Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles
Open accessAbstract
Cells chemically isolate molecules in compartments to both facilitate and regulate their interactions. In addition to membrane-encapsulated compartments, cells can form proteinaceous and membraneless organelles, including nucleoli, Cajal and PML bodies, and stress granules. The principles that determine when and why these structures form have remained elusive. Here, we demonstrate that the disordered tails of Ddx4, a primary constituent of nuage or germ granules, form phase-separated organelles both in live cells and in vitro. These bodies are stabilized by patterned electrostatic interactions that are highly sensitive to temperature, ionic strength, arginine methylation, and splicing. Sequence determinants are used to identify proteins found in both membraneless organelles and cell adhesion. Moreover, the bodies provide an alternative solvent environment that can concentrate single-stranded DNA but largely exclude double-stranded DNA. We propose that phase separation of disordered proteins containing weakly interacting blocks is a general mechanism for forming regulated, membraneless organelles.
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Evidence for chromatin LLPS and its functional significance in gene control is still incomplete.
“Whilst LLPS in general has been demonstrated both in vitro and in vivo [421, 422], evidence for chromatin LLPS and its functional significance in gene control is still incomplete.”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [421]
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Funnels, pathways, and the energy landscape of protein folding: A synthesis
Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340210302 · Cited by 2,648 · cited 1× · see citing works
“Ddx4 Organelles Are Likely Minimally Stable to Enable Regulation by PTMs The folded structures of proteins have been recognized as being minimally stable, a property that facilitates the relative motion of domains and enables function (Bryngelson et al., 1995).”
BackgroundKato, M., Han, T. W., Xie, S., Shi, K., Du, X., Wu, L. C., Mirzaei, H., Goldsmith, E. J., Longgood, J., Pei, J., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.017 · Cited by 2,012 · see citing works
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Research works printed but not linked: 46
- Balagopal V. Parker R. Polysomes, P bodies and stress granules: states and fates of eukaryotic mRNAs Curr. Opin. Cell Biol. 21 2009 403 408 19394210 PMC2740377
- Baldwin A.J. Knowles T.P. Tartaglia G.G. Fitzpatrick A.W. Devlin G.L. Shammas S.L. Waudby C.A. Mossuto M.F. Meehan S. Gras S.L. Metastability of native proteins and the phenomenon of amyloid formation J. Am. Chem. Soc. 133 2011 14160 14163 21650202
- Brangwynne C.P. Eckmann C.R. Courson D.S. Rybarska A. Hoege C. Gharakhani J. Jülicher F. Hyman A.A. Germline P granules are liquid droplets that localize by controlled dissolution/condensation Science 324 2009 1729 1732 19460965
- Brangwynne C.P. Mitchison T.J. Hyman A.A. Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes Proc. Natl. Acad. Sci. USA 108 2011 4334 4339 21368180 PMC3060270
- Brown C.J. Johnson A.K. Dunker A.K. Daughdrill G.W. Evolution and disorder Curr. Opin. Struct. Biol. 21 2011 441 446 21482101 PMC3112239
- Chen C. Jin J. James D.A. Adams-Cioaba M.A. Park J.G. Guo Y. Tenaglia E. Xu C. Gish G. Min J. Pawson T. Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi Proc. Natl. Acad. Sci. USA 106 2009 20336 20341 19918066 PMC2787181
- Chen C. Nott T.J. Jin J. Pawson T. Deciphering arginine methylation: Tudor tells the tale Nat. Rev. Mol. Cell Biol. 12 2011 629 642 21915143
- de Thé H. Chomienne C. Lanotte M. Degos L. Dejean A. The t(15;17) translocation of acute promyelocytic leukaemia fuses the retinoic acid receptor alpha gene to a novel transcribed locus Nature 347 1990 558 561 2170850
- Decker C.J. Teixeira D. Parker R. Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae J. Cell Biol. 179 2007 437 449 17984320 PMC2064791
