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Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

Abstract

Elementary mode analysis is a useful metabolic pathway analysis tool to identify the structure of a metabolic network that links the cellular phenotype to the corresponding genotype. The analysis can decompose the intricate metabolic network comprised of highly interconnected reactions into uniquely organized pathways. These pathways consisting of a minimal set of enzymes that can support steady state operation of cellular metabolism represent independent cellular physiological states. Such pathway definition provides a rigorous basis to systematically characterize cellular phenotypes, metabolic network regulation, robustness, and fragility that facilitate understanding of cell physiology and implementation of metabolic engineering strategies. This mini-review aims to overview the development and application of elementary mode analysis as a metabolic pathway analysis tool in studying cell physiology and as a basis of metabolic engineering.

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Acknowledgement

We thank NIH for supporting this work (GM077529).

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Correspondence to Friedrich Srienc.

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Trinh, C.T., Wlaschin, A. & Srienc, F. Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Microbiol Biotechnol 81, 813–826 (2009). https://doi.org/10.1007/s00253-008-1770-1

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Keywords

  • Metabolic pathway analysis
  • Metabolic engineering
  • Elementary mode
  • Extreme pathway
  • Weighting factors
  • Rational strain design
  • Genetic knockout analysis
  • Metabolic flux ratio
  • Minimal cut set
  • Control effective flux
  • Robustness
  • Minimal cell