1. Biochemistry and Chemical Biology
  2. Cell Biology
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Multiplex image-based autophagy RNAi screening identifies SMCR8 as ULK1 kinase activity and gene expression regulator

  1. Jennifer Jung
  2. Arnab Nayak
  3. Véronique Schaeffer
  4. Tatjana Starzetz
  5. Achim Klaus Kirsch
  6. Stefan Müller
  7. Ivan Dikic
  8. Michel Mittelbronn
  9. Christian Behrends  Is a corresponding author
  1. Goethe University School of Medicine, Germany
  2. Goethe University, Germany
  3. PerkinElmer, Inc., Germany
Research Article
  • Cited 39
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Cite this article as: eLife 2017;6:e23063 doi: 10.7554/eLife.23063

Abstract

Autophagy is an intracellular recycling and degradation pathway that depends on membrane trafficking. Rab GTPases are central for autophagy but their regulation especially through the activity of Rab GEFs remains largely elusive. We employed a RNAi screen simultaneously monitoring different populations of autophagosomes and identified 34 out of 186 Rab GTPase, GAP and GEF family members as potential autophagy regulators, amongst them SMCR8. SMCR8 uses overlapping binding regions to associate with C9ORF72 or with a C9ORF72-ULK1 kinase complex holo-assembly, which function in maturation and formation of autophagosomes, respectively. While focusing on the role of SMCR8 during autophagy initiation, we found that kinase activity and gene expression of ULK1 are increased upon SMCR8 depletion. The latter phenotype involved association of SMCR8 with the ULK1 gene locus. Global mRNA expression analysis revealed that SMCR8 regulates transcription of several other autophagy genes including WIPI2. Collectively, we established SMCR8 as multifaceted negative autophagy regulator.

Article and author information

Author details

  1. Jennifer Jung

    Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9436-4021
  2. Arnab Nayak

    Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  3. Véronique Schaeffer

    Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  4. Tatjana Starzetz

    Neurological Institute, Goethe University, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  5. Achim Klaus Kirsch

    PerkinElmer, Inc., Hamburg, Germany
    Competing interests
    No competing interests declared.
  6. Stefan Müller

    Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  7. Ivan Dikic

    Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
    Competing interests
    Ivan Dikic, Senior Editor eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8156-9511
  8. Michel Mittelbronn

    Neurological Institute, Goethe University, Frankfurt, Germany
    Competing interests
    No competing interests declared.
  9. Christian Behrends

    Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
    For correspondence
    behrends@em.uni-frankfurt.de
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9184-7607

Funding

Deutsche Forschungsgemeinschaft (SFB1177)

  • Stefan Müller
  • Ivan Dikic
  • Christian Behrends

Munich Cluster of Systems Neurology (EXC 1010 SyNergy)

  • Christian Behrends

Goethe-Universität Frankfurt am Main (EXC115)

  • Ivan Dikic

LOEWE Zentrum (Ub-net)

  • Stefan Müller
  • Ivan Dikic
  • Christian Behrends

European Research Council (ERC,282333-XABA)

  • Christian Behrends

Deutsche Forschungsgemeinschaft (DI 931/3-1)

  • Ivan Dikic

LOEWE Zentrum (Gene and Cell Therapy Frankfurt)

  • Christian Behrends

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

Reviewing Editor

  1. Noboru Mizushima, The University of Tokyo, Japan

Publication history

  1. Received: November 7, 2016
  2. Accepted: February 13, 2017
  3. Accepted Manuscript published: February 14, 2017 (version 1)
  4. Version of Record published: February 23, 2017 (version 2)
  5. Version of Record updated: September 13, 2017 (version 3)

Copyright

© 2017, Jung 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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