DNA transposons (also called Class II transposable elements) are a group of transposable elements (TEs) that can move in the DNA of an organism via a single- or double-stranded DNA intermediate. DNA transposons have been found in both prokaryotic and eukaryotic organisms. They can make up a significant portion of an organism's genome, particularly in eukaryotes. In prokaryotes, TE's can facilitate the horizontal transfer of antibiotic resistance or other genes associated with virulence.
There are autonomous, as well as nonautonomous DNA transposons. The latter use the enzymatic machinery of the former for their amplification in a genome. It is estimated, that there are around 300,000 copies of DNA transposon fossils in the human genome and they make up around 3% of it.
Movement of DNA transposons
DNA transposons can move around in the genome. The system requires a transposase enzyme that catalyzes the movement of the DNA from its current location in the genome and inserts it in a new location. Transposition requires three DNA sites on the transposon two at each end of the transposon called terminal inverted repeats and another at the target site. The transposase will bind to the terminal inverted repeats of the transposon and mediate synapsis of the transposon ends. The transposase then disconnects the element from the flanking DNA of the original donor site and mediates the joining reaction that link the transposon to the new insertion site. The ends of the mobile element attack the target DNA at staggered positions such that the newly inserted transposon is flanked by short gaps. Host systems repair these gaps resulting in the target sequence duplication that are characteristic of transposition. In many reactions, the transposon is completely excised from the donor site in what is called a "cut and paste" transposition and inserted into the target DNA to form a simple insertion.Occasionally, genetic material not originally in the transposable element gets copied and moved as well. The ability of these elements to excise and insert themselves creates a mechanism for lateral gene transfer from one organism to another via a transposon migrating from one cell to another.
Helitrons are a group of eukaryotic class II transposable elements. This group does not move via the "cut and paste" method. Instead, helitrons replicate and move around the genome using a "rolling circle" mechanism, where a single stranded piece of donor DNA rolls in to a circular intermediate and inserts itself in to a target elsewhere in the genome. This systems creates duplicates of the gene sequence in the genome each time the TE moves.
Polintons are a group of eukaryotic class II transposable elements. They contain genes with homology to viral proteins and which are often found in eukaryotic genomes. They are the largest and most complex known DNA transposons. Polintons encode up to 10 individual proteins and derive their name from two key proteins, a DNA polymerase and a retroviral-like integrase, proteins necessary to replicate themselves.
As of the most recent update in 2015, 23 superfamilies of DNA transposons were recognized and annotated in Repbase, a database of repetitive DNA elements maintained by the Genetic Information Research Institute:
Barbara McClintock first discovered and described DNA transposons in Zea mays, during the 1940s; an achievement that would earn her the Nobel Prize in 1983. She described the Ac/Ds system where the Ac unit (activator) was autonomous but the Ds genomic unit required the presence of the activator in order to move.
The Mariner transposon, found in many animals but studied in Drosophila was first described by Jacobson and Hartl. Mariner is well known for being able to excise and insert horizontally in to a new organism. Thousands of copies of the TE have been found interspersed in the human genome as well as other animals.
The Hobo transposons in Drosophila have been extensively studied due to their ability to cause gonadal dysgenesis. The insertion and subsequent expression of hobo-like sequences results in the loss of germ cells in the gonads of developing flies.
Bacterial transposons are especially good at facilitating horizontal gene transfer between microbes. Transposition facilitates the transfer and accumulation of antibiotic resistance genes. In bacteria, transposable elements can easily jump between the chromosomal genome and plasmids. In a study by Devaud et al. in 1982, a multi-drug resistant strain of Acinetobacter isolated and examined. Evidence pointed to the transfer of a plasmid in to the bacterium, where the resistance genes were transposed in to the chromosomal genome.
Class II TE Activity in Humans
Class II transposable elements make up about 3% of the human genome. Today, there are no active DNA Transposons in the human genome. Therefore, the elements found in the human genome are called "fossils".
