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-Knock; Jacob H. Hanna; Yifat Merbl; Ludo Van Den Bosch; Paul Anderson; Pavel Ivanov; Tamar Geiger; Eran Hornstein

doi:10.1016/j.molcel.2020.10.032

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

Human Molecular Genetics Biochemistry

Research output: Contribution to journal › Article › peer-review

154 Scopus citations

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 language	English
Pages (from-to)	876-891.e6
Journal	Molecular Cell
Volume	80
Issue number	5
DOIs	https://doi.org/10.1016/j.molcel.2020.10.032
State	Published - 3 Dec 2020

Funding

Funders	Funder number
Maria Halphen
Merck
Benoziyo Center Neurological Disease
Kekst Family Institute for Medical Genetics
Ministry of Industry, Trade and Labor
Université de Genève
E-Rare
Jefferson University
Engineering Research Centers
Julius and Ray Charlestein Foundation
Motor Neurone Disease Association
National Institutes of Health
Fraida Foundation
Charlene Vener New Scientist Fund
Weizmann Institute of Science
Roy Beck Barkai and Eran Perlson
Crown Human Genome Center
Wolfson Family Charitable Trust
Ron Rotkof
Seventh Framework Programme	617351
RADALA Foundation
Tel Aviv University
Minerva Foundation
European Research Council
Federal German Ministry for Education and Research
Abney Foundation
Fondation Thierry Latran
Assaf Kacen
Israel Science Foundation	135/16
Horizon 2020 Framework Programme	845692
NIH Office of the Director	P40OD018537
National Institute of General Medical Sciences	R35GM126901, R01GM126150
EU Horizon 2020 Programme for Research and Innovation Marie Skłodowska-Curie actions	R35 GM126901, RO1 GM126150
AFM-Téléthon	20576
Iowa Science Foundation	118945, 828/17

Keywords

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

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10.1016/j.molcel.2020.10.032

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Marmor-Kollet, H., Siany, A., Kedersha, N., Knafo, N., Rivkin, N., Danino, Y. M., Moens, T. G., Olender, T., Sheban, D., Cohen, N., Dadosh, T., Addadi, Y., Ravid, R., Eitan, C., Toth Cohen, B., Hofmann, S., Riggs, C. L., Advani, V. M., Higginbottom, A., ... Hornstein, E. (2020). Spatiotemporal Proteomic Analysis of Stress Granule Disassembly Using APEX Reveals Regulation by SUMOylation and Links to ALS Pathogenesis. Molecular Cell, 80(5), 876-891.e6. https://doi.org/10.1016/j.molcel.2020.10.032

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

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.",

keywords = "ALS, APEX, RNA binding proteins, amyotrophic lateral sclerosis, condensates, membraneless organelles, neurodegeneration, phase separation, stress granules, sumoylation",

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

note = "Publisher Copyright: {\textcopyright} 2020 Elsevier Inc.",

year = "2020",

month = dec,

day = "3",

doi = "10.1016/j.molcel.2020.10.032",

language = "אנגלית",

volume = "80",

pages = "876--891.e6",

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Marmor-Kollet, H, Siany, A, Kedersha, N, Knafo, N, Rivkin, N, Danino, YM, Moens, TG, Olender, T, Sheban, D, Cohen, N, Dadosh, T, Addadi, Y, Ravid, R, Eitan, C, Toth Cohen, B, Hofmann, S, Riggs, CL, Advani, VM, Higginbottom, A, Cooper-Knock, J, Hanna, JH, Merbl, Y, Van Den Bosch, L, Anderson, P, Ivanov, P, Geiger, T & Hornstein, E 2020, 'Spatiotemporal Proteomic Analysis of Stress Granule Disassembly Using APEX Reveals Regulation by SUMOylation and Links to ALS Pathogenesis', Molecular Cell, vol. 80, no. 5, pp. 876-891.e6. https://doi.org/10.1016/j.molcel.2020.10.032

TY - JOUR

T1 - Spatiotemporal Proteomic Analysis of Stress Granule Disassembly Using APEX Reveals Regulation by SUMOylation and Links to ALS Pathogenesis

AU - Marmor-Kollet, Hagai

AU - Siany, Aviad

AU - Kedersha, Nancy

AU - Knafo, Naama

AU - Rivkin, Natalia

AU - Danino, Yehuda M.

AU - Moens, Thomas G.

AU - Olender, Tsviya

AU - Sheban, Daoud

AU - Cohen, Nir

AU - Dadosh, Tali

AU - Addadi, Yoseph

AU - Ravid, Revital

AU - Eitan, Chen

AU - Toth Cohen, Beata

AU - Hofmann, Sarah

AU - Riggs, Claire L.

AU - Advani, Vivek M.

AU - Higginbottom, Adrian

AU - Cooper-Knock, Johnathan

AU - Hanna, Jacob H.

AU - Merbl, Yifat

AU - Van Den Bosch, Ludo

AU - Anderson, Paul

AU - Ivanov, Pavel

AU - Geiger, Tamar

AU - Hornstein, Eran

PY - 2020/12/3

Y1 - 2020/12/3

N2 - 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.

AB - 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.

KW - ALS

KW - APEX

KW - RNA binding proteins

KW - amyotrophic lateral sclerosis

KW - condensates

KW - membraneless organelles

KW - neurodegeneration

KW - phase separation

KW - stress granules

KW - sumoylation

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U2 - 10.1016/j.molcel.2020.10.032

DO - 10.1016/j.molcel.2020.10.032

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C2 - 33217318

AN - SCOPUS:85097406351

SN - 1097-2765

VL - 80

SP - 876-891.e6

JO - Molecular Cell

JF - Molecular Cell

IS - 5

ER -

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

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