Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism

Abstract

The Tricarboxylic Acid Cycle (TCA) cycle is arguably the most critical metabolic cycle in physiology and exists as an essential interface coordinating cellular metabolism, bioenergetics, and redox homeostasis. Despite decades of research, a comprehensive investigation into the consequences of TCA cycle dysfunction remains elusive. Here, we targeted two TCA cycle enzymes, fumarate hydratase (FH) and succinate dehydrogenase (SDH), and combined metabolomics, transcriptomics, and proteomics analyses to fully appraise the consequences of TCA cycle inhibition (TCAi) in murine kidney epithelial cells. Our comparative approach shows that TCAi elicits a convergent rewiring of redox and amino acid metabolism dependent on the activation of ATF4 and the integrated stress response (ISR). Furthermore, we also uncover a divergent metabolic response, whereby acute FHi, but not SDHi, can maintain asparagine levels via reductive carboxylation and maintenance of cytosolic aspartate synthesis. Our work highlights an important interplay between the TCA cycle, redox biology and amino acid homeostasis.

Data availability

All the transcriptomics. proteomics and uncropped blots data have been deposited in Dryad.

The following data sets were generated
    1. Ryan D
    (2021) Label-free proteomics - thenoyltrifluoroacetone (TTFA)
    Dryad Digital Repository, doi:10.5061/dryad.h44j0zpkt.
    1. Ryan D
    (2021) TruSeq stranded mRNA - Atpenin A5 (AA5)
    Dryad Digital Repository, doi:10.5061/dryad.08kprr536.
    1. Ryan D
    (2021) Western blot uncropped blots
    Dryad Digital Repository, doi:10.5061/dryad.08kprr537.

Article and author information

Author details

  1. Dylan Gerard Ryan

    MRC Cancer Unit, Hutchison MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Ming Yang

    MRC Cancer Unit, Hutchison MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Hiran A Prag

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Giovanny Rodriguez Blanco

    Edinburgh Cancer Research UK Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Efterpi Nikitopoulou

    MRC Cancer Unit, Hutchison MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Marc Segarra-Mondejar

    MRC Cancer Unit, Hutchison MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Christopher A Powell

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7501-0586
  8. Tim Young

    MRC Cancer Unit, Hutchison MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1831-3473
  9. Nils Burger

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  10. Jan Lj Miljkovic

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  11. Michal Minczuk

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  12. Michael P Murphy

    MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1115-9618
  13. Alex von Kriegsheim

    Edinburgh Cancer Research UK Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  14. Christian Frezza

    MRC Cancer Unit, Hutchison MRC Research Centre, University of Cambridge, Cambridge, United Kingdom
    For correspondence
    cf366@cam.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3293-7397

Funding

Medical Research Council (MRC_MC_UU_12022/6.)

  • Christian Frezza

H2020 European Research Council (ERC819920)

  • Dylan Gerard Ryan

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

Reviewing Editor

  1. Matthew G Vander Heiden, Massachusetts Institute of Technology, United States

Publication history

  1. Preprint posted: July 27, 2021 (view preprint)
  2. Received: July 28, 2021
  3. Accepted: December 21, 2021
  4. Accepted Manuscript published: December 23, 2021 (version 1)
  5. Version of Record published: January 6, 2022 (version 2)
  6. Version of Record updated: February 2, 2022 (version 3)

Copyright

© 2021, Ryan 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. Dylan Gerard Ryan
  2. Ming Yang
  3. Hiran A Prag
  4. Giovanny Rodriguez Blanco
  5. Efterpi Nikitopoulou
  6. Marc Segarra-Mondejar
  7. Christopher A Powell
  8. Tim Young
  9. Nils Burger
  10. Jan Lj Miljkovic
  11. Michal Minczuk
  12. Michael P Murphy
  13. Alex von Kriegsheim
  14. Christian Frezza
(2021)
Disruption of the TCA cycle reveals an ATF4-dependent integration of redox and amino acid metabolism
eLife 10:e72593.
https://doi.org/10.7554/eLife.72593

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