Transposable Element ISHp608 of Helicobacter pylori: Nonrandom Geographic Distribution, Functional Organization, and Insertion Specificity

The hundreds of known insertion sequences (ISs) of prokaryotes are diverse in overall structure and in detailed mechanism, specificity, and regulation of transposition (8, 21, 36). Typically, an IS found in one bacterial strain will be absent from many other strains of that species yet be closely related to ISs in other microbes. This pattern bears witness to a rich heritage of interspecies DNA transfer, which has resulted in the spread of individual ISs to taxonomic groups remote from those in which they arose. Their abundance also reflects the action of transposase proteins, which mediate IS movement without need for extensive DNA sequence homology; to the ability of these elements to proliferate in host genomes by transposition itself; and to contributions that these elements or genes associated with them (e.g., in composite drug resistance transposons) sometimes make to bacterial fitness. Many ISs and other tranposable elements specify just one transposase protein that acts as a multimer on matched (inverted repeat) sequences at each element end. Others, exemplified by Tn7, specify two different proteins that form a more complex transposase. With Tn7, each transposase protein has a distinct role in transposition, and additional Tn7-encoded proteins help select insertion sites and affect the efficiency of transposition, in part through interactions with host proteins (9, 31). A third type of element, exemplified by IS605 of the gastric pathogen Helicobacter pylori, contains just two transposition-related genes, each of which has protein level homology to the single putative transposase genes of other simpler one-gene ISs and thus may be of different phylogenetic origin (18, 19). The termini of these latter two types of elements tend to have less inverted repeat character, which implies that each end may be acted on differently by proteins of the transposition complex. Each of the two other ISs found to date in H. pylori (IS606 and IS607) is related to IS605 by protein level homologies in orfB (some 25 to 35% amino acid sequence identity) (18, 19), as is the new ISHp608 element described here (Fig. ​(Fig.1A).1A). This orfB (putative transposase gene) is also related to gipA, a gene found in a Salmonella prophage that contributes to virulence during murine infection (32). FIG. 1. IS element maps. (A) Structures of ISs of H. pylori. ISHp608 is 1,833 bp long, making it slightly smaller than its three other known H. pylori relatives (size range, 1,888 to 2,028 bp [18, 19]). Boxes represent ORFs: those with the same shading pattern ... Two branches of the IS605 family can be distinguished based on protein level homologies in orfA, one represented by IS607, whose transposition was found to be orfA dependent and orfB independent (19), and the other represented by IS605 and IS606 (18) and also the present ISHp608. The orfAs of IS605, IS606, and ISHp608 are protein level homologs of the putative transposase gene of IS200, an element that is abundant in natural isolates of Salmonella and Escherichia coli. Only a few cases of IS200 transposition have ever been detected, however, and the mechanisms of its movement are not understood (8, 21, 36). Sequences of IS605, IS606, and IS607 were each found in only a subset of H. pylori strains, always in chimeric (two-gene) elements, as depicted in Fig. ​Fig.1A.1A. In particular, none of the several hundred H. pylori strains tested to date was found to contain only orfA (or only orfB) without the cognate orfB (or orfA), positioned as in Fig. ​Fig.1A1A (18, 19). Formal models to explain such association include (i) OrfA and OrfB proteins serving together as the functional transposase, at least in H. pylori; (ii) transposition mediated by just one of these proteins but regulated (in terms of efficiency or specificity) by the other; (iii) each protein mediating transposition in a different set of bacterial species (implying relatively recent acquisition by H. pylori); or (iv) one gene needed for transposition and the other contributing to fitness. As background to the present studies, H. pylori chronically infects more than half of all people worldwide and is implicated in peptic ulcer disease and gastric cancer. Infections often begin in infancy, resulting from preferential transmission within the family or perhaps the local community, and tend to last for decades once established; new adult infections are rare (10, 12, 27, 38). H. pylori is also one of the most genetically diverse of bacterial species: independent isolates typically differ from one another by some 3 to 5% in DNA sequence in essential genes and can also differ markedly in gene content and chromosomal gene arrangement (1, 3, 4). This diversity is enhanced by recombination. In general, little if any linkage is found between alleles at different polymorphic sites in collections of strains from the same geographic region, a pattern referred to as free recombination (33). Superimposed on the extensive recombination between strains from the same region are indications that H. pylori gene pools differ geographically. This is based primarily on distributions of DNA sequence motifs in the virulence-associated vacA and cagA genes and of insertion and deletion motifs downstream of cagA (17, 20, 26, 37, 39). Strains from Europe, India, and East Asia were generally easily distinguished from one another using these tests, whereas those from a largely native population in Lima, Peru, seemed closely related to those of Spain. Much of the genetic diversity in local H. pylori populations and geographic differences in gene pools can be attributed to H. pylori's patterns of transmission (preferentially to children and within families), the extraordinary chronicity of infection, and the relative isolation of the strain(s) carried by any given person, noted above. In consequence, strains diverge from one another by random genetic drift and by selection for adaptation to the new gastric environments each person may present (15). Despite occasional mixed infection, there is only limited direct competition between H. pylori strains of different lineages and no effective selection for just a few genotypes that might be best suited for most people worldwide. Here we describe the discovery and characterization of ISHp608, found first in an H. pylori strain from Peru, features of its structure and transposition behavior, and its remarkably nonrandom distribution in human populations.