Classification of prokaryotic cellular features:

Classification of prokaryotic cellular features:
Variant (or NOT common to all) -Cell wall (chemistry varies; some don’t have one) -Endospores (heavy-duty life support strategy) -Bacterial Flagella (appendages for movement) -Pili (genetic exchange) -Fimbriae (surface attachment) -Inclusion Bodies (granules for storage) -Gas vesicles (movement)

Formation of the endospore

Endospores are a highly resistant differentiated bacterial cell produced by certain gram-positive Bacteria. -mostly soil bacteria of phyum Firmiculites (evolved just once) -most common in Clostridium, Bacillus -agents of survival -metabolically inert, highly dehydrated (10-15% water) -most resistant biological structure known: heat, dryness -can survive 100’s (perhaps 1000’s) of years Exospores are formed by pinching off of tips of filamentous bacteria (and of fungi) -Streptomyces, Myxobacteria -agents of dispersal

Endospore cycle BAD conditions Loss of flagella Endospore forms
Cell disintegrates Vegetative cell GOOD conditions Forms a new rod Spore germinates Bad conditions: dense population, dwindling nutrients Good conditions: nutrients are sensed

Sporulation

Spore-specific proteins
Bacillus megaterium Spore-specific proteins Loose peptidoglycan Thin protein coating Bacillus subtilis Surrounds spore protoplast Cytoplasm is dehydrated and gel-like: Resistant to heat and free radicals in this form.

 

(a) Structure of Dipicolinic Acid
(b) Crosslinked with Ca++ Figure: 04-61a-b Caption: Dipicolinic acid (DPA). (a) Structure of DPA. (b) How CO2 + cross-links DPA molecules to form a complex. -Reduces water availability -Complexes with DNA and stabilizes against heat denaturation

Morpology of the bacterial endospore:
(a) Terminal (b) Subterminal (c) Central

Botulism Pathogen: Clostridium botulinum Signs/Symptoms:
Food-borne: abdominal pain, dry mouth, nausea, dysphagia, vomiting, diarrhea, dyspnea, ptosis, descending paralysis Infant: lethargic, weak cry, don’t eat, floppy baby syndrome, constipation. Typically <6mo. Most common form in US. SIDS connection? Wound: similar to foodborne. Longer incubation Virulence factor: Botulism toxins A-G: neurotoxins Acid stable, heat labile (80C, 20min) 30g of toxin would kill entire population of US! Pathogenesis: Gram (+), anaerobic, central endospore Growth in intestinal tract of infants -> toxemia 1-4d incubation period (food-wound) Transmission: Infected foods: canned foods (pH>4.5), honey (infants) Very low dose (licking a spoon! ->death) Botulism Wound botulism Food-borne botulism

Tetanus Pathogen: Clostridium tetani Signs/Symptoms:
Stiff neck and jaw muscles, drooling, sweating, back spasms, anger, irregular heartbeat, fluctuating blood pressure. Incubation 3d-15w Differential: TMJ, Meningitis Virulence factor: Tetanospasmin: neurotoxin. Released on cell death Prevents GABA and lysine release (inhibitory neurotransmitters) in spinal cord - non reversible Pathogenesis: Gram (+), anaerobic, terminal endospore Toxemia Transmission: Wound contamination. Splinters, nails, cuts, drug use Endospores in soil and animal feces 1M cases/year 50% mortality untreated Diagnosis and treatment: Metronidazole (Penicillin may increase contractions) Antitoxin intrathecally (into CNS), wound debridement Vaccination: tetanus toxoid. Boost every 10yr Tetanus

Variant (or NOT common to all) -Cell wall (chemistry varies; some don’t have one) -Endospores (heavy-duty life support strategy) -Capsules/Slime Layer (exterior to cell wall) -Bacterial Flagella (appendages for movement) -Pili (genetic exchange) -Fimbriae (surface attachment) -Inclusion Bodies (granules for storage) -Gas vesicles (vertical movement in liquid medium)

Prokaryotes may contain cell surface layers composed of any of these:
-a two-dimensional array of protein called an S-layer -polysaccharide capsules -a more diffuse polysaccharide matrix (slime layer). glycocalyx

Glycocalyx S. pneumonia Bacteroides Sugar & protein coating
Tight - capsule Loose - slime layer Sticky Immune evasion

(a) Acinetobacter sp. (b) Rhizobium trifolii
Bacterial Capsules: (a) Acinetobacter sp. (b) Rhizobium trifolii A B negative stain

Capsule/EPS as virulence factor
Bacterial exudate is a common diagnostic sign of a plant pathogenic bacterium Exudate is polysaccharide mixture Like Ralstonia wilt of many plants, or Stewart’s wilt of corn caused by P. stewartii.

