reduce iron
absorption
MAOIs St. John’s wort may intensify the
effects of MAOIs, possibly
causing very high blood
pressure that requires
emergency treatment
Photosensitizing drugs (such as When taken with these drugs,
lansoprazole, omeprazole, St. John’s wort may increase the
piroxicam, and sulfonamide risk of sun sensitivity
antibiotics)
Selective serotonin reuptake St. John’s wort may intensify the
inhibitors (such as fluoxetine, effects of these drugs
paroxetine, and sertraline)
Warfarin St. John’s wort may reduce blood
levels of warfarin, making it less
effective and clot formation
more likely
Valerian Anesthetics Valerian may prolong sedation
time
Barbiturates Valerian may intensify the effects
of barbiturates, causing
excessive sedation
14.3.1 Medical Risks in the Use of Kava Kava (Piper

methysticum): A Case Study
Kava kava is a herbal ingredient derived from the plant Piper methysticum G. Forst.,
which is a member of the pepper family (Piperaceae). It is native to many Pacific
Ocean islands. The leaves and the root of the plant are used in herbal food and
medicinal products. In recent years it has become popular in Europe in herbal reme-
dies used to treat anxiety, tension, and restlessness.
It is considered a sacred plant by many of the traditional Polynesian cultures and
has been used in prayer and ritual as well as for a wide variety of ailments ranging
from asthma and rheumatism to weary muscles and sleeplessness. The main active
components in kava kava (kavalactones) are found in the root of the plant. Kavalac-
tones are thought to affect levels of neurotransmitters in the blood, which can affect
the body’s fight-or-flight response. While kava root was traditionally chewed or
made into a beverage, it is now primarily taken as a natural anxiety remedy in cap-
sule, tablet, beverage, tea, and liquid extract forms.
Evidence has mounted that in rare cases the use of products containing kava
kava (mostly in the form of herbal medicines) has been associated with severe liver
damage. Research indicates that this may be largely due to the use of stems and
leaves in dietary supplements, which were not used indigenously. The occurrence of
liver damage is unpredictable and the mechanism is unclear. Some of the compounds
found in Kava extracts block several subtypes of the enzyme cytochrome P450,
which may result in adverse interactions with concomitant use of other drugs and
alcohol (Mathews et al., 2002). Because of these reports, regulatory agencies in
Europe and Canada now warn consumers of the potential risks associated with kava
kava and even remove kava-containing products from the market. Based on these
and other reports in the United States, the Food and Drug Administration (FDA)
issued a consumer advisory in March of 2002 regarding the “rare” but potential risk
of liver failure associated with kava-containing products.
14.3.2 Medical Risks in the Use of Ephedra (Ephedra sinica):

A Case Study (Modified from Data Provided
by www.rand.org/health)
The herb ephedra, also known as ma huang (Ephedra sinica Stapf.), is a small
shrub native to Asia, where it has a long history of medicinal use, as documented
in ancient medical treatises from India and China. In traditional Chinese and Indian
medicine, branches of the herb are used to treat colds, and it is also used as a diuretic.
Modern European practitioners of herbal medicine use ephedra only to treat symp-
toms of respiratory diseases, such as bronchial asthma.
In the United States, the active components of ephedra are known as ephedrine
alkaloids. They include ephedrine, pseudoephedrine, and norephedrine (also
known as phenylpropanolamine and norpseudoephedrine). These constituents are
commonly found in over-the-counter cold and allergy medications. The ephedrine

alkaloids are stimulants similar to, but much weaker than, amphetamines. These
ephedra stimulants can increase heart rate and blood pressure and relax bronchial tis-
sue, easing shortness of breath. At low doses, they are reputed to decrease appetite,
increase alertness and productivity, improve mood, and decrease fatigue; at higher
doses, they may promote anxiety, restlessness, and insomnia.
The use of ephedra to promote weight loss and to enhance athletic performance
began to gain popularity in the United States in the early 1990s. The increase in pop-
ularity of herbal products, and over-the-counter medications that seem to promote
weight loss, is probably due to a combination of factors. These include the recent
precipitous rise in obesity rates, the reluctance of many obese people to talk with
their doctors about weight control, and the growing belief on the part of many peo-
ple that natural substances such as herbs are safer to use than synthetic prescription
medicines.
Products that contain the herb ephedra have been promoted and used in the
United States since the 1980s in order to increase weight loss and to enhance ath-
letic performance. Yet, despite manufacturers’ claims, little research has been done
to assess whether or not ephedra products are safe. Furthermore, the research stud-
ies that have been done have been too small to allow any firm conclusions to be
drawn.
The questionable effectiveness of these products might not have raised public
concern, had the US Food and Drug Administration (FDA) and major manufac-
turers of ephedra-containing products not become the targets of growing numbers
of consumer complaints in the late 1990s. Reports of adverse events, including seri-
ous adverse side effects and even deaths, many in apparently healthy young people,
began increasing during this time. Prominent among the victims have been several
college and professional athletes. Thus, in recent years, several major consumer
health groups have called on the FDA to ban sales of ephedra-containing products.
The FDA classifies products containing herbal ephedra as dietary supplements,
which are regulated by the Dietary Supplement Health and Education Act of 1994
(DSHEA). Under the DSHEA, dietary supplements are generally “presumed safe.”
Thus, manufacturers are required only to notify the FDA of their intent to market
new products. However, they are not required to establish the safety or the effec-
tiveness of their products. Once a dietary supplement is on the market, the FDA can
restrict its use or ban sales of the product only if it can demonstrate convincingly
that the product is unsafe.
The studies that have been conducted (see Shekelle et al., 2003a and 2003b) sug-
gest that ephedra- and ephedrine-containing products may be modestly effective in
promoting weight loss, but the evidence on enhancing athletic performance is not
definitive. However, the use of ephedra or ephedrine does cause an increase in jitter-
iness, mood changes, palpitations, nausea, and vomiting. Moreover, the adverse-
event reports raise serious concerns about the safety of ephedra and ephedrine
products.
In response to the reporting of these studies, the federal government quickly
moved to propose stricter labeling of ephedra products and solicited public comment
on whether the safety evidence thus far warrants further restrictions. By itself, the
existing evidence is insufficient to link these products conclusively with death and
other serious health problems. However, an analysis of the existing studies and their
shortcomings suggests that a more definitive answer to questions about ephedra’s
safety could be obtained by doing what is called a “case–control” study.
Such a study would compare ephedra use by individuals who suffered death or
another illness with use by similar individuals who have not suffered severe health
problems. A study of this type could also be used to compare the safety of ephedra-
containing supplements and products containing ephedrine. Finally, a case-control
study could help answer safety questions quickly, thus avoiding the expense and
time that would be needed to conduct a large-scale randomized controlled trial and
potentially saving lives.
14.3.3 Risks Associated with the Use of Vaccinium: A Case Study
The genus Vaccinium is composed of approximately 450 species, many of which

have been important food and medicinal plants for cultures worldwide through-
out the millennia. All are considered nontoxic, although palatability and compo-
sition across such a wide range of species are, understandably, diverse. Interest
in Vaccinium-based dietary supplements has increased dramatically over the past
decade as consumers have become aware through the media of the numerous health
benefits of V. corymbosum (highbush blueberry) and V. angustifolium (lowbush
or “wild” blueberry). In fact, these fruits have been categorized, among a select
group of other fruits and vegetables, as “superfoods” in consumer-oriented mar-
keting campaigns. Although this claim is arguably legitimate, based on their replete
flavonoid content and generally recognized safety profile, some considerations must
apply.
Consumers face a dizzying array of products based on Vaccinium in the form
of capsules, powders, liquid formulas, sports drinks, energy bars and as an ingre-
dient in dairy, grain, and other food matrices. Although consumers are familiar,
conceptually, with antioxidants and free radicals, they are often misled by claims of
superior antioxidant activity of different products, which are usually based only on
testing of a limited spectrum of antioxidant activities. One group sought to compare
directly and make example of various commercial fruit juices through (1) evaluation
of the total polyphenol content [by gallic acid equivalents (GAEs)]; (2) four tests
of antioxidant potency including Trolox equivalent antioxidant capacity (TEAC),
total oxygen radical absorbance capacity (ORAC), free radical scavenging capacity
by 2,2-diphenyl-1-picrylhydrazyl (DPPH), and ferric reducing antioxidant power
(FRAP); and (3) a test of antioxidant functionality, that is, inhibition of low-
density lipoprotein (LDL) oxidation by peroxides and malondialdehyde meth-
ods of polyphenol-rich beverages in the marketplace (Seeram et al., 2008). In
this study, total polyphenol content, composite antioxidant potency, and ability to
inhibit LDL oxidation were consistent in classifying the antioxidant capacity of the
polyphenol-rich beverages in descending order: Punica granatum L. (pomegranate)
juice > red wine > Vitis x labruscana (Concord grape) juice > V. corymbosum
(blueberry) juice > Prunus serotina Ehrh. (black cherry) juice, Euterpe oleracea
Mart. (a,caí) juice, V. macrocarpon (cranberry) juice > Citrus sinensis (L.)
Osbeck (orange) juice, iced tea beverages, Malus domestica Borkh. (apple)
juice.
While these results are interesting and arguably legitimate, different sample
brands could alter readily the order of observed antioxidant potency. In many prod-
ucts, the amount of Vaccinium included is often very low, although its contribution
to the final product may be inflated through labeling in order to use it as the market-
ing “handle.” Furthermore, the quality of Vaccinium preparations used in a finished
product, whether in dried or extract forms, may be inconsistent. The fresh fruit
source is of utmost importance, as notable differences have been documented not
only between species but also between cultivars, growth conditions, harvest time,
storage, and ultimate processing – even for the same species. Drying technologies
differ in terms of temperature and time required for the process, and the amount
of flavonoids retained, especially the anthocyanins, significantly decreases under
harsher conditions. Similarly, the yield of bioactive flavonoids is dependent upon
the method employed to produce an extract. In recent years, advanced analytical
methods have become available to assess the authenticity and quality of Vaccinium
compositions for research purposes and standardization of commercial products for
dietary supplements and clinical applications (Zhang et al., 2004; Määttä-Riihinen
et al., 2004; Tian et al., 2005; Burdulis et al., 2007; Cassinese et al., 2007; Harris
et al., 2007; Lin and Harnly, 2007; Grant and Helleur, 2008). Whereas the quality
control of herbal medicinal products used by health-care practitioners is regulated
in detail (e.g., German Commission E), no uniform requirements for food-derived
supplements currently exist. A standardized preparation, typically an extract,
is one with a consistent and guaranteed percentage of a definable bioactive com-
pound or group of compounds. For Vaccinium dietary supplements, standardization
is a voluntary effort by manufacturers to offer a high-quality product. The princi-
pal components of interest from Vaccinium, anthocyanins and proanthocyanidins,
are notoriously difficult among all flavonoids to analyze quantitatively with accu-
racy (Krenn et al., 2007). Yet other biotechnological methods have been devel-
oped to improve yield and composition and mitigate against detrimental effects
of storage and processing on the stability of flavonoids from Vaccinium in foods,
nutraceuticals, and phytopharmaceutical dosage forms (Kalt et al., 1999; Connor
et al., 2002; Gunes et al., 2002; Wang and Stretch, 2002; Lyons et al., 2003; Zheng
et al., 2003; Lohachoompol et al., 2004; Vattem et al., 2005; Song and Sink, 2006;
Srivastava et al., 2007; Puupponen-Pimiä et al., 2008; Brambilla et al., 2008; Wang
et al., 2008).
Since flavonoids are known to be potent antioxidants, and compartments such as
plasma, tissues, and urine have been shown to increase in antioxidant capacity fol-
lowing consumption of flavonoid-rich substances, a reasonable assumption is that
they are readily bioavailable (Cao and Prior, 1998; Prior and Cao, 1999; Prior and
Cao, 2000; Vinson et al., 2008). In fact, flavonoids are relatively abundant micronu-
trients in the diet, but bioavailability differs greatly from one type to another. Thus,
the most abundant dietary flavonoids are not necessarily those leading to the highest
concentrations of active metabolites in target compartments.
Employing data from 97 studies, based on a single ingestion of pure compound,
extract, or whole food/beverage, one group of investigators calculated mean values
for the maximal plasma concentration, the time to reach the maximal plasma con-
centration, the area under the plasma concentration–time curve, the elimination of
half-life, and the relative urinary excretion for 18 major flavonoids (Manach et al.,
2005). They found gallic acid and isoflavones to be the best absorbed flavonoids, fol-
lowed by catechins, flavanones, and quercetin glucosides, but with different kinet-
ics. The least well-absorbed polyphenols are proanthocyanidins, galloylated tea
catechins, and anthocyanins. Data were too limited for the assessment of hydrox-
ycinnamic acids and other polyphenols. As a result of digestive and hepatic activ-
ity, the metabolites present in blood usually differ from the parent compounds.
Depending on the flavonoid, plasma concentrations of total metabolites ranged from
0 to 4 μmol·L−1 from an intake of 50 mg aglycone equivalents, and the relative uri-
nary excretion ranged from 0.3 to 43% of the ingested dose.
Intervention studies have indicated the type and magnitude of effects among
humans in vivo, on the basis of short-term changes in biomarkers. A review
of 93 such studies led workers to conclude that flavonoids have varying physi-
ological effects (Williamson and Manach, 2005). They propose that isoflavones
(i.e., genistein and daidzein) have weak hormonal effects, but significant ones
on processes affecting bone health in postmenopausal women. Monomeric cate-
chins, which occur in exceptional amounts in tea, influence energy metabolism
as well as plasma antioxidant biomarkers. Proanthocyanidins, which are widely
distributed in many foods, red wine, and supplements such as Pycnogenol
(http://www.pycnogenol.com), have pronounced effects on the vasculature that are
not limited to antioxidant activity. Quercetin, the principal flavonol in plant-based
foods, red wine, and Ginkgo supplements, appears to influence certain markers of
carcinogenesis and exerts small effects in vivo on plasma antioxidant biomark-
ers; nonetheless, some studies failed to corroborate those findings. In fact, the
largest randomized, double-blind, placebo-controlled clinical trial ever conducted
on a botanical medicine failed to show that extracts of Ginkgo biloba L. prevented
dementia. Five academic medical centers in the United States between 2000 and
2008 evaluated 3069 community volunteers aged 75 years or older with normal
cognition (n = 2587) or MCI (mild cognitive impairment; n = 482) (Dekosky et al.,
2008). Proponents of Ginkgo may argue that this study does not undermine what has
already been observed with regard to the usefulness of Ginkgo extract in providing
symptomatic relief in persons who already suffer from dementia or Alzheimer’s
disease or prevent progression in younger, middle-age subjects.
Other workers have found an apparent lack of correlation between the effec-
tiveness of anthocyanins, such as those derived from Vaccinium, in laboratory
model systems and in humans, especially as cancer chemopreventive agents, as
evidenced by epidemiological studies, further illustrating the importance of study
design (Wang and Stoner, 2008). A discrepancy exists in the antioxidant and other
bioactivities of flavonoids, which are powerful in assays conducted in vitro; the
measured in vivo activities are far more subtle. The reasons for incongruity are cited
as (1) lack of validated in vivo biomarkers, especially in the area of carcinogenesis;
(2) lack of understanding or consideration of bioavailability and the inherent com-
plexity of flavonoid interactions in the in vitro experiments, which are subsequently
used for the design of in vivo studies; and (3) lack of long-term observations. In the
design of in vitro and in vivo studies, these issues mandate careful consideration.
The length of human intervention studies should be increased, particularly to more
closely reflect the consequences of long-term dietary consumption of flavonoids.
The Physicians Desk Reference (PDR) for Herbal Medicines is an authori-
tative source for efficacy and safety guidelines regarding phytotherapeutics and
plant-based dietary supplements (Gruenwald et al., 2007). Although PDR does
not endorse specific brands, a select few have contributed indirectly to its con-
tent through academic and independent citations therein. PDR employs a consistent
format for reporting data, and the categories mirror those for FDA-approved pre-
scription pharmaceuticals. The basic data include a plant’s common name and Latin
binomial. A description section follows and specifies the medicinal part(s), botanical
characteristics, and features of the flower and fruit, leaves, stems and roots, habitat,
production, and alternative (common) names. Next is a section on actions and phar-
macology that lists known compounds present in the medicinal parts, with a sub-
section on effects. Clinical trials, if available, comprise the third section, followed
by six sections that encompass indications and usage (segregated by approved and
unproven uses), contraindications, precautions and adverse reactions, drug interac-
tions, dosage, and, lastly, supporting literature citations.
Three Vaccinium species presented in the PDR include V. myrtillus (European
bilberry), V. macrocarpon (cranberry), and V. uliginosum (bog bilberry). The PDR
cites their beneficial effects but, notably, these presumably innocuous fruits also
possess clear risks. V. myrtillusis contraindicated during pregnancy and should not
be used while breastfeeding, whereas V. macrocarpon is contraindicated for use in
patients with aspirin allergy, atrophic gastritis, diabetes (when product, such as juice,
is sweetened with sugar), hypochlorhydria, and kidney stones. Use of the latter dur-
ing pregnancy has been reviewed, in light of possible mitigation against elevated
risk of urinary tract infections associated with this condition, and no adverse events
came to light in a survey of 400 women (Dugoua et al., 2008). Alternatively, no
evidence is available for safety during lactation. Although contraindications are not
cited for V. uliginosum, an overdosage warning is given for signs of poisoning after
consumption of large quantities and includes nausea, vomiting, states of intoxica-
tion, feelings of weakness, and visual disorders. Presumably, these untoward effects
may be traced back to natural contamination of the fruit by a fungus.
Precautions and adverse reactions for V. myrtillus include side effects relating to
the skin, gastrointestinal tract, and nervous system. Digestive complaints, includ-
ing nausea, are due to the substantive tannin content of the fruit. High doses and
prolonged use may lead to chronic intoxication; chronic administration to animals
(1.5 g·kg−1 per day minimum) has been reported to be fatal. V. macrocarponis gen-
erally well tolerated, but high doses may also cause gastrointestinal upset and diar-
rhea. Since scientific evidence is not available for use during pregnancy, precaution
rather than contraindication is considered prudent. Side effects of V. uliginosum have

