General features and properties of insertion sequence elements

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Host factors

Transposition activity is frequently modulated by various host factors. These effects are generally specific for each element. A non-exhaustive list of such factors includes the DNA chaperones (or histone-like proteins), IHF, HU, HNS, and FIS, the replication initiator DnaA, the protein chaperone/proteases ClpX, P, and A, the SOS control protein LexA, and the Dam DNA methylase. In addition, proteins which govern DNA supercoiling in the cell can also influence transposition.


DNA chaperones may play roles in assuring the correct three dimensional architecture in the evolution of various nucleoprotein complexes necessary for productive transposition. They may also be involved in regulating Tpase expression. IHF, HU, HNS, and FIS have all been variously implicated in the case of bacteriophage Mu, in the control of Mu gene expression or directly in the transposition process (see (Chaconas et al., 1996)for review).

Several elements carry specific binding sites for IHF within, or close to, their terminal IRs. These can lie within (e.g. IS1: (Gamas et al., 1985); IS903: see (Grindley & Joyce, 1980) or close to (IS10: (Kleckner, et al., 1996)) the Tpase promoter. IHF appears to influence the nature of IS10 transposition products by binding to a site 43 bp from one end (Signon & Kleckner, 1995), (Chalmers, et al., 1998), (Sakai, et al., 1995).IHF also stimulates Tpase binding to the ends of the Tn3 family member, Tn1000 or γδ (Wiater & Grindley, 1988). Ironically, although IS1 was the first element in which IHF sites were identified (one within each IR), conditions have not yet been found in which IHF shows a clear effect on transposition or gene expression (D. Zerbib and M.C. unpublished results). The multiple roles of several of these proteins in both the IS10 and Tn5 (IS50) systems and the dynamics of their involvement has been determined in detail (Ward, et al., 2007, Singh, et al., 2008, Wardle, et al., 2009, Whitfield, et al., 2009, Haniford & Ellis, 2015)(Liu, et al., 2005)(Chalmers, et al., 1998, Crellin & Chalmers, 2001, Sewitz, et al., 2003, Crellin, et al., 2004)

The histone-like nucleoid structuring protein H-NS, a global transcriptional regulator, has also been implicated in the regulation of bacterial transposition systems, including Tn10 (Wardle, et al., 2005, Ward, et al., 2007, Wardle, et al., 2009). It appears to promote transposition by binding directly to the transposition complex (or transpososome).


In the case of IS50, an element of the same family as IS10, both the protein Fis and the replication initiator protein DnaA have been reported to intervene in transposition (see(Reznikoff, 1993). Finally another "histone-like" protein, HNS, has been reported to stimulate transposition of IS1 in certain circumstances (Shiga, et al., 1999).

Although their mode of action is at present unknown, several other host proteins with otherwise entirely different functions have been implicated in transposition.

Accessory proteins: Acyl carrier protein (ACP), ribosomal protein L29, PepA and ArgR

Acyl carrier protein (ACP) was independently shown to stimulate 3' end cleavage of Tn3 by its cognate Tpase (Maekawa, et al., 1996) and, together with ribosomal protein L29, to greatly increase binding of TnsD (a protein involved in Tn7 target selection) to the chromosomal insertion site, attTn7 (Sharpe & Craig, 1998). Moreover ACP and L29 moderately stimulate Tn7 transposition in vitro while L29 alone has a significant stimulatory effect in vivo (Sharpe & Craig, 1998). The mode of action of these proteins may be similar to that of the accessory proteins PepA and ArgR which modify the architecture of the synaptic complex in certain XerC/XerD-mediated site-specific recombination reactions (Hallet & Sherratt, 1997)

ClpX, ClpP, and Lon

Certain factors involved in protein "management" such as ClpX, ClpP, and Lon have been implicated in transposition. ClpX is essential for Mu growth (Mhammedi-Alaoui, et al., 1994) where it is required for disassembling the transposase-DNA complex or the transpososome strand transfer complex in preparation for the assembly of a replication complex (Kruklitis, et al., 1996), (Levchenko, et al., 1995). Recognition of Mu transposase, pA, by ClpX requires the terminal 10 amino acids of pA (Levchenko, et al., 1997). Together with ClpP, ClpX also plays a role in proteolysis of the Mu repressor (Laachouch, et al., 1996), (Welty, et al., 1997). The Lon protease is implicated in proteolysis of the IS903 transposase (Derbyshire, et al., 1990, Derbyshire & Grindley, 1996).

At present the involvement of these proteins in the transposition of other elements has not been well documented.