Flagellar Motility  Motility in most microorganisms is due to flagella.  In prokaryotes the flagellum is a complex structure made of several proteins, most of which are anchored in the cell wall and cytoplasmic membrane. The flagellum filament is: -made of a single kind of protein (flagellin) -rotates at the expense of the proton motive force (which drives the flagellar motor).

Flagella Monotrichous Peritrichous Lophotrichous Amphitrichous

Flagellar Motility: Relationship of flagellar rotation
to bacterial movement. Chemotaxis and phototaxis che genes mediate chemotaxis ccw rotation moves forward cw rotation tumbles

Flagellar Motility: Relationship of flagellar rotation
to bacterial movement. (both)

Flagella Complex structure Immunogenic
(flagellin recognized by mammalian immune system) Rotates to swim G- have two extra rings (bushings) to anchor and allow rotation in peptidoglycan and OM)

Structure of the bacterial flagellum ~20 different proteins MotA and MotB = motor FliG, FliM, FliN form “switch”, control direction Flagellin = filament

Proton Transport-Coupled Rotation of the Flagellum
MotA and MotB proteins surround MS/C ring, and may form a structure having two half-channels. One model for the mechanism of coupling rotation to a proton gradient requires protons to be taken up into the outer half-channel and transferred to the MS ring. The MS ring rotates in a CCW direction, and the protons are released into the inner half-channel. The flagellum is linked to the MS ring and so the flagellum rotates as well.

Chemotaxis Signaling Pathway
Chemotaxis Signaling Pathway. Receptors in the plasma membrane initiate a signaling pathway leading to the phosphorylation of the CheY protein. Phosphorylated CheY binds to the flagellar motor and favors CW rotation. When an attractant binds to the receptor, this pathway is blocked, and CCW flagellar rotation and, hence, smooth swimming results. When a repellant binds, the pathway is stimulated, leading to an increased concentration of phosphoylated CheY and, hence, more frequent CW rotation and tumbling.

Flagellar Motility: Take Home Message
 Motility in most microorganisms is due to flagella.  In prokaryotes the flagellum is a complex structure made of several proteins, most of which are anchored in the cell wall and cytoplasmic membrane.  The flagellum filament, which is made of a single kind of protein, rotates at the expense of the proton motive force, which drives the flagellar motor.

Type IV pilus (sex pilus)
“Sex” pilus used in bacterial conjugation of E. coli cells: F pilus adheres to receptors on recipient cell surface; then retraction of pilus via pilin subunit depolymerization brings cells closer till contact and DNA transfer (not through pilus).

Conjugation Conjugal transfer occurs from ‘male’ to ‘female’ Spreads plasmids and antibiotic resistance Agrobacterium: DNA to eukaryotic cells… others can too!

The Type IV pilus of Agrobacterium tumefaciens is a DNA conduit for this natural genetic engineer
Ubiquitous gram-negative, soil-dwelling bacterium Plant pathogen, causes crown gall disease Very broad host range (dicots) Only plant pathogen known to utilize a Type IV secretion system I know you are all familiar with Agrobacterium tumefaciens, the bacterial pathogen that causes crown gall tumors by transfering its DNA into plant cells, so I will just briefly remind you of some of the more interesting things about its biology. First of all, this soilborne phytopathogen has a very broad host range which can be extendened even further under laboratory conditions. In nature, it is attracted to plant wounds, where the plant exudates activate it to form a pilus structure that transfers DNA into plant cells. This pilus is not like the one found in most bacterial pathogens, that is, the hrp pilus or Type III secretion system. Agrobacterium’s pilus is more closely related to pili used to transfer plasmids between bacterial cells during conjugation.

