Precision methylome and in vivo methylation kinetics characterization of Klebsiella pneumoniae

Abstract

Klebsiella pneumoniae (K. pneumonia) is an important pathogen that can cause severe hospital-/community-acquired infections. To panoramically analyze K. pneumoniaes methylation features, we completed the whole genome sequences of 14 K. pneumoniae strains covering various serotypes, multilocus-sequence typings (MLSTs), clonal groups (CG), viscosity/virulence and drug-resistances, and further characterized their methylomes using PacBio-SMRT and bisulfite technologies. We identified 15 methylation motifs (13 6mA and two 5mC motifs), among which eight were novel ones. Their corresponding MTases were further validated. Additionally, we analyzed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains, and identified differential distributive patterns of some hemi/un-methylated GATC motifs tending to locate in the intergenic regions (IGRs). Specifically, we characterized the in vivo methylation kinetics at single-base resolution on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalyzed re-methylation. The slower methylation-rates of the GATC motifs in the replication origins (oriC) and IGRs suggest an epigenetic mechanism implicated in the regulation of replication-initiation and transcription. Our findings illustrate the first comprehensive dynamic methylome map of K. pneumonia at single base resolution, and provide an efficient means and important reference for a better understanding of epigenetic regulation in bacteria.