Cluster of Type IV Secretion Genes inHelicobacter pylori's Plasticity Zone

Abstract

Some genes present in only certain strains of the genetically diverse gastric pathogen Helicobacter pylori may affect its phenotype and/or evolutionary potential. Here we describe a new 16.3-kb segment, 7 of whose 16 open reading frames are homologs of type IV secretion genes (virB4, virB7 to virB11, and virD4), the third such putative secretion gene cluster found in H. pylori. This segment, to be called tfs3, was discovered by subtractive hybridization and chromosome walking. Full-length and truncated tfs3 elements were found in 20 and 19%, respectively, of 94 strains tested, which were from Spain, Peru, India, and Japan. A tfs3 remnant (6 kb) was found in an archived stock of reference strain J99, although it was not included in this strain's published genome sequence. PCR and DNA sequence analyses indicated the following. (i) tfs3's ends are conserved. (ii) Right-end insertion occurred at one specific site in a chromosomal region that is varied in gene content and arrangement, the "plasticity zone." (iii) Left-end insertion occurred at different sites in each of nine strains studied. (iv) Sequences next to the right-end target in tfs3-free strains were absent from most strains carrying full-length tfs3 elements. These patterns suggested insertion by a transposition-like event, but one in which targets are chosen with little or no specificity at the left end and high specificity at the right end, thereby deleting the intervening DNA.

DNA transfer in the gastric pathogen Helicobacter pylori

“…In addition, H. pylori uses the ComB T4SS for uptake of naked DNA during natural transformation, a very effective source to gain genetic variability [31], shown to be important for promoting chronic H. pylori infection [32]. The T4SS member tfs3 has also been postulated to have a function in horizontal DNA transfer [33]. Later on, a role in DNA transfer has also been proposed for another chromosomal locus named tfs4 [34].…”

“…Tfs3 is composed of 16 ORFs in the first described H. pylori strain, PeCan18B, and seven of them exhibit homology to those previously described for the virB/D4 operon in A. tumefaciens [33]. The functional role of tfs3, however, is still not clear, but some researchers suggested a possible implication in DNA transfer [33]. Interestingly, full-length and partially truncated tfs3 genes were found in 20 and 19 %, respectively, of 94 clinical H. pylori strains tested [33].…”

“…Due to the low G?C content in the tfs3 gene cluster as compared to the rest of the genome, it has been suggested that it was acquired by horizontal DNA transfer from another bacterial species [33]. Tfs3 is composed of 16 ORFs in the first described H. pylori strain, PeCan18B, and seven of them exhibit homology to those previously described for the virB/D4 operon in A. tumefaciens [33]. The functional role of tfs3, however, is still not clear, but some researchers suggested a possible implication in DNA transfer [33].…”

“…Apart from the cagPAI and comB T4SS genes, Kersulyte et al [33] identified a novel 16.3 kb gene cluster located in one of the three plasticity regions in H. pylori, which encodes a putative third T4SS, named as Tfs3 (Fig. 2).…”

Biochemical Characterization of Protein Complexes from the Helicobacter pylori Protein Interaction Map

“…Note that the Cag type IV secretion system is not the only type IV secretion system encoded by H. pylori. Two other gene clusters encoding such systems have been recently characterized: the ComB system, which serves as a DNA uptake machinery, and the Tfs3 system, which serves as conjugation system (30,31).…”