How does Agrobacterium
initiate infection?

Agrobacterium Plant Cell LB RB Ti plasmid 4. Transport 3. T-DNA
processing LB RB 7. Phytohormone and opine synthesis V virD2 i D 2 virE2 virE2 virD2 virE2 virD2 V i D 2 5. Nuclear targeting T-STRAND T-DNA vir genes VirB/VirD4 Ti plasmid tra nucleus This is a cartoon depicting the mechanics of DNA transfer between the bacterium and the plant. Wounds allow the release of plant exudates that act as chemoattractants for Agrobacterium. These include specific monosaccharides and phenolic molecules. Higher concentrations of these molecules (closer to wound) halt chemotaxis, and activate a signal transduction system that results in expression of virulence, or vir, genes on the Ti plasmid. These genes code for many proteins that work together to cause DNA from the pathogen to be carried into the host plant, where it genetically engineers the plant and is expressed. For example, DNA processing enzymes nick and release single stranded DNA from between two short repeats known as border sequences. The resultant ssDNA, or T-DNA, is presumably chauffered by the VirD2 protein to the translocation apparatus. The translocation apparatus, known as the virB pilus, has been elaborated by the virB and virD4 gene products. The TDNA, D2, and other proteins are also transported through or along the virB pilus into the host cell. Once across, the TDNA is targeted to the nucleus, where it is integrated into the plant genome. Genes that are transferred have their own eukaryotic promoters, and include those for IAA and cytokinin biosynthesis, as well as for opines, amino acid derivatives that Agrobacterium can metabolize. Gall formation ensues, and the engineered plant cells produce food for Agrobacterium. occ VirG 6. Integration and expression VirG P VirA Phenolics sugars, acid 2. vir expression 1. Induction

The Type IV pilus of Agrobacterium tumefaciens
Agrobacterium tumefaciens attached to a plant cell. Image by Martha Hawes Agrobacterium tumefaciens Type IV pilus structure. Li et al., Trends in Microbiology

Type III secretion pilus and effectors
Effector proteins injected via needle complex directly into host cytoplasm Delivery of “effectors”: Contribute to pathogen spread in susceptible hosts Induce resistance response in non-hosts Besides toxins, bacteria may be secreting other molecules to aid in its attack. One example is protein effectors, secreted by what is called a Type III secretion system. These protein effectors travel through a specialized channel, directly from the cytoplasm of the bacterial cell to the cytoplasm of the host cell. Thus, the bacterial secretory apparatus that secretes these must cross both bacterial and plant cell membranes. Here are some micrographs. Now, it turns out that this secretion apparatus is very important in determining hosts and non-host plants for bacteria in the genera Pseudomonas, Xanthomonas, Erwinia, and Ralstonia. The proteins secreted by this system cause two very different responses. In host plants, the plant cells seem to be oblivious to the presence of the bacteria, and allow them to multiply and eventually cause disease symptoms. On nonhosts, cells at the site of infection quickly die, in a response called the Hypersensitive response. In HR, reaction is fast, localized (within ½ cm of infection site) but in normal plant immune response it’s slower, nonlocalized. Since the proteins are involved in both the hypersensitive response and in pathogenicity, they and their pilus are called HrP pilus and hrp effectors, or harpins.

Schematic representation of the flagellum (a), Ysc injectisome (b), injectisome from EPECs (c) and the injectisome from plant pathogens (d). Cornelis Nature Reviews Microbiology 4, 811–825 (November 2006) | doi: /nrmicro1526

Salmonella, Shigella, Yersinia, etc.
Plant and mammalian pathogens share this mechanism of injecting host cells with bacterial proteins: Salmonella, Shigella, Yersinia, etc. Cornelis Nature Reviews Microbiology 4, 811–825 (November 2006) | doi: /nrmicro1526

a Transmission electron micrograph of Yersinia enterocolitica E40
a Transmission electron micrograph of Yersinia enterocolitica E40. One needle (arrow) protrudes from the cell surface. b 3D structure of the needle complex encoded by Shigella flexneri (top) and by Salmonella enterica serovar Typhimurium (bottom), reconstructed by averaging cryo-electron micrograph images. Cornelis Nature Reviews Microbiology 4, 811–825 (November 2006) | doi: /nrmicro1526

