Groups with DDE Transposases

DDE enzymes, so-called because of a conserved Asp, Asp, Glu triad of amino acids which coordinate essential metal ions, use OH (e.g. H₂0) as a nucleophile in a transesterification reaction (Mizuuchi & Baker, 2002, Hickman & Dyda, 2015) (Figs 1.7.1 and 1.8.1).

IS with DDE enzymes are the most abundant type in the public databases (Fig 1.4.2). This is partly due to the fact that the definition of an IS became implicitly coupled to the presence of a DDE Tpase, an idea probably reinforced by the similarity between Tpases of IS (and other TE) and the retroviral integrases (Fig. 1.8.1) (Fayet, et al., 1990, Khan, et al., 1991, Kulkosky, et al., 1992) particularly in the region including the catalytic site. More precisely, for these TE, the triad is DD(35)E in which the second D and E are separated by 35 residues. As more DDE transposases were identified, the distance separating the D and E residues was found to vary slightly (Table 2: MGE transposases examined using secondary structure prediction programmes) (Hickman, et al., 2010). However, for certain IS, this distance was significantly larger. In these cases, the Tpases include an "insertion domain" between the second D and E residues (Hickman, et al., 2010) with either α-helical or β-strand configurations (Fig 1.8.3). Although in most cases this is a prediction, it has been confirmed by crystallographic studies for the IS50 [β-strand; (Davies, et al., 1999)] and Hermes [α-helical; (Hickman, et al., 2005)] Tpases. The function of these "insertion domains" is not entirely clear (Hickman, et al., 2010).

Although DDE-type transposons share basic transposition chemistry, different TE vary in the steps leading to formation of a unique insertion intermediate (Fig 1.8.2) (Hickman, et al., 2010, Hickman & Dyda, 2015). They catalyze cleavage of a single DNA strand to generate a 3'OH at the TE ends which is subsequently used as a nucleophile to attack the DNA target phosphate backbone. This is known as the transferred strand. The variations are due to the way in which the second (non-transferred) strand is processed (Turlan & Chandler, 2000, Curcio & Derbyshire, 2003). There are several ways in which second strand processing can occur (Fig 1.8.2): for certain IS, the second strand is not cleaved but replication following transfer of the first strand fuses donor and target molecules to generate cointegrates with a directly repeated copy at each donor/target junction. This is known as replicative transposition (e.g. IS6, Tn3) or more precisely, Target Primed Replicative Transposition (TPRT) (Fig 1.8.2 pathway a). In the other pathways, the flanking donor DNA can be shed in several different ways: the non-transferred strand may be cleaved initially several bases within the IS prior to cleavage of the transferred strand [e.g. IS630 and Tc1;(Plasterk, 1996, Feng & Colloms, 2007)]. (Fig 1.8.2 pathway d); the 3'OH generated by first strand cleavage may be used to attack the second strand to form a hairpin structure at the IS ends liberating the IS from flanking DNA and subsequently hydrolyzed to regenerate the 3'OH known as conservative or cut-and-paste transposition (e.g. IS4; (Haniford & Ellis, 2015)(Fig 1.8.2 pathway f)(IS4.4; IS4.5; IS4.6; IS4.7); the 3'OH of the transferred strand from one IS end may attack the other to generate a donor molecule with a single strand bridge which is then replicated to produce a double strand transposon circle intermediate and regenerating the original donor molecule known as copy-paste or more precisely Donor Primed Replicative Transposition (DPRT) (e.g. IS3; (Chandler, et al., 2015)(Fig 1.8.2 pathway e)(IS911 movie); or the 3'OH at the flank of the non-transferred strand may attack the second strand to form a hairpin on the flanking DNA and a 3'OH on the transferred strand (at present this has only been demonstrated for eukaryotic TE of the hAT family and in V(D)J recombination (Zhou, et al., 2004)) (Fig 1.8.2 pathway g). Clearly, many families produce double-strand circular intermediates but this does not necessarily mean that they all use the copy-paste DPRT mechanism since a circle could formally be generated by excision involving recombination of both strands (Hickman & Dyda, 2015). These differences are reflected in the different IS families.

References :

• Chandler M, Fayet O, Rousseau P, Ton Hoang B & Duval-Valentin G (2015) Copy-out-Paste-in Transposition of IS911: A Major Transposition Pathway. Microbiol Spectr 3.
• Curcio MJ & Derbyshire KM (2003) The outs and ins of transposition: from Mu to Kangaroo. Nat Rev Mol Cell Biol 4: 865-877.
• Davies DR, Braam LM, Reznikoff WS & Rayment I (1999) The three-dimensional structure of a Tn5 transposase-related protein determined to 2.9-A resolution. J.Biol.Chem. 274: 11904-11913.
• Fayet O, Ramond P, Polard P, Prere MF & Chandler M (1990) Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences? Mol Microbiol 4: 1771-1777.
• Feng X & Colloms SD (2007) In vitro transposition of ISY100, a bacterial insertion sequence belonging to the Tc1/mariner family. Mol Microbiol 65: 1432-1443.
• Haniford DB & Ellis MJ (2015) Transposons Tn10 and Tn5. Microbiol Spectr 3: MDNA3-0002-2014.
• Hickman AB & Dyda F (2015) Mechanisms of DNA Transposition. Microbiol Spectr 3: MDNA3-0034-2014.
• Hickman AB, Chandler M & Dyda F (2010) Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Critical Reviews in Biochemistry and Molecular Biology 45: 50-69.
• Hickman AB, Perez ZN, Zhou L, et al. (2005) Molecular architecture of a eukaryotic DNA transposase. Nat Struct Mol Biol 12: 715-721.
• Khan E, Mack JP, Katz RA, Kulkosky J & Skalka AM (1991) Retroviral integrase domains: DNA binding and the recognition of LTR sequences [published erratum appears in Nucleic Acids Res 1991 Mar 25;19(6):1358]. Nucleic Acids Res. 19: 851-860.
• Kulkosky J, Jones KS, Katz RA, Mack JP & Skalka AM (1992) Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol.Cell Biol. 12: 2331-2338.
• 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.
• Plasterk RH (1996) The Tc1/mariner transposon family. Curr.Top.Microbiol.Immunol. 204: 125-143.
• Turlan C & Chandler M (2000) Playing second fiddle: second-strand processing and liberation of transposable elements from donor DNA. Trends Microbiol 8: 268-274.
• Zhou L, Mitra R, Atkinson PW, Burgess Hickman A, Dyda F & Craig NL (2004) Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432: 995-1001.