Functional Organization and Insertion Specificity of IS 607 , a Chimeric Element of Helicobacter pylori

Abstract

ABSTRACT 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 IS 607 , which further PCR and hybridization tests indicated was present in about one-fifth of H. pylori strains worldwide. IS 607 contained two open reading frames (ORFs) of possibly different phylogenetic origin. One ORF ( orfB ) exhibited protein-level homology to one of two putative transposase genes found in several other chimeric elements including IS 605 (also of H. pylori ) and IS 1535 (of Mycobacterium tuberculosis ). The second IS 607 gene ( orfA ) was unrelated to the second gene of IS 605 and might possibly be chimeric itself: it exhibited protein-level homology to merR bacterial regulatory genes in the first ∼50 codons and homology to the second gene of IS 1535 (annotated as “resolvase,” apparently due to a weak short recombinase motif) in the remaining three-fourths of its length. IS 607 was found to transpose in Escherichia coli , and analyses of sequences of IS 607 -target DNA junctions in H. pylori and E. coli indicated that it inserted either next to or between adjacent GG nucleotides, and generated either a 2-bp or a 0-bp target sequence duplication, respectively. Mutational tests showed that its transposition in E. coli required orfA but not orfB , suggesting that OrfA protein may represent a new, previously unrecognized, family of bacterial transposases.