Novel sequence organization and insertion specificity of IS605 and IS606: Chimaeric transposable elements of Helicobacter pylori

IS605, an insertion sequence (IS) that is unusual in containing homologs of genes for the single putative transposases of two other unrelated IS elements (IS200 and IS1341), was found in nearly one-third of a set of 238 independent isolates of the gastric pathogen Helicobacter pylori. Hybridization and PCR tests indicated that any strain carrying one of these ORFs also carried the other, which implies that both ORFs are in the same unit of transposition. The IS605 ends and target sites for insertion were identified by sequencing eight preexisting insertions in strain NCTC11638, corresponding empty sites in other strains, and new transpositions in E. coli of an IS605 derivative marked with a selectable chloramphenicol-resistance gene. These tests showed that IS605 is also unusual in: (1) having unique, not inverted repeat, ends; (2) not duplicating (or deleting) target sequences during transposition; and (3) inserting with its left (IS200-homolog) end next to 5'-TTTAA or 5'-TTTAAC. IS605 was implicated in at least two genome rearrangements in strain NCTC11638. A second member of the IS605 family, called IS606 (25% amino acid identity to IS605 in inferred proteins) was found in one-third of 38 H. pylori strains tested, many of which did not carry IS605. The features of these two chimaeric IS elements are discussed in terms of possible transposition mechanisms, IS element evolution, and effects of IS elements on genome organization and evolution in the microbes that they inhabit.