Fimbriae E. coli Fimbriae help cells stick; have adhesin proteins in the protein fibrils. Some minor adhesins at tip of fimbriae recognize and bind host cell receptors. Uropathogenic E. coli use fimbriae to adhere to urinary tract Hold ‘tighter’ in high flow, release and swim in low flow Neisseria gonorrhoeae binds oligosaccharides in receptors of urogenital tract Critical pathogenicity factor: adhesins = hemagglutinin, causes erythrocytes to clump

Biofilms Capsule and fimbria promote adherence Bacterial communities Chemical communication alters lifestyle Protect against antimicrobial agents Colonization of medical equipment Important in human infections Cystic fibrosis and dental plaque

Variant (or NOT common to all) -Cell wall (chemistry varies; some don’t have one) -Endospores (heavy-duty life support strategy) -Capsules/Slime Layer (exterior to cell wall) -Bacterial Flagella (appendages for movement) -Pili (conduit for genetic exchange) -Inclusion Bodies (granules for storage) -Gas vesicles (vertical movement in liquid medium)

Storage of PHB (or other carbon polymers like glycogen; energy reserve like Gü or battery)

Elemental sulfur globules inside the purple sulfur
bacterium Isochromatium buderi: oxidation of H2S

Magnetotactic bacteria with Fe3O4 (magnetite) particles called magnetosomes – function unknown

Variant (or NOT common to all) -Cell wall (chemistry varies; some don’t have one) -Endospores (heavy-duty life support strategy) -Capsules/Slime Layer (exterior to cell wall) -Bacterial Flagella (appendages for movement) -Pili (conduit for genetic exchange) -Inclusion Bodies (granules for storage) -Gas vesicles (vertical movement in liquid medium)

Gas Vesicles: Cyanobacteria, photosynthetic bacteria, some non-photosynthetic bacteria Stratified lakes where light, temperature, nutrients vary; less common in isothermally mixed waters (a) Anabaena flos-aquae (b) Microcystis sp. A B

Model of how the two proteins that make up the
gas vesicle, GvpA and GvpC, interact to form a watertight but gas-permeable structure (GoreTex). β-sheet α-helix

Microbial Diversity and Classification

Evolution is the change in a line of descent (e. g
Evolution is the change in a line of descent (e.g. heritable change) over time leading to new species or varieties. The evolutionary relationships between life forms are the subject of the science of phylogeny. Woese tree suggests that all life forms we share the Earth with have been evolving for the same amount of time from a common universal ancestor… there are no more “ancient” life forms than others, although some appear to have changed at a more rapid rate over the eons.

Carl Woese: Demonstrated that differences in rRNA sequences usefully reflect evolutionary relationships. Used to show 3 domains of life. Brought taxonomy to prokaryotes.

Why rRNA? “Molecular chronometer” universally distributed functionally homologous sequence conservation so DNA can be aligned sequence change should reflect evolutionary change in organism as a whole rRNA, ATPase, RecA, DNA polymerase, etc.

Comparative ribosomal RNA sequencing has defined the three domains of life: Bacteria, Archaea, and Eukarya. Multicellularity evolved in only a small percentage of life on Earth

Although species of Bacteria and Archaea share a prokaryotic cell structure, they differ dramatically in their evolutionary history.

Molecular sequencing has also shown that the major organelles of Eukarya have evolutionary roots in the Bacteria mitochondria chloroplast Diplomonads: nucleus, but no mitochondria

Spirulina (a cyanobacterium)
Culturing Spirulina

Acquisition of genomes and compartments during evolution:
Endosymbiosis Raven et al. Genome Biology :209

Microbial Diversity Several lineages are present in the domains Bacteria and Archaea, and an enormous diversity of cell morphologies and physiologies are represented there.

Prokaryotes represent a huge metabolic and ecological diversity (reservoir of possibilities for life on Earth?)

