Evolutionary dynamics of the vapD gene in Helicobacter pylori and its wide distribution among bacterial phyla

The vapD gene is present in microorganisms from different phyla and encodes for the virulence-associated protein D (vapD). In some microorganisms, it has been suggested that vapD participates in either protecting the bacteria from respiratory burst within the macrophage or in facilitating the persistence of the microorganism within the respiratory epithelial cell. The aim of this study was to define the phylogenetic relationship of the Helicobacter pylori vapD gene with other vapD genes of different bacterial species from different phyla and to estimate the genealogy of vapD gene within H. pylori species. Sixteen sequences of Helicobacter pylori vapD gene obtained from Mexican patients and 211 vapD sequences from 72 species of six bacterial phyla were analysed. Our results showed that the vapD region is a hot spot that presents a greater diversity in the Mexican strains of H. pylori to that previously reported. Rearrangements in the vapD region led to the formation of new ORFs in Mexican strains, which were not seen as being fortuitous, suggesting that these chromosomal rearrangements might provide some type of advantage to the bacteria. Phylogenetic analysis, codon usage bias and GC content indicated that vapD was acquired by horizontal gene transfer. Then, in some H. pylori strains it was incorporated and fixed into the bacterial chromosome and maintained in these strains in a similar fashion as an essential gene. Genealogical analysis of the H. pylori vapD gene showed two divisions: one that grouped most of the strains from different parts of the world and the other that grouped only Mexican strains together with the 60190 and 26695 reference strains. Keywords: vapD gene; Helicobacter pylori; Genealogy; Phylogeny; Horizontal Gene Transfer.