Cited by 7,452

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

The Complete Genome Sequence of Escherichia coli K-12

Blattner, Frederick R., Plunkett, Guy, Bloch, Craig A., Perna, Nicole T., Burland, Valerie, Riley, Monica, Collado-Vides, Julio, Glasner, Jeremy D., Rode, Christopher K., Mayhew, George F., Gregor, Jason, Davis, Nelson Wayne, Kirkpatrick, Heather A., Goeden, Michael A., Rose, Debra J., Mau, Bob, Shao, Ying·1997·Science

DOI 10.1126/science.277.5331.1453

Open this paper in CoChat — free account

Abstract

The 4,639,221–base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.

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

Crossref · 10.1126/science.277.5331.1453

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

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.

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
Sharp, P. M., & Li, W.-H. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.3.1281 · Cited by 3,992

Show all 2 references

Items 101–149 of 149

Clostridioides difficile Senses and Hijacks Host Heme for Incorporation into an Oxidative Stress Defense System
Knippel, R. J., Wexler, A. G., Miller, J. M., Beavers, W. N., Weiss, A., de Crécy-Lagard, V., Edmonds, K. A., Giedroc, D. P., & Skaar, E. P. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.05.015 · Cited by 62
Role of nonadsorbing polymers in bacterial aggregation
Eboigbodin, K. E., Newton, J. R. A., Routh, A. F., & Biggs, C. A. (2005) · Langmuir · doi:10.1021/la051740u · Cited by 62
A novel aldo-keto reductase from Escherichia coli can increase resistance to methylglyoxal toxicity
Grant, A. W., Steel, G., Waugh, H., & Ellis, E. M. (2003) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2003.tb11503.x · Cited by 57
A New Sugar for an Old Phage: a c-di-GMP-Dependent Polysaccharide Pathway Sensitizes Escherichia coli for Bacteriophage Infection
(2021) · doi:10.1128/mbio.03246-21 · Cited by 56
Inter-membrane association of the Sec and BAM translocons for bacterial outer-membrane biogenesis.
Alvira, S., Watkins, D. W., Troman, L. A., Allen, W. J., Lorriman, J. S., Degliesposti, G., Cohen, E. J., Beeby, M., Daum, B., Gold, V. A., et al. (2020) · eLife · doi:10.7554/elife.60669 · Cited by 51
Tunable recombinant protein expression in E. coli: Promoter systems and genetic constraints
Marschall, L., Sagmeister, P., & Herwig, C. (2017) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-016-8045-z · Cited by 55
Abundance of 4Feâ4S motifs in the genomes of methanogens and other prokaryotes
Major, T. A., Burd, H., & Whitman, W. B. (2004) · FEMS Microbiology Letters · doi:10.1016/j.femsle.2004.08.027 · Cited by 55
Effects of SecE Depletion on the Inner and Outer Membrane Proteomes of Escherichia coli
Baars, L., Wagner, S., Wickström, D., Klepsch, M., Ytterberg, A. J., van Wijk, K. J., & de Gier, J.-W. (2008) · Journal of Bacteriology · doi:10.1128/jb.01631-07 · Cited by 52
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli
Lenski, R. E. (2023) · Journal of Molecular Evolution · doi:10.1007/s00239-023-10095-3 · Cited by 62
First insights into the unexplored two-component system YehU/YehT in Escherichia coli
Kraxenberger, T., Fried, L., Behr, S., & Jung, K. (2012) · Journal of Bacteriology · doi:10.1128/jb.00409-12 · Cited by 46
Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms
Amann, T., Schmieder, V., Faustrup Kildegaard, H., Borth, N., & Andersen, M. R. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.27101 · Cited by 46
A cut above: Discovery of an alternative excision repair pathway in bacteria
Van Houten, B., Eisen, J. A., & Hanawalt, P. C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.062062599 · Cited by 44
Siderophore-mediated iron acquisition by Klebsiella pneumoniae
Kumar, A., Chakravorty, S., Yang, T., Russo, T. A., Newton, S. M., & Klebba, P. E. (2024) · Journal of Bacteriology · doi:10.1128/jb.00024-24 · Cited by 42
NhaK, a novel monovalent cation/H+ antiporter of Bacillus subtilis
Fujisawa, M., Kusumoto, A., Wada, Y., Tsuchiya, T., & Ito, M. (2005) · Archives of Microbiology · doi:10.1007/s00203-005-0011-6 · Cited by 43
The Immune Protein Calprotectin Impacts Clostridioides difficile Metabolism through Zinc Limitation
Lopez, C. A., Beavers, W. N., Weiss, A., Knippel, R. J., Zackular, J. P., Chazin, W., & Skaar, E. P. (2019) · mBio · doi:10.1128/mbio.02289-19 · Cited by 42
An Improved Natural Transformation Protocol for the Cyanobacterium Synechocystis sp. PCC 6803
Pope, M. A., Hodge, J. A., & Nixon, P. J. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.00372 · Cited by 42
