The DOI matches its Crossref record; 44 of the 45 references it cites were found in a registry or an index.
The complete genome sequence of the gastric pathogen Helicobacter pylori
Open accessAbstract
Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“The complete genome sequences of two H. pylori strains, 26695 and J99 (1, 34), have been published elsewhere and demonstrate that this organism contains only two rRNA operons, increasing the likelihood that rRNA mutations could arise.”
From Mutations in the 16S rRNA Genes of Helicobacter pylori Mediate Resistance to Tetracycline (2002) · cites this paper as [34]
In the citing paper
“Analysis of the H. pylori genome sequences (1, 34) indicates that the smallest distances between rdxA and one of the 16S rRNA genes are 193 kb in strain 26695 and 205 kb in strain J99.”
From Mutations in the 16S rRNA Genes of Helicobacter pylori Mediate Resistance to Tetracycline (2002) · cites this paper as [34]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Escherichia coli and Salmonella :cellular and molecular biology
Neidhardt, F. C. (1996) · ASM Press eBooks · Cited by 8,197
Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd
Fleischmann, R. D., Adams, M. D., White, O. R., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J.-F., Dougherty, B. A., Merrick, J. M., et al. (1995) · Science · doi:10.1126/science.7542800 · Cited by 5,731
Self-citationIdentification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
Nielsen, H., Engelbrecht, J., Brunak, S., & von HEIJNE, G. (1997) · Protein Engineering Design and Selection · doi:10.1093/protein/10.1.1 · Cited by 5,343
UNIDENTIFIED CURVED BACILLI ON GASTRIC EPITHELIUM IN ACTIVE CHRONIC GASTRITIS
ROBINWARREN, J. (1983) · The Lancet · doi:10.1016/s0140-6736(83)92719-8 · Cited by 3,597
The Minimal Gene Complement of Mycoplasma genitalium
Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., et al. (1995) · Science · doi:10.1126/science.270.5235.397 · Cited by 2,545
Self-citationComplete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
Bult, C. J., White, O. R., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., Fitzgerald, L. M., Clayton, R. A., Gocayne, J. D., et al. (1996) · Science · doi:10.1126/science.273.5278.1058 · Cited by 2,086
Self-citationCensini, S., Lange, C., Xiang, Z., Crabtree, J. E., GHIARA, P., Borodovsky, M. Y., Rappuoli, R., & Covacci, A. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.25.14648 · Cited by 1,872
Self-citationEscherichia coli and Salmonella.
Neidhart, F. C. (1996) · Cited by 1,577
Mosaicism in Vacuolating Cytotoxin Alleles of Helicobacter pylori
Atherton, J. C., Cao, P., Peek, R. M., Tummuru, M. K. R., Blaser, M. J., & Cover, T. L. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.30.17771 · Cited by 1,564
Molecular biology of microbial ureases
Mobley, H. L. T., Island, M. D., & Hausinger, R. P. (1995) · Microbiological Reviews · doi:10.1128/mr.59.3.451-480.1995 · Cited by 1,471
Attachment of Helicobacter pylori to Human Gastric Epithelium Mediated by Blood Group Antigens
Borén, T., Falk, P. G., Roth, K. A., Larson, G., & Normark, S. J. (1993) · Science · doi:10.1126/science.8018146 · Cited by 1,185
TopPred II: an improved software for membrane protein structure predictions
Claros, M. G., & von HEIJNE, G. (1994) · Computer applications in the biosciences · doi:10.1093/bioinformatics/10.6.685 · Cited by 939
Adaptive evolution of highly mutable loci in pathogenic bacteria
Moxon, E. R., Rainey, P. B., Nowak, M. A., & Lenski, R. E. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00005-1 · Cited by 755
Tummuru, M. K. R., Sharma, S., & Blaser, M. J. (1995) · Molecular Microbiology · doi:10.1111/j.1365-2958.1995.18050867.x · Cited by 391
Functions of the gene products of Escherichia coli
Riley, M. A. (1993) · Microbiological Reviews · doi:10.1128/mr.57.4.862-952.1993 · Cited by 367
Phase variation of gonococcal pili by frameshift mutation in pilC, a novel gene for pilus assembly.
Jonsson, A., Nyberg, G., & Normark, S. J. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07970.x · Cited by 300
Helicobacter pylori and gastric acid: Biological and therapeutic implications
McGowan, C., Cover, T. L., & Blaser, M. (1996) · Gastroenterology · doi:10.1053/gast.1996.v110.pm8608904 · Cited by 227
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism
Karp, P. D. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.50 · Cited by 221
Self-citationBuilding bridges: disulphide bond formation in the cell
Bardwell, J. C. A. (1994) · Molecular Microbiology · doi:10.1111/j.1365-2958.1994.tb01281.x · Cited by 215
Adaptation of a conjugal transfer system for the export of pathogenic macromolecules
Winans, S. C., Burns, D., & Christie, P. J. (1996) · Trends in Microbiology · doi:10.1016/0966-842x(96)81513-7 · Cited by 190
tRNA-dependent asparagine formation
Curnow, A. W., Ibba, M., & Söll, D. G. (1996) · Nature · doi:10.1038/382589b0 · Cited by 155
Cover, T. L., & Blaser, M. J. (1996) · PubMed · Cited by 149
Determinants of Helicobacter pylori pathogenicity.
