The EcoCyc Database

Overview

Journal EcoSal Plus

Publisher American Society for Microbiology

Specialty Microbiology

Date 2018 Nov 9

PMID 30406744

Citations 52

Authors

Peter D Karp

Wai Kit Ong

Suzanne Paley

Richard Billington

Ron Caspi

Carol Fulcher

Anamika Kothari

Markus Krummenacker

Mario Latendresse

Peter E Midford

Pallavi Subhraveti

Socorro Gama-Castro

Luis Muniz-Rascado

Cesar Bonavides-Martinez

Alberto Santos-Zavaleta

Amanda Mackie

Julio Collado-Vides

Ingrid M Keseler

Ian Paulsen

Affiliations

Soon will be listed here.

Abstract

EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of . EcoCyc is an electronic reference source for biologists and for biologists who work with related microorganisms. The database includes information pages on each gene product, metabolite, reaction, operon, and metabolic pathway. The database also includes information on gene essentiality and on nutrient conditions that do or do not support the growth of . The website and downloadable software contain tools for analysis of high-throughput data sets. In addition, a steady-state metabolic flux model is generated from each new version of EcoCyc and can be executed via EcoCyc.org. The model can predict metabolic flux rates, nutrient uptake rates, and growth rates for different gene knockouts and nutrient conditions. This review outlines the data content of EcoCyc and of the procedures by which this content is generated.

Citing Articles

Core and accessory genomic traits of Vibrio cholerae O1 drive lineage transmission and disease severity.

Maciel-Guerra A, Babaarslan K, Baker M, Rahman A, Hossain M, Sadique A Nat Commun. 2024; 15(1):8231.

PMID: 39313510 PMC: 11420230. DOI: 10.1038/s41467-024-52238-0.

Development of a logic regression-based approach for the discovery of host- and niche-informative biomarkers in and their application for microbial source tracking.

Yu D, Andersson-Li M, Maes S, Andersson-Li L, Neumann N, Odlare M Appl Environ Microbiol. 2024; 90(7):e0022724.

PMID: 38940567 PMC: 11267920. DOI: 10.1128/aem.00227-24.

Genetic evidence for functional diversification of gram-negative intermembrane phospholipid transporters.

Rai A, Sawasato K, Bennett H, Kozlova A, Sparagna G, Bogdanov M PLoS Genet. 2024; 20(6):e1011335.

PMID: 38913742 PMC: 11226057. DOI: 10.1371/journal.pgen.1011335.

Emergence of potentially disinfection-resistant, naturalized Escherichia coli populations across food- and water-associated engineered environments.

Yu D, Stothard P, Neumann N Sci Rep. 2024; 14(1):13478.

PMID: 38866876 PMC: 11169474. DOI: 10.1038/s41598-024-64241-y.

Spatio-temporal organization of the chromosome from base to cellular length scales.

Royzenblat S, Freddolino L EcoSal Plus. 2024; 12(1):eesp00012022.

PMID: 38864557 PMC: 11636183. DOI: 10.1128/ecosalplus.esp-0001-2022.

References

. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2012; 41(Database issue):D43-7. PMC: 3531094. DOI: 10.1093/nar/gks1068. View

Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M . Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006; 2:2006.0008. PMC: 1681482. DOI: 10.1038/msb4100050. View

Serres M, Riley M . MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb Comp Genomics. 2001; 5(4):205-22. DOI: 10.1089/omi.1.2000.5.205. View

Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich J . Global transcriptional regulatory network for robustly connects gene expression to transcription factor activities. Proc Natl Acad Sci U S A. 2017; 114(38):10286-10291. PMC: 5617254. DOI: 10.1073/pnas.1702581114. View

Orth J, Conrad T, Na J, Lerman J, Nam H, Feist A . A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol Syst Biol. 2011; 7:535. PMC: 3261703. DOI: 10.1038/msb.2011.65. View

Monk J, Lloyd C, Brunk E, Mih N, Sastry A, King Z . iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol. 2017; 35(10):904-908. PMC: 6521705. DOI: 10.1038/nbt.3956. View

Latendresse M . Efficiently gap-filling reaction networks. BMC Bioinformatics. 2014; 15:225. PMC: 4094995. DOI: 10.1186/1471-2105-15-225. View

AbuOun M, Suthers P, Jones G, Carter B, Saunders M, Maranas C . Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain. J Biol Chem. 2009; 284(43):29480-8. PMC: 2785581. DOI: 10.1074/jbc.M109.005868. View

Varma A, Boesch B, Palsson B . Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol. 1993; 59(8):2465-73. PMC: 182307. DOI: 10.1128/aem.59.8.2465-2473.1993. View

10.

Karp P, Riley M, Paley S, Pellegrini-Toole A, Krummenacker M . Eco Cyc: encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 1998; 27(1):55-8. PMC: 148095. DOI: 10.1093/nar/27.1.55. View

11.

Perez-Acle T, Fuenzalida I, Martin A, Santibanez R, Avaria R, Bernardin A . Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach. Biochem Biophys Res Commun. 2017; 498(2):342-351. DOI: 10.1016/j.bbrc.2017.11.138. View

12.

Paley S, Karp P . The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res. 2006; 34(13):3771-8. PMC: 1557788. DOI: 10.1093/nar/gkl334. View

13.

Karp P, Keseler I, Shearer A, Latendresse M, Krummenacker M, Paley S . Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 2007; 35(22):7577-90. PMC: 2190727. DOI: 10.1093/nar/gkm740. View

14.

Stephanopoulos G, Vallino J . Network rigidity and metabolic engineering in metabolite overproduction. Science. 1991; 252(5013):1675-81. DOI: 10.1126/science.1904627. View

15.

Mackie A, Paley S, Keseler I, Shearer A, Paulsen I, Karp P . Addition of Escherichia coli K-12 growth observation and gene essentiality data to the EcoCyc database. J Bacteriol. 2013; 196(5):982-8. PMC: 3957686. DOI: 10.1128/JB.01209-13. View

16.

Karimpour-Fard A, Leach S, Gill R, Hunter L . Predicting protein linkages in bacteria: which method is best depends on task. BMC Bioinformatics. 2008; 9:397. PMC: 2570368. DOI: 10.1186/1471-2105-9-397. View

17.

Karp P, Riley M, Paley S, Pellegrini-Toole A, Krummenacker M . EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 1998; 26(1):50-3. PMC: 147256. DOI: 10.1093/nar/26.1.50. View

18.

Delepine B, Duigou T, Carbonell P, Faulon J . RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metab Eng. 2017; 45:158-170. DOI: 10.1016/j.ymben.2017.12.002. View

19.

Moreno-Hagelsieb G, Jokic P . The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective. Nucleic Acids Res. 2012; 40(15):7104-12. PMC: 3424573. DOI: 10.1093/nar/gks443. View

20.

Patrick W, Quandt E, Swartzlander D, Matsumura I . Multicopy suppression underpins metabolic evolvability. Mol Biol Evol. 2007; 24(12):2716-22. PMC: 2678898. DOI: 10.1093/molbev/msm204. View