Database Authors
Summary Helicobacter pylori is a Gram-negative bacterium that is often found in the human stomach. It is helix-shaped (giving the genus its name), presumably to help it penetrate the mucoid lining of the stomach and reach the epithelial cells underneath, where it escapes the acidic environment of the stomach [Amieva08].

Helicobacter pylori infections are common and usually have no symptoms. In 2015 it was estimated that more than 50% of the world's population is colonized by the bacterium. However, in 10-20% of the cases an infection results in gastritis (stomach inflammation) or ulcers. In some cases the infection may lead to the development of certain cancers [Blaser06]. Pathogenicity is correlated with the presence of pathogenicity islands in the genome [Broutet01, Miehlke01, Baldwin07, ZawilakPawlik19]. However, disease outcome depends on additional factors, such as the host's physiology, genotype and dietary habits.

Helicobacter pylori was discovered only in 1982 [Warren83, Marshall84]. It is highly motile owing to four to six flagella. While it is a heterotroph, it can also produce energy by oxidizing molecular hydrogen (H2) produced by other intestinal bacteria [Olson02]. It produces large amounts of the ammonia-producing enzyme urease, which helps it overcome the stomach acidity. Its O antigen (external part of the lipopolysaccharide) is often fucosylated to mimic the Lewis blood group antigens found on the human gastric epithelium [Kusters06].

Helicobacter pylori 26695, originally known as Campylobacter pyloridis NE 26695, was isolated in 1986 from a human gastric biopsy of a patient in Southampton, England, as part of the collection of Dr D.R. Morgan from Norwich Eaton Pharmaceuticals Inc. [Morgan87, Morgan87a, Leunk88]. The genome of Helicobacter pylori 26695 was originally sequenced in 1997 [Tomb97]. This Pathway/Genome Database (PGDB) was generated by the PathoLogic component [Karp11] of the Pathway Tools software version 25.5 [Karp16] and MetaCyc version 25.5 [Caspi18] on 21 Jun 2021, using a genome annotation by RefSeq that was generated on 02 Apr 2021. The database was subsequently upgraded by limited manual curation.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
chromosome1,5851,44745931,667,867RefSeq:NC_000915
Ortholog data available?Yes
Database Contents
Genes1,585
Pathways171
Enzymatic Reactions826
Transport Reactions61
Polypeptides1,467
Protein Complexes139
Enzymes502
Transporters93
Compounds643
Transcription Units745
tRNAs36
Growth Media2
Transcriptional Regulation34
Protein Features1,825
GO Terms17,127
Gene Essentiality Datasets2
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Campylobacterota
Epsilonproteobacteria
Campylobacterales
Helicobacteraceae
Helicobacter
Helicobacter pylori
Helicobacter pylori 26695
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603995
NCBI BioProjectPRJNA224116
NCBI-Taxonomy85962
Collection Date1986
Relationship to Oxygenmicroaerophilic
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipmutualistic
Pathogenicityhuman
Human Microbiome Body Sitegastrointestinal-tract
Annotation ProviderNCBI RefSeq
Annotation Date2021-04-2
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.1
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
Copyright 2021, SRI International. All Rights Reserved.


References

Amieva08: Amieva MR, El-Omar EM (2008). "Host-bacterial interactions in Helicobacter pylori infection." Gastroenterology 134(1);306-23. PMID: 18166359

Baldwin07: Baldwin DN, Shepherd B, Kraemer P, Hall MK, Sycuro LK, Pinto-Santini DM, Salama NR (2007). "Identification of Helicobacter pylori genes that contribute to stomach colonization." Infect Immun 75(2);1005-16. PMID: 17101654

Blaser06: Blaser MJ (2006). "Who are we? Indigenous microbes and the ecology of human diseases." EMBO Rep 7(10);956-60. PMID: 17016449

Broutet01: Broutet N, Marais A, Lamouliatte H, de Mascarel A, Samoyeau R, Salamon R, Megraud F (2001). "cagA Status and eradication treatment outcome of anti-Helicobacter pylori triple therapies in patients with nonulcer dyspepsia." J Clin Microbiol 39(4);1319-22. PMID: 11283049

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Kusters06: Kusters JG, van Vliet AH, Kuipers EJ (2006). "Pathogenesis of Helicobacter pylori infection." Clin Microbiol Rev 19(3);449-90. PMID: 16847081

Leunk88: Leunk RD, Johnson PT, David BC, Kraft WG, Morgan DR (1988). "Cytotoxic activity in broth-culture filtrates of Campylobacter pylori." J Med Microbiol 26(2);93-9. PMID: 3385767

Marshall84: Marshall BJ, Warren JR (1984). "Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration." Lancet 1(8390);1311-5. PMID: 6145023

Miehlke01: Miehlke S, Yu J, Schuppler M, Frings C, Kirsch C, Negraszus N, Morgner A, Stolte M, Ehninger G, Bayerdorffer E (2001). "Helicobacter pylori vacA, iceA, and cagA status and pattern of gastritis in patients with malignant and benign gastroduodenal disease." Am J Gastroenterol 96(4);1008-13. PMID: 11316139

Morgan87: Morgan, D. R., Fitzpatrick, P. M., David, K. L., Kraft, W. G. (1987). "Susceptibility patterns of Campylobacter pyloridis." FEMS Microbiology Letters 42(2-3):245-248.

Morgan87a: Morgan DR, Freedman R, Depew CE, Kraft WG (1987). "Growth of Campylobacter pylori in liquid media." J Clin Microbiol 25(11);2123-5. PMID: 3693542

Olson02: Olson JW, Maier RJ (2002). "Molecular hydrogen as an energy source for Helicobacter pylori." Science 298(5599);1788-90. PMID: 12459589

Tomb97: Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC (1997). "The complete genome sequence of the gastric pathogen Helicobacter pylori." Nature 388(6642);539-47. PMID: 9252185

Warren83: Warren JR, Marshall B (1983). "Unidentified curved bacilli on gastric epithelium in active chronic gastritis." Lancet 1(8336);1273-5. PMID: 6134060

ZawilakPawlik19: Zawilak-Pawlik A, Zarzecka U, Zyla-Uklejewicz D, Lach J, Strapagiel D, Tegtmeyer N, Bohm M, Backert S, Skorko-Glonek J (2019). "Establishment of serine protease htrA mutants in Helicobacter pylori is associated with secA mutations." Sci Rep 9(1);11794. PMID: 31409845


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Please cite the following article in publications resulting from the use of Gcf_000008525Cyc: Development of this PGDB was supported by BioCyc subscription revenues
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