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Biomolecular Condensates: Structure, Functions, Methods of Research

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Abstract

The term “biomolecular condensates” is used to describe membraneless compartments in eukaryotic cells, accumulating proteins and nucleic acids. Biomolecular condensates are formed as a result of liquid–liquid phase separation (LLPS). Often, they demonstrate properties of liquid-like droplets or gel-like aggregates; however, some of them may appear to have a more complex structure and high-order organization. Membraneless microcompartments are involved in diverse processes both in cytoplasm and in nucleus, among them ribosome biogenesis, regulation of gene expression, cell signaling, and stress response. Condensates properties and structure could be highly dynamic and are affected by various internal and external factors, e.g., concentration and interactions of components, solution temperature, pH, osmolarity, etc. In this review, we discuss variety of biomolecular condensates and their functions in live cells, describe their structure variants, highlight domain and primary sequence organization of the constituent proteins and nucleic acids. Finally, we describe current advances in methods that characterize structure, properties, morphology, and dynamics of biomolecular condensates in vitro and in vivo.

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Fig. 1.
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Abbreviations

ER:

endoplasmic reticulum

IDR:

intrinsically disordered regions

LCD:

low complexity domains

LLPS:

liquid–liquid phase separation

RNP:

ribonucleoprotein

References

  1. Nelson, D., and Cox, M. (2012) Lehninger Principles of Biochemistry [in Russian], BINOM, Laboratoriya Znaniy, Moscow, p. 694.

  2. Hyman, A. A., Weber, C. A., and Jülicher, F. (2014) Liquid-liquid phase separation in biology, Annu. Rev. Cell Dev. Biol., 30, 39-58, https://doi.org/10.1146/annurev-cellbio-100913-013325.

    Article  CAS  PubMed  Google Scholar 

  3. Bogolyubov, D. S. (2019) Membrane-less organelles of the eucaryotic cell: basic concepts and principles of formation [in Russian], Tsytology, 61, 683-703, https://doi.org/10.1134/S0041377119090049.

    Article  Google Scholar 

  4. Banani, S. F., Lee, H. O., Hyman, A. A., and Rosen, M. K. (2017) Biomolecular condensates: organizers of cellular biochemistry, Nat. Rev. Mol. Cell Biol., 18, 285-298, https://doi.org/10.1038/nrm.2017.7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Martin, E. W., Holehouse, A. S., Peran, I., Farag, M., Incicco, J. J., and Bremer, A. (1979) Valence and patterning of aromatic residues determine the phase behavior of prion-like domains, Science, 367, 694-699, https://doi.org/10.1126/science.aaw8653.

    Article  CAS  ADS  Google Scholar 

  6. Alberti, S., Gladfelter, A., and Mittag, T. (2019) Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates, Cell, 176, 419-434, https://doi.org/10.1016/j.cell.2018.12.035.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Harmon, T. S., Holehouse, A. S., Rosen, M. K., and Pappu, R. V. (2017) Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins, Elife, 6, e30294, https://doi.org/10.7554/eLife.30294.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Alberti, S., and Hyman, A. A. (2021) Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing, Nat. Rev. Mol. Cell Biol., 22, 196-213, https://doi.org/10.1038/s41580-020-00326-6.

    Article  CAS  PubMed  Google Scholar 

  9. Brangwynne, C. P. (2013) Phase transitions and size scaling of membrane-less organelles, J. Cell Biol., 203, 875-681, https://doi.org/10.1083/jcb.201308087.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Munder, M. C., Midtvedt, D., Franzmann, T., Nüske, E., Otto, O., and Herbig, M. (2016) A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy, Elife, 5, e09347, https://doi.org/10.7554/eLife.09347.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Wolf, N., Priess, J., and Hirsh, D. (1983) Segregation of germline granules in early embryos of Caenorhabditis elegans: an electron microscopic analysis, J. Embryol. Exp. Morph., 73, 297-306, https://doi.org/10.1242/dev.73.1.297.

    Article  CAS  PubMed  Google Scholar 

  12. Strome, S., and Wood, W. B. (1983) Generation of asymmetry and segregation of germ-line granules in early C. elegans embryos, Cell, 35, 15-25, https://doi.org/10.1016/0092-8674(83)90203-9.

    Article  CAS  PubMed  Google Scholar 

  13. Updike, D., and Strome, S. (2010) P granule assembly and function in Caenorhabditis elegans germ cells, J. Androl., 31, 53-60, https://doi.org/10.2164/jandrol.109.008292.

    Article  CAS  PubMed  Google Scholar 

  14. Brangwynne, C. P., Eckmann, C. R., Courson, D. S., Rybarska, A., Hoege, C., and Gharakhani, J. (2009) Germline P Granules are liquid droplets that localize by controlled dissolution/condensation, Science, 324, 1729-1732, https://doi.org/10.1126/science.1172046.

    Article  CAS  PubMed  ADS  Google Scholar 

  15. Brangwynne, C. P., Mitchison, T. J., and Hyman, A. A. (2011) Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes, Proc. Natl. Acad. Sci. USA, 108, 4334-4339, https://doi.org/10.1073/pnas.1017150108.

    Article  PubMed  PubMed Central  ADS  Google Scholar 

  16. McSwiggen, D. T., Mir, M., Darzacq, X., and Tjian, R. (2019) Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences, Genes Dev., 33, 1619-1634, https://doi.org/10.1101/gad.331520.119.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Yang, P., Mathieu, C., Kolaitis, R. M., Zhang, P., Messing, J., and Yurtsever, U. (2020) G3BP1 is a tunable switch that triggers phase separation to assemble stress granules, Cell, 181, 325-345.e28, https://doi.org/10.1016/j.cell.2020.03.046.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Riback, J. A., Katanski, C. D., Kear-Scott, J. L., Pilipenko, E. V., Rojek, A. E., and Sosnick, T. R. (2017) Stress-triggered phase separation is an adaptive, evolutionarily tuned response, Cell, 168, 1028-1040.e19, https://doi.org/10.1016/j.cell.2017.02.027.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kroschwald, S., Munder, M. C., Maharana, S., Franzmann, T. M., Richter, D., and Ruer, M. (2018) Different material states of pub1 condensates define distinct modes of stress adaptation and recovery, Cell Rep., 23, 3327-3339, https://doi.org/10.1016/j.celrep.2018.05.041.

    Article  CAS  PubMed  Google Scholar 

  20. Ivanov, P., Kedersha, N., and Anderson, P. (2019) Stress granules and processing bodies in translational control, Cold Spring Harb. Perspect. Biol., 11, a032813, https://doi.org/10.1101/cshperspect.a032813.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kroschwald, S., Maharana, S., Mateju, D., Malinovska, L., Nüske, E., and Poser, I. (2015) Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules, Elife, 4, e06807, https://doi.org/10.7554/eLife.06807.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Rao, B. S., and Parker, R. (2017) Numerous interactions act redundantly to assemble a tunable size of P bodies in Saccharomyces cerevisiae, Proc. Natl. Acad. Sci. USA, 114, E9569-E9578, https://doi.org/10.1073/pnas.1712396114.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  23. Luo, Y., Na, Z., and Slavoff, S. A. (2018) P-bodies: composition, properties, and functions, Biochemistry, 57, 2424-2431, https://doi.org/10.1021/acs.biochem.7b01162.

