Investigating the DNA methylation landscape of Staphylococcus aureus

Abstract

Staphylococcus aureus is a leading causative agent of healthcare-associated infections. One aspect of the organism that remains unknown is the methylome, specifically that of the whole genome. In prokaryotes, methylation is facilitated by methyltransferases, usually part of the organism’s Restriction Modification system (RM). It is well established that RM are involved in cellular defense but have also been attributed to have secondary regulatory functions in host physiology and virulence by modulating gene expression through DNA methylation in numerous bacterial species.

In S. aureus the main RM present are Type I RM Sau1, which potential epigenetic role has not yet been studied. Using PacBio SMRT sequencing this study investigates the variability and distribution of sau1 DNA binding specificity unit (hsdS) alleles and explores the frequency of whole genome 6mA methylation within the species using a historically and phylogenetically variable collection of S. aureus isolates part of the NCTC3000 project. The results revealed lineage specific methylation patterns randomly distributed throughout the chromosome, but preferential methylation of the coding sequence and the core genome. Between the 24 represented STs, the detailed protein structure of 40 different HsdS homologs were characterised and matched to corresponding 6mA target recognition sequences, greatly augmenting the current knowledge of Sau1 methylation signatures.

Differential methylation was also investigated in novel ST622 hybrid strains as a natural experiment (variable methylation signatures across an identical sequence region between chimeric and closely related ST45 and ST22 donor strains) effectively looking at the effect of large-scale recombination on whole genome methylation using RNA-Sequencing. Mutagenesis of hsdS and further transcriptomic studies revealed that deletion of 6mA methylation by Sau1 in a set of isogenic mutants in multiple sequence backgrounds causes a pleotropic shift in expression of metabolic genes. This is not likely due to an epigenetic regulatory mechanism, but rather and induced global stress response.