Genomic Comparison of cag pathogenicity island (PAI)-positive and -negative Helicobacter pylori strains: identification of novel markers for cag PAI-positive strains

Association of Interleukin-1B gene Polymorphism with H. pylori infected Dyspeptic Gastric Diseases and Healthy Population

Objective:

The aim of study was to investigate the association of IL 1B gene polymorphism with involvement of H. pylori and other gastric diseases.

Methods:

Blood samples of dyspeptic patients were collected from endoscopy department of Allied Hospital Faisalabad from January 2017 to January 2019 and were qualitatively assayed for serological detection of CagA H. pylori antibodies. PCR followed by direct sequencing was performed for proinflammatory IL-1B gene polymorphism detection. Sequence analysis was performed in software SnapGene viewer for haplotypes.

Results:

Demographic characteristics of seropositive patients showed maximum 25% gastritis in age groups of 20-40 years and 41-60 years, predominantly (41.7%) in females. While in seronegative patient’s gastritis (33.3%) was found in age group of 20-40 years mainly in males (41.7%). Among studied groups, higher expression of IL-1B-511 genotype (33.3%) polymorphism was found in healthy individuals as compared to H. pylori seropositive (25%) and seronegative (8.3%). While IL-1B-31 genotype showed maximum 33.3% polymorphism rate in seropositive gastric diseased group. Moreover, haplotypes frequencies IL-1B-511CC and IL-1B-31TT were predominantly (20%) found in seropositive gastric diseased group.

Conclusions:

In H. pylori seropositive patients, gastric disease was commonly found, however, gastric disease was not only associated with H. pylori as seronegative patients were also carrying gastric complications. Interleukin IL-1B polymorphism was partially associated with H. pylori infection in studied dyspeptic population.

Outer inflammatory protein a (OipA) of Helicobacter pylori is regulated by host cell contact and mediates CagA translocation and interleukin-8 response only in the presence of a functional cag pathogenicity island type IV secretion system

OipA is a phase-variable virulence factor of Helicobacter pylori. Mutations in oipA to turn the gene phase on in a cag pathogenicity island (PAI)-negative strain of H. pylori (J68) or phase off in a cag PAI-positive strain (26695) demonstrated that phase on oipA alleles in both strains had both increased oipA mRNA and human gastric adenocarcinoma (AGS) cell adherence compared to isogenic oipA phase off mutants. An oipA phase off mutant of H. pylori 26695 demonstrated decreased IL-8 secretion by AGS cells and failure to translocate the cag PAI effector CagA. Increased attachment by OipA expressing cag PAI-negative H. pylori J68 failed to alter secreted IL-8 levels. Thus, OipA is necessary but not sufficient for the induction of IL-8; however, it is necessary for translocation of the oncoprotein CagA. Perhaps the nearly invariant phase on status of oipA alleles among cag PAI-positive H. pylori isolates relates to the role of this outer membrane protein in effective translocation of CagA. oipA mRNA comparisons between AGS cell-adherent and non-adherent H. pylori 26695 revealed significantly greater levels in the adherent cells. This may allow H. pylori to adapt to conditions of host cell contact by altering expression of this virulence factor.

Association of CagPAI integrity with severeness of Helicobacter pylori infection in patients with gastritis

BACKGROUND AND AIM

The Helicobacter pylori cag pathogenicity island (cagPAI) is involved in delivery of CagA effector protein and peptidoglycan into host cells and also in IL-8 induction in the human gastric tissue. Diversity of cagPAI may affect disease status and clinical outcome of the infected patients. Our study was aimed to investigate diversity of this island and its intactness in Iranian patients to investigate possible associations between cagPAI integrity and pathological changes of the infected tissue.

MATERIAL/PATIENTS AND METHODS

Out of the 75 patients, H. pylori strains were obtained from 30 patients with severe active gastritis (SAG) (n=11), moderate chronic gastritis (CG) (n=14) and intestinal metaplasia/dysplasia (IM) (n=5). Intactness of the cagPAI was determined using 12 sets of primer pairs specific for functionally important loci of cagPAI by polymerase chain reaction (PCR).

RESULTS

The cagPAI positive strains were significantly observed in patients with SAG (52.4%) in comparison to those presenting CG (33.3%) and IM (14.3%). In addition, the presence of intact cagPAI was 87.5% in H. pylori strains isolated from patients with SAG, which was higher than those obtained from patients with CG (12.5%) or IM (0%). A significant increase in the frequency of cagα-cagY and cagW-cagT segments, as exterior proteins of the CagPAI, was illustrated in strains from SAG patients compared with those from patients with CG.

CONCLUSIONS

Overall, these results strongly proposed an association between the severity of histopathological changes and intactness of cagPAI in the gastric tissue of patients infected with H. pylori.

Molecular characterization and polyclonal antibody generation against core component CagX protein of Helicobacter pylori type IV secretion system

Gram-negative bacteria Helicobacter pylori cause gastric ulcer, duodenal cancer, and found in almost half of the world's residents. The protein responsible for this disease is secreted through type IV secretion system (TFSS) of H. pylori. TFSS is encoded by 40-kb region of chromosomal DNA known as cag-pathogenicity island (PAI). TFSS comprises of three major components: cytoplasmic/inner membrane ATPase, transmembrane core-complex and outer membranous pilli, and associated subunits. Core complex consists of CagX, CagT, CagM, and Cag3(δ) proteins as per existing knowledge. In this study, we have characterized one of the important component of core-complex forming sub-unit protein, i.e., CagX. Complete ORF of CagX except signal peptide coding region was cloned and expressed in pET28a vector. Purification of CagX protein was performed, and polyclonal anti-sera against full-length recombinant CagX were raised in rabbit model. We obtained a very specific and high titer, CagX anti-sera that were utilized to characterize endogenous CagX. Surface localization of CagX was also seen by immunofluorescence microscopy. In short for the first time a full-length CagX was characterized, and we showed that CagX is the part of high molecular weight core complex, which is important for assembly and function of H. pylori TFSS.

