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.
Highlights
Methylated bases can be found in the genomes of organisms from all three domains of life as well as in the genome of viruses [1,2,3,4]
Our findings reveal a strong link between CcrM-dependent methylation and cell cycle control in C. crescentus that is likely to exist in many other Alphaproteobacteria
The functions of the CcrM family of N6-adenine methyltransferases have been studied in a limited number of Alphaproteobacteria, including C. crescentus, Agrobacterium tumefaciens, Rhizobium meliloti and Brucella abortus [33,38,39,40]
Summary
Methylated bases can be found in the genomes of organisms from all three domains of life as well as in the genome of viruses [1,2,3,4]. The functions of DNA methylation have been poorly investigated for most of the bacterial kingdom [6]. Bacterial DNA methyltransferases are mostly associated with endonucleases in restriction-modification systems, which are generally considered as a defense mechanism that bacteria use to identify and destroy differentially methylated foreign DNA [7,8,9]. A number of ‘orphan’ DNA methyltransferases that are not associated with a cognate endonuclease have been identified [7,10,11,12]. The best studied examples are the DNA adenine methyltransferases Dam and CcrM. Dam methylates 50-GATC-30 (hereafter called GATC) motifs in the genomes of a subset of Gammaproteobacteria [13], whereas CcrM methylates 50-GANTC-30 (hereafter called GANTC) motifs in the genomes of many Alphaproteobacteria
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