not been observed in conjunction with proper administration of designated therapeu-
tic dosages.
Drug interactions are some of the most serious considerations associated with
Vaccinium preparations and supplements. V. myrtillus is considered a “moderate
risk” when used with anticoagulants, antiplatelet and antithrombotic agents, and
low-molecular-weight heparins. Clinical management requires close monitoring for
signs and symptoms of bleeding with adjustment of anticoagulant dose if the patient
regularly takes a consistent and standardized product. V. macrocarpon is consid-
ered a “high risk” for bleeding when used in conjunction with warfarin and clinic
management involves discouraging patients from excessive use of these products.
V. macrocarpon is a moderate risk when used with histamine2 -receptor antago-
nist (H2 blocker) medications that are used to treat heartburn, gastroesophageal
reflux disease, and ulcers. H2 blockers and concomitant use may reduce effective-
ness of the drug. Patients taking H2 blockers should avoid regular consumption of
these extracts or juice, although occasional use is probably not harmful. Caution
is also prudent for patients taking H2 blockers because the effect of V. macrocar-
pon extracts on gastric acids is not known. Furthermore, V. macrocarpon supple-
ments may result in reduced effectiveness of gastric proton pump inhibitors with
concurrent use and requires similar clinical management as for H2 blockers. V. ulig-
inosum may be anticipated to have similar interactions with anticoagulants or gas-
trointestinal drugs at very high doses, but no report of such effects is published in the
literature.
Health-conscious consumers and medical practitioners must be careful about
excessive intake of Vaccinium extracts and other dosage forms for additional rea-
sons cited in the scientific literature. Their proposed use as anticarcinogens, and
cardioprotective and neuroprotective agents, has prompted a dramatic increase in
their consumption as dietary supplements (Skibola and Smith, 2000). Despite the
fact that flavonoid preparations, many of which derive from Vaccinium, are mar-
keted as herbal medicines or dietary supplements for a variety of alleged nontoxic
therapeutic effects, most have yet to pass controlled clinical trials for efficacy (Galati
and O’Brien, 2004). Although most of the work done to date indicates a chemo-
preventive activity of these compounds, some studies show cancer-inducing or no
effects. Current knowledge about flavonoid toxicity, albeit limited, relates to poten-
tial dietary flavonoid/phenolic-induced adverse events, including their pro-oxidant
activity, mitochondrial toxicity, and interactions with drug-metabolizing enzymes.
The chemopreventive activity observed in animal experiments may result from their
ability to inhibit phase I and induce phase II carcinogen metabolizing enzymes
that initiate carcinogenesis. They also inhibit the promotion stage of carcinogen-
esis by inhibiting oxygen radical-forming enzymes, those acting as ATP mimics
and inhibitors of protein kinases that contribute to proliferative signal transduction
enzymes, and others that contribute to DNA synthesis. Finally, they may prevent
tumor development by inducing tumor cell apoptosis by inhibiting DNA topoiso-
merase II and p53 downregulation but, at the same time, potentially elicit mitochon-
drial DNA apoptosis. While most flavonoids/phenolics indeed are considered safe,
flavonoid/phenolic therapy or chemopreventive use needs to be assessed carefully,

as there have been reports of toxic flavonoid–drug interactions, contact dermati-
tis, hemolytic anemia, liver failure, and estrogenic-related concerns such as breast
cancer and male reproductive health associated with dietary flavonoid/phenolic
exposures. At higher doses, flavonoids may act as mutagens, pro-oxidants that
generate free radicals, and as inhibitors of key enzymes involved in hormone
metabolism. Phenolic acids, anthocyanins, stilbenes, catechins, and other flavonoids
have documented effects on the cytochrome P-450 system (Rodeiro et al., 2008).
There are several common mechanisms by which these chemicals exert their
effects that could be conducive to additive, synergistic, or antagonistic interactions
(Nichenametla et al., 2006). Since flavonoids readily cross the placenta, the unborn
fetus may be especially at risk. Thus, the adverse effects of flavonoids may out-
weigh their beneficial ones at high doses. These high levels are above those typically
obtained from a balanced vegetarian diet.
There are many different kinds of risks associated with herbal preparations, as
delineated in the chapter “Abstract.” We document many of these risks in case stud-
ies on herbal preparations of ephedra, kava kava, and Vaccinium. It turns out that
the most serious risks are those associated with adverse interactions that can occur
between herbal preparations and pharmaceutical prescription drugs (Table 14.1).
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Chapter 15
Risks Associated with Overcollection
of Medicinal Plants in Natural Habitats
Maureen McKenzie, Ara Kirakosyan, and Peter B. Kaufman
Abstract Human exploitation of fragile plant communities and ecosystems has

been occurring in recent times at an accelerating pace. In general, worldwide loss of
habitat has resulted from human overpopulation, global warming, resource extrac-
tion, creeping agricultural developments (especially on marginal lands), extensive
use of herbicides (as in Vietnam), construction of highways, desertification, fire,
flooding/tsunamis, alien invasive species, and disease/insect attacks. This is hap-
pening in tropical rain forests worldwide due, in particular, to habitat destruction
from mining, removal of forest trees through cutting and the use of fire, livestock
overgrazing, and farming. In temperate regions the predominant causes are clear-
cutting of forests, collecting wood from trees and shrubs for fuel, overgrazing by
livestock, mining, damming river systems, and allowing urban sprawl to replace
forest ecosystems. In Arctic regions, ecosystem destruction is the result of massive
clear-cuts of boreal forests for pulpwood for paper manufacture, lumber, and wood
products.
The Worldwatch Institute in Washington, D.C. has successfully documented these
calamities over the past two decades. Unfortunately, their prognosis is not good for
the future regarding the Earth’s natural resources. Humans, with their burgeoning
populations, continue to be engaged, despite sufficient warning, in overly exploitive
activities that squander natural products that occur in vast ecosystems. As a result,
the population is living way beyond the carrying capacity in many regions of the
planet.
The purpose of this chapter is to point out ways which might reverse this trend.
Critical considerations involve preserving natural and wilderness areas; commit-
ment to sustainable harvesting of plants in these ecosystems; saving rare, threatened,
and endangered species of plants in “gene banks,” seed banks, tissue culture banks,
nurseries, botanical gardens and arboreta, and parks and shrines; and cultivating
plants in an ecologically friendly way. Following these strategies, the supply of nat-
ural products of medicinal value obtained from plants will be available in perpetuity
M. McKenzie (B)
Denali BioTechnologies, L.L.C. 35555 Spur Highway, PMB 321, Soldotna, Alaska 99669, USA

and, at the same time, help to provide a livelihood for many people who depend
upon these products for their income.
15.1 Causes for Loss of Medicinal Plant Diversity

Plants are recognized universally as a vital part of the world’s biological diversity
and an essential resource for the planet. In addition to the relatively small number
of crop plants developed for food, fuel, and fibers, many thousands of wild plants
have enormous economic and cultural importance and potential, providing nutrition
and medicine to populations throughout world.
Many species of plants, including those of medicinal value, are becoming threat-
ened, endangered, rare, nearly extinct, or extinct because of misguided human activ-
ities (see further). The primary causes for loss of medicinal plant diversity are
destruction and overcollection of medicinal plants in their natural habitats. The
exact definitions for these different categories, as defined by the IUCN (Interna-
tional Union for Conservation of Nature), are as follows:
• Extinct: the last remaining member of the species had died or is presumed beyond
reasonable doubt to have died.
• Extinct in the wild: captive individuals survive, but there is no free-living, natural
population.
• Critically endangered: faces an extremely high risk of extinction in the immediate
future.
• Endangered: faces a very high risk of extinction in the near future.
• Vulnerable: faces a high risk of extinction in the medium term.
• Least concern: no immediate threat to the survival of the species.
The Botanic Gardens Conservation International (BGCI), which represents botanic

gardens in 120 countries, stated that “400 medicinal plants are at risk of extinction,
from over-collection and deforestation, threatening the discovery of future cures for
disease.” (BGCI, January 18, 2008). The most notable are Yew trees (Taxus spp.)
(from which the bark is used for the cancer drug, paclitaxel); Hoodia gordonii Sweet
ex Decne. (a source of weight loss supplements from Namibia); half of Magnolia
spp. (used as Chinese medicine for 5,000 years to fight cancer, dementia, and heart
disease); and Autumn crocus (Colchicum autumnale L. prescribed for gout). The
group also found that 5 billion people benefit from traditional plant-based medicine
for health care.
Many medicinal plants have been overcollected almost to the point of extinc-
tion in their natural habitats. In the United States, notable examples include
Pacific yew (Taxus brevifolia Nutt.), ginseng (Panax ginseng C.A. Mey.), gold-
enseal (Hydrastis canadensis L.), black cohosh (Cimicifuga racemosa (L.) Nutt.
or Caulophyllum thalictroides (L.) Michx.), American ginseng (Panax quinque-
folius L.), bloodroot (Sanguinaria canadensis L.), prairie coneflower or echinacea
(Echinacea spp.), helonias root (Chamaelirium luteum (L.) A. Gray), kava kava
15 Risks Associated with Overcollection of Medicinal Plants 365
(Piper methysticum G. Forst.; Hawaii only), lady’s slipper orchid (Cypripedium

spp.), Lomatium (Lomatium dissectum (Nutt.) Mathias & Constance), osha (Ligus-
ticum porteri J.M. Coult. & Rose), partridge berry (Mitchella repens L.), peyote or
mescal button (Lophophora williamsii (Lem. ex Salm-Dyck) J.M. Coult.), slippery
elm (Ulmus rubra Muhl.), sundew (Drosera spp.), trillium (Trillium spp.), true uni-
corn (Aletris farinosa L.), Venus’ flytrap (Dionaea muscipula J. Ellis), and wild yam
(Dioscorea villosa L.) (Source: United Plant Savers, www.unitedplantsavers.org).
15.2 Use of Biotechnology to Rescue Rare or Endangered