SOS system, RecA, RecBC

The third class of host factor includes host cell systems which act to limit DNA damage and maintain chromosome integrity. Studies with IS10 (see (Kleckner, et al., 1996) and IS1 (Lane, et al., 1994) have demonstrated that high levels of Tpase in the presence of suitable terminal IRs lead to induction of the host SOS system. As discussed previously (Mahillon & Chandler, 1998), some controversy still exists concerning the role of RecA in Tn5 (IS50) transposition (Kuan, et al., 1991, Kuan & Tessman, 1991), (Weinreich, et al., 1991). Reznikoff and colleagues have provided genetic evidence that transposition is inhibited by induction of the SOS system in a manner which does not require the proteolytic activity of RecA (Weinreich, et al., 1991). On the other hand, Tessman and collaborators (Kuan, et al., 1991, Kuan & Tessman, 1991, Kuan & Tessman, 1992) using a different transposition assay have found that constitutive SOS conditions actually enhance Tn5 transposition. Moreover, using yet another assay system, Ahmed (Ahmed, 1986) has concluded that intermolecular transposition of Tn5 is stimulated by RecA. Further investigation is clearly required to understand these apparently incompatible results.

Ahmed has also concluded that intermolecular transposition of the IS1-based transposon, Tn9, behaves in a similar way to that of Tn5 with respect to the recA allele (Ahmed, 1986). In contrast, however, the frequency of adjacent deletions mediated by IS1 was significantly increased in the absence of RecA. This has received some independent support using a physical assay where it was shown that deletion products accumulate in a recA but not in a wildtype host. Moreover, like IS1 induction of the SOS system, accumulation of such adjacent deletions was dependent on recBC (Zablweska et al., unpublished observations). The recBC genes are also implicated in the behavior of transposons such as Tn10 and Tn5 (Ahmed, 1986), (Lundblad, et al., 1984) where they affect precise and imprecise excision in a process independent of transposition per se. This is more pronounced with composite transposons in which the component insertion sequences IS10 and IS50 are present as inverted repeats, and is stimulated when the transposon is carried by a transfer-proficient conjugative plasmid. It seems probable that such excisions occur by a process involving replication fork slippage (see (Galas & Chandler, 1989),(Nagel & Chan, 2000), (Reddy & Gowrishankar, 2000) for further discussion).

PolI and gyrase

Both DNA polymerase I (Sasakawa, et al., 1981), (Syvanen, et al., 1982) and DNA gyrase (Isberg & Syvanen, 1982), (Sternglanz, et al., 1981) are implicated in the transposition of Tn5. While the effect of gyrase may reflect a requirement for optimal levels of supercoiling, the role of PolI remains a matter of speculation. It may be involved in DNA synthesis necessary to repair the single strand gaps resulting from staggered cleavage of the target and which gives rise to the DRs. DNA gyrase has also been shown to be important in transposition of bacteriophage Mu (Pato, et al., 1995, Pato & Banerjee, 1996).

Dam methylase

Another host function, the Dam DNA methylase can be important in modulating both Tpase expression and activity. IS10, IS50 and IS903 all carry methylation sites (GATC) in the transposase promoter regions and in each case, promoter activity is increased in a dam- host (Roberts, et al., 1985), (Yin, et al., 1988). Additional evidence has been presented that the methylation status of GATC sites within the terminal inverted repeats also modulates the activity of these ends (Roberts, et al., 1985). For IS50, this can now be understood in terms of steric interference in the transposase active site, as recently revealed by the determination of the crystal structure of a synpatic complex including its Tpase and a pair of precleaved transposon ends (Davies, et al., 1999). Similar methylation sites have been previously observed in IS3, IS4, and IS5. A survey of the elements included in the data base has shown that most groups or families contain members which have GATC sites within the first 50 bp of one or both extremities. The IS3, IS5 and IS256 families include the most members carrying such sites. Except for IS3 itself where strong stimulation of transposition has been observed in a dam-host, in most of these cases the biological relevance of these sites is unknown. Moreover, it should be pointed out that the probability that any 100 bp DNA sequence carries the GATC tetranucleotide is about 40%. The role of Dam methylation in IS10 and IS50 transposition is described in detail in the appropriate sections dealing with these elements.

Metabolic control elements

In a screen of over 20,000 independent insertion mutants for host factors that influence IS903 transposition the Derbyshire lab isolated more than 100 mutants that increased or decreased transposition and also altered its timing during colony growth (Twiss, et al., 2005). These included independent mutations in a gene required for fermentative metabolism during anaerobic growth resulting in "early" transposition during colony growth and was suppressed by addition of fumarate, and other mutations in genes associated with DNA metabolism, intermediary metabolism, transport, cellular redox, protein folding and proteolysis. Other mutations were isolated in pur genes involved in purine biosynthesis. Further analysis suggested that this phenotype was due to a requirement for GTP in IS903 transposition (Coros, et al., 2005). It should be noted that some of these mutants also affected transposition of IS10 and of Tn552.


Finally, the RNA chaperone Hfq has also been implicated in the regulation of Tn10 transposition by promoting RNAout interaction with transposase mRNA (Ross, et al., 2013, Ellis, et al., 2015, Ellis, et al., 2015).

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