Methyltransferase DnmA is responsible for genome-wide N6-methyladenosine modifications at non-palindromic recognition sites in Bacillus subtilis

Abstract

The genomes of organisms from all three domains of life harbor endogenous base modifications in the form of DNA methylation. In bacterial genomes, methylation occurs on adenosine and cytidine residues to include N6-methyladenine (m6A), 5-methylcytosine (m5C), and N4-methylcytosine (m4C). Bacterial DNA methylation has been well characterized in the context of restriction-modification (RM) systems, where methylation regulates DNA incision by the cognate restriction endonuclease. Relative to RM systems less is known about how m6A contributes to the epigenetic regulation of cellular functions in Gram-positive bacteria. Here, we characterize site-specific m6A modifications in the non-palindromic sequence GACGmAG within the genomes of Bacillus subtilis strains. We demonstrate that the yeeA gene is a methyltransferase responsible for the presence of m6A modifications. We show that methylation from YeeA does not function to limit DNA uptake during natural transformation. Instead, we identify a subset of promoters that contain the methylation consensus sequence and show that loss of methylation within promoter regions causes a decrease in reporter expression. Further, we identify a transcriptional repressor that preferentially binds an unmethylated promoter used in the reporter assays. With these results we suggest that m6A modifications in B. subtilis function to promote gene expression.

Methylation by multiple type I restriction modification systems avoids influencing gene regulation in uropathogenicEscherichia coli

“…All together, the three RMSs we examined account for 1818 distinct methylation sites that would vary in methylation status among the strains we studied. The number of intergenic methylation sites in UTI89, which are expected to be more likely to affect gene regulation (46,(77)(78)(79)(80), are comparable for the three Type I RMSs (31-40 intergenic sites) (S5 Table ). Using RNA-seq, we again found no gene expression changes for any of the "methylation-switch" strains compared with the parental wt UTI89, except for one hypothetical gene that was close to both the FDR and fold-change cutoffs (Fig 4C and 4D MG1655 and wt UTI89 at any concentration, consistent with our previous interpretation that the single difference identified between UTI89 and UTI89ΔhsdSMR was a false positive (Fig 1D, S4 Table ).…”

Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix

“…Post-synthetic methylations of DNA are common, and play significant roles, in a wide range of bacterial and archaeal cellular functions 16 – 19 , such as adenine methylation-directed mismatch repair in Escherichia coli by Dam 20 , and essential functions of the cell-cycle regulated adenine methyltransferase (MTase) CcrM in Caulobactor crescentus 21 . The majority of known bacterial and archaeal DNA MTases function to protect a cell’s own DNA from digestion by a paired (cognate) restriction endonuclease 22 .…”

Protoplast fusion inBacillusspecies produces frequent, unbiased, genome-wide homologous recombination

“…We hypothesized that differential methylation patterns in the two parents might bias recombination directionality and localization. Methylation analysis of our PacBio sequencing data confirmed the known GAGGAC methylation motif in strain 168 (39) To investigate more subtle influences on recombination, we examined the correlation between local recombination frequencies and several features of the genomic context, including proximity to methylation sites, local GC content, and SNP density (Figure 3). We performed these analyses using all recombination regions in the 168 HK x RO-NN-1 ME prototrophic progeny where we identified extensive genetic variability ( Figure 1B).…”