Medicinal Plant Species That Are Rare or Threatened
by Extinction in Their Natural Habitats
The primary expertise to bridge the gap between conservation and scientific research
is in plant systematics and floristics – the primary collection, inventory, description,
and assimilation of information about plants. Once this information is obtained,
modern biotechnology techniques have many possible contributions to offer medic-
inal plant conservation efforts. The following sections delineate plant conservation
strategies that are aimed at rescuing medicinal plant species that are rare or threat-
ened by extinction in their natural habitats.
15.2.1 Preservation of Natural Habitats and Ecosystems
National Parks: Natural resource policies aim to provide people the opportunity
to enjoy and benefit from natural environments evolving by natural processes with
minimal influence by human actions. The National Park Service ( NPS) will ensure
that lands are protected within park boundaries. Where parks contain nonfederal
lands, the NPS uses cost-effective protection methods. Preservation of character and
resources of wilderness areas designated within a park, while providing for appro-
priate use, represent the primary management responsibility. The National Parks
and Conservation Association is a national nonprofit membership organization ded-
icated to defending, promoting, and enhancing our national parks, and educating the
public about the NPS. It was established in 1919 to protect parks and monuments
against private interests and commercialism and to block inappropriate development
within parks. Most recently, this organization has done a magnificent job of mobi-
lizing citizen action to prevent clear-cutting of timber and mining within and adja-
cent to the national parks. They have also helped to protect these parks from undue
human intrusion with recreational vehicles, helicopters, campers, and “vehicles” of
all types (including boats, jeeps, motorcycles, mountain bikes, snowmobiles, and
dune buggies). Limiting access to the national parks because of “people pressure”
and consequently over-crowding has become the norm. Together, these efforts help,
but citizen action groups, such as the National Parks and Conservation Associa-
tion, the Sierra Club, the Nature Conservancy, the Wilderness Society, the Natural
Resources Defense Fund, and the many other organizations who operate in the indi-
vidual states, must be ever vigilant and ready for concerted action.
Sustainable Biopreserves for Indigenous Peoples: Based on a recent United
Nations Conference on Environment and Development (UNCED), the United States
has placed forest management and protection as a priority of UNCED. Further, dis-
cussions by the US government agencies and nongovernmental organizations have
concluded that a provision needs to be included on the needs of indigenous peo-
ples who use the forests for their livelihood, social organization, or cultural identity,
and who have an economic stake in sustainable forest use (Plotkin and Famolare,
1992). Actions include promoting means for indigenous peoples and members of
local communities to actively participate in decision-making processes for any pro-
posed forest-related actions where their interests are affected (Plotkin and Famolare,
1992). Other propositions are to identify ways to enhance the value of standing
forests through policy reform, more accurately reflecting the costs and benefits of
alternative forestry activities, in addition to identifying economically valuable forest
species, including timber and nontimber species, and the development of improved
and sustainable extraction methods (Moran, 1992).
Nabhan (1992) has indicated that the following criteria offer the best guidelines
for ensuring that indigenous peoples and other peasant communities benefit from
applied ethnobotanical development, and that projects sustain rather than deplete or
destroy biodiversity.
• The project should attempt to improve the objective and subjective well-being
of local communities rather than seeking cheap production sites and importing
inexpensive labor.
• Cultivation in fields or agroforestry management should be considered if there
are threats that wild harvests will deplete the resource.
• Wildland management and sensitive harvesting practices should be introduced
in cases where the resource might sustain economic levels of extraction in the
habitat.
• The plant(s) chosen should offer multiple products or be adapted to diversified
production systems.
• When possible, programs should build on local familiarity, use, and conservation
traditions for the plant being developed.
• If possible, these programs should be based on locally available genetic
resources, technologies, and social organizations to enable local people to retain
control over the future of the resource.
15.2.2 Organizations Involved in Conservation of Medicinal Plants

and Their Ecosystems
The important topic of ethnobotany and the sustainable use of plant resources
is based principally on the work of the World Wildlife Fund (WWF), the United
Nations Educational, Scientific and Cultural Organization (UNESCO), and the
Royal Botanic Gardens at Kew, United Kingdom. The People and Plants Initia-
tive is creating support for ethnobotanists from developing countries who work with
local people on issues relating to conservation of plant resources and indigenous
ecological knowledge. Rather than promoting the discovery and marketing of new
products, emphasis is placed on subsistence use and small-scale commercialization
of plants which benefit rural communities. In cases of large-scale commercialization
of wild plants, emphasis is on improving harvesting methods and mechanisms which
allow communities an increasing share of profits (The Royal Botanic Gardens, Kew,
1996a).
One example is provided by the Kuna Indians of Panama. They have success-
fully established the world’s first internationally recognized forest park created by
indigenous people. The reserve provides revenues directly to the Kuna from the
sale of research rights, and from ecotourists who come to learn about the rainfor-
est. Coupled with this, it helps protect and preserve their native heritage. Scientists
conducting research in the park are required to hire the Kuna to assist and accom-
pany them during their stay. The Kuna control access to sites and require reports on
all research. These terms allow the Kuna to patrol and protect outlying areas while
learning from the scientists.
Head and Heismann (1990) in Lessons of the Rainforest, tell about the organiza-
tion called Environmental Restoration in Southern Colombia (CRIC). It is composed
of 56 Indian communities that are organized to protect Indian lands, resources, cul-
ture, and rights in an area where the forest has been destroyed by mines and cattle
ranches. CRIC began a forestry program with three tree nurseries which provided
seedlings to those communities that agree to plant a minimum of 1000 trees of native
species. To date, one community has completed nine reforestation programs.
15.2.2.1 The Nature Conservancy

The main objective of the Nature Conservancy is to protect plants, animals, and
ecological communities that represent biodiversity. To do this, they rely on conser-
vation science to guide its work. Conservation science programs encompass biolog-
ical, ecological, and technological knowledge that are used to identify and protect
sensitive biodiversity, and in management methods and practices used to ensure its
survival. The Natural Heritage Program and the Conservation Data Center Network
programs collectively track in their databases the protected status and locations or
rare and endangered species and ecological communities. Over the last four decades,
the Nature Conservancy has protected more than 8.1 million acres (3.28 million ha)
of habitat based on information about the location, range, and status of rare species.
This number is even higher for total acreage protected to date: it is 9.3 million acres
(3.77 million ha) of land in the United States and 40 million acres (16.19 million
ha) throughout Latin America, the Carribean, and the Asia/Pacific regions. Indeed,
it operates the largest system of privately owned nature preserves in the world.
In carrying out its work, the Nature Conservancy addresses ecological function
and influences of people and develop better conservation planning methods and
tools that will allow planning across immense biologically defined regions and the
range of a particular ecological community. Stewardship of land and its resources

are an important component of the work of the Conservancy. In protecting areas
identified as critical for biodiversity protection, boundaries of those areas are care-
fully chosen to encompass important biological components and the ecological pro-
cesses that sustain them. Its presence in local communities enables it to address
ecosystem protection, find solutions to environmental problems, and form partner-
ships. An organization-wide network electronically links all the Nature Conser-
vancy’s offices to support the information systems plan which provides up-to-date
information (The Nature Conservancy, 1996).
15.2.2.2 The World Wildlife Fund

The World Wildlife Fund (WWF) has several important objectives, including (1)
halting global trade in endangered animals and plants; (2) creating and preserving
parks and protected areas around the world; (3) working to create strongholds for
thousands of irreplaceable plant and animal species as well as protecting those and
other areas from threats beyond their boundaries; (4) working with local leaders,
groups, governments, and international funding institutions to coordinate conserva-
tion and improve living standards to help alleviate development pressures that may
put wildlands in danger; and (5) organizing, supporting, and strengthening conser-
vation efforts around the world (World Wildlife Fund, 1995).
The WWF uses Geographic Information Systems (GIS) technology to iden-
tify priority areas with the greatest biological wealth and the greatest degree of
threat, with a focus on conservation priorities. The WWF works closely with the
North American Commission for Environmental Cooperation to help ensure that
its work promotes conservation initiatives, such as the North American ecoregion
mapping and planning project for biodiversity management. It follows the trade
agreement’s effect on commodities production and health of forests, wildlife, and
natural resources in North America. It also supports the Forest Stewardship Council
which has developed criteria for identifying timber companies that produce envi-
ronmentally sound, economically viable products. This Council consists of social,
environmental, and indigenous groups from more than 24 countries, as well as rep-
resentatives from the timber industry whose mission is to promote ecologically sus-
tainable forest management. In Madagascar, the WWF brokered a debt-for-nature
swap which has trained more than 350 local conservation agents and created a net-
work of locally managed tree plantations. It is also helping to develop alternatives
to cattle production and slash-and-burn agriculture in order to protect native forests
(World Wildlife Fund, 1995).
15.2.2.3 The Sierra Club

The Sierra Club was founded by John Muir in 1892 in San Francisco, California, to
help preserve the pristine beauty of the Sierra Nevada mountain range in California.
Today, it is a national organization with chapters throughout the United States.
It continues to expand, stop abuse of wilderness lands, save endangered species,
and protect the global environment. It helps to create and enlarge national parks,
preserve forests, designate wilderness areas, halt dams, and prevent destruction of
priceless habitats. The Sierra Club helped save Alaska’s Arctic National Wildlife
Refuge from imprudent utilization by oil companies, establish National Park and
Wilderness Preservation Systems, and safeguard more than 132 million acres of
public land.
This organization launched the Critical Ecosystems Program, which is designed
to protect and restore 21 regional ecosystems in the United States and Canada. This
program is involved in designing protection for public and private lands that are
the core habitats for native species. It established task forces for each ecoregion,
drawing together activists with expertise in various areas to develop strategies to
save those regions. What are these strategies for the different ecoregions?
• Atlantic Coast and Great Northern Forest – preserve biodiversity by restoring and
sustaining habitat for the full array of native plants and animals, establish sound
forestry policy, and preserve wilderness.
• Central Appalachia, Southern Appalachian Highlands, and American Southeast –
saving from development, as much as possible, the shoreline stretching 2000
miles (3200 km) from Florida to the mouth of the Rio Grand River.
• Interior Highlands, Great Lakes, Great North American Prairie – establish a sys-
tem of national parks, reform Forest Service policies on grazing, oil and gas
development, and coal mining on grasslands.
• Mississippi Basin, Rocky Mountains, and Colorado Plateau – enact legislation
to protect 5 million roadless acres in Utah, eliminate timber sales that threaten
old-growth ponderosa pine stands, do away with subsidized timber sales in all
national forests, and protect the Grand Canyon by restricting development on its
boundaries.
• Southwest Deserts, Great Basin/High Desert, Sierra Nevada, Pacific Northwest,
and Pacific Coast – permanently protect the remaining ancient forests on federal
land.
• Alaska Rainforests (Tongass and Chugach National Forests), the Boreal Forest
extending from Alaska to Newfoundland, Hudson Bay/James Bay Watershed,
the Arctic, and Hawaii – prevent further destruction of endangered and threatened
plant and animal habitats (Elder, 1994).
15.2.3 Growing Rare and Endangered Plants in Botanical

Gardens and Arboreta
According to the New York Botanical Garden, of approximately 250,000 species of

flowering plants, it is estimated that some 60,000 of these may become extinct by the
year 2050, and more than 19,000 species of plants are considered to be threatened
or endangered from around the world. More than 2,000 species of plants native to
the United States are threatened or endangered, with as many as 700 species becom-
ing extinct in the next 10 years (The New York Botanical Garden, 1995). The New
York Botanical Garden currently grows 10 species of plants in the Federal Endan-
gered Species List. They are striving to preserve rare and endangered plants and
participate with other institutions in doing this. The Garden is a Participating Insti-
tution in the Center for Plant Conservation (CPC), serving as a rescue center for six
native plant species that are imminently threatened, which form part of the National
Collection of Endangered Plants, and are grown and studied to be conserved (The
New York Botanical Garden, 1995). The CPC is located at the Missouri Botanical
Garden in St. Louis, MO. This center is dedicated to conserving rare plants native
to the United States in an integrated plant conservation context through a collabo-
rative program of ex situ plant conservation, research, and education. It is made up
of a consortium of 25 botanical gardens and arboreta (Center for Plant Conserva-
tion, 1996). A national survey by the CPC in 1988 found that over three-quarters of
the endangered flora of the United States is in six areas: Hawaii, California, Texas,
Florida, Puerto Rico, and the Virgin Islands. It has designated these areas as con-
servation priority regions. The CPC Priority Regions Program addresses the need
for conservation through programs of land conservation, management, offsite col-
lection in seed banks, botanical gardens and other institutions, research, and site
surveys (Center for Plant Conservation, 1996). The National Collection of Endan-
gered Plants contains seeds, cuttings, and whole plants of 496 rare plant species
native to the United States. The collection is stored at 25 gardens and arboreta that
form part of the CPC.
The Royal Botanic Gardens at Kew, United Kingdom, support six ex situ and
in situ conservation projects. The activities range from acting as the UK Scientific
Authority for Plants for CITES (Convention on International Trade in Endangered
Species of Wild Fauna and Flora), cooperating in the recovery and reintroduction of
endangered species, and in production of management plans for sustainable devel-
opment and protected areas (Royal Botanic Gardens, Kew, 1996b).
The Wrigley Memorial and Botanical Gardens at Catalina Island, CA, is still
another example. The garden places its emphasis on California island endemic
plants. Many of these plants are extremely rare, with some listed on the Endangered
Species List.
15.2.4 Plant Tissue Culture as a Method to Clone and Rescue

Rare and Endangered Plant Species
Plant tissue culture has been the primary method used to rescue rare and endangered
plant species and to increase their numbers of genetically similar offspring. It is a
practice used to propagate plants under sterile conditions, often to produce clones
of a plant. The most useful plant tissue culture protocols involve shoot-tip cul-
ture (mericloning), embryo culture, and shoot multiplication using elite germplasm.
Germplasm of vegetatively propagated plant material is cheaper to maintain in tis-
sue culture (Akerele et al., 1991), is less expensive to ship, and has the potential to
yield more plants more quickly. It is one of the preferred ways to preserve rare and
endangered plant species and to distribute these species to other botanical gardens
and arboreta around the world. Where conditions allow, some tissue-cultured plant
material can be used to reintroduce species that have become lost or extinct in
the wild.
The different techniques of plant tissue culture offer certain advantages over tra-
ditional methods of plant propagation including
• the production of exact copies of plants that produce particularly good flowers,
fruits, or have other desirable traits;
• to quickly produce mature plants;
• the production of multiples of plants in the absence of seeds or necessary polli-
nators to produce seeds;
• the regeneration of whole plants from plant cells that have been genetically
modified;
• the production of plants in sterile containers that allows them to be moved with
greatly reduced chances of transmitting diseases, pests, and pathogens;
• the production of plants from seeds that otherwise have very low chances of ger-
minating and growing, i.e., orchids and nepenthes; and
• to clean particular plant of viral and other infections and to quickly multiply these
plants as “cleaned stock” for horticulture and agriculture.
Plant tissue culture relies on the fact that many plant cells have the ability to regen-
erate a whole plant (totipotency). Single cells, plant cells without cell walls (proto-
plasts), pieces of leaves, or (less commonly) roots can often be used to generate a
new plant on culture media given the required nutrients and plant hormones.
Plant tissue culture is performed under aseptic conditions under filtered air. Liv-
ing plant materials from the environment are naturally contaminated on their sur-
faces (and sometimes interiors) with microorganisms, so surface sterilization in
chemical solutions (usually alcohol or bleach) is required of starting materials. The
tissue which is obtained from the plant to start the culture is called an explant.
Explants are then usually placed on the surface of a solid culture medium, but are
sometimes placed directly into a liquid medium, particularly when cell suspension
cultures are desired. Solid and liquid media are generally composed of inorganic
salts plus a few organic nutrients, vitamins, and plant hormones. Solid media are pre-
pared from liquid media with the addition of a gelling agent, usually purified agar.
The composition of the medium, particularly the plant hormones and the nitrogen
source (nitrate versus ammonium salts or amino acids), has profound effects on the
morphology of the tissues that grow from the initial explant. For example, an excess
of auxin will often result in a proliferation of roots, while an excess of cytokinin
may yield shoots. A balance of both auxin and cytokinin will often produce an
unorganized growth of cells or callus, but the morphology of the outgrowth will
depend on the plant species as well as the medium composition. As cultures grow,
pieces are typically sliced off and transferred to new media (subcultured) to allow
for growth or to alter the morphology of the culture. As shoots emerge from a culture
(Fig. 15.1), they may be sliced off and rooted with auxin to produce plantlets which,
Fig. 15.1 In vitro shoot (a)

and callus (b) cultures of
Hypericum perforatum L.
when mature, can be transferred to potting soil for further growth as normal plants
in the greenhouse.
The skill and experience of the tissue culturist are important in judging which
pieces to culture and which to discard. Based on work with certain model systems,
particularly tobacco, it has often been claimed that a totipotent explant can be grown
from any part of the plant. However, this concept has been vitiated in practice. In
many species, explants of various organs vary in their rates of growth and regenera-
tion, while some do not grow at all. The choice of explant material also determines
if the plantlets developed via tissue culture are haploid or diploid. Also the risk of
microbial contamination is increased with inappropriate explants. Thus, an appro-
priate choice of explant made prior to tissue culture is very important.
The specific differences in the regeneration potential of different organs and
explants have various explanations. The significant factors include differences in
the stage of the cells in the cell cycle, the availability of or ability to transport
endogenous growth regulators, and the metabolic capabilities of the cells. The most
commonly used tissue explants are the meristematic ends of the plants like the stem
tip, auxiliary bud tip, and root tip. These tissues have high rates of cell division
and either concentrate or produce required growth-regulating substances including

