DNA methylation, catalysed by DNA methyltransferases (MTases), guides numerous biological processes including genomic defence against foreign DNA, DNA replication and repair, transposition and regulation of gene expression and virulence1. MTases are often encoded on mobile genetic elements (MGEs), which have a key role in E. coli evolution. Third generation sequencing technologies allow us to de novo assemble complete genomes, resolve complex MGEs and define the genome-wide complement of DNA methylation (methylome). Our investigations reveal several distinct narratives on how the methylome may contribute to the evolution of extraintestinal pathogenic E. coli (ExPEC).
(i) In E. coli Sequence Type (ST)101, we showed strain-specific methylation differences, where an additional MTase encoded on a MGE resulted in differential methylome patterns within the promoter regions of 31 genes, suggestive of functional differences between two almost identical strains.
(ii) In ST101, we also showed how recombination events at a single genomic locus encoding a restriction-modification system methylating approx. 500 sites throughout the genome, caused global methylome changes within the lineage.
(iii) In the ST131 strain EC958, we found that the distribution of MTase sites is not random between the core and accessory genome. For Dam methylation, this difference is partially accounted by large (>=1 kbp) methylation-free regions in MGEs, suggestive of evolutionary pressure and selection against Dam methylation in MGEs.
(iv) Investigations of knockout mutants of global regulators in EC958 showed that transcription factors have a much larger role in the regulation of E. coli methylation than previously thought, resulting in both repression and activation of EC958 MTases.
Our findings suggest numerous possible functional roles for DNA MTases in ExPEC, particularly genome-wide gene regulation. These studies highlight the need for fine-scale genomic and methylome characterisations for a full understanding of the impact of DNA methylation on ExPEC evolution.