Biotechnol Lett. 2013 Dec;35(12):2039-44. doi: 10.1007/s10529-013-1328-x.

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

Shayan Tabe-Bordbar, Sayed-Amir Marashi

PMID: 24078125 DOI: 10.1007/s10529-013-1328-x

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.

MeSH terms

• Escherichia coli / genetics
• Escherichia coli / metabolism
• Metabolic Networks and Pathways*
• Models, Biological*
• Systems Biology / methods

Publication Types

• Journal Article