CoChat
Sign Up
Cited by 1,249RNA Research and SplicingRNA and protein synthesis mechanismsProtein Structure and Dynamics

G3BP1 is a tunable switch that triggers phase separation to assemble stress granules

Open access
Yang, Peiguo, Mathieu, Cécile, Kolaitis, Regina-Maria, Zhang, Peipei, Messing, James, Yurtsever, Ugur, Yang, Zemin, Wu, Jinjun +7 more·2020·Cell
DOI 10.1016/j.cell.2020.03.046PMC PMC7448383
Open this paper in CoChat — free accountOpen PDF

Abstract

The mechanisms underlying ribonucleoprotein (RNP) granule assembly, including the basis for establishing and maintaining RNP granules with distinct composition, are unknown. One prominent type of RNP granule is the stress granule (SG), a dynamic and reversible cytoplasmic assembly formed in eukaryotic cells in response to stress. Here, we show that SGs assemble through liquid-liquid phase separation (LLPS) arising from interactions distributed unevenly across a core protein-RNA interaction network. The central node of this network is G3BP1, which functions as a molecular switch that triggers RNA-dependent LLPS in response to a rise in intracellular free RNA concentrations. Moreover, we show that interplay between three distinct intrinsically disordered regions (IDRs) in G3BP1 regulates its intrinsic propensity for LLPS, and this is fine-tuned by phosphorylation within the IDRs. Further regulation of SG assembly arises through positive or negative cooperativity by extrinsic G3BP1-binding factors that strengthen or weaken, respectively, the core SG network.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.cell.2020.03.046

