Reaction mechanisms

There are a limited number of transposase types defined by their chemistry.

The main groups

Two groups whose mechanisms are the best understood are the DDE and the HUH superfamilies named after the amino acids which constitute the active sites. The reaction mechanisms involved in transposition using DDE enzymes have been treated in depth (e.g. (Mizuuchi, 1992, Mizuuchi, 1997, Mizuuchi & Baker, 2002, Hickman & Dyda, 2015)) as have those of the HUH enzymes (see (Chandler, et al., 2013, He, et al., 2015)).

Other enzymes

Other types of transposase include: the DEDD enzymes (Buchner, et al., 2005) whose chemistry presumably resembles that of the DDE enzymes (since they also have an RNaseH fold (Ariyoshi, et al., 1994)) but resemble the RuvC four-way Holliday junction resolvase; Serine transposases which are thought to use chemistry similar to their Serine-site-specific recombinase cousins; and a group of novel transposons, casposons, thought to be primitive ancestors of the CRISPR system (Krupovic, et al., 2014).

The transpososome.

Most transposition reactions can be divided into several defined steps generally comprising: binding of the transposase to the ends; elaboration of a synaptic complex involving the transposase, perhaps accessory proteins, and both transposon ends - this step involves either concomitant or subsequent (depending on the element) recruitment of the target DNA; cleavage and strand transfer of the transposon ends into the target; and processing of the strand transfer complex to a final product. The protein-DNA complexes assembled during this process are called transpososomes.

Enzymes or reaction components?

An important point which has not yet been fully addressed is whether transposases are true enzymes which can be recycled or whether they are themselves reaction components which are consumed during the process. The fact that many transposases show a preference for action on the element from which they are expressed (in cis) and the coupling between transposase translation and DNA binding (Duval-Valentin & Chandler, 2011) imposes strong constraints on transposase recycling. Moreover, at least in the case of bacteriophage Mu, special machinery in place for removing transposase from the transposition complex following insertion which includes ClpX (Mhammedi-Alaoui, et al., 1994) (Kruklitis, et al., 1996), (Levchenko, et al., 1995). In addition, the Lon protease is implicated in proteolysis of the IS903 transposase (Derbyshire, et al., 1990, Derbyshire & Grindley, 1996).

References :

• Ariyoshi M, Vassylyev DG, Iwasaki H, Nakamura H, Shinagawa H & Morikawa K (1994) Atomic structure of the RuvC resolvase: a holliday junction-specific endonuclease from E. coli. Cell 78: 1063-1072.
• Buchner JM, Robertson AE, Poynter DJ, Denniston SS & Karls AC (2005) Piv Site-Specific Invertase Requires a DEDD Motif Analogous to the Catalytic Center of the RuvC Holliday Junction Resolvases. 10.1128/JB.187.10.3431-3437.2005. J. Bacteriol. 187: 3431-3437.
• Chandler M, de la Cruz F, Dyda F, Hickman AB, Moncalian G & Ton-Hoang B (2013) Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol 11: 525-538.
• Derbyshire KM & Grindley ND (1996) Cis preference of the IS903 transposase is mediated by a combination of transposase instability and inefficient translation. Mol Microbiol 21: 1261-1272.
• Derbyshire KM, Kramer M & Grindley ND (1990) Role of instability in the cis action of the insertion sequence IS903 transposase. Proc Natl Acad Sci U S A 87: 4048-4052.
• Duval-Valentin G & Chandler M (2011) Cotranslational control of DNA transposition: a window of opportunity. Mol Cell 44: 989-996.
• He S, Corneloup A, Guynet C, et al. (2015) The IS200/IS605 Family and "Peel and Paste" Single-strand Transposition Mechanism. Microbiol Spectr 3.
• Hickman AB & Dyda F (2015) Mechanisms of DNA Transposition. Microbiol Spectr 3: MDNA3-0034-2014.
• Kruklitis R, Welty DJ & Nakai H (1996) ClpX protein of Escherichia coli activates bacteriophage Mu transposase in the strand transfer complex for initiation of Mu DNA synthesis. EMBO J. 15: 935-944.
• Krupovic M, Makarova KS, Forterre P, Prangishvili D & Koonin EV (2014) Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity. BMC Biol 12: 36.
• Levchenko I, Luo L & Baker TA (1995) Disassembly of the Mu transposase tetramer by the ClpX chaperone. Genes Dev 9: 2399-2408.
• Mhammedi-Alaoui A, Pato M, Gama MJ & Toussaint A (1994) A new component of bacteriophage Mu replicative transposition machinery: the Escherichia coli ClpX protein. Mol.Microbiol. 11: 1109-1116.
• Mizuuchi K (1992) Polynucleotidyl transfer reactions in transpositional DNA recombination. J Biol Chem 267: 21273-21276.
• Mizuuchi K (1997) Polynucleotidyl transfer reactions in site-specific DNA recombination. Genes Cells 2: 1-12.
• Mizuuchi K & Baker TA (2002) Chemical mechanisms for mobilizing DNA. Mobile DNA, Vol. II (Craig NL, Craigie R, Gellert M & Lambowitz A, ed.^eds.), p.^pp. 12-23. ASM press, Washington DC.