Labigne, A., & Reuse, H. D. (1996) · PubMed · Cited by 142
Hughes, N. J., Chalk, P. A., Clayton, C. L., & Kelly, D. J. (1995) · Journal of Bacteriology · doi:10.1128/jb.177.14.3953-3959.1995 · Cited by 122
Peterson, S. N., Bailey, C. C., Jensen, J. S., Borre, M. B., King, E. S., Bott, K. F., & Hutchison, C. A. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.25.11829 · Cited by 112
Self-citationAdaptive mutation and cocolonization during Helicobacter pylori infection of gnotobiotic piglets
Akopyants, N. S., Eaton, K. A., & Berg, D. E. (1995) · Infection and Immunity · doi:10.1128/iai.63.1.116-121.1995 · Cited by 105
Self-citationIntrinsic and extrinsic approaches for detecting genes in a bacterial genome
Borodovsky, M. Y., Rudd, K. E., & Koonin, E. V. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4756 · Cited by 104
Self-citationCloning and Membrane Topology of a P type ATPase from Helicobacter pylori
Melchers, K., Weitzenegger, T., Buhmann, A., Steinhilber, W., Sachs, G. M., & Schäfer, K. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.1.446 · Cited by 100
The role of lipopolysaccharide in Helicobacter pylori pathogenesis.
Moran, A. P. (1996) · Alimentary Pharmacology & Therapeutics · doi:10.1046/j.1365-2036.1996.22164004.x · Cited by 97
Frazier, B. A., Pfeifer, J. D., Russell, D. G., Falk, P., Olsén, A., Hammar, M., Westblom, T. U., & Normark, S. J. (1993) · Journal of Bacteriology · doi:10.1128/jb.175.4.966-972.1993 · Cited by 85
Odenbreit, S., Till, M., & Haas, R. (1996) · Molecular Microbiology · doi:10.1111/j.1365-2958.1996.tb02623.x · Cited by 79
Evans, D. J., Evans, D. G., Lampert, H. C., & Nakano, H. (1995) · Gene · doi:10.1016/0378-1119(94)00774-m · Cited by 77
Impact of Infection by Helicobacter pylori on the Risk and Severity of Endemic Cholera
Clemens, J. D., Albert, M. J., Rao, M. R., Qadri, F., Huda, S. N., Kay, B. A., LOON, F. P. L. V., Sack, D. A., PRADHAN, B., & Sack, R. B. (1995) · The Journal of Infectious Diseases · doi:10.1093/infdis/171.6.1653 · Cited by 74
Aminoacid utilization by Helicobacter pylori
Mendz, G. L., & Hazell, S. L. (1995) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/1357-2725(95)00069-2 · Cited by 71
MacPattern: protein pattern searching on the Apple Macintosh
Fuchs, R. (1991) · Computer applications in the biosciences · doi:10.1093/bioinformatics/7.1.105 · Cited by 66
Isolation and characterization of a conserved porin protein from Helicobacter pylori
Doig, P. C., Exner, M. M., Hancock, R. E. W., & Trevor J. TRUST (1995) · Journal of Bacteriology · doi:10.1128/jb.177.19.5447-5452.1995 · Cited by 63
The complex flagella of gastric Helicobacter species
Suerbaum, S. (1995) · Trends in Microbiology · doi:10.1016/s0966-842x(00)88913-1 · Cited by 63
Díaz, J. F., Wroblowski, B., Schlitter, J., & Engelborghs, Y. (1997) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199707)28:3 · Cited by 63
[42] Posttranslational processing of type IV prepilin and homologs by PilD of Pseudomonas aeruginosa
Strom, M. S., Nunn, D. N., & Lory, S. (1994) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(94)35168-6 · Cited by 56
Matin, A., Zychlinsky, E., Keyhan, M., & Sachs, G. M. (1996) · Infection and Immunity · doi:10.1128/iai.64.4.1434-1436.1996 · Cited by 38
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism
Karp, P. D., Riley, M. A., Paley, S., Pellegrini-Toole, A., & Krummenacker, M. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.43 · Cited by 38
Self-citationBaker, P. J., Hrabă, T., Taylor, C. E., Stashak, P. W., Fauntleroy, M. B., Zähringer, U., Takayama, K., Sievert, T. R., Hronowski, X. L., & Cotter, R. J. (1994) · Infection and Immunity · doi:10.1128/iai.62.6.2257-2269.1994 · Cited by 31
Bacterial chromosome origins of replication
Marczynski, G. T., & Shapiro, L. (1993) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(05)80098-x · Cited by 30
How does Helicobacter pylori cause duodenal ulcer disease: The bug, the host, or both?