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 71

  1. Banani SF, Lee HO, Hyman AA, and Rosen MK (2017). Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 18, 285– 298. 28225081 PMC7434221
  2. Banani SF, Rice AM, Peeples WB, Lin Y, Jain S, Parker R, and Rosen MK (2016). Compositional Control of Phase-Separated Cellular Bodies. Cell 166, 651– 663. 27374333 PMC4967043
  3. Bernado P, Mylonas E, Petoukhov MV, Blackledge M, and Svergun DI (2007). Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc 129, 5656– 5664. 17411046
  4. Brown PH, and Schuck P (2006). Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophys J 90, 4651– 4661. 16565040 PMC1471869
  5. Buchan JR (2014). mRNP granules. Assembly, function, and connections with disease. RNA Biol 11, 1019– 1030. 25531407 PMC4615263
  6. Buchan JR, Kolaitis RM, Taylor JP, and Parker R (2013). Eukaryotic stress granules are cleared by autophagy and Cdc48/VCP function. Cell 153, 1461– 1474. 23791177 PMC3760148
  7. Cohn EJ, and Edsall JT (1943). Density and apparent specific volume of proteins In Proteins, amino acids, and peptides, Cohn EJ, and Edsall JT, eds. (Princeton, NJ: Van Nostrand-Reinhold), pp. 370– 381.
  8. Crick SL, Ruff KM, Garai K, Frieden C, and Pappu RV (2013). Unmasking the roles of N- and C-terminal flanking sequences from exon 1 of huntingtin as modulators of polyglutamine aggregation. Proc Natl Acad Sci U S A 110, 20075– 20080. 24282292 PMC3864320
  9. Dundr M (2012). Nuclear bodies: multifunctional companions of the genome. Curr Opin Cell Biol 24, 415– 422. 22541757 PMC3372688
  10. Edupuganti RR, Geiger S, Lindeboom RGH, Shi H, Hsu PJ, Lu Z, Wang SY, Baltissen MPA, Jansen P, Rossa M, (2017). N(6)-methyladenosine (m(6)A) recruits and repels proteins to regulate mRNA homeostasis. Nat Struct Mol Biol 24, 870– 878. 28869609 PMC5725193
  11. Fabrini R, De Luca A, Stella L, Mei G, Orioni B, Ciccone S, Federici G, Lo Bello M, and Ricci G (2009). Monomer-dimer equilibrium in glutathione transferases: a critical re-examination. Biochemistry 48, 10473– 10482. 19795889
  12. Figley MD, Bieri G, Kolaitis RM, Taylor JP, and Gitler AD (2014). Profilin 1 associates with stress granules and ALS-linked mutations alter stress granule dynamics. J Neurosci 34, 8083– 8097. 24920614 PMC4051967
  13. Gallouzi IE, Parker F, Chebli K, Maurier F, Labourier E, Barlat I, Capony JP, Tocque B, and Tazi J (1998). A novel phosphorylation-dependent RNase activity of GAP-SH3 binding protein: a potential link between signal transduction and RNA stability. Mol Cell Biol 18, 3956– 3965. 9632780 PMC108980
  14. Gilks N, Kedersha N, Ayodele M, Shen L, Stoecklin G, Dember LM, and Anderson P (2004). Stress granule assembly is mediated by prion-like aggregation of TIA-1. Mol Biol Cell 15, 5383– 5398. 15371533 PMC532018
  15. Goktug AN, Ong SS, and Chen T (2012). GUItars: a GUI tool for analysis of high-throughput RNA interference screening data. PLoS One 7, e49386. 23185323 PMC3502531
  16. Gomes E, and Shorter J (2019). The molecular language of membraneless organelles. J Biol Chem 294, 7115– 7127. 30045872 PMC6509512
  17. Hopkins JB, Gillilan RE, and Skou S (2017). BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis. J Appl Crystallogr 50, 1545– 1553. 29021737 PMC5627684
  18. Huang da W, Sherman BT, and Lempicki RA (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44– 57. 19131956
  19. Humphrey W, Dalke A, and Schulten K (1996). VMD: visual molecular dynamics. J Mol Graph 14, 33– 38, 27–38. 8744570
  20. Ivanov P, Kedersha N, and Anderson P (2019). Stress Granules and Processing Bodies in Translational Control. Cold Spring Harb Perspect Biol 11. PMC6496347 30082464
  21. Jain S, Wheeler JR, Walters RW, Agrawal A, Barsic A, and Parker R (2016). ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure. Cell 164, 487– 498. 26777405 PMC4733397
  22. Jeong H, Mason SP, Barabasi AL, and Oltvai ZN (2001). Lethality and centrality in protein networks. Nature 411, 41– 42. 11333967
  23. Kapust RB, Tozser J, Fox JD, Anderson DE, Cherry S, Copeland TD, and Waugh DS (2001). Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng 14, 993– 1000. 11809930
  24. Kedersha N, Panas MD, Achorn CA, Lyons S, Tisdale S, Hickman T, Thomas M, Lieberman J, McInerney GM, Ivanov P, (2016). G3BP-Caprin1-USP10 complexes mediate stress granule condensation and associate with 40S subunits. J Cell Biol 212, 845– 860. 27022092 PMC4810302
  25. Khong A, Matheny T, Jain S, Mitchell SF, Wheeler JR, and Parker R (2017). The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules. Mol Cell 68, 808– 820 e805. 29129640 PMC5728175
  26. Kiebler MA, and Bassell GJ (2006). Neuronal RNA granules: movers and makers. Neuron 51, 685– 690. 16982415
  27. Kirby N, Cowieson N, Hawley AM, Mudie ST, McGillivray DJ, Kusel M, Samardzic-Boban V, and Ryan TM (2016). Improved radiation dose efficiency in solution SAXS using a sheath flow sample environment. Acta Crystallogr D Struct Biol 72, 1254– 1266. 27917826 PMC5137223
  28. Kwon S, Zhang Y, and Matthias P (2007). The deacetylase HDAC6 is a novel critical component of stress granules involved in the stress response. Genes Dev 21, 3381– 3394. 18079183 PMC2113037
  29. Li P, Banjade S, Cheng HC, Kim S, Chen B, Guo L, Llaguno M, Hollingsworth JV, King DS, Banani SF, (2012). Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336– 340. 22398450 PMC3343696
  30. Lin Y, Protter DS, Rosen MK, and Parker R (2015). Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins. Mol Cell 60, 208– 219. 26412307 PMC4609299
  31. Mackenzie IR, Nicholson AM, Sarkar M, Messing J, Purice MD, Pottier C, Annu K, Baker M, Perkerson RB, Kurti A, (2017). TIA1 Mutations in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Promote Phase Separation and Alter Stress Granule Dynamics. Neuron 95, 808– 816 e809. 28817800 PMC5576574
  32. Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, Luo EC, Krach F, Yang D, Sen A, (2018). Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules. Cell 172, 590– 604 e513. 29373831 PMC5969999
  33. Martin EW, Holehouse AS, Grace CR, Hughes A, Pappu RV, and Mittag T (2016a). Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation. J Am Chem Soc 138, 15323– 15335. 27807972 PMC5675102
  34. Martin S, Bellora N, Gonzalez-Vallinas J, Irimia M, Chebli K, de Toledo M, Raabe M, Eyras E, Urlaub H, Blencowe BJ, (2016b). Preferential binding of a stable G3BP ribonucleoprotein complex to intron-retaining transcripts in mouse brain and modulation of their expression in the cerebellum. J Neurochem 139, 349– 368. 27513819
  35. Marzahn MR, Marada S, Lee J, Nourse A, Kenrick S, Zhao H, Ben-Nissan G, Kolaitis RM, Peters JL, Pounds S, (2016). Higher-order oligomerization promotes localization of SPOP to liquid nuclear speckles. EMBO J 35, 1254– 1275. 27220849 PMC4910529
