| Sonstiges: |
- Nachgewiesen in: MEDLINE
- Sprachen: English
- Publication Type: Journal Article; Research Support, Non-U.S. Gov't; Review
- Language: English
- [FEBS J] 2020 May; Vol. 287 (10), pp. 1924-1935. <i>Date of Electronic Publication: </i>2020 Mar 14.
- MeSH Terms: Lipid Bilayers / *chemistry ; Organelles / *chemistry ; Protein Processing, Post-Translational / *genetics ; Proteins / *genetics ; Cytoplasm / chemistry ; Cytoplasm / genetics ; Humans ; Lipid Bilayers / metabolism ; Organelles / genetics ; Proteins / chemistry
- References: Banani SF, Lee HO, Hyman AA & Rosen MK (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 18, 285-298. ; Shin Y & Brangwynne CP (2017) Liquid phase condensation in cell physiology and disease. Science 357, eaaf4382. ; Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, Schymkowitz J, Shorter J, Wolozin B, Van Den Bosch L et al. (2018) Protein phase separation: a new phase in cell biology. Trends Cell Biol 28, 420-435. ; Wu H & Fuxreiter M (2016) The structure and dynamics of higher-order assemblies: amyloids, signalosomes, and granules. Cell 165, 1055-1066. ; Pancsa R, Schad E, Tantos A & Tompa P (2019) Emergent functions of proteins in non-stoichiometric supramolecular assemblies. Biochim Biophys Acta Proteins Proteom 1867, 970-979. ; Case LB, Zhang X, Ditlev JA & Rosen MK (2019) Stoichiometry controls activity of phase-separated clusters of actin signaling proteins. Science 363, 1093-1097. ; Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N, Henry L, Gerlich DW, Redding S & Rosen MK (2019) Organization of chromatin by intrinsic and regulated phase separation. Cell 179, 470-484. e21. ; Franzmann TM & Alberti S (2019) Protein phase separation as a stress survival strategy. Cold Spring Harb Perspect Biol 11, a034058. ; Li P, Banjade S, Cheng HC, Kim S, Chen B, Guo L, Llaguno M, Hollingsworth JV, King DS, Banani SF et al. (2012) Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336-340. ; Milovanovic D, Wu Y, Bian X & De Camilli P (2018) A liquid phase of synapsin and lipid vesicles. Science 361, 604-607. ; Kilic S, Lezaja A, Gatti M, Bianco E, Michelena J, Imhof R & Altmeyer M (2019) Phase separation of 53BP1 determines liquid-like behavior of DNA repair compartments. EMBO J 38, e101379. ; Alberti S, Gladfelter A & Mittag T (2019) Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell 176, 419-434. ; Alberti S & Dormann D (2019) Liquid-liquid phase separation in disease. Annu Rev Genet 53, 171-194. ; Elbaum-Garfinkle S (2019) Matter over mind: liquid phase separation and neurodegeneration. J Biol Chem 294, 7160-7168. ; Meszaros B, Erdos G, Szabo B, Schad E, Tantos A, Abukhairan R, Horvath T, Murvai N, Kovacs OP, Kovacs M et al. (2019) PhaSePro: the database of proteins driving liquid-liquid phase separation. Nucleic Acids Res 48, D360-D367. ; Ning W, Guo Y, Lin S, Mei B, Wu Y, Jiang P, Tan X, Zhang W, Chen G, Peng D et al. (2020) DrLLPS: a data resource of liquid-liquid phase separation in eukaryotes. Nucleic Acids Res 48, D288-D295. ; Banani SF, Rice AM, Peeples WB, Lin Y, Jain S, Parker R & Rosen MK (2016) Compositional control of phase-separated cellular bodies. Cell 166, 651-663. ; Lin Y, Currie SL & Rosen MK (2017) Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs. J Biol Chem 292, 19110-19120. ; van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT et al. (2014) Classification of intrinsically disordered regions and proteins. Chem Rev 114, 6589-6631. ; Tompa P, Davey NE, Gibson TJ & Babu MM (2014) A million peptide motifs for the molecular biologist. Mol Cell 55, 161-169. ; Wright PE & Dyson HJ (2015) Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol 16, 18-29. ; Mitrea DM, Cika JA, Stanley CB, Nourse A, Onuchic PL, Banerjee PR, Phillips AH, Park CG, Deniz AA & Kriwacki RW (2018) Self-interaction of NPM1 modulates multiple mechanisms of liquid-liquid phase separation. Nat Commun 9, 842. ; Zhang P, Fan B, Yang P, Temirov J, Messing J, Kim HJ & Taylor JP (2019) Chronic optogenetic induction of stress granules is cytotoxic and reveals the evolution of ALS-FTD pathology. Elife, 8. ; Taylor JP, Brown RH Jr & Cleveland DW (2016) Decoding ALS: from genes to mechanism. Nature 539, 197-206. ; Guenther EL, Cao Q, Trinh H, Lu J, Sawaya MR, Cascio D, Boyer DR, Rodriguez JA, Hughes MP & Eisenberg DS (2018) Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation. Nat Struct Mol Biol 25, 463-471. ; Conicella AE, Zerze GH, Mittal J & Fawzi NL (2016) ALS mutations disrupt phase separation mediated by alpha-helical structure in the TDP-43 low-complexity C-terminal domain. Structure 24, 1537-1549. ; Fromm SA, Kamenz J, Noldeke ER, Neu A, Zocher G & Sprangers R (2014) In vitro reconstitution of a cellular phase-transition process that involves the mRNA decapping machinery. Angew Chem Int Ed Engl 53, 7354-7359. ; Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J et al. (2012) Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149, 753-767. ; Burke KA, Janke AM, Rhine CL & Fawzi NL (2015) Residue-by-residue view of in vitro FUS granules that bind the C-terminal domain of RNA polymerase II. Mol Cell 60, 231-241. ; Wang J, Choi JM, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D et al. (2018) A Molecular Grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174, 688-699. e16. ; Bakthavachalu B, Huelsmeier J, Sudhakaran IP, Hillebrand J, Singh A, Petrauskas A, Thiagarajan D, Sankaranarayanan M, Mizoue L, Anderson EN et al. (2018) RNP-granule assembly via ataxin-2 disordered domains is required for long-term memory and neurodegeneration. Neuron 98, 754-766.e4. ; Hanazawa M, Yonetani M & Sugimoto A (2011) PGL proteins self associate and bind RNPs to mediate germ granule assembly in C. elegans. J Cell Biol 192, 929-937. ; Saha S, Weber CA, Nousch M, Adame-Arana O, Hoege C, Hein MY, Osborne-Nishimura E, Mahamid J, Jahnel M, Jawerth L et al. (2016) Polar positioning of phase-separated liquid compartments in cells regulated by an mRNA competition mechanism. Cell 166, 1572-1584. e16. ; Feric M, Vaidya N, Harmon TS, Mitrea DM, Zhu L, Richardson TM, Kriwacki RW, Pappu RV & Brangwynne CP (2016) Coexisting Liquid phases underlie nucleolar subcompartments. Cell 165, 1686-1697. ; Ader C, Frey S, Maas W, Schmidt HB, Gorlich D & Baldus M (2010) Amyloid-like interactions within nucleoporin FG hydrogels. Proc Natl Acad Sci USA 107, 6281-6285. ; Riback JA, Katanski CD, Kear-Scott JL, Pilipenko EV, Rojek AE, Sosnick TR & Drummond DA (2017) Stress-triggered phase separation is an adaptive evolutionarily tuned response. Cell 168, 1028-1040, e19. ; True HL & Lindquist SL (2000) A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature 407, 477-483. ; Yoo H, Triandafillou C & Drummond