Get CO2 from organic molecules
ENERGY CARBON Fix CO2 for carbon (autotrophy) Get CO2 from organic molecules (heterotrophy)

All cells need carbon and energy sources.
Chemoorganotrophs obtain their energy from the oxidation of organic compounds. Chemolithotrophs obtain their energy from the oxidation of inorganic compounds. Phototrophs contain pigments that allow them to use light as an energy source.

Much diversity: Extremophiles thrive under environmental conditions in which eukaryotic organisms cannot survive.

1990: Retrieval and analysis of ribosomal RNA genes from cells in natural samples have shown that many phylogenetically distinct but as yet uncultured prokaryotes exist in nature. Filter a lot of seawater Extract DNA PCR with rRNA primers Sequence PCR product

Today: Retrieval and analysis of genomes from cells in natural samples have shown that many phylogenetically distinct but as yet uncultured prokaryotes exist in nature. J. Craig Venter sails around the world in Sorcerer II, 100 ft sailboat

In a barrel (~20 L) of seawater in the nutrient-poor Sargasso Sea, Venter found ,000 new species (depending on how one defines a species)! 1 mL seawater contains 1,000,000 bacteria 1 mL seawater contains 10,000,000 viruses < 1% have been characterized (Most don’t grow in the lab)

“genome of the Earth”?

Archaea in particular represent a huge diversity. Four phyla…
From hot springs and Antarctic waters Methanogens, halophiles 1 community: all from Yellowstone 1 species; parasite of another archeon

Respiration & fermentation
Are Archaea more like Bacteria or Eukarya? Bacteria Archaea Eukaryotes Archaea resemble Bacteria Cell volume 1 to 100 μm3 (usually) 1 to 106 μm3 DNA chromosome Circular (usually) Linear Gene organization operons; few introns Many introns Metabolism Denitrification, N2 fixation, lithotrophy, respiration and fermentation Respiration & fermentation Nuclear membrane None Multicellularity Simple Complex Ribosome size ~70s ~80s

Are Archaea more like Bacteria or Eukarya?
Bacteria Archaea Eukaryotes Archaea resemble Eukaryotes Cell wall Peptidoglycan (nearly always) No PG in most species (Methanogens have pseudopeptidoglycan) Ribosome sensitivity to Cm, Kn, and Sr Sensitive Resistant Ribosomes sensitive to Diptheria toxin Translation initiator Formyl-Met Methionine (except mitochondrial F-Met) RNA polymerase Bacterial 4 subunit Eukaryotic 8+ subunits Transcription factors Bind ribosome

Are Archaea more like Bacteria or Eukarya?
Bacteria Archaea Eukaryotes Archaea Differ from Bacteria and Eukaryotes Methanogenesis No Yes Thermophilic growth > 80ºC > 100ºC > 60ºC Photosynthesis Many species. bacterio-chlorophyll Halobacteria only; bacterio-rhodopsin Many species; bacterial chlorophyll Chlorophyll light absorption Red and blue Green Membrane lipids (major) Ester-linked fatty acids Ether-linked isoprenoids Pathogens that infect animals or plants Many pathogens No pathogens

Archaeal cell membranes
Some (but not all) hyperthermophilic Archaea also have monolayers of lipids as membranes. More stable at high temperatures. Bacteria and Eukarya only have lipid bilayer membranes. Bacteria and eukaryotes use fatty acid side chains in membrane lipids. Archaeal membrane lipids are derived from isoprene (5-carbon molecule that is also precursor to natural rubber). More stable at high temperatures. Isoprene = chemical fossil; residues persist (stable…) in sediments that are the oldest known on Earth (3.8 billion years old).

How do we classify all these diverse life forms?
We know < 1% of prokaryotes. Estimates of actual prokaryotic species: 100,000 to 10,000,000

Classification/Nomenclature
Classifying prokaryotes: Appearance (size, shape, staining characteristics) Metabolic capabilities (ability to break down various compounds) Other easy-to-observe characteristics (flourescence, pathogenicity) DNA sequences Ribosomal RNA genes

Classification/Nomenclature
Domain - a collection of similar kingdoms Kingdom - a collection of similar phyla or classes Phylum/division - a collection of similar classes Class - a collection of similar orders Order - a collection of similar families Family - a collection of similar genera Genus - a collection of related species Species - a group of related isolates or strains Escherichia coli (E. coli) E. coli K12 - a specific strain often used in laboratory research E. coli O157:H7 - a group of strains able to cause a severe diarrheal disease

