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The  Helicobacter pylori  phase variable gene  modH , typified by gene HP1522 in strain 26695, encodes a N 6 -adenosine type III DNA methyltransferase. Our previous studies identified multiple strain-specific  modH  variants ( modH1  –  modH19 ) and showed that phase variation of  modH5  in  H. pylori  P12 influenced expression of motility-associated genes and outer membrane protein gene  hopG . However, the ModH5 DNA recognition motif and the mechanism by which ModH5 controls gene expression were unknown. Here, using comparative single molecule real-time sequencing, we identify the DNA site methylated by ModH5 as 5′-G m6 ACC-3′. This motif is vastly underrepresented in  H. pylori  genomes, but overrepresented in a number of virulence genes, including motility-associated genes, and outer membrane protein genes. Motility and the number of flagella of  H. pylori  P12 wild-type were significantly higher than that of isogenic  modH5  OFF or Δ modH5  mutants, indicating that phase variable switching of  modH5  expression plays a role in regulating  H. pylori  motility phenotypes. Using the flagellin A ( flaA ) gene as a model, we show that ModH5 modulates  flaA  promoter activity in a GACC methylation-dependent manner. These findings provide novel insights into the role of ModH5 in gene regulation and how it mediates epigenetic regulation of  H. pylori  motility.

Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori