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Nucleic Acids Res. 2014 Apr;42(6):3720-35. doi: 10.1093/nar/gkt1352. Epub 2014 Jan 7.

The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach.

Author information

1
Department of Fundamental Microbiology, University of Lausanne, Lausanne, CH 1015, Switzerland, Department of Developmental Biology, Stanford University, CA 94305, USA and Department of Chemistry, Stanford University, CA 94305, USA.

Abstract

DNA methylation is involved in a diversity of processes in bacteria, including maintenance of genome integrity and regulation of gene expression. Here, using Caulobacter crescentus as a model, we exploit genome-wide experimental methods to uncover the functions of CcrM, a DNA methyltransferase conserved in most Alphaproteobacteria. Using single molecule sequencing, we provide evidence that most CcrM target motifs (GANTC) switch from a fully methylated to a hemi-methylated state when they are replicated, and back to a fully methylated state at the onset of cell division. We show that DNA methylation by CcrM is not required for the control of the initiation of chromosome replication or for DNA mismatch repair. By contrast, our transcriptome analysis shows that >10% of the genes are misexpressed in cells lacking or constitutively over-expressing CcrM. Strikingly, GANTC methylation is needed for the efficient transcription of dozens of genes that are essential for cell cycle progression, in particular for DNA metabolism and cell division. Many of them are controlled by promoters methylated by CcrM and co-regulated by other global cell cycle regulators, demonstrating an extensive cross talk between DNA methylation and the complex regulatory network that controls the cell cycle of C. crescentus and, presumably, of many other Alphaproteobacteria.

PMID:
24398711
PMCID:
PMC3973325
DOI:
10.1093/nar/gkt1352
[Indexed for MEDLINE]
Free PMC Article

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