- Dedmon M.M. Lindorff-Larsen K. Christodoulou J. Vendruscolo M. Dobson C.M. Mapping long-range interactions in α-synuclein using spin-label NMR and ensemble molecular dynamics simulations J. Am. Chem. Soc. 127 2005 476 477 15643843
- Dellaire G. Ching R.W. Dehghani H. Ren Y. Bazett-Jones D.P. The number of PML nuclear bodies increases in early S phase by a fission mechanism J. Cell Sci. 119 2006 1026 1033 16492708
- Dellaire G. Eskiw C.H. Dehghani H. Ching R.W. Bazett-Jones D.P. Mitotic accumulations of PML protein contribute to the re-establishment of PML nuclear bodies in G1 J. Cell Sci. 119 2006 1034 1042 16492707
- Dobson C.M. Protein folding and misfolding Nature 426 2003 884 890 14685248
- Dundr M. Misteli T. Biogenesis of nuclear bodies Cold Spring Harb. Perspect. Biol. 2 2010 a000711 21068152 PMC2982170
- Fanfoni M. Tomellini M. The Johnson-Mehl-Avrami-Kohnogorov model: A brief review Il Nuovo Cimento D 20 1998 1171 1182
- Fitzpatrick A.W. Debelouchina G.T. Bayro M.J. Clare D.K. Caporini M.A. Bajaj V.S. Jaroniec C.P. Wang L. Ladizhansky V. Müller S.A. Atomic structure and hierarchical assembly of a cross-β amyloid fibril Proc. Natl. Acad. Sci. USA 110 2013 5468 5473 23513222 PMC3619355
- Forman-Kay J.D. Mittag T. From sequence and forces to structure, function, and evolution of intrinsically disordered proteins Structure 21 2013 1492 1499 24010708 PMC4704097
- Frey S. Richter R.P. Görlich D. FG-rich repeats of nuclear pore proteins form a three-dimensional meshwork with hydrogel-like properties Science 314 2006 815 817 17082456
- Gallivan J.P. Dougherty D.A. Cation-π interactions in structural biology Proc. Natl. Acad. Sci. USA 96 1999 9459 9464 10449714 PMC22230
- Gromiha M.M. Santhosh C. Ahmad S. Structural analysis of cation-π interactions in DNA binding proteins Int. J. Biol. Macromol. 34 2004 203 211 15225993
- Hearst S.M. Gilder A.S. Negi S.S. Davis M.D. George E.M. Whittom A.A. Toyota C.G. Husedzinovic A. Gruss O.J. Hebert M.D. Cajal-body formation correlates with differential coilin phosphorylation in primary and transformed cell lines J. Cell Sci. 122 2009 1872 1881 19435804 PMC2684838
- Hyman A.A. Brangwynne C.P. Beyond stereospecificity: liquids and mesoscale organization of cytoplasm Dev. Cell 21 2011 14 16 21763600
- Kim H.J. Kim N.C. Wang Y.-D. Scarborough E.A. Moore J. Diaz Z. MacLea K.S. Freibaum B. Li S. Molliex A. Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS Nature 495 2013 467 473 23455423 PMC3756911
- Kirino Y. Vourekas A. Kim N. de Lima Alves F. Rappsilber J. Klein P.S. Jongens T.A. Mourelatos Z. Arginine methylation of vasa protein is conserved across phyla J. Biol. Chem. 285 2010 8148 8154 20080973 PMC2832966
- Kotaja N. Sassone-Corsi P. The chromatoid body: a germ-cell-specific RNA-processing centre Nat. Rev. Mol. Cell Biol. 8 2007 85 90 17183363
- Kotaja N. Bhattacharyya S.N. Jaskiewicz L. Kimmins S. Parvinen M. Filipowicz W. Sassone-Corsi P. The chromatoid body of male germ cells: similarity with processing bodies and presence of Dicer and microRNA pathway components Proc. Natl. Acad. Sci. USA 103 2006 2647 2652 16477042 PMC1413789
- Li P. Banjade S. Cheng H.C. Kim S. Chen B. Guo L. Llaguno M. Hollingsworth J.V. King D.S. Banani S.F. Phase transitions in the assembly of multivalent signalling proteins Nature 483 2012 336 340 22398450 PMC3343696
- Liang L. Diehl-Jones W. Lasko P. Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities Development 120 1994 1201 1211 8026330
- Liu K. Chen C. Guo Y. Lam R. Bian C. Xu C. Zhao D.Y. Jin J. MacKenzie F. Pawson T. Min J. Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain Proc. Natl. Acad. Sci. USA 107 2010 18398 18403 20937909 PMC2972943
- Marsh J.A. Forman-Kay J.D. Sequence determinants of compaction in intrinsically disordered proteins Biophys. J. 98 2010 2383 2390 20483348 PMC2872267
- Meikar O. Da Ros M. Korhonen H. Kotaja N. Chromatoid body and small RNAs in male germ cells Reproduction 142 2011 195 209 21652638
- Melnick A. Licht J.D. Deconstructing a disease: RARalpha, its fusion partners, and their roles in the pathogenesis of acute promyelocytic leukemia Blood 93 1999 3167 3215 10233871
- Misteli T. Cáceres J.F. Clement J.Q. Krainer A.R. Wilkinson M.F. Spector D.L. Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo J. Cell Biol. 143 1998 297 307 9786943 PMC2132840
