Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein

TL;DR

Cytosine methylation in Caulobacter helps protect cells from DNA damage and improves fitness when a Vsr-like protein is present.

Contribution

The study reveals a novel role of cytosine methylation in stabilizing solitary methyltransferase genes through Vsr-like proteins.

Findings

Unmethylated DNA motifs in Caulobacter can cause genotoxic stress and fitness loss.

Vsr-like proteins are involved in DNA damage responses and may prevent mutations.

Vsr-like proteins help maintain cytosine methyltransferase genes in bacterial genomes.

Abstract

The role of methylated cytosines introduced into bacterial genomes by solitary DNA methyltransferases often remains elusive. Here, we show that the solitary cytosine methyltransferase ScmA of Caulobacter crescentus methylates thousands of YGCCGGCR motifs in its genome and that wild-type cells outcompete ΔscmA mutant cells. Transcriptomic and single-cell analyses reveal that a DNA damage response is turned on in a significant proportion of ΔscmA cells and that this response is strictly dependent on the Vsr-like protein VsrA. Although the vsrA gene is not genetically linked to scmA or to any other cytosine methyltransferase gene, VsrA is predicted to be a mismatch repair (MMR) endonuclease preventing 5mC-to-T mutations. In ΔscmA cells, VsrA may accidentally cause double-strand breaks (DSBs) during MMR, leading to reduced fitness. These findings suggest that vsr-like genes can stabilize solitary cytosine methyltransferase genes in bacterial genomes, potentially explaining their prevalence despite the frequent absence of detectable regulatory roles.

•Unmethylated DNA motifs can expose Caulobacter to genotoxic stresses and fitness losses•Vsr-like proteins can be induced during bacterial DNA damage responses•Vsr-like proteins can stabilize cytosine methyltransferase genes in bacterial genomes•Cytosine methyltransferases may not be genetically linked with their cognate Vsr

Unmethylated DNA motifs can expose Caulobacter to genotoxic stresses and fitness losses

Vsr-like proteins can be induced during bacterial DNA damage responses

Vsr-like proteins can stabilize cytosine methyltransferase genes in bacterial genomes

Cytosine methyltransferases may not be genetically linked with their cognate Vsr

Properties of biomolecules; Epigenetics; Microbial genomics; Transcriptomics

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