Background: Helicobacter pylori (Hp) is a bacterial carcinogenic pathogen infecting about 50% of the human population. Hp is genetically highly diverse and harbors one of the largest portfolios of restriction-modification (RM) systems. Several RM systems have been related to gene regulation and we have shown previously that this effect is partially mediated by direct methylation of promoter regions.

Aims and Methods: Here, we analyzed M.HpyAVII, an ATTAAT-specific methyltransferase, aiming to understand its role in transcriptional regulation of Hp and underlying mechanisms. The M.HpyAVII gene is highly conserved in Hp, and also its only strictly orphan MTase. We performed bioinformatic analyses, transcriptomic assays and phenotypic characterization of Hp wild-type strains and M.HpyAVII mutants.

Results and Conclusions: RNA-Seq analyses showed a pronounced effect of ATTAAT methylation on the Hp transcriptome. Yet, only part of these changes could be explained as direct methylation effects by the presence of an ATTAAT motif in promoter regions. However, pathways related to acid stress and iron metabolism can be observed among differentially regulated genes lacking a motif in their promoters, suggesting that the MTase might influence transcription indirectly through regulation cascades. Following this hypothesis, we could show that the targeted disruption of a methylated motif within a promoter could lead to a significant change in expression not only on the downstream gene but on other distant, functionally related genes as well. Furthermore, we also demonstrate that this type of methylation-dependent regulation cascade can be associated with phenotypic changes, such as copper, nickel and iron sensitivity.

In summary, we combined genome-wide and targeted analysis of gene expression to provide new insights into the regulatory effects of methyltransferases in H. pylori.

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Ailloud F, Gottschall W & Suerbaum S. Commun Biol. 2023