Abstract
DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (>94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium’s lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.
Highlights
DNA methyltransferases (MTases) are enzymes that catalyze the transfer of a methyl group from the universal methyl donor S-Adenosylmethionine (SAM) to a nucleotide[1]
We investigated whether changes in DNA methylation pattern occur within the antimicrobial peptides (AMPs)-resistant subpopulation responsible for insect virulence, or after the Dam overexpression that leads to major phenotypic changes in P. luminescens
We investigated whether the high proportion (99.8%, Table 2) of the methylated GATC motifs identified in a reference condition could be increased by Dam MTase overexpression
Summary
DNA methyltransferases (MTases) are enzymes that catalyze the transfer of a methyl group from the universal methyl donor S-Adenosylmethionine (SAM) to a nucleotide[1]. Dcm adds a methyl group to the second cytosine of CCWGG motifs This solitary MTase has been shown to be involved in drug resistance, translation[25] and stationary phase gene expression[26]. In addition to Dam, the best known example of solitary MTase involved in epigenetic mechanisms in bacteria[27] is the CcrM (Cell cycle regulated MTase) found in many Alphaproteobacteria. SMRT sequencing can detect all DNA methylation marks in genomes, opening opportunities to detect new methylated motifs[7]. This new-generation sequencing technology has been used to describe the methylome of several microorganisms. There has been a strong focus on animal pathogens, but the methylomes of some plant pathogens have been reported[32,33,34,35,36,37,38,39,40,41]
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