Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes

Significance New technologies have fostered renewed interest in bacterial epigenetics, with DNA modifications defending against other microbes and controlling gene expression. Here, we describe how two diverse modifications, adenine methylation ( 6m A) and phosphorothioation (PT), have evolved to occupy the same genomic sites in bacteria. Using mass spectrometry, single-molecule real-time sequencing, and genetic engineering, we discovered coincident PT and 6m A in G PS 6m AAC and G PS 6m ATC, representing PT consensus sequences, a GA-containing consensus for an unknown methyltransferase, and the GATC consensus for Dam methyltransferase. 6m A was found in all G PS ATC sites in vivo, with 6m A substituting for PT in preventing DNA cleavage by PT restriction enzymes. These findings show how different DNA modification systems have evolved to avoid conflict.