title: The complete methylome of Helicobacter pylori UM032.
abstract: BACKGROUND
  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 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).
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  Consistent 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.
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. woonching.lee@gmail.com.
authors.forename: Woon Ching
authors.initials: WC
authors.lastname: Lee
authors.affiliation: New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA. anton@neb.com.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Anton
authors.affiliation: Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 94025, USA. swang@pacificbiosciences.com.
authors.forename: Susana
authors.initials: S
authors.lastname: Wang
authors.affiliation: Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 94025, USA. pbaybayan@pacificbiosciences.com.
authors.forename: Primo
authors.initials: P
authors.lastname: Baybayan
authors.affiliation: PacBio Singapore, Singapore, Singapore. ssingh@pacificbiosciences.com.
authors.forename: Siddarth
authors.initials: S
authors.lastname: Singh
authors.affiliation: Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 94025, USA. mashby@pacbiosciences.com.
authors.forename: Meredith
authors.initials: M
authors.lastname: Ashby
authors.affiliation: Marshall Centre, School of Pathology & Laboratory Medicine, The University of Western Australia, 6009, Perth, Australia. eng.chua@uwa.edu.au.
authors.forename: Eng Guan
authors.initials: EG
authors.lastname: Chua
authors.affiliation: Marshall Centre, School of Pathology & Laboratory Medicine, The University of Western Australia, 6009, Perth, Australia. alfred.tay@uwa.edu.au.
authors.forename: Chin Yen
authors.initials: CY
authors.lastname: Tay
authors.affiliation: Marshall Centre, School of Pathology & Laboratory Medicine, The University of Western Australia, 6009, Perth, Australia. fanny.thirriot@uwa.edu.au.
authors.forename: Fanny
authors.initials: F
authors.lastname: Thirriot
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. lokemunfai@um.edu.my.
authors.forename: Mun Fai
authors.initials: MF
authors.lastname: Loke
authors.affiliation: Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. gohkl@um.edu.my.
authors.forename: Khean Lee
authors.initials: KL
authors.lastname: Goh
authors.affiliation: Marshall Centre, School of Pathology & Laboratory Medicine, The University of Western Australia, 6009, Perth, Australia. barry.marshall@uwa.edu.au.
authors.forename: Barry J
authors.initials: BJ
authors.lastname: Marshall
authors.affiliation: New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA. roberts@neb.com.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia. jamuna@um.edu.my.
authors.forename: Jamuna
authors.initials: J
authors.lastname: Vadivelu
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000378:metabolism; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D008780:Methyltransferases / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D008780:Methyltransferases; D004262:DNA Restriction Enzymes