Evolutionary Dynamics of Insertion Sequences in Helicobacter pylori

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Abstract
Prokaryotic insertion sequence (IS) elements behave like parasites in terms of their ability to invade and proliferate in microbial gene pools and like symbionts when they coevolve with their bacterial hosts. Here we investigated the evolutionary history of IS 605 and IS 607 of Helicobacter pylori , a genetically diverse gastric pathogen. These elements contain unrelated transposase genes ( orfA ) and also a homolog of the Salmonella virulence gene gipA ( orfB ). A total of 488 East Asian, Indian, Peruvian, and Spanish isolates were screened, and 18 and 14% of them harbored IS 605 and IS 607 , respectively. IS 605 nucleotide sequence analysis ( n = 42) revealed geographic subdivisions similar to those of H. pylori ; the geographic subdivision was blurred, however, due in part to homologous recombination, as indicated by split decomposition and homoplasy tests (homoplasy ratio, 0.56). In contrast, the IS 607 populations ( n = 44) showed strong geographic subdivisions with less homologous recombination (homoplasy ratio, 0.2). Diversifying selection (ratio of nonsynonymous change to synonymous change, ≫1) was evident in ∼15% of the IS 605 orfA codons analyzed but not in the IS 607 orfA codons. Diversifying selection was also evident in ∼2% of the IS 605 orfB and ∼10% of the IS 607 orfB codons analyzed. We suggest that the evolution of these elements reflects selection for optimal transposition activity in the case of IS 605 orfA and for interactions between the OrfB proteins and other cellular constituents that potentially contribute to bacterial fitness. Taken together, similarities in IS elements and H. pylori population genetic structures and evidence of adaptive evolution in IS elements suggest that there is coevolution between these elements and their bacterial hosts.