Identification of the periplasmic DNA receptor for natural transformation of Helicobacter pylori

AbstractHorizontal gene transfer through natural transformation is a major driver of antibiotic resistance spreading in many pathogenic bacterial species. In the case of Gram-negative bacteria, and in particular of Helicobacter pylori, the mechanisms underlying the handling of the incoming DNA within the periplasm are poorly understood. Here we identify the protein ComH as the periplasmic receptor for the transforming DNA during natural transformation in H. pylori. ComH is a DNA-binding protein required for the import of DNA into the periplasm. Its C-terminal domain displays strong affinity for double-stranded DNA and is sufficient for the accumulation of DNA in the periplasm, but not for DNA internalisation into the cytoplasm. The N-terminal region of the protein allows the interaction of ComH with a periplasmic domain of the inner-membrane channel ComEC, which is known to mediate the translocation of DNA into the cytoplasm. Our results indicate that ComH is involved in the import of DNA into the periplasm and its delivery to the inner membrane translocator ComEC.

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Slow Genetic Divergence of Helicobacter pylori Strains during Long-Term Colonization

Infection and Immunity ◽

10.1128/iai.73.8.4818-4822.2005 ◽

2005 ◽

Vol 73 (8) ◽

pp. 4818-4822 ◽

Cited By ~ 27

Author(s):

Annelie Lundin ◽

Britta Björkholm ◽

Ilya Kupershmidt ◽

Magnus Unemo ◽

Peter Nilsson ◽

...

Keyword(s):

Helicobacter Pylori ◽

Genetic Divergence ◽

Bacterial Species ◽

Pcr Amplification ◽

Genetic Change ◽

Genetic Changes ◽

Single Strain ◽

Divergent Gene ◽

Asymptomatic Adult ◽

H Pylori

ABSTRACT The genetic variability of Helicobacter pylori is known to be high compared to that of many other bacterial species. H. pylori is adapted to the human stomach, where it persists for decades, and adaptation to each host results in every individual harboring a distinctive bacterial population. Although clonal variants may exist within such a population, all isolates are generally genetically related and thus derived from a common ancestor. We sought to determine the rate of genetic change of H. pylori over 9 years in two asymptomatic adult patients. Arbitrary primed PCR confirmed the relatedness of individual subclones within a patient. Furthermore, sequencing of 10 loci (∼6,000 bp) in three subclones per time and patient revealed only two base pair changes among the subclones from patient I. All sequences were identical among the patient II subclones. However, PCR amplification of the highly divergent gene amiA revealed great variation in the size of the gene between the subclones within each patient. Thus, both patients harbored a single strain with clonal variants at both times. We also studied genetic changes in culture- and mouse-passaged strains, and under both conditions no genetic divergence was found. These results suggest that previous estimates of the rate of genetic change in H. pylori within an individual might be overestimates.

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Structural insights into a novel family of integral membrane siderophore reductases

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2101952118 ◽

2021 ◽

Vol 118 (34) ◽

pp. e2101952118

Author(s):

Inokentijs Josts ◽

Katharina Veith ◽

Vincent Normant ◽

Isabelle J. Schalk ◽

Henning Tidow

Keyword(s):

Iron Uptake ◽

Bacterial Species ◽

Gram Negative Bacteria ◽

Inner Membrane ◽

Gram Negative ◽

Inner Membrane Protein ◽

Uptake Studies ◽

Structural Insights

Gram-negative bacteria take up the essential ion Fe3+ as ferric-siderophore complexes through their outer membrane using TonB-dependent transporters. However, the subsequent route through the inner membrane differs across many bacterial species and siderophore chemistries and is not understood in detail. Here, we report the crystal structure of the inner membrane protein FoxB (from Pseudomonas aeruginosa) that is involved in Fe-siderophore uptake. The structure revealed a fold with two tightly bound heme molecules. In combination with in vitro reduction assays and in vivo iron uptake studies, these results establish FoxB as an inner membrane reductase involved in the release of iron from ferrioxamine during Fe-siderophore uptake.

