An environmental perspective on metabolism

Thomas Handorf, Nils Christian, Oliver Ebenhoeh, Daniel Kahn

Research output: Contribution to journalArticle

40 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)530-537
Number of pages8
JournalJournal of Theoretical Biology
Volume252
Issue number3
Early online date4 Nov 2007
DOIs
Publication statusPublished - 7 Jun 2008

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Metabolic Network
Metabolic Networks and Pathways
Metabolism
metabolism
organisms
Nutritional Requirements
Resources
Metabolites
nutrient requirements
Inverse problems
Inverse Problem
Maintenance
metabolites
Robustness
Calculate
Predict
Requirements
Growth
Knowledge
methodology

Keywords

  • nutrient
  • scope
  • metabolic network
  • evolution

Cite this

Handorf, T., Christian, N., Ebenhoeh, O., & Kahn, D. (2008). An environmental perspective on metabolism. Journal of Theoretical Biology, 252(3), 530-537. https://doi.org/10.1016/j.jtbi.2007.10.036

An environmental perspective on metabolism. / Handorf, Thomas; Christian, Nils; Ebenhoeh, Oliver; Kahn, Daniel.

In: Journal of Theoretical Biology, Vol. 252, No. 3, 07.06.2008, p. 530-537.

Research output: Contribution to journalArticle

Handorf, T, Christian, N, Ebenhoeh, O & Kahn, D 2008, 'An environmental perspective on metabolism', Journal of Theoretical Biology, vol. 252, no. 3, pp. 530-537. https://doi.org/10.1016/j.jtbi.2007.10.036
Handorf, Thomas ; Christian, Nils ; Ebenhoeh, Oliver ; Kahn, Daniel. / An environmental perspective on metabolism. In: Journal of Theoretical Biology. 2008 ; Vol. 252, No. 3. pp. 530-537.
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