scholarly journals Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anubhav Tamrakar ◽  
Rahul Singh ◽  
Amit Kumar ◽  
Ravindra D. Makde ◽  
Ashish ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Protein Interactions ◽  
Structural Information ◽  
Outer Membrane Proteins ◽  
In Silico Analysis ◽  
Structural Aspect ◽  
Globular Domain ◽  
H Pylori

AbstractHelicobacter pylori is a Gram-negative bacterium that causes chronic inflammations in the stomach area and is involved in ulcers, which can develop into gastric malignancies. H. pylori attaches and colonizes to the human epithelium using some of their outer membrane proteins (OMPs). HomB and HomA are the most studied OMPs from H. pylori as they play a crucial role in adherence, hyper biofilm formation, antibiotic resistance and are also associated with severe gastric malignancies. The role of HomA and HomB in pathogenesis concerning their structure and function has not been evaluated yet. In the present study, we explored the structural aspect of HomA and HomB proteins using various computational, biophysical and small-angle X-ray scattering (SAXS) techniques. Interestingly, the in-silico analysis revealed that HomA/B consists of 8 discontinuous N and C terminal β-strands forming a small β-barrel, along with a large surface-exposed globular domain. Further, biophysical experiments suggested that HomA and HomB are dimeric and most likely the cysteine residues present on surface-exposed loops participate in protein–protein interactions. Our study provides essential structural information of unexplored proteins of the Hom family that can help in a better understanding of H. pylori pathogenesis.

scholarly journals Assembly of the β-Barrel Outer Membrane Proteins in Gram-Negative Bacteria, Mitochondria, and Chloroplasts

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Rajeev Misra
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Protein Interactions ◽  
Structural Information ◽  
Outer Membrane Proteins ◽  
Model Systems ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
The Core ◽  
Assembly Pathways

In the last decade, there has been an explosion of publications on the assembly of β-barrel outer membrane proteins (OMPs), which carry out diverse cellular functions, including solute transport, protein secretion, and assembly of protein and lipid components of the outer membrane. Of the three outer membrane model systems—Gram-negative bacteria, mitochondria and chloroplasts—research on bacterial and mitochondrial systems has so far led the way in dissecting the β-barrel OMP assembly pathways. Many exciting discoveries have been made, including the identification of β-barrel OMP assembly machineries in bacteria and mitochondria, and potentially the core assembly component in chloroplasts. The atomic structures of all five components of the bacterial β-barrel assembly machinery (BAM) complex, except the β-barrel domain of the core BamA protein, have been solved. Structures reveal that these proteins contain domains/motifs known to facilitate protein-protein interactions, which are at the heart of the assembly pathways. While structural information has been valuable, most of our current understanding of the β-barrel OMP assembly pathways has come from genetic, molecular biology, and biochemical analyses. This paper provides a comparative account of the β-barrel OMP assembly pathways in Gram-negative bacteria, mitochondria, and chloroplasts.

scholarly journals Genome-wide mutation analysis of Helicobacter pylori after inoculation to Mongolian gerbils

Gut Pathogens ◽  
2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Rumiko Suzuki ◽  
Kazuhito Satou ◽  
Akino Shiroma ◽  
Makiko Shimoji ◽  
Kuniko Teruya ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Outer Membrane Proteins ◽  
Human Stomach ◽  
Next Generation Sequencing Data ◽  
Mongolian Gerbils ◽  
New Host ◽  
Model Animal ◽  
H Pylori

Abstract Background Helicobacter pylori is a pathogenic bacterium that causes various gastrointestinal diseases in the human stomach. H. pylori is well adapted to the human stomach but does not easily infect other animals. As a model animal, Mongolian gerbils are often used, however, the genome of the inoculated H. pylori may accumulate mutations to adapt to the new host. To investigate mutations occurring in H. pylori after infection in Mongolian gerbils, we compared the whole genome sequence of TN2 wild type strain (TN2wt) and next generation sequencing data of retrieved strains from the animals after different lengths of infection. Results We identified mutations in 21 loci of 17 genes of the post-inoculation strains. Of the 17 genes, five were outer membrane proteins that potentially influence on the colonization and inflammation. Missense and nonsense mutations were observed in 15 and 6 loci, respectively. Multiple mutations were observed in three genes. Mutated genes included babA, tlpB, and gltS, which are known to be associated with adaptation to murine. Other mutations were involved with chemoreceptor, pH regulator, and outer membrane proteins, which also have potential to influence on the adaptation to the new host. Conclusions We confirmed mutations in genes previously reported to be associated with adaptation to Mongolian gerbils. We also listed up genes that mutated during the infection to the gerbils, though it needs experiments to prove the influence on adaptation.