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In Vitro Anti-Helicobacter pyloriActivities of New Rifamycin Derivatives, KRM-1648 and KRM-1657

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.43.5.1072 ◽

1999 ◽

Vol 43 (5) ◽

pp. 1072-1076 ◽

Cited By ~ 45

Author(s):

Junko K. Akada ◽

Mutsunori Shirai ◽

Kenji Fujii ◽

Kiwamu Okita ◽

Teruko Nakazawa

Keyword(s):

Helicobacter Pylori ◽

Cell Lysis ◽

Antimicrobial Activities ◽

Gram Negative Bacteria ◽

Gram Negative ◽

Bactericidal Activities ◽

H Pylori ◽

Time Kill

ABSTRACT The new rifamycin derivatives KRM-1657 and KRM-1648 were evaluated for their in vitro antimicrobial activities against 44 strains ofHelicobacter pylori. Although the drugs were not very active against other gram-negative bacteria, the MICs at which 90% of isolates are inhibited for these drugs were lower (0.002 and 0.008 μg/ml, respectively) than those of amoxicillin and rifampin forH. pylori. Time-kill studies revealed that the bactericidal activities of these agents were due to cell lysis. The results presented here indicate that these new rifamycin derivatives may be useful for the eradication of H. pylori infections.

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Helicobacter pylori Peptidoglycan Modifications Confer Lysozyme Resistance and Contribute to Survival in the Host

mBio ◽

10.1128/mbio.00409-12 ◽

2012 ◽

Vol 3 (6) ◽

Cited By ~ 39

Author(s):

Ge Wang ◽

Leja F. Lo ◽

Lennart S. Forsberg ◽

Robert J. Maier

Keyword(s):

Cell Wall ◽

Helicobacter Pylori ◽

Double Mutant ◽

Lytic Enzyme ◽

Permeability Barrier ◽

Gram Negative Bacteria ◽

Gram Negative ◽

Content Type ◽

H Pylori ◽

Modification Enzyme

ABSTRACTThe prominent host muramidase lysozyme cleaves bacterial peptidoglycan (PG), and the enzyme is abundant in mucosal secretions. The lytic enzyme susceptibility of Gram-negative bacteria and mechanisms they use to thwart lytic enzyme activity are poorly studied. We previously characterized aHelicobacter pyloriPG modification enzyme, an N-deacetylase (PgdA) involved in lysozyme resistance. In this study, another PG modification enzyme, a putative PG O-acetyltransferase (PatA), was identified. Mass spectral analysis of the purified PG demonstrated that apatAstrain contained a greatly reduced amount of acetylated muropeptides, indicating a role for PatA inH. pyloriPG O-acetylation. The PG modification mutant strains (pgdA,patA, orpgdA patA) were more susceptible to lysozyme killing than the parent, but this assay required high lysozyme levels (up to 50 mg/ml). However, addition of host lactoferrin conferred lysozyme sensitivity toH. pylori, at physiologically relevant concentrations of both host components (3 mg/ml lactoferrin plus 0.3 mg/ml lysozyme). ThepgdA patAdouble mutant strain was far more susceptible to lysozyme/lactoferrin killing than the parent. Peptidoglycan purified from apgdA patAmutant was five times more sensitive to lysozyme than PG from the parent strain, while PG from both single mutants displayed intermediate sensitivity. Both sensitivity assays for whole cells and for purified PGs indicated that the modifications mediated by PgdA and PatA have a synergistic effect, conferring lysozyme tolerance. In a mouse infection model, significant colonization deficiency was observed for the double mutant at 3 weeks postinoculation. The results show that PG modifications affect the survival of a Gram-negative pathogen.IMPORTANCEPathogenic bacteria evade host antibacterial enzymes by a variety of mechanisms, which include resisting lytic enzymes abundant in the host. Enzymatic modifications to peptidoglycan (PG, the site of action of lysozyme) are a known mechanism used by Gram-positive bacteria to protect against host lysozyme attack. However, Gram-negative bacteria contain a thin layer of PG and a recalcitrant outer membrane permeability barrier to resist lysis, so molecular modifications to cell wall structure in order to combat lysis remain largely unstudied. Here we show that twoHelicobacter pyloriPG modification enzymes (PgdA and PatA) confer a clear protective advantage to a Gram-negative bacterium. They protect the bacterium from lytic enzyme degradation, albeit via different PG modification activities. Many pathogens are Gram negative, so some would be expected to have a similar cell wall-modifying strategy. Understanding such strategies may be useful for combating pathogen growth.

