Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation
- University of Fribourg, Switzerland
- University of Milano-Bicocca, Italy
- University of Freiburg, Germany
- 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
Article and author information
Author details
Claudio De Virgilio
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.
Reviewing Editor
- Kevin Struhl, Harvard Medical School, United States
Version history
- Preprint posted: October 18, 2022 (view preprint)
- Received: October 25, 2022
- Accepted: February 6, 2023
- Accepted Manuscript published: February 7, 2023 (version 1)
- Version of Record published: February 17, 2023 (version 2)
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.
Metrics
-
- 2,515
- views
-
- 396
- downloads
-
- 15
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation
eLife 12:e84319.
https://doi.org/10.7554/eLife.84319
Further reading
-
- Biochemistry and Chemical Biology
Transporter research primarily relies on the canonical substrates of well-established transporters. This approach has limitations when studying transporters for the low-abundant micromolecules, such as micronutrients, and may not reveal physiological functions of the transporters. While d-serine, a trace enantiomer of serine in the circulation, was discovered as an emerging biomarker of kidney function, its transport mechanisms in the periphery remain unknown. Here, using a multi-hierarchical approach from body fluids to molecules, combining multi-omics, cell-free synthetic biochemistry, and ex vivo transport analyses, we have identified two types of renal d-serine transport systems. We revealed that the small amino acid transporter ASCT2 serves as a d-serine transporter previously uncharacterized in the kidney and discovered d-serine as a non-canonical substrate of the sodium-coupled monocarboxylate transporters (SMCTs). These two systems are physiologically complementary, but ASCT2 dominates the role in the pathological condition. Our findings not only shed light on renal d-serine transport, but also clarify the importance of non-canonical substrate transport. This study provides a framework for investigating multiple transport systems of various trace micromolecules under physiological conditions and in multifactorial diseases.
-
- Biochemistry and Chemical Biology
- Cell Biology
Mediator of ERBB2-driven Cell Motility 1 (MEMO1) is an evolutionary conserved protein implicated in many biological processes; however, its primary molecular function remains unknown. Importantly, MEMO1 is overexpressed in many types of cancer and was shown to modulate breast cancer metastasis through altered cell motility. To better understand the function of MEMO1 in cancer cells, we analyzed genetic interactions of MEMO1 using gene essentiality data from 1028 cancer cell lines and found multiple iron-related genes exhibiting genetic relationships with MEMO1. We experimentally confirmed several interactions between MEMO1 and iron-related proteins in living cells, most notably, transferrin receptor 2 (TFR2), mitoferrin-2 (SLC25A28), and the global iron response regulator IRP1 (ACO1). These interactions indicate that cells with high MEMO1 expression levels are hypersensitive to the disruptions in iron distribution. Our data also indicate that MEMO1 is involved in ferroptosis and is linked to iron supply to mitochondria. We have found that purified MEMO1 binds iron with high affinity under redox conditions mimicking intracellular environment and solved MEMO1 structures in complex with iron and copper. Our work reveals that the iron coordination mode in MEMO1 is very similar to that of iron-containing extradiol dioxygenases, which also display a similar structural fold. We conclude that MEMO1 is an iron-binding protein that modulates iron homeostasis in cancer cells.
