title: DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates.
abstract: The Gram-negative bacterium Neisseria meningitidis features extensive genetic variability. To present, proposed virulence genotypes are also detected in isolates from asymptomatic carriers, indicating more complex mechanisms underlying variable colonization modes of N. meningitidis. We applied the Single Molecule, Real-Time (SMRT) sequencing method from Pacific Biosciences to assess the genome-wide DNA modification profiles of two genetically related N. meningitidis strains, both of serogroup A. The resulting DNA methylomes revealed clear divergences, represented by the detection of shared and of strain-specific DNA methylation target motifs. The positional distribution of these methylated target sites within the genomic sequences displayed clear biases, which suggest a functional role of DNA methylation related to the regulation of genes. DNA methylation in N. meningitidis has a likely underestimated potential for variability, as evidenced by a careful analysis of the ORF status of a panel of confirmed and predicted DNA methyltransferase genes in an extended collection of N. meningitidis strains of serogroup A. Based on high coverage short sequence reads, we find phase variability as a major contributor to the variability in DNA methylation. Taking into account the phase variable loci, the inferred functional status of DNA methyltransferase genes matched the observed methylation profiles. Towards an elucidation of presently incompletely characterized functional consequences of DNA methylation in N. meningitidis, we reveal a prominent colocalization of methylated bases with Single Nucleotide Polymorphisms (SNPs) detected within our genomic sequence collection. As a novel observation we report increased mutability also at 6mA methylated nucleotides, complementing mutational hotspots previously described at 5mC methylated nucleotides. These findings suggest a more diverse role of DNA methylation and Restriction-Modification (RM) systems in the evolution of prokaryotic genomes.
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland.|Universität Basel, Petersplatz 1, Basel, Switzerland.|SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Mohamad R Abdul
authors.initials: MR
authors.lastname: Sater
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland.|Universität Basel, Petersplatz 1, Basel, Switzerland.
authors.forename: Araceli
authors.initials: A
authors.lastname: Lamelas
authors.affiliation: Yale Center for Genomic Analysis, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Guilin
authors.initials: G
authors.lastname: Wang
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland.|Universität Basel, Petersplatz 1, Basel, Switzerland.
authors.forename: Katharina
authors.initials: K
authors.lastname: Röltgen
authors.affiliation: Yale Center for Genomic Analysis, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Shrikant
authors.initials: S
authors.lastname: Mane
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland.|Universität Basel, Petersplatz 1, Basel, Switzerland.
authors.forename: Gerd
authors.initials: G
authors.lastname: Pluschke
authors.affiliation: Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel, Switzerland.|Universität Basel, Petersplatz 1, Basel, Switzerland.|SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Christoph D
authors.initials: CD
authors.lastname: Schmid
mesh_terms: D000225:Adenine / Q000378:metabolism; D003596:Cytosine / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D044127:Epigenesis, Genetic; D015870:Gene Expression; D016680:Genome, Bacterial; D008589:Meningococcal Infections / Q000382:microbiology / Q000473:pathology; D008969:Molecular Sequence Data; D009154:Mutation; D009345:Neisseria meningitidis / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity*; D059372:Nucleotide Motifs; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods; D065288:Serogroup; D014774:Virulence
chemical_list: D004269:DNA, Bacterial; D003596:Cytosine; D004248:DNA (Cytosine-5-)-Methyltransferases; D000225:Adenine