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Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism

Biotechnology Letters volume 35, pages 2039–2044 (2013)Cite this article

Abstract

Elementary modes (EMs) are steady-state metabolic flux vectors with minimal set of active reactions. Each EM corresponds to a metabolic pathway. Therefore, studying EMs is helpful for analyzing the production of biotechnologically important metabolites. However, memory requirements for computing EMs may hamper their applicability as, in most genome-scale metabolic models, no EM can be computed due to running out of memory. In this study, we present a method for computing randomly sampled EMs. In this approach, a network reduction algorithm is used for EM computation, which is based on flux balance-based methods. We show that this approach can be used to recover the EMs in the medium- and genome-scale metabolic network models, while the EMs are sampled in an unbiased way. The applicability of such results is shown by computing “estimated” control-effective flux values in Escherichia coli metabolic network.

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Authors and Affiliations

  1. Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran

    Shayan Tabe-Bordbar & Sayed-Amir Marashi

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  1. Shayan Tabe-Bordbar
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  2. Sayed-Amir Marashi
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Correspondence to Sayed-Amir Marashi.

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Tabe-Bordbar, S., Marashi, SA. Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism. Biotechnol Lett 35, 2039–2044 (2013). https://doi.org/10.1007/s10529-013-1328-x

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  • DOI: https://doi.org/10.1007/s10529-013-1328-x

Keywords

  • Constraint-based modeling
  • Elementary flux modes
  • Flux balancing analysis
  • Flux coupling analysis
  • Metabolic networks
  • Metabolic pathways
  • Random sampling