IS200
IS200 was originally identified in S. typhimurium (270) but related elements have since been found in a variety of bacterial species including certain Shigella (157), Clostridia (58), and S. pneumoniae (Claverys, J.P. Personnal communication). The most recent sequence determination (38) indicates that IS200 is 707 bp long with a single orf preceded by several sequences capable of forming hairpin structures (Fig.). One of these, identified within 20 bp of the end, is thought to act as a transcriptional terminator and to prevent impinging transcription from activating the element (270), while another may sequester the ribosome binding site of the Tpase gene (38). IS200 does not carry terminal IRs. Despite much effort, few cases of IS200 transposition or other forms of rearrangement have been documented (177). In the few examples of IS200 insertions in the S. typhimurium genome where the sequence of the unoccupied target site is also known, it seems clear that transposition resulted from a simple insertion of IS200 alone (38,64).
IS605
Although IS200 has been described as an autonomous element, it is often associated with other orfs in the form of a composite element ( Fig.). This was first observed with IS605 from Helicobacter pylori (246, 476) where it was called orfA and is associated with a second divergently transcribed orf, orfB. OrfB is related to the putative Tpase of IS1341. It is also related to the gipA gene of the the Gifsy-1 phage of S. typhimurium which, since it affects the survival of its host in Peyer's Patches, has been implicated in virulence functions (454). IS605 is found in over one third of nearly 300 independent H. pylori isolates (246). It is repeated several times in the genome of various strains and both reading frames are always associated (246,476). That IS605 is a transposable unit was demonstrated in a mating-out assay in E. coli using a native copy to supply transposition functions and a derivative in which orfA and orfB had been partially replaced by a CmR gene (246). Moreover, analysis of the metronidazole resistant strain NCTC11637 indicated that resistance was due to interruption of the nitroreductase gene by a mini-IS605 and an adjacent deletion (105). The mini-IS605 was similar to that found at one end of the cag pathogenicity island in strain N11638 (72). It includes 41 bp from the left and 33 bp from the right end of IS605 and is present in multiple copies in strains 26695 and J99 (105). Comparison of occupied and unoccupied sites in various H. pylori strains and in the pOX38 plasmid used as a target in the E. coli mating out assay indicated that IS605 inserts with high sequence specificity 3' to the sequences 5'-TTTAA-3' or 5'-TTTAAC-3' such that the left (IS200 homolog) end is proximal to the target sequence. A second related sequence, IS606, was also identified in Helicobacter pylori. This was present in one third of nearly 40 strains, many of which many did not carry IS605. The potential products of orfA and orfB reading frames share 25% and 28% identity respectively to those of IS605 itself.
IS605 is not restricted to Helicobacter pylori (Fig.). A significant number of IS200-like isolates from many other species have been found adjacent to orfs resembling orfB (Table). However, the genes are not always found in a divergent orientation. In Deinococcus radiodurans (IS8301), Dichelobacter nodosus (IS1253: 43) and Thermotoga maritima for example, they occur in the same orientation and may overlap. A similar arrangement, without overlap, is found in the Halobacterium element ISH1-8 in which orfB is related to the putative Tpase of IS891. Apparently isolated copies of OrfB-related orfs have been reported. This is the case for IS891, which has been reported to transpose (21) and IS1136 (122) and IS1341 (342) which have not.
Copies of orfB-related reading frames have also been found associated with alternative orfA frames (Fig.). IS607 identified in a clone obtained from a gastritis strain of H. pylori is present in about one fifth of H. pylori strains tested (247). It is composed of two consecutive orfs with a nine codon overlap. The downstream frame is related to orfB while the upstream frame is related to potential "resolvase" genes associated with other ISs. IS607 was shown to transpose at a low frequency in E. coli and requires orfA but not orfB. Comparison of occupied and unoccupied sites in H. pylori and in the E. coli system indicated that IS607 terminates with the dinucleotide 5'-GC-3', carries rather imperfect terminal inverted repeats of approximately 45 bp and inserts between two adjacent G nucleotides without generating DRs (247).
Another element, IS1535, was previously identified as a repeated sequence in the M. tuberculosis H37Rv genome where is was proposed to consitute a new IS family (163). IS1535 (together with IS1537, IS1538 and IS1539) exhibits ends very similar to those of IS607, and, like IS607, is flanked by a G nucleotide in the target site. It also carries two consecutive orfs. The downstream orfB shows significant similarity with that of IS605 and IS607 and the upstream orfA shows similarity with orfA of IS607.
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.
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Last modification : December 20 2001