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An environmental perspective on metabolism

Abstract : In principle the knowledge of an organism's metabolic network allows to infer its biosynthetic capabilities. Handorf et al. [2005. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol. 61, 498-512] developed a method of network expansion generating the set of all possible metabolites that can be produced from a set of compounds, given the structure of a metabolic network. Here we investigate the inverse problem: which chemical compounds or sets of compounds must be provided as external resources in order to sustain the growth or maintenance of an organism, given the structure of its metabolic network? Although this problem is highly combinatorial, we show that it is possible to calculate locally minimal nutrient sets that can be interpreted in terms of resource types. Using these types we predict broad nutritional requirements for 447 organisms, providing clues for possible environments from the knowledge of their metabolic networks.
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https://hal.archives-ouvertes.fr/hal-00428159
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Submitted on : Wednesday, October 7, 2015 - 8:14:43 PM
Last modification on : Tuesday, July 20, 2021 - 5:20:05 PM

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Thomas Handorf, Nils Christian, Oliver Ebenhöh, Daniel Kahn. An environmental perspective on metabolism. Journal of Theoretical Biology, Elsevier, 2008, 252 (3), pp.530-537. ⟨10.1016/j.jtbi.2007.10.036⟩. ⟨hal-00428159v2⟩

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