auxins and cytokinins.
Some explants, like the root tip, are hard to isolate and are contaminated with soil
microflora that become problematic during the tissue culture process. Certain soil
microflora can form tight associations with the root systems or even grow within the
root. Soil particles bound to roots are difficult to remove without injury to the roots,
a circumstance that then allows microbial attack. These root-associated microflora
generally will overgrow the tissue culture medium before there is significant growth
of plant tissue.
Aerial (above soil) explants are also rich in undesirable microflora. However, they
are more easily removed from the explant by gentle rinsing, and the remainder usu-
ally can be killed by surface sterilization with 10% sodium hypochlorite (NaClO4 ).
Most of the surface microflora do not form tight associations with the plant tis-
sue. Such associations can usually be found by visual inspection as a mosaic, de-
colorization or localized necrosis (blackening or death of tissues) on the surface of
the explant, and removed before culture.
An alternative for obtaining uncontaminated explants is to take explants from
seedlings which are aseptically grown from surface-sterilized seeds. The hard sur-
face of the seed is less permeable to penetration of harsh surface-sterilizing agents,
such as hypochlorite, so the acceptable conditions of sterilization used for seeds can
be much more stringent than for vegetative tissues.
One of the preferred methods of tissue culture is shoot-tip culture (mericloning).
It is becoming the preferred tissue for exchange of clonal material. Tissue cultures
produced from shoot-tip cultures can produce disease-free germplasm, particularly
with respect to viruses. Shoot-tip explants, devoid of any vascular tissue, is typically
free of any viral pathogens. This protocol was developed by George Morel in France
as a way to rescue virus-infected orchid plants and rapidly propagate virus-free
stock. This process is used for the micropropagation of virus-free stock of any plant
species. Great success stories are seen in the shoot-tip propagation of virus-free
potatoes, strawberries, cassava, pelargoniums, and orchids (Kyte and Kleyn, 1996).
In vitro (“in glass”, microorganism-free cultures) disease elimination techniques
help to ensure international exchange of germplasm, particularly since viral trans-
mission through seed is known to occur (Akerele et al., 1991). It allows for a far
greater number of plants to be produced in a given time than by conventional prop-
agation methods. The Micropropagation Unit at Kew Botanic Gardens propagates
plants which are rare, endangered, or difficult to propagate conventionally. Tech-
niques include micropropagation from vegetative material and in vitro germination
of seeds and spores. A large number of tropical epiphytic (growing on other plants)
and terrestrial (growing in the soil) orchids are grown from seed in vitro under ster-
ile conditions. Of these, many are members of island floras and are in jeopardy.
Plant tissue culture is used widely in plant science; it also has a number of com-
mercial applications. These applications include the following:
• Micropropagation is widely used in forestry and in floriculture. Micropropagation

can also be used to conserve rare or endangered plant species.
• A plant breeder may use tissue culture to screen cells rather than plants for advan-
tageous characters, e.g., herbicide resistance/tolerance.
• Large-scale growth of plant cells in liquid culture inside bioreactors as a source
of secondary products, like recombinant proteins used as biopharmaceuticals.
• To cross distantly related species by protoplast fusion and regeneration of the
novel hybrid.
• To cross-pollinate distantly related species and then tissue culture the resulting
embryo which would otherwise normally die (embryo rescue).
• For production of doubled monoploid plants from haploid cultures to achieve
homozygous lines more rapidly in breeding programs, usually by treatment with
colchicine which causes doubling of the chromosome number.
• As a tissue for transformation, followed by either short-term testing of genetic
constructs or regeneration of transgenic plants.
• Certain techniques such as shoot apical meristem tip culture (mericloning) may
be employed that can be used to produce clean plant material from virused stock,
such as potatoes and many species of soft fruit.
15.2.5 Plant Seed Banks for Germplasm Preservation
15.2.5.1 Plant-Introduction Stations in the United States

Four regional plant-introduction stations in the United States occur in Pullman, WA,
Ames, IA, Geneva, NY, and Griffin, GA. They are responsible for the management,
regeneration, characterization, evaluation, and distribution of seeds of more than
one-third of the accessions of the national system (i.e., nearly 197,000 accessions of
almost 4,000 plant species). At Ames, approximately 40,079 accessions are held; the
primary crops preserved include maize, grain amaranth, oilseed brassicas (e.g., rape,
canola, mustard), sweet clover, cucumber, pumpkin, summer squash, acorn squash,
zucchini squash, gourds, beets, carrots, sunflower, and millets. At Geneva, approx-
imately 14,180 accessions are held; the primary crops preserved include tomato,
birdsfoot trefoil, brassicas, and onion. At Griffin, approximately 82,277 accessions
are held; the primary crops preserved here include sweet potato, sorghum, peanut,
pigeon pea, forage grasses, forage legumes, cowpea, mung bean, pepper, okra, mel-
ons, sesame, and eggplant. At the Pullman station, approximately 60,277 accessions
are held; the primary crops preserved there include common bean, onion, lupine,
pea, safflower, chickpea, clovers, wild rye, lettuce, lentils, alfalfa, forage grasses,
horsebean, common vetch, and milk vetch.
15.2.5.2 National Center for Genetic Resources Preservation in Fort

Collins, CO
This center houses the base collection for long-term, backup storage of the National
Plant Germplasm Storage active collections. It has recently expanded and remod-
eled its facilities, quadrupling the storage area, and adding modern research and
processing laboratories. It features quality cold-storage facilities for conventional

seed storage and cryopreservation (low-temperature preservation, using liquid nitro-
gen at –196◦ C) storage capacity for seeds, pollen, and vegetatively propagated
germplasm. The National Seed Storage Laboratory (NSSL) can store more than
1 million samples. The base collection of the NSSL is not duplicated in its entirety
in any other gene bank. Furthermore, of the more than 268,000 accessions, about
60,628 are not duplicated at other sites.
15.2.5.3 International Rice Research Institute in Los Baños, Philippines

Rice (Oryza sativa L.) is the third best-represented crop in plant gene banks. This is
most likely due to the fact that rice is a staple food crop in much of the Third World,
particularly Asia. One of the main gene banks for tropical rice is at the International
Rice Research Institute (IRRI). Japan and the United States maintain major collec-
tions of temperate rices and act as a backup for IRRI and the International Institute
for Tropical Agriculture (IITA) materials. IRRI has assembled the world’s largest
rice collection. It represents the largest germplasm collection for any crop and is
regarded as one of the best-managed gene banks. It has computerized rice collec-
tion data on samples that contain 45 morphological and agronomic characteristics
for each entry. As many as 38 genetic evaluation and utilization traits are added,
covering disease and pest resistance to tolerance to adverse soils and climates. Its
germplasm collection is gradually regenerated and fresh seed is put in medium and
long-term storage. Approximately 2000 rice varieties and much wild material still
remain to be collected. The gene bank at IRRI is expected to continue growing until
it reaches about 130,000 accessions (Plucknett et al., 1987).
15.2.5.4 International Potato Center in Lima, Peru

Potato (Solanum tuberosum L.) is the fourth leading world crop, exceeding all other
in annual production of starch, protein, and several other important “nutrients”
(Niederhauser, 1993). It is susceptible to many diseases and pests and is one of the
heavy users of chemical inputs of any crop (Martin, 1988). Improved potato culti-
vars present a great potential benefit to the economic, environmental, and nutritional
future of the world potato growers and consumers (Bamberg et al., 1995).
The International Potato Center (CIP) accepted the global mandate for potato
genetic resources when it was founded. By 1980, more than 80% of total cultivated
potato germplasm had been collected. Wild species of potato have also been sys-
tematically collected. The cultivated potato collection samples are grown annually
at high altitudes and stored in conservation facilities. Duplicates of all lines are
replaced by a new CIP harvest in each succeeding year (Reid et al., 1993).
Potato cultivars are distributed worldwide from CIP. Microtubers are more tol-
erant of physical and environmental disturbances and a few cultures are tolerant
of delays in transit (Bamberg et al., 1995). They are now in use for distributing
germplasm of potato from CIP and yam from the IITA. The CIP helped to initiate a
joint database with potato gene banks around the world by sharing evaluation data
and technical procedures, professional exchanges, cooperation on prioritization and

organization of collecting expeditions, duplicate storage of accessions, and cooper-
ative research (Bamberg et al., 1995).
15.2.5.5 Crucifer Genetics Center in Madison, WI

The Crucifer Genetics Center (CrGC) has been established for the purpose of devel-
oping, acquiring, maintaining, and distributing information about seed stocks of
various crucifers (members of the cabbage family, Brassicaceae) as well as crucifer-
specific symbionts, namely, pathogens (organisms which cause disease in crucifers).
It distributes seed from various genetic stocks of rapid-cycling brassicas (short life
cycle from seed to seed), some wild crucifer species, a large number of mutants of
Brassica, Raphanus (radish), and Arabidopsis (a cress), and pathogen symbiont cul-
tures. The CrGC has been instrumental in introducing rapid-cycling brassicas into
laboratory teaching experiments for students in elementary and high school and in
colleges and universities for the study of plant genetics, development (flowering and
fruiting), physiology (gravitropism, phototropism, and hormone action), and plant
pathology. One of these plants, Arabidopsis, has been shown to develop from seed to
seed in outer space on NASA’s Space Shuttle. For humans, conservation of crucifer
germplasm, as done at the CrGC, is important for humans; many of the brassicas
are important in preventing cancer in humans (e.g., broccoli).
15.2.5.6 Commercial Seed Companies That Save and Sell Heirloom Seeds
of Rare and Endangered Medicinal and Other Plants
Because of the loss of crop diversity with the advent of the green revolution and
the breeding of crop varieties grown as monocultures, we have lost thousands of
varieties of plants because they are no longer available for sale. This has happened
with rice, wheat, and maize. Also witnessed with the loss of crop diversity, is a
loss in disease and insect pest resistance, a loss or protein and essential nutrients in
many of the grain crops, a loss in desirable flavor and texture in many vegetables,
and an increase in the use of fertilizers, pesticides, and irrigation water. Many of the
desirable cultivars of apples and roses, once grown very widely, almost completely
disappeared from commercial seed or nursery catalogues.
The situation today is changing rapidly. Many of the “old-fashioned” rose cul-
tivars or apple cultivars are now reappearing in the catalogues, primarily driven
by consumer demand for more plant diversity and varieties that do not require so
much in the way of fertilizer, pesticide, and water inputs. The same can be said
for cucurbits (squash and melon), maize, legume crops (peas, beans, and their rel-
atives), herbs, prairie plants, medicinal plants, woodland wild flowers, native trees
and shrubs useful in landscaping and in forest restoration projects, aquatic plant
species used in ponds to purify water polluted water from sewage treatment plants,
and species of plants which are good scavengers of heavy metal pollutants in soils.
Let us cite just a few examples of sources of seeds of rare and endangered plants.
• Henry Doubleday Institute at Ryton Gardens, Coventry, UK, has a heritage seed
program whereby it distributes heirloom and rare varieties of seed plants which
are generally not commercially available. The seed is not registered with the
European Community, so, it cannot be sold, but it can be donated. We do not
know if their seeds are exportable to the United States.
• The Seed Guild is an organization located in Lanark, UK, which buys seed
from botanical gardens throughout the world, making them available to amateur
gardeners and commercial outlets. The guild provides an opportunity to obtain
unusual and rare seeds which are not generally on commercial seed lists. Their
annual newsletter provides information on seed collecting expeditions and new
sources of seed supply.
• Three commercial seed companies: Redwood Seed Company (PO Box 361, Red-
wood City, CA 94064) is an alternative seed company; Sandy’s Exotic Plant Seed
Company (7179A Nebraska, Fairchild, WA 99011) has available rare, exotic, and
unusual seeds from around the world; and Prairie Moon Nursery (Route 3, Box
163 Winona, MN 55987) sells seeds of rare ferns, cacti, forbs (herbaceous plants),
grasses, sedges, rushes, trees, shrubs, vines, and prairie mixtures.
15.2.5.7 Seed Banks in Botanical Gardens Established for International

Seed Exchange
The Royal Botanic Gardens Kew Seed Bank, located at Wakehurst Place, UK, was
founded in 1974. It provides storage for seeds of some 4,000 plant species from
more than 100 countries. It is the most diverse collection anywhere in the world.
It also holds a long-term collection of seeds sampled from wild populations within
the United Kingdom and the world’s arid and semi-arid lands. Their emphasis is
placed on threatened plant populations and in the drylands, especially for plants of
local economic value. Some 3,750 plant species are conserved according to inter-
nationally accepted standards for long-term conservation. When numbers permit,
seed is offered for distribution. Samples are made available through a List of Seeds
published every other year and distributed to organizations doing research work and
subject to a commercialization agreement in the event of any commercial success,
a policy of apportioning profits to the seeds’ country of origin. This policy aims to
abide with the spirit of the 1992 Rio Earth Summit and to keep pace with subsequent
changes in national and international attitudes and legislation (The Royal Botanic
Gardens, Kew, 1996a).
The CPC, located at the Missouri Botanic Garden in St. Louis, MO, maintains
a Memorandum of Understanding (MOU) with the US Department of Agriculture
NSSL in Ft. Collins, CO. Under this MOU, the NSSL stores seeds from rare US
plants in the center’s National Collection of Endangered Plants at no cost to the
center or its participating institutions. The CPC’s National Collection of Endan-
gered Plants represents perhaps the most fundamental reserve of plant germplasm
for many of the rarest plants in the United States.
15.2.6 Botanical Prospecting – Ethnobotanical Field Research