- Monsellier E. Chiti F. Prevention of amyloid-like aggregation as a driving force of protein evolution EMBO Rep. 8 2007 737 742 17668004 PMC1978086
- Morozova N. Allers J. Myers J. Shamoo Y. Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures Bioinformatics 22 2006 2746 2752 16966360
- Phair R.D. Misteli T. High mobility of proteins in the mammalian cell nucleus Nature 404 2000 604 609 10766243
- Shammas S.L. Knowles T.P. Baldwin A.J. Macphee C.E. Welland M.E. Dobson C.M. Devlin G.L. Perturbation of the stability of amyloid fibrils through alteration of electrostatic interactions Biophys. J. 100 2011 2783 2791 21641324 PMC3117150
- Sun Z. Diaz Z. Fang X. Hart M.P. Chesi A. Shorter J. Gitler A.D. Molecular determinants and genetic modifiers of aggregation and toxicity for the ALS disease protein FUS/TLS PLoS Biol. 9 2011 e1000614 21541367 PMC3082519
- Tang J. Frankel A. Cook R.J. Kim S. Paik W.K. Williams K.R. Clarke S. Herschman H.R. PRMT1 is the predominant type I protein arginine methyltransferase in mammalian cells J. Biol. Chem. 275 2000 7723 7730 10713084
- Tycko R. Solid-state NMR studies of amyloid fibril structure Annu. Rev. Phys. Chem. 62 2011 279 299 21219138 PMC3191906
- Wilkins D.K. Grimshaw S.B. Receveur V. Dobson C.M. Jones J.A. Smith L.J. Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques Biochemistry 38 1999 16424 16431 10600103
- Wilson E.B. The structure of protoplasm Science 10 1899 33 45 17829686
- Wooderchak W.L. Zang T. Zhou Z.S. Acuña M. Tahara S.M. Hevel J.M. Substrate profiling of PRMT1 reveals amino acid sequences that extend beyond the “RGG” paradigm Biochemistry 47 2008 9456 9466 18700728
- Yaffe M.B. Leparc G.G. Lai J. Obata T. Volinia S. Cantley L.C. A motif-based profile scanning approach for genome-wide prediction of signaling pathways Nat. Biotechnol. 19 2001 348 353 11283593
- Yamaguchi A. Kitajo K. The effect of PRMT1-mediated arginine methylation on the subcellular localization, stress granules, and detergent-insoluble aggregates of FUS/TLS PLoS ONE 7 2012 e49267 23152885 PMC3496700
- Yeo G.C. Keeley F.W. Weiss A.S. Coacervation of tropoelastin Adv. Colloid Interface Sci. 167 2011 94 103 21081222
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- Authors
- Nott, T. J., Petsalaki, E., Farber, P., Jervis, D., Fussner, E., Plochowietz, A., Craggs, T. D., Bazett-Jones, D. P., Pawson, T., Forman-Kay, J. D., & Baldwin, A. J.
- Affiliations
- Mount Sinai Hospital (CA)
- Hospital for Sick Children (CA)
- University of Toronto (CA)
- University of Oxford (GB)
- Corresponding author
- Forman-Kay, Julie D.
- Baldwin, Andrew J.
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2015-03
- Volume
- 57
- Issue
- 5
- Pages
- 936-947
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC4352761
- OpenAlex
- W2168639701
- Cited by
- 1,803
- References
- 2
- Citations by year
- 2026: 125 · 2025: 176 · 2024: 194 · 2023: 195 · 2022: 198 · 2021: 246 · 2020: 195 · 2019: 165 · 2018: 136 · 2017: 78 · 2016: 65 · 2015: 23 · 2014: 2
- FWCI
- 43.73
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Molecular Cell (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Health Canada
- Canadian Institutes of Health Research (-MOP-6849)
- Biotechnology and Biological Sciences Research Council (BB/J014346/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- phase separation, biomolecular condensates, intrinsically disordered proteins, DDX4, nuage, germ granules, electrostatic interactions, arginine methylation, splicing, single-stranded DNA, temperature sensitivity, ionic strength, cell adhesion, liquid-liquid phase separation
- MeSH terms
- Amino Acid Sequence, Cell Nucleus, Cytoplasmic Granules, DNA, HeLa Cells, Humans, Intracellular Membranes, Luminescent Proteins, Methylation, Microscopy, Fluorescence, Molecular Sequence Data, Mutation, Osmolar Concentration, Organelles, Sequence Homology, Amino Acid, Microscopy, Confocal, Transition Temperature, Phase Transition, DEAD-box RNA Helicases, Static Electricity, Time-Lapse Imaging
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