Advances in analysis of microbial metabolic fluxes via 13C isotopic labeling

Authors

  • Yinjie J. Tang,

    1. Joint Bio-Energy Institute, Emeryville, CA
    2. Virtual Institute for Microbial Stress and Survival, Berkeley, CA
    3. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA
    4. Department of Chemical Engineering, University of California, Berkeley, CA
    Current affiliation:
    1. Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO.
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  • Hector Garcia Martin,

    1. Joint Bio-Energy Institute, Emeryville, CA
    2. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA
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  • Samuel Myers,

    1. Department of Chemical Engineering, University of California, Berkeley, CA
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  • Sarah Rodriguez,

    1. Department of Molecular Cell Biology, University of California, Berkeley, CA
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  • Edward E.K. Baidoo,

    1. Virtual Institute for Microbial Stress and Survival, Berkeley, CA
    2. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA
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  • Jay D. Keasling

    Corresponding author
    1. Joint Bio-Energy Institute, Emeryville, CA
    2. Virtual Institute for Microbial Stress and Survival, Berkeley, CA
    3. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA
    4. Department of Chemical Engineering, University of California, Berkeley, CA
    5. Department of Bioengineering, University of California, Berkeley, CA
    • Joint Bio-Energy Institute, 5885 Hollis, Emeryville, CA 94608.
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  • JDK has a consulting relationship with and a financial interest in Amyris and a financial interest in LS9, both of which stand to benefit from the commercialization of the results of this research.

  • YJT and HGM contributed equally to this study.

Abstract

Metabolic flux analysis via 13C labeling (13C MFA) quantitatively tracks metabolic pathway activity and determines overall enzymatic function in cells. Three core techniques are necessary for 13C MFA: (1) a steady state cell culture in a defined medium with labeled-carbon substrates; (2) precise measurements of the labeling pattern of targeted metabolites; and (3) evaluation of the data sets obtained from mass spectrometry measurements with a computer model to calculate the metabolic fluxes. In this review, we summarize recent advances in the 13C-flux analysis technologies, including mini-bioreactor usage for tracer experiments, isotopomer analysis of metabolites via high resolution mass spectrometry (such as GC-MS, LC-MS, or FT-ICR), high performance and large-scale isotopomer modeling programs for flux analysis, and the integration of fluxomics with other functional genomics studies. It will be shown that there is a significant value for 13C-based metabolic flux analysis in many biological research fields. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:362–375, 2009

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