    Article  CAS  PubMed  Google Scholar 

  24. Latonen, L. (2019) Phase-to-phase with nucleoli – stress responses, protein aggregation and novel roles of RNA, Front. Cell. Neurosci., 13, 151, https://doi.org/10.3389/fncel.2019.00151.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Khodyuchenko, T. A., and Krasikova, A. V. (2014) Cajal bodies and Histon locus bodies: molecular composition and functions [in Russian], Ontogenez, 45, 363-379, https://doi.org/10.7868/S0475145014060068.

    Article  Google Scholar 

  26. Sawyer, I. A., Bartek, J., and Dundr, M. (2019) Phase separated microenvironments inside the cell nucleus are linked to disease and regulate epigenetic state, transcription and RNA processing, Semin. Cell Dev. Biol., 90, 94-103, https://doi.org/10.1016/j.semcdb.2018.07.001.

    Article  CAS  PubMed  Google Scholar 

  27. Taliansky, M. E., Love, A. J., Kołowerzo-Lubnau, A., and Smoliński, D. J. (2023) Cajal bodies: evolutionarily conserved nuclear biomolecular condensates with properties unique to plants, Plant Cell, 35, 3214-3235, https://doi.org/10.1093/plcell/koad140.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Ilik, İ. A., Malszycki, M., Lübke, A. K., Schade, C., Meierhofer, D., and Aktaş, T. (2020) SON and SRRM2 are essential for nuclear speckle formation, Elife, 9, e60579, https://doi.org/10.7554/eLife.60579.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Dion, W., Balance, H., Lee, J., Pan, Y., Irfan, S., and Edwards, C. (2022) Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis, Sci. Adv., 8, eabl4150, https://doi.org/10.1126/sciadv.abl4150.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  30. Hur, W., Kemp, J. P., Tarzia, M., Deneke, V. E., Marzluff, W. F., and Duronio, R. J. (2020) CDK-regulated phase separation seeded by Histone genes ensures precise growth and function of histone locus bodies, Dev. Cell, 54, 379-394.e6, https://doi.org/10.1016/j.devcel.2020.06.003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Larson, A. G., Elnatan, D., Keenen, M. M., Trnka, M. J., Johnston, J. B., Burlingame, A. L. (2017) Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin, Nature, 547, 236-240, https://doi.org/10.1038/nature22822.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  32. Tang, S. C., Vijayakumar, U., Zhang, Y., and Fullwood, M. J. (2022) Super-enhancers, phase-separated condensates, and 3D genome organization in cancer, Cancers (Basel), 14, 2866, https://doi.org/10.3390/cancers14122866.

    Article  CAS  PubMed  Google Scholar 

  33. Nag, N., Sasidharan, S., Uversky, V. N., Saudagar, P., and Tripathi, T. (2022) Phase separation of FG-nucleoporins in nuclear pore complexes, Biochim. Biophys. Acta Mol. Cell Res., 1869, 119205, https://doi.org/10.1016/j.bbamcr.2021.119205.

    Article  CAS  PubMed  Google Scholar 

  34. Woodruff, J. B., Ferreira Gomes, B., Widlund, P. O., Mahamid, J., Honigmann, A., and Hyman, A. A. (2017) The centrosome is a selective condensate that nucleates microtubules by concentrating tubulin, Cell, 169, 1066-1077.e10, https://doi.org/10.1016/j.cell.2017.05.028.

    Article  CAS  PubMed  Google Scholar 

  35. Su, X., Ditlev, J. A., Hui, E., Xing, W., Banjade, S., and Okrut, J. (2016) Phase separation of signaling molecules promotes T cell receptor signal transduction, Science, 352, 595-599, https://doi.org/10.1126/science.aad9964.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  36. Case, L. B., Ditlev, J. A., and Rosen, M. K. (2019) Regulation of transmembrane signaling by phase separation, Annu. Rev. Biophys., 48, 465-494, https://doi.org/10.1146/annurev-biophys-052118-115534.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Lin, C. C., Suen, K. M., Jeffrey, P. A., Wieteska, L., Lidster, J. A., and Bao, P. (2022) Receptor tyrosine kinases regulate signal transduction through a liquid-liquid phase separated state, Mol. Cell, 82, 1089-1106.e12, https://doi.org/10.1016/j.molcel.2022.02.005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Sołtys, K., Tarczewska, A., Bystranowska, D., and Sozańska, N. (2022) Getting closer to decrypting the phase transitions of bacterial biomolecules, Biomolecules, 12, 907, https://doi.org/10.3390/biom12070907.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Yeong, V., Werth, E. G., Brown, L. M., and Obermeyer, A. C. (2020) Formation of biomolecular condensates in bacteria by tuning protein electrostatics, ACS Cent. Sci., 6, 2301-2310, https://doi.org/10.3390/biom12070907.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Emenecker, R. J., Holehouse, A. S., and Strader, L. C. (2020) Emerging roles for phase separation in plants, Dev. Cell, 55, 69-83, https://doi.org/10.1016/j.devcel.2020.09.010.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Strom, A. R., Emelyanov, A. V., Mir, M., Fyodorov, D. V., Darzacq, X., and Karpen, G. H. (2017) Phase separation drives heterochromatin domain formation, Nature, 547, 241-245, https://doi.org/10.1038/nature22989.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  42. Zhang, L., Geng, X., Wang, F., Tang, J., Ichida, Y., and Sharma, A. (2022) 53BP1 regulates heterochromatin through liquid phase separation, Nat. Commun., 13, 1088, https://doi.org/10.1038/s41467-022-28019-y.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  43. Wang, L., Hu, M., Zuo, M. Q., Zhao, J., Wu, D., and Huang, L. (2020) Rett syndrome-causing mutations compromise MeCP2-mediated liquid–liquid phase separation of chromatin, Cell Res., 30, 393-407, https://doi.org/10.1038/s41422-020-0288-7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Pandya-Jones, A., Markaki, Y., Serizay, J., Chitiashvili, T., Mancia Leon, W. R., and Damianov, A. (2020) A protein assembly mediates Xist localization and gene silencing, Nature, 587, 145-151, https://doi.org/10.1038/s41586-020-2703-0.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  45. Wang, Y. L., Zhao, W. W., Bai, S. M., Feng, L. L., Bie, S. Y., and Gong, L. (2022) MRNIP condensates promote DNA double-strand break sensing and end resection, Nat. Commun., 13, 2638, https://doi.org/10.1038/s41467-022-30303-w.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  46. Pessina, F., Giavazzi, F., Yin, Y., Gioia, U., Vitelli, V., and Galbiati, A. (2019) Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors, Nat. Cell Biol., 21, 1286-1299, https://doi.org/10.1038/s41556-019-0392-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Dall’Agnese, G., Dall’Agnese, A., Banani, S. F., Codrich, M., Malfatti, M. C., and Antoniali, G. (2023) Role of condensates in modulating DNA repair pathways and its implication for chemoresistance, J. Biol. Chem., 299, 104800, https://doi.org/10.1016/j.jbc.2023.104800.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Spegg, V., and Altmeyer, M. (2021) Biomolecular condensates at sites of DNA damage: more than just a phase, DNA Repair (Amst), 106, 103179, https://doi.org/10.1016/j.dnarep.2021.103179.

