Analysis of comprehensive local and global bacterial genome methylation and epigenetics in the model bacterium Helicobacter pylori detects strain-specific methylation and various internal and external influencing factors

Background and Questions. Bacterial epigenetics is a recently expanding field of study. All bacterial species express methyltransferases (Mtases) which methylate genomic DNA at specific nucleotide motifs. Known functions of DNA methylation include the protection of genomic DNA integrity, DNA replication, exclusion of heterologous DNA and damage repair. Recently, DNA Mtase functions were also shown to include regulation of genomic transcripts, governing both housekeeping functions and virulence. We are using the model bacterium Helicobacter pylori which possesses the highest number and the most variably expressed set of DNA Mtases. We have a basic understanding of H. pylori epigenetics, we need to better characterize the activity, expression and basic biology of the complete set of methyltransferases under various environmental conditions. We also would like to investigate global and local genome methylation in a more quantitative manner, including single nucleotide resolution of changes in methylation.

Methods and Results. We have established novel methods, including enzymatically aided detection, biochemical methods, long-read sequencing, and mutant analyses, to quantitate specific methylation patterns of the H. pylori genome under various conditions. We have also expressed and purified active DNA methyltransferases. This has helped us to gather reproducible information on local quantitative methylation. DNA Mtase expression and activity are significantly strain and growth condition specific. We have also identified Mtase enzymes that show and overall high methylation, versus such which lead to a lower percentage of local methylation. Furthermore, basic conditions that modulate genome-wide nucleotide methylation in H. pylori include growth phase and methionine availability. We have started to use targeted intervention strategies to alter global and local DNA methylation.

Conclusions. We have obtained quantitative information on diverse global and local genome methylation in H. pylori under various conditions. In the future this knowledge will support to develop novel bacterial epigenetic modulation strategies which may also have therapeutic uses.