Other techniques to use rRNA, other sequences, or PHENOTYPES in taxonomy
-GC Ratios -DNA:DNA hybridization -Ribotyping -Multilocus sequence typing -Fatty Acid Analysis (FAME)

Ranges of DNA base composition

Hyperchromic Effect of DNA
In ds DNA, absorption is less than in ss DNA due to base-stacking interactions. When DNA is denatured, these interactions are disrupted and an increase in absorbance is seen. This change is called the hyperchromic effect.

Dissimilar Tm = dissimilar GC/sequence and
G+C Ratios: Dissimilar Tm = dissimilar GC/sequence and similar Tm = similar GC, but similar GC ≠ sequence identity

DNA:DNA hybridization
(Excess) MIX!

Hydroxyapatite binds ds DNA. Only 75% radioactive signal (ssDNA) flows thru hydroxyapatite column in mixed sample: 25% of Genome 1 is complementary to Genome 2

70% or greater; considered same species… What does that really mean in a haploid organism?

Ribotyping, a.k.a. Molecular Fingerprinting:
PCR to amplify rRNA Digest with 1 or more restriction enzymes: polymorphisms in sequence = different cut patterns 3. Gel electrophoresis 4. Probe to “light up” sequences of interest 5. Analyze pattern

Multi-locus sequence typing:

FAME analysis

FAME analysis: can differentiate closely related prokaryotes,
but not so useful for distantly related organisms

Taxonomy Summary Classical physiological descriptions of microbes (%GC, FAME, morphology, metabolism) constitute a taxonomy (is A like B?), but do not describe evolutionary relationships (is A related to B?). Methods such as ribotyping, MLST, and DNA-DNA hybridization establish relationships, but only if organisms are closely related. Not applicable on broad evolutionary landscapes. All these methods require pure cultivation of organisms for characterization, but we can't cultivate much of what is out there.

Less than

Importance of a Molecular Biological Approach
Traditional culturing techniques isolate ~1% of the total bacteria in marine ecosystems, thereby severely underestimating diversity and community structure. Because nutrient-rich culture media have been historically used during enrichment procedures, bacteria which may be dominant in natural communities are selected against in favor of copiotrophic (weedy) bacteria. Ribosomal RNAs (rRNAs) and its respective genes (DNA) are excellent descriptors of microbial taxa based on phylogeny.

How do we classify all these diverse life forms
How do we classify all these diverse life forms? Prokaryotic ribosomes and rRNA rRNA in the small subunit is called 16S rRNA. It’s responsible for codon-anticodon recognition, translocation, and binding to the mRNA transcript (Shine-Delgarno sequence). SSU (30S) Large subunit contains 23S rRNA and its tiny 5S rRNA partner, totaling ~3000 nucleotides We now know that rRNA in the large subunit is a ribozyme (performs the peptidyltransferase reaction in protein synthesis). This is such an ancient reaction that something like it must’ve initiated protein synthesis in the progenitor of life! LSU (50S)

A side note about rRNA: lots of antibiotics target this entity
A side note about rRNA: lots of antibiotics target this entity. Very ancient microbial warfare?

16S rRNA in 2-D

16S rRNA in 3-D Pink: 16S rRNA. Lots of tertiary structure.
Blue: protein

Regarding Molecular Phylogeny
The Root of the Problem: Unlike zoology and botany, microbiology developed without the knowledge of phylogenetic relationships among the organisms studied. Milestone #1: Zuckerkandl and Pauling (1965): Molecules as documents of evolutionary history. Milestone #2: Pace (1986): Applied rRNA concept to microbial ecology's need to take a census (“see” without culturing). Milestone #3: Woese (1987): Applied rRNA concept to redefine microbial systematics or the need to understand microbial genealogy.

