Abstract
We present the first exact method based on the topology of a metabolic network to find minimal sets of metabolites (called precursors) sufficient to produce a set of target metabolites. In contrast with previous proposals, our model takes into account self-regenerating metabolites involved in cycles, which may be used to generate target metabolites from potential precursors. We analyse the complexity of the problem and we propose an algorithm to enumerate all minimal precursor sets for a set of target metabolites. The algorithm can be applied to identify a minimal medium necessary for a cell to ensure some metabolic functions. It can be used also to check inconsistencies caused by misannotations in a metabolic network. We present two illustrations of these applications.
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References
Caspi, R., et al.: MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 34(Database issue), D511–D516 (2006)
Francke, C., Siezen, R.J., Teusink, B.: Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol. 13(11), 550–558 (2005)
Garey, M.R., Johnson, D.S.: Computers and Intractability (A guide to the theory of NP-completeness). W.H. Freeman and Company, New York (1979)
Handorf, T., Christian, N., Ebenhöh, O., Kahn, D.: An environmental perspective on metabolism. J. Theor. Biol (November 2007)
Kanehisa, M., et al.: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34(Database issue), D354–D357 (2006)
Keseler, I.M., et al.: EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33(Database issue), D334–D337 (2005)
Nakabachi, A., et al.: The 160-kilobase genome of the bacterial endosymbiont carsonella. Science 314, 267 (2006)
Romero, P.R., Karp, P.: Nutrient-related analysis of pathway/genome databases. In: Pac. Symp. Biocomput., pp. 471–482 (2001)
Tamames, J., Gil, R., Latorre, A., Peretó, Silva, F., Moya, A.: The frontier between cell and organelle: genome analysis of candidatus carsonella ruddii. BMC Evol. Biol. 7, 181 (2007)
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Cottret, L. et al. (2008). Enumerating Precursor Sets of Target Metabolites in a Metabolic Network. In: Crandall, K.A., Lagergren, J. (eds) Algorithms in Bioinformatics. WABI 2008. Lecture Notes in Computer Science(), vol 5251. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87361-7_20
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DOI: https://doi.org/10.1007/978-3-540-87361-7_20
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-87360-0
Online ISBN: 978-3-540-87361-7
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