UNIT -4

Transposable elements
Prokaryotic transposable elements – Insertion Sequences, composite and non-composite
transposons, Replicative and Non replicative transposition, Mu transposon Eukaryotic
transposable elements - Yeast (Ty retrotransposon), Drosophila (P elements), Maize Ac/Ds)
Uses of transposons and transposition.
Transposable elements definition
Transposable elements (TE) or transposons can be defined as small, mobile DNA sequences
that move around chromosomes with no regard for homology, and insertion of these
elements may produce deletions, inversions, chromosomal fusions, and even more
complicated rearrangements.
● Transposons are mobile genetic elements that often carry an antimicrobial resistance
gene.
● These elements can insert randomly, move from plasmids to the chromosome, and vice
versa, and can be moved from one bacterium to another by conjugation,
transformation, or transduction.
● Transposable elements make up a significant fraction of the genome and are
responsible for much of the mass of DNA in a eukaryotic cell.
● Transposable elements were discovered by Barbara McClintock (1965) through an
analysis of genetic instability in maize (corn).

Characteristics of Transposable Elements

What are Transposable Elements?
Transposable elements are DNA sequences that contain the instructions for enzymes that
allow them to copy themselves and move to a new location in the DNA.
● Transposition: Transposons are involved in transposition, a process where they move
around in the DNA. This movement can involve recombination (exchange of genetic
material) and replication (copying). This usually results in two copies of the
transposable element: one stays at the original site, and the other moves to a new
target site.
● Gene Disruption: When transposons insert into genes, they can disrupt the normal
function of those genes. This is because the transposons interrupt the gene’s
sequence.
● Gene Activation: Transposons can also activate dormant genes. Some transposons
contain sequences that start the process of RNA synthesis, which can "wake up"
previously inactive genes.
● No Origin of Replication: Transposons don’t have their own origin of replication (the
site where DNA replication starts). This means they can’t replicate on their own like
plasmids or viruses; they rely on the host DNA to replicate.
● No Homology: Transposons don’t require any specific sequence to insert themselves
into the host DNA. They can insert randomly into almost any part of the host
chromosome or plasmid. While some transposons have preferred spots (called "hot
spots"), they don’t always insert in those areas.
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Types of Transposable Elements
Transposable elements come in two main types:
. Insertion Sequences (IS) or Simple Transposons
○ These are short DNA sequences (around 800 to 1500 base pairs long).
○ They don’t code for proteins, but they do contain the genetic information
needed for their own movement.
○ IS elements contain a gene for an enzyme called transposase, which is needed
for the transposition process.
○ These elements have been found in bacteriophages, plasmids (like the F
factor), and in many bacteria.
. Transposons (Tn) or Complex Transposons
○ These are much larger than insertion sequences, often several thousand base
pairs long.
○ They carry genes that code for proteins, including antibiotic resistance genes
in bacteria.
○ A key feature of transposons is the presence of inverted terminal repeats (IRs)
at both ends of the element, which are sequences that are repeated but in
opposite directions. These repeats help the transposon move.
○ Transposons also have a short sequence (less than 10 base pairs) on either side.
○ When a transposon inserts itself into a new location, it causes a duplication of
the target sequence, creating direct repeats (identical sequences) on both
sides of the inserted element. However, these repeats are not part of the
transposon itself—they behave like IS elements.

There are two types of transposons: composite transposons and non-composite

transposons.
(a) Composite Transposons:
Composite transposons are large, complex elements. They consist of a central region, which
usually carries genes for things like antibiotic resistance, and two IS elements at both ends.
These IS elements help the transposon move by producing transposase.
For example, Tn10 is a composite transposon that is 9,300 base pairs long and carries a
gene for tetracycline resistance. The two IS elements (IS10L and IS10R) are at the ends, and
they help the transposon move. Transposition of composite transposons is rare because it
doesn’t happen very often (once every 10 generations).
(b) Non-Composite Transposons:
Non-composite transposons, like Tn3, also carry genes for functions like antibiotic
resistance, but they don't have IS elements at their ends. Instead, they have inverted repeats
(similar to IS elements) at their ends, which are necessary for movement.
Tn3, for example, carries three genes. One gene codes for β-lactamase, which makes
bacteria resistant to antibiotics like ampicillin. The other two genes code for enzymes
needed for transposition: transposase and resolvase.
Non-composite transposons also create target site duplications when they move.
How Do Transposons Move? There are two main ways transposons move:
 ● Replicative transposition: The transposon makes a copy of itself, so there’s one copy
at the old location and one at the new location.
● Conservative (non-replicative) transposition: The transposon is excised (cut out)
from the old location and inserted into a new one. No new copy is made.

