Fig. 6
Quantitative DNA methylation of genome-wide cytosine motifs in H. pylori wild type compared for different culture conditions that impair methyl donor homeostasis. A to C show the comparison for the genome-wide aggregated quantitative data of the three cytosine-methylated motifs for H. pylori N6 under conditions of methionine (methyl donor) supplementation (methionine-replete) or methionine depletion. N6-wt designates standard liquid culture condition for the H. pylori N6 strain; N6-Met indicates methionine-depleted liquid medium; N6 + Met indicates methionine-depleted medium supplemented with a defined methionine concentration (50 µg/ml methionine). Box plots with whiskers were prepared summarizing the genome-wide cytosine methylation of each single genomic motif (as conversion frequency in [%]) for each condition (average for each site, summarized in box, with median). A GCGC motif; B CCTC motif; C TCTTC motif. Two biological and technical replicates are included for each condition. Chi-square p-values for significant differences between conditions: * < 0.05, ** < 0.01, *** < 0.001, **** < 0.0001. D Genome-wide averaged quantitative DNA methylation of CCTC cytosine motifs in H. pylori wild type (N6-wt) compared to an isogenic mutant in luxS (N6-luxS) in liquid medium. Box plot with whiskers for CCTC motif methylation (shown as conversion frequency [%]) is depicted including two biological and technical replicates of each strain. Chi-square p-values for significant differences between strains: * < 0.05, ** < 0.01, *** < 0.001, **** < 0.0001. E MTase-Glo assay for quantitating MTase activities in bulk between the N6 wild type strain (N6-wt) and the isogenic luxS insertion mutants (N6-luxS), shown for two independently obtained luxS mutant clones (cl.6 and cl.7). Background luminescence of a control condition without bacterial lysates was subtracted. F qRT-PCR for transcript quantification of MTase gene HP0051 (M.HpyAII), encoding MTase which methylates the CCTC motif), normalized against 16S rRNA transcript, in H. pylori N6 wild type and luxS mutant clones (two clones shown; three biological replicates were performed in technical triplicates [6 replicates] and summarized for each strain), which was increased in the mutants, corresponding to increased cytosine motif CCTC methylation shown in panel D. Full single-base conversion data in Additional file 3: Table S2