The colorful patterns that we see in maize kernels also have an important scientific significance.

Modern research has shown that the stripes and spots on maize kernels are the result of a genetic
phenomenon called Transposition.

Within the maize genome— indeed, within the genomes of most organisms—geneticists have
found DNA sequences that can move from one position to another. These transposable
elements—or, more simply, transposons—constitute an appreciable fraction of the genome.

When transposable elements move from one location to another, they may break chromosomes
or mutate genes. Thus, these elements have a profound genetic significance.
 TEs can positively and negatively impact a genome

➢ can promote gene inactivation,

➢ modulate gene expression
➢ induce illegitimate recombination.
➢ by insertion within introns, exons or regulatory regions

➢ In some cases, transposable elements have been “domesticated” by the

host to perform a specific function in the cell.
➢ RAG proteins, which participate in V(D)J recombination during antibody
class switching.
MODULE IV: Transposons
➢Transposable elements make up a substantial proportion of the total DNA in
most, if not all, eukaryotic genomes.

➢ These elements fall into two classes: the retrotransposons that transpose by a
process involving reverse transcription, and the transposons that move by an
excision-insertion mechanism.
➢ Transposase
➢ inverted terminal repeats (ITRs)
encode Gag, protease (PR), reverse transcriptase (RT), and
integrase (IN)
• encode Gag, protease (PR), reverse
transcriptase (RT), and integrase (IN)
activities critical for retrotransposition.

• The 5’ LTR contains a promoter that is

recognized by the host RNA
polymerase II and produces the mRNA
of the TE

• Gag (small pink circles) assembles into

virus like particles containing TE
mRNA, RT, and IN

• The RT copies the TE mRNA into a full-

length double stranded DNA

• IN (purple circles) inserts the DNA

into the new target site
• The transcription of non-LTR
retrotransposons (indicate arrow as in
panel b) also leads to the production
of a full-length mRNA.

• these elements mobilize by target-site

primed reverse transcription (TPRT)

• An element-encoded endonuclease
generates a single-strand “nick” in
genomic DNA, liberating a 3’OH that is
used to prime reverse transcription of
the RNA.
 Non LTR Retrotransposons - LINE
➢Originally discovered in mammalian genomes have now been detected in a wide range
of species from protozoa to fungi.
 Where Do Transposons Integrate ?

• Some TEs preferentially integrate into gene-dense regions of the genome

• others target regions such as heterochromatin, telomeres
• some appear to insert throughout the genome

• Many TEs integrate into gene rich regions although they use mechanisms that prevent
the disruption of open reading frames (ORFs). An extreme example is the E. coli Tn7 DNA
TE. Tn7 encodes a sequence specific DNA binding protein, TnsD, which mediates
integration into a specific position in the host chromosome, termed attnTn7, and
thereby avoids damaging the host genome.
Certain non-LTR retrotransposons encode endonucleases that target specific sites in
genomic DNA. For example, the R1 and R2 elements of insects encode sequence-specific
endonucleases that cleave at specific positions within the 28S rDNA locus to initiate
targetprimed reverse transcription (TPRT)
• LTR-retrotransposons also have evolved
strategies to integrate into gene rich regions,
while ensuring minimal damage to their
hosts.
• Integration of Ty3 occurs one or two bp
upstream of tRNA genes.

• This pattern requires Brf1 and TBP,

components of TFIIIB that recruit integrase
(IN, gray oval) to the target site.

• The factor Bdp1 is a component of TFIIIB

(green circles) that is required to recruit the
chromatin remodeling complex Isw2 (light
blue semi-circle).

S. cerevisiae
S. cerevisiae
The degradation of transposon mRNA by RNAi
 RETROTRANSPOSONS

In the third category, transposition is accomplished through a process that involves the insertion of copies of an element
that were synthesized from the element’s RNA.

An enzyme called reverse transcriptase uses the element’s RNA as a template to synthesize DNA molecules, which are
then inserted into new chromosomal sites.

Because this mechanism reverses the usual direction in which genetic information flows in cells—that is, it flows from
RNA to DNA instead of from DNA to RNA—geneticists refer to it as RETROTRANSPOSITION. We will refer to the elements
in
this category as RETROTRANSPOSONS.

Some of the elements that transpose in this way are related to a special group of viruses that utilize the enzyme
REVERSE TRANSCRIPTASE—the retroviruses; consequently, they are called RETROVIRUSLIKE ELEMENTS.

