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The below mentioned article provides a study note on transposable elements.
The term “transposon” was coined by Hedges and Jacob in 1974 for mobile discrete DNA sequences in the genome; such sequences are able to transport themselves from one location to the other locations within the genome. These sequences are also called transposable genetic elements.
Transposable genetic elements are found in both, prokaryotes and eukaryotes. Each bacterial transposon carries genes coding for the enzyme needed for its own transposition. Similar systems occur in eukaryotic organisms also.
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Transposons promote rearrangement of the genomes sinne (a) transposition causes deletion or inversion and (b) transposable elements act as regions of homology for recombination, resulting in translocations, inversions, deletions and insertions.
1. IS (Insertion Sequences) Elements:
They are small bacterial transposons that carry only the genes coding for the proteins required for their own transposition. They are the normal constituents of plasmids, transposons and bacterial chromosomes. The first IS element identified was designated as ISI which was detected through mutations within various loci involved in galactose metabolism in E. coli.
Subsequently, several other IS elements were discovered, and they were found to be responsible for duplications inversions and deletions. Several copies of a single IS element may be present in the genome. IS elements are relatively small, i.e., around 1000 base pairs in length, and have terminal repeats of few bases at both their ends (Table 5.1).
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After IS elements are denatured into single strands, the terminal inverted repeats of a strand may pair together to produce loop or “lollipop” structure. Such structures can be recognized under the electron microscope (Fig. 5.1).
IS elements are inserted in the host DNA at the target site. During their insertion in the host DNA, the target site of the IS elements become duplicated to yield direct repeats at both the ends of the IS element.
For example, the target site 
is duplicate and flanks the IS element on both sides as direct repeats (Fig. 5.2). The length of the direct repeat for any particular IS element is constant the most common being 9 bases.
The protein responsible for transposition of IS element is called transposase; the gene coding for transposase falls between the terminal inverted repeats. IS1 has two separate reading frames, while other IS elements have only one reading frame. The general rate of transposition is 10-3 to 10-4 cells per IS element per generation.
2. Composite Transposons:
Composite transposons are larger transposons which possess a central region bracketed on each side by IS elements, and one or both the IS elements may enable the transposition of the complete transposon.
The IS element located on one side of the transposon is designated L (left), while that on the other side is designated as R (right) (Fig. 5.3).
Composite transposons carry genes for drug resistance or other functions besides the functions related to transposition. Some transposons contain genes for resistance to antibiotics like ampicillin (ampR), tetracycline (tetR), kannamycin (kanR) etc. Table (5.2). Composite transposons are designated by Tn, followed by a number, e.g., Tn5, Tn9, Tn10 and Tn 903 etc.
The transposon Tn9 contains IS1 as direct repeat on both the sides, while Tn903 contains IS903 as inverted repeats on both its sides. But some Tn elements have IS modules at their two ends that differ from each other to a limited extent, e.g., Tn5 contains IS50 but the left (L) and right (R) modules differ for one base pair so that the left module has become nonfunctional (Table 5.2).
Both the IS1 modules of Tn9 are presumed functional. The IS10R of Tn10 is functional, while IS10L is nonfunctional. The functional IS module can transpose either alone or along with the whole transposon. The gene coding for the enzyme transposase is located within the IS module. This enzyme creates a target site and also recognizes the two ends of the complete transposon.
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Sometimes a plasmid may contain several composite transposons of varying sizes; each of these transposons may carry resistance genes for different antibiotics thereby conferring multiple drug resistance to the organism (cell) carrying such a plasmid (Fig 5.4).
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3. Mechanism of Transposition:
Transcription of the gene producing transposase is regulated by a repressor. The repressor also regulates its own synthesis. The transposase produces a staggered cleavage at the target site in the host DNA in which the Tn element is to transpose. The staggered cuts enable the joining of the single stranded ends of the host DNA with the ends of the transposon.
After the joining of the ends, the single stranded (open) target sequences at the ends of the transposon support DNA synthesis leading to gap filling, then the ligation of the nicks causes the duplication of the target sequences that make a direct repeat at both the ends of the inserted transposon (Fig. 5.5).
The mechanisms of transposition are of the following three types:
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(1) Replicative,
(2) Non-replicative
(3) Conservative.
1. Replicative transposition:
The transposon is duplicated during the process of transposition; one copy of the Tn element remains at the original site while the duplicated copy is inserted at a new site. Such type of transposition is a characteristic of TnA group of transposons (see later).
In this type of transpositions the number of copies of the transposon increases. Two endonucleases are involved in transposition: the enzyme transposase acts on the ends of the original transposon while another enzyme resolvase acts on the duplicated copy.
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2. No-Replicative Transposition:
In this case, the transposable element moves from one site into the other. Since there is no duplication of the transposon, it is lost from the original site.
This process involves a single enzyme, the transposon. Transposition of all IS elements and of the composite transposons Tn5 and Tn10 occurs according to this mechanism.
3. Conservative Transposition:
This is also a type of non-replicative transposition where the transposon is cleaved from one site and inserted into a new site. But every nucleotide bond is conserved during this process. This process is quite similar to the intergration of phage lambda (λ) into the E. coli chromosome. In such transposons, the transposes belong to λ-integrase family. Large transposons utilize the conservative mechanism of transposition.
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Mu Transposon:
The bacteriophage Mu is very large and is regarded as a giant mutator Tn element. It possesses a number of genes for its head and tail formation. This transposon has the ability to insert into E. coli chromosome at different non-homologous positions. The enzyme Mu transposase cuts both the ends of the transposon from the donor molecule. A staggered cleavage of 5 bases occurs at the target site of insertion.
