Recent trends in studies of biomolecular phase separation
2
조회
0
다운로드
2
인용
0
참고문헌
키워드
초록
Biomolecular phase separation has recently attracted broad interest,due to its role in the spatiotemporal compartmentalizationof living cells. It governs the formation, regulation, anddissociation of biomolecular condensates, which play multipleroles in vivo, from activating specific biochemical reactions toorganizing chromatin. Interestingly, biomolecular phase separationseems to be a mainly passive process, which can be explainedby relatively simple physical principles and reproducedin vitro with a minimal set of components. This Mini reviewfocuses on our current understanding of the fundamental principlesof biomolecular phase separation and the recent progressin the research on this topic.
Abstract
Biomolecular phase separation has recently attracted broad interest,due to its role in the spatiotemporal compartmentalizationof living cells. It governs the formation, regulation, anddissociation of biomolecular condensates, which play multipleroles in vivo, from activating specific biochemical reactions toorganizing chromatin. Interestingly, biomolecular phase separationseems to be a mainly passive process, which can be explainedby relatively simple physical principles and reproducedin vitro with a minimal set of components. This Mini reviewfocuses on our current understanding of the fundamental principlesof biomolecular phase separation and the recent progressin the research on this topic.
참고문헌 (75)
- Harmon TS, "Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins", eLife, 6, pp.e30294~ (2017)
- Shin Y, "Liquid phase condensation in cell physiology and disease", Science, 357, pp.eaaf4382~ (2017)
- Ryu JK, "Current understanding of molecular phase separation in chromosomes", Int J Mol Sci, 22, pp.10736~ (2021)
- Banani SF, "Compositional control of phase-separated cellular bodies", Cell, 166, pp.651~663 (2016)
- Feric M, "Coexisting liquid phases underlie nucleolar subcompartments", Cell, 165, pp.1686~1697 (2016)
- Banjade S, "Phase transitions of multivalent proteins can promote clustering of membrane receptors", eLife, 3, pp.e04123~ (2014)
- Kroschwald S, "Gel or Die : phase separation as a survival strategy", Cell, 168, pp.947~948 (2017)
- Riback JA, "Stress-triggered phase separation is an adaptive, evolutionarily tuned response", Cell, 168, pp.1028~1040 (2017)
- Molliex A, "Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization", Cell, 163, pp.123~133 (2015)
- Sheu-Gruttadauria J, "Phase transitions in the assembly and function of human miRISC", Cell, 173, pp.946~957 (2018)
- Xiao Q, "Phase separation in immune signalling", Nat Rev Immunol, 22, pp.188~199 (2022)
- Wippich F, "Dual specificity kinase dyrk3 couples stress granule condensation", dissolution to mTORC1 signaling, 2013, pp.152, 791~805
- Fujioka Y, "Phase separation organizes the site of autophagosome formation", Nature, 578, pp.301~305 (2020)
- Nicolas E, "Involvement of human ribosomal proteins in nucleolar structure and p53-dependent nucleolar stress", Nat Commun, 7, pp.11390~ (2016)
- Cho WK, "Mediator and RNA polymerase II clusters associate in transcriptiondependent condensates", Science, 361, pp.412~415 (2018)
- Boyko S, "Tau liquid–liquid phase separation in neurodegenerative diseases", Trends Cell Biol, 32, pp.611~623 (2022)
- Wang B, "Liquid–liquid phase separation in human health and diseases", Signal Transduct Target Ther, 6, pp.290~ (2021)
- Alberti S, "Liquid–liquid phase separation in disease", Ann Rev Genet, 53, pp.171~194 (2019)
- Brangwynne Clifford P, "Polymer physics of intracellular phase transitions", Nat Phys, 11, pp.899~904 (2015)
