Figure 4. MTase JHP1050 inactivation causes phenotypic effects that vary between strains: growth, viability and ... Figure 4. MTase JHP1050 inactivation.

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Figure 4. MTase JHP1050 inactivation causes phenotypic effects that vary between strains: growth, viability and ... Figure 4. MTase JHP1050 inactivation causes phenotypic effects that vary between strains: growth, viability and morphology. (A) Growth curves for four wild type strains and mutants and for the complemented strains J99-compl, 26695-compl and BCM-300-compl were measured for 72 h. The doubling time for H. pylori was calculated to be 3.87 h (46). Statistics: two-way ANOVA, *P < 0.05, **P < 0.01, ****P < 0.0001, bars: SD. (B) Viability of the strains was studied using epifluorescence microscopy after live/dead staining. Statistics: two-way ANOVA, *P < 0.05, bars: SD. (C) Bacterial morphology was quantitated from epifluorescence microscopy pictures using ImageJ. A value of 0 represents completely elongated bacteria, while a value of 1 means a complete circle (coccoid bacteria). Statistics: one-way ANOVA, **P < 0.01, bars: 95% confidence interval (CI). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 47, Issue 5, 09 January 2019, Pages 2336–2348, https://doi.org/10.1093/nar/gky1307 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. Quantification of transcript amounts of jhp0832 in H Figure 3. Quantification of transcript amounts of jhp0832 in H. pylori strains J99, J99-mut and the J99 mutants with ... Figure 3. Quantification of transcript amounts of jhp0832 in H. pylori strains J99, J99-mut and the J99 mutants with point mutations within the GCGC motifs. qPCR results are represented in the right panel, three different biological replicates were performed. Statistics: One-way ANOVA, **P < 0.01, ****P < 0.0001, bars: SD. Legend: The jhp0832 gene is shown as a gray arrow. The predicted promoter is represented by a black arrow. Crosses represent methylated motifs while vertical lines mean unmethylated motifs (due to site-directed mutation, or to inactivation of the MTase in strain J99-mut). The GCGC motifs appear in blue and the motifs mutated to GAGC are colored in pink. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 47, Issue 5, 09 January 2019, Pages 2336–2348, https://doi.org/10.1093/nar/gky1307 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. Graphical representation of the percentage of genes with GCGC motifs 500 bp of sequence upstream of the start ... Figure 2. Graphical representation of the percentage of genes with GCGC motifs 500 bp of sequence upstream of the start codon for differentially expressed genes (DEGs) and genes not showing differential expression (Non-DEGs). Non-DEGs versus DEGs in BCM-300 (A) and J99 (C). DEGs in J99 shared with BCM-300 versus the rest of the J99 genes (B). DEGs in J99 shared with BCM-300 versus the rest of the J99 DEGs (all DEGs) (D). Statistics: Chi-square, *P < 0.05, **P < 0.01. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 47, Issue 5, 09 January 2019, Pages 2336–2348, https://doi.org/10.1093/nar/gky1307 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 1. Phylogenetic analysis of the GCGC-specific R–M system JHP1050/1049 (M.Hpy99III/Hpy99III) in H. pylori. ... Figure 1. Phylogenetic analysis of the GCGC-specific R–M system JHP1050/1049 (M.Hpy99III/Hpy99III) in H. pylori. Neighbour-Joining trees based on the nucleotide sequences of MTase M.Hpy99III (A) and REase Hpy99III (B). In both cases, strain symbols are colored according to the phylogeographic population assignment based on seven gene MLST and STRUCTURE analysis (see right panel for color coding). Filled circles represent strains without REase gene, while unfilled circles are used for strains containing both MTase and REase genes. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 47, Issue 5, 09 January 2019, Pages 2336–2348, https://doi.org/10.1093/nar/gky1307 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. MTase JHP1050 inactivation causes phenotypic effects that vary between strains: natural competence, ... Figure 5. MTase JHP1050 inactivation causes phenotypic effects that vary between strains: natural competence, resistance to copper, and adherence to host cells. (A) Transformation experiments were performed with 1 μg/ml of gDNA. Statistics: Welch’s unpaired t test, **P < 0.01, ****P < 0.0001, bars: SD. (B) The growth of J99 wild type, J99-mut, BCM-300 wild type and BCM-300-mut strains was measured 24 h post-inoculation after addition of different concentrations of copper sulfate to the cultures. Data was normalized to a control culture without copper. Statistics: One-Way ANOVA, **P < 0.01, ***P < 0.001, ****P < 0.0001, bars: SD. (C) Adherence of H. pylori wild type and mutant strains to fixed AGS cells. Statistics: unpaired t-test, *P < 0.05, bars: SD. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 47, Issue 5, 09 January 2019, Pages 2336–2348, https://doi.org/10.1093/nar/gky1307 The content of this slide may be subject to copyright: please see the slide notes for details.