title: The complex methylome of the human gastric pathogen Helicobacter pylori.
abstract: The genome of Helicobacter pylori is remarkable for its large number of restriction-modification (R-M) systems, and strain-specific diversity in R-M systems has been suggested to limit natural transformation, the major driving force of genetic diversification in H. pylori. We have determined the comprehensive methylomes of two H. pylori strains at single base resolution, using Single Molecule Real-Time (SMRT®) sequencing. For strains 26695 and J99-R3, 17 and 22 methylated sequence motifs were identified, respectively. For most motifs, almost all sites occurring in the genome were detected as methylated. Twelve novel methylation patterns corresponding to nine recognition sequences were detected (26695, 3; J99-R3, 6). Functional inactivation, correction of frameshifts as well as cloning and expression of candidate methyltransferases (MTases) permitted not only the functional characterization of multiple, yet undescribed, MTases, but also revealed novel features of both Type I and Type II R-M systems, including frameshift-mediated changes of sequence specificity and the interaction of one MTase with two alternative specificity subunits resulting in different methylation patterns. The methylomes of these well-characterized H. pylori strains will provide a valuable resource for future studies investigating the role of H. pylori R-M systems in limiting transformation as well as in gene regulation and host interaction.
authors.affiliation: Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany, German Center for Infection Research, Hannover-Braunschweig Site, Carl-Neuberg-Straße 1, 30625 Hannover, Germany, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany and Pacific Biosciences, 1380 Willow Road, Menlo Park, CA 94025, USA.
authors.forename: Juliane
authors.initials: J
authors.lastname: Krebes
authors.forename: Richard D
authors.initials: RD
authors.lastname: Morgan
authors.forename: Boyke
authors.initials: B
authors.lastname: Bunk
authors.forename: Cathrin
authors.initials: C
authors.lastname: Spröer
authors.forename: Khai
authors.initials: K
authors.lastname: Luong
authors.forename: Raphael
authors.initials: R
authors.lastname: Parusel
authors.forename: Brian P
authors.initials: BP
authors.lastname: Anton
authors.forename: Christoph
authors.initials: C
authors.lastname: König
authors.forename: Christine
authors.initials: C
authors.lastname: Josenhans
authors.forename: Jörg
authors.initials: J
authors.lastname: Overmann
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.forename: Sebastian
authors.initials: S
authors.lastname: Suerbaum
mesh_terms: D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics*; D009154:Mutation; D017422:Sequence Analysis, DNA
chemical_list: D015254:DNA Modification Methylases