Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation

  1. Marco Caligaris
  2. Raffaele Nicastro  Is a corresponding author
  3. Zehan Hu
  4. Farida Tripodi
  5. Johannes Erwin Hummel
  6. Benjamin Pillet
  7. Marie-Anne Deprez
  8. Joris Winderickx
  9. Sabine Rospert
  10. Paola Coccetti
  11. Jörn Dengjel
  12. Claudio De Virgilio  Is a corresponding author
  1. University of Fribourg, Switzerland
  2. University of Milano-Bicocca, Italy
  3. University of Freiburg, Germany
  4. KU Leuven, Belgium

Abstract

The AMP-activated protein kinase (AMPK) and the target of rapamycin complex 1 (TORC1) are central kinase modules of two opposing signaling pathways that control eukaryotic cell growth and metabolism in response to the availability of energy and nutrients. Accordingly, energy depletion activates AMPK to inhibit growth, while nutrients and high energy levels activate TORC1 to promote growth. Both in mammals and lower eukaryotes such as yeast, the AMPK and TORC1 pathways are wired to each other at different levels, which ensures homeostatic control of growth and metabolism. In this context, a previous study (Hughes Hallet et. al, 2015) reported that AMPK in yeast, i.e. Snf1, prevents the transient TORC1 reactivation during the early phase following acute glucose starvation, but the underlying mechanism has remained elusive. Using a combination of unbiased mass spectrometry (MS)-based phosphoproteomics, genetic, biochemical, and physiological experiments, we show here that Snf1 temporally maintains TORC1 inactive in glucose-starved cells primarily through the TORC1-regulatory protein Pib2. Our data, therefore, extend the function of Pib2 to a hub that integrates both glucose and, as reported earlier, glutamine signals to control TORC1. We further demonstrate that Snf1 phosphorylates the TORC1 effector kinase Sch9 within its N-terminal region and thereby antagonizes the phosphorylation of a C-terminal TORC1-target residue within Sch9 itself that is critical for its activity. The consequences of Snf1-mediated phosphorylation of Pib2 and Sch9 are physiologically additive and sufficient to explain the role of Snf1 in short-term inhibition of TORC1 in acutely glucose-starved cells.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1-6 and Supplementary figures 1-3. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD037381

The following data sets were generated

Article and author information

Author details

  1. Marco Caligaris

    Department of Biology, University of Fribourg, Fribourg, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1732-7694
  2. Raffaele Nicastro

    Department of Biology, University of Fribourg, Fribourg, Switzerland
    For correspondence
    raffaele.nicastro2@unifr.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5420-2228
  3. Zehan Hu

    Department of Biology, University of Fribourg, Fribourg, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Farida Tripodi

    Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
    Competing interests
    The authors declare that no competing interests exist.
  5. Johannes Erwin Hummel

    Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Benjamin Pillet

    Department of Biology, University of Fribourg, Fribourg, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7313-4304
  7. Marie-Anne Deprez

    Functional Biology, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  8. Joris Winderickx

    Functional Biology, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3133-7733
  9. Sabine Rospert

    Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Paola Coccetti

    Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
    Competing interests
    The authors declare that no competing interests exist.
  11. Jörn Dengjel

    Department of Biology, University of Fribourg, Friborug, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9453-4614
  12. Claudio De Virgilio

    Department of Biology, University of Fribourg, Fribourg, Switzerland
    For correspondence
    Claudio.DeVirgilio@unifr.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8826-4323

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_166474/184671)

  • Marco Caligaris
  • Raffaele Nicastro
  • Benjamin Pillet
  • Claudio De Virgilio

Deutsche Forschungsgemeinschaft (RO 1028/5-2)

  • Sabine Rospert

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_184781)

  • Zehan Hu
  • Jörn Dengjel

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (316030_177088)

  • Zehan Hu
  • Jörn Dengjel

Fonds Wetenschappelijk Onderzoek (G069413)

  • Marie-Anne Deprez
  • Joris Winderickx

Fonds Wetenschappelijk Onderzoek (G0C7222N)

  • Marie-Anne Deprez
  • Joris Winderickx

Katholieke Universiteit Leuven (C14/17/063)

  • Marie-Anne Deprez
  • Joris Winderickx

Katholieke Universiteit Leuven (C14/21/095)

  • Marie-Anne Deprez
  • Joris Winderickx

Ministero dell'Università e della Ricerca (2020-ATE-0329)

  • Farida Tripodi
  • Paola Coccetti

Deutsche Forschungsgemeinschaft (Project-ID 403222702 - SFB 1381,TP B08)

  • Johannes Erwin Hummel
  • Sabine Rospert

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

Copyright

© 2023, Caligaris 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. Marco Caligaris
  2. Raffaele Nicastro
  3. Zehan Hu
  4. Farida Tripodi
  5. Johannes Erwin Hummel
  6. Benjamin Pillet
  7. Marie-Anne Deprez
  8. Joris Winderickx
  9. Sabine Rospert
  10. Paola Coccetti
  11. Jörn Dengjel
  12. Claudio De Virgilio
(2023)
Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation
eLife 12:e84319.
https://doi.org/10.7554/eLife.84319

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https://doi.org/10.7554/eLife.84319

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