DA (2019) Cellular sensing by phase separation: using the process, not just the products. J Biol Chem 294, 7151-7159. ; Franzmann TM, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nuske E, Richter D, Baumeister W, Grill SW, Pappu RV et al. (2018) Phase separation of a yeast prion protein promotes cellular fitness. Science 359, eaao5654. ; Zhang Y, Bertulat B, Tencer AH, Ren X, Wright GM, Black J, Cardoso MC & Kutateladze TG (2019) MORC3 forms nuclear condensates through phase separation. iScience 17, 182-189. ; Tress ML, Abascal F & Valencia A (2017) Alternative splicing may not be the key to proteome complexity. Trends Biochem Sci 42, 98-110. ; Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD et al. (2015) Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol Cell 57, 936-947. ; Brady JP, Farber PJ, Sekhar A, Lin YH, Huang R, Bah A, Nott TJ, Chan HS, Baldwin AJ, Forman-Kay JD et al. (2017) Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation. Proc Natl Acad Sci USA 114, E8194-E8203. ; Ambadipudi S, Biernat J, Riedel D, Mandelkow E & Zweckstetter M (2017) Liquid-liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau. Nat Commun 8, 275. ; Kistler KE, Trcek T, Hurd TR, Chen R, Liang FX, Sall J, Kato M & Lehmann R (2018) Phase transitioned nuclear Oskar promotes cell division of Drosophila primordial germ cells. Elife 7, e37949. ; Zeng M, Shang Y, Araki Y, Guo T, Huganir RL & Zhang M (2016) Phase transition in postsynaptic densities underlies formation of synaptic complexes and synaptic plasticity. Cell 166, 1163-1175. e12. ; Su X, Ditlev JA, Hui E, Xing W, Banjade S, Okrut J, King DS, Taunton J, Rosen MK & Vale RD (2016) Phase separation of signaling molecules promotes T cell receptor signal transduction. Science 352, 595-599. ; Fath I, Schweighoffer F, Rey I, Multon MC, Boiziau J, Duchesne M & Tocque B (1994) Cloning of a Grb2 isoform with apoptotic properties. Science 264, 971-974. ; Li C, Peng Q, Wan X, Sun H & Tang J (2017) C-terminal motifs in promyelocytic leukemia protein isoforms critically regulate PML nuclear body formation. J Cell Sci 130, 3496-3506. ; Xiang S, Kato M, Wu LC, Lin Y, Ding M, Zhang Y, Yu Y & McKnight SL (2015) The LC domain of hnRNPA2 adopts similar conformations in hydrogel polymers, liquid-like droplets, and nuclei. Cell 163, 829-839. ; Gueroussov S, Weatheritt RJ, O'Hanlon D, Lin ZY, Narula A, Gingras AC & Blencowe BJ (2017) Regulatory expansion in mammals of multivalent hnRNP assemblies that globally control alternative splicing. Cell. 170, 324-339. e23. ; Deshaies JE, Shkreta L, Moszczynski AJ, Sidibe H, Semmler S, Fouillen A, Bennett ER, Bekenstein U, Destroismaisons L, Toutant J et al. (2018) TDP-43 regulates the alternative splicing of hnRNP A1 to yield an aggregation-prone variant in amyotrophic lateral sclerosis. Brain 141, 1320-1333. ; Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R et al. (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338, 1587-1593. ; Weatheritt RJ, Davey NE & Gibson TJ (2012) Linear motifs confer functional diversity onto splice variants. Nucleic Acids Res 40, 7123-7131. ; Hunter T (2012) Why nature chose phosphate to modify proteins. Philos Trans R Soc Lond B Biol Sci 367, 2513-2516. ; Guillen-Boixet J, Buzon V, Salvatella X & Mendez R (2016) CPEB4 is regulated during cell cycle by ERK2/Cdk1-mediated phosphorylation and its assembly