The complete methylome of Helicobacter pylori UM032

Abstract

Background: The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian H. pylori clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome).

Results: The N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome during normal growth was characterized by cloning.

Conclusion: Consistent with previously-studied H. pylori strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of H. pylori.

Figure 1

Schematic representation of the specificity switching of the Type IIG MTase HpyUM032XIII. (A) The S1 and S2 subunits are separated by a homopolymeric tract of 12 G residues at the location shown by ▼, which appears to create a natural frameshift. (B) Reducing the tract length from 12 to 11 corrects the frameshift at ▼, thereby fusing the S1 and S2 subunits. This ‘corrected’ sequence is denoted by ‘mut’, to create fusion of S1 and S2 subunits. (C–D) Expression of individual S subunits with the RM gene shows that the S1 subunit is active in the absence of S2.