Functional organization and insertion specificity of IS607, a chimeric element of Helicobacter pylori

A search by subtractive hybridization for sequences present in only certain strains of Helicobacter pylori led to the discovery of a 2-kb transposable element to be called IS607, which further PCR and hybridization tests indi cated was present in about one-fifth of H. pylori strains worldwide, IS607 contained two open reading frames (ORFs) of possibly different phylogenetic origin. One ORF (orfB) exhibited protein-level homolog to one of two putat ive transposase genes found in several other chimeric elements including IS 605 (also of H, pylori) and IS1535 (of Mycobacterium tuberculosis). The sec ond IS607 gene (orfA) was unrelated to the second gene of IS605 and might p ossibly be chimeric itself: it exhibited protein-level homology to merR bac terial regulatory genes in the first similar to 50 codons and homology to t he second gene of IS1535 (annotated as "resolvase," apparently due to a wea k short recombinase motif) in the remaining three-fourths of its length, IS 607 was found to transpose in Escherichia coli, and analyses of sequences o f IS607-target DNA junctions in H. pylori and E. coli indicated that it ins erted either next to or between adjacent CG nucleotides, and generated eith er a 2-bp or a 0-bp target sequence duplication, respectively, Mutational t ests showed that its transposition in E. coli required orfA but not orfB, s uggesting that OrfA protein may represent a new, preciously unrecognized, f amily of bacterial transposases.