    Article  CAS  PubMed  Google Scholar 

  49. Jiang, L., Shao, C., Wu, Q. J., Chen, G., Zhou, J., and Yang, B. (2017) NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing, Nat. Struct. Mol. Biol., 24, 816-824, https://doi.org/10.1038/nsmb.3455.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Fox, A. H., Nakagawa, S., Hirose, T., and Bond, C. S. (2018) Paraspeckles: where long noncoding RNA meets phase separation, Trends Biochem. Sci., 43, 124-135, https://doi.org/10.1016/j.tibs.2017.12.001.

    Article  CAS  PubMed  Google Scholar 

  51. West, J. A., Mito, M., Kurosaka, S., Takumi, T., Tanegashima, C., and Chujo, T. (2016) Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization, J. Cell Biol., 214, 817-830, https://doi.org/10.1083/jcb.201601071.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Pollock, C., and Huang, S. (2010) The perinucleolar compartment, Cold Spring Harb. Perspect. Biol., 2, a000679, https://doi.org/10.1101/cshperspect.a000679.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Do Amaral, M. J., de Andrade Rosa, I., Andrade, S. A., Fang, X., Andrade, L. R., and Costa, M. L. (2022) The perinuclear region concentrates disordered proteins with predicted phase separation distributed in a 3D network of cytoskeletal filaments and organelles, Biochim. Biophys. Acta Mol. Cell Res., 1869, 119161, https://doi.org/10.1016/j.bbamcr.2021.119161.

    Article  CAS  PubMed  Google Scholar 

  54. Nathanailidou, P., Taraviras, S., and Lygerou, Z. (2020) DNA replication control: liquid-liquid phase separation comes into play, J. Mol. Biochem., 9, 54-56.

    PubMed  PubMed Central  Google Scholar 

  55. Parker, M. W., Bell, M., Mir, M., Kao, J. A., Darzacq, X., and Botchan, M. R. (2019) A new class of disordered elements controls DNA replication through initiator self-assembly, Elife, 8, e48562, https://doi.org/10.7554/eLife.48562.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Parker, M. W., Kao, J. A., Huang, A., Berger, J. M., and Botchan, M. R. (2021) Molecular determinants of phase separation for Drosophila DNA replication licensing factors, Elife, 10, e70535, https://doi.org/10.7554/eLife.70535.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Liu, S., Wang, T., Shi, Y., Bai, L., Wang, S., and Guo, D. (2021) USP42 drives nuclear speckle mRNA splicing via directing dynamic phase separation to promote tumorigenesis, Cell Death Differ., 28, 2482-2498, https://doi.org/10.1038/s41418-021-00763-6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Sabari, B. R., Dall’Agnese, A., Boija, A., Klein, I. A., Coffey, E. L., and Shrinivas, K. (2018) Coactivator condensation at super-enhancers links phase separation and gene control, Science, 361, eaar3958, https://doi.org/10.1126/science.aar3958.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Coffey, E. L (2021) Biomolecular Condensates in Transcriptional Regulation: Ph. D. Thesis, Massachusetts Institute of Technology, Cambridge, Massachussets, p. 125.

  60. Jack, A., Kim, Y., Strom, A. R., Lee, D. S. W., Williams, B., and Schaub, J. M. (2022) Compartmentalization of telomeres through DNA-scaffolded phase separation, Dev. Cell, 57, 277-290.e9, https://doi.org/10.1016/j.devcel.2021.12.017.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Navascues, J., Berciano, M. T., Tucker, K. E., Lafarga, M., and Matera, A. G. (2004) Targeting SMN to Cajal bodies and nuclear gems during neuritogenesis, Chromosoma, 112, 398-409, https://doi.org/10.1007/s00412-004-0285-5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Nesterov, S. V., Ilyinsky, N. S., and Uversky, V. N. (2021) Liquid-liquid phase separation as a common organizing principle of intracellular space and biomembranes providing dynamic adaptive responses, Biochim. Biophys. Acta Mol. Cell Res., 1868, 119102, https://doi.org/10.1016/j.bbamcr.2021.119102.

    Article  CAS  PubMed  Google Scholar 

  63. Hampoelz, B., Schwarz, A., Ronchi, P., Bragulat-Teixidor, H., Tischer, C., and Gaspar, I. (2019) Nuclear pores assemble from nucleoporin condensates during oogenesis, Cell, 179, 671-686.e17, https://doi.org/10.1016/j.cell.2019.09.022.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Yoshizawa, T., and Guo, L. (2021) Karyopherin-βs play a key role as a phase separation regulator, J. Biochem., 170, 15-23, https://doi.org/10.1093/jb/mvab072.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Feric, M., Vaidya, N., Harmon, T. S., Mitrea, D. M., Zhu, L., and Richardson, T. M. (2016) Coexisting liquid phases underlie nucleolar subcompartments, Cell, 165, 1686-1697, https://doi.org/10.1016/j.cell.2016.04.047.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Pombo, A. (1998) Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle, EMBO J., 17, 1768-1778, https://doi.org/10.1093/emboj/17.6.1768.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Harrigan, J. A., Belotserkovskaya, R., Coates, J., Dimitrova, D. S., Polo, S. E., and Bradshaw, C. R. (2011) Replication stress induces 53BP1-containing OPT domains in G1 cells, J. Cell Biol., 193, 97-108, https://doi.org/10.1083/jcb.201011083.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Seif, E., Kang, J. J., Sasseville, C., Senkovich, O., Kaltashov, A., and Boulier, E. L. (2020) Phase separation by the polyhomeotic sterile alpha motif compartmentalizes Polycomb Group proteins and enhances their activity, Nat. Commun., 11, 5609, https://doi.org/10.1038/s41467-020-19435-z.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  69. Guo, Y., Zhao, S., and Wang, G. G. (2021) Polycomb gene silencing mechanisms: PRC2 chromatin targeting, H3K27me3 “Readout”, and phase separation-based compaction, Trends Genet., 37, 547-565, https://doi.org/10.1016/j.tig.2020.12.006.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Guo, Y., and Wang, G. G. (2022) Modulation of the high-order chromatin structure by Polycomb complexes, Front. Cell Dev. Biol., 10, 1021658, https://doi.org/10.3389/fcell.2022.1021658.

    Article  PubMed  PubMed Central  Google Scholar 

  71. Corpet, A., Kleijwegt, C., Roubille, S., Juillard, F., Jacquet, K., and Texier, P. (2020) PML nuclear bodies and chromatin dynamics: catch me if you can! Nucleic Acids Res., 48, 11890-11912, https://doi.org/10.1093/nar/gkaa828.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Wu, W., Tan, Y., Yin, H., Jiang, M., Jiang, Y., and Ma, X. (2023) Phase separation is required for PML nuclear body biogenesis and function, FASEB J., 37, e22986, https://doi.org/10.1096/fj.202300216R.

