1. Biochemistry and Chemical Biology
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Underground isoleucine biosynthesis pathways in E. coli

  1. Charles AR Cotton
  2. Iria Bernhardsgrütter
  3. Hai He
  4. Simon Burgener
  5. Luca Schulz
  6. Nicole Paczia
  7. Beau Dronsella
  8. Alexander Erban
  9. Stepan Toman
  10. Marian Dempfle
  11. Alberto De Maria
  12. Joachim Kopka
  13. Steffen N Lindner
  14. Tobias J Erb
  15. Arren Bar-Even  Is a corresponding author
  1. Max Planck Institute of Molecular Plant Physiology, Germany
  2. Max Planck Institute of Terrestrial Microbiology, Germany
  3. Max Planck Insitute of Molecular Plant Physiology, Germany
Research Article
  • Cited 4
  • Views 2,121
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Cite this article as: eLife 2020;9:e54207 doi: 10.7554/eLife.54207

Abstract

The promiscuous activities of enzymes provide fertile ground for the evolution of new metabolic pathways. Here, we systematically explore the ability of E. coli to harness underground metabolism to compensate for the deletion of an essential biosynthetic pathway. By deleting all threonine deaminases, we generated a strain in which isoleucine biosynthesis was interrupted at the level of 2-ketobutyrate. Incubation of this strain under aerobic conditions resulted in the emergence of a novel 2-ketobutyrate biosynthesis pathway based upon the promiscuous cleavage of O-succinyl-L-homoserine by cystathionine γ-synthase (MetB). Under anaerobic conditions, pyruvate formate-lyase enabled 2-ketobutyrate biosynthesis from propionyl-CoA and formate. Surprisingly, we found this anaerobic route to provide a substantial fraction of isoleucine in a WT strain, when propionate is available in the medium. This study demonstrates the selective advantage underground metabolism offers, providing metabolic redundancy and flexibility which allow for the best use of environmental carbon sources.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 2 and 7 as well as for the metabolomic analysis.

Article and author information

Author details

  1. Charles AR Cotton

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Iria Bernhardsgrütter

    Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5019-8188
  3. Hai He

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1223-2813
  4. Simon Burgener

    Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Luca Schulz

    Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Nicole Paczia

    Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Beau Dronsella

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Alexander Erban

    Dept. III, Max Planck Insitute of Molecular Plant Physiology, Potsdam-Golm, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Stepan Toman

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Marian Dempfle

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Alberto De Maria

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  12. Joachim Kopka

    Dept. III, Max Planck Insitute of Molecular Plant Physiology, Potsdam-Golm, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9675-4883
  13. Steffen N Lindner

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3226-3043
  14. Tobias J Erb

    Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  15. Arren Bar-Even

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    For correspondence
    Bar-Even@mpimp-golm.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1039-4328

Funding

Max Planck Society

  • Arren Bar-Even

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

Reviewing Editor

  1. Pimchai Chaiyen, Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand

Publication history

  1. Received: December 5, 2019
  2. Accepted: August 22, 2020
  3. Accepted Manuscript published: August 24, 2020 (version 1)
  4. Version of Record published: September 7, 2020 (version 2)

Copyright

© 2020, Cotton 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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