Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity

Abstract

DNA methylations play an important role in the biology of bacteria. Often associated with restriction modification (RM) systems, they are important drivers of bacterial evolution interfering in horizontal gene transfer events by providing a defence against foreign DNA invasion or by favouring genetic transfer through production of recombinogenic DNA ends. Little is known regarding the methylome of the Mycoplasma genus, which encompasses several pathogenic species with small genomes. Here, genome-wide detection of DNA methylations was conducted using single molecule real-time (SMRT) and bisulphite sequencing in several strains of Mycoplasma agalactiae , an important ruminant pathogen and a model organism. Combined with whole-genome analysis, this allowed the identification of 19 methylated motifs associated with three orphan methyltransferases (MTases) and eight RM systems. All systems had a homolog in at least one phylogenetically distinct Mycoplasma spp. Our study also revealed that several superimposed genetic events may participate in the M. agalactiae dynamic epigenomic landscape. These included (i) DNA shuffling and frameshift mutations that affect the MTase and restriction endonuclease content of a clonal population and (ii) gene duplication, erosion, and horizontal transfer that modulate MTase and RM repertoires of the species. Some of these systems were experimentally shown to play a major role in mycoplasma conjugative, horizontal DNA transfer. While the versatility of DNA methylation may contribute to regulating essential biological functions at cell and population levels, RM systems may be key in mycoplasma genome evolution and adaptation by controlling horizontal gene transfers.

Unraveling the adaptive strategies of Mycoplasma hominis through proteogenomic profiling of clinical isolates

“…Analysis of the distribution of methylated motifs and their functional significance in strains of M. genitalium and M. pneumoniae showed a potential regulatory role of methylation in the cell cycle and gene expression. The same role of DNA methylation was shown for M. agalactiae ( Dordet-Frisoni et al., 2022 ). Experimentally, it has been shown that some RM systems play an important role in the conjugative horizontal DNA transfer of Mycoplasma , i.e., DNA methylation can not only contribute to the regulation of vital biological functions at the cellular and population levels but also plays a significant role in the evolution and adaptation of the Mycoplasma genome, controlling horizontal gene transfer (HGT).…”

The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing

“…This species exhibits DNA inversions involving IRs located in various oppositely oriented hsdS genes that can modify the DNA sequence, generating enzyme variants with different DNA binding motifs. In Mycoplasma agalactiae , the organization of the hsd locus resembles that of M. pulmonis ( Dordet-Frisoni et al., 2022 ). The variability of the Type I profile detected in several M. agalactiae strains may be explained by potential recombination events.…”

Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates

“…RM systems play a pivotal role in regulating bacterial HGT by protecting the genome against incoming mobile genetic elements, or by facilitating recombination with the introduced DNA [77]. A strong correlation has been reported between the presence of active Type II RM systems and the presence of mobile genetic elements and ICEs within M. agalactiae genomes, indicating the facilitative role of Type II RM systems in HGT in mycoplasmas [78].…”