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Anti-Helicobacter pylori Activity of the Methanolic Extract of Geum iranicum and its Main Compounds

Zeitschrift für Naturforschung C ◽

10.1515/znc-2012-3-409 ◽

2012 ◽

Vol 67 (3-4) ◽

pp. 172-180 ◽

Cited By ~ 6

Author(s):

Somayeh Shahani ◽

Hamid R. Monsef-Esfahani ◽

Soodabeh Saeidnia ◽

Parastoo Saniee ◽

Farideh Siavoshi ◽

...

Keyword(s):

Helicobacter Pylori ◽

Clinical Isolates ◽

Diffusion Method ◽

Phenolic Glycoside ◽

Gram Negative Bacteria ◽

Gram Positive ◽

Aqueous Fraction ◽

Gram Negative ◽

Effective Fraction ◽

H Pylori

Geum iranicum Khatamsaz, belonging to the Rosaceae family, is an endemic plant of Iran. The methanol extract of the roots of this plant showed signifi cant activity against one of the clinical isolates of Helicobacter pylori which was resistant to metronidazole. The aim of this study was the isolation and evaluation of the major compounds of G. iranicum effective against H. pylori. The compounds were isolated using various chromatographic methods and identifi ed by spectroscopic data (1H and 13C NMR, HMQC, HMBC, EI-MS). An antimicrobial susceptibility test was performed employing the disk diffusion method against clinical isolates of H. pylori and a micro dilution method against several Gram-positive and Gram-negative bacteria; additionally the inhibition zone diameters (IZD) and minimum inhibitory concentrations (MIC) values were recorded. Nine compounds were isolated: two triterpenoids, uvaol and niga-ichigoside F1, three sterols, β-sitosterol, β-sitosteryl acetate, and β-sitosteryl linoleate, one phenyl propanoid, eugenol, one phenolic glycoside, gein, one fl avanol, (+)-catechin, and sucrose. The aqueous fraction, obtained by partitioning the MeOH extract with water and chloroform, was the most effective fraction of the extract against all clinical isolates of H. pylori. Further investigation of the isolated compounds showed that eugenol was effective against H. pylori but gein, diglycosidic eugenol, did not exhibit any activity against H. pylori. The subfraction D4 was the effective fraction which contained tannins. It appeared that tannins were probably the active compounds responsible for the anti-H. pylori activity of G. iranicum. The aqueous fraction showed a moderate inhibitory activity against both Gram-positive and Gram-negative bacteria. The MIC values indicated that Gram-positive bacteria including Staphylococcus aureus, Staphylococcus epidermidis, and Bacillus subtilis are more susceptible than Gram-neagative bacteria including Escherichia coli and Pseudomonas aeruginosa.

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Molecular and Structural Analysis of the Helicobacter pylori cag Type IV Secretion System Core Complex

mBio ◽

10.1128/mbio.02001-15 ◽

2016 ◽

Vol 7 (1) ◽

Cited By ~ 67

Author(s):

Arwen E. Frick-Cheng ◽

Tasia M. Pyburn ◽

Bradley J. Voss ◽

W. Hayes McDonald ◽

Melanie D. Ohi ◽

...

Keyword(s):