- Flory PJ, "Thermodynamics of high polymer solutions", J Chem Phys, 10, pp.51~61 (1942)
- Hyman AA, "Liquidliquid phase separation in biology", Annu Rev Cell Dev Biol, 30, pp.39~58 (2014)
- Dolgin E, "What lava lamps and vinaigrette can teach us about cell biology", Nature, 555, pp.300~303 (2018)
- Martin EW, "Valence and patterning of aromatic residues determine the phase behavior of prion-like domains", Science, 367, pp.694~699 (2020)
- Wang J, "A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins", Cell, 174, pp.688~699 (2018)
- Rubinstein M, "Thermoreversible gelation in solutions of associating polymers. 2. Linear dynamics", Macromolecules, 31, pp.1386~1397 (1998)
- Choi J-M, "Generalized models for bond percolation transitions of associative polymers", Phys Rev E, 102, pp.042403~ (2020)
- Huggins ML, "Theory of solutions of high polymers1", J Am Chem Soc, 64, pp.1712~1719 (1942)
- Banani SF, "Biomolecular condensates : organizers of cellular biochemistry", Nat Rev Mol Cell Biol, 18, pp.285~298 (2017)
- Choi J-M, "Physical principles underlying the complex biology of intracellular phase transitions", Annu Rev Biophys, 49, pp.107~133 (2020)
- Jia P, "ZMYND8 mediated liquid condensates spatiotemporally decommission the latent superenhancers during macrophage polarization", Nat Commun, 12, pp.6535~ (2021)
- Zhang H, "Liquid-liquid phase separation in biology : mechanisms, physiological functions and human diseases", Sci China Life Sci, 63, pp.953~985 (2020)
- Paloni M, "Unraveling molecular interactions in liquid–liquid phase separation of disordered proteins by atomistic simulations", J Phys Chem B, 124, pp.9009~9016 (2020)
- Bremer A, "Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains", Nat Chem, 14, pp.196~207 (2022)
- Buchan JR, "Eukaryotic stress granules : the ins and outs of translation", Mol Cell, 36, pp.932~941 (2009)
- Fong K, "Whole-genome screening identifies proteins localized to distinct nuclear bodies", J Cell Biol, 203, pp.149~164 (2013)
- Song D, "Client proximity enhancement inside cellular membrane-less compartments governed by client-compartment interactions", Nat Commun, 11, pp.1~13 (2020)
- RuffKM, "Ligand effects on phase separation of multivalent macromolecules", Proc Natl Acad Sci U S A, 118, pp.10~ (2021)
- Rhine K, "RNA droplets", Annu Rev Biophys, 49, pp.247~265 (2020)
- Roden C, "RNA contributions to the form and function of biomolecular condensates", Nat Rev Mol Cell Biol, 22, pp.183~195 (2021)
- Wei MT, "Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles", Nat Chem, 9, pp.1118~1125 (2017)
- Le Vay K, "Enhanced ribozyme-catalyzed recombination and oligonucleotide assembly in peptide-RNA condensates", Angew Chem Int Ed, 60, pp.26096~26104 (2021)
- Grese ZR, "Specific RNA interactions promote TDP-43 multivalent phase separation and maintain liquid properties", EMBO Rep, 22, pp.e53632~ (2021)
- Shao W, "Phase separation of RNA-binding protein promotes polymerase binding and transcription", Nat Chem Biol, 18, pp.70~80 (2022)
- Li P, "Phase transitions in the assembly of multivalent signalling proteins", Nature, 483, pp.336~340 (2012)
- Azaldegui CA, "The emergence of phase separation as an organizing principle in bacteria", Biophys J, 120, pp.1123~1138 (2021)
- Fritsch AW, "Local thermodynamics govern formation and dissolution of Caenorhabditis elegans P granule condensates", Proc Natl Acad Sci U S A, 118, pp.e2102772118~ (2021)
- Hong K, "Behavior control of membrane-less protein liquid condensates with metal ioninduced phase separation", Nat Commun, 11, pp.5554~ (2020)
- Zbinden A, "Phase separation and neurodegenerative diseases : a disturbance in the force", Dev Cell, 55, pp.45~68 (2020)
