The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori

Abstract

Helicobacter pylori encodes a large number of restriction–modification (R–M) systems despite its small genome. R–M systems have been described as ‘primitive immune systems’ in bacteria, but the role of methylation in bacterial gene regulation and other processes is increasingly accepted. Every H. pylori strain harbours a unique set of R–M systems resulting in a highly diverse methylome. We identified a highly conserved GCGC-specific m5C MTase (JHP1050) that was predicted to be active in all of 459 H. pylori genome sequences analyzed. Transcriptome analysis of two H. pylori strains and their respective MTase mutants showed that inactivation of the MTase led to changes in the expression of 225 genes in strain J99, and 29 genes in strain BCM-300. Ten genes were differentially expressed in both mutated strains. Combining bioinformatic analysis and site-directed mutagenesis, we demonstrated that motifs overlapping the promoter influence the expression of genes directly, while methylation of other motifs might cause secondary effects. Thus, m5C methylation modifies the transcription of multiple genes, affecting important phenotypic traits that include adherence to host cells, natural competence for DNA uptake, bacterial cell shape, and susceptibility to copper.

Cytosine N4-Methylation via M.Ssp6803II Is Involved in the Regulation of Transcription, Fine- Tuning of DNA Replication and DNA Repair in the Cyanobacterium Synechocystis sp. PCC 6803

“…Comparable observations have recently been made in different H. pylori strains. The mutation of a DNA methyltransferase conserved in all known H. pylori genomes also resulted in the changed gene expression of several genes; but similar to our observations here, only 10 genes showed changes consistently (Estibariz et al, 2019).…”

“…The regulatory role of DNA methylation by orphan methyltransferases is best understood in the bacterial model system Caulobacter crescentus , where DNA methylation is crucial for cell cycle control and many other processes (Fioravanti et al, 2013; Mouammine and Collier, 2018). The combined characterization of the methylome and transcriptome in wild-type and methyltransferase-defective mutant cells revealed that DNA methylation also impacts gene expression patterns in the pathogenic bacteria Vibrio cholera (Chao et al, 2015) and Helicobacter pylori (Estibariz et al, 2019). In Borrelia burgdorferi DNA methylation through the natural RM system also impacts the global transcriptome (Casselli et al, 2018).…”

DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes

“…coli , Campylobacter jejuni , Salmonella enterica serovar Typhimurium, Vibrio breoganii , Geobacter metallireducens , Chromhalobacter salexigens , Bacillus cereus , and Borrelia burgdorferi [33–35, 56, 57]. Additional evidence of 5-methylcytosine (m5C) DNA modifications influencing transcriptional expression of multiple genes with an impact on several phenotypic traits has recently been described in Helicobacter pylori , further expanding the recognized influence of prokaryotic methylation modifications [58]. Some of the DNA modifications described have been linked to orphan MTases without an associated endonuclease, such as DNA Adenine Methyltransferase (Dam) of S .…”

Comparison of the Diagnostic Performance of qPCR, Sanger Sequencing, and Whole-Genome Sequencing in Determining Clarithromycin and Levofloxacin Resistance in Helicobacter pylori

“…Specifically, quantitative realtime PCR assays (qPCR) combined with melting curve analysis enable the timely assessment of H. pylori and its drug resistance specimens (Schabereiter-Gurtner et al, 2004;Gazi et al, 2013;Beńejat et al, 2018, Redondo et al, 2018 however, published data are limited to 23SrDNA. Design of a qPCR for gyrA remains a complex challenge due to the high sequence variation of H. pylori (Ailloud et al, 2019;Estibariz et al, 2019). To date and to our knowledge, only Genotype HelicoDR (Cambau et al, 2009) is used as a commercial test (with CE-IVD label) for the combined detection of different mutations of 23SrDNA and gyrA.…”

“…However, this commercial kit is based on a timeconsuming non-realtime PCR followed by hybridization which includes many incubation steps (Jehanne et al, 2020). Additionally, hybridization probes based analysis of gyrA gene (which have to differentiate between 1 bp sequence variation but only at relevant codon 87 and 91) conflicts with the abovementioned extraordinary genetic diversity (Ailloud et al, 2019;Estibariz et al, 2019).…”