    Article  CAS  PubMed  Google Scholar 

  73. Lallemand-Breitenbach, V., and de Thé, H. (2010) PML nuclear bodies, Cold Spring Harb. Perspect. Biol., 2, a000661, doi: 10.1101/cshperspect.a000661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Kim, S., Kalappurakkal, J. M., Mayor, S., and Rosen, M. K. (2019) Phosphorylation of nephrin induces phase separated domains that move through actomyosin contraction, Mol. Biol. Cell, 30, 2996-3012, https://doi.org/10.1091/mbc.E18-12-0823.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Banjade, S., and Rosen, M. K. (2014) Phase transitions of multivalent proteins can promote clustering of membrane receptors, Elife, 3, e04123, https://doi.org/10.7554/eLife.04123.

    Article  PubMed  PubMed Central  Google Scholar 

  76. Baymiller, M., and Moon, S. L. (2023) Stress granules as causes and consequences of translation suppression, Antioxid. Redox Signal., 39, 390-409, https://doi.org/10.1089/ars.2022.0164.

    Article  CAS  PubMed  Google Scholar 

  77. Grousl, T., Vojtova, J., Hasek, J., and Vomastek, T. (2022) Yeast stress granules at a glance, Yeast, 39, 247-261, https://doi.org/10.1002/yea.3681.

    Article  CAS  PubMed  Google Scholar 

  78. Decker, C. J., and Parker, R. (2012) P-bodies and stress granules: possible roles in the control of translation and mRNA degradation, Cold Spring Harb. Perspect. Biol., 4, a012286, https://doi.org/10.1101/cshperspect.a012286.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Grimes, B., Jacob, W., Liberman, A. R., Kim, N., Zhao, X., and Masison, D. C. (2023) The properties and domain requirements for phase separation of the Sup35 prion protein in vivo, Biomolecules, 13, 1370, https://doi.org/10.3390/biom13091370.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Nunes, C., Mestre, I., Marcelo, A., Koppenol, R., Matos, C. A., and Nóbrega, C. (2019) MSGP: the first database of the protein components of the mammalian stress granules, Database (Oxford), 2019, baz031, https://doi.org/10.1093/database/baz031.

    Article  CAS  PubMed  Google Scholar 

  81. Deis, R., and Elkouby, Y. M. (2022) Microtubules control Buc phase separation and Balbiani body condensation in zebrafish oocyte polarity, bioRxiv, https://doi.org/10.1101/2022.03.11.484019.

    Article  Google Scholar 

  82. Boke, E., Ruer, M., Wühr, M., Coughlin, M., Lemaitre, R., Gygi, S. P., Alberti, S., Drechsel, D., Hyman, A. A., and Mitchison, T. J. (2016) Amyloid-like self-assembly of a cellular compartment, Cell, 166, 637-650, https://doi.org/10.1016/j.cell.2016.06.051.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Nott, T. J., Petsalaki, E., Farber, P., Jervis, D., Fussner, E., and Plochowietz, A. (2015) Phase transition of a disordered Nuage protein generates environmentally responsive membraneless organelles, Mol. Cell, 57, 936-947, https://doi.org/10.1016/j.molcel.2015.01.013.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Pushpalatha, K. V., and Besse, F. (2019) Local translation in axons: when membraneless RNP granules meet membrane-bound organelles, Front. Mol. Biosci., 6, 129, https://doi.org/10.3389/fmolb.2019.00129.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Zwicker, D., Decker, M., Jaensch, S., Hyman, A. A., and Jülicher, F. (2014) Centrosomes are autocatalytic droplets of pericentriolar material organized by centrioles, Proc. Natl. Acad. Sci. USA, 111, E2636-E2645, https://doi.org/10.1073/pnas.1404855111.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  86. Patel, P. H., Barbee, S. A., and Blankenship, J. T. (2016) GW-bodies and P-bodies constitute two separate pools of sequestered non-translating RNAs, PLoS One, 11, e0150291, https://doi.org/10.1371/journal.pone.0150291.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Putnam, A., Cassani, M., Smith, J., and Seydoux, G. (2019) A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos, Nat. Struct. Mol. Biol., 26, 220-226, https://doi.org/10.1038/s41594-019-0193-2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Smith, J., Calidas, D., Schmidt, H., Lu, T., Rasoloson, D., and Seydoux, G. (2016) Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3, Elife, 5, e21337, https://doi.org/10.7554/eLife.21337.

    Article  PubMed  PubMed Central  Google Scholar 

  89. Buckingham, M., and Liu, J. L. (2011) U bodies respond to nutrient stress in Drosophila, Exp. Cell Res., 317, 2835-2844, https://doi.org/10.1016/j.yexcr.2011.09.001.

    Article  CAS  PubMed  Google Scholar 

  90. Liu, J. L., and Gall, J. G. (2007) U bodies are cytoplasmic structures that contain uridine-rich small nuclear ribonucleoproteins and associate with P bodies, Proc. Natl. Acad. Sci. USA, 104, 11655-11659, https://doi.org/10.1073/pnas.0704977104.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  91. Tsalikis, J., Tattoli, I., Ling, A., Sorbara, M. T., Croitoru, D. O., and Philpott, D. J. (2015) Intracellular bacterial pathogens trigger the formation of U small nuclear RNA bodies (U Bodies) through metabolic stress induction, J. Biol. Chem., 290, 20904-20918, https://doi.org/10.1074/jbc.M115.659466.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Franzmann, T. M., Jahnel, M., Pozniakovsky, A., Mahamid, J., Holehouse, A. S., and Nüske, E. (2018) Phase separation of a yeast prion protein promotes cellular fitness, Science, 359, eaao5654, https://doi.org/10.1126/science.aao5654.

    Article  CAS  PubMed  Google Scholar 

  93. Du, M., and Chen, Z. J. (2018) DNA-induced liquid phase condensation of cGAS activates innate immune signaling, Science, 361, 704-709, https://doi.org/10.1126/science.aat1022.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  94. Ladbury, J. E., Lin, C. C., and Suen, K. M. (2023) Phase separation enhances probability of receptor signalling and drug targeting, Trends Biochem. Sci., 48, 428-436, https://doi.org/10.1016/j.tibs.2023.01.005.

    Article  CAS  PubMed  Google Scholar 

  95. Jalihal, A. P., Schmidt, A., Gao, G., Little, S. R., Pitchiaya, S., and Walter, N. G. (2021) Hyperosmotic phase separation: condensates beyond inclusions, granules and organelles, J. Biol. Chem., 296, 100044, https://doi.org/10.1074/jbc.REV120.010899.

