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

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• 作者：Shayan Tabe-Bordbar (1)
  Sayed-Amir Marashi (1)
  
• 关键词：Constraint ; based modeling ; Elementary flux modes ; Flux balancing analysis ; Flux coupling analysis ; Metabolic networks ; Metabolic pathways ; Random sampling
• 刊名：Biotechnology Letters
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：35
• 期：12
• 页码：2039-2044
• 全文大小：
• 作者单位：Shayan Tabe-Bordbar (1)
  Sayed-Amir Marashi (1)
  
  1. Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
  
• ISSN：1573-6776

文摘

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.