into liquid-like droplets. Elife 5, e19298. ; Monahan Z, Ryan VH, Janke AM, Burke KA, Rhoads SN, Zerze GH, O'Meally R, Dignon GL, Conicella AE, Zheng W et al. (2017) Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity. EMBO J 36, 2951-2967. ; Wang A, Conicella AE, Schmidt HB, Martin EW, Rhoads SN, Reeb AN, Nourse A, Ramirez Montero D, Ryan VH, Rohatgi R et al. (2018) A single N-terminal phosphomimic disrupts TDP-43 polymerization, phase separation, and RNA splicing. EMBO J 37, e97452. ; Tsang B, Arsenault J, Vernon RM, Lin H, Sonenberg N, Wang LY, Bah A & Forman-Kay JD (2019) Phosphoregulated FMRP phase separation models activity-dependent translation through bidirectional control of mRNA granule formation. Proc Natl Acad Sci USA 116, 4218-4227. ; Nonaka T, Suzuki G, Tanaka Y, Kametani F, Hirai S, Okado H, Miyashita T, Saitoe M, Akiyama H, Masai H et al. (2016) Phosphorylation of TAR DNA-binding protein of 43 kDa (TDP-43) by truncated casein Kinase 1delta triggers mislocalization and accumulation of TDP-43. J Biol Chem 291, 5473-5483. ; Drazic A, Myklebust LM, Ree R & Arnesen T (2016) The world of protein acetylation. Biochim Biophys Acta 1864, 1372-1401. ; Saito M, Hess D, Eglinger J, Fritsch AW, Kreysing M, Weinert BT, Choudhary C & Matthias P (2019) Acetylation of intrinsically disordered regions regulates phase separation. Nat Chem Biol 15, 51-61. ; Cohen TJ, Hwang AW, Restrepo CR, Yuan CX, Trojanowski JQ & Lee VM (2015) An acetylation switch controls TDP-43 function and aggregation propensity. Nat Commun 6, 5845. ; Qamar S, Wang G, Randle SJ, Ruggeri FS, Varela JA, Lin JQ, Phillips EC, Miyashita A, Williams D, Strohl F et al. (2018) FUS phase separation is modulated by a molecular chaperone and methylation of arginine cation-pi interactions. Cell 173, 720-734. e15. ; Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R et al. (2018) Tdrd6a regulates the aggregation of buc into functional subcellular compartments that drive germ cell specification. Dev Cell 46, 285-301.e9. ; Ries RJ, Zaccara S, Klein P, Olarerin-George A, Namkoong S, Pickering BF, Patil DP, Kwak H, Lee JH & Jaffrey SR (2019) m(6)A enhances the phase separation potential of mRNA. Nature 571, 424-428. ; Dao TP, Kolaitis RM, Kim HJ, O'Donovan K, Martyniak B, Colicino E, Hehnly H, Taylor JP & Castaneda CA (2018) Ubiquitin modulates liquid-liquid phase separation of UBQLN2 via disruption of multivalent interactions. Mol Cell 69, 965-978. e6. ; Hebron ML, Lonskaya I, Sharpe K, Weerasinghe PP, Algarzae NK, Shekoyan AR & Moussa CE (2013) Parkin ubiquitinates Tar-DNA binding protein-43 (TDP-43) and promotes its cytosolic accumulation via interaction with histone deacetylase 6 (HDAC6). J Biol Chem 288, 4103-4115. ; Rhoads SN, Monahan ZT, Yee DS & Shewmaker FP (2018) The role of post-translational modifications on prion-like aggregation and liquid-phase separation of FUS. Int J Mol Sci 19, e886. ; Dignon GL, Zheng W, Kim YC & Mittal J (2019) Temperature-controlled liquid-liquid phase separation of disordered proteins. ACS Cent Sci 5, 821-830. ; Dumetz AC, Chockla AM, Kaler EW & Lenhoff AM (2008) Protein phase behavior in aqueous solutions: crystallization, liquid-liquid phase separation, gels, and aggregates. Biophys J 94, 570-583. ; Simon CM, Dai Y, Van Alstyne M, Koutsioumpa C, Pagiazitis JG, Chalif JI, Wang X, Rabinowitz JE, Henderson CE, Pellizzoni