    Article  CAS  PubMed  Google Scholar 

  96. Ambadipudi, S., Biernat, J., Riedel, D., Mandelkow, E., and Zweckstetter, M. (2017) Liquid–liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau, Nat. Commun., 8, 275, https://doi.org/10.1038/s41467-017-00480-0.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  97. Patel, A., Lee, H. O., Jawerth, L., Maharana, S., Jahnel, M., and Hein, M. Y. (2015) A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation, Cell, 162, 1066-1077, https://doi.org/10.1016/j.cell.2015.07.047.

    Article  CAS  PubMed  Google Scholar 

  98. Conicella, A. E., Zerze, G. H., Mittal, J., and Fawzi, N. L. (2016) ALS mutations disrupt phase separation mediated by α-helical structure in the TDP-43 low-complexity C-terminal domain, Structure, 24, 1537-1549, https://doi.org/10.1016/j.str.2016.07.007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Peskett, T. R., Rau, F., O’Driscoll, J., Patani, R., Lowe, A. R., and Saibil, H. R. (2018) A liquid to solid phase transition underlying pathological huntingtin exon1 aggregation, Mol. Cell, 70, 588-601.e6, https://doi.org/10.1016/j.molcel.2018.04.007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Mehta, S., and Zhang, J. (2022) Liquid–liquid phase separation drives cellular function and dysfunction in cancer, Nat. Rev. Cancer, 22, 239-252, https://doi.org/10.1038/s41568-022-00444-7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Roberts, S., Dzuricky, M., and Chilkoti, A. (2015) Elastin-like polypeptides as models of intrinsically disordered proteins, FEBS Lett., 589, 2477-2486, https://doi.org/10.1016/j.febslet.2015.08.029.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Vrhovski, B., and Weiss, A. S. (1998) Biochemistry of tropoelastin, Eur. J. Biochem., 258, 1-18, https://doi.org/10.1046/j.1432-1327.1998.2580001.x.

    Article  CAS  PubMed  Google Scholar 

  103. Olins, A. L., Gould, T. J., Boyd, L., Sarg, B., and Olins, D. E. (2020) Hyperosmotic stress: in situ chromatin phase separation, Nucleus, 11, 1-18, https://doi.org/10.1080/19491034.2019.1710321.

    Article  PubMed  PubMed Central  Google Scholar 

  104. Frey, S., and Görlich, D. (2007) A saturated FG-repeat hydrogel can reproduce the permeability properties of nuclear pore complexes, Cell, 130, 512-523, https://doi.org/10.1016/j.cell.2007.06.024.

    Article  CAS  PubMed  Google Scholar 

  105. Kato, M., and McKnight, S. L. (2017) Cross-β polymerization of low complexity sequence domains, Cold Spring Harb. Perspect. Biol., 9, a023598, https://doi.org/10.1101/cshperspect.a023598.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Kato, M., Han, T. W., Xie, S., Shi, K., Du, X., and Wu, L. C. (2012) Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels, Cell, 149, 753-767, https://doi.org/10.1016/j.cell.2012.04.017.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Shimamoto, Y., Maeda, Y. T., Ishiwata, S., Libchaber, A. J., and Kapoor, T. M. (2011) Insights into the micromechanical properties of the metaphase spindle, Cell, 145, 1062-1074, https://doi.org/10.1016/j.cell.2011.05.038.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Rog, O., Köhler, S., and Dernburg, A. F. (2017) The synaptonemal complex has liquid crystalline properties and spatially regulates meiotic recombination factors, Elife, 6, e21455, https://doi.org/10.7554/eLife.21455.

    Article  PubMed  PubMed Central  Google Scholar 

  109. Guillén-Boixet, J., Kopach, A., Holehouse, A. S., Wittmann, S., Jahnel, M., and Schlüßler, R. (2020) RNA-induced conformational switching and clustering of G3BP drive stress granule assembly by condensation, Cell, 181, 346-361.e17, https://doi.org/10.1016/j.cell.2020.03.049.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Lang, M., Jegou, T., Chung, I., Richter, K., Münch, S., and Udvarhelyi, A. (2010) Three-dimensional organization of promyelocytic leukemia nuclear bodies, J. Cell Sci., 123, 392-400, https://doi.org/10.1242/jcs.053496.

    Article  CAS  PubMed  Google Scholar 

  111. Fare, C. M., Villani, A., Drake, L. E., and Shorter, J. (2021) Higher-order organization of biomolecular condensates, Open Biol., 11, 210137, https://doi.org/10.1098/rsob.210137.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Otzen, D., and Riek, R. (2019) Functional amyloids, Cold Spring Harb. Perspect. Biol., 11, a033860, https://doi.org/10.1101/cshperspect.a033860.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Sergeeva, A. V., and Galkin, A. P. (2020) Functional amyloids of eukaryotes: criteria, classification, and biological significance, Curr. Genet., 66, 849-866, https://doi.org/10.1007/s00294-020-01079-7.

    Article  CAS  PubMed  Google Scholar 

  114. Rubel, M. S., Fedotov, S. A., Grizel, A. V., Sopova, J. V., Malikova, O. A., Chernoff, Y. O., and Rubel, A. A. (2020) Functional mammalian amyloids and amyloid-like proteins, Life, 10, 156, https://doi.org/10.3390/life10090156.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  115. 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, https://doi.org/10.1083/jcb.201010106.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Ishov, A. M., Sotnikov, A. G., Negorev, D., Vladimirova, O. V., Neff, N., and Kamitani, T. (1999) Pml is critical for Nd10 formation and recruits the Pml-interacting protein Daxx to this nuclear structure when modified by Sumo-1, J. Cell Biol., 147, 221-234, https://doi.org/10.1083/jcb.147.2.221.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Groušl, T., Ivanov, P., Frydlová, I., Vašicová, P., Janda, F., and Vojtová, J. (2009) Robust heat shock induces eIF2α-phosphorylation-independent assembly of stress granules containing eIF3 and 40S ribosomal subunits in budding yeast, Saccharomyces cerevisiae, J. Cell Sci., 122, 2078-2088, https://doi.org/10.1242/jcs.045104.

    Article  CAS  PubMed  Google Scholar 

  118. Buchan, J. R., and Parker, R. (2009) Eukaryotic stress granules: the ins and outs of translation, Mol. Cell, 36, 932-341, https://doi.org/10.1016/j.molcel.2009.11.020.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Mittag, T., and Parker, R. (2018) Multiple modes of protein–protein interactions promote RNP granule assembly, J. Mol. Biol., 430, 4636-4649, https://doi.org/10.1016/j.jmb.2018.08.005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Molliex, A., Temirov, J., Lee, J., Coughlin, M., Kanagaraj, A. P., and Kim, H. J. (2015) Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization, Cell, 163, 123-133, https://doi.org/10.1016/j.cell.2015.09.015.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Peran, I., and Mittag, T. (2020) Molecular structure in biomolecular condensates, Curr. Opin. Struct. Biol., 60, 17-26, https://doi.org/10.1016/j.sbi.2019.09.007.