Examples of Transposable Elements

. Tn3 Transposon in E. coli
○ The Tn3 transposon is 4957 base pairs long and contains three genes:
◆ TnpA: Codes for transposase, an enzyme that helps the transposon move.
◆ TnpR: Codes for resolvase, a repressor enzyme that controls transposase
activity.
◆ Bla: Codes for β-lactamase, an enzyme that breaks down ampicillin,
giving bacteria resistance to this antibiotic.
. Bacteriophage Mu (Mu Phage)
○ Phage Mu is a temperate bacteriophage (a virus that infects bacteria).
○ It has properties similar to transposons because it can insert itself into the
bacterial DNA at random locations, causing mutations at the insertion site.
○ Because of this random insertion, it’s called a “mutator” phage.
. Yeast Ty Elements
○ Ty elements are transposons found in yeast (Saccharomyces cerevisiae).
○ These elements are about 5900 base pairs long and are surrounded by direct
repeats (5 base pairs long) that are created when the Ty element inserts into the
DNA.

Applications of Transposable Elements

Transposable elements have several useful applications:
● Genetic Research: They are used as tools to study gene expression (how genes are
turned on or off) and protein function.
● Genetic Engineering: Transposable elements are used in genetic engineering to
insert or remove specific DNA sequences. They can also cause frameshift mutations,
which change the reading frame of a gene.
● Gene Therapy: Some transposons, like the Tc1/mariner-class and Sleeping Beauty
transposon systems, are being studied for use in human gene therapy, where they
could help treat genetic disorders by adding or correcting genes.

Negative Effects of Transposable Elements

While transposons have useful applications, they can also have negative effects:
● Gene Disruption: When a transposon inserts into a functional gene, it can disable that
gene, causing loss of function.
● Chromosome Pairing Problems: Having multiple copies of the same transposon can
interfere with chromosome pairing during cell division, leading to chromosome
duplication or other problems.
● Disease-Causing Proteins: Some transposons carry genes that produce harmful
proteins, which can negatively affect the normal functioning of the cell and may even
contribute to disease.
Mu Transposon (Bacteriophage Mu)
The Mu transposon (often just called Mu or Phage Mu) is a type of bacteriophage (a virus
that infects bacteria). It is unique because, although it's a virus, it shares many
characteristics with transposable elements (pieces of DNA that can move around within a
genome). Here's a breakdown of its features and behavior:
Key Features of Mu Transposon
. Size and Structure:
○ The Mu phage has a large genome, around 36,000 nucleotides long.
○ It is a temperate phage, meaning it can exist in a dormant form inside a host cell
or enter into the lytic cycle (where the host cell is destroyed and new phages are
made).
. Random Insertion:
○ Mu transposons can insert themselves randomly into the bacterial
chromosome or plasmids, much like other transposons.
○ The insertion occurs at random locations in the host genome, and this process
leads to mutations at the site where Mu inserts itself. This is why the phage is
named Mu (short for "mutator"), because its insertion can cause mutations.
. Inverted Repeats (IRs):
○ Mu has inverted terminal repeats (IRs), similar to other transposable elements.
These IRs are essential for the transposition process and help the phage insert
into new locations in the genome.
. Mutation Induction:
○ When Mu inserts itself into the host DNA, it can cause a mutation at the
insertion site. This is because the insertion disrupts the normal sequence of the
gene, making it non-functional or altering its function.
Mu’s Mechanism of Action
. Insertion:
When Mu phage enters a bacterial cell, it can attach itself to the bacterial DNA, either
in the chromosome or a plasmid.
The Mu transposase enzyme, made by the phage, cuts the bacterial DNA and inserts
the Mu DNA at a random spot.
. Excision and Duplication:
After Mu DNA is inserted, it can sometimes be removed (excised) from the bacterial
DNA. When this happens, a copy of Mu stays behind in the host's DNA.
The excised Mu phage can now make more copies of itself and infect other bacteria,
repeating the process of causing mutations.

Transposable Elements (TEs) in Eukaryotes:

Transposable elements, also known as "jumping genes," are small pieces of DNA that can
move around within a genome. This means they can change their position from one location
to another within the same organism's DNA. This movement is known as transposition. TEs
can cause genetic changes that affect the structure and function of a genome.
In eukaryotes (organisms with complex cells, like humans, animals, plants, and fungi),
transposons (another name for TEs) play a significant role in the evolution and diversity of
genomes. They are found in all eukaryotic organisms and contribute to genetic variation.
There are two main classes of transposable elements in eukaryotes:
. Class 1: Retro-transposons
. Class 2: DNA transposons
Each class has its own way of moving and specific characteristics. Let’s explore each type in
detail.

