title: Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution.
abstract: In the bacterial world, methylation is most commonly associated with restriction-modification systems that provide a defense mechanism against invading foreign genomes. In addition, it is known that methylation plays functionally important roles, including timing of DNA replication, chromosome partitioning, DNA repair, and regulation of gene expression. However, full DNA methylome analyses are scarce due to a lack of a simple methodology for rapid and sensitive detection of common epigenetic marks (ie N(6)-methyladenine (6 mA) and N(4)-methylcytosine (4 mC)), in these organisms. Here, we use Single-Molecule Real-Time (SMRT) sequencing to determine the methylomes of two related human pathogen species, Mycoplasma genitalium G-37 and Mycoplasma pneumoniae M129, with single-base resolution. Our analysis identified two new methylation motifs not previously described in bacteria: a widespread 6 mA methylation motif common to both bacteria (5'-CTAT-3'), as well as a more complex Type I m6A sequence motif in M. pneumoniae (5'-GAN(7)TAY-3'/3'-CTN(7)ATR-5'). We identify the methyltransferase responsible for the common motif and suggest the one involved in M. pneumoniae only. Analysis of the distribution of methylation sites across the genome of M. pneumoniae suggests a potential role for methylation in regulating the cell cycle, as well as in regulation of gene expression. To our knowledge, this is one of the first direct methylome profiling studies with single-base resolution from a bacterial organism.
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain. maria.lluch@crg.es
authors.forename: Maria
authors.initials: M
authors.lastname: Lluch-Senar
authors.forename: Khai
authors.initials: K
authors.lastname: Luong
authors.forename: Verónica
authors.initials: V
authors.lastname: Lloréns-Rico
authors.forename: Javier
authors.initials: J
authors.lastname: Delgado
authors.forename: Gang
authors.initials: G
authors.lastname: Fang
authors.forename: Kristi
authors.initials: K
authors.lastname: Spittle
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.forename: Eric
authors.initials: E
authors.lastname: Schadt
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Turner
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
mesh_terms: D019175:DNA Methylation / Q000235:genetics*; D019848:Gene Expression Regulation, Archaeal; D016680:Genome, Bacterial; D006801:Humans; D008780:Methyltransferases / Q000235:genetics; D045704:Mycoplasma genitalium / Q000235:genetics / Q000378:metabolism; D009177:Mycoplasma pneumoniae / Q000235:genetics / Q000378:metabolism; D059372:Nucleotide Motifs / Q000235:genetics*
chemical_list: D008780:Methyltransferases