DNA Sequence Conservation and Diversity in Transposable Element IS605 of Helicobacter pylori

Background. IS605, a transposable element-like sequence identified in the virulence-associated cag region of Helicobacter pylori reference strain NCTC11638, is unusual in containing two oppositely-oriented open reading frames whose products are homologues of the single transposases of the unrelated elements, IS200 and IS1341. Methods. One hundred independent H. pylori isolates from different parts of the world were screened by PCR and dot blot hybridization to determine the presence of IS605. For some positive isolates, southern hybridizations and sequence analyses were done. Results. Of the 100 isolates, 31 were found to contain sequences related to each ORF with orientation and spacing matching those in canonical IS605-hybridizing sequences. No isolate containing just one ORF and not the other was found. The frequencies of IS605 carriage were independent of geographical origin (U.S. vs. non-U.S.), and of the probable virulence of the isolate (cag status, toxin production or vacA alleles, patient symptoms). Southern blot hybridization of six IS605-containing strains revealed one to nine IS605 copies per genome. Two types of DNA sequence diversity were found: first, a specific 100 bp deletion in two isolates; second, base substitution divergence of 0.4% to 7.5% in pairwise comparisons among the eight isolates characterized, a level of divergence similar to that seen in other H. pylori chromosomal genes. Conclusions. Based on these findings, we speculate that IS605 is a relatively ancient component of the H. pylori gene pool that has proliferated in this species by horizontal gene transfer, homologous recombination, and transposition.