IS1 was one of the first bacterial insertion sequences to be isolated and characterized (139, 199). The original examples were obtained from an F'lac-proB plasmid (IS1K [230]) and the multiple drug resistance plasmid R100 (IS1R [357]). The nucleotide sequences of several variants of this IS from Escherichia and Shigella species have been determined (278, 485, 530). Of the 17 initially compared, three were duplicates and one only partially complete. Nine of the others exhibited sequence divergence of between 0.52 and 10% at the nucleic acid level. These were called IS1 isoforms. Two examples, IS1N and IS1H,are significantly different from the others (45 to 47% divergence in nucleotide sequence; 55 to 58% divergence at the protein level) but similar to each other (14 to 19% divergence at the protein level) and might be considered distinct members of the family. Except for IS1K(A) and IS1R(G), transposition of these elements has not been directly demonstrated experimentally in a controlled way but is implied from the isolation of mutants with spontaneous mutations in various genes. IS1 is a component of several compound transposons such as Tn9 (301) and Tn1681 (447), where it is present in direct or inverted orientation flanking a chloramphenicol acetyltrans-ferase and heat-stable toxin gene, respectively.
Although IS1 was thought to be restricted to the enterobacteria, a distant relative, IS1Sa, has recently been detected in the nucleotide sequence of the Synechocystis genome (233, 311). There are 3 integral copies of 802 bp and 11 partial or vestigal copies of varying length all of which can be considered as isoforms. This is illustrated in the dendrogram presented in Fig. 6A based on the relationship between the InsB region (see below). The InsB frame shows about 25-30% identity at the protein level with their E. coli relatives. However, the InsA frame (see below) and the 22 bp terminal inverted repeats are significantly different (Fig.B). Another relative, not included in this figure, has recently been identified in the Sulfolobus solfataricus genome (Y18930; coordinates 254390 - 255563). It carries a single orf spanning both insA and insB, is longer (1174 bp) and appears to have long IRs of > 50 bp. It is also related to sequences from Aquifex aeolicus and Halobacterium sp. (34).
Integration of IS1 is accompanied by duplication of generally 9 bp in the target DNA at the site of insertion (66, 165).Direct target repeats of 8, 10, and 14 bp (215, 302, 434) have also been observed. The frequency of their appearance is increased by mutations within the Tpase gene (302). The element exhibits a strong preference for insertion into AT-rich target regions (146, 328, 526).
IS1 (Fig.) is one of the smallest "autonomous" bacterial insertion sequences isolated so far. It is 768 bp long, includes two approximately 23 bp imperfect inverted repeats (IRL and IRR) located at its ends (230, 356), and two partly overlapping open reading frames (insA and insB') located in the 0 and -1 relative translational phases, respectively (Fig.A). The integrity of these frames is essential for transposition (227, 304).
An IS1 transcript is initiated from a promoter, pIRL, partially located in IRL (514) and is translated to give two products : InsA and InsAB'. The first and more abundant protein is encoded by the insA frame alone. The small, basic InsA protein binds specifically to the IRs (527, 529) and represses transcription from pIRL (303, 529). It also appears to inhibit transposition, probably by competing with the Tpase for binding to the ends of the element (131). In IS1Sa, InsA is longer at its C-terminal end by about 50 amino acids. The second protein, InsAB', is the Tpase of the element. Its production results from a programmed translational frameshift between the insA and insB’ frames which occurs at a frequency of approximately 1%. The site of frameshifting is an A6 C motif located at the 39 end of the upstream insA frame (131, 431) (Fig.B). A possible A7 frameshift signal followed by potential secondary structures can also be found in IS1Sa. Natural transposition of IS1 occurs at a relatively low frequency (approximately10-7 in a standard mating assay). Insertion of an additional A residue within the A6 C motif to yield A7 C or replacement of the motif with GA2 GA3 C fuses the two reading frames, leading to constitutive production of the Tpase while eliminating the production of InsA. This results in levels of transposition of between 0.1 and 1% in vivo (130, 131). Indirect evidence has been presented suggesting that a translational restart within the insA frame gives rise to an InsAB' protein with an N-terminal deletion. It has been proposed that this protein is the true Tpase (320, 321). No independent product of the downstream frame, insB’, alone has been detected. Transposition activity appears to depend on the InsAB9/InsA ratio (131). Since this is relatively insensitive to the intensity of transcription, this arrangement ensures that IS1 is not activated by high levels of impinging transcription following insertion into highly expressed genes.
An additional control of Tpase expression may be exercised at the level of transcription termination. Early studies on the organization of IS1 identified a region at the end of the insA gene which behaves as a Rho-dependent transcription terminator (210, 381). Premature transcription termination would therefore result in the production of an mRNA lacking the insB’ frame. The role of this sequence in the control of IS1 transposition remains to be determined.
IS1 generates both simple insertions and replicon fusions (cointegrates) composed of two directly repeated copies of the IS, one at each junction between the target and donor replicons. The occurrence of stable cointegrates as transposition end products led to the suggestion that transposition of IS1 can proceed in a replicative manner (148) while simple insertions may occur without replication (41). Thus, IS1 may be capable of both replicative and conservative transposition. More convincing evidence in support of a duplicative transposition pathway has recently been obtained by analyzing the products of intramolecular transposition (482). In addition, these and other studies (428) detected excised circular copies of the IS1-derived transposon, and it was suggested that, as in the case of IS911 (see "IS3 family"), such forms may integrate into a target molecule to give rise to simple insertions. A related type of transposition mechanism was previously proposed for IS1 transposition (390). Recent experiments have confirmed that such circles in which the IS ends are separated by a spacer of 6-9 bp are active in transposition and integrate with high efficiency. Insertion generates a typical target DR and is accompanied by loss of the spacer sequence (440).
High levels of InsAB' in the presence of suitable IS1 ends induce the host SOS response, possibly reflecting endonucleolytic activity of the IS1 Tpase (274). By using this in vivo assay system, originally developed for screening mutants of the IS10 Tpase (see " IS4 family"), it was possible to show that for relatively short artificial derivatives of IS1, the level of response depends in a periodic manner on the distance between the ends. The periodicity was found to be about 10 to 11 bp and was also reflected in the transposition activity, suggesting a requirement for correct helical positioning of both ends. Two directly repeated ends were also capable of eliciting the SOS response, although they were not capable of giving productive transposition.
The notion that a C-terminal H[200] R[203] Y[231] triad of InsAB' is catalytically important for IS1 as it is in integrases of the phage l family (436) should probably be reevaluated. Although the relative activities of mutants at these positions in IS1 parallel those of similar mutants in the Flp recombinase (436), this triad is not fully conserved in IS1Sa: while the R residue is conserved, the upstream H occurs one residue further upstream and the conserved Y is replaced by an F residue. Moreover, although neither IS1N (356) nor IS1H (530) have been analysed for their transposition activity, in both the H[200] is substituted for an R residue.
Mahillon J. and
Chandler M. (1998)
Microbiology
and Molecular Biology Reviews.
62 : 725-774
Chandler, M. and Mahillon, J.(2002) Insertion Sequences Revisited
Mobile DNA II Edited by N.L., Craig et al. ASM
Press 305-366
with permission of American Society of Microbiology the 10-26-01.
Last modification : December 20 2001