Expanding metabolic networks

scopes of compounds, robustness, and evolution

Thomas Handorf, Oliver Ebenhöh, Reinhart Heinrich

Research output: Contribution to journalArticle

109 Citations (Scopus)

Abstract

A new method for the mathematical analysis of large metabolic networks is presented. Based on the fact that the occurrence of a metabolic reaction generally requires the existence of other reactions providing its substrates, series of metabolic networks are constructed. In each step of the corresponding expansion process those reactions are incorporated whose substrates are made available by the networks of the previous generations. The method is applied to the set of all metabolic reactions included in the KEGG database. Starting with one or more seed compounds, the expansion results in a final network whose compounds define the scope of the seed. Scopes of all metabolic compounds are calculated and it is shown that large parts of cellular metabolism can be considered as the combined scope of simple building blocks. Analyses of various expansion processes reveal crucial metabolites whose incorporation allows for the increase in network complexity. Among these metabolites are common cofactors such as NAD+, ATP, and coenzyme A. We demonstrate that the outcome of network expansion is in general very robust against elimination of single or few reactions. There exist, however, crucial reactions whose elimination results in a dramatic reduction of scope sizes. It is hypothesized that the expansion process displays characteristics of the evolution of metabolism such as the temporal order of the emergence of metabolic pathways.
Original languageEnglish
Pages (from-to)498-512
Number of pages15
JournalJournal of Molecular Evolution
Volume61
Issue number4
DOIs
Publication statusPublished - 1 Oct 2005

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Metabolic Networks and Pathways
Seeds
seed
substrate
mathematical analysis
seeds
NAD
biochemical pathways
metabolite
Adenosine Triphosphate
Databases
metabolites
methodology
method
incorporation

Keywords

  • adenosine triphosphate
  • coenzymes
  • molecular evolution
  • glucose
  • glycolysis
  • metabolism
  • organic chemicals
  • metabolic networks
  • scope
  • evolution of metabolic pthways
  • stoichiometry
  • KEGG database
  • robustness
  • optimization
  • organization
  • pathways

Cite this

Expanding metabolic networks : scopes of compounds, robustness, and evolution. / Handorf, Thomas; Ebenhöh, Oliver; Heinrich, Reinhart.

In: Journal of Molecular Evolution, Vol. 61, No. 4, 01.10.2005, p. 498-512.

Research output: Contribution to journalArticle

Handorf, Thomas ; Ebenhöh, Oliver ; Heinrich, Reinhart. / Expanding metabolic networks : scopes of compounds, robustness, and evolution. In: Journal of Molecular Evolution. 2005 ; Vol. 61, No. 4. pp. 498-512.
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