- Dfam, a database of repeating DNA sequences
- Repbase, a database and classification system for repeating DNA sequences
- DNA transposon derived genes, in HGNC database
- Wicker, Thomas; Sabot, François; Hua-Van, Aurélie; Bennetzen, Jeffrey L.; Capy, Pierre; Chalhoub, Boulos; Flavell, Andrew; Leroy, Philippe; Morgante, Michele (2007). "A unified classification system for eukaryotic transposable elements". Nature Reviews Genetics. 8 (12): 973–982. doi:10.1038/nrg2165. PMID 17984973.
- Feschotte, Cédric; Pritham, Ellen J. (December 2007). "DNA Transposons and the Evolution of Eukaryotic Genomes". Annual Review of Genetics. 41 (1): 331–368. doi:10.1146/annurev.genet.40.110405.090448. PMC 2167627. PMID 18076328.
- International Human Genome Sequencing Consortium (Feb 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011.
- Berg and Howe, Douglas E. and Martha M. (1989). Mobile DNA II. ASM Press. p. 98. ISBN 9781555812096.
- Madigan M, Martinko J, eds. (2006). Brock Biolog of Microorganisms (11th ed.). Prentice Hall. Template:0-13-144329-1.
- Kapitonov VV, Jurka J. Trends Genet. 2007 Oct;23(10):521-9. Epub 2007 Sep 11. Review. PMID 17850916
- Kapitonov, V. V.; Jurka, J. (14 March 2006). "Self-synthesizing DNA transposons in eukaryotes". Proceedings of the National Academy of Sciences. 103 (12): 4540–4545. doi:10.1073/pnas.0600833103. PMC 1450207. PMID 16537396.
- Pritham, Ellen J.; Putliwala, Tasneem; Feschotte, Cédric (April 2007). "Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses". Gene. 390 (1–2): 3–17. doi:10.1016/j.gene.2006.08.008. PMID 17034960.
- Krupovic, Mart; Koonin, Eugene V. (22 December 2014). "Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution". Nature Reviews Microbiology. 13 (2): 105–115. doi:10.1038/nrmicro3389. PMC 5898198. PMID 25534808.
- Yutin, Natalya; Shevchenko, Sofiya; Kapitonov, Vladimir; Krupovic, Mart; Koonin, Eugene V. (11 November 2015). "A novel group of diverse Polinton-like viruses discovered by metagenome analysis". BMC Biology. 13 (1): 95. doi:10.1186/s12915-015-0207-4. PMC 4642659. PMID 26560305.
- Krupovic, Mart; Koonin, Eugene V (June 2016). "Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems". Current Opinion in Microbiology. 31: 25–33. doi:10.1016/j.mib.2016.01.006. PMC 4899294. PMID 26836982.
- Bao, Weidong; Kojima, Kenji K.; Kohany, Oleksiy (2 June 2015). "Repbase Update, a database of repetitive elements in eukaryotic genomes". Mobile DNA. 6 (1): 11. doi:10.1186/s13100-015-0041-9. PMC 4455052. PMID 26045719.
- McClintock, Barbara (June 1950). "The origin and behavior of mutable loci in maize". Proc Natl Acad Sci U S A. 36 (6): 344–55. Bibcode:1950PNAS...36..344M. doi:10.1073/pnas.36.6.344. PMC 1063197 . PMID 15430309.
- Jacobson JW, Medhora MM, Hartl DL. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8684-8. PMID 3022302
- Lohe AR, Moriyama EN, Lidholm DA, Hartl DL (January 1995). "Horizontal transmission, vertical inactivation, and stochastic loss of mariner-like transposable elements". Mol. Biol. Evol. 12 (1): 62–72. doi:10.1093/oxfordjournals.molbev.a040191. PMID 7877497.
- Deprá M, Valente VL, Margis R, Loreto EL. Gene. 2009 Dec 1;448(1):57-63. doi: 10.1016/j.gene.2009.08.012. Epub 2009 Aug 29. PMID 19720121
- Devaud M, Kayser FH, Bächi B. Antimicrob Agents Chemother. 1982 Aug;22(2):323-9. PMID 6100428