Spatiotemporal Proteomic Analysis of Stress Granule Disassembly Using APEX Reveals Regulation by SUMOylation and Links to ALS Pathogenesis

Hagai Marmor-Kollet, Aviad Siany, Nancy Kedersha, Naama Knafo, Natalia Rivkin, Yehuda M. Danino, Thomas G. Moens, Tsviya Olender, Daoud Sheban, Nir Cohen, Tali Dadosh, Yoseph Addadi, Revital Ravid, Chen Eitan, Beata Toth Cohen, Sarah Hofmann, Claire L. Riggs, Vivek M. Advani, Adrian Higginbottom, Johnathan Cooper-KnockJacob H. Hanna, Yifat Merbl, Ludo Van Den Bosch, Paul Anderson, Pavel Ivanov, Tamar Geiger*, Eran Hornstein*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Stress granules (SGs) are cytoplasmic assemblies of proteins and non-translating mRNAs. Whereas much has been learned about SG formation, a major gap remains in understanding the compositional changes SGs undergo during normal disassembly and under disease conditions. Here, we address this gap by proteomic dissection of the SG temporal disassembly sequence using multi-bait APEX proximity proteomics. We discover 109 novel SG proteins and characterize distinct SG substructures. We reveal dozens of disassembly-engaged proteins (DEPs), some of which play functional roles in SG disassembly, including small ubiquitin-like modifier (SUMO) conjugating enzymes. We further demonstrate that SUMOylation regulates SG disassembly and SG formation. Parallel proteomics with amyotrophic lateral sclerosis (ALS)-associated C9ORF72 dipeptides uncovered attenuated DEP recruitment during SG disassembly and impaired SUMOylation. Accordingly, SUMO activity ameliorated C9ORF72-ALS-related neurodegeneration in Drosophila. By dissecting the SG spatiotemporal proteomic landscape, we provide an in-depth resource for future work on SG function and reveal basic and disease-relevant mechanisms of SG disassembly.

Original languageEnglish
Pages (from-to)876-891.e6
JournalMolecular Cell
Volume80
Issue number5
DOIs
StatePublished - 3 Dec 2020

Funding

FundersFunder number
Assaf Kacen
Benoziyo Center Neurological Disease
Charlene Vener New Scientist Fund
EU Horizon 2020 Programme for Research and Innovation Marie Skłodowska-Curie actions845692
Federal German Ministry for Education and Research
Fraida Foundation
Jefferson University
Julius and Ray Charlestein Foundation
Kekst Family Institute for Medical Genetics
Maria Halphen
RADALA Foundation
Ron Rotkof
Roy Beck Barkai and Eran Perlson
National Institutes of HealthP40OD018537, RO1 GM126150
National Institute of General Medical SciencesR35GM126901
Abney Foundation
Merck
Fondation Thierry Latran
Seventh Framework Programme617351
Iowa Science Foundation118945, 828/17
Engineering Research Centers
E-Rare
Motor Neurone Disease Association
European Research Council
Minerva Foundation
Weizmann Institute of Science
Israel Science Foundation135/16
Tel Aviv University
Ministry of Industry, Trade and Labor
AFM-Téléthon20576
Seventh Framework Programme
Université de Genève
Wolfson Family Charitable Trust
Crown Human Genome Center

    Keywords

    • ALS
    • APEX
    • RNA binding proteins
    • amyotrophic lateral sclerosis
    • condensates
    • membraneless organelles
    • neurodegeneration
    • phase separation
    • stress granules
    • sumoylation

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