Other elements that engage in retrotransposition are simply called RETROPOSONS.

 RETROTRANSPOSONS

❖ RETROVIRUSLIKE ELEMENTS [also called LONG TERMINAL REPEATS (LTR)]

Example Host Organism

Ty1 ELEMENTS YEAST

COPIA ELEMENTS DROSOPHILA
GYPSY ELEMENTS DROSOPHILA

❖ RETROPOSONS

Example Host Organism

TELOMERIC RETROPOSONS DROSOPHILA

LINES HUMAN
SINES HUMAN
 Non LTR Retrotransposons

➢ target-site duplications flanking them vary in both length and sequence.

➢ integration at ‘random’ breaks in chromosomal DNA.

➢ subset of non-LTR retrotransposons that insert at specific sequences.

➢ Example (specific integration) - elements found only at specific sites within

ribosomal RNA genes of insects, and elements inserted within the mini-exon
genes of some trypanosomes.

➢ R2Bm element that inserts within the 28S rRNA genes of Bombyx mori.
Non LTR Retrotransposons - LINE
Mode of Transposition of DNA Transposons
Although each kind of transposable element has its own special characteristics, most can be classified
into one of three categories based on the mechanism of transposition.

CUT AND PASTE TRANSPOSONS

In the first category, transposition is accomplished by excising an element from its position in a
chromosome and inserting it into another position.

The excision and insertion events are catalyzed by an enzyme called the TRANSPOSASE, which is
usually encoded by the element itself.

Geneticists refer to this mechanism as cut-and-paste transposition because the element is physically
cut out of one site in a chromosome and pasted into a new site, which may even be on a different
chromosome.

Example Host Organism

IS ELEMENTS Bacteria

COMPOSITE TRANSPOSONS (Tn5) Bacteria

Ac/Ds ELEMENTS Maize

P ELEMENTS Drosophila
 REPLICATIVE TRANSPOSON

In the second category, transposition is accomplished through a process that involves replication of the transposable
element’s DNA. A transposase encoded by the element mediates an interaction between the element and a potential
insertion site.

During this interaction, the element is replicated, and one copy of it is inserted at the new site; one copy also remains at
the original site. Because there is a net gain of one copy of the element, geneticists refer to this mechanism as
REPLICATIVE TRANSPOSITION.

Example Host Organism

Tn3 ELEMENTS Bacteria

Cut and Paste Model for Replicative Transposition
 Transposase

➢ Transposases or transposition proteins bind to the ends of a transposon

and catalyze its movement to another part of the genome by a cut-and-paste
mechanism.

➢ Mu transposase (MuA) is essential for integration, replication-transposition

and excision of bacteriophage Mu DNA into multiple sites of bacterial genome.
➢ Hermes transposase is a fly protein.

➢ Dra2 transposase is a Deinococcus radiodurans protein

➢ Tn5 transposase active site contains the DDE motif which catalyzes the
movement of the transposon.
Shapiro Model for Replicative Transposition
 Transposable Elements in Bacteria

Bacterial transposons move within and between chromosomes and plasmids

Although transposable elements were originally discovered in eukaryotes, bacterial transposons were the first to be
studied at the molecular level.

There are three main types:

❖ Insertion sequences, (IS elements)

❖ Composite transposons (Tn5 Elements)

❖ Tn3-like elements.

These three types of transposons differ in size and structure.

The IS elements are the simplest, containing only genes that encode proteins involved in transposition.

The Composite transposons and Tn3-like elements are more complex containing some genes that encode products
unrelated to the transposition process.
 IS ELEMENTS

The simplest bacterial transposons are the insertion sequences, or IS elements, so named because they can insert at
many different sites in bacterial chromosomes and plasmids.

IS elements were first detected in certain lac mutations of E. coli. These mutations had the unusual property of
reverting to wild-type at a high rate.

Molecular analyses revealed that these unstable mutations possessed extra DNA in or near the lac genes.

When DNA from the wild-type revertants of these mutations was compared with that from the mutations themselves,
it was found that the extra DNA had been lost.

Thus, these genetically unstable mutations were caused by DNA sequences that had inserted into E. coli genes, and
reversion to wild-type was caused by excision of these sequences.

Similar insertion sequences have been found in many other bacterial species.
Transposons - Examples
 ORGANIZATION OF IS ELEMENTS

IS elements are compactly organized.