Mu utilizes both the replicative and non-replicative pathways of transposition. Its integration into the host genome occurs through the non-replicative process, while the multiplication of Mu occurs through the replicative mechanism. The Mu transposon can produce 100 copies by its transposition to 100 different target sites in a single E. coli chromosome.
The enzyme Mu transposase recognizes the terminal sequences and makes staggered cleavages at the end of the Mu and also at the target site in the chromosomal DNA. One cut end of the Mu joins with the cut end of the target site of the recipient chromosome producing a cross-shaped structure (Fig. 5.6). Subsequently, one of the following two pathways is followed.
(i) A cleavage in the donor molecule near the transposon causes the insertion of the transposon in the target DNA. The single-stranded region formed by the staggered cleavage is filled by repair synthesis. This is the non-replicative mechanisms in which donor DNA suffers a double-stranded break and loses the Mu transposon (Fig. 5.6).
(ii) In the implicative mechanism, no further cleavage occurs in the cross-shaped structure. DNA synthesis occurs complementary to the single-stranded region that was formed by staggered cleavage. Synthesis continues through the transposon and separates the duplex into a single large DNA molecule consisting of both, the donor and recipient chromosomes.
This molecule contains two copies of the transposon and is called a co-integrate (Fig. 5.6). The transposons are located at the joining of the donor and the recipient replicons.
Tn10 Transposon:
Tn10 is a composite transposon carrying the gene for tetracycline resistance (tetR) and has inverted IS10L and IS10R at its ends. These IS modules are oriented inward (Fig. 5.7). The IS modules have short inverted repeats of 22 base pairs at their ends.
The IS10R is an active element, while the IS10L is functionally defective. Transposition of Tn10 generates direct repeats of 9 bases on the target DNA at both its ends. The target site has the sequence NGCTNACN, where N represents any base. When Tn10 is inserted into NCGANTCGN circular DNA (plasmid), there occur the following two regions of the DNA in relation to the IS modules and the DNA region flanked by them (Fig. 5.7):
(i) On one side of the IS modules, there lies the transposon carrying the gene tetR… The inverted IS modules are oriented inside.
(ii) On the other side of the IS modules, there lies the host chromosome carrying the host genes.
The IS modules can transpose either of the above two regions, i.e., either the coding region of the transposon, or the entire sequence of the plasmid (Fig. 5.7). In the case of the former (transposon Tn10 is mobilized), the tetR gene is transposed.
But in the case of latter (the IS modules transpose the plasmid DNA), a new “inside-out” transposon is generated that carries the markers of the host chromosome (Fig. 5.7). In this new transposon also, the IS modules are inverted but their orientation is to wards outside.
The active module IS10R contains two promoters PIN and POUT near its outside end (Fig. 5.8). The promoter Pw promotes the transcription of IS 10R regions (inside) to produce the enzyme “transposase”, a protein having molecular weight of 47,000 Daltons.
The promoter POUT however, transcribes towards outside. Sometimes the Pout transcription extends into the host DNA, thus activating the adjacent bacterial genes. The POUT transcript contains 69 bases of which 40 bases overlap (i.e., are complementary to) 5′ terminal region of the PIN RNA.
The Pout actsas antisense RNA and produces RNA-RNA duplex with the Pm RNA. This prevents the synthesis of transposase, thereby causing inhibition of transposition. Consequently, when IS10R is present in many copies the transposition of Tn10 on the bacterial chromosome is inhibited.
6. TnA Transposons:
Transposons of TnA group, such as, Tn3, Tn100 (γδ) etc. are large transposable elements containing about 5000 base pairs. Notably, they are devoid of IS elements, but they carry genes required for transposition along with the genes for resistance to antibiotics such as, ampicillin (ampR). Their terminal sequences are about 38 base pairs long in form of inverted repeats.
The enzymes “transposase” coded by the gene tnpA and “resolvase” coded by the gene tnpR are involved in transposition of TnA transposons. The transposase binds to a sequence of 25 base pairs located within the 38 base pair inverted terminal repeat. This enzyme makes a staggered cleavage of 5 base pairs at the target DNA.
The product of gene tnpR (resolvase) functions as a repressor of tnpA as well as tnpR itself. The repression of gene tnpR or a mutation in the gene tnpR results in an increased synthesis of transposase; this leads to a higher frequency of transposition. The enzyme resolvase is involved in site specific recombination between two transposons present as direct repeats in a co-integrate molecule.
7. Rearrangement of Host DNA Caused by Transposons:
Transposons may often bring about change in the host DNA as they may cause deletions, duplications and inversions etc. When a copy of a transposon is mobilized and inserted into the same chromosome near its original site, recombination may occur between the two copies. There are two situations depending on whether the orientation of the repeats is direct (e.g., Tn9) or inverted (e.g., in Tn903).
(i) Direct repeats:
In case of Tn9, IS1 is present on both the ends as direct repeats. Recombination between a pair of direct repeats produces a circular DNA molecule that contains only one copy of the direct repeat (IS1 module); the other copy of the direct repeat (IS1 module) remains within the chromosome (Fig. 5.9). The circular DNA molecule is lost from the cell and thus a deletion occurs.
(ii) Inverted repeats. The transposon Tn903 consists of inverted repeats of IS 903 at its two ends. A recombination between a pair of inverted repeats does not cause a deletion but it results in an inversion of the central region (Fig. 5.10).