Non‐invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator
Arce‐Rodríguez, A., Volke, D. C., Bense, S., Häussler, S., & Nikel, P. I. (2019) · Microbial Biotechnology · doi:10.1111/1751-7915.13439 · Cited by 40
Towards a Reconstruction of Ancestral Genomes by Gene Cluster Alignment
Wächtershäuser, G. (1998) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(98)80058-1 · Cited by 39
Dissecting the Fidelity of Bacteriophage RB69 DNA Polymerase: Site-Specific Modulation of Fidelity by Polymerase Accessory Proteins
Bebenek, A., Carver, G. T., Dressman, H. K., Kadyrov, F. A., Haseman, J. K., Petrov, V., Konigsberg, W. H., Karam, J. D., & Drake, J. W. (2002) · Genetics · doi:10.1093/genetics/162.3.1003 · Cited by 39
ZupT Facilitates Clostridioides difficile Resistance to Host-Mediated Nutritional Immunity
Zackular, J. P., Knippel, R. J., Lopez, C. A., Beavers, W. N., Maxwell, C. N., Chazin, W. J., & Skaar, E. P. (2020) · mSphere · doi:10.1128/msphere.00061-20 · Cited by 35
Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
Kocurek, K. I., Stones, L., Bunch, J., May, R. C., & Cooper, H. J. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1718-8 · Cited by 37
“YahO was identified following cleavage of a 21 amino acid sequence peptide from the intact protein, previously inferred from protein sequence [52] and experimentally confirmed here by LESA MS.”
Method
Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli : application to DNA replication
Atlas, J. C., Nikolaev, E. V., Browning, S. T., & Shuler, M. L. (2008) · IET Systems Biology · doi:10.1049/iet-syb:20070079 · Cited by 31
Structural and Functional Analysis of the Signal-Transducing Linker in the pH-Responsive One-Component System CadC of Escherichia coli
Buchner, S., Schlundt, A., Lassak, J., Sattler, M., & Jung, K. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.05.001 · Cited by 32
Fluorescent sensors of siderophores produced by bacterial pathogens
Kumar, A., Yang, T., Chakravorty, S., Majumdar, A., Nairn, B. L., Six, D. A., Marcondes dos Santos, N., Price, S. L., Lawrenz, M. B., Actis, L. A., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101651 · Cited by 28
Evidence for Horizontal Transfer of the Eco T38I Restriction- Modification Gene to Chromosomal DNA by the P2 Phage and Diversity of Defective P2 Prophages in Escherichia coli TH38 Strains
Kita, K., Kawakami, H., & Tanaka, H. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.7.2296-2305.2003 · Cited by 31
Effects of Co-culture on Improved Productivity and Bioresource for Microalgal Biomass Using the Floc-Forming Bacteria Melaminivora Jejuensis
Kim, D.-H., Yun, H.-S., Kim, Y.-S., & Kim, J.-G. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.588210 · Cited by 28
Frontline Science: LPS-inducible SLC30A1 drives human macrophage-mediated zinc toxicity against intracellular Escherichia coli
Stocks, C. J., von Pein, J. B., Curson, J. E. B., Rae, J., Phan, M.-D., Foo, D., Bokil, N. J., Kambe, T., Peters, K. M., Parton, R. G., et al. (2021) · Journal of Leukocyte Biology · doi:10.1002/jlb.2hi0420-160r · Cited by 28
Oxygen-Dependent Cell-to-Cell Variability in the Output of the Escherichia coli Tor Phosphorelay
Roggiani, M., & Goulian, M. (2015) · Journal of Bacteriology · doi:10.1128/jb.00074-15 · Cited by 24
Mathematical Modelling of Toxic Metal Uptake and Efflux Pump in Metal-Resistant Bacterium Bacillus cereus Isolated From Heavy Crude Oil
Shaw, D. R., & Dussan, J. (2015) · Water, Air, & Soil Pollution · doi:10.1007/s11270-015-2385-7 · Cited by 21
Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments
Shen, B. A., Hustmyer, C. M., Roston, D., Wolfe, M. B., & Landick, R. (2022) · iScience · doi:10.1016/j.isci.2022.104429 · Cited by 20
IS-Linked Movement of a Restriction-Modification System
Takahashi, N., Ohashi, S., Sadykov, M. R., Mizutani-Ui, Y., & Kobayashi, I. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016554 · Cited by 18
Enhanced expression of soluble antibody fragments by low-temperature and overdosing with a nitrogen source
Kim, S. J., Ha, G. S., Lee, G., Lim, S. I., Lee, C. M., Yang, Y. H., Lee, J., Kim, J. E., Lee, J. H., Shin, Y., et al. (2018) · Enzyme and Microbial Technology · doi:10.1016/j.enzmictec.2018.04.002 · Cited by 17
Identification of antigen Ag43 in uropathogenic Escherichia coli Dr+ strains and defining its role in the pathogenesis of urinary tract infections
Zalewska-Pia˛tek, B., Pia˛tek, R., Olszewski, M., & Kur, J. (2015) · Microbiology · doi:10.1099/mic.0.000072 · Cited by 15
