Direct target repeats

Another general feature of IS elements is that, on insertion, most generate short directly repeated sequences (DR) of the target DNA flanking the IS. Attack of each DNA strand at the target site by one of the two transposon ends in a staggered way during insertion provides an explanation for this observation. The DR is generated by repair of the "gap" between cleavage sites (Fig 1.28.1). The length of the DR, generally between 2 and 14 bp, is characteristic for a given element and a given element will generally generate a duplication of fixed length. This is determined by the architecture of the transposition complex or transpososome which imposes constraints on the distance between cleavages on each strand of the target DNA (Gueguen, et al., 2005), (Dyda, et al., 2012), (Montano & Rice, 2011). However, certain ISs have been shown to generate DRs of atypical length at a low frequency, presumably reflecting small variations in the geometry of the transpososome (see (Hickman & Dyda, 2015)). Although some notable exceptions exist in which there is a systematic absence of DRs (either within a given family or in several independent transposition events of a given element), care should be taken in interpreting the absence of DRs in isolated cases. A lack of DRs can simply result from homologous inter- or intra-molecular recombination between two IS elements, each with a different DR sequence. This would result in a hybrid element carrying one DR of each parent. It can also arise from the formation of adjacent deletions resulting from duplicative intramolecular transposition. In this case, a single copy of the DR is located on each of the reciprocal deletion products (see for example (Weinert, et al., 1983) and (Turlan & Chandler, 1995) or, more recently in a clinical context, (He, et al., 2015).

Three IS, IS1549, IS1634 and IS1630, have been identified which appear to generate long DRs of quite variable length (Calcutt, et al., 1999), (Plikaytis, et al., 1998), (Vilei, et al., 1999). Two, IS1549 and IS1634, are distantly related to the IS4 family and one, IS1630, belongs to the IS30 family. The mechanism involved in generating such long DRs is at present unknown. However, it seems reasonable to propose that the target DNA may be able to form a loop within the transpososome and thereby bringing somewhat distant phophodiester bonds into close proximity.

References :

• Calcutt MJ, Lavrrar JL & Wise KS (1999) IS1630 of mycoplasma fermentans, a novel IS30-type insertion element that targets and duplicates inverted repeats of variable length and sequence during insertion. J.Bacteriol. 181: 7597-7607.
• Dyda F, Chandler M & Hickman AB (2012) The emerging diversity of transpososome architectures. Q Rev Biophys 45: 493-521.
• Gueguen E, Rousseau P, Duval-Valentin G & Chandler M (2005) The transpososome: control of transposition at the level of catalysis. Trends Microbiol 13: 543-549.
• He S, Hickman AB, Varani AM, Siguier P, Chandler M, Dekker JP & Dyda F (2015) Insertion Sequence IS26 Reorganizes Plasmids in Clinically Isolated Multidrug-Resistant Bacteria by Replicative Transposition. MBio 6: e00762.
• Hickman AB & Dyda F (2015) Mechanisms of DNA Transposition. Microbiol Spectr 3: MDNA3-0034-2014.
• Montano SP & Rice PA (2011) Moving DNA around: DNA transposition and retroviral integration. Curr Opin Struct Biol 21: 370-378.
• Plikaytis BB, Crawford JT & Shinnick TM (1998) IS1549 from Mycobacterium smegmatis forms long direct repeats upon insertion. J.Bacteriol. 180: 1037-1043.
• Turlan C & Chandler M (1995) IS1-mediated intramolecular rearrangements: formation of excised transposon circles and replicative deletions. Embo J 14: 5410-5421.
• Vilei EM, Nicolet J & Frey J (1999) IS1634, a Novel Insertion Element Creating Long, Variable-Length Direct Repeats Which Is Specific for Mycoplasma mycoides subsp. mycoides Small- Colony Type. J.Bacteriol. 181: 1319-1323.
• Weinert TA, Schaus NA & Grindley ND (1983) Insertion sequence duplication in transpositional recombination. Science 222: 755-765.