scholarly journals Role of the Helicobacter pylori outer-membrane proteins AlpA and AlpB in colonization of the guinea pig stomach

2004 ◽  
Vol 53 (5) ◽  
pp. 375-379 ◽  
Author(s):  
Ramon de Jonge ◽  
Zarmina Durrani ◽  
Sjoerd G. Rijpkema ◽  
Ernst J. Kuipers ◽  
Arnoud H.M. van Vliet ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Guinea Pig ◽  
Outer Membrane ◽  
Type Strain ◽  
Wild Type Strain ◽  
Outer Membrane Proteins ◽  
Wild Type ◽  
H Pylori

The human gastric pathogen Helicobacter pylori expresses several putative outer-membrane proteins (OMPs), but the role of individual OMPs in colonization of the stomach by H. pylori is still poorly understood. The role of four such OMPs (AlpA, AlpB, OipA and HopZ) in a guinea pig model of H. pylori infection has been investigated. Single alpA, alpB, hopZ and oipA isogenic mutants were constructed in the guinea pig-adapted, wild-type H. pylori strain GP15. Guinea pigs were inoculated intragastrically with the wild-type strain, single mutants or a mixture of the wild-type and a single mutant in a 1 : 1 ratio. Three weeks after infection, H. pylori could be isolated from stomach sections of all animals that were infected with the wild-type, the hopZ mutant or the oipA mutant, but from only five of nine (P = 0.18) and one of seven (P = 0.02) animals that were infected with the alpA or alpB mutants, respectively. The hopZ and oipA mutants colonized the majority of animals that were inoculated with the strain mixture, whereas alpA and alpB mutants could not be isolated from animals that were infected with the strain mixture (P < 0.01). Specific IgG antibody responses were observed in all animals that were infected with either the wild-type or a mutant, but IgG levels were lower in animals that were infected with either the alpA or the alpB mutants, compared to the wild-type strain (P < 0.05). In conclusion, absence of AlpA or AlpB is a serious disadvantage for colonization of the stomach by H. pylori.

scholarly journals Comparative Genomics of Helicobacter pylori: Analysis of the Outer Membrane Protein Families

2000 ◽  
Vol 68 (7) ◽  
pp. 4155-4168 ◽  
Author(s):  
Richard A. Alm ◽  
James Bina ◽  
Beth M. Andrews ◽  
Peter Doig ◽  
Robert E. W. Hancock ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Outer Membrane Proteins ◽  
Gene Families ◽  
Ancestral Gene ◽  
Related Function ◽  
Paralogous Family ◽  
H Pylori ◽  
Complete Genomic

ABSTRACT The two complete genomic sequences of Helicobacter pylori J99 and 26695 were used to compare the paralogous families (related genes within one genome, likely to have related function) of genes predicted to encode outer membrane proteins which were present in each strain. We identified five paralogous gene families ranging in size from 3 to 33 members; two of these families contained members specific for either H. pylori J99 or H. pylori26695. Most orthologous protein pairs (equivalent genes between two genomes, same function) shared considerable identity between the two strains. The unusual set of outer membrane proteins and the specialized outer membrane may be a reflection of the adaptation of H. pylori to the unique gastric environment where it is found. One subfamily of proteins, which contains both channel-forming and adhesin molecules, is extremely highly related at the sequence level and has likely arisen due to ancestral gene duplication. In addition, the largest paralogous family contained two essentially identical pairs of genes in both strains. The presence and genomic organization of these two pairs of duplicated genes were analyzed in a panel of independentH. pylori isolates. While one pair was present in every strain examined, one allele of the other pair appeared partially deleted in several isolates.

scholarly journals Antigenic Properties of HpaA and Omp18, Two Outer Membrane Proteins of Helicobacter pylori

2003 ◽  
Vol 71 (7) ◽  
pp. 3837-3843 ◽  
Author(s):  
Petra Voland ◽  
Nadia Hafsi ◽  
Marco Zeitner ◽  
Stephanie Laforsch ◽  
Hermann Wagner ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Dendritic Cells ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Mononuclear Cells ◽  
Human Peripheral Blood ◽  
Outer Membrane Proteins ◽  
Interleukin 12 ◽  
Antigenic Properties ◽  
H Pylori