Typically, they consist of fewer than 2500 nucleotide pairs and contain only genes whose products are involved in
promoting or regulating transposition.

Each type of IS element is demarcated by short identical, or nearly identical, sequences at its ends.

Because these terminal sequences are always in inverted orientation with respect to each other, they are called
TERMINAL INVERTED REPEATS. Their lengths range from 9 to 40 nucleotide pairs.

When nucleotides in these repeats are mutated, the transposon usually loses its ability to move. These mutations
therefore demonstrate that terminal inverted repeats play an important role in the transposition process.
IS elements usually encode an enzyme, the transposase, that is required for transposition.

Transposase binds at or near the ends of the element and then cuts both strands of the DNA.

This cleavage excises the element from the chromosome or plasmid, so that it can be inserted at a new position in
the same or a different DNA molecule.

IS elements are therefore cut-and-paste transposons.

When IS elements insert into chromosomes or plasmids, they create a duplication of part of the DNA sequence at
the site of the insertion.

One copy of the duplication is located on each side of the element.

These short (2 to 13 nucleotide pairs), directly repeated sequences, called TARGET SITE DUPLICATIONS, arise from
staggered cleavage of the double-stranded DNA molecule.
Production of target site duplications by the insertion of an IS element.
Transposons in Maize
The Ac - Ds system in maize (Zea): genetic analysis of
"jumping genes"
 P ELEMENTS AND HYBRID DYSGENESIS IN DROSOPHILA

Some of the most extensive research on transposable elements has focused on the P elements of
Drosophila melanogaster.

Crosses between certain strains of Drosophila produce hybrids with an assortment of aberrant traits, including
frequent mutation, chromosome breakage, and sterility.

The term hybrid dysgenesis, derived from Greek roots meaning “a deterioration in quality,” was used to denote this
syndrome of abnormalities.

Drosophila strains were classified into two main types based on whether or not they produce dysgenic hybrids in
testcrosses. The two types of strains are denoted as M and P.

Only crosses between M and P strains can produce dysgenic hybrids, and they do so only if the male in the cross is
from the P strain.

Crosses between two different P strains, or between two different M strains, produce hybrids that are normal.
DNA sequence analysis has shown that P elements vary in size.

The largest P elements are 2907 nucleotide pairs long, including terminal inverted repeats of 31 nucleotide pairs.

These complete P elements carry a gene that encodes a transposase.

When the transposase cleaves DNA near the ends of a complete P element, it can move that element to a new
location in the genome.

Incomplete P elements lack the ability to produce the transposase because some of their internal sequences are
deleted; however, they do possess the terminal inverted repeat sequences recognized by the transposase.

Consequently, Incomplete P elements can be mobilized if a complete P element is present somewhere in the genome.
 HYBRID DYSGENESIS IS STRICTLY A GERM LINE PHENOMENON

In dysgenic hybrids, P elements transpose only in the germ line cells.

Somatic cells are unable to remove one of the introns from the P element’s pre-mRNA (Alternative Splicing)

When these wrongly spliced mRNAs are translated, it produces a non-functional transposase, unable to catalyze the
movement of P elements.

As a result, P elements are inactive in somatic cells.

In germ line cells, pre-mRNAs produced from the P elements are properly spliced to produce active Transposase.
 We can summarize the phenotypes of the hybrid offspring from these different crosses in a simple table:

The parents of the different strains therefore contribute maternally or paternally to the formation of dysgenic hybrids—
hence, their designations as M and P.
 Generation of Hfr strains

A bacterial chromosome may contain several copies of a particular type of IS element. For example,
6 to 10 copies of IS1 are found in the E. coli chromosome.

Plasmids may also contain IS elements. The F plasmid, for example, typically has at least two different IS
elements, IS2 and IS3.

When a particular IS element resides in two different DNA molecules, it creates the opportunity for
HOMOLOGOUS RECOMBINATION between them.

For instance, an IS element in the F plasmid may pair and recombine with the same kind of IS element in the
E. coli chromosome.

Both the E. coli chromosome and the F plasmid are circular DNA molecules. When an IS element mediates
recombination between these molecules, the smaller plasmid is integrated into the larger chromosome,
creating a single circular molecule.

Such integration events produce Hfr strains capable of transferring their chromosomes during conjugation.