Abstract
BackgroundThe genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian H. pylori clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome).ResultsThe N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome during normal growth was characterized by cloning.ConclusionConsistent with previously-studied H. pylori strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of H. pylori.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1585-2) contains supplementary material, which is available to authorized users.
Highlights
The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain
Nucleotide sequence accession number The first annotated H. pylori UM032 genome sequence was deposited in DDBJ/EMBL/GenBank with the accession number CP005490 [37]
The methylated motif GANNNNNNNTAYG, which was reported in H. pylori strain F32, was not assigned to a MTase in H. pylori UM032 genome
Summary
The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The Gram-negative spiral-shaped bacterium Helicobacter pylori persistently colonizes the human stomach and is often associated with chronic gastritis and peptic ulceration. This bacterium is implicated in more severe gastric diseases that are regarded as an early risk factor for gastric cancer. Previous analyses of H. pylori genomes have revealed the presence of a large number of restriction-modification (R-M) systems in several strains [3,4,5].
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