Sequence Organization and Insertion Specificity of the Novel Chimeric IS Hp609 Transposable Element of Helicobacter pylori

Abstract

ABSTRACT Here we describe IS Hp609 of Helicobacter pylori , a new member of the IS 605 mobile element family that is novel and contains two genes whose functions are unknown, jhp960 and jhp961 , in addition to homologs of two other H. pylori insertion sequence (IS) element genes, orfA , which encodes a putative serine recombinase-transposase, and orfB , whose homologs in other species are also often annotated as genes that encode transposases. The complete four-gene element was found in 10 to 40% of strains obtained from Africa, India, Europe, and the Americas but in only 1% of East Asian strains. Sequence comparison of 10 representative IS Hp609 elements revealed higher levels of DNA sequence matches (99%) than those seen in normal chromosomal genes (88 to 98%) or in other IS elements (95 to 97% for IS 605 , IS 606 , and IS 607 ) from the same H. pylori populations. Sequence analysis suggested that IS Hp609 can insert at many genomic sites with its left end preferentially next to TAT, with no target specificity for its right end, and without duplicating or deleting target sequences. A deleted form of IS Hp609 , containing just jhp960 and jhp961 and 37 bp of orfA , found in reference strain J99, was at the same chromosomal site in 15 to 40% of the strains from many geographic regions but again in only 1% of the East Asian strains. The abundance and sequence homogeneity of IS Hp609 and of this nonmobile remnant suggested a recent bottleneck and then rapid spread in H. pylori populations, possibly selected by the contributions of the elements to bacterial fitness.