Go, M. F., & Graham, D. Y. (1994) · Journal of Gastroenterology and Hepatology · doi:10.1111/j.1440-1746.1994.tb01294.x · Cited by 28
Flagged first, then by citations
1 of the 45 references couldn’t be matched to a known paper.
Research works printed but not linked: 7
- Akopyants, N. S., Kersulyte, D. & Berg, D. E. DNA rearrangement in the 40 kb cag (virulence) region in the Helicobacter pylori genome. Gut 39 (suppl. 2), A67 (1996).
- Peek, R. M., Thompson, S. A., Atherton, J. C., Blaser, M. J. & Miller, G. G. Expression of iceA, a novel ulcer-associated Helicobacter pylori gene, is induced by contact with gastric epithelial cells and is associated with enhanced mucosal IL-8. Gut 39 (suppl. 2), A71 (1996).
- Jones, A. C., Foynes, S., Cockayne, A. & Penn, C. W. Gene cloning of a flagellar sheath protein of Helicobacter pylori shows its identity with the putative adhesin, HpaA. Gut 39 (suppl. 2), A62 (1996).
- Ilver, D.et al. The Helicobacter pylori blood group antigen binding adhesin. Gut 39 (suppl. 2), A55 (1996).
- Earhart, C. F. in Escherichia coli and Salmonella Cellular and Molecular Biology(eds Neidhardt, F. C. et al.) 1075–1090 (ASM, Washington DC, (1996)).
- Melchers, K.et al. Cloning and analysis of two P type ion pumps of Helicobacter pylori, a cation resistance ATPase and a membrane pump necessary for urease activity. Gut 39 (suppl. 2), A67 (1996).
- Sonnhammer, E. L. L., Eddy, S. R. & Durbin, R. Pfam: A comprehensive database of protein families based on seed alignments. Proteins(in the press).
Cited by
Sorted by citations
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Self-citationVersatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Molecular Basis of Bacterial Outer Membrane Permeability Revisited
Nikaido, H. (2003) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.67.4.593-656.2003 · Cited by 4,316
The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessières, P., Bolotin, A., Borchert, S., et al. (1997) · Nature · doi:10.1038/36786 · Cited by 3,679
A genomic perspective on protein families.
Tatusov, R., Koonin, E., & Lipman, D. (1997) · Science · doi:10.1126/science.278.5338.631 · Cited by 3,777
Metadata
- Authors
- Tomb, J.-F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., Ketchum, K. A., Klenk, H. P., Gill, S., Dougherty, B. A., Nelson, K., Quackenbush, J., Zhou, L., Kirkness, E. F., Peterson, S., Loftus, B., Richardson, D., Dodson, R., Khalak, H. G., Glodek, A., McKenney, K., Fitzegerald, L. M., Lee, N., Adams, M. D., Hickey, E. K., Berg, D. E., Gocayne, J. D., Utterback, T. R., Peterson, J. D., Kelley, J. M., Cotton, M. D., Weidman, J. M., Fujii, C., Bowman, C., Watthey, L., Wallin, E., Hayes, W. S., Borodovsky, M., Karp, P. D., Smith, H. O., Fraser, C. M., & Venter, J. C.
- Affiliations
- Washington University in St. Louis (US)
- Stockholm University (SE)
- Georgia Institute of Technology (US)
- SRI International (US)
- Johns Hopkins University (US)
- Corresponding author
- Tomb, Jean-F.
- ORCID
- Venue
- Nature
- Published
- 1997-08-07
- Volume
- 388
- Issue
- 6642
- Pages
- 539-547
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2110132014
- Cited by
- 3,529
- References
- 45
- Citations by year
- 2026: 23 · 2025: 41 · 2024: 36 · 2023: 45 · 2022: 36 · 2021: 60 · 2020: 43 · 2019: 50 · 2018: 71 · 2017: 66 · 2016: 92 · 2015: 82 · 2014: 148 · 2013: 101 · 2012: 102
- FWCI
- 324.03
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- European Synchrotron Radiation Facility
- National Institutes of Health
- National Center for Research Resources
- Topics
- Health Sciences › Medicine › Gastroenterology › Helicobacter pylori-related gastroenterology studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Helicobacter pylori, complete genome sequence, motility genes, iron acquisition, adhesins, outer membrane proteins, lipoproteins, host-pathogen interaction, antigenic variation, slipped-strand mispairing, recombination, regulatory networks, acid resistance, membrane potential, strain 26695
- MeSH terms
- Antigenic Variation, Bacterial Adhesion, Bacterial Proteins, Base Sequence, Cell Division, DNA Repair, DNA, Bacterial, Biological Evolution, Hydrogen-Ion Concentration, Molecular Sequence Data, Recombination, Genetic, Transcription, Genetic, Protein Biosynthesis, Virulence, Gene Expression Regulation, Bacterial, Helicobacter pylori, Genome, Bacterial
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