  36. Meyer C, Garzia A, Mazzola M, Gerstberger S, Molina H, and Tuschl T (2018). The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression. Mol Cell 69, 622– 635 e626. 29429924 PMC5816707
  37. Molliex A, Temirov J, Lee J, Coughlin M, Kanagaraj AP, Kim HJ, Mittag T, and Taylor JP (2015). Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell 163, 123– 133. 26406374 PMC5149108
  38. Nedelsky NB, and Taylor JP (2019). Bridging biophysics and neurology: aberrant phase transitions in neurodegenerative disease. Nat Rev Neurol 15, 272– 286. 30890779
  39. Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD, (2015). Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 57, 936– 947. 25747659 PMC4352761
  40. Ohn T, Kedersha N, Hickman T, Tisdale S, and Anderson P (2008). A functional RNAi screen links O-GlcNAc modification of ribosomal proteins to stress granule and processing body assembly. Nat Cell Biol 10, 1224– 1231. 18794846 PMC4318256
  41. Onomoto K, Jogi M, Yoo JS, Narita R, Morimoto S, Takemura A, Sambhara S, Kawaguchi A, Osari S, Nagata K, (2012). Critical role of an antiviral stress granule containing RIG-I and PKR in viral detection and innate immunity. PLoS One 7, e43031. 22912779 PMC3418241
  42. Panas MD, Ivanov P, and Anderson P (2016). Mechanistic insights into mammalian stress granule dynamics. J Cell Biol 215, 313– 323. 27821493 PMC5100297
  43. Panas MD, Kedersha N, Schulte T, Branca RM, Ivanov P, and Anderson P (2019). Phosphorylation of G3BP1-S149 does not influence stress granule assembly. J Cell Biol 218, 2425– 2432. 31171631 PMC6605800
  44. Panas MD, Schulte T, Thaa B, Sandalova T, Kedersha N, Achour A, and McInerney GM (2015). Viral and cellular proteins containing FGDF motifs bind G3BP to block stress granule formation. PLoS Pathog 11, e1004659. 25658430 PMC4450067
  45. Patel A, Lee HO, Jawerth L, Maharana S, Jahnel M, Hein MY, Stoynov S, Mahamid J, Saha S, Franzmann TM, (2015). A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation. Cell 162, 1066– 1077. 26317470
  46. Posey AE, Ruff KM, Harmon TS, Crick SL, Li A, Diamond MI, and Pappu RV (2018). Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers. J Biol Chem 293, 3734– 3746. 29358329 PMC5846159
  47. Rollins CT, Rivera VM, Woolfson DN, Keenan T, Hatada M, Adams SE, Andrade LJ, Yaeger D, van Schravendijk MR, Holt DA, (2000). A ligand-reversible dimerization system for controlling protein-protein interactions. Proc Natl Acad Sci U S A 97, 7096– 7101. 10852943 PMC16505
  48. Sahoo PK, Lee SJ, Jaiswal PB, Alber S, Kar AN, Miller-Randolph S, Taylor EE, Smith T, Singh B, Ho TS, (2018). Axonal G3BP1 stress granule protein limits axonal mRNA translation and nerve regeneration. Nat Commun 9, 3358. 30135423 PMC6105716
  49. Samir P, Kesavardhana S, Patmore DM, Gingras S, Malireddi RKS, Karki R, Guy CS, Briard B, Place DE, Bhattacharya A, (2019). DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome. Nature 573, 590– 594. 31511697 PMC6980284
  50. Schuck P (2000). Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys J 78, 1606– 1619. 10692345 PMC1300758
  51. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, (2015). STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43, D447– 452. 25352553 PMC4383874
  52. Thedieck K, Holzwarth B, Prentzell MT, Boehlke C, Klasener K, Ruf S, Sonntag AG, Maerz L, Grellscheid SN, Kremmer E, (2013). Inhibition of mTORC1 by astrin and stress granules prevents apoptosis in cancer cells. Cell 154, 859– 874. 23953116
  53. Tourriere H, Chebli K, Zekri L, Courselaud B, Blanchard JM, Bertrand E, and Tazi J (2003). The RasGAP-associated endoribonuclease G3BP assembles stress granules. J Cell Biol 160, 823– 831. 12642610 PMC2173781
  54. Tsai WC, Gayatri S, Reineke LC, Sbardella G, Bedford MT, and Lloyd RE (2016). Arginine Demethylation of G3BP1 Promotes Stress Granule Assembly. J Biol Chem 291, 22671– 22685. 27601476 PMC5077203
  55. Tsai WC, and Lloyd RE (2014). Cytoplasmic RNA Granules and Viral Infection. Annu Rev Virol 1, 147– 170. 26958719 PMC4867093
  56. Valentin-Vega YA, Wang YD, Parker M, Patmore DM, Kanagaraj A, Moore J, Rusch M, Finkelstein D, Ellison DW, Gilbertson RJ, (2016). Cancer-associated DDX3X mutations drive stress granule assembly and impair global translation. Sci Rep 6, 25996. 27180681 PMC4867597
  57. Van Treeck B, and Parker R (2018). Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies. Cell 174, 791– 802. 30096311 PMC6200146
  58. Van Treeck B, Protter DSW, Matheny T, Khong A, Link CD, and Parker R (2018). RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome. Proc Natl Acad Sci U S A 115, 2734– 2739. 29483269 PMC5856561
  59. Vognsen T, Moller IR, and Kristensen O (2013). Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup repeat specificity. PLoS One 8, e80947. 24324649 PMC3852005
  60. Wasserman S, and Faust K (1994). Social Network Analysis: Methods and Applications (Cambridge University Press).
  61. Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46, W296– W303. 29788355 PMC6030848
  62. Wippich F, Bodenmiller B, Trajkovska MG, Wanka S, Aebersold R, and Pelkmans L (2013). Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. Cell 152, 791– 805. 23415227
  63. Youn JY, Dunham WH, Hong SJ, Knight JDR, Bashkurov M, Chen GI, Bagci H, Rathod B, MacLeod G, Eng SWM, (2018). High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Mol Cell 69, 517– 532 e511. 29395067
  64. Zhang B, and Horvath S (2005). A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol 4, Article17. 16646834
  65. Zhang K, Daigle JG, Cunningham KM, Coyne AN, Ruan K, Grima JC, Bowen KE, Wadhwa H, Yang P, Rigo F, (2018). Stress Granule Assembly Disrupts Nucleocytoplasmic Transport. Cell 173, 958– 971 e917. 29628143 PMC6083872
  66. Zhang XD (2007). A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high-throughput screening assays. J Biomol Screen 12, 645– 655. 17517904
  67. Zhang XD (2011). Illustration of SSMD, z score, SSMD*, z* score, and t statistic for hit selection in RNAi high-throughput screens. J Biomol Screen 16, 775– 785. 21515799
  68. Zhang XD, Yang XC, Chung N, Gates A, Stec E, Kunapuli P, Holder DJ, Ferrer M, and Espeseth AS (2006). Robust statistical methods for hit selection in RNA interference high-throughput screening experiments. Pharmacogenomics 7, 299– 309. 16610941
  69. Zhao BS, Roundtree IA, and He C (2017). Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol 18, 31– 42. 27808276 PMC5167638
  70. Zhao H, Brautigam CA, Ghirlando R, and Schuck P (2013). Overview of current methods in sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation. Curr Protoc Protein Sci Chapter 20, Unit20 12. PMC3652391 23377850
  71. Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, (2015). A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. PLoS One 10, e0126420. 25997164 PMC4440767

