General features
The IS5 family, like the IS4 family, is also a relatively heterogeneous group and also includes sequences from both eubacteria and the archae. The majority carry only a single orf. Their lengths range from 850 bp (IS869) to 1643 bp (IS493). The latter carries a second open reading frame upstream of the "Tpase" frame which is inessential for transposition (20). Similarly, IS4811 (Tn4811 (83)), which is greater than 5kb, clearly contains other as yet uncharacterised genes. The major feature which defines this group is the similarities between their putative Tpases (404). In particular this includes the N2, N3 and C1 domains carried by the IS4 group (Fig). However, Tpases of the IS5 family exhibit a spacing between the N3 and C1 domains of approximately 40 residues, a distance more consistent with the canonical DDE motif. This group had been divided into 6 or 7 subgroups according to the depth of branching between them (Fig.A) (310). Analysis of the largely increased number of members generally confirms these subgroups. Members within each group also generate DRs of similar lengths (IS5, 4 bp; ISL2, 2-3 bp; IS1031, 3-4 bp; IS903, 8-9 bp; and IS427, 2-3 bp). The IS903 subgroup appears distinct from the halobacterial ISH1, ISH28 and ISH9 elements which form a cluster. Although included in this figure for convenience, they have been placed in "Emerging families" The division is supported by similarities in the terminal IRs (Fig. 10B), by correlation with the length of the target duplication and, to a lesser extent, by the typical length of the entire IS (Table). It is important to note that most members of the IS427 subgroup exhibit two partially overlapping open reading frames in a configuration in which the downstream frame is in phase -1 compared to the upstream frame and most have a potential -1 frameshift window. In order to perform the analysis shown in Fig.A these orfs were artificially fused. Several members of the family are associated with compound transposons. These include IS903 and IS602, which form part of the kanamycin resistance transposons Tn903 (166) and Tn602 (457) respectively, and ISVa1/ISVa2 which form part of a transposon carrying iron transport genes (475).
Several members exhibit GATC sites within their terminal 50 bp. This includes all members of the IS903 subgroup and many members of the IS1031 and IS427 subgroups. IS903 transposition activity has been shown to be modulated by Dam in vivo (cited in 408).
A preferred target sequence, YTAR (often CTAG), is observed for two subgroups, IS5 and IS427, and for two members of the ISL2 group (IS112 and IS1373) in which either all four base pairs or the central TA are duplicated on insertion. It is important to underline that, in many cases, the sequence of the original target site before insertion is not available. This can introduce ambiguities not only in estimating the number of duplicated target base pairs but also in defining the IRs. It is particularly important in several cases where the target repeat is symmetrical (e.g. CTAG) and where it is impossible to distinguish whether the element duplicates 2 or 4 bp and therefore to determine the exact ends of the element. Alignment of the ends of these elements in subgroups has permitted a number of ambiguities to be resolved. Members of the ISL2 group which generate 3 bp DRs exhibit a preference for ANT while those from the IS1031 group (which generate exclusively a 3 bp DR) exhibits a preference for insertion sites with the sequence TNA. Neither the small ISH1 group (8 bp DRs) nor the IS903 group (9 bp DRs) exhibit marked target specificity (see IS903 and also Target specificity).
Only two of these elements, IS5 and IS903, have received significant attention.
IS5
In spite of the importance of IS5 in generating mutations, the published work concerning this element is largely directed to an understanding of its coding capacity and expression properties. IS5 carries one large orf, ins5A, spanning the entire element and shown to be essential for transposition (see 421), and two small orfs (ins5B and 5C, 234) whose relevance to transposition remains to be demonstrated. Nothing is known about the transposition mechanism of this element.
IS903
The ends of IS903 carry IRs of 18 bp which exhibit the typical two-domain organisation ( Fig) (114). Transposase has been shown to bind specifically to the ends using a region located in the amino-terminal portion of the protein (112, 469). In addition, a region possibly involved in the formation of higher order multimers has been identified and residues probably involved in catalysis have been pinpointed among the conserved residues in the catalytic DDE domain (469). An elegant genetic analysis provided strong evidence that IS903 is not only capable of undergoing direct insertion but can also generate adjacent deletions in a duplicative manner (356). Moreover, point mutations in the terminal base pair of the IRs decrease overall transposition frequency but increase the frequency of cointegrate formation (467). Similarly, mutation of the first nucleotide flanking an IR also influences the level of cointegrate formation (468). The level of cointegrate formation can also be increased by mutation of the Tpase. The molecular nature of these effects requires further investigation.
As discussed above (see Target specificity) a two fold symmetric consensus target sequence has been elaborated for IS903 and is highly efficient (207).
Jacques Mahillon and Michael Chandler (1998)
Microbiology and Molecular Biology
Reviews. 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.
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last modification : January 4 2002