title: Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori.
abstract: Recombination plays a dominant role in the evolution of the bacterial pathogen Helicobacter pylori, but its dynamics remain incompletely understood. Here we use an in vitro transformation system combined with genome sequencing to study chromosomal integration patterns after natural transformation. A single transformation cycle results in up to 21 imports, and repeated transformations generate a maximum of 92 imports (8% sequence replacement). Import lengths show a bimodal distribution with averages of 28 and 1,645 bp. Reanalysis of paired H. pylori genomes from chronically infected people demonstrates the same bimodal import pattern in vivo. Restriction endonucleases (REases) of the recipient bacteria fail to inhibit integration of homeologous DNA, independently of methylation. In contrast, REases limit the import of heterologous DNA. We conclude that restriction-modification systems inhibit the genomic integration of novel sequences, while they pose no barrier to homeologous recombination, which reconciles the observed stability of the H. pylori gene content and its highly recombinational population structure.
authors.affiliation: Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.|DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bubendorfer
authors.affiliation: Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.|DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
authors.forename: Juliane
authors.initials: J
authors.lastname: Krebes
authors.affiliation: Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.|DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
authors.forename: Ines
authors.initials: I
authors.lastname: Yang
authors.affiliation: DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.|Institute of Virology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
authors.forename: Elias
authors.initials: E
authors.lastname: Hage
authors.affiliation: DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.|Institute of Virology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Schulz
authors.affiliation: Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
authors.forename: Christelle
authors.identifier: 0000-0003-2728-2397
authors.initials: C
authors.lastname: Bahlawane
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London W2 1PG, UK.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.|DZIF-German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany.
authors.forename: Sebastian
authors.identifier: 0000-0001-9583-7505
authors.initials: S
authors.lastname: Suerbaum
mesh_terms: D002876:Chromosomes, Bacterial; D004247:DNA / Q000235:genetics; D004262:DNA Restriction Enzymes / Q000378:metabolism; D015280:DNA Restriction-Modification Enzymes / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000235:genetics* / Q000378:metabolism*; D006801:Humans; D016296:Mutagenesis; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial; D004247:DNA; D004262:DNA Restriction Enzymes