Class 1: Retro-transposons
Retro-transposons are a type of transposon that move using RNA as an intermediate.
Here's a breakdown of how they work:
. RNA Intermediate: First, the DNA of the retro-transposon is transcribed into RNA.
This RNA copy is then converted back into DNA (this process is called reverse
transcription) by an enzyme called reverse transcriptase.
. Reverse Transcription: After the RNA is turned back into DNA, this newly created DNA
copy is inserted into a new location in the genome. This means that retro-transposons
"copy and paste" themselves, leaving behind their original copy while also creating a
new one elsewhere in the genome.
Retro-transposons are classified into two main groups based on whether or not they have
long terminal repeats (LTRs)at the ends of their sequences:
1. LTR Retro-transposons
● Structure: These retro-transposons have long terminal repeats (LTRs) at both ends
of their DNA sequence. LTRs are short, repetitive sequences that help in the
transposition process.
● How They Work: LTR retro-transposons behave in a way similar to retroviruses (like
HIV). The LTR sequences are recognized by reverse transcriptase, which copies the
RNA into DNA. Then, this new DNA is inserted at a new location in the genome.
● Example: One example is the Ty1 element in yeast. It has two genes (TyA and TyB)
that help in the process of making RNA and turning it into DNA.
2. Non-LTR Retro-transposons
● Structure: These retro-transposons do not have LTRs. Instead, they have a short
sequence of A:T base pairs at one end, which is a result of the modification of the RNA
(called a poly-A tail).
● How They Work: Like LTR retro-transposons, non-LTR retro-transposons also use RNA
as an intermediate. However, they lack LTR sequences and instead rely on a process
called reverse transcription to insert themselves into a new spot in the genome.
● Examples: LINEs (Long Interspersed Nuclear Elements) and SINEs (Short Interspersed
Nuclear Elements) are two common types of non-LTR retro-transposons in humans.

Class 2: DNA Transposons

DNA transposons are a different type of transposable element that move directly as DNA.
They don’t go through an RNA intermediate like retro-transposons do. Instead, DNA
transposons use a "cut-and-paste" mechanism to move around in the genome. Here’s how
they work:
. Cut and Paste Mechanism: The DNA transposon is cut out of its original location in
 .
the genome by an enzyme called transposase. After it’s cut out, the transposon is
then pasted into a new location within the genome.
. Transposase: This enzyme is responsible for recognizing the inverted repeat
sequences at both ends of the transposon and cutting the DNA. Once the DNA is cut,
transposase helps insert the transposon into a new spot in the genome.
DNA transposons are often shorter than retro-transposons, and they do not use RNA in their
movement. This mechanism is very similar to the way some bacterial transposons move.
Example: P Element in Drosophila
The P element is a DNA transposon found in the fruit fly (Drosophila). The P element has:
● Inverted repeats at both ends of the sequence.
● A single gene called transposase that cuts and inserts the transposon into new
locations.
This P element causes a phenomenon called hybrid dysgenesis in Drosophila, where hybrid
offspring (offspring from a cross between different strains of flies) show unexpected
changes like sterility and high mutation rates. This happens because the P elements in one
strain (wild-type) are not silenced in the hybrid offspring, leading to transposition and
damage to the genome.

How Transposons Affect the Genome

Transposable elements, through their movement and insertion into new parts of the genome,
can cause a variety of genetic changes, some of which may have significant effects on the
organism.
. Gene Disruption: When a transposon inserts itself into a gene, it can disrupt that
gene’s normal function, which may lead to a loss of function or a new function for the
gene.
. Exon Shuffling: Transposons can move exons (coding parts of a gene) to new
positions in the genome. This process can lead to the creation of new genes or
variations in gene function.
. Genome Size and Variation: Transposons make up a large portion of the genome in
many organisms. For example, in humans, about 44% of the genome is made up of
repetitive sequences, most of which are transposons. The presence of transposons
adds a lot of genetic diversity to a population, allowing for evolution and adaptation
over time.
. Regulation of Gene Expression: Some transposons have regulatory elements that
affect how nearby genes are turned on or off. In this way, transposons can influence
the expression of genes that are important for the development and function of the
organism.

Why Are Transposons Important?

