TheHelicobacter pyloriMethylome is Acid-Responsive due to Regulation by the Two-Component System ArsRS and the Type I DNA Methyltransferase HsdM1 (HP0463)

Abstract

AbstractIn addition to its role in genome protection, DNA methylation can regulate gene expression. In this study, we characterized the impact of acidity, phase variation, and the ArsRS TCS on the expression of the Type I m6A DNA methyltransferase HsdM1 (HP0463) ofHelicobacter pylori26695 and their subsequent effects on the methylome. Transcription ofhsdM1 increases at least 4-fold in the absence of the sensory histidine kinase ArsS, the major acid-sensing protein ofH. pylori.hsdM1 exists in the phase-variable operonhsdR1-hsdM1. Phase-lockinghsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription ofhsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples cultured at pH 7 or pH 5. We found differentially methylated motifs between these growth conditions, and that deletions ofarsSand/orhsdM1 interfere with the epigenetic acid response. Deletion ofarsSleads to altered activity of HsdM1 and multiple other methyltransferases under both pH conditions indicating that the ArsRS TCS, in addition to direct effects on regulon transcription during acid acclimation, may also indirectly impact gene expression via regulation of the methylome. We determined the target motif of HsdM1 (HP0463) to be the complementary bipartite sequence pair 5’-(HH)TCAm6AVN6TGY-3’ and 3’-AGTN6GAm6ACA-5’. The Type II m5C DNA methyltransferase M.HpyAVIII (HP1121) is regulated by ArsS and HsdM1. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection byH. pylori.ImportanceThis study expands the possibilities for complex, epigenomic regulation inHelicobacter pylori. We demonstrate that theH. pylorimethylome is plastic and acid-sensitive via the two-component system ArsRS and the DNA methyltransferase HsdM1. The control of a methyltransferase by ArsRS may allow for a layered response to changing acidity. Likely, an early response whereby ArsR∼P affects regulon expression, including the methyltransferasehsdM1. Then, a somewhat later effect as the altered methylome, due to altered HsdM1 expression, subsequently alters the expression of other genes involved in acclimation. The intermediate methylation of certain motifs supports the hypothesis that methyltransferases play a regulatory role. Untangling this additional web of regulation could play a key role in understandingH. pyloricolonization and persistence.