    Article  CAS  PubMed  Google Scholar 

  122. Grizel, A. V., Rubel, A. A., and Chernoff, Y. O. (2016) Strain conformation controls the specificity of cross-species prion transmission in the yeast model, Prion, 10, 269-282, https://doi.org/10.1080/19336896.2016.1204060.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Chernoff, Y. O., Grizel, A. V., Rubel, A. A., Zelinsky, A. A., Chandramowlishwaran, P., and Chernova, T. A. (2020) Application of yeast to studying amyloid and prion diseases, Adv. Genet., 105, 293-380, https://doi.org/10.1016/bs.adgen.2020.01.002.

    Article  CAS  PubMed  Google Scholar 

  124. Martin, E. W., and Mittag, T. (2018) Relationship of sequence and phase separation in protein low-complexity regions, Biochemistry, 57, 2478-2487, https://doi.org/10.1021/acs.biochem.8b00008.

    Article  CAS  PubMed  Google Scholar 

  125. Wang, J., Choi, J. M., Holehouse, A. S., Lee, H. O., Zhang, X., and Jahnel, M. (2018) A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins, Cell, 174, 688-699.e16, https://doi.org/10.1016/j.cell.2018.06.006.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Ozawa, Y., Anbo, H., Ota, M., and Fukuchi, S. (2023) Classification of proteins inducing liquid–liquid phase separation: sequential, structural and functional characterization, J. Biochem., 173, 255-264, https://doi.org/10.1093/jb/mvac106.

    Article  CAS  PubMed  Google Scholar 

  127. Fomicheva, A., and Ross, E. (2021) From prions to stress granules: defining the compositional features of prion-like domains that promote different types of assemblies, Int. J. Mol. Sci., 22, 1251, https://doi.org/10.3390/ijms22031251.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Kulichikhin, K. Y., Malikova, O. A., Zobnina, A. E., Zalutskaya, N. M., and Rubel, A. A. (2023) Interaction of proteins involved in neuronal proteinopathies, Life, 13, 1954, https://doi.org/10.3390/life13101954.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  129. Semenov, A. N., and Rubinstein, M. (1998) Thermoreversible gelation in solutions of associative polymers. 1. Statics, Macromolecules, 31, 1373-1385, https://doi.org/10.1021/ma970616h.

    Article  CAS  ADS  Google Scholar 

  130. Ginell, G. M., and Holehouse, A. S. (2023) An introduction to the stickers-and-spacers framework as applied to biomolecular condensates, Methods Mol. Biol., 2563, 95-116, https://doi.org/10.1007/978-1-0716-2663-4_4.

    Article  CAS  PubMed  Google Scholar 

  131. Murthy, A. C., Dignon, G. L., Kan, Y., Zerze, G. H., Parekh, S. H., and Mittal, J. (2019) Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain, Nat. Struct. Mol. Biol., 26, 637-648, https://doi.org/10.1038/s41594-019-0250-x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Saar, K. L., Morgunov, A. S., Qi, R., Arter, W. E., Krainer, G., and Lee, A. A. (2021) Learning the molecular grammar of protein condensates from sequence determinants and embeddings, Proc. Natl. Acad. Sci. USA, 118, e2019053118, https://doi.org/10.1073/pnas.2019053118.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Devarajan, D. S., Wang, J., Nikoubashman, A., Kim, Y. C., and Mittal, J. (2023) Sequence-dependent material properties of biomolecular condensates, bioRxiv, https://doi.org/10.1101/2023.05.09.540038.

    Article  PubMed  PubMed Central  Google Scholar 

  134. Fisher, R. S., and Elbaum-Garfinkle, S. (2020) Tunable multiphase dynamics of arginine and lysine liquid condensates, Nat. Commun., 11, 4628, https://doi.org/10.1038/s41467-020-18224-y.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  135. De Sancho, D. (2022) Phase separation in amino acid mixtures is governed by composition, Biophys. J., 121, 4119-4127, https://doi.org/10.1016/j.bpj.2022.09.031.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  136. Vernon, R. M., Chong, P. A., Tsang, B., Kim, T. H., Bah, A., and Farber, P. (2018) Pi-Pi contacts are an overlooked protein feature relevant to phase separation, eLife, 7, e31486, https://doi.org/10.7554/eLife.31486.

    Article  PubMed  PubMed Central  Google Scholar 

  137. Nomoto, A., Nishinami, S., and Shiraki, K. (2021) Solubility parameters of amino acids on liquid–liquid phase separation and aggregation of proteins, Front. Cell Dev. Biol., 9, 691052, https://doi.org/10.3389/fcell.2021.691052.

    Article  PubMed  PubMed Central  Google Scholar 

  138. Crick, S. L., Ruff, K. M., Garai, K., Frieden, C., and Pappu, R. V. (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. USA, 110, 20075-20080, https://doi.org/10.1073/pnas.1320626110.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  139. Li, J., Zhang, M., Ma, W., Yang, B., Lu, H., and Zhou, F. (2022) Post-translational modifications in liquid-liquid phase separation: a comprehensive review, Mol. Biomed., 3, 13, https://doi.org/10.1186/s43556-022-00075-2.

    Article  PubMed  PubMed Central  Google Scholar 

  140. Wang, J. T., Smith, J., Chen, B. C., Schmidt, H., Rasoloson, D., and Paix, A. (2014) Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans, eLife, 3, e04591, https://doi.org/10.7554/eLife.04591.

    Article  PubMed  PubMed Central  Google Scholar 

  141. López-Palacios, T. P., and Andersen, J. L. (2023) Kinase regulation by liquid–liquid phase separation, Trends Cell Biol., 33, 649-666, https://doi.org/10.1016/j.tcb.2022.11.009.

    Article  CAS  PubMed  Google Scholar 

  142. Qamar, S., Wang, G., Randle, S. J., Ruggeri, F. S., Varela, J. A., and Lin, J. Q. (2018) FUS phase separation is modulated by a molecular chaperone and methylation of arginine cation-π interactions, Cell, 173, 720-734.e15, https://doi.org/10.1016/j.cell.2018.03.056.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Zhang, H., Romero, H., Schmidt, A., Gagova, K., Qin, W., and Bertulat, B. (2022) MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation, Nucleus, 13, 1-34, https://doi.org/10.1080/19491034.2021.2024691.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Cheng, X. (2023) Protein SUMOylation and phase separation: partners in stress? Trends Biochem. Sci., 48, 417-419, https://doi.org/10.1016/j.tibs.2022.12.003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Keiten-Schmitz, J., Röder, L., Hornstein, E., Müller-McNicoll, M., and Müller, S. (2021) SUMO: glue or solvent for phase-separated ribonucleoprotein complexes and molecular condensates? Front. Mol. Biosci., 8, 673038, https://doi.org/10.3389/fmolb.2021.673038.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  146. Sahin, U., Ferhi, O., Jeanne, M., Benhenda, S., Berthier, C., and Jollivet, F. (2014) Oxidative stress-induced assembly of PML nuclear bodies controls sumoylation of partner proteins, J. Cell Biol., 204, 931-945, https://doi.org/10.1083/jcb.201305148.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Li, X., Pinou, lv., Du, Y., Chen, X., and Liu, C. (2023) Emerging roles of O-glycosylation in regulating protein aggregation, phase separation, and functions, Curr. Opin. Chem. Biol., 75, 102314, https://doi.org/10.1016/j.cbpa.2023.102314.

