During each round of replicative transposition, a transposon duplicated (replicated) and inserted in a new position. Both DNA and retrotransposons follow the replicative mechanism of transposition.
Tn3, phage Mu are some of the examples of the replicative transposons in bacteria.
The DNA doubled by the replication mechanism. Even, the replication helps to seal the gaps and breaks during the DNA repair process.
The DNA polymerase helps to do so.
Transposable elements are the short-repeated DNA sequences, that cannot encode any proteins. It can jump from one location to another location into the genome, called a transposition.
The transposition can be done by one of the two mechanisms: by replicative transposition or by the non-replicative transposition.
With using the replicative mechanism of transposition, the transposons replicate a new copy of it by leaving the old copy behind,
Whereas, in the non-replicative transposition, the transposons move from one place to another by leaving a gap in the older place.
See the image below,
Transposition of the DNA transposons occurs via the strand transfer mechanism in the replicative transposition.
In the present article, we will understand the mechanism of replicative transposition for DNA transposons and retrotransposons.
Replicative transposition of DNA transposons:
The explanation of the strand transfer mechanism for DNA transposon is given below,
At the beginning of the replicative transposition, the transposase enzyme assembles at the two ends of the transposable element.
This assembly migrates the entire transposons at another location.
This assembly creates the actual transposon, it helps in cutting the transposon at one location and inserting it to another location, simply called a “Cleaving and joining reaction.”
The second step is catalysed by the transposase protein.
The transposase protein cleaves the DNA at the two terminal of the TE itself and creates the free 3′ OH ends.
Furthermore, it also creates a gap in the target DNA sequences at which the transposon will be inserted.
The transposase proteins cleave the ends of the transposons as well as the host DNA.
Overall, 4 nicks are created, two at both the ends of transposons and two in the target DNA.
The nicking process in the transposons is ” sequence-specific nicking”, two nicks that created on both ends of the transposons contain the same sequences because they are inverted terminal repeats.
One of the important even happened here,
The transposase creates a free 3′ end at both ends of the transposon terminus.
These 3′ ends are very essential in the synthesis of DNA by a polymerase. Contrary, nicking and 3′ end generation lacks in cut and paste mechanism.
In this step, a double branched DNA molecule formed by the strand transfer mechanism.
The 3′ end generated in the previous step is now joined to the 5′ ends of the host DNA or the target DNA. The bond between them is covalent, contrary to this, the 5′ ends of the transposon sequence remain bound with the old DNA.
See the figure below,
In the next step, the intermediate strand transfer complex creates two replication forks that facilitate a normal replication into the target DNA.
Here, cleavage on the target DNA at 3′ end accommodates a primer for the replication.
The replication machinery of the host cell assembled at the replication fork junction, the 3′ free end serves as a primer, replication occurred through the transposon and ends at another end.
In the last step, at the end of the replication, two DNA molecules each with the transposon are generated at the end of the process.
The transposon is flanked by the short direct target site duplication.
These target site duplication will move with the transposons to another location and inserted TSDs to another location, in future.
Deletion and chromosomal inversions are very often in the replicative transposition mechanism which is the major limitation of it.
The entire mechanism is shown in the figure below,
- How to set up a DNA extraction lab: A comprehensive guide (chemicals, instruments and other utilities).
- What are the different components used in the PCR reaction buffer?
In the plasmid DNA, the replicative transposition occurred through the cointegrate structure.
The replicative transposition starts by the fusion of two plasmids, donor and recipient. The structure called cointegrate is generated via transposase-mediated catalytic activity.
The transposon replicates in the cointegrate structure and creates another molecule of it in the same direction.
In the next step, a recombination event occurs between both transposons mediated by the transposons as well as the resolvase at the “res” site.
The resolvase is another bacterial protein that suppresses the transposition process.
After that, the two molecules are detached and two plasmids with two transposons are generated.
See the figure below,
Replicative transposition of Retrotransposon:
The retrotransposons also follow the replicative strand transfer mechanism of transposition.
Instead of direct replication, here the reverse transcription mediates the transposition of DNA, via the RNA intermediate.
In the very first step, using the cellular RNA polymerase, the RNA is synthesised from the DNA of the retrovirus or retrovirus-like particle through the mechanism of transcription.
The long terminal repeats of the transposons are non-coding DNA sequences having a promoter region.
Here, from one of the LTR, the full-length RNA molecule is generated by the transcription machinery and from that RNA, the DNA is synthesised back using the reverse transcription enzyme by the reverse transcription mechanism.
The DNA generated from the RNA does not contain a copy of the previous host DNA. It is called as the cDNA or complementary DNA.
A double-stranded cDNA is generated through the reverse transcription.
In the next step,
The recombination is occurred via the recognition of the integrase protein by the cDNA. Once the integrase is recognized by cDNA, it is assembled on both the ends of the DNA.
Likewise the strand transfer mechanism of the DNA transposition, the gap is generated at the 3′ end of each strand of the DNA by cleaving some of the nucleotides from this end by the integrase.
By using the DNA strand transfer mechanism, the integrase catalyzes the insertion of the modified DNA into the host genome DNA.
Once the gaps are filled by the DNA repair mechanism by a DNA repair enzyme, The process of recombination is completed
After the completion of recombination, the target site duplication is generated on both the ends of a new transposon possibly because of the same DNA repair mechanism on both sides.
This is a complete process of replicative transposition for DNA transposons and retrotransposons.
TY element in yeast and copia element in Drosophila whereas Tn3, Tn5 and phage Mu follows the replicative mechanism for transposition.
Our additional resources related to this topic:
- History, overview, DNA transposons, retrotransposons.
- Bacterial transposons, Is elements, composite transposons, transposons and antibiotic resistance.
- Transposons in Drosophila, transposons in maize, transposons in yeast.
- How transposons involve in the process of evolution.
External resources related to the present topic:
In a replicative transposition, a new copy of transposon is inserted at a new location by leaving the original TE at its native position. Both the DNA and retrotransposons follow the replicative transposition. New alleles are originated due to these types of transposition.
Replicative transposition played an important role in the process of evolution and generation of new variations into nature.