Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points

  1. Uri Barenholz  Is a corresponding author
  2. Dan Davidi
  3. Eduard Reznik
  4. Yinon Bar-On
  5. Niv Antonovsky
  6. Elad Noor
  7. Ron Milo  Is a corresponding author
  1. The Weizmann Institute of Science, Israel
  2. The Weizmann Institute for Science, Israel
  3. Memorial Sloan Kettering Cancer Center, United States
  4. ETH Zurich, Switzerland

Abstract

A set of chemical reactions that require a metabolite to synthesize more of that metabolite is an autocatalytic cycle. Here we show that most of the reactions in the core of central carbon metabolism are part of compact autocatalytic cycles. Such metabolic designs must meet specific conditions to support stable fluxes, hence avoiding depletion of intermediate metabolites. As such, they are subjected to constraints that may seem counter-intuitive: the enzymes of branch reactions out of the cycle must be overexpressed and the affinity of these enzymes to their substrates must be relatively weak. We use recent quantitative proteomics and fluxomics measurements to show that the above conditions hold for functioning cycles in central carbon metabolism of E.coli. This work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzymes and lead to seemingly wasteful enzyme usage.

Article and author information

Author details

  1. Uri Barenholz

    Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
    For correspondence
    uri.barenholz@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3097-9681
  2. Dan Davidi

    Department of Plant and Environmental Sciences, The Weizmann Institute for Science, Rehovot, Israel
    Competing interests
    The authors declare that no competing interests exist.
  3. Eduard Reznik

    Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6511-5947
  4. Yinon Bar-On

    Department of Plant and Environmental Sciences, The Weizmann Institute for Science, Rehovot, Israel
    Competing interests
    The authors declare that no competing interests exist.
  5. Niv Antonovsky

    Department of Plant and Environmental Sciences, The Weizmann Institute for Science, Rehovot, Israel
    Competing interests
    The authors declare that no competing interests exist.
  6. Elad Noor

    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  7. Ron Milo

    Department of Plant and Environmental Sciences, The Weizmann Institute for Science, Rehovot, Israel
    For correspondence
    ron.milo@weizmann.ac.il
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1641-2299

Funding

Israel Science Foundation (740/16)

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

European Research Council (NOVCARBFIX 646827)

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

Beck-Canadian Center for Alternative Energy Research

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

Dana and Yossie Hollander

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

Helmsley Charitable Foundation

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

The Larson Charitable Foundation

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

Wolfson Family Charitable Trust

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

Charles Rothchild

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

Selmo Nussenbaum

  • Uri Barenholz
  • Dan Davidi
  • Yinon Bar-On
  • Niv Antonovsky
  • Ron Milo

Alternative sustainable Energy Research Initiative (Graduate Student Fellowship)

  • Uri Barenholz

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Daniel Segre

Version history

  1. Received: August 15, 2016
  2. Accepted: February 1, 2017
  3. Accepted Manuscript published: February 7, 2017 (version 1)
  4. Version of Record published: March 2, 2017 (version 2)

Copyright

© 2017, Barenholz et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Uri Barenholz
  2. Dan Davidi
  3. Eduard Reznik
  4. Yinon Bar-On
  5. Niv Antonovsky
  6. Elad Noor
  7. Ron Milo
(2017)
Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points
eLife 6:e20667.
https://doi.org/10.7554/eLife.20667

Share this article

https://doi.org/10.7554/eLife.20667

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