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Pancsa R, Vranken W, Mészáros B. Computational resources for identifying and describing proteins driving liquid-liquid phase separation. Brief Bioinform 2021; 22:6124912. [PMID: 33517364 PMCID: PMC8425267 DOI: 10.1093/bib/bbaa408] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/23/2020] [Accepted: 12/12/2020] [Indexed: 01/06/2023] Open
Abstract
One of the most intriguing fields emerging in current molecular biology is the study of membraneless organelles formed via liquid–liquid phase separation (LLPS). These organelles perform crucial functions in cell regulation and signalling, and recent years have also brought about the understanding of the molecular mechanism of their formation. The LLPS field is continuously developing and optimizing dedicated in vitro and in vivo methods to identify and characterize these non-stoichiometric molecular condensates and the proteins able to drive or contribute to LLPS. Building on these observations, several computational tools and resources have emerged in parallel to serve as platforms for the collection, annotation and prediction of membraneless organelle-linked proteins. In this survey, we showcase recent advancements in LLPS bioinformatics, focusing on (i) available databases and ontologies that are necessary to describe the studied phenomena and the experimental results in an unambiguous way and (ii) prediction methods to assess the potential LLPS involvement of proteins. Through hands-on application of these resources on example proteins and representative datasets, we give a practical guide to show how they can be used in conjunction to provide in silico information on LLPS.
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Affiliation(s)
- Rita Pancsa
- Enzymology Institute of the Research Centre for Natural Sciences, Budapest, Hungary
| | - Wim Vranken
- Computer Science, chemistry and biomedical sciences at the Vrije Universiteit Brussel
| | - Bálint Mészáros
- Structural and Computational Biology Unit at the European Molecular Biology Laboratory, Heidelberg 69117, Germany
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52
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Uversky VN. Recent Developments in the Field of Intrinsically Disordered Proteins: Intrinsic Disorder-Based Emergence in Cellular Biology in Light of the Physiological and Pathological Liquid-Liquid Phase Transitions. Annu Rev Biophys 2021; 50:135-156. [PMID: 33503380 DOI: 10.1146/annurev-biophys-062920-063704] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review deals with two important concepts-protein intrinsic disorder and proteinaceous membrane-less organelles (PMLOs). The past 20 years have seen an upsurge of scientific interest in these phenomena. However, neither are new discoveries made in this century, but instead are timely reincarnations of old ideas that were mostly ignored by the scientific community for a long time. Merging these concepts in the form of the intrinsic disorder-based biological liquid-liquid phase separation provides a basis for understanding the molecular mechanisms of PMLO biogenesis.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, USA; .,Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
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53
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Sehgal PB, Yuan H, Scott MF, Deng Y, Liang FX, Mackiewicz A. Murine GFP-Mx1 forms nuclear condensates and associates with cytoplasmic intermediate filaments: Novel antiviral activity against VSV. J Biol Chem 2020; 295:18023-18035. [PMID: 33077519 PMCID: PMC7939456 DOI: 10.1074/jbc.ra120.015661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/30/2020] [Indexed: 11/06/2022] Open
Abstract
Type I and III interferons induce expression of the "myxovirus resistance proteins" MxA in human cells and its ortholog Mx1 in murine cells. Human MxA forms cytoplasmic structures, whereas murine Mx1 forms nuclear bodies. Whereas both HuMxA and MuMx1 are antiviral toward influenza A virus (FLUAV) (an orthomyxovirus), only HuMxA is considered antiviral toward vesicular stomatitis virus (VSV) (a rhabdovirus). We previously reported that the cytoplasmic human GFP-MxA structures were phase-separated membraneless organelles ("biomolecular condensates"). In the present study, we investigated whether nuclear murine Mx1 structures might also represent phase-separated biomolecular condensates. The transient expression of murine GFP-Mx1 in human Huh7 hepatoma, human Mich-2H6 melanoma, and murine NIH 3T3 cells led to the appearance of Mx1 nuclear bodies. These GFP-MuMx1 nuclear bodies were rapidly disassembled by exposing cells to 1,6-hexanediol (5%, w/v), or to hypotonic buffer (40-50 mosm), consistent with properties of membraneless phase-separated condensates. Fluorescence recovery after photobleaching (FRAP) assays revealed that the GFP-MuMx1 nuclear bodies upon photobleaching showed a slow partial recovery (mobile fraction: ∼18%) suggestive of a gel-like consistency. Surprisingly, expression of GFP-MuMx1 in Huh7 cells also led to the appearance of GFP-MuMx1 in 20-30% of transfected cells in a novel cytoplasmic giantin-based intermediate filament meshwork and in cytoplasmic bodies. Remarkably, Huh7 cells with cytoplasmic murine GFP-MuMx1 filaments, but not those with only nuclear bodies, showed antiviral activity toward VSV. Thus, GFP-MuMx1 nuclear bodies comprised phase-separated condensates. Unexpectedly, GFP-MuMx1 in Huh7 cells also associated with cytoplasmic giantin-based intermediate filaments, and such cells showed antiviral activity toward VSV.
