Abstract
BackgroundThe human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. Its persistence in the stomach mucosa is facilitated by several mechanisms of immune evasion and immune modulation, but also by an unusual genetic variability which might account for the capability to adapt to changing environmental conditions during long-term colonization. This variability is reflected by the fact that almost each infected individual is colonized by a genetically unique strain. Strain-specific genes are dispersed throughout the genome, but clusters of genes organized as genomic islands may also collectively be present or absent.ResultsWe have comparatively analysed such clusters, which are commonly termed plasticity zones, in a high number of H. pylori strains of varying geographical origin. We show that these regions contain fixed gene sets, rather than being true regions of genome plasticity, but two different types and several subtypes with partly diverging gene content can be distinguished. Their genetic diversity is incongruent with variations in the rest of the genome, suggesting that they are subject to horizontal gene transfer within H. pylori populations. We identified 40 distinct integration sites in 45 genome sequences, with a conserved heptanucleotide motif that seems to be the minimal requirement for integration.ConclusionsThe significant number of possible integration sites, together with the requirement for a short conserved integration motif and the high level of gene conservation, indicates that these elements are best described as integrating conjugative elements (ICEs) with an intermediate integration site specificity.
Highlights
The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections
That genome plasticity plays a role in bacterial persistence is further supported by the observation that natural transformation competence, which is upregulated upon DNA stress [8], promotes persistent colonization in mice [9]
Possible integration sites are located on the integrating conjugative elements (ICEs) elements themselves, and we found several cases where one ICE is integrated into another
Summary
The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. With the availability of more sequencing data and more complete H. pylori genome sequences, it became clear that parts of the plasticity regions are usually organized as genomic islands that may be integrated in one of several different genetic loci They generally contain complete sets of genes required to produce type IV secretion machineries, as well as genes encoding different DNAprocessing proteins [11,15,16], suggesting that they are mobile genetic elements capable of horizontal gene transfer between bacterial cells, and that they might be best described as conjugative transposons or integrating conjugative elements (ICEs)
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