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DNA methylomes of <i>Helicobacter pylori</i> strains are complex due to the large number of DNA methyltransferases (MTases) they possess. <i>H. pylori</i> J99 M.Hpy99III is a 5-methylcytosine (^m5C) MTase that converts GCGC motifs to G^m5CGC. Homologs of M.Hpy99III are found in essentially all <i>H. pylori</i> strains. Most of these homologs are orphan MTases that lack a cognate restriction endonuclease, and their retention in <i>H. pylori</i> strains suggest they have roles in gene regulation. To address this hypothesis, green fluorescent protein (GFP) reporter genes were constructed with six putative promoters that had a GCGC motif in the extended −10 region, and the expression of the reporter genes was compared in wild-type <i>H. pylori</i> G27 and a mutant lacking the M.Hpy99III homolog (M.HpyGIII). The expression of three of the GFP reporter genes was decreased significantly in the mutant lacking M.HpyGIII. In addition, the growth rate of the <i>H. pylori</i> G27 mutant lacking M.HpyGIII was reduced markedly compared to that of the wild type. These findings suggest that the methylation of the GCGC motif in many <i>H. pylori</i> GCGC-containing promoters is required for the robust expression of genes controlled by these promoters, which may account for the universal retention of M.Hpy99III homologs in <i>H. pylori</i> strains.