Journal of Molecular Evolution

, Volume 61, Issue 4, pp 498–512 | Cite as

Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution

  • Thomas Handorf
  • Oliver Ebenhöh
  • Reinhart Heinrich
Article

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.

Keywords

Metabolic networks Scope Evolution of metabolic pathways Stoichiometry KEGG database Robustness 

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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Thomas Handorf
    • 1
  • Oliver Ebenhöh
    • 1
  • Reinhart Heinrich
    • 1
  1. 1.Institute of Biology, Department of Theoretical BiophysicsHumboldt University BerlinGermany

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