Why ribosomal RNAs? Found among all living organisms (for 3.8 of the last 4.5 billion years). Integral part of protein synthesis machinery. Cell component analyses provide culture-independent means of investigating questions in microbial ecology (lack of morphology). rRNAs offer a type of sequence information that makes them excellent descriptors of an organism's evolutionary history. No detectable horizontal gene transfer, especially important for the prokaryotes. Large and growing database; RDP contains ~100K SSU rRNAs.

rRNA for classifying diverse life forms
Phylogenetic trees based on ribosomal RNA have now been prepared for all the major prokaryotic and eukaryotic groups. -called SSU (small subunit) RNA sequencing or 16S or 18S sequencing. Differences in nucleotide or amino acid sequence of functionally similar (homologous) macromolecules are a function of their evolutionary distance. Can’t accumulate many mutations in such an important macromolecule… so, evolutionary distance between rRNAs reflects evolutionary distance betweent organisms. A huge database of rRNA sequences exists. For example, the Ribosomal Database Project (RDP) contains a large collection of such sequences, now numbering over 100,000.

What is a microbial “species”?
Eukaryotic species = interbreeding populations. Microbes are asexual. > 70% DNA hybridization > 97% rRNA sequence identity

How do new species arise?
Major components of evolution: Vertical inheritance (traits passed from parents to offspring) Descent with modification (traits passed on imperfectly: mutation, recombination) Natural selection (selects among variants) A (progenitor) A A A B

How do we reconstruct evolutionary relationships?
Observe Biological records Fossils Geology (geochemistry) Infer from data of current organisms (chemistry, gene sequence, protein sequence) A (progenitor) A A A B

How do we infer evolutionary relationships?
-Key word is inference (not always correct!) -none of the organisms in the “Tree of Life” are ancient; they are all modern organisms. -Some may have characteristics of ancient organisms

What did the first cell look like? We don’t know…
Planet Earth is approximately 4.6 billion years old. The first evidence for microbial life can be found in rocks about 3.86 billion years old. These are geochemical/ fossil records. We can’t include them in our rRNA trees.

Estimating evolutionary
distance ED to map on phylogenetic tree Parsimony: what you see is what you get Figure: 11-10a-c Caption: Preparing a phylogenetic distance tree from 16S ribosomal RNA sequences. For illustrative purposes, only short sequences are shown. The evolutionary distance (ED) in (b) is calculated as the percentage of nonidentical sequences between the RNAs of any two organisms. The corrected ED is a statistical correction necessary to account for either back mutations to the original genotype or additional forward mutations at the same site that could have occurred. The tree (c) is ultimately generated by computer analysis of the data to give the best fit. The total length of the branches separating any two organisms is proportional to the calculated evolutionary distance between them. In actual analyses a statistical process called bootstrapping is typically used whereby the computer generates hundreds of versions of the tree to confirm that the final tree is indeed the best fit to the data set. In addition, insertions of several nucleotides may separate regions of sequence homology in two organisms’ rRNA, and these insertions are “masked” (not considered) in the actual analyses.

Signature sequences can be obtained at any
level of taxonomic hierarchy…

Fluorescent in situ hybridization (FISH)

Take Home Message Phylogenies may be right or wrong; we try to infer it the best we can. Phylogeny allows us to ask testable questions, e.g., hypothesis testing. - microbial ecology relationships can now be truly examined - relationships between microbes can be studies -relationships among microbial genes can be studied -can infer dynamics of sequence change (Rolex vs Timex)

Single origin for all life on Earth... ● Central Dogma intact.
Some Lessons from the BIG TREE: Map of the Biological Record Single origin for all life on Earth... ● Central Dogma intact. ● ATP and PMF are universal themes. General topology implies: ● Three “primary lines of evolutionary descent.” ● The Eukarya “nuclear” lineage almost as old as other two. ● Prokaryotes split between Bacteria and Archaea. ● Tree represents only a limited number of organisms. ● Mitochondria and chloroplasts proven to be of bacterial origin.

Classification of prokaryotic cellular features:

Similar presentations

Presentation on theme: "Classification of prokaryotic cellular features:"— Presentation transcript:

Similar presentations

About project

Feedback

Log in

Auth with social network:

Classification of prokaryotic cellular features:

Similar presentations

Presentation on theme: "Classification of prokaryotic cellular features:"— Presentation transcript:

Similar presentations

About project

Feedback