There is a correlation between plant genetic resources and the development of
new pharmaceutical products. This correlation integrates biological, ecological,
chemical, medical, legal, and economic aspects. The issues can involve property,
resource and access right, reciprocity, technology transfer, export, and patent and
royalty rights (Reid et al., 1993). The force behind biodiversity-prospecting is the
demand for new genes and chemical compounds and to research the supply of these
resources in wildland diversity. Interest has increased in the pharmaceutical indus-
try. Development and improvement of screening techniques has increased the rate
for chemical testing. Ethnopharmacology is another force. This field, which involves
the use of plants and animals in traditional medicine, can greatly increase the prob-
ability of finding a valuable drug. Drug exploration based on indigenous knowledge
may prove to be more cost- and time-effective than random screenings.
In the United States, approximately 25% of prescriptions are of drugs with
ingredients that are derived from plant extracts or their derivatives. The demand
for genetic resources in agriculture will grow as techniques for genetic manipu-
lation improve and research investments show a return. Between 1985 and 1990,
the number of biotechnology patent applications grew by 15% annually (Raines,
1991–1992). As an example, two cancer drugs derived from the rosy periwinkle
(Catharanthus roseus (L.) G. Don), vincristine and vinblastine, alone earned $100
million per drug for Eli Lilly Company (Farnsworth, 1988). In addition, Paclitaxel
(taxol) sold more than $600 million in 1996, and etoposide (from Podophyllum
peltatum L. or mayapple) more than half that figure.
The stakes in drug development are high and payoff is uncertain. Finding a valu-
able compound has a high cost since the probability of locating one with a desired
action is low. It is often necessary to test as many as 10,000 substances in order to
find one that may reach the drug market (Reid et al., 1993). Developing a successful
drug can require screening of some 1000 plant species. Research and development
costs are generally high, at an average of $868 million per drug for those developed
between 1989 and 2002, with nearly 12 years needed to go from discovery to market
(DiMasi et al., 2003).
International laws directly affect biodiversity-prospecting. Intellectual Property
Rights and Human and Indigenous Rights are measures to be used for the protec-
tion of traditional cultural manifestations, including cultivated plants, medicines,
and knowledge of useful properties of plants (Akerele et al., 1991). These laws
guarantee rights to participate in the use, management, access, and conservation of
these resources and should involve sharing in the benefits. The objectives of such
laws should include conservation of plant and animal diversity, sustainable develop-
ment of genetic resources, and the fair and equitable sharing of the resultant benefits
(Reid et al., 1993).
A Costa Rican private, nonprofit organization, Instituto Nacional de Biodiversi-
dad (INBio), was established to facilitate conservation and sustainable use of bio-
diversity. Other private, nonprofit intermediaries are based in developed countries.
In the United States, for example, the New York Botanical Garden, the Missouri
Botanical Garden, and the University of Chicago have all contracted with private
pharmaceutical companies and public research organizations to provide samples of
biodiversity for pharmaceutical development. It is important that pharmaceutical
companies involved in such contracts return an equitable share of their profits from
any plant-derived drugs they develop from such plants to the indigenous peoples
from whom these plants and the knowledge about their medical uses are obtained.
Good role models are provided by DENALI BioTechnologies, LLC (DENALI),
Kenai, Alaska 99611, and the former Shaman Pharmaceuticals from South San
Francisco, CA.
15.2.7 Integration of Traditional Knowledge and Biotechnology

to Address and Prevent Overcollection of Medicinal
Plant Species in Their Natural Habitats
Overcollected medicinal plants in the United States (see above) were originally
important to its Native American cultures. Settlers and immigrants to the land
learned the healing values of these indigenous plants, but generally poor stewardship
imposed through indifferent, thoughtless, and destructive practices has led to their
demise. A similar lack of respect for traditional knowledge and habitat destruction
has led to the loss of many species in biodiversity-rich tropical regions.
A little studied area of the world that is facing habitat change is the circumpo-
lar Arctic. While presumably less diverse in number of species than temperate or
tropical flora, the plants of this region are uniquely adapted to harsh conditions.
Despite the vigor of individual species, plants in Arctic habitats are particularly
interwoven and vulnerable to mismanagement, making their recovery from unto-
ward events slow and often incomplete. Paradoxically, this environment is both
robust and fragile.
The diverse Native cultures of Alaska have witnessed many changes to their tra-
ditional lifestyles in the last few decades. Since Alaska achieved statehood in 1959,
and the Alaska Native Claims Settlement Act of 1971 extinguished the sovereign
rights of Alaska Native tribes in exchange for $962 million (ANCSA, 1971), a rapid
introduction of a currency-based economy, influx of new residents, aggressive natu-
ral resource exploration and development, and installation of military facilities and
related technologies during the former Cold War transformed their lives forever.
Current changes in the global climate further challenge the traditional, subsistence
existence (defined as taking only what one needs from plants and animal resources
to survive) that served them for thousands of years. Important medicinal and nutri-
tional plants are regarded still with reverence and typically are guarded with ferocity.
DENALI, Alaska’s only biotechnology company, is working with Native orga-
nizations throughout the state to develop medicinal plant resources through genetic
analysis and modification, secondary metabolite identification, and bioactive com-
pound quantification, with the intent to generate pharmaceutical agents. DENALI’s
collection program for research specimens follows a strict protocol for selection
and harvesting practices. Working with elders and healers, plants in the Alaska flora
have been prioritized based on documentation of medicinal efficacy, abundance,
sustainability of harvest, and potential economic value to the Native cultures who
used them for subsistence purposes. Priority plants are harvested in small quantities
(e.g., 1 quart to 2.5 gallon Zip-loc R bags) and specimen locations are marked by
global positioning satellite (GPS) technology. Less than one-third of the biomass
in any location is harvested at a given time in order to preserve material for future
collection. Specimens are stored frozen prior to undergoing low-volume extraction,
typically with 5–10 g of tissue per extraction and five solvents of highly different
polarity. Subsequently, extracts are fingerprinted by high-performance liquid chro-
matography (HPLC) and mass spectrometry. If the occurrence of a specific com-
pound is sought, HPLC analyses are conducted in the presence and absence of a
reference standard (e.g., artemisinin in wormwood (Artemisia spp.) extracts).
Fractions containing novel compounds are pursued in assays that demonstrate
bioactivity. In the event a bioactive(s) is identified, locations that were previously
harvested are revisited; but, for large harvests (up to 1,000 kg), numerous locations
are added in order to obtain additional biomass while minimizing the “footprint” of
collection activity. The biomass is immediately dried by a rapid and gentle process
known as Refractance Window R Drying (MCD Technologies, Inc., Tacoma, WA)
and vacuum sealed so as to maintain stability for at least 3 years. This material
is extracted on a larger scale with the preferred solvent and conditions delineated
on a small scale (as above) to obtain the pure “lead” compound or “new chemical
entity” (NCE) of interest. At this point, the compound is ready to undergo pre-
clinical evaluations in animal models and early phases of human trials.
Today, Alaska Natives appreciate the need to integrate into the fabric of modern
life, but they strive to maintain their resources and traditional knowledge of use
and management. Examples of traditional medicinal plants under investigation and
development include devil’s club, also called Alaska ginseng (Oplopanax horridus
C.A. Mey.), wormwood, also known by an alternative common name, stinkweed,
(Artemisia tilesii Ledeb.), and blueberries (Vaccinium spp.) (Fortuine, 1988).
Devil’s club is the panacea plant of the Tlingit, Haida, and Gitskan of Southeast
Alaska and British Columbia (Fortuine, 1988; Moerman, 1998; Johnson, 2006). Tra-
ditionally, it is used for treatment of a variety of ailments including, but not limited
to, wounds, infections, colds, cough, fever, arthritis, and diabetes. Due to protest
over its special cultural significance, commercialization of the plant has not occurred
on an industrial scale. Tribal elders and healers recognize that devil’s club requires
many years to reach maturity and medicinal value; thus, overcollection would be
devastating to this species which currently grows abundantly in its natural habitat.
Modern science has demonstrated in vitro antioxidant, anti-proliferative, anti-
bacterial, anti-tubercular, anti-fungal, anti-inflammatory, and anti-viral activity
against respiratory syncytial virus; this is consistent with traditional uses
(McCutcheon et al., 1995; Kobaisy et al., 1997; Tai et al. 2006; Inui et al., 2007).
Notably, authentic ginsengs are used for very similar medicinal purposes. Devil’s
club constituents resemble those of authentic ginseng species and, as a result, it
has been discussed as a substitute to overcollected ginseng species (Panax spp.)
for medicinal and nutritional supplement purposes. A partial list of bioactive com-
pounds found in devil’s club through HPLC profiling of extracts includes trans-
nerolidol, sterols, including daucosterol and beta-sitosterol, syringin, a series of
triterpenoid saponins, and a group of polyynes (Kobaisy et al., 1997; Gruber et al.,
2004). Some of these compounds, known also to occur in Panax species, were iden-
tified in closely related Oplopanax elatus Nakai (as judged by sequences in ITS
regions of nuclear rDNA), which is indigenous to the Russian Far East (Zhang et al.,
1993; Wang et al., 1996; 1997; 2004; Artiukova et al., 2005).
The major bioactive ingredients of ginseng are ginsenosides, which are also clas-
sified as triterpene saponins. Because ginseng cultivation is relatively expensive,
time-consuming, and labor-intensive, and because the productivity of ginseng cell
and tissue culture is low, it has become important to provide alternatives to ginseng
propagation through other biotechnological methods (Liang and Zhao, 2008).
Ribosomal and biosynthesis-related gene sequence analyses offer taxonomic
positioning of devil’s club in the family Araliaceae (Artiukova et al., 2005). Fur-
ther taxonomic proximity may be established through comparison of conserved
DNA sequences in the ribosomal ITS1-5.8S-ITS2 region between authentic gin-
seng, already characterized in six species, Panax ginseng C. A. Mey., Panax quin-
quefolius L., Panax japonicus C. A. Mey. (Japanese ginseng), Panax notoginseng
(Burkill) F. H. Chen (Sanchi), Panax trifolius L., and Panax major Ting (Ngan et al.
1999). Once established as a ginseng, or close relative, the possibility for using
devil’s club (also referred to as Panax horridus C. A. Mey.) as a surrogate for gin-
senoside production becomes viable.
Ongoing research strives to understand and improve ginsenoside levels in Panax
by metabolic engineering that is based on the biosynthetic pathway of ginsenosides.
Candidate enzymes include squalene synthase, oxidosqualene cyclase, involved in
the cyclization reaction of 2,3-oxidosqualene, cytochrome P450 isoforms, various
glycosyltransferses and, in particular, dammarenediol-II synthase, the first dedicated
enzyme for dammarane-type ginsenoside biosynthesis, versus oleanane-type com-
pounds that also occur in the genus Panax (Jung et al., 2003; Lee et al., 2004). DNA
sequences that encode enzymes of ginsenoside biosynthesis should be compared
between Panax species and devil’s club. Expressed sequence tags (ESTs) provide
a valuable tool that can be used to identify secondary metabolite-associated genes
and help to predict the potential for ginsenoside production in devil’s club (Jung
et al., 2003). Because devil’s club offers similarities to overcollected Panax, and is
unthreatened in the wild, it may prove to be an acceptable substitute for metabolic
engineering of a ginsenoside pathway in preparation of responsible cultivation and
management in its natural habitat.
Wormwood is the most important medicinal plant of the Yu’pik Eskimos of the
Yukon-Kuskokwim Delta region and the Athabascans of Interior Alaska. Worm-
wood has been used traditionally for many of the same purposes as devil’s club,
although it belongs to the family Asteraceae and is, taxonomically, quite dis-
similar. As its common name would imply, some of the most interesting tradi-
tional uses were as an anti-parasitic and ethnoveterinary anti-helminthic for sled
dogs. The closely related Chinese species, Artemisia annua L. (sweet wormwood),
has received extensive scientific and medical attention because of its compound,
artemisinin, which is active against the malaria parasite, Plasmodium (Weina, 2008).
These clues, derived from thousands of years of medicinal use, should trigger a
similar investigative program on wormwood as that described above for devils’
club. Recent research on A. annua is focused on secondary metabolite biosyn-
thetic pathways for enhancement of artemisinin yield. As an unthreatened, prolific
Artemisia species, Alaska wormwood may prove to be an alternative natural source
of artemisinin, amenable to metabolite engineering for artemisinin production, or as
a reservoir of other promising novel bioactive molecules, most of which await study
and development.
15.2.8 The Concept of “Ranching” Wild Vaccinium Species

with Superior Properties as a Nutraceutical
and Potential Pharmaceutical
The beneficial properties of berries were understood instinctively by humans

throughout the millennia and, of these, Vaccinium species have been revered by
indigenous peoples for their food and medicinal values. Modern science now pro-
vides a biochemical basis for the health-promoting effects of Vaccinium, a staple
wherever humans established a culture in cooler, higher latitude or altitude regions
of the world and where a large variety of food plants were unavailable.
Several Vaccinium species of worldwide economic importance occur in the
United States. The most widely cultivated is Vaccinium corymbosum L. (highbush
blueberry), grown from the Mid-Atlantic to California, Oregon, and Washington,
and from the Upper Midwest to the Mid-South, with Michigan and New Jersey
leading production. Vaccinium angustifolium Ait. (lowbush, or “wild”, blueberry)
is adapted to the far North and is commercially important in Maine and Eastern
Canada, as well as in parts of New Hampshire, Massachusetts, Michigan, and
Wisconsin. Vaccinium ashei Reade (rabbiteye blueberry) is well-adapted to the
warmer climates of the South. In addition to blueberries, the genus also includes
Vaccinium macrocarpon Ait. (cranberry), another principal crop of more Northern
locations.
During the past decade, demand for blueberries and cranberries has grown dra-
matically as a result of increasing awareness in the scientific community and by
consumers of their healthful properties. In addition to greater amounts consumed
annually as fresh, frozen, and processed fruit, these berries have become important
components of nutraceuticals or dietary supplements. Cranberry extract, used pri-
marily for maintenance of urinary tract health, was the 14th most popular dietary
supplement, whereas Vaccinium myrtillus L. (European bilberry), a close relative of
V. angustifolium, was placed no. 21 for its beneficial effects on retinal and vascular
health (Nutrition Business Journal, 2004). Extracts of V. myrtillus are widely used
in prescription and over-the-counter medications. Preparations derived from its fruit
are recognized in “The Complete German Commission E Monograph: Therapeutic
Guide to Herbal Medicines” (Blumenthal, 1998) and in the “PDR for Herbal
Medicine”, which also cites the bog bilberry, Vaccinium uliginosum L. (Gruenwald,
2004). There are currently over 180 Vaccinium phytopharmaceutical products avail-
able worldwide. As these medications become increasingly popular, European crops
can no longer meet the global demand. In response to this shortfall, extracts of gen-
erally similar North American V. angustifolium are now being considered as an alter-
native to more expensive V. myrtillus extracts (Kalt and Dufour, 1997).
Three species that are not currently used in commerce, but stand out with regard
to their recognized importance in the subsistence diets of Native Americans and
Alaska Natives, are Vaccinium ovatum Pursh (evergreen huckleberry), Vaccinium
ovalifolium Sm. (Alaska black huckleberry), and V. uliginosum. Although V. ovatum
possesses a remarkable array of flavonoids with beneficial properties (Taruscio et al.,
2004), its occurrence within its natural range and adaptability to cultivation is con-
sidered too limited to be commercially viable. V. ovalifolium is equally remarkable
as V. ovatum in its profile of flavonoid compounds (Taruscio et al., 2004) and, like
V. uliginosum, grows prolifically without cultivation of any sort, throughout Alaska.
Some experts estimate that hundreds of millions of pounds of Vaccinium species are
available each growing season (Matz, 1996).
V. ovalifolium forms dense thickets up to subalpine levels, and is the most com-
mon woodland and coastal forest berry, providing most of those picked in maritime,
rainforest habitats of Alaska. V. uliginosum occurs on vast expanses of wet tun-
dra habitat throughout the state, and is a ubiquitous, low spreading, dwarf, alpine
species, and is the best-known and most-used berry in Alaska for food purposes
(Hulten, 1968; Matz, 1996). Despite spectacular annual yield, these berries are cycli-
cal in year-to-year productivity, and occur in remote areas with extremely rugged
terrain that makes harvest of large quantities difficult and expensive. As a result,
picking machinery cannot be employed and berries must be hand-gathered with
claw-like implements. While these physical obstacles are considerable, there is the
additional inherent danger of gathering berries where grizzly and black bears are
eating voraciously in preparation for hibernation.
Irrespective of barriers to large-scale commercialization, DENALI has gathered
sufficient quantities of V. ovalifolium (which in the wild extensively introgresses
with the closely related species Vaccinium alaskaense How.) and V. uliginosumto
formulate its first nutraceutical product, AuroraBlue R
. Replete with flavonoids,
including 15 prominent anthocyanins, a multitude of polyphenolics, high levels
of monomeric, oligomeric, and, most importantly, high molecular weight proan-
thocyanidin polymers, AuroraBlue is comprised of biomass from >90% V. ovali-
folium/V. alaskaense, <10% V. uliginosum and subspecies, and <1% of various other
Vaccinium species that occur concomitantly in wild stands. The unique profile con-
tributed to AuroraBlue by V. ovalifolium×V. alaskaense suggests a chemotaxonomic
position for this species somewhere between the blueberry, bilberry, huckleberry,
and cranberry, with the individual health-promoting characteristics of each bundled
into one (DENALI BioTechnologies, 2008). Very recent studies reveal that prepa-
rations of wild V. ovatumand V. ovalifolium are the most effective oxygen radical
scavengers in the Ericaceae and V. ovalifolium specimens growing at high latitudes
(greater than the 55th parallel) have the highest oxygen radical absorbing capac-
ity (ORAC) values of any Vaccinium species tested to date (Taruscio et al., 2004;
DENALI BioTechnologies, 2008).
As demand for AuroraBlue has been increasing, DENALI embarked on a “ranch-