Transposons play a critical role in the evolution of genomes. Their ability to move around
and create genetic variation can lead to the development of new traits in organisms. They
can cause mutations, changes in gene expression, and increases in genetic diversity,
which can help organisms adapt to their environment.
Transposons are also important in genetic research. Scientists use transposons in genetic
engineering and gene therapybecause they can be used to insert new genes into organisms
or cells.

Examples:
Class 1: Retro-transposons
These are transposable elements that use an RNA intermediate for transposition. They are
further divided into LTR retro-transposons and non-LTR retro-transposons.
1. LTR Retro-transposons (Retrovirus-like)
Examples:
● Ty1 elements in yeast:
○ Ty1 is a retro-transposon in yeast, which is about 5.9 kbp long. The Ty1
elements have LTRs at both ends, and the transposition process involves
reverse transcriptase.
● Copia elements in Drosophila:
○ The Copia elements in Drosophila are another example of LTR retro-
transposons. They are similar to retroviruses because they have long terminal
repeats (LTRs) that are important for their replication and transposition.
● Human retroviral-like elements:
○ HERVs (Human Endogenous Retroviruses) are a family of LTR
retrotransposons found in the human genome. They are remnants of ancient
retroviral infections that have become integrated into the human genome over
millions of years.
2. Non-LTR Retro-transposons (Retroposons)
Examples:
● LINEs (Long Interspersed Nuclear Elements):
○ L1 is the most well-known LINE in humans. It makes up a significant part of the
human genome (about 17%of the genome) and is active in transposing by
reverse transcription.
○ L2 and L3 are two other types of LINEs in humans, although they are mostly
inactive and do not transpose.
● SINEs (Short Interspersed Nuclear Elements):
○ Alu elements:
◆ Alu elements are the most abundant SINEs in the human genome. They
make up about 10% of the human genome and are highly active in
transposition.
◆ These elements rely on LINEs for the reverse transcriptase enzyme
needed for their transposition since SINEs themselves don't encode the
enzymes required for transposition.
○ MIR (Mammalian Interspersed Repetitive sequences):
◆ MIRs are another example of SINEs found in mammals, but they are much
less abundant than Alu elements.

Class 2: DNA Transposons

These transposable elements move via a "cut and paste" mechanism and do not involve
RNA intermediates. They are commonly found in both prokaryotes and eukaryotes.
Examples of DNA Transposons:
● P elements in Drosophila (Fruit flies):
○ P elements are DNA transposons that were discovered in Drosophila (fruit
flies). The P element has inverted terminal repeats at both ends and encodes a
transposase enzyme that cuts and pastes the element from one position to
another in the genome.
○ The P element was originally studied because it causes hybrid dysgenesis in
Drosophila, a phenomenon where hybrid offspring (offspring of a cross between
different strains) exhibit genetic defects like sterility and high mutation rates.
● Ac/Ds system in maize (corn):
○ The Ac (Activator) and Ds (Dissociation) elements were the first DNA
transposons discovered by Barbara McClintock in maize.
○ Ac is a transposase-encoding element that can move around the genome. Ds is
a non-autonomous element (it does not encode its own transposase), but it
relies on Ac to facilitate its movement.
○ These elements are responsible for the phenomenon of "somatic mosaicism" in
maize, where the presence of the transposons can cause color variation in
maize kernels.
● hAT (hobo, Activator, and Tam3) transposons in fruit flies, plants, and other
organisms:
○ The hAT family of transposons is another example of DNA transposons that are
found in various organisms, including Drosophila (fruit flies), plants, and other
eukaryotes.
○ These transposons have similar inverted repeat sequences and use transposase
enzymes to move around the genome.
● Mariner transposons:
○ The mariner transposons are found in a variety of eukaryotic species, including
humans and fruit flies. These elements are part of a more ancient family of DNA
transposons and can be found across many different animal species.

Sure! Let's explore each of these examples in more detail:

1. Yeast: Ty Retrotransposons
In yeast (a type of fungus), Ty elements are a type of LTR (long terminal repeat)
retrotransposon. They are similar to retroviruses, as they use an RNA intermediate to move
within the genome. Here’s a breakdown of the Ty retrotransposon in yeast:
Characteristics of Ty Elements:
● Structure: Ty elements are typically around 5.9 kbp (kilobase pairs) long. They have
long terminal repeats (LTRs) at both ends (around 340 base pairs each), which are
essential for their transposition process.
● Genes: Ty elements have two main genes:
○ TyA: Encodes a gag-like protein (related to retrovirus proteins).
○ TyB: Encodes a pol-like protein, which includes reverse transcriptase
(important for converting RNA into DNA).
 ● Transposition Process:
○ Transcription: The Ty element DNA is first transcribed into RNA.
○ Reverse Transcription: The RNA is then reverse-transcribed into double-
stranded DNA by the reverse transcriptase encoded by TyB.
○ Integration: The newly synthesized DNA is inserted back into the genome at a
new location, creating a new copy of the Ty element.
Importance of Ty Elements:
● Genetic Diversity: Ty elements contribute to genetic diversity in yeast by randomly
inserting themselves into different regions of the genome.
● Regulation of Gene Expression: Their insertion can affect the expression of nearby
genes, sometimes causing beneficial mutations, or in other cases, disrupting the
normal function of genes.

