Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes

The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles ofDNAmethylation in these organisms. Methyltransferases (MTases), the enzymes responsible for DNA methylation, are exchanged between prokaryotes through horizontal gene transfer and can function either as part of restriction-modification systems or in apparent isolation as single (orphan) genes. The patterns of DNA methylation they confer on the host chromosome can have significant effects on gene expression, DNA replication, and other cellular processes. Some processes require very stable patterns of methylation, resulting in conservation of persistent MTases in a particular lineage. Other processes require patterns that are more dynamic yet more predictable than what is afforded by horizontal gene transfer and gene loss, resulting in phase-variable or recombination-driven MTase alleles. In this review, we discuss what is currently known about the functions of DNA methylation in prokaryotes in light of these evolutionary patterns.

Automated summary

The increase in bacterial and archaeal genome sequence and methylome data has shed new light on the functional roles of DNA methylation in these organisms. Methyltransferases (MTases) responsible for DNA methylation are exchanged between prokaryotes through horizontal gene transfer, affecting host chromosome DNA methylation patterns which in turn impact gene expression and other cellular processes. The conservation of persistent MTases in certain lineages and the existence of phase-variable or recombination-driven MTase alleles reflect the different requirements for stable and dynamic DNA methylation patterns.