title: Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer.
abstract: The availability of multiple bacterial genome sequences has revealed a surprising extent of variability among strains of the same species. The human gastric pathogen Helicobacter pylori is known as one of the most genetically diverse species. We have compared the genome sequence of the duodenal ulcer strain P12 and six other H. pylori genomes to elucidate the genetic repertoire and genome evolution mechanisms of this species. In agreement with previous findings, we estimate that the core genome comprises about 1200 genes and that H. pylori possesses an open pan-genome. Strain-specific genes are preferentially located at potential genome rearrangement sites or in distinct plasticity zones, suggesting two different mechanisms of genome evolution. The P12 genome contains three plasticity zones, two of which encode type IV secretion systems and have typical features of genomic islands. We demonstrate for the first time that one of these islands is capable of self-excision and horizontal transfer by a conjugative process. We also show that excision is mediated by a protein of the XerD family of tyrosine recombinases. Thus, in addition to its natural transformation competence, conjugative transfer of genomic islands has to be considered as an important source of genetic diversity in H. pylori.
authors.affiliation: Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität, Pettenkoferstr. 9a, D-80336 München, Germany. fischer@mvp.uni-muenchen.de
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Fischer
authors.forename: Lukas
authors.initials: L
authors.lastname: Windhager
authors.forename: Stefanie
authors.initials: S
authors.lastname: Rohrer
authors.forename: Matthias
authors.initials: M
authors.lastname: Zeiller
authors.forename: Arno
authors.initials: A
authors.lastname: Karnholz
authors.forename: Reinhard
authors.initials: R
authors.lastname: Hoffmann
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.forename: Rainer
authors.initials: R
authors.lastname: Haas
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D044404:Genomic Islands; D016480:Helicobacter pylori / Q000201:enzymology / Q000235:genetics*; D008969:Molecular Sequence Data; D045522:Recombinases / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D045522:Recombinases