ABSTRACT Outer membrane proteins (OMPs) are incorporated into the outer plasma membrane of Helicobacter pylori and are important for, e.g., ion transport, adherence, structural and osmotic stability, and bacterial virulence but may also be antigenic due to their surface exposure. Previous proteome-based approaches with H. pylori lysates determined a strong serological reaction towards two H. pylori OMPs, HpaA (TIGR HP0797) and Omp18 (TIGR HP1125). PCR was used to detect DNA encoding the two proteins, and a positive signal was found in all H. pylori strains tested. Proteins were cloned and expressed in the human kidney cell line HK293 with the QiaExpressionist system with a C-terminal His tag. Only sera from infected persons showed a positive reaction with the recombinant proteins. Recombinant HpaA (rHpaA) and rOmp18 were incubated with human peripheral blood mononuclear cells and induced secretion of interleukin-12 (IL-12) and IL-10 from these cells. To determine the effect on antigen-presenting cells, human blood monocytic and dendritic cells (DCs) were isolated by magnetic cell separation. rOmp18 and rHpaA strongly stimulated major histocompatibility class II and CD83 expression 7- to 10-fold on isolated DCs. rHpaA and rOmp18 failed to stimulate IL-8 secretion from monocytes but increased secretion of IL-12 and IL-10 from DCs significantly. In summary, HpaA and Omp18 are recognized by human dendritic cells and induce their maturation as well as antigen presentation. HpaA and Omp18 of H. pylori thereby appear to have a specific antigenic potential in humans.

scholarly journals Selective pressure on membrane proteins drives the evolution of Helicobacter pylori Colombian subpopulations

2021 ◽  
Author(s):  
Alix Andrea Guevara Tique ◽  
Roberto C. Torres ◽  
Fabian Leonardo Castro Valencia ◽  
John Jairo Suárez ◽  
Ángel Alexandro Criollo Rayo ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Population Structure ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Selective Pressure ◽  
Outer Membrane Proteins ◽  
Geographic Origin ◽  
Population Structure Analysis ◽  
Genes Encoding ◽  
H Pylori

Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America H. pylori has evolved in several subpopulations specific for regions or even countries. In this study we analyzed the genome of 163 Colombian strains along with 1,113 strains that represent worldwide H. pylori populations to better discern the ancestry and adaption to Colombian people. Population structure was inferred with FineStructure and chromosome painting identifying the proportion of ancestries in Colombian isolates. Phylogenetic relationship was analyzed using the SNPs present in the core genome. Also, a Fst analysis was done to identify the gene variants with the strongest fixation in the identified Colombian subpopulations in relation to their parent population hspSWEurope. Worldwide, population structure analysis allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia. In addition, three subgroups of H. pylori were identified within hspColombia that follow their geographic origin. The Colombian H. pylori subpopulations represent an admixture of European, African and Native indigenous ancestry; although some genomes showed a high proportion of self-identity, suggesting a strong adaption to these mestizo Colombian groups. The Fst analysis identified 82 SNPs significantly fixed in 26 genes of the hspColombia subpopulation that encode mainly for outer membrane proteins and proteins involved in central metabolism. The strongest fixation indices were identified in genes encoding the membrane proteins HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations following a geographical structure, evolving to an autochthonous genetic pool, drive by a positive selective pressure especially on genes encoding for outer membrane proteins.

scholarly journals NikR Mediates Nickel-Responsive Transcriptional Repression of the Helicobacter pylori Outer Membrane Proteins FecA3 (HP1400) and FrpB4 (HP1512)

2006 ◽  
Vol 74 (12) ◽  
pp. 6821-6828 ◽  
Author(s):  
Florian D. Ernst ◽  
Jeroen Stoof ◽  
Wannie M. Horrevoets ◽  
Ernst J. Kuipers ◽  
Johannes G. Kusters ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Transcriptional Repression ◽  
Outer Membrane Proteins ◽  
Regulatory Protein ◽  
Start Codon ◽  
Recognition Sequence ◽  
Nickel Uptake ◽  
H Pylori

ABSTRACT The transition metal nickel plays an important role in gastric colonization and persistence of the important human pathogen Helicobacter pylori, as it is the cofactor of the abundantly produced acid resistance factor urease. Nickel uptake through the inner membrane is mediated by the NixA protein, and the expression of NixA is controlled by the NikR regulatory protein. Here we report that NikR also controls the nickel-responsive expression of the FecA3 (HP1400) and FrpB4 (HP1512) outer membrane proteins (OMPs), as well as the nickel-responsive expression of an ExbB-ExbD-TonB system, which may function in energization of outer membrane transport. Transcription and expression of the frpB4 and fecA3 genes were repressed by nickel in wild-type H. pylori 26695, but they were independent of nickel and derepressed in an isogenic nikR mutant. Both the frpB4 and fecA3 genes were transcribed from a promoter directly upstream of their start codon. Regulation by NikR was mediated via nickel-dependent binding to specific operators overlapping either the +1 or −10 sequence in the frpB4 and fecA3 promoters, respectively, and these operators contained sequences resembling the proposed H. pylori NikR recognition sequence (TATWATT-N11-AATWATA). Transcription of the HP1339-1340-1341 operon encoding the ExbB2-ExbD2-TonB2 complex was also regulated by nickel and NikR, but not by Fur and iron. In conclusion, H. pylori NikR controls nickel-responsive expression of the HP1400 (FecA3) and HP1512 (FrpB4) OMPs. We hypothesize that these two NikR-regulated OMPs may participate in the uptake of complexed nickel ions and that this process is energized by the NikR-regulated ExbB2-ExbD2-TonB2 system, another example of the specific adaptation of H. pylori to the gastric lifestyle.

