EcoCyc: a Comprehensive View of Escherichia Coli Biology

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2008 Nov 1

PMID 18974181

Citations 171

Authors

Ingrid M Keseler

Cesar Bonavides-Martinez

Julio Collado-Vides

Socorro Gama-Castro

Robert P Gunsalus

D Aaron Johnson

Markus Krummenacker

Laura M Nolan

Suzanne Paley

Ian T Paulsen

Martin Peralta-Gil

Alberto Santos-Zavaleta

Alexander Glennon Shearer

Peter D Karp

Affiliations

Soon will be listed here.

Abstract

EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the regulatory network of E. coli. Recent EcoCyc developments include a new initiative to represent and curate all types of E. coli regulatory processes such as attenuation and regulation by small RNAs. EcoCyc has started to curate Gene Ontology (GO) terms for E. coli and has made a dataset of E. coli GO terms available through the GO Web site. The curation and visualization of electron transfer processes has been significantly improved. Other software and Web site enhancements include the addition of tracks to the EcoCyc genome browser, in particular a type of track designed for the display of ChIP-chip datasets, and the development of a comparative genome browser. A new Genome Omics Viewer enables users to paint omics datasets onto the full E. coli genome for analysis. A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc.

Citing Articles

Metabolic engineering of for efficient production of α-glucosidase inhibitor1-deoxynojirimycin.

Li X, Zhang M, Lu Y, Wu N, Chen J, Ji Z Synth Syst Biotechnol. 2023; 8(3):378-385.

PMID: 37692204 PMC: 10485785. DOI: 10.1016/j.synbio.2023.05.002.

The EcoCyc Database (2023).

Karp P, Paley S, Caspi R, Kothari A, Krummenacker M, Midford P EcoSal Plus. 2023; 11(1):eesp00022023.

PMID: 37220074 PMC: 10729931. DOI: 10.1128/ecosalplus.esp-0002-2023.

Small RNAs beyond Model Organisms: Have We Only Scratched the Surface?.

Boutet E, Djerroud S, Perreault J Int J Mol Sci. 2022; 23(8).

PMID: 35457265 PMC: 9029176. DOI: 10.3390/ijms23084448.

Quantitative Genetic Screens for Mapping Bacterial Pathways and Functional Networks.

Gagarinova A, Hosseinnia A, Babu M Methods Mol Biol. 2021; 2381:3-37.

PMID: 34590268 DOI: 10.1007/978-1-0716-1740-3_1.

Regulates the Growth of in the Presence of a Subinhibitory Concentration of Gentamicin and Mediates the Adaptive Resistance to Gentamicin.

Zhou S, Zhuang Y, Zhu X, Yao F, Li H, Li H Front Microbiol. 2019; 10:1180.

PMID: 31191496 PMC: 6545925. DOI: 10.3389/fmicb.2019.01180.

References

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

Shen-Orr S, Milo R, Mangan S, Alon U . Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet. 2002; 31(1):64-8. DOI: 10.1038/ng881. View

Plumbridge J . Co-ordinated regulation of amino sugar biosynthesis and degradation: the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites. EMBO J. 1995; 14(16):3958-65. PMC: 394474. DOI: 10.1002/j.1460-2075.1995.tb00067.x. View

Ma H, Kumar B, Ditges U, Gunzer F, Buer J, Zeng A . An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res. 2004; 32(22):6643-9. PMC: 545451. DOI: 10.1093/nar/gkh1009. View

Keseler I, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen I . EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 2004; 33(Database issue):D334-7. PMC: 540062. DOI: 10.1093/nar/gki108. View

Nonaka G, Blankschien M, Herman C, Gross C, Rhodius V . Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress. Genes Dev. 2006; 20(13):1776-89. PMC: 1522074. DOI: 10.1101/gad.1428206. View

Wade J, Castro Roa D, Grainger D, Hurd D, Busby S, Struhl K . Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol. 2006; 13(9):806-14. DOI: 10.1038/nsmb1130. View

Chen Z, Lewis K, Shultzaberger R, Lyakhov I, Zheng M, Doan B . Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res. 2007; 35(20):6762-77. PMC: 2189734. DOI: 10.1093/nar/gkm631. View

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

10.

Caspi R, Foerster H, Fulcher C, Kaipa P, Krummenacker M, Latendresse M . The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2007; 36(Database issue):D623-31. PMC: 2238876. DOI: 10.1093/nar/gkm900. View

11.

Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola M, Contreras-Moreira B . RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 2007; 36(Database issue):D120-4. PMC: 2238961. DOI: 10.1093/nar/gkm994. View

12.

Salgado H, Santos-Zavaleta A, Gama-Castro S, Peralta-Gil M, Penaloza-Spinola M, Martinez-Antonio A . The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinformatics. 2006; 7:5. PMC: 1382256. DOI: 10.1186/1471-2105-7-5. View

13.

Urban J, Vogel J . Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol. 2008; 6(3):e64. PMC: 2267818. DOI: 10.1371/journal.pbio.0060064. View

14.

Reichenbach B, Maes A, Kalamorz F, Hajnsdorf E, Gorke B . The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli. Nucleic Acids Res. 2008; 36(8):2570-80. PMC: 2377431. DOI: 10.1093/nar/gkn091. View