    Article  CAS  PubMed  Google Scholar 

  148. Roden, C., and Gladfelter, A. S. (2021) RNA contributions to the form and function of biomolecular condensates, Nat. Rev. Mol. Cell Biol., 22, 183-195, https://doi.org/10.1038/s41580-020-0264-6.

    Article  CAS  PubMed  Google Scholar 

  149. Bounedjah, O., Desforges, B., Wu, T. D., Pioche-Durieu, C., Marco, S., and Hamon, L., (2014) Free mRNA in excess upon polysome dissociation is a scaffold for protein multimerization to form stress granules, Nucleic Acids Res., 42, 8678-8691, https://doi.org/10.1093/nar/gku582.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Van Treeck, B., Protter, D., Matheny, T., Khong, A., Link, C. D., and Parker, R. (2018) RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome, Proc. Natl. Acad. Sci. USA, 115, 2734-2739, https://doi.org/10.1073/pnas.180003811.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  151. Khong, A., Matheny, T., Jain, S., Mitchell, S. F., Wheeler, J. R., and Parker, R. (2017) The stress granule transcriptome reveals principles of mRNA accumulation in stress granules, Mol. Cell, 68, 808-820.e5, https://doi.org/10.1016/j.molcel.2017.10.015.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Hubstenberger, A., Courel, M., Bénard, M., Souquere, S., Ernoult-Lange, M., and Chouaib, R., (2017) P-body purification reveals the condensation of repressed mRNA regulons, Mol. Cell, 68, 144-157.e5, https://doi.org/10.1016/j.molcel.2017.09.003.

    Article  CAS  PubMed  Google Scholar 

  153. Schisa, J., Pitt, N. J., and Priess, R. J. (2001) Analysis of RNA associated with P granules in germ cells of C. elegans adults, Development, 128, 1287-1298, https://doi.org/10.1242/dev.128.8.1287.

    Article  CAS  PubMed  Google Scholar 

  154. Namkoong, S., Ho, A., Woo, Y. M., Kwak, H., and Lee, J. H. (2018) Systematic Characterization of Stress-Induced RNA Granulation, Mol. Cell, 70, 175-187.e8, https://doi.org/10.1016/j.molcel.2018.02.025.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Berry, J., Weber, S. C., Vaidya, N., Haataja, M., and Brangwynne, C. P. (2015) RNA transcription modulates phase transition-driven nuclear body assembly, Proc. Natl. Acad. Sci. USA, 112, E5237-E5245, https://doi.org/10.1073/pnas.1509317112.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  156. Boeynaems, S., Holehouse, A. S., Weinhardt, V., Kovacs, D., Van Lindt, J., and Larabell, C. (2019) Spontaneous driving forces give rise to protein–RNA condensates with coexisting phases and complex material properties, Proc. Natl. Acad. Sci. USA, 116, 7889-7898, https://doi.org/10.1073/pnas.1821038116.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  157. Jain, A., and Vale, R. D. (2017) RNA phase transitions in repeat expansion disorders, Nature, 546, 243-247, https://doi.org/10.1038/nature22386.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  158. Smith, J. A., Curry, E. G., Blue, R. E., Roden, C., Dundon, S., and Rodríguez-Vargas, A., (2020) FXR1 splicing is important for muscle development and biomolecular condensates in muscle cells, J. Cell Biol., 219, e201911129, https://doi.org/10.1083/jcb.201911129.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Su, Y., Maimaitiyiming, Y., Wang, L., Cheng, X., and Hsu, C. (2021) Modulation of phase separation by RNA: a glimpse on N6-methyladenosine modification, Front. Cell Dev. Biol., 9, 786454, https://doi.org/10.3389/fcell.2021.786454.

    Article  PubMed  PubMed Central  Google Scholar 

  160. Langdon, E. M., Qiu, Y., Ghanbari Niaki, A., McLaughlin, G. A., Weidmann, C. A., and Gerbich, T. M. (2018) mRNA structure determines specificity of a polyQ-driven phase separation, Science, 360, 922-927, https://doi.org/10.1126/science.aar7432.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  161. Mitrea, D. M., Chandra, B., Ferrolino, M. C., Gibbs, E. B., Tolbert, M., and White, M. R. (2018) Methods for physical characterization of phase-separated bodies and membraneless organelles, J. Mol. Biol., 430, 4773-4805, https://doi.org/10.1016/j.jmb.2018.07.006.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Molenaar, C., and Weeks, K. L. (2018) Nucleocytoplasmic shuttling: the ins and outs of quantitative imaging, Clin. Exp. Pharmacol., 45, 1087-1094, https://doi.org/10.1111/1440-1681.12969.

    Article  CAS  Google Scholar 

  163. Jonkman, J., and Brown, C. M. (2015) Any way you slice it – a comparison of confocal microscopy techniques, J. Biomol. Tech., 26, 54-65, https://doi.org/10.7171/jbt.15-2602-003.

    Article  PubMed  PubMed Central  Google Scholar 

  164. Watanabe, K., Morishita, K., Zhou, X., Shiizaki, S., Uchiyama, Y., and Koike, M. (2021) Cells recognize osmotic stress through liquid–liquid phase separation lubricated with poly(ADP-ribose), Nat. Commun., 12, 1353, https://doi.org/10.1038/s41467-021-21614-5.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  165. Khan, T., Kandola, T. S., Wu, J., Venkatesan, S., Ketter, E., and Lange, J. J. (2018) Quantifying nucleation in vivo reveals the physical basis of prion-like phase behavior, Mol. Cell, 71, 155-168.e7, https://doi.org/10.1016/j.molcel.2018.06.016.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Kroschwald, S., Maharana, S., and Alberti, S. (2017) Hexanediol: a chemical probe to investigate the material properties of membrane-less compartments, Matters, 3, e201702000010, https://doi.org/10.19185/matters.201702000010.

    Article  Google Scholar 

  167. Weihs, D., Mason, T. G., and Teitell, M. A. (2006) Bio-microrheology: a frontier in microrheology, Biophys. J., 91, 4296-4305, https://doi.org/10.1529/biophysj.106.081109.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  168. Andersen, J. S., Lyon, C. E., Fox, A. H., Leung, A., Lam, Y. W., and Steen, H. (2002) Directed proteomic analysis of the human nucleolus, Curr. Biol., 12, 1-11, https://doi.org/10.1016/s0960-9822(01)00650-9.

    Article  PubMed  Google Scholar 

  169. Youn, J. Y., Dunham, W. H., Hong, S. J., Knight, J. D. R., Bashkurov, M., and Chen, G. I. (2018) High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies, Mol. Cell, 69, 517-532.e11, https://doi.org/10.1016/j.molcel.2017.12.020.

