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.
- 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.
TA, Schaus NA & Grindley ND (1983) Insertion sequence duplication in
transpositional recombination. Science 222: 755-765.