Dead end metabolites - defining the known unknowns of the E. coli metabolic network

Amanda Mackie, Ingrid M. Keseler, Laura Nolan, Peter D. Karp, Ian T. Paulsen

    Research output: Contribution to journalArticle

    14 Citations (Scopus)
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    Abstract

    The EcoCyc database is an online scientific database which provides an integrated view of the metabolic and regulatory network of the bacterium Escherichia coli K-12 and facilitates computational exploration of this important model organism. We have analysed the occurrence of dead end metabolites within the database - these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their production or consumption within the metabolic network. 127 dead end metabolites were identified from the 995 compounds that are contained within the EcoCyc metabolic network. Their presence reflects either a deficit in our representation of the network or in our knowledge of E. coli metabolism. Extensive literature searches resulted in the addition of 38 transport reactions and 3 metabolic reactions to the database and led to an improved representation of the pathway for Vitamin B12 salvage. 39 dead end metabolites were identified as components of reactions that are not physiologically relevant to E. coli K-12 - these reactions are properties of purified enzymes in vitro that would not be expected to occur in vivo. Our analysis led to improvements in the software that underpins the database and to the program that finds dead end metabolites within EcoCyc. The remaining dead end metabolites in the EcoCyc database likely represent deficiencies in our knowledge of E. coli metabolism.

    Original languageEnglish
    Article numbere75210
    Pages (from-to)1-11
    Number of pages11
    JournalPLoS ONE
    Volume8
    Issue number9
    DOIs
    Publication statusPublished - 23 Sep 2013

    Bibliographical note

    Copyright the Author(s) 2013. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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