A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen

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.

The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori

“…Moreover, there were more DEGs with higher number of motifs within the coding sequence than expected when compared with the non-DEGs (Supplementary Figure 6A). These results are similar to reports from Vibrio cholerae , where a significant correlation between differential regulation and the number of motifs within the coding sequence was reported for a m5 C MTase (21).…”

“…These MTase-dependent regulons were termed phasevarions (19). As described previously, adenine methylation has been shown to play a key role in transcriptional regulation but the influence of cytosine methylation in gene expression has so far only been investigated in very few studies (20,21).…”

The Nucleoid Binding Protein H-NS Biases Genome-Wide Transposon Insertion Landscapes

“…(A) Pie graphs depicting the relative frequencies of V. cholerae genes from reference 22, now classified as underrepresented or neutral. Frequencies are depicted for all classified genes and for the subsets of these genes with GC content of ≥40% and <40%.…”

A conserved RNA seed‐pairing domain directs small RNA‐mediated stress resistance in enterobacteria

“…To test whether micV is controlled by r E , we generated an rpoE deletion mutant in V. cholerae. The rpoE gene is considered essential in V. cholerae and to avoid unpredictable suppressor mutations, we first deleted the vchM gene, encoding a known suppressor of r E (Chao et al, 2015), followed by deletion of rpoE. The vchM deletion did not affect the expression of MicV or VrrA ( Fig EV1B).…”

“…The rpoE gene is considered essential in V. cholerae and to avoid unpredictable suppressor mutations, we first deleted the vchM gene, encoding a known suppressor of r E (Chao et al, 2015), followed by deletion of rpoE. The rpoE gene is considered essential in V. cholerae and to avoid unpredictable suppressor mutations, we first deleted the vchM gene, encoding a known suppressor of r E (Chao et al, 2015), followed by deletion of rpoE.…”