Identification of chromosomal HP0892-HP0893 toxin-antitoxin proteins in Helicobacter pylori and structural elucidation of their protein-protein interaction

Bacterial chromosomal toxin-antitoxin (TA) systems have been proposed not only to play an important role in the stress response, but also to be associated with antibiotic resistance. Here, we identified the chromosomal HP0892-HP0893 TA proteins in the gastric pathogen, Helicobacter pylori, and structurally characterized their protein-protein interaction. Previously, HP0892 protein was suggested to be a putative TA toxin based on its structural similarity to other RelE family TA toxins. In this study, we demonstrated that HP0892 binds to HP0893 strongly with a stoichiometry of 1:1, and HP0892-HP0893 interaction occurs mainly between the N-terminal secondary structure elements of HP0892 and the C-terminal region of HP0893. HP0892 cleaved mRNA in vitro, preferentially at the 5' end of A or G, and the RNase activity of HP0892 was inhibited by HP0893. In addition, heterologous expression of HP0892 in Escherichia coli cells led to cell growth arrest, and the cell toxicity of HP0892 was neutralized by co-expression with HP0893. From these results and a structural comparison with other TA toxins, it is concluded that HP0892 is a toxin with intrinsic RNase activity and HP0893 is an antitoxin against HP0892 from a TA system of H. pylori. It has been known that hp0893 gene and another TA antitoxin gene, hp0895, of H. pylori, are both genomic open reading frames that correspond to genes that are potentially expressed in response to interactions with the human gastric mucosa. Therefore, it is highly probable that TA systems of H. pylori are involved in virulence of H. pylori.

Structural analysis of hypothetical proteins from Helicobacter pylori: an approach to estimate functions of unknown or hypothetical proteins

Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc. Based on genomic research of H. pylori, over 1600 genes have been functionally identified so far. However, H. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the function of genes have not been characterized in any other bacterial systems; and (iii) sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in H. pylori. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of H. pylori. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information.

Diversity in the cag pathogenicity island of Helicobacter pylori isolates in populations from North and South India

The cag pathogenicity island (cagPAI) has been reported to be the major virulence determinant in Helicobacter pylori-related diseases. In the present study, the diversity of the cagA gene and the integrity of the cagPAI in 158 H. pylori strains from Varanasi (North India) and Hyderabad (South India) were studied by amplifying the cagA gene (approximately 3.5 kb), followed by PCR-RFLP analysis. The results revealed significant differences in the cagA gene and the integrity of the cagPAI between North and South Indian isolates. Of 158 isolates, 40 (34.8 %) from Varanasi and 20 (46.5 %) from Hyderabad were found to carry an intact cagPAI. A partially deleted cagPAI was present in 75 (65.2 %) isolates from Varanasi and 23 (53.5 %) from Hyderabad. None of the isolates showed complete deletion of the cagPAI. Differences in the cagA 5' and 3' regions were also noted, and 11 isolates (8 from Varanasi and 3 from Hyderabad) that were cagA negative with primers for the 5' region turned out to be cagA positive with primers for the 3' variable region. It is tentatively concluded that the 3' variable region may be a better marker for cagA typing. The results also showed that the majority of the isolates harboured the Western-type EPIYA motif. PCR-RFLP analysis of the cagA gene showed 29 distinguishable digestion patterns, and cluster analysis of RFLP types from a random selection of 32 isolates placed all of the isolates into 5 groups. These results demonstrate that significant differences in the cagPAI occur among isolates from North and South India, and that RFLP of cagA could be employed for elucidating genetic variations among various isolates of H. pylori.

Differences in genome content among Helicobacter pylori isolates from patients with gastritis, duodenal ulcer, or gastric cancer reveal novel disease-associated genes

Helicobacter pylori establishes a chronic infection in the human stomach, causing gastritis, peptic ulcer, or gastric cancer, and more severe diseases are associated with virulence genes such as the cag pathogenicity island (PAI). The aim of this work was to study gene content differences among H. pylori strains isolated from patients with different gastroduodenal diseases in a Mexican-Mestizo patient population. H. pylori isolates from 10 patients with nonatrophic gastritis, 10 patients with duodenal ulcer, and 9 patients with gastric cancer were studied. Multiple isolates from the same patient were analyzed by randomly amplified polymorphic DNA analysis, and strains with unique patterns were tested using whole-genome microarray-based comparative genomic hybridization (aCGH). We studied 42 isolates and found 1,319 genes present in all isolates, while 341 (20.5%) were variable genes. Among the variable genes, 127 (37%) were distributed within plasticity zones (PZs). The overall number of variable genes present in a given isolate was significantly lower for gastric cancer isolates. Thirty genes were significantly associated with nonatrophic gastritis, duodenal ulcer, or gastric cancer, 14 (46.6%) of which were within PZs and the cag PAI. Two genes (HP0674 and JHP0940) were absent in all gastric cancer isolates. Many of the disease-associated genes outside the PZs formed clusters, and some of these genes are regulated in response to acid or other environmental conditions. Validation of candidate genes identified by aCGH in a second patient cohort allowed the identification of novel H. pylori genes associated with gastric cancer or duodenal ulcer. These disease-associated genes may serve as biomarkers of the risk for severe gastroduodenal diseases.