title: Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N(6)-adenine DNA methyltransferases of Neisseria meningitidis.
abstract: Phase variation (random ON/OFF switching) of gene expression is a common feature of host-adapted pathogenic bacteria. Phase variably expressed N(6)-adenine DNA methyltransferases (Mod) alter global methylation patterns resulting in changes in gene expression. These systems constitute phase variable regulons called phasevarions. Neisseria meningitidis phasevarions regulate genes including virulence factors and vaccine candidates, and alter phenotypes including antibiotic resistance. The target site recognized by these Type III N(6)-adenine DNA methyltransferases is not known. Single molecule, real-time (SMRT) methylome analysis was used to identify the recognition site for three key N. meningitidis methyltransferases: ModA11 (exemplified by M.NmeMC58I) (5'-CGY M6A: G-3'), ModA12 (exemplified by M.Nme77I, M.Nme18I and M.Nme579II) (5'-AC M6A: CC-3') and ModD1 (exemplified by M.Nme579I) (5'-CC M6A: GC-3'). Restriction inhibition assays and mutagenesis confirmed the SMRT methylome analysis. The ModA11 site is complex and atypical and is dependent on the type of pyrimidine at the central position, in combination with the bases flanking the core recognition sequence 5'-CGY M6A: G-3'. The observed efficiency of methylation in the modA11 strain (MC58) genome ranged from 4.6% at 5'-GCGC M6A: GG-3' sites, to 100% at 5'-ACGT M6A: GG-3' sites. Analysis of the distribution of modified sites in the respective genomes shows many cases of association with intergenic regions of genes with altered expression due to phasevarion switching.
authors.affiliation: Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.
authors.forename: Kate L
authors.initials: KL
authors.lastname: Seib
authors.affiliation: Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.
authors.forename: Freda E-C
authors.initials: FE
authors.lastname: Jen
authors.affiliation: Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.
authors.forename: Aimee
authors.initials: A
authors.lastname: Tan
authors.affiliation: Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.
authors.forename: Adeana L
authors.initials: AL
authors.lastname: Scott
authors.affiliation: Department of Biochemistry, Indian Institute of Science, Bangalore, India.
authors.forename: Ritesh
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Power
authors.affiliation: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Li-Tzu
authors.initials: LT
authors.lastname: Chen
authors.affiliation: Center for Molecular Medicine, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan.
authors.forename: Hsing-Ju
authors.initials: HJ
authors.lastname: Wu
authors.affiliation: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Andrew H-J
authors.initials: AH
authors.lastname: Wang
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: Dorothea M C
authors.initials: DM
authors.lastname: Hill
authors.affiliation: New England Biolabs, Ipswich, MA 01938, USA.
authors.forename: Yvette A
authors.initials: YA
authors.lastname: Luyten
authors.affiliation: New England Biolabs, Ipswich, MA 01938, USA.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Morgan
authors.affiliation: New England Biolabs, Ipswich, MA 01938, USA.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: Martin C J
authors.initials: MC
authors.lastname: Maiden
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Boitano
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.affiliation: Department of Biochemistry, Indian Institute of Science, Bangalore, India.
authors.forename: Desirazu N
authors.initials: DN
authors.lastname: Rao
authors.affiliation: Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia m.jennings@griffith.edu.au.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Jennings
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D044127:Epigenesis, Genetic; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008745:Methylation; D008969:Molecular Sequence Data; D009345:Neisseria meningitidis / Q000201:enzymology* / Q000235:genetics; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)
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