Helicobacter Pylori ◽

Bacterial Species ◽

Secretion System ◽

Effector Proteins ◽

Type Iv Secretion ◽

Secretion Systems ◽

Core Complex ◽

Type Iv ◽

Membrane Spanning ◽

H Pylori

ABSTRACT Bacterial type IV secretion systems (T4SSs) can function to export or import DNA, and can deliver effector proteins into a wide range of target cells. Relatively little is known about the structural organization of T4SSs that secrete effector proteins. In this report, we describe the isolation and analysis of a membrane-spanning core complex from the Helicobacter pylori cag T4SS, which has an important role in the pathogenesis of gastric cancer. We show that this complex contains five H. pylori proteins, CagM, CagT, Cag3, CagX, and CagY, each of which is required for cag T4SS activity. CagX and CagY are orthologous to the VirB9 and VirB10 components of T4SSs in other bacterial species, and the other three Cag proteins are unique to H. pylori . Negative stain single-particle electron microscopy revealed complexes 41 nm in diameter, characterized by a 19-nm-diameter central ring linked to an outer ring by spoke-like linkers. Incomplete complexes formed by Δ cag3 or Δ cagT mutants retain the 19-nm-diameter ring but lack an organized outer ring. Immunogold labeling studies confirm that Cag3 is a peripheral component of the complex. The cag T4SS core complex has an overall diameter and structural organization that differ considerably from the corresponding features of conjugative T4SSs. These results highlight specialized features of the H. pylori cag T4SS that are optimized for function in the human gastric mucosal environment. IMPORTANCE Type IV secretion systems (T4SSs) are versatile macromolecular machines that are present in many bacterial species. In this study, we investigated a T4SS found in the bacterium Helicobacter pylori. H. pylori is an important cause of stomach cancer, and the H. pylori T4SS contributes to cancer pathogenesis by mediating entry of CagA (an effector protein regarded as a “bacterial oncoprotein”) into gastric epithelial cells. We isolated and analyzed the membrane-spanning core complex of the H. pylori T4SS and showed that it contains unique proteins unrelated to components of T4SSs in other bacterial species. These results constitute the first structural analysis of the core complex from this important secretion system.

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Quantitative Effect of luxS Gene Inactivation on the Fitness of Helicobacter pylori

Applied and Environmental Microbiology ◽

10.1128/aem.01291-06 ◽

2006 ◽

Vol 72 (10) ◽

pp. 6615-6622 ◽

Cited By ~ 17

Author(s):

Woo-Kon Lee ◽

Keiji Ogura ◽

John T. Loh ◽

Timothy L. Cover ◽

Douglas E. Berg

Keyword(s):

Helicobacter Pylori ◽

Competitive Ability ◽

Reference Strain ◽

Bacterial Species ◽

Soft Agar ◽

Autoinducer 2 ◽

Methyl Cycle ◽

Adenosyl Methionine ◽

Unrelated Strain ◽

H Pylori

ABSTRACT Furanone metabolites called AI-2 (autoinducer 2), used by some bacterial species for signaling and cell density-regulated changes in gene expression, are made while regenerating S-adenosyl methionine (SAM) after its use as a methyl donor. The luxS-encoded enzyme, in particular, participates in this activated methyl cycle by generating both a pentanedione, which is transformed chemically into these AI-2 compounds, and homocysteine, a precursor of methionine and SAM. Helicobacter pylori seems to contain the genes for this activated methyl cycle, including luxS, but not genes for AI-2 uptake and transcriptional regulation. Here we report that deletion of luxS in H. pylori reference strain SS1 diminished its competitive ability in mice and motility in soft agar, whereas no such effect was seen with an equivalent ΔluxS derivative of the unrelated strain X47. These different outcomes are consistent with H. pylori's considerable genetic diversity and are reminiscent of phenotypes seen after deletion of another nonessential metabolic gene, that encoding polyphosphate kinase 1. We suggest that synthesis of AI-2 by H. pylori may be an inadvertent consequence of metabolite flux in its activated methyl cycle and that impairment of this cycle and/or pathways affected by it, rather than loss of quorum sensing, is deleterious for some H. pylori strains. Also tenable is a model in which AI-2 affects other microbes in H. pylori's gastric ecosystem and thereby modulates the gastric environment in ways to which certain H. pylori strains are particularly sensitive.

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comH, a Novel Gene Essential for Natural Transformation of Helicobacter pylori

Journal of Bacteriology ◽

10.1128/jb.182.14.3948-3954.2000 ◽

2000 ◽

Vol 182 (14) ◽

pp. 3948-3954 ◽

Cited By ~ 54

Author(s):

Leonard C. Smeets ◽

Jetta J. E. Bijlsma ◽

Sacha Y. Boomkens ◽

Christina M. J. E. Vandenbroucke-Grauls ◽

Johannes G. Kusters

Keyword(s):