ing”program in 2002 with its Alaska Native collaborators to facilitate gathering and
supply of commercial quantities of berries. Consistent with the truly wild features of
the product, ranched plants are neither genetically manipulated nor supported with
conventional fertilizers, pesticides, or herbicides. In ranching stands, soil pH, nutri-
ent composition and other characteristics must mimic the original growth habitat.
Should adjustment of nutrient composition of the soil be required, compost of wild
salmon waste and chips of the white spruce Picea glauca (Moench) Voss constitute
the fertilizer of choice. These efforts are directed not only to improving yield, but
also to protecting and preserving the fragile and special ecosystems of the only tem-
perate rainforests, as well as diverse tundra, in the world. The challenges DENALI
faces are associated with successfully using nonintrusive approaches for greater
productivity and preservation of the unique biochemical composition of ranched
V. ovalifolium and V. uliginosum. Based on region-specific history and experience,
DENALI’s principal ranching approaches include the following:
Utilization of clear-cut stands. Left over from logging activities of the paper and
pulp industry in Alaska’s forested lands, clear-cut stands typically support vigor-
ous growth of Vaccinium plants previously restricted by shade from the old-growth
tree canopy. In most cases, Vaccinium is dependent upon the presence of associated
plants of other genera that comprise its communities or complexes in the forest, and
clear-cut stands retain these critical ecological relationships (Tirmentein, 1990). As
a result of enhanced exposure to more intense sunlight, each bush grows taller with
larger leaves, and fruit is more abundant, larger, and darker in epidermal pigmenta-
tion. The desirable flavonoid composition of plants in clear-cut stands is maintained,
also, as the phenylpropanoid pathway from which flavonoids arise, is triggered by
UV-B light (Dixon and Paiva, 1995). Thus, clear-cuts offer excellent areas for Vac-
cinium ranching.
Utilization of burned stands. Whereas controlled burning is a management tech-
nique employed in other areas, annual summertime wildfires are typical throughout
Alaska. Subsequent to naturally occurring forest fires, some of the earliest and most
prolific re-growth may be achieved by Vaccinium, but for V. ovalifolium, re-growth
is variable (Tirmentein, 1990). Above ground portions of the plants are commonly
killed by fire, but underground rhizomes survive wildfires or controlled burns. Sur-
vival typically decreases with higher fire intensity and severity, although some rhi-
zomes survive even hot wildfires, as long as soil is sufficiently deep to offer some
protection. Some plants may survive even after lethal heat penetration to depths
of 3.5–4.7 inches (9–12 cm). If affected, rhizomes are typically most susceptible
to heat damage during the period of active growth in the spring and early sum-
mer, which is prior to the most prevalent time for wildfires later in the season. The
advantage of burning is freedom from competing genera that recover more slowly
for some years following the burn.
Enrichment. In DENALI’s experience over the past 5 years, stands that have
been heavily picked by hand tend to produce more fruit over the following years,
as a considerable percentage of berries removed from the bush fall to the ground
for reseeding. That noted, individual, established plants within a stand appear to be
on a 2-year cycle for fruiting. The stands seem to display a modest subsequent gain
in plant density, as well as in fruit density per plant. In general, Vaccinium seeds
are thought to be poorly viable, although refrigerated and frozen fruit can be used
to begin seedlings for over 10 years after being held in storage (Tirmentein, 1990).
Interestingly, refrigerated berries appear as fresh as when picked for up to 6 months
at 4◦ C. As a result of these observations, thinly populated stands are enriched with
seeds from plants originating in nearby more heavily populated stands. Since these
seeds are likely to be borne on plants emergent from the same rhizome system, they
are considered to be genetically comparable.
Wild species are preferably relocated directly to ranching stands through hard-
wood cuttings, bare root specimens, or by container (USDA, NRCS, 2004). Speci-
mens are transferred from their native habitat during dormancy, typically before the
snow has melted in the spring and after leaves have dropped in the fall. Compared
to cultivated highbush blueberries that thrive at a planting density of 1400–1700 per
acre (Dailey, personal communication, 2005), wild stock prefers a higher planting
density of 2700–4800 per acre. Like cultivated Vaccinium species, wild species can
be propagated vegetatively through hardwood cuttings that are rooted and raised in
a greenhouse for about 1 year before planting out, but will require at least 2–3 years
of acclimation before fruiting. Although tissue-cultured plants also succeed in the
field, they may have a different form than plants derived from hardwood cuttings,
tending to spread at the base, making ultimate machine harvesting difficult, whereas
hardwood cuttings will grow more upright. Tissue-cultured stock is no longer con-
sidered wild, and that distinction may lower the market value in certain segments
of berries used for nutraceutical grade AuroraBlue. Similarly, genetically modified
Vaccinium may not represent the most valuable source material for products based
on totally natural marketing messages but, conversely, may serve as valuable sources
of extractable flavonoids for pharmaceutical/phytopharmaceutical formulations.
Despite the target market for the above-said product, ranching will provide a
more economical approach to provision of commercial quantities of truly wild
Alaskan berries. As a result of these efforts, Alaska will be able to develop a sustain-
able economic sector based on a renewable resource that is far more environmental
friendly than the traditional industries of oil drilling and extraction, logging, mining,
fishing, and tourism. Valuable relationships are being formed between DENALI and
state and borough economic development organizations, rural villages, native cor-
porations and associations, and private landholders to create an emergent nutraceu-
tical industry in Alaska. This industry will provide benefits to all who produce and
consume wonderful Vaccinium fruits for their widely appreciated health-promoting
properties.
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Chapter 16
The Potential of Biofumigants as
Alternatives to Methyl Bromide for the Control
of Pest Infestation in Grain and Dry Food
Products
Eli Shaaya and Moshe Kostyukovsky
Abstract Fumigation is still one of the most effective methods for the protection of
stored grain and dry food from insect infestations. Phosphine and methyl bromide
are the most widely used fumigants for the control of stored-product insects. Phos-
phine is mainly used today, but there are repeated reports that a number of storage
pests have developed resistance to this fumigant. Methyl bromide has been identi-
fied as a contributor to ozone depletion by the United Nations World Meteorological
Organization in 1995 and, thus, was phased out in most developed countries. Thus,
there is an urgent need to develop alternatives with the potential to replace these
fumigants.
The primary aims of the current study are to evaluate the potential use of essential
oils obtained from aromatic plants as insect fumigants and to evaluate the toxic-
ity of the known isothiocyanates (ITCs) as compared to a new ITC isolated from
Eruca sativa (salad rocket) as fumigants for the control of stored-product insects.
Also, the biological activity of carbon disulphide (CS2 ), methyl iodide (CH3 I), and
benzaldehyde (C7 H6 O) is evaluated.
The toxicity of the various fumigants was assessed against adults, larvae, and
pupae of six major stored-product insects. Two essential oils isolated from Lami-
aceae plants were found to be the most potent fumigants as compared with a
large number of other essential oils. ITCs are also potential candidates, especially
methylthio-butyl isothiocyanate, the main bioactive component in E. sativa, because
of its low toxicity. Comparative studies with CH3 I, CS2 , and C7 H6 O showed that
CH3 I was the most active compound against stored-product insects, followed by
CS2 and C7 H6 O. CH3 I was also found to be less sorptive and less penetrative in
wheat than CS2 .
E. Shaaya (B)
ARO, the Volcani Center, Department of Food Science, Bet Dagan 50250, Israel

390 E. Shaaya and M. Kostyukovsky
16.1 Introduction
In developing countries, the post-harvest losses of cereals and other durable com-
modities caused by insect damage and other bio-agents range from 10 to 40% (Raja
et al., 2001).
Fumigation with methyl bromide or phosphine is a quick and effective tool for
the control of stored-product insect pests. In view of the scheduled phaseout of
methyl bromide under the Montreal protocol, the role of phosphine in grain pro-
tection has increased and stands as the main alternative to methyl bromide. Lately,
insect resistance to phosphine has become an important issue for effective grain
treatment (Nakakita and Winks, 1981; Tyler et al., 1983; Rajendran and Karanth,
2000). A global survey of pesticide susceptibility demonstrated that 9.7% of the
strains tested showed resistance to phosphine (Champ and Dyte, 1976). Another
compound, 2,2 dichlorovinyl dimethyl phosphate, which is widely used as a fog
fumigant for insect control in empty structures, is classified by the US Environ-
mental Agency as a possible human carcinogen (Mueller, 1998). Therefore, there
is an urgent need for new strategies. Thus, in recent years, research has focused on
a search for alternative fumigants for the control of stored-product insects. In this
chapter, we present a comprehensive laboratory and semi-field studies to evaluate
the potential use of essential oils (EOs) obtained from aromatic plants and isothio-
cyanates (ITCs), methyl iodide (CH3 I), carbon disulfide (CS2 ), and benzaldehyde
(C7 H6 O) for the control of stored-product insects.
During previous centuries, traditional agriculture in developing countries has
developed effective means for insect control using botanicals. Their efficiency and
optimal use still need to be assessed in order to make these means of insect control
cheap and simple for users. Lately, a new field has evolved which emphasizes the
use of phytochemicals for insect pest management. The bioactivity of essential oils
(EOs), the major volatile in aromatic plants, and their constituents, has been well
documented against a large number of insect pests. An example is the EO obtained
from the leaves of Thugopsis dolabrata hondai which was found to have high bioac-
tivity against the cockroach (Periplaneta fuliginosa), the mite (Dermatophagoids
farinae), and the termite (Coptotermes farmosanus) (Asada et al., 1989; Lee, 2004).
Some EOs were found to exhibit repellent activity against various insects (Kalemba
et al., 1991; Hassalani and Lwande, 1989; Mwangi et al., 1992). Others were found
to be potent growth inhibitors and anti-feedants (Jermy et al., 1981; Koul et al.,
1990). These essential oils were also found to be effective as nematicidal (Oka et al.,
2000), anti-bacterial (Matasyoh et al., 2007), virucidal (Schuhmacher et al., 2003),
and repellents against ectoparasites (Mumcuoglu et al., 1996).
The efficacy of essential oils as fumigants for the control of pest infestations
in grain and dry food products was also evaluated. EOs and their constituents are
known to possess insecticidal (Wilson and Shaaya, 1999; Shaaya et al., 1997) and
insect repellent activity (Jilani et al., 1988) and to cause a reduction in progeny
(Regnault-Roger and Hamraoui, 1995). For example, the fumigant toxic activity,
anti-feedant, and reproduction inhibition induced by a number of EOs and their
monoterpenoids were evaluated against the bean weevil Acanthoscelides obtectus
16 Biofumigants for the Control of Pest Infestation 391
(Say) and Callosobruchus maculatus (F.) (Klingauf et al., 1983; Regnault-Roger

and Hamraoui, 1995; Raja et al., 2001). EOs extracted from Pogostemon heyneanus,
Ocimum basilicum (basal), and Eucalyptus showed insecticidal activity against
Sitophilus oryzae, Stegobium paniceum, Tribolium castaneum, and Callosobruchus
chinensis (Deshpande et al., 1974; Deshpande and Tipnis, 1977).
In our laboratory, in order to isolate active EOs, we screened a large number of
EOs extracted from aromatic plants and isolated their main constituents. We have
already isolated many such compounds from the EOs of a large number of aromatic
plants (Shaaya et al., 1991, 1994, 1997). Using space fumigation (see Shaaya et al.,
1997), two EOs obtained from Lamiaceae plants were found to be the most potent
fumigants of all oils tested. The main component of one of the oils is pulegone. The
other is not yet identified and it is called SEM76 (Shaaya and Kostyukovsky, 2006).
In our study of the mode of action of EOs, we could show that the target for
EO’s neurotoxicity is the octopaminergic system in insects. We can thus postulate
that EOs may affect octopaminergic target sites (Kostyukovsky et al., 2002; Shaaya
et al., 2002).
ITCs were chosen for this study because of the pesticidal properties of these
chemicals (Fenwick at al., 1983) and because of the potential use of methyl ITC as
fumigant for wheat (Ducom, 1994). In our study on the rates of sorption of homol-
ogous series of ITCs on wheat, we could show that the rate of sorption decreases
with increasing molecular weight (Shaaya and Desmarchelier, 1995). In the case of
methyl ITC, a withholding period over 1 week would be required before residues
decayed to levels near the limit of detection (Shaaya and Desmarchelier, 1995).
Comparative studies with CH3 I, CS2 , and C7 H6 O showed that CH3 I was the
most potent compound against stored-product insects, followed by CS2 and C7 H6 O.
CS2 , according to Winburn (1952), was one of the most effective grain fumigants
as viewed from efficiency and low cost points of view. C7 H6 O occurs in kernels
of bitter almonds, has low toxicity to mammals, and has widespread use in topical
antiseptics.
16.2 The Materials and Methods
The materials and methods employed in the current study are described as follows.
The tested stored-product insects were laboratory strains of S. oryzae, Rhyzop-
ertha dominica, Oryzaephilus surinamensis, T. casteneum, Trogoderma granarium,
Plodia interpunctella, and Ephestia cautella.
The isothiocyanates (ITCs) are obtained by putting 100 g ground seeds into round
bottom flask containing buffer solution (1% ascorbic acid). The flask is held in a
water bath (temperature = 70◦ C) for 2 h to facilitate the hydrolysis of sinigrin to
ITC by the enzyme myrosinase which is found inside the seeds. The second step
is steam distillation with use of the Dean–Stark apparatus (Leoni et al., 1997). The
yellow upper layer is then separated and extracted with petroleum ether. Finally,
the petroleum ether is evaporated under a stream of air. The unknown ITC obtained
from the seeds of E. sativa was identified as methyl thio-butyl isothiocyanate by gas
chromatography (GC), nuclear magnetic resonance (NMR), and infra-red (IR) spec-
troscopy. CS2 , CH3 I, and C7 H6 O were purchased from Sigma Chemical Company,
St. Louis, MO, USA. The essential oils from the aromatic plants were obtained from
freshly harvested leaves and stems by steam distillation.
Three types of bioassays were performed to evaluate the activity of the fumi-
gants. The first screening of the compounds was space fumigation in glass chambers
of 3.4-L capacity (for details see Shaaya et al., 1991). The highly active compounds
were then assayed in 600-mL glass chambers, filled to 70% by volume with wheat
(11% moisture content). Pilot tests were carried out in simulation glass columns of
10 cm in diameter × 120 cm in height, filled to 70% by volume with wheat (11%
moisture content). The insects were introduced in cages, each holding 20 insects
of the same species together with food. Groups of four cages were suspended by a
steel wire at different heights from the bottom of the column. Percentage of insect
mortality was then determined.
The essential oils (EOs) of aromatic plant families are volatiles that can be easily
extracted by hot water vapors. The main components of the EOs are monoterpenes
and, to a lesser extent, sesquiterpenes (Brielmann et al., 2006). The majority of EOs
contain a limited number of main constituents, although minor compounds in the
oil can also play an important role in the fragrance and biological activity.
In order to isolate bioactive EOs, we screened a large number of EOs extracted
from aromatic plants and isolated their main constituents by methods cited in
Shaaya et al. (1991, 1994, 1997). Using space fumigation methodology, the two
EOs obtained from our experimental Lamiaceae plants were found to be the most
potent fumigants as compared with all other essential oils obtained from a large
number of aromatic plant species tested against stored-product insects (Table 16.1)
.
Table 16.1 List of aromatic plants whose essential oils were tested for bioactivity
Species Family Species Family
Apium graveolens Apiaceae Micromeria fruticosa Lamiaceae

