title: Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria.
abstract: Heritable DNA methylation imprints are ubiquitous and underlie genetic variability from bacteria to humans. In microbial genomes, DNA methylation has been implicated in gene transcription, DNA replication and repair, nucleoid segregation, transposition and virulence of pathogenic strains. Despite the importance of local (hypo)methylation at specific loci, how and when these patterns are established during the cell cycle remains poorly characterized. Taking advantage of the small genomes and the synchronizability of α-proteobacteria, we discovered that conserved determinants of the cell cycle transcriptional circuitry establish specific hypomethylation patterns in the cell cycle model system Caulobacter crescentus. We used genome-wide methyl-N6-adenine (m6A-) analyses by restriction-enzyme-cleavage sequencing (REC-Seq) and single-molecule real-time (SMRT) sequencing to show that MucR, a transcriptional regulator that represses virulence and cell cycle genes in S-phase but no longer in G1-phase, occludes 5'-GANTC-3' sequence motifs that are methylated by the DNA adenine methyltransferase CcrM. Constitutive expression of CcrM or heterologous methylases in at least two different α-proteobacteria homogenizes m6A patterns even when MucR is present and affects promoter activity. Environmental stress (phosphate limitation) can override and reconfigure local hypomethylation patterns imposed by the cell cycle circuitry that dictate when and where local hypomethylation is instated.
authors.affiliation: Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland.
authors.forename: Silvia
authors.identifier: http://orcid.org/0000-0003-4346-8124
authors.initials: S
authors.lastname: Ardissone
authors.affiliation: Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland.
authors.forename: Peter
authors.identifier: http://orcid.org/0000-0002-3619-632X
authors.initials: P
authors.lastname: Redder
authors.affiliation: Functional Genomics Center Zurich, ETH/University of Zürich, Zürich, Switzerland.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Russo
authors.affiliation: Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland.
authors.forename: Antonio
authors.initials: A
authors.lastname: Frandi
authors.affiliation: Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland.
authors.forename: Coralie
authors.identifier: http://orcid.org/0000-0002-6969-3111
authors.initials: C
authors.lastname: Fumeaux
authors.affiliation: Functional Genomics Center Zurich, ETH/University of Zürich, Zürich, Switzerland.
authors.forename: Andrea
authors.initials: A
authors.lastname: Patrignani
authors.affiliation: Functional Genomics Center Zurich, ETH/University of Zürich, Zürich, Switzerland.
authors.forename: Ralph
authors.identifier: http://orcid.org/0000-0002-7488-4262
authors.initials: R
authors.lastname: Schlapbach
authors.affiliation: Biochemistry Unit, Dept. of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland.
authors.forename: Laurent
authors.identifier: http://orcid.org/0000-0001-8102-7579
authors.initials: L
authors.lastname: Falquet
authors.affiliation: Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland.
authors.forename: Patrick H
authors.identifier: http://orcid.org/0000-0002-5249-9910
authors.initials: PH
authors.lastname: Viollier
mesh_terms: D016935:Caulobacter crescentus / Q000235:genetics*; D002453:Cell Cycle / Q000235:genetics*; D002455:Cell Division / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D004261:DNA Replication / Q000187:drug effects / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D064349:Genome, Microbial; D008780:Methyltransferases / Q000235:genetics; D010710:Phosphates / Q000378:metabolism; D011401:Promoter Regions, Genetic; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific) / Q000235:genetics; D013217:Starvation / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D010710:Phosphates; D008780:Methyltransferases; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)