scholarly journals Helicobacter pylori Physiology Predicted from Genomic Comparison of Two Strains

1999 ◽  
Vol 63 (3) ◽  
pp. 675-707 ◽  
Author(s):  
Peter Doig ◽  
Boudewijn L. de Jonge ◽  
Richard A. Alm ◽  
Eric D. Brown ◽  
Maria Uria-Nickelsen ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Sulfur Metabolism ◽  
Outer Membrane Proteins ◽  
Anaerobic Respiration ◽  
Phase Variation ◽  
Carbohydrate Utilization ◽  
Wide Range ◽  
H Pylori

SUMMARY Helicobacter pylori is a gram-negative bacteria which colonizes the gastric mucosa of humans and is implicated in a wide range of gastroduodenal diseases. This paper reviews the physiology of this bacterium as predicted from the sequenced genomes of two unrelated strains and reconciles these predictions with the literature. In general, the predicted capabilities are in good agreement with reported experimental observations. H. pylori is limited in carbohydrate utilization and will use amino acids, for which it has transporter systems, as sources of carbon. Energy can be generated by fermentation, and the bacterium possesses components necessary for both aerobic and anaerobic respiration. Sulfur metabolism is limited, whereas nitrogen metabolism is extensive. There is active uptake of DNA via transformation and ample restriction-modification activities. The cell contains numerous outer membrane proteins, some of which are porins or involved in iron uptake. Some of these outer membrane proteins and the lipopolysaccharide may be regulated by a slipped-strand repair mechanism which probably results in phase variation and plays a role in colonization. In contrast to a commonly held belief that H. pylori is a very diverse species, few differences were predicted in the physiology of these two unrelated strains, indicating that host and environmental factors probably play a significant role in the outocme of H. pylori-related disease.

scholarly journals Proteins Released by Helicobacter pylori In Vitro

2002 ◽  
Vol 184 (22) ◽  
pp. 6155-6162 ◽  
Author(s):  
Nayoung Kim ◽  
David L. Weeks ◽  
Jai Moo Shin ◽  
David R. Scott ◽  
Mary K. Young ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Proteins ◽  
Dna Binding ◽  
Outer Membrane ◽  
Nalidixic Acid ◽  
Outer Membrane Proteins ◽  
Gastric Epithelium ◽  
Synthesis Inhibitor ◽  
Vitro Analysis

ABSTRACT Secretion of proteins by Helicobacter pylori may contribute to gastric inflammation and epithelial damage. An in vitro analysis was designed to identify proteins released by mechanisms other than nonspecific lysis. The radioactivity of proteins in the supernatant was compared with that of the intact organism by two-dimensional gel phosphorimaging following a 4-h pulse-chase. The ratio of the amount of UreB, a known cytoplasmic protein, in the supernatant to that in the pellet was found to be 0.25, and this was taken as an index of lysis during the experiments (n = 6). Ratios greater than that of UreB were used to distinguish proteins that were selectively released into the medium. Thus, proteins enriched more than 10-fold in the supernatant compared to UreB were identified by mass spectrometry. Sixteen such proteins were present in the supernatant: VacA; a conserved secreted protein (HP1286); putative peptidyl cis-trans isomerase (HP0175); six proteins encoded by HP0305, HP0231, HP0973, HP0721, HP0129, and HP0902; thioredoxin (HP1458); single-stranded-DNA-binding 12RNP2 precursor (HP0827); histone-like DNA-binding protein HU (HP0835); ribosomal protein L11 (HP1202); a putative outer membrane protein (HP1564); and outer membrane proteins Omp21 (HP0913) and Omp20 (HP0912). All except HP0902, thioredoxin, HP0827, HP0835, and HP1202 had a signal peptide. When nalidixic acid, a DNA synthesis inhibitor, was added to inhibit cell division but not protein synthesis, to decrease possible contamination due to outer membrane shedding, two outer membrane proteins (Omp21 and Omp20) disappeared from the supernatant, and the amount of VacA also decreased. Thus, 13 proteins were still enriched greater than 10-fold in the medium after nalidixic acid treatment, suggesting these were released specifically, possibly by secretion. These proteins may be implicated in H. pylori-induced effects on the gastric epithelium.

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