Artemisia arborescens Compositae O. basilicum Lamiaceae
A. judaica Compositae O. gratissimum Lamiaceae
Carum carvi Apiaceae Origanum vulgare Lamiaceae
Pelargonium
Citrus limonum Rutaceae Geraniaceae
graveoleus
Coriandrum sativum Apiaceae Petroselinum crispum Apiaceae
Cuminum cyminum Apiaceae Pimpinella anisum Apiaceae
Cymbopogon citrates Poaceae Rosmarinus officinalis Lamiaceae
Foeniculum vulgare Apiaceae Ruta chalepensis Rutaceae
Laurus nobilis Lauraceae Salvia dominica Lamiaceae
Lavandula officinalis Lamiaceae Salvia fruticosa Lamiaceae
Majorana siriaca Lamiaceae Salvia officinalis Lamiaceae
Matricaria camomilla Asteraceae Salvia sclarea Lamiaceae
Mentha piperita Lamiaceae Satureja thymbra Lamiaceae
M. rotundifolia Lamiaceae Thymus vulgaris Lamiaceae
Table 16.2 Fumigant toxicity of SEM76 and pulegone on some stored-product insects (space
fumigation)
Exposure time –24 h.

Third instar larvae and 3-day old pupae were used.
The main component of one of the oils was pulegone and of the other is not yet
totally identified, and it is called SEM76. In space fumigation, these two volatiles
caused total mortality of all adults tested at very low concentrations of 0.5 μL·L−1
air and exposure time of 24 h. A higher concentration of 4 μL·L−1 air was needed
to kill larvae of Tribolium, Trogoderma, and Plodia. Limonene which is regarded as
active monoterpene has much lower activity (Table 16.2).
Table 16.3 Fumigant toxicity of SEM76, with and without CO2 , against five stored-product
insects on winter wheat, in columns 70% filling, in pilot tests
% Mortality (7 days after treatment)

Concentration,
Stage μL·L−1 Sitophilus Tribolium Oryzaephilus Rhyzopertha Plodia
Adults 70 100 66 100 70 –

50 + 15%
100 96 100 100 –
CO2
70 + 15%
100 100 100 100 –
CO2
Pupae 70 + 15%
– 75 – – 100
CO2
Larvae 70 – 60 – – 87
70 + 15%
– 80 – – 100
CO2
Exposure time – 7 days.

Pilot tests in simulation glass columns filled to 70% volume with wheat, under
conditions similar to those present in large grain bins, showed that SEM76 at a con-
centration of 70 μL·L−1 air (equivalent to 70 g·m−3 ) and 7 days exposure time
caused 100% kill of adults of Sitophilus and Oryzaephilus, but not of Rhyzop-
ertha and Tribolium (Table 16.3). Supplementation of 15% CO2 (200 g·m−3 ) caused
reduction in the effective volatile concentration. A concentration of 50 μL·L−1 air
was enough to cause 96–100% kill of all adult insects tested. For pupae and larvae
of Tribolium and Plodia, a higher concentration is needed (Table 16.3).
16.3 Efficacy of Isothiocyanates (ITCs) as Fumigants

for the Control of Pest Infestations in Grain
and Dry Food Products
Mustard family (Brassicaceae) seeds contain ITCs, volatile essential oils that are
known to possess insecticidal activity. By screening a number of various species of
Brassicaceae seeds, namely, Brassica nigra, B. carinata, B. tournefortii, Lepidium
Table 16.4 The fumigant toxicity of four active isothiocyanates compared with methylthio-butyl
ITC against adults of major stored grain insects. (Space fumigation)
Methylthio-butyl ITC was isolated from the plant Eruca sativa.

sativa, Sisymbrium irio, Sinapis alba, S. arvensis, E. sativa, and Diplotaxis spp.,
only in the last three species was it possible to isolate from the seed oil an unknown
ITC at concentrations of 98, 92, and 33%, respectively. Later, this compound was
identified as methylthio-butyl ITC. In space fumigation, the biological activity of
this compound was compared with four common ITCs, namely, allyl, methyl, butyl,
and ethyl. Allyl and methyl ITCs were found to be the most active against adults of
four stored-product insects. A concentration of 1 μL·L−1 air and exposure time of
3 h were enough to kill all the tested adult insects. The activity of methylthio-butyl
ITC was comparable to that of allyl and methyl ITCs except for Tribolium, which
was found to be much more susceptible to the two ITCs (Table 16.4).
In the case of Plodia larva also, a concentration of 1.5 μL·L−1 air of the three
active ITCs and exposure time of 3 h were enough to get 100% kill. For larvae of
Tribolium and Trogoderma, a higher concentration of 2.5 μL·L−1 air and exposure
time of 3 h were needed. The pupae of these three insect species were the most
resistant to the ITCs tested (Table 16.5).
Using high columns filled to 70% wheat to evaluate the toxicity of allyl ITC
in grain, we could show that 20 μL·L−1 air (=20 g m−3 ) and exposure time of
1 day were not effective in killing the insects at the bottom of the column when the
fumigant was applied at the upper layer of the grain. Addition of CO2 and circulation
caused 100% kill at the different heights. Increasing the exposure time to 4 days and
cycling was enough to obtain 100% kill (Table 16.6).
Table 16.5 The fumigant toxicity of four active isothiocyanates compared with methylthio-butyl
ITC against larvae and pupae of major stored grain insects. (Space fumigation)
Methylthio-butyl ITC was isolated from the plant Eruca sativa.

Third instar larvae and 3-day old pupae were used
Table 16.6 Toxicity of allyl ITC against stored-product insects, using high columns filled with
70% wheat with and without CO2
16.4 Efficacy of CH 3 I, CS2 , and C7 H6 O as Fumigants

for the Control of Stored-Product Insects
In space fumigation, CH3 I was very effective against all insect stages tested. Expo-
sure to a concentration of 3–5 μL·L−1 for 3 h was lethal and caused 100% mor-
tality of all stages of the test insects, except for Trogoderma larvae (Table 16.7).
Adults of Tribolium were found to be the most tolerant, followed by Oryzaephilus,
Rhyzopertha, and Sitophilus. In the case of larvae and pupae, Trogoderma was the
most tolerant, followed by Tribolium and Plodia (Table 16.7).
CS2 was less effective than CH3 I and needed a concentration of 6–9 μL·L−1
air for 1 day to achieve total mortality of all the test insects except for Trogoderma
larvae. In the case of CS2 , adults of Tribolium were found to be the most resistant,
followed by Sitophilus, Oryzaephilus, and Rhyzopertha. The larvae of Trogoderma
were more resistant than Tribolium (Table 16.8).
In experiments with 600-mL glass chambers filled to 70% volume with wheat,
CH3 I also showed higher activity than CS2 . The concentration of CH3 I and expo-
sure time needed to obtain a total mortality of the test insects were comparable to
those in space fumigation tests (see Table 16.7). For CS2 , higher concentrations
Table 16.7 Toxicity of CH3 I against stored-product insects, in space fumigation and in 600-mL
chambers filled with 70% wheat
Specific gravity of CH3I –2.28

Third instar larvae and 3-day old pupae were used.
were needed (see Table 16.8). The large difference in the activity between the two
compounds was probably due to higher sorption rate of CS2 in wheat, as compared
with that of CH3 I. In the pilot tests, in glass columns filled to 70% wheat, CH3 I again
showed higher activity than CS2 , when circulation was applied. A concentration of
5 μL·L−1 air and exposure time of 3 h were enough to obtain 100% kill (Table 16.9)
as compared with 20 μL·L−1 air CS2 and 24 h exposure time (Table 16.10). In grav-
ity applications, CS2 penetrated better than CH3 I, but needed a higher concentration
and exposure time to achieve total mortality (Tables 16.9 and 16.10). It should be
mentioned that for methyl bromide fumigation the recommended concentration is
30–50 g·m−3 .
16.5 Conclusions
Our findings, as well as those of other researchers, suggest that certain plant essen-
tial oils and their active constituents, mainly terpenoids, have potentially high bioac-
tivity against a range of insects and mites. They are also highly selective to insects,
since they are probably targeted to the insect-selective octopaminergic receptor, a
Table 16.8 Toxicity of CS2 against stored-product insects, in space fumigation and in 600-mL
chambers filled with 70% wheat
Specific gravity of CS2– 1.26

Third instar larvae were used.
non-mammalian target. The worldwide availability of plant essential oils and their
terpenoids, and their use in cosmetics and as flavoring agents in food and beverages,
is a good indication of their relative safety to warm-blooded animals and humans.
They are also classified as generally recognized as safe (GRAS). The ultimate goal
is the introduction of these phytochemicals with low toxicity, which comply with
health and environmental standards, as alternatives to methyl bromide and phos-
phine for the preservation of grain and dry food.
C7 H6 O was less active than CH3 I and CS2 in space fumigation bioassays. A
concentration of 3 μL·L−1 air and exposure time of 1 day caused 100% adult mor-
tality of Sitophilus, Rhyzopertha, and Oryzaephilus. In the case of Tribolium, 65%
mortality for adults and no effect on eggs and pupae were recorded (Table 16.11).
In the case of Ephestia, this concentration caused 100% mortality of the eggs, but
had no effect on pupae (data not shown). In studies with 600-mL fumigation cham-
bers, a concentration of 50 μL·L−1 air and exposure time of 7 days caused 100%
mortality of the adults tested except for Tribolium. Increasing the concentration to
100 μL·L−1 air yielded very low mortality of larvae, pupae, and adults of Tribolium
(Table 16.11).
Table 16.9 Penetration of CH3 I in 120-cm high columns filled with 70% wheat by gravity or
circulation
ITCs are also potential candidates because only very low concentrations are
needed for the control of stored-product insects. It should be mentioned that
E. sativa (salad rocket) is used worldwide as a food supplement, and methyl thio-
butyl ITC, the main bioactive component in this plant, has lower mammalian
toxicity as compared to the other active ITCs tested. The lower toxicity makes
this fumigant a promising candidate for the disinfestation of grain and dry food
products.
Comparative studies with CH3 I, CS2 , and C7 H6 O showed that CH3 I was the
most toxic compound to stored-product insects, followed by CS2 and C7 H6 O. CH3 I
was found to be less sorptive and less penetrative in wheat than CS2 . CH3 I is toxic to
humans and its use in food as a fumigant is therefore limited. It should be mentioned
that CS2 is flammable and used mainly as a supplement to increase the activity
of other fumigants. In fact, a mixture of trichloroethylene, carbon disulphide, and
carbon tetrachloride (CalandrexR ) in a ratio of 64:26:10, respectively, was developed
by us and was found to be effective against stored-product insects (Polachek et al.,
1960). C7 H6 O has low toxicity to mammals, but it is less effective against stored-
product insects than all other fumigants tested. CH3 I, CS2 , and C7 H6 O may play a
role mainly as supplements to increase the activity of other fumigants.
In this context, we should keep in mind that a general consensus is very difficult
to achieve in order to introduce broad-spectrum fumigants like methyl bromide or
400
Table 16.10 Penetration of CS2 in 120-cm high columns filled with 70% wheat by gravity or circulation
Insects’ % Mortality (7 days after treatment)
Concentration, Exposure height, cm
Method used μL·L-1 time, h (top–bottom) Rhyzopertha Oryzaephilus Sitophilus Tribolium
Gravity 20 48 Top 100 100 100 100

20 100 0 30 10
120
Bottom
20 72 Top to bottom 100% mortality of all insects
Circulation 20 24 Top to bottom 100% mortality of all insects
3 × 45 min
E. Shaaya and M. Kostyukovsky
Table 16.11 Fumigant toxicity of benzaldehyde against various developmental stages of stored-
product insects using space fumigation and fumigation in 600-mL chambers filled with 70%
wheat
Adult mortality in control was less than 5. Third instar larvae and 3-day old pupae were used.
phosphine. Because of this, alternative fumigants could be developed against partic-

ular species of insects or used for a specific food product commodity.
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Index
A Bioenergy, 164
ABE fermentation, 186 Biofertilizer, 146, 150
Abiotic stress, 79, 81, 156–157 Biofuel, 164
Additive, 213 Biogas, 193–200
ADME, 214, 216 Biogasoline, 186
Agricultural sector, 107–116 Bioheat, 188
Agrol, 175 Bioinformatics, 20, 21
Alkaloids, 23 Biomass, 163
Allergenicity, 342 Biomethane, 193–194, 196, 199
American process, 182 Biopharming, 76
Anabolism, 29 Biopriming, 146
AND/OR logic gates, 218 Biotechnology, 3
Angiogenesis, 256 Bliss independence, 219–220
Antagonistic, 213 Blocking catabolism or competitive pathways,
Anthocyanidins, 297 29
Anthocyanins, 232, 383 Botanicals, 390
Anti-sense gene, 11, 24, 25, 26–27, 29 Brown fields, 119, 120
technology, 11
Apoplast, 53 C
Apoptosis, 218, 243 Calvin cycle, 70, 80
Aspirin, 290 Camelid serum antibody, 38
AtNHX1 transcripts, 31 Canada oil/Canola, 190
AuroraBlue, R 258, 383 Cancer, 233–262
Autoinducers, 156 Carbon neutral, 166
Auxins, 144 Carotenes, 293
Carotenoids, 233, 293
B Cartagena Protocol on Biosafety (CPB), 343
Bacillus thuringiensis (milky spore bacterium), Case-control study, 354
66, 334, 340 Catabolism, 29
Bagasse, 164, 170, 173–174 Catechins, 297
Bean, 73 Cauliflower mosaic virus 35S promoter (CaMV
Bean arc5-I promoter, 52 35S), 52, 73, 74, 75, 77, 81, 311
“B” factor, 187 Cellulolysis, 181, 183, 185
Bioaccumulation, 120 Cellulose, 26
Bioassays, 392 Cellulosic ethanol, 187
Biobutanol, 186 Center for Plant Conservation (CPC), 370
Biocontrol, 139 Choline oxidase, 31
Biodegradable substances, 113 C-Jun protein, 253
Biodiesel, 187–188 Classical plant biotechnology, 6–10
405
406 Index
Clean coal technology, 172 Essential oils (Eos), 392