- Wang B, "Liquid-liquid phase separation in human health and diseases", Signal Transduct Target Ther, 6, pp.290~290 (2021)
- Lednev IK, "Amyloid fibrils : the eighth wonder of the world in protein folding and aggregation", Biophys J, 106, pp.1433~1435 (2014)
- Malki A, "Intrinsically disordered tardigrade proteins self-assemble into fibrous gels in response to environmental stress", Angew Chem Int Ed, 61, pp.e202109961~ (2022)
- Shen C, "Phase separation drives RNA virus-induced activation of the NLRP6 inflammasome", Cell, 184, pp.5759~5774 (2021)
- Bergeron-Sandoval LP, "Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling", Proc Natl Acad Sci U S A, 118, pp.e2113789118~ (2021)
- Zhu P, "Cold-induced Arabidopsis FRIGIDA nuclear condensates for FLC repression", Nature, 599, pp.657~661 (2021)
- Sun M, "NuMA regulates mitotic spindle assembly, structural dynamics and function via phase separation", Nat Commun, 12, pp.7157~ (2021)
- Babl L, "CTP-controlled liquid–liquid phase separation of ParB", J Mol Biol, 434, pp.167401~ (2022)
- Hnisz D, "A phase separation model for transcriptional control", Cell, 169, pp.13~23 (2017)
- Palacio M, "Merging established mechanisms with new insights : condensates, hubs, and the regulation of rna polymerase II transcription", J Mol Biol, 434, pp.167216~ (2022)
- Pérez-Schindler J, "RNA-bound PGC-1α controls gene expression in liquidlike nuclear condensates", Proc Natl Acad Sci U S A, 118, pp.e2105951118~ (2021)
- Shi Y, "Formation of nuclear condensates by the mediator complex subunit Med15 in mammalian cells", BMC Biol, 19, pp.245~ (2021)
- Kim GH, "Distinct roles of hnRNPH1low-complexity domains in splicing and transcription", Proc Natl Acad Sci U S A, 118, pp.e2109668118~ (2021)
- Lee R, "CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates", Nucleic Acid Res, 50, pp.207~226 (2022)
- Long Q, "Phase separation drives the self-assembly of mitochondrial nucleoids for transcriptional modulation", Nat Struct Mol Biol, 28, pp.900~908 (2021)
- Hallegger M, "TDP-43condensation properties specify its RNA-binding and regulatory repertoire", Cell, 184, pp.4680~4696 (2021)
- Sawner AS, "Modulating α-synuclein liquid–liquid phase separation", Biochemistry, 60, pp.3676~3696 (2021)
- Ishiguro A, "ALS-linked FUS mutations dysregulate G-quadruplexdependent liquid–liquid phase separation and liquid-tosolid transition", J Biol Chem, 297, pp.101284~ (2021)
- Wurtz JD, "Chemical-reaction-controlled phase separated drops : formation, size selection, and coarsening", Phys Rev Lett, 120, pp.078102~ (2018)
- Folkmann AW, "Regulation of biomolecular condensates by interfacial protein clusters", Science, 373, pp.1218~1224 (2021)
- Qi Y, "Chromatin network retards nucleoli coalescence", Nat Commun, 12, pp.6824~ (2021)
- Abbas M, "A short peptide synthon for liquid–liquid phase separation", Nat Chem, 13, pp.1046~1054 (2021)
- Scott WA, "Active controlled and tunable coacervation using side-chain functional α-helical homopolypeptides", J Am Chem Soc, 143, pp.18196~18203 (2021)
- Lee T, "The flexibility-based modulation of DNA nanostar phase separation", Nanoscale, 13, pp.17638~17647 (2021)
- Sato Y, "Capsule-like DNA hydrogels with patterns formed by lateral phase separation of DNA nanostructures", J Am Chem Soc Au, 2, pp.159~168 (2022)
- Agarwal A, "An intrinsically disordered pathological prion variant Y145Stop converts into self-seeding amyloids via liquidliquid phase separation", Proc Natl Acad Sci U S A, 118, pp.e2100968118~ (2021)
- Liu Q, "Glycogen accumulation and phase separation drives liver tumor initiation", Cell, 184, pp.5559~5576 (2021)
