The ULK1-FBXW5-SEC23B nexus controls autophagy

  1. Yeon-Tae Jeong
  2. Daniele Simoneschi
  3. Sarah Keegan
  4. David Melville
  5. Natalia S Adler
  6. Anita Saraf
  7. Laurence Florens
  8. Michael P Washburn
  9. Claudio N Cavasotto
  10. David Fenyö
  11. Ana Maria Cuervo
  12. Mario Rossi  Is a corresponding author
  13. Michele Pagano  Is a corresponding author
  1. New York University School of Medicine, United States
  2. Howard Hughes Medical Institute, University of California, Berkeley, United States
  3. Instituto de Investigación en Biomedicina de Buenos Aires, CONICET-Partner Institute of the Max Planck Society, Argentina
  4. The Stowers Institute for Medical Research, United States
  5. Albert Einstein College of Medicine, United States

Abstract

In response to nutrient deprivation, the cell mobilizes an extensive amount of membrane to form and grow the autophagosome, allowing the progression of autophagy. By providing membranes and stimulating LC3 lipidation, COPII (Coat Protein Complex II) promotes autophagosome biogenesis. Here, we show that the F-box protein FBXW5 targets SEC23B, a component of COPII, for proteasomal degradation and that this event limits the autophagic flux in the presence of nutrients. In response to starvation, ULK1 phosphorylates SEC23B on Serine 186, preventing the interaction of SEC23B with FBXW5 and, therefore, inhibiting SEC23B degradation. Phosphorylated and stabilized SEC23B associates with SEC24A and SEC24B, but not SEC24C and SEC24D, and they re-localize to the ER-Golgi intermediate compartment, promoting autophagic flux. We propose that, in the presence of nutrients, FBXW5 limits COPII-mediated autophagosome biogenesis. Inhibition of this event by ULK1 ensures efficient execution of the autophagic cascade in response to nutrient starvation.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Mass spectrometry data is available at http://www.stowers.org/research/publications/libpb‐1118 (ftp://odr.stowers.org/LIBPB-1118) and has also been deposited to the MassIVE repository. Source data files have been provided for Figures 1, 3, 4, 5, 6, 7, Figure 2-figure supplement 1, and Figure 4-figure supplement 1.

The following data sets were generated

Article and author information

Author details

  1. Yeon-Tae Jeong

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Daniele Simoneschi

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Sarah Keegan

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. David Melville

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Natalia S Adler

    Instituto de Investigación en Biomedicina de Buenos Aires, CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
    Competing interests
    The authors declare that no competing interests exist.
  6. Anita Saraf

    The Stowers Institute for Medical Research, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Laurence Florens

    The Stowers Institute for Medical Research, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Michael P Washburn

    The Stowers Institute for Medical Research, Kansas City, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7568-2585
  9. Claudio N Cavasotto

    Instituto de Investigación en Biomedicina de Buenos Aires, CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1372-0379
  10. David Fenyö

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5049-3825
  11. Ana Maria Cuervo

    Department of DevelopmentalandMolecular Biology, Albert Einstein College of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Mario Rossi

    Instituto de Investigación en Biomedicina de Buenos Aires, CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
    For correspondence
    mrossi@ibioba-mpsp-conicet.gov.ar
    Competing interests
    The authors declare that no competing interests exist.
  13. Michele Pagano

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
    For correspondence
    michele.pagano@nyumc.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3210-2442

Funding

National Institutes of Health (R01‐CA076584)

  • Michele Pagano

National Institutes of Health (R01‐GM057587)

  • Michele Pagano

Agencia Nacional de Promoción Científica y Tecnológica (PICT‐2014‐0458)

  • Mario Rossi

Agencia Nacional de Promoción Científica y Tecnológica (PICT2016‐2620)

  • Mario Rossi

Agencia Nacional de Promoción Científica y Tecnológica (PICT‐ 2014‐3599)

  • Claudio N Cavasotto

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

Copyright

© 2018, Jeong 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

  • 3,523
    views
  • 738
    downloads
  • 67
    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)

  1. Yeon-Tae Jeong
  2. Daniele Simoneschi
  3. Sarah Keegan
  4. David Melville
  5. Natalia S Adler
  6. Anita Saraf
  7. Laurence Florens
  8. Michael P Washburn
  9. Claudio N Cavasotto
  10. David Fenyö
  11. Ana Maria Cuervo
  12. Mario Rossi
  13. Michele Pagano
(2018)
The ULK1-FBXW5-SEC23B nexus controls autophagy
eLife 7:e42253.
https://doi.org/10.7554/eLife.42253

Share this article

https://doi.org/10.7554/eLife.42253

Further reading

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Santi Mestre-Fos, Lucas Ferguson ... Jamie HD Cate
    Research Article

    Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the role of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP and alternative polyadenylation (APA) Seq, we show eIF3 crosslinks predominantly with 3’ untranslated region (3’-UTR) termini of multiple mRNA isoforms, adjacent to the poly(A) tail. Furthermore, we find that eIF3 engagement at 3’-UTR ends is dependent on polyadenylation. High eIF3 crosslinking at 3’-UTR termini of mRNAs correlates with high translational activity, as determined by ribosome profiling, but not with translational efficiency. The results presented here show that eIF3 engages with 3’-UTR termini of highly translated mRNAs, likely reflecting a general rather than specific regulatory function of eIF3, and supporting a role of mRNA circularization in the mechanisms governing mRNA translation.

    1. Cell Biology
    Ling Cheng, Ian Meliala ... Mikael Björklund
    Research Article

    Mitochondrial dysfunction is involved in numerous diseases and the aging process. The integrated stress response (ISR) serves as a critical adaptation mechanism to a variety of stresses, including those originating from mitochondria. By utilizing mass spectrometry-based cellular thermal shift assay (MS-CETSA), we uncovered that phosphatidylethanolamine-binding protein 1 (PEBP1), also known as Raf kinase inhibitory protein (RKIP), is thermally stabilized by stresses which induce mitochondrial ISR. Depletion of PEBP1 impaired mitochondrial ISR activation by reducing eukaryotic translation initiation factor 2α (eIF2α) phosphorylation and subsequent ISR gene expression, which was independent of PEBP1’s role in inhibiting the RAF/MEK/ERK pathway. Consistently, overexpression of PEBP1 potentiated ISR activation by heme-regulated inhibitor (HRI) kinase, the principal eIF2α kinase in the mitochondrial ISR pathway. Real-time interaction analysis using luminescence complementation in live cells revealed an interaction between PEBP1 and eIF2α, which was disrupted by eIF2α S51 phosphorylation. These findings suggest a role for PEBP1 in amplifying mitochondrial stress signals, thereby facilitating an effective cellular response to mitochondrial dysfunction. Therefore, PEBP1 may be a potential therapeutic target for diseases associated with mitochondrial dysfunction.