title: The methylomes of six bacteria.
abstract: Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and C. jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N(6)-methyladenine ((m6)A) and N(4)-methylcytosine ((m4)C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. In 15 cases, it was possible to match MTase genes with MTase recognition sequences without further sub-cloning. Two Type I restriction systems required sub-cloning to differentiate their recognition sequences, while four MTase genes that were not expressed in the native organism were sub-cloned to test for viability and recognition sequences. Two of these proved active. No attempt was made to detect 5-methylcytosine ((m5)C) recognition motifs from the SMRT® sequencing data because this modification produces weaker signals using current methods. However, all predicted (m6)A and (m4)C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active but also revealing their recognition sequences.
authors.affiliation: New England Biolabs, 240 County Road, Ipswich, MA 01938, USA.
authors.forename: Iain A
authors.initials: IA
authors.lastname: Murray
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.forename: Richard D
authors.initials: RD
authors.lastname: Morgan
authors.forename: Matthew
authors.initials: M
authors.lastname: Boitano
authors.forename: Brian P
authors.initials: BP
authors.lastname: Anton
authors.forename: Khai
authors.initials: K
authors.lastname: Luong
authors.forename: Alexey
authors.initials: A
authors.lastname: Fomenkov
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Turner
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
mesh_terms: D000225:Adenine / Q000031:analogs & derivatives / Q000032:analysis; D001409:Bacillus cereus / Q000235:genetics; D016123:Campylobacter jejuni / Q000235:genetics; D055353:Chromohalobacter / Q000235:genetics; D003596:Cytosine / Q000031:analogs & derivatives / Q000032:analysis; D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D016680:Genome, Bacterial; D045302:Geobacter / Q000235:genetics; D017422:Sequence Analysis, DNA; D014733:Vibrio / Q000235:genetics
chemical_list: D000225:Adenine; D003596:Cytosine; D015254:DNA Modification Methylases; D004269:DNA, Bacterial; C039052:N(4)-methylcytosine; C000730567:6-methyladenine