CoChat
Sign Up
Cited by 875Microbial Metabolic Engineering and BioproductionGene Regulatory Network AnalysisBioinformatics and Genomic Networks

The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities

Open access
Edwards, J. S., Palsson, B. O.·2000·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.97.10.5528PMC PMC25862
Open this paper in CoChat — free accountOpen PDF

Abstract

The Escherichia coli MG1655 genome has been completely sequenced. The annotated sequence, biochemical information, and other information were used to reconstruct the E. coli metabolic map. The stoichiometric coefficients for each metabolic enzyme in the E. coli metabolic map were assembled to construct a genome-specific stoichiometric matrix. The E. coli stoichiometric matrix was used to define the system's characteristics and the capabilities of E. coli metabolism. The effects of gene deletions in the central metabolic pathways on the ability of the in silico metabolic network to support growth were assessed, and the in silico predictions were compared with experimental observations. It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined. Herein, it is demonstrated that the synthesis of in silico metabolic genotypes based on genomic, biochemical, and strain-specific information is possible, and that systems analysis methods are available to analyze and interpret the metabolic phenotype.

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1073/pnas.97.10.5528

Cites

51 of 51 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.

A few free checks a day · papers already verified open instantly · results are public

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?

  • Integration of bibliographic, metabolomic, and genomic data has been used to reconstruct the dynamic range of metabolome flow of organisms, first in Escherichia coli and extended to yeast, mice, and humans.

    “For example, the integration of bibliographic, metabolomic, and genomic data have been used to reconstruct the dynamic range of metabolome flow of organisms, first performed in Escherichia coli [35] and since extended to yeast [36, 37] and to individual tissues in mice [38] and humans [39].”

    From Multi-omics approaches to disease (2017) · cites this paper as [35]

Self-check

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

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

Cites

Flagged first, then by citations

Research works printed but not linked: 20

  1. Palsson, B. O., Joshi, A. & Ozturk, S. S. (1987) Fed. Proc. 46, 2485-2489.
  2. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 13-16.
  3. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 189-198.
  4. Edwards, J. S. (1999) Ph.D thesis (Univ. of California-San Diego, La Jolla).
  5. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 391-407.
  6. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 542-560.
  7. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 358-379.
  8. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 2, pp. 1715-1902.
  9. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 408-433.
  10. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 600-611.
  11. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 580-599.
  12. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 721-730.
  13. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 687-694.
  14. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 680-686.
  15. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 642-656.
  16. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 1035-1063.
  17. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 1149-1174.
  18. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 307-342.
  19. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 189-198.
  20. Neidhardt, F. C. (Am. Soc. Microbiol., Washington, DC), Vol. 1, pp. 283-306.

Cited by

Sorted by citations

Related

Authors
Edwards, J. S., & Palsson, B. O.
Affiliations
  • Harvard University (US)
  • Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412
ORCID
Edwards, J. S.
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2000-05-09
Volume
97
Issue
10
Pages
5528-5533
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.97.10.5528
PMC
PMC25862
OpenAlex
W2153373497
Cited by
875
References
51
Citations by year
2026: 13 · 2025: 10 · 2024: 12 · 2023: 14 · 2022: 19 · 2021: 23 · 2020: 20 · 2019: 19 · 2018: 24 · 2017: 30 · 2016: 27 · 2015: 36 · 2014: 38 · 2013: 40 · 2012: 51
FWCI
10.60
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Science Foundation (9873384)
  • National Institutes of Health
  • National Institute of General Medical Sciences (GM 27089, R01GM057089)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
Escherichia coli MG1655, genome-scale metabolic networks, stoichiometric matrix, central metabolic pathways, capacity constraints, genome annotation
MeSH terms
Bacterial Proteins, Chromosome Mapping, Enzymes, Escherichia coli, Genotype, Kinetics, Models, Biological, Models, Chemical, Genome, Bacterial, Biomass

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