    Article  CAS  PubMed  Google Scholar 

  170. Hughes, M. P., Sawaya, M. R., Boyer, D. R., Goldschmidt, L., Rodriguez, J. A., and Cascio, D. (2018) Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks, Science, 359, 698-701, https://doi.org/10.1126/science.aan6398.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  171. Sun, Y., Zhang, S., Hu, J., Tao, Y., Xia, W., and Gu, J. (2022) Molecular structure of an amyloid fibril formed by FUS low-complexity domain, iScience, 25, 103701, https://doi.org/10.1016/j.isci.2021.103701.

    Article  CAS  PubMed  ADS  Google Scholar 

  172. Gibbs, E. B., Cook, E. C., and Showalter, S. A. (2017) Application of NMR to studies of intrinsically disordered proteins, Arch. Biochem. Biophys., 628, 57-70, https://doi.org/10.1016/j.abb.2017.05.008.

    Article  CAS  PubMed  Google Scholar 

  173. Stetefeld, J., McKenna, S. A., and Patel, T. R. (2016) Dynamic light scattering: a practical guide and applications in biomedical sciences, Biophys. Rev., 8, 409-427, https://doi.org/10.1007/s12551-016-0218-6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. Kikhney, A. G., and Svergun, D. I. (2015) A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins, FEBS Lett., 589, 2570-2577, https://doi.org/10.1016/j.febslet.2015.08.027.

    Article  CAS  PubMed  Google Scholar 

  175. Maharana, S., Wang, J., Papadopoulos, D. K., Richter, D., Pozniakovsky, A., and Poser, I. (2018) RNA buffers the phase separation behavior of prion-like RNA binding proteins, Science, 360, 918-921, https://doi.org/10.1126/science.aar7366.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  176. Mahato, J., Ray, S., Maji, S. K., and Chowdhury, A. (2023) Spectrally resolved FRET microscopy of α-synuclein phase-separated liquid droplets, Methods Mol. Biol., 2551, 425-447, https://doi.org/10.1007/978-1-0716-2597-2_27.

    Article  CAS  PubMed  Google Scholar 

  177. Ray, S., Singh, N., Patel, K., Krishnamoorthy, G., and Maji, S. K. (2023) FRAP and FRET investigation of α-synuclein fibrillization via liquid-liquid phase separation in vitro and in HeLa cells, Methods Mol. Biol., 2551, 395-423, https://doi.org/10.1007/978-1-0716-2597-2_26.

    Article  CAS  PubMed  Google Scholar 

  178. Ganser, L. R., and Myong, S. (2020) Methods to study phase-separated condensates and the underlying molecular interactions, Trends Biochem. Sci., 45, 1004-1005, https://doi.org/10.1016/j.tibs.2020.05.011.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Elson, E. L. (2011) Fluorescence correlation spectroscopy: past, present, future, Biophys. J., 101, 2855-2870, https://doi.org/10.1016/j.bpj.2011.11.012.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  180. Erdős, G., Pajkos, M., and Dosztányi, Z. (2021) IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation, Nucleic Acids Res., 49, W297-W303, https://doi.org/10.1093/nar/gkab408.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Holehouse, A. S., Das, R. K., Ahad, J. N., Richardson, M. G., and Pappu, R. (2017) CIDER: resources to analyze sequence-ensemble relationships of intrinsically disordered proteins, Biophys. J., 112, 16-21, https://doi.org/10.1016/j.bpj.2016.11.3200.

    Article  CAS  PubMed  PubMed Central  ADS  Google Scholar 

  182. Cascarina, S. M., and Ross, E. D. (2022) The LCD-composer webserver: high-specificity identification and functional analysis of low-complexity domains in proteins, Bioinformatics, 38, 5446-5448, https://doi.org/10.1093/bioinformatics/btac699.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Lancaster, A. K., Nutter-Upham, A., Lindquist, S., and King, O. D. (2014) PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition, Bioinformatics, 30, 2501-2502, https://doi.org/10.1093/bioinformatics/btu310.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Huang, Y. J., Acton, T. B., and Montelione, G. T. (2014) DisMeta: a meta server for construct design and optimization, Methods Mol. Biol., 1091, 3-16, https://doi.org/10.1007/978-1-62703-691-7_1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., and Xue, B. (2012) D2P2: database of disordered protein predictions, Nucleic Acids Res., 41, D508-D516, https://doi.org/10.1093/nar/gks1226.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Piovesan, D., Del Conte, A., Clementel, D., Monzon, A. M., Bevilacqua, M., and Aspromonte, M. C. (2023) MobiDB: 10 years of intrinsically disordered proteins, Nucleic Acids Res., 51, D438-D444, https://doi.org/10.1093/nar/gkac1065.

    Article  CAS  PubMed  Google Scholar 

  187. Goldschmidt, L., Teng, P. K., Riek, R., and Eisenberg, D. (2010) Identifying the amylome, proteins capable of forming amyloid-like fibrils, Proc. Natl. Acad. Sci. USA, 107, 3487-3492, https://doi.org/10.1073/pnas.0915166107.

    Article  PubMed  PubMed Central  ADS  Google Scholar 

  188. Chen, Z., Hou, C., Wang, L., Yu, C., Chen, T., and Shen, B. (2022) Screening membraneless organelle participants with machine-learning models that integrate multimodal features, Proc. Natl. Acad. Sci. USA, 119, e2115369119, https://doi.org/10.1073/pnas.2115369119.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Cai, H., Vernon, R. M., and Forman-Kay, J. D. (2022) An interpretable machine-learning algorithm to predict disordered protein phase separation based on biophysical interactions, Biomolecules, 12, 1131, https://doi.org/10.3390/biom12081131.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

The authors thank Maria S. Rubel, Konstantin Y. Kulichikhin, and Yury O. Chernoff for discussion, critical reading of the manuscript, and valuable comments. The authors acknowledge support from the St. Petersburg State University (project ID 95444727) and are grateful to the Core Facility “Chromas” (Research Park, St. Petersburg State University) for technical assistance.

Funding

This work was funded by the Russian Science Foundation, grant no. 20-14-00148-П.

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Authors and Affiliations

  1. St. Petersburg State University, 199034, St. Petersburg, Russia

    Natalia A. Gorsheneva, Julia V. Sopova, Vladimir V. Azarov & Aleksandr A. Rubel

  2. School of Biological Sciences, Georgia Institute of Technology, 30332, Atlanta, Georgia, USA

    Anastasia V. Grizel

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  1. Natalia A. Gorsheneva
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  2. Julia V. Sopova
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  3. Vladimir V. Azarov
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N.A.G. preparation of the original draft of the manuscript, V.V.A., A.V.G., and A.A.R. writing and editing manuscript; J.V.S. visualization and editing manuscript.

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Correspondence to Anastasia V. Grizel or Aleksandr A. Rubel.

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This work does not contain any studies involving human and animal subjects. The authors of this work declare that they have no conflicts of interest.

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Translated from Uspekhi Biologicheskoi Khimii, 2024, Vol. 64, pp. 397-430.

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Gorsheneva, N.A., Sopova, J.V., Azarov, V.V. et al. Biomolecular Condensates: Structure, Functions, Methods of Research. Biochemistry Moscow 89 (Suppl 1), S205–S223 (2024). https://doi.org/10.1134/S0006297924140116

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