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Sci Rep. 2017 Nov 23;7(1):16140. doi: 10.1038/s41598-017-15721-x.

Methylomic and phenotypic analysis of the ModH5 phasevarion of Helicobacter pylori.

Author information

1
Department of Microbiology, Monash University, Clayton, 3800, Victoria, Australia.
2
Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, 3010, Victoria, Australia.
3
Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia.
4
Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Victoria, Australia.
5
Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia.
6
Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia.
7
Bioinformatics Platform, Monash University, Clayton, 3800, Victoria, Australia.
8
Pacific Biosciences, Menlo Park, CA, 94025, USA.
9
Department of Molecular and Translational Science, Hudson Institute of Medical Research, Monash University, Clayton, 3800, Victoria, Australia.
10
Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia. m.jennings@griffith.edu.au.
11
Department of Microbiology, Monash University, Clayton, 3800, Victoria, Australia. terry.kwok@monash.edu.
12
Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia. terry.kwok@monash.edu.
13
Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Victoria, Australia. terry.kwok@monash.edu.
14
Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Victoria, Australia. terry.kwok@monash.edu.

Abstract

The Helicobacter pylori phase variable gene modH, typified by gene HP1522 in strain 26695, encodes a N6-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'-Gm6ACC-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 ΔmodH5 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.

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