A Cytosine Methyltransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen [corrected

Michael C Chao,Satoshi Kimura,Matthew K Waldor,Gang Fang,Shijia Zhu,Brigid M Davis,Eric E Schadt

doi:10.1371/journal.pgen.1005666

Abstract

DNA methylation is a key epigenetic regulator in all domains of life, yet the effects of most bacterial DNA methyltransferases on cellular processes are largely undefined. Here, we used diverse techniques, including bisulfite sequencing, transcriptomics, and transposon insertion site sequencing to extensively characterize a 5-methylcytosine (5mC) methyltransferase, VchM, in the cholera pathogen, Vibrio cholerae. We have comprehensively defined VchM’s DNA targets, its genetic interactions and the gene networks that it regulates. Although VchM is a relatively new component of the V. cholerae genome, it is required for optimal V. cholerae growth in vitro and during infection. Unexpectedly, the usually essential σE cell envelope stress pathway is dispensable in ∆vchM V. cholerae, likely due to its lower activation in this mutant and the capacity for VchM methylation to limit expression of some cell envelope modifying genes. Our work illuminates how an acquired DNA methyltransferase can become integrated within complex cell circuits to control critical housekeeping processes.

Highlights

DNA methylation—the covalent attachment of methyl moieties to specific nucleotides in the genome by DNA methyltransferases (MTases)—is a fundamental mechanism for epigenetic regulation in all domains of life
Methylation of DNA is used by numerous organisms to regulate a wide variety of cellular processes, but specific roles for most DNA methyltransferases have not been defined
We studied one such enzyme in Vibrio cholerae, the cholera pathogen, using genome-wide approaches to compare DNA methylation, gene expression, and the sets of genes required or dispensable for growth in bacterial strains that produced or lacked this enzyme

Summary

Introduction

DNA methylation—the covalent attachment of methyl moieties to specific nucleotides in the genome by DNA methyltransferases (MTases)—is a fundamental mechanism for epigenetic regulation in all domains of life (reviewed in [1,2]). Most bacterial MTases are components of restriction-modification (R-M) systems; these MTases modify target DNA sequences in order to protect them from digestion by a cognate restriction enzyme, which is typically co-transcribed. R-M systems enable digestion of horizontally acquired DNA sequences that lack appropriate methylation marks, and protect bacteria from selfish elements and phage predation [5]. A subset of MTase genes are not accompanied by a cognate restriction enzyme, and a few of these so-called ‘orphan’ MTases are known to regulate diverse host cell processes (reviewed in [2,6,7]). Roles for the majority of bacterial MTases—which are predicted in over 90% of genomes [18]—have not been defined

Methods

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Discussion

Conclusion