Letter | Published:

Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo

Nature Biotechnology volume 31, pages 357361 (2013) | Download Citation

Abstract

Recent data suggest that the majority of proteins bind specific metabolites1,2 and that such interactions are relevant to metabolic and gene regulation3,4,5. However, there are no methods to systematically identify functional allosteric protein-metabolite interactions4,6. Here we present an experimental and computational approach for using dynamic metabolite data to discover allosteric regulation that is relevant in vivo. By switching the culture conditions of Escherichia coli every 30 s between medium containing either pyruvate or 13C-labeled fructose or glucose, we measured the reversal of flux through glycolysis pathways and observed rapid changes in metabolite concentration. We fit these data to a kinetic model of glycolysis and systematically tested the consequences of 126 putative allosteric interactions on metabolite dynamics. We identified allosteric interactions that govern the reversible switch between gluconeogenesis and glycolysis, including one by which pyruvate activates fructose-1,6-bisphosphatase. Thus, from large sets of putative allosteric interactions, our approach can identify the most likely ones and provide hypotheses about their function.

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Acknowledgements

We thank E. Zamora-Sillero, L. Gerosa, M. Zampieri and R. Milo for discussions. This work was supported by Deutsche Forschungsgemeinschaft grant Li 1993/1-1.

Author information

Affiliations

  1. Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland.

    • Hannes Link
    • , Karl Kochanowski
    •  & Uwe Sauer
  2. Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland.

    • Karl Kochanowski

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Contributions

H.L. co-wrote the manuscript, performed and conceived experiments and computational analysis, K.K. performed experiments and constructed strains and edited the final draft, U.S. co-wrote the manuscript and directed the project.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Uwe Sauer.

Supplementary information

PDF files

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    Supplementary Text and Figures

    Supplementary Tables 2–5, Supplementary Figures 1–8 and Supplementary Methods

Excel files

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    Supplementary Table 1

    Metabolite data of the glucose switch, the fructose switch and the control sample without substrate switching.

About this article

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DOI

https://doi.org/10.1038/nbt.2489

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