Codex Alimentarius Commission Codex, 343 components: monoterpenes, 232
Commercial Seed Companies, 376–377 Ethnopharmacology, 378
Communities genomics, 157 Ethylene, 144
Competitive pathways, 24, 25, 29 Exothermic reaction, 197–198
Conservation Data Center Network, 367 Expressed sequence tags (ESTs), 381
Convention on International Trade in Exteins, 83
Endangered Species of Wild Fauna and Extinct (plant species), 364
Flora (CITES), 370 in wild, 364
Cooperative Research Centre (CRC) for
International Food Manufacture and F
Packaging Science, 115 FAME, 188
Cordite, 186 Farm chemurgy movement, 175
Corn stover, 182 Feedback regulation, 27–28
Co-suppression, 334, 341 Flavanols, 232, 297
Coumarins, 232 Flavanones, 297
Coverage, 220 Flavodoxin (Fld), 65, 78–82
Critical Ecosystems Program, 369 Flavones, 297
Critically endangered (plant species), 364 Flavonoid compounds, 383
Crucifer Genetics Center (CrGC) in Madison, Flavonoids, 23, 232, 296–299
WI, 376 Flavonols, 297
Cytochrome P450-dependent monooxygenase, Flex-fuel vehicles, 176, 180
237 French paradox, 303
Cytokinins, 143–144 Functional foods, 158
Cytosolic mevalonic acid pathway, 295 Functional metabolites, 158, 289, 290
D G
Dehulling, 112 Generally recognized as safe(GRAS),
DENALI BioTechnologies, LLC (DENALI), 51, 398
379 Gene targeting, 51, 54
Depression, 268–276 Genetically modified(GM) plants, 4, 333
Dianthrone derivatives, 232 goals ofgenetic engineers in developing,
Diester, 189–190 334
Diterpenes, 232 risk assessment, 336
DNA microarray, 20–21 Genetically modified organisms (GMOs), 10,
Docking targets, 27 11, 45, 108, 116, 320, 340
Drug, 216 Gene transfer, 31, 342
Genomics, 19–22, 157
E Geographic Information Systems (GIS), 368
Elastin-like peptides (ELPs), 53 Gibberellins, 143–144
Elicitors, 137, 152 Glycine betaine, 31
Endangered (plant species), 364 Gober gas, 195
Endangered species list, 370 Green crude, 201–202
Endothermic reaction, 198 Green energy, 165
Energy Green fluorescent protein (GFP),
crisis, 164–167 18, 83, 157
crop, 169 Grow gardens, 110
security, 166
Enrichment, 384–385 H
Ephedra (ma huang), 352 Henry Doubleday Institute, 377
Ephedrine alkaloids, 352, 353 Heterologous gene overexpression, 28
Epidermal growth factor(EGF), 217 H/KDEL C–terminal tetrapeptide tag, 53
Epiphytic, 373 Human and Indigenous Rights, 378
Error function, 224 Hybridoma cell line, 37, 38
Index 407
Hydrated ethanol, 180 Monoterpenes, 392

Hydroponics, 111 Multidrug resistance, 215
Hyperaccumulators, 128
N
I N-acyl-homoserine lactone (AHL),
IC50 value, 250 156, 157
Indole alkaloid pathway, 26 NAD(P)H:(quinone-acceptor) oxidoreductase
Induced systemic resistance(ISR), 146 (QR), 237
Induction of Defense Metabolism, 154 n-Alkanols, 232
Industrial sector, 107–116 National Center for Genetic Resources
Inteins, 83 Preservation in Fort Collins, CO,
Intellectual Property Rights, 378 374–375
International Institute for Tropical Agriculture National Collection of Endangered Plants, 370,
(IITA), 375 377
International Potato Center (CIP) in Lima, 375 National Parks, 365, 369
International Rice Research Institute (IRRI), National Parks and Conservation Association,
375 365
International Rice Research Institute in Los National Park Service (NPS), 365
Baños, Philippines, 375 National Seed Storage Laboratory (NSSL), 375
International Union for Conservation of Nature Natural Heritage Program, 367
(IUCN), 364 Natural Resources Defense Fund, 365–366
Inverse metabolic engineering (IME), 29–30 Nature Conservancy, 365, 367–368
Isoflavones, 232, 297 New York Botanical Garden, 369–370, 378
Niche exclusion, 139, 149
L Non-methane organic compounds (NMOCs),
Landfill Directive, 197 197
Least concern, 364 Non-photochemical quenching (NPQ), 294
Lignans, 232 Nutraceuticals, 290, 382
Lignocellulose, 173, 181, 182, 183, 184, 185, Nutragenomics, 290
205
Lipid rafts, 218, 219 O
Loewe additivity, 220 On/off switch, 218
Loewe index, 222 Oil, 112
Oilgae, 201
M Omics, 19, 21
Maize, 29, 41, 42, 45, 74, 168, 169, 182, 196, Organic contaminants, 123
298, 311, 333, 334, 335, 342, 374, 376 Organic farming, 107
Materials and methods (biofumigants), advantages, 108
391–394 disadvantages, 108
Meal, 112 reasons for implementation, 108
Mechanical gene activation, 52 Organization of Petroleum Exporting Countries
Median-effect method, 220, 221 (OPEC), 165
Mericloning, 370, 373, 374 Osmoprotectant compounds, 31
Metabolic flux, 23, 24, 26, 317 Outcrossing, 342
analysis, 23, 24 Oxygen radical absorbing capacity (ORAC),
Metabolomics, 19–20 241, 242, 243, 244, 245, 256, 259, 302,
Metagenomic approach, 157, 158 354, 383
Methylerythritol 4-phosphate (MEP) pathway, Oxygen radical scavengers, 383
295
Methyl tertiary butyl ether(MBTE), 176 P
Missouri Botanical Garden, 370 Parkinson’s disease(PD), 231–276
MixLow method, 221–228 People and Plants Initiative, 367
Modern plant biotechnology, 3, 4, 10–12 Petrodiesel, 187
Molecular switch, 84 Pharmacodynamic, 216
408 Index
Pharmacokinetic, 216 Reactive oxygen species (ROS), 31, 79, 147,

Phenolic corboxylic acids, 232 238, 239, 240, 303
Phloroglucinol derivatives, 232 Refining, 112
hyperforin, secohyperforin, 232 Refractance Window R Drying, 258, 380
Photomorphogenesis, 293, 313 Regiospecificity, 10
Photosynthetic electron transport chain Regulatory genes, 293, 296, 299, 303, 304,
(PETC), 79 316, 317
Phyllosecretion, 49 Reverse genetics, 21
Phytochemicals, 290 Rhizofiltration, 119, 122, 124, 126–131
Phytodegradation, 122, 124 Rhizosecretion, 49
Phytoextraction, 122, 127 Rhizosphere, 124, 137, 138
Phytofiltration, 127 Ribosomal and biosynthesis-related gene
Phytonutrients, 137, 290 sequence analyses, 381
Phytoremediation, 12, 119–133, 336, 340 RNA interference (RNAi), 304
Phytostabilization, 122, 129 Royal Botanic Gardens, Kew, 367, 370, 377
Phytosterols, 233 Rubisco, 70, 318
Plackett & Burman, 17
Plant biotechnology, 3–6 S
Plant Growth Promoting Rhizobacteria Sanitary and Phytosanitary Agreement of
(PGPR), 139 the World Trade Organization (SPS
case study, 145–146 Agreement), 343
direct mechanisms, 139 Seed Banks in Botanical Gardens Established
indirect mechanisms, 139 for International Seed Exchange, 377
Plant metabolic engineering, 22–23 Seed Guild, 377
Plant systematics and floristics, 365 Serial analysis of gene expression (SAGE), 20
Plant tissue culture, 370–374 Sespuiterpenes, 232
Polyethylene terephthalate (PET/PETE), 116 Sesquiterpenes, 392
Polyphenolics, 235, 244, 383 Shaman Pharmaceuticals, 379
Polyvinyl chloride (PVC), 114 Shooty teratomas, 49
Potato virus X (PVX), 48 Siderophores, production of, 141–142
PPLEX, 52 The Sierra Club, 368–369
Presscake, 250 Soaking (soyabean), 112
Priming, 146 Soybean meal, 112, 113
Proanthocyanidin polymers, 383 Soybean oil, 112–113
Proanthocyanidins, 297 application in industrial products
(protective coatings), 113
Probes, 20–21
pure and crude, 112
Protein A, 55
Standardized preparation, 355
Protein G affinity chromatography, 55
Stereospecificity, 10
Proteomics, 19, 21
Stress-inducible transcription, 31
Pyrolysis, 198
Structural genes, 293, 297, 299, 303, 309, 311,
Pyrosequencing, 204
315
Subcellular targeting, 53
Q Superoxide anion, 239
Quantitative trait loci (QTLs), 206, 292, 304, Sustainable Biopreserves for Indigenous
306 Peoples, 366
Quorum sensing (QS), 156 Synergistic, 213
effect, 311
R Systemic acquired resistance(SAR), 147
Ranching program, 384
properties as a nutraceutical and potential T
pharmaceutical, 382–385 Targeted metabolic profiling, 20
Ras (protein), 218 Targeted therapy, 214
Rate-limiting steps, 24, 25, 27–28, 70, 72 Terpenoids, 23
Index 409
Terpens: Sesquiterpenes, 232 V

Terrestrial, 373 Vacuolar Na super(+)/H super(+) antiport, 31
Tetraterpenes, 232 In vitro bioconversion, 8
Toasting and Grinding, 112 In vivo enzymatic bioconversion, 8
Tobacco mosaic virus (TMV), 48 Volatile organic compounds (VOCs), 197
Town gas, 198 Vulnerable (plant species), 364
Traditional biotechnology, 3
Trans-esterification, 188, 189
W
Transpiration, 110
Water evapo-transpiration, 110
Triterpenes, 232
Wilderness Society, 365
Wild Vaccinium species, study, 259–260
U
Wood gas, 172, 185, 194, 197–199
Ubiquitin-1 (ubi-1) promoter, 52
World Health Organization (WHO), 268, 340
The United Nations Educational, Scientific and
World Wildlife Fund (WWF), 366, 368
Cultural Organization (UNESCO), 366
Useful genes, 30 Wrigley Memorial and Botanical Gardens, 370
U.S. Food and Drug Administration (FDA),
38, 268, 274, 275, 276, 352, 353 X
Utilization of burned stands, 384 Xanthones, 232
Utilization of clear-cut stands, 384 Xanthophylls, 293, 310
UV-B light, 384 Xenobiotics, 236

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Recent Advances in Plant Biotechnology

Ara Kirakosyan · Peter B. Kaufman

Recent Advances in Plant

ISBN 978-1-4419-0193-4 e-ISBN 978-1-4419-0194-1

Library of Congress Control Number: 2009928135

c Springer Science+Business Media, LLC 2009

Printed on acid-free paper

Springer is part of Springer Science+Business Media (www.springer.com)

Ann Arbor, MI Peter B. Kaufman

Part I Plant Biotechnology from Inception to the Present

Part II Applications of Plant Biotechnology in Agriculture

9 Plants as Sources of Energy . . . . . . . . . . . . . . . . . . . . . 163

Part III Use of Plant Secondary Metabolites in Medicine

Part IV Risks and Benefits Associated with Plant Biotechnology

Ara Kirakosyan, Ph.D., D.Sc. is an associate professor of biology at Yerevan

John Boik Department of Statistics Clark, Room S.264, Stanford University,

Néstor Carrillo Instituto de Biologı́a Molecular y Celular de Rosario (IBR,

Leland J. Cseke Department of Biological Sciences, The University of Alabama

Rainer Fischer Fraunhofer Institute for Molecular Biology and

Mohammad-Reza Hajirezaei Leibniz-Institute of Plant Genetics and

Hiroaki Hayashi School of Pharmacy. Iwate Medical University. 2-1-1

Peter B. Kaufman University of Michigan, Ann Arbor MI 48109-0646, USA,

Ara Kirakosyan University of Michigan, Ann Arbor, MI 48109-0646, USA,

Ilan Levin Department of Vegetable Research, Institute of Plant Sciences, The

Carl Li Department of Social and Preventive Medicine, State University of

Ara Kirakosyan, Peter B. Kaufman, and Leland J. Cseke

Abstract In this chapter, we first define what is meant by plant biotechnology.

1.1 What Is Plant Biotechnology All About?

A. Kirakosyan, P.B. Kaufman, Recent Advances in Plant Biotechnology, 3

Besides the evaluation of some compounds as chemotaxonomic markers, one can

Reproduction Natural dyes

Plant defense Oils

Fig. 1.1 A schematic representation of plant biotechnology applications

lite biosynthesis is regulated by particular enzymes, transcription factors, substrate

1.2 Tracing the Evolution of Classical Plant Biotechnology

capable of producing a variety of pharmaceuticals, adhesives, and compounds used

Application of Functional genomics

Metabolic and Gene Engineering

1.3 Modern Plant Biotechnology

Present-day studies are progressing in several different directions. It is notewor-

Ara Kirakosyan, Leland J. Cseke, and Peter B. Kaufman

Abstract In this chapter, we bring together up-to-date information concerning

A. Kirakosyan, P.B. Kaufman, Recent Advances in Plant Biotechnology, 15

2.1 Plant Cell Factories as a Source of High-Value Metabolites

2.2 Applications Through the Use of Functional Genomics

phenotype or phytochemical database for a plant organism. This can be used to

Fig. 2.1 Application of Genomics Proteomics Transcriptomics Metabolomics

Using Omics Database for the Selection of Target Genes,

Plant Cell Biotechnology Application

biotechnology. We now may simultaneously analyze the expression or silencing

2.3 Metabolic Engineering

of several end-products. Additionally cofactors are essential for many enzymatic

2.3.1 Increasing Total Carbon Flux Through Metabolic Pathways

Branch point Increasing Desired

5 ’.-A -G-U -C-A -C-U -U -U -G-C-A -A -C-G-.3 ’

a >50,000-fold range, and the isolation of mechanistically informative prephenate

2.3.2 Introduction of an Antisense Gene of the Competing Enzyme

Metabolic engineering of a zeaxanthin-rich potato by antisense inactivation and

dry weight. As a consequence of this metabolic engineering manipulation, the