On the flexibility of the cellular amination network in E. coli

  1. Helena Schulz-Mirbach
  2. Alexandra Müller
  3. Tong Wu
  4. Pascal Pfister
  5. Selçuk Aslan
  6. Lennart Schada von Borzyskowski
  7. Tobias J Erb
  8. Arren Bar-Even
  9. Steffen N Lindner  Is a corresponding author
  1. Max Planck Institute of Molecular Plant Physiology, Germany
  2. Max Planck Institute for Terrestrial Microbiology, Germany

Abstract

Ammonium (NH4+) is essential to generate the nitrogenous building blocks of life. It gets assimilated via the canonical biosynthetic routes to glutamate and is further distributed throughout metabolism via a network of transaminases. To study the flexibility of this network, we constructed an Escherichia coli glutamate auxotrophic strain. This strain allowed us to systematically study which amino acids serve as amine sources and found that several amino acids complement the auxotrophy, either by producing glutamate via transamination reactions or by their conversion to glutamate. In this network, we identified aspartate transaminase AspC as a major connector between many amino acids and glutamate. Additionally, we extended the transaminase network by the amino acids β-alanine, alanine, glycine, and serine as new amine sources and identified d-amino acid dehydrogenase (DadA) as an intracellular amino acid sink removing substrates from transaminase reactions. Finally, ammonium assimilation routes producing aspartate or leucine were introduced. Our study reveals the high flexibility of the cellular amination network, both in terms of transaminase promiscuity and adaptability to new connections and ammonium entry points.

Data availability

sequencing data has been deposited at Dryad

The following data sets were generated

Article and author information

Author details

  1. Helena Schulz-Mirbach

    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:" 0000-0002-5376-9185
  2. Alexandra Müller

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Tong Wu

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Pascal Pfister

    Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Selçuk Aslan

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Lennart Schada von Borzyskowski

    Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Tobias J Erb

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

    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:" 0000-0002-1039-4328
  9. Steffen N Lindner

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    For correspondence
    Lindner@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:" 0000-0003-3226-3043

Funding

Bundesministerium für Bildung und Forschung (031B0825B)

  • Steffen N Lindner

Deutsche Forschungsgemeinschaft (SFB987)

  • Tobias J Erb

Max Planck Institute of Molecular Plant Physiology (open access funding)

  • Helena Schulz-Mirbach
  • Alexandra Müller
  • Tong Wu
  • Selçuk Aslan
  • Arren Bar-Even
  • Steffen N Lindner

Max Planck Institute for Terrestrial Microbiology (open access funding)

  • Pascal Pfister

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

Reviewing Editor

  1. Ahmad S Khalil, Boston University, United States

Publication history

  1. Preprint posted: January 27, 2022 (view preprint)
  2. Received: February 1, 2022
  3. Accepted: July 22, 2022
  4. Accepted Manuscript published: July 25, 2022 (version 1)
  5. Version of Record published: September 1, 2022 (version 2)

Copyright

© 2022, Schulz-Mirbach 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. Helena Schulz-Mirbach
  2. Alexandra Müller
  3. Tong Wu
  4. Pascal Pfister
  5. Selçuk Aslan
  6. Lennart Schada von Borzyskowski
  7. Tobias J Erb
  8. Arren Bar-Even
  9. Steffen N Lindner
(2022)
On the flexibility of the cellular amination network in E. coli
eLife 11:e77492.
https://doi.org/10.7554/eLife.77492

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