The core genome <sup>m5</sup>C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in <i>Helicobacter pylori</i>

Estibariz, Iratxe; Overmann, Annemarie; Ailloud, Florent; Krebes, Juliane; Josenhans, Christine; Suerbaum, Sebastian

doi:10.1101/393710

Cited by 12 publications

(14 citation statements)

References 64 publications

(66 reference statements)

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“…DNA methylation can have a profound effect on gene transcription, both up-regulating and down-regulating transcript levels in bacteria ( 39–41 ). To study the potential transcriptional effects of the different methylation patterns in the locked mutants, we performed RNA-Seq analysis.…”

Section: Resultsmentioning

confidence: 99%

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

Ben-Assa

Coyne

Fomenkov

et al. 2020

Nucleic Acids Research

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The genomes of gut Bacteroidales contain numerous invertible regions, many of which contain promoters that dictate phase-variable synthesis of surface molecules such as polysaccharides, fimbriae, and outer surface proteins. Here, we characterize a different type of phase-variable system of Bacteroides fragilis, a Type I restriction modification system (R-M). We show that reversible DNA inversions within this R-M locus leads to the generation of eight specificity proteins with distinct recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. By creating mutants, each able to produce only one specificity protein from this region, we identified the R-M recognition sites of four of these S-proteins using SMRT sequencing. Transcriptome analysis revealed that the locked specificity mutants, whether grown in vitro or isolated from the mammalian gut, have distinct transcriptional profiles, likely creating different phenotypes, one of which was confirmed. Genomic analyses of diverse strains of Bacteroidetes from both host-associated and environmental sources reveal the ubiquity of phase-variable R-M systems in this phylum.

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Section: Resultsmentioning

confidence: 99%

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

Ben-Assa

Coyne

Fomenkov

et al. 2020

Nucleic Acids Research

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“…The literature search mostly yielded basic research studies investigating a broad spectrum of fundamental mechanism in H. pylori like the presence of genes associated with bacterial virulence[99-104] and biofilm formation[105,106], the characterization of methylases[107], nudix hydrolases[108], restriction-modification (R-M) systems[109], exo- and endo-ribonucleases[110] ; and the transcriptional response of H. pylori to exposition to different salt concentrations[111], different pH conditions[112], heat shock[113] and chemical agents like bismuth[114] and nickel[115]. Most of these studies initially depleted ribosomal RNA, either using RiboZero eukaryotic rRNA depletion treatment (Epicentre, Illumina)[112,113,116] or a rRNA modified capture hybridization approach[110], and performed sequencing on an Illumina platform (Illumina, United States).…”

Section: Next Generation Sequencing and Helicobacter Pylorimentioning

confidence: 99%

Review of current diagnostic methods and advances inHelicobacter pyloridiagnostics in the era of next generation sequencing

Pohl

Keller

Bordier

et al. 2019

WJG

115

113

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Helicobacter pylori ( H. pylori ) infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers, mucosa associated tissue lymphoma and gastric adenocarcinoma. In recent years, an alarming increase in antimicrobial resistance and subsequently failing empiric H. pylori eradication therapies have been noted worldwide, also in many European countries. Therefore, rapid and accurate determination of H. pylori ’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important. Traditionally, detection of H.pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time. Recent advances in diagnostics provide new tools, like real-time polymerase chain reaction (PCR) and line probe assays, to diagnose H. pylori infection and antimicrobial resistance to certain antibiotics, directly from clinical specimens. Moreover, high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome, thereby allowing identification of resistance mutations and associated antibiotic resistance. In the first part of this review, we will give an overview on currently available diagnostic methods for detection of H. pylori and its drug resistance and their implementation in H. pylori management. The second part of the review focusses on the use of next generation sequencing technology in H. pylori research. To this end, we conducted a literature search for original research articles in English using the terms “ Helicobacter ”, “transcriptomic”, “transcriptome”, “next generation sequencing” and “whole genome sequencing”. This review is aimed to bridge the gap between current diagnostic practice (histology, rapid urease test, H. pylori culture, PCR and line probe assays) and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H. pylori management guidelines and subsequently improve public health.

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“…HPG27_1233, called JHP1050 in H. pylori J99, was recently demonstrated to affect the transcription of multiple genes, adherence to host cell, natural competence and bacterial cells shape (Estibariz, Overmann et al 2019). Here we demonstrated that HPG27_1233 also affects biofilm growth and its inactivation results in a significant decrease in biofilm formation of H. pylori G27.…”

Section: Genes Essential For Biofilm Formationmentioning

confidence: 99%

Helicobacter pylori biofilm cells are metabolically distinct, express flagella, and antibiotic tolerant

Hathroubi

Zerebinski

Ottemann

2019

Preprint

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Biofilm growth protects bacteria against harsh environments, antimicrobials, and immune responses. Helicobacter pylori is a bacterium that has a robust ability to maintain colonization in a challenging environment. Over the last decade, H. pylori biofilm formation has begun to be characterized, however, there are still gaps in our understanding about how this growth mode is defined and its impact on H. pylori physiology. To provide insights into H. pylori biofilm growth properties, we characterized the antibiotic susceptibility, gene expression, and genes required for biofilm formation of a strong biofilm-producing H. pylori. H. pylori biofilms developed complex 3D structures and were recalcitrant to multiple antibiotics. Disruption of the protein-based matrix decreased this antibiotic tolerance. Using both transcriptomic and genomic approaches, we discovered that biofilm cells demonstrated lower transcripts for TCA cycle enzymes but higher ones for hydrogenase and acetone metabolism. Interestingly, several genes encoding for the natural competence Type IV secretion system 4 (tfs4) were up-regulated during biofilm formation along with several genes encoding for restriction-modification (R-M) systems, suggesting DNA exchange activities in this mode of growth. Flagella genes were also discovered through both approaches, consistent with previous reports about the importance of these filaments in H. pylori biofilm. Together, these data suggest that H. pylori is capable of adjusting its phenotype when grown as biofilm, changing its metabolism and elevating specific surface proteins including those encoding tfs4 and flagella.

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

Cited by 12 publications

References 64 publications

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

Review of current diagnostic methods and advances inHelicobacter pyloridiagnostics in the era of next generation sequencing

Helicobacter pylori biofilm cells are metabolically distinct, express flagella, and antibiotic tolerant

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

Cited by 12 publications

References 64 publications

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

Review of current diagnostic methods and advances inHelicobacter pyloridiagnostics in the era of next generation sequencing

Helicobacter pylori biofilm cells are metabolically distinct, express flagella, and antibiotic tolerant

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