Literature DB >> 33169001

A framework for understanding the functions of biomolecular condensates across scales.

Andrew S Lyon1, William B Peeples1, Michael K Rosen2.   

Abstract

Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes. They are also implicated in a wide range of cellular functions, organizing molecules that act in processes ranging from RNA metabolism to signalling to gene regulation. Early work in the field focused on identifying condensates and understanding how their physical properties and regulation arise from molecular constituents. Recent years have brought a focus on understanding condensate functions. Studies have revealed functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating localization of cellular materials and homeostatic responses). In this Roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the recent literature and organize these functions into a series of non-exclusive classes across the different length scales. We conclude with a discussion of areas of current interest and challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology.

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Year:  2020        PMID: 33169001      PMCID: PMC8574987          DOI: 10.1038/s41580-020-00303-z

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  196 in total

1.  mRNA structure determines specificity of a polyQ-driven phase separation.

Authors:  Erin M Langdon; Yupeng Qiu; Amirhossein Ghanbari Niaki; Grace A McLaughlin; Chase A Weidmann; Therese M Gerbich; Jean A Smith; John M Crutchley; Christina M Termini; Kevin M Weeks; Sua Myong; Amy S Gladfelter
Journal:  Science       Date:  2018-04-12       Impact factor: 47.728

2.  Valence and patterning of aromatic residues determine the phase behavior of prion-like domains.

Authors:  Erik W Martin; Alex S Holehouse; Ivan Peran; Mina Farag; J Jeremias Incicco; Anne Bremer; Christy R Grace; Andrea Soranno; Rohit V Pappu; Tanja Mittag
Journal:  Science       Date:  2020-02-07       Impact factor: 47.728

Review 3.  Theories for Sequence-Dependent Phase Behaviors of Biomolecular Condensates.

Authors:  Yi-Hsuan Lin; Julie D Forman-Kay; Hue Sun Chan
Journal:  Biochemistry       Date:  2018-03-13       Impact factor: 3.162

4.  Pi-Pi contacts are an overlooked protein feature relevant to phase separation.

Authors:  Robert McCoy Vernon; Paul Andrew Chong; Brian Tsang; Tae Hun Kim; Alaji Bah; Patrick Farber; Hong Lin; Julie Deborah Forman-Kay
Journal:  Elife       Date:  2018-02-09       Impact factor: 8.140

5.  [Cyclophosphan and prednisolone immunosuppressant therapy of a patient with hypoplastic anemia].

Authors:  T N Postriganeva; B V Afanas'ev; A Iu Zaritskiĭ; M A Saĭdali; T S Zabelina
Journal:  Ter Arkh       Date:  1980       Impact factor: 0.467

6.  A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins.

Authors:  Jie Wang; Jeong-Mo Choi; Alex S Holehouse; Hyun O Lee; Xiaojie Zhang; Marcus Jahnel; Shovamayee Maharana; Régis Lemaitre; Andrei Pozniakovsky; David Drechsel; Ina Poser; Rohit V Pappu; Simon Alberti; Anthony A Hyman
Journal:  Cell       Date:  2018-06-28       Impact factor: 41.582

7.  Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels.

Authors:  Masato Kato; Tina W Han; Shanhai Xie; Kevin Shi; Xinlin Du; Leeju C Wu; Hamid Mirzaei; Elizabeth J Goldsmith; Jamie Longgood; Jimin Pei; Nick V Grishin; Douglas E Frantz; Jay W Schneider; She Chen; Lin Li; Michael R Sawaya; David Eisenberg; Robert Tycko; Steven L McKnight
Journal:  Cell       Date:  2012-05-11       Impact factor: 41.582

8.  Phase transitions in the assembly of multivalent signalling proteins.

Authors:  Pilong Li; Sudeep Banjade; Hui-Chun Cheng; Soyeon Kim; Baoyu Chen; Liang Guo; Marc Llaguno; Javoris V Hollingsworth; David S King; Salman F Banani; Paul S Russo; Qiu-Xing Jiang; B Tracy Nixon; Michael K Rosen
Journal:  Nature       Date:  2012-03-07       Impact factor: 49.962

9.  RNA phase transitions in repeat expansion disorders.

Authors:  Ankur Jain; Ronald D Vale
Journal:  Nature       Date:  2017-05-31       Impact factor: 49.962

10.  Organization of Chromatin by Intrinsic and Regulated Phase Separation.

Authors:  Bryan A Gibson; Lynda K Doolittle; Maximillian W G Schneider; Liv E Jensen; Nathan Gamarra; Lisa Henry; Daniel W Gerlich; Sy Redding; Michael K Rosen
Journal:  Cell       Date:  2019-09-19       Impact factor: 41.582

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  94 in total

Review 1.  Generic nature of the condensed states of proteins.

Authors:  Monika Fuxreiter; Michele Vendruscolo
Journal:  Nat Cell Biol       Date:  2021-06-09       Impact factor: 28.824

Review 2.  Nuclear compartmentalization as a mechanism of quantitative control of gene expression.

Authors:  Prashant Bhat; Drew Honson; Mitchell Guttman
Journal:  Nat Rev Mol Cell Biol       Date:  2021-08-02       Impact factor: 94.444

Review 3.  Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing.

Authors:  Simon Alberti; Anthony A Hyman
Journal:  Nat Rev Mol Cell Biol       Date:  2021-01-28       Impact factor: 94.444

4.  p62-containing, proteolytically active nuclear condensates, increase the efficiency of the ubiquitin-proteasome system.

Authors:  Afu Fu; Victoria Cohen-Kaplan; Noa Avni; Ido Livneh; Aaron Ciechanover
Journal:  Proc Natl Acad Sci U S A       Date:  2021-08-17       Impact factor: 11.205

Review 5.  Phase separation in transcription factor dynamics and chromatin organization.

Authors:  Kaustubh Wagh; David A Garcia; Arpita Upadhyaya
Journal:  Curr Opin Struct Biol       Date:  2021-07-22       Impact factor: 6.809

6.  Generation and Biochemical Characterization of Phase-Separated Droplets Formed by Nucleic Acid Binding Proteins: Using HP1 as a Model System.

Authors:  Serena Sanulli; Geeta J Narlikar
Journal:  Curr Protoc       Date:  2021-05

Review 7.  Autophagosome biogenesis comes out of the black box.

Authors:  Chunmei Chang; Liv E Jensen; James H Hurley
Journal:  Nat Cell Biol       Date:  2021-04-26       Impact factor: 28.824

8.  Mechanistic dissection of increased enzymatic rate in a phase-separated compartment.

Authors:  William Peeples; Michael K Rosen
Journal:  Nat Chem Biol       Date:  2021-05-25       Impact factor: 15.040

Review 9.  Combating deleterious phase transitions in neurodegenerative disease.

Authors:  April L Darling; James Shorter
Journal:  Biochim Biophys Acta Mol Cell Res       Date:  2021-02-05       Impact factor: 4.739

10.  Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates.

Authors:  Ibraheem Alshareedah; George M Thurston; Priya R Banerjee
Journal:  Biophys J       Date:  2021-01-14       Impact factor: 4.033

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