L et al. (2017) Converging mechanisms of p53 activation drive motor neuron degeneration in spinal muscular atrophy. Cell Rep 21, 3767-3780. ; Koga S, Williams DS, Perriman AW & Mann S (2011) Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model. Nat Chem 3, 720-724. ; Van Lindt J, Bratek-Skicki A, Pakravan D, Van Den Bosch L, Maes D & Tompa P (2019) A generic approach for studying the kinetics of liquid-liquid phase separation under near-native conditions. BioRxiv. http://biorxiv.org/cgi/content/short/563700v563701. “[PREPRINT]”. ; Nakashima KK, Vibhute MA & Spruijt E (2019) Biomolecular chemistry in liquid phase separated compartments. Front Mol Biosci 6, 21. ; Maharana S, Wang J, Papadopoulos DK, Richter D, Pozniakovsky A, Poser I, Bickle M, Rizk S, Guillen-Boixet J, Franzmann TM et al. (2018) RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science 360, 918-921. ; Zhang H, Elbaum-Garfinkle S, Langdon EM, Taylor N, Occhipinti P, Bridges AA, Brangwynne CP & Gladfelter AS (2015) RNA controls PolyQ protein phase transitions. Mol Cell 60, 220-230. ; Milin AN & Deniz AA (2018) Reentrant phase transitions and non-equilibrium dynamics in membraneless organelles. Biochemistry 57, 2470-2477. ; Langdon EM, Qiu Y, Ghanbari Niaki A, McLaughlin GA, Weidmann CA, Gerbich TM, Smith JA, Crutchley JM, Termini CM, Weeks KM et al. (2018) mRNA structure determines specificity of a polyQ-driven phase separation. Science 360, 922-927. ; Elbaum-Garfinkle S, Kim Y, Szczepaniak K, Chen CC, Eckmann CR, Myong S & Brangwynne CP (2015) The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics. Proc Natl Acad Sci USA 112, 7189-7194. ; Mitrea DM, Cika JA, Guy CS, Ban D, Banerjee PR, Stanley CB, Nourse A, Deniz AA & Kriwacki RW (2016) Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA. Elife 5, e13571. ; Boeynaems S, Bogaert E, Kovacs D, Konijnenberg A, Timmerman E, Volkov A, Guharoy M, De Decker M, Jaspers T, Ryan VH et al. (2017) Phase separation of C9orf72 dipeptide repeats perturbs stress granule dynamics. Mol Cell 65, 1044-1055. e5. ; Molliex A, Temirov J, Lee J, Coughlin M, Kanagaraj AP, Kim HJ, Mittag T & Taylor JP (2015) Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell 163, 123-133. ; Kaur T, Alshareedah I, Wang W, Ngo J, Moosa MM & Banerjee PR (2019) Molecular crowding tunes material states of ribonucleoprotein condensates. Biomolecules 9, e71. ; Ghosh A, Mazarakos K & Zhou HX (2019) Three archetypical classes of macromolecular regulators of protein liquid-liquid phase separation. Proc Natl Acad Sci USA 116, 19474-19483. ; Khong A, Matheny T, Jain S, Mitchell SF, Wheeler JR & Parker R (2017) The stress granule transcriptome reveals principles of mrna accumulation in stress granules. Mol Cell 68, 808-820. e5. ; Ciryam P, Lambert-Smith IA, Bean DM, Freer R, Cid F, Tartaglia GG, Saunders DN, Wilson MR, Oliver SG, Morimoto RI et al. (2017) Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS. Proc Natl Acad Sci USA 114, E3935-E3943.
- Contributed Indexing: Keywords: interaction partner; liquid; liquid phase separation; membraneless organelle; phase transition; post-translational modification
- Substance Nomenclature: 0 (Lipid Bilayers) ; 0 (Proteins)
- Entry Date(s): Date Created: 20200222 Date Completed: 20210422 Latest Revision: 20210422
- Update Code: 20231215
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