Helicobacter Pylori ◽

Natural Transformation ◽

Bacterial Genome ◽

Uptake System ◽

Dna Uptake ◽

Mutant Library ◽

Chromosomal Dna ◽

Orthologous Genes ◽

Helicobacter Felis ◽

H Pylori

ABSTRACT Helicobacter pylori is naturally competent for transformation, but the DNA uptake system of this bacterium is only partially characterized, and nothing is known about the regulation of competence in H. pylori. To identify other components involved in transformation or competence regulation in this species, we screened a mutant library for competence-deficient mutants. This resulted in the identification of a novel,Helicobacter-specific competence gene (comH) whose function is essential for transformation of H. pyloriwith chromosomal DNA fragments as well as with plasmids. Complementation of comH mutants in transcompletely restored competence. Unlike other transformation genes ofH. pylori, comH does not belong to a known family of orthologous genes. Moreover, no significant homologs ofcomH were identified in currently available databases of bacterial genome sequences. The comH gene codes for a protein with an N-terminal leader sequence and is present in both highly competent and less-efficient transforming H. pyloristrains. A comH homolog was found in Helicobacter acinonychis but not in Helicobacter felis andHelicobacter mustelae.

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Interplay and cooperation of Helicobacter pylori and gut microbiota in gastric carcinogenesis

BMC Microbiology ◽

10.1186/s12866-021-02315-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Seyedeh Zahra Bakhti ◽

Saeid Latifi-Navid

Keyword(s):

Helicobacter Pylori ◽

Gut Microbiota ◽

Intestinal Microbiota ◽

Bacterial Species ◽

Short Chain Fatty Acids ◽

Gastric Carcinogenesis ◽

Oncogenic Signaling ◽

Comprehensive Overview ◽

H Pylori ◽

Oncogenic Signaling Pathways

AbstractChronic Helicobacter pylori infection is a critical risk factor for gastric cancer (GC). However, only 1–3 % of people with H. pylori develop GC. In gastric carcinogenesis, non-H. pylori bacteria in the stomach might interact with H. pylori. Bacterial dysbiosis in the stomach can strengthen gastric neoplasia development via generating tumor-promoting metabolites, DNA damaging, suppressing antitumor immunity, and activating oncogenic signaling pathways. Other bacterial species may generate short-chain fatty acids like butyrate that may inhibit carcinogenesis and inflammation in the human stomach. The present article aimed at providing a comprehensive overview of the effects of gut microbiota and H. pylori on the development of GC. Next, the potential mechanisms of intestinal microbiota were discussed in gastric carcinogenesis. We also disserted the complicated interactions between H. pylori, intestinal microbiota, and host in gastric carcinogenesis, thus helping us to design new strategies for preventing, diagnosing, and treating GC.

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Overview of Helicobacter pylori Detection Using Rapid Urease Test and Giemsa Modification Staining in Chronic Tonsillitis Patients

Open Access Macedonian Journal of Medical Sciences ◽

10.3889/oamjms.2020.5244 ◽

2020 ◽

Vol 8 (B) ◽

pp. 1105-1109

Author(s):

Ade Asyari ◽

Ferdy Azman ◽

Novialdi Novialdi ◽

Aziz Djamal ◽

Hafni Bachtiar ◽

...

Keyword(s):

Helicobacter Pylori ◽

Descriptive Study ◽

Chronic Tonsillitis ◽

Rapid Urease Test ◽

Gram Negative Bacteria ◽

Gram Negative ◽

Tonsillar Tissue ◽

Urease Test ◽

Tonsil Tissue ◽

H Pylori

BACKGROUND: Helicobacter pylori (H. pylori) is a Gram-negative bacteria and has been known for its role in causing gastric infection aused diseases such as gastric ulcer. H. pylori also implied to play a role in chronic tonsillitis, but this theory remains controversial. Many researches have different and contradictory results due to difficulty to accurately detect H. pylori in tonsillar tissue. There is still no appropriate method that able to detect H. pylori in tonsil tissue. AIM: The aim of the study was to detect H. pylori colonization in chronic tonsillitis and understand some of the methods of examination that can be done to detect H. pylori in tonsillar tissue. METHODS: This study is a descriptive study conducted on 25 respondents. Each sample was taken from patients with chronic tonsillitis who underwent tonsillectomy. Then, the rapid urease test (RUT) and the Giemsa modification staining were carried out to determine the presence of H. pylori. RESULTS: There were 19 people (76%) positive and 6 people (24%) negative for H. pylori using RUT. On examination with Giemsa modification staining obtained 19 people (76%) positive and 6 people (24%) negative for H. pylori. CONCLUSION: H. pylori can be found in most of chronic tonsillitis. Combination RUT and Giemsa modification staining examination can be a good option in detecting H. pylori in chronic tonsillitis.

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