Cited by

Sorted by citations

Authors
Yang, P., Mathieu, C., Kolaitis, R.-M., Zhang, P., Messing, J., Yurtsever, U., Yang, Z., Wu, J., Li, Y., Pan, Q., Yu, J., Martin, E. W., Mittag, T., Kim, H. J., & Taylor, J. P.
Affiliations
St. Jude Children's Research Hospital (US)
Corresponding author
Taylor, J. Paul
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2020-04
Volume
181
Issue
2
Pages
325-345.e28
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2020.03.046
PMC
PMC7448383
OpenAlex
W3016592635
Cited by
1,249
References
4
Citations by year
2026: 241 · 2025: 245 · 2024: 211 · 2023: 191 · 2022: 152 · 2021: 160 · 2020: 48 · 2012: 1
FWCI
44.14
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Cell
Funders
Howard Hughes Medical Institute
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
G3BP1, stress granules, liquid-liquid phase separation, ribonucleoprotein granules, intrinsically disordered regions, phosphorylation, cooperativity
MeSH terms
RNA Recognition Motif Proteins, Poly-ADP-Ribose Binding Proteins, Cytoplasm, Cytoplasmic Granules, DNA Helicases, Humans, Phosphorylation, Ribonucleoproteins, RNA, RNA Helicases, Cytoplasmic Structures, Cell Line, Tumor, HEK293 Cells

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review