Ght protein of Neisseria meningitidis is involved in the regulation of lipopolysaccharide biosynthesis
Putker, F., Grutsch, A., Tommassen, J., & Bos, M. P. (2014) · Journal of Bacteriology · doi:10.1128/jb.00943-13 · Cited by 14
Urogenital colonization and pathogenicity of E. Coli in the vaginal microbiota during pregnancy
Boutouchent, N., Vu, T. N. A., Landraud, L., & Kennedy, S. P. (2024) · Scientific Reports · doi:10.1038/s41598-024-76438-2 · Cited by 14
Specificity and mechanism of TonB-dependent ferric catecholate uptake by Fiu
Yang, T., Zou, Y., Ng, H. L., Kumar, A., Newton, S. M., & Klebba, P. E. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1355253 · Cited by 11
Lineage-specific expansions provide genomic complexity among sea urchin GTPases
Beane, W. S., Voronina, E., Wessel, G. M., & McClay, D. R. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.046 · Cited by 10
Cross-evaluation of E. coli’s operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons
Sun, G., DeFelice, M. M., Gillies, T. E., Ahn-Horst, T. A., Andrews, C. J., Krummenacker, M., Karp, P. D., Morrison, J. H., & Covert, M. W. (2024) · Cell Systems · doi:10.1016/j.cels.2024.02.002 · Cited by 9
A four-point molecular handover during Okazaki maturation
Botto, M. M., Borsellini, A., & Lamers, M. H. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01071-y · Cited by 9
A phage protein screen identifies triggers of the bacterial innate immune system
Nagy, T. A., Gersabeck, G. W., Conte, A. N., & Whiteley, A. T. (2026) · Nature Microbiology · doi:10.1038/s41564-025-02239-6 · Cited by 8
Compaction and Segregation of DNA in Escherichia coli
(2024) · doi:10.3390/life14060660 · Cited by 8
The Escherichia coli replication initiator DnaA is titrated on the chromosome
Olivi, L., Köstlbacher, S., Ludwig, C., Langendoen, M., Claassens, N. J., Ettema, T. J. G., van der Oost, J., ten Wolde, P. R., Hohlbein, J., & Staals, R. H. J. (2025) · Nature Communications · doi:10.1038/s41467-025-63147-1 · Cited by 7
AdiY acts as a cytoplasmic pH sensor via histidine protonation to regulate acid stress adaptation in Escherichia coli
Gallo, G., Brameyer, S., Kuppermann, S., Schneider, S., Kielkowski, P., & Jung, K. (2026) · Journal of Bacteriology · doi:10.1128/jb.00542-25 · Cited by 4
A large‐scale evolutionary and structural analysis of CLC channels and transporters
Mishra, A., Díaz Vázquez, G., & Robertson, J. L. (2025) · Protein Science · doi:10.1002/pro.70389 · Cited by 3
“Escherichia coli have three CLC genes: CLC-ec1, CLC-ec2, and the uncharacterized ecYfeO (Blattner et al., 1997; Iyer et al., 2002).”
Strategies to identify and edit improvements in synthetic genome segments episomally
Rudolph, A., Nyerges, A., Chiappino-Pepe, A., Landon, M., Baas-Thomas, M., & Church, G. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad692 · Cited by 3
Lipopolysaccharide confinement in the bacterial outer membrane is governed by interactions within the conserved Lipid A anchor
Nabarro, J., Leaman, R. M., Lenton, S., Mantion, L., Spears, R. J., Coles, M. C., Pushkin, D. O., Fascione, M. A., & Baumann, C. G. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00711-5 · Cited by 3
Impact of ovotransferrin on the membrane integrity of Salmonella Enteritidis under egg-white conditions
Legros, J., Bonnassie, S., Cochet, M.-F., Jan, S., Andrews, S. C., & Baron, F. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1539663 · Cited by 2
Adsorption of phage T2 is inhibited due to inversion of cryptic prophage DNA by the serine recombinase PinQ
(2025) · doi:10.1093/nar/gkaf1041 · Cited by 1
Subtle Variations in a Client Protein Determine Bacterial Hsp90 Dependence
Corteggiani, M., Ali Chaouche, A., Bahun, M., Honoré, F. A., Byrne, D., Dementin, S., Rebeaud, M. E., & Genest, O. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169378

Authors: Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., & Shao, Y.
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 1997-09-05
Volume: 277
Issue: 5331
Pages: 1453-1462
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.277.5331.1453
OpenAlex: W2134153749
Cited by: 7,452
References: 2
FWCI: 126.90
Type: journal article
Language: en
Open access: closed

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

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

The Complete Genome Sequence of Escherichia coli K-12

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Self-check

Citations

Cites

Cited by

Metadata

Record

About these checks

Data sources