2. Drosophila (Fruit Flies): P Elements

P elements in Drosophila are a type of DNA transposon that move via the cut-and-paste
mechanism, similar to bacterial transposons. P elements were first discovered by Margaret
Kidwell when studying a phenomenon called hybrid dysgenesis in fruit flies.
Characteristics of P Elements:
● Structure:
○ P elements have inverted terminal repeats (similar to other DNA transposons).
○ They also contain a single open reading frame (ORF), which codes for the
transposase enzyme responsible for cutting the element out of one location and
inserting it into another.
● Size: P elements range in size from 0.5 to 2.9 kbp.
Transposition Process:
● Cut and Paste Mechanism: The transposase enzyme produced by the P element
recognizes the terminal repeats, cuts the element out of its original location, and then
inserts it into a new location in the genome.
Hybrid Dysgenesis:
● Dysgenesis Phenomenon: This is a phenomenon where hybrid offspring (offspring
from two genetically different strains of Drosophila) show genetic defects like
sterility, high mutation rates, and chromosomal aberrations.
○ In the M cytotype (female flies without P elements), the P elements are inactive.
In the P cytotype (male flies with P elements), the P elements are active.
○ When an M female (no P elements) mates with a P male (with P elements), the
P elements become activated in the progeny, leading to disruption in their
genome and causing dysgenesis.
○ In contrast, when a P female mates with an M male, the P elements are already
silenced in the female, and no dysgenesis occurs in the offspring.
Significance of P Elements:
● Regulation of Gene Expression: Like other transposons, P elements can affect the
function of the host genes by inserting into or near important genomic regions.
● Genetic Tool: P elements are also widely used in genetic research and in creating
transgenic Drosophila because they can be easily inserted or used to introduce
foreign genes into the Drosophila genome.
3. Maize (Corn): Ac/Ds Transposon System
Ac/Ds elements were discovered by Barbara McClintock in maize and are one of the best-
studied examples of DNA transposons. These elements are famous for their role in genetic
variability and somatic mosaicism in plants.
Characteristics of Ac and Ds Elements:
● Ac (Activator) Element:
○ Ac is a transposase-encoding DNA transposon. It has terminal inverted
repeats and is capable of moving throughout the genome, thanks to the
transposase enzyme it encodes.
● Ds (Dissociation) Element:
○ Ds is a non-autonomous transposon, meaning it does not encode its own
transposase enzyme. Instead, it relies on the presence of an active Ac element
in the same genome to provide the transposase.
Transposition Process:
● The Ac element encodes transposase, which recognizes the terminal repeats of the
Ac or Ds elements, cuts the element out from its current location, and inserts it into a
new site in the genome.
● The Ds element, lacking transposase, depends on an active Ac element to move.
When Ac is active, it can cause the Ds element to transpose to new locations.
Somatic Mosaicism and Genetic Effects:
● Somatic Mosaicism: The movement of Ac/Ds elements within the somatic cells of the
plant can cause patches of cells with different genetic makeup. This results in
variegated colors in maize kernels, a phenomenon that was central to McClintock's
discoveries.
○ For example, the color of maize kernels can be affected by the insertion of Ds
elements into color genes. If Ac is present, it can activate Ds, leading to color
changes in patches of kernels where Ds has inserted itself into the color gene.
● Transposition and Mutations: The movement of Ac and Ds elements can cause
mutations by inserting into functional genes. This can lead to gene disruption and
genetic diversity within the plant population.
Significance of Ac/Ds Elements:
● Genetic Diversity: The Ac/Ds system contributes to the genetic diversity of maize by
causing mutations and by promoting the shuffling of genetic material.
● Historical Discovery: McClintock's work on Ac/Ds elements led to her Nobel Prize in
Physiology or Medicine in 1983. She demonstrated the concept of "jumping genes"
and the idea that genes can move within and between chromosomes, a groundbreaking
discovery in genetics.