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Affiliation(s)
- Pravin B Sehgal
- Departments of Cell Biology and Anatomy, New York Medical College, Valhalla, New York, USA; Department of Medicine, New York Medical College, Valhalla, New York, USA.
| | - Huijuan Yuan
- Departments of Cell Biology and Anatomy, New York Medical College, Valhalla, New York, USA
| | - Mia F Scott
- Departments of Cell Biology and Anatomy, New York Medical College, Valhalla, New York, USA
| | - Yan Deng
- Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Feng-Xia Liang
- Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Andrzej Mackiewicz
- Department of Medical Biotechnology, University School of Medical Sciences, Poznań, Poland; Department of Diagnostics and Immunology of Cancer, Greater Poland Cancer Center, Poznań, Poland
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54
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Salladini E, Jørgensen MLM, Theisen FF, Skriver K. Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications. Int J Mol Sci 2020; 21:E9755. [PMID: 33371315 PMCID: PMC7767404 DOI: 10.3390/ijms21249755] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering.
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Affiliation(s)
| | | | | | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; (E.S.); (M.L.M.J.); (F.F.T.)
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55
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Martins PM, Navarro S, Silva A, Pinto MF, Sárkány Z, Figueiredo F, Pereira PJB, Pinheiro F, Bednarikova Z, Burdukiewicz M, Galzitskaya OV, Gazova Z, Gomes CM, Pastore A, Serpell LC, Skrabana R, Smirnovas V, Ziaunys M, Otzen DE, Ventura S, Macedo-Ribeiro S. MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments. Front Mol Neurosci 2020; 13:582488. [PMID: 33328883 PMCID: PMC7729192 DOI: 10.3389/fnmol.2020.582488] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.
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Affiliation(s)
- Pedro M Martins
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alexandra Silva
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria F Pinto
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory - Department of Atomic Structure - Composition of Materials, Braga, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Annalisa Pastore
- UK-DRI Centre at King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rostislav Skrabana
- Department of Neuroimmunology, Axon Neuroscience R&D Services SE, Bratislava, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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56
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Dysregulated ribonucleoprotein granules promote cardiomyopathy in RBM20 gene-edited pigs. Nat Med 2020; 26:1788-1800. [PMID: 33188278 PMCID: PMC9270981 DOI: 10.1038/s41591-020-1087-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/21/2020] [Indexed: 12/12/2022]
Abstract
Ribonucleoprotein (RNP) granules are biomolecular condensates-liquid-liquid phase-separated droplets that organize and manage messenger RNA metabolism, cell signaling, biopolymer assembly, biochemical reactions and stress granule responses to cellular adversity. Dysregulated RNP granules drive neuromuscular degenerative disease but have not previously been linked to heart failure. By exploring the molecular basis of congenital dilated cardiomyopathy (DCM) in genome-edited pigs homozygous for an RBM20 allele encoding the pathogenic R636S variant of human RNA-binding motif protein-20 (RBM20), we discovered that RNP granules accumulated abnormally in the sarcoplasm, and we confirmed this finding in myocardium and reprogrammed cardiomyocytes from patients with DCM carrying the R636S allele. Dysregulated sarcoplasmic RBM20 RNP granules displayed liquid-like material properties, docked at precisely spaced intervals along cytoskeletal elements, promoted phase partitioning of cardiac biomolecules and fused with stress granules. Our results link dysregulated RNP granules to myocardial cellular pathobiology and heart failure in gene-edited pigs and patients with DCM caused by RBM20 mutation.
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57
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Babinchak WM, Dumm BK, Venus S, Boyko S, Putnam AA, Jankowsky E, Surewicz WK. Small molecules as potent biphasic modulators of protein liquid-liquid phase separation. Nat Commun 2020; 11:5574. [PMID: 33149109 PMCID: PMC7643064 DOI: 10.1038/s41467-020-19211-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of proteins that leads to formation of membrane-less organelles is critical to many biochemical processes in the cell. However, dysregulated LLPS can also facilitate aberrant phase transitions and lead to protein aggregation and disease. Accordingly, there is great interest in identifying small molecules that modulate LLPS. Here, we demonstrate that 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) and similar compounds are potent biphasic modulators of protein LLPS. Depending on context, bis-ANS can both induce LLPS de novo as well as prevent formation of homotypic liquid droplets. Our study also reveals the mechanisms by which bis-ANS and related compounds modulate LLPS and identify key chemical features of small molecules required for this activity. These findings may provide a foundation for the rational design of small molecule modulators of LLPS with therapeutic value.
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Affiliation(s)
- W Michael Babinchak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin K Dumm
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science & Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - Solomiia Boyko
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Andrea A Putnam
- Center for RNA Science & Therapeutics, Case Western Reserve University, Cleveland, OH, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eckhard Jankowsky
- Center for RNA Science & Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA.
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58
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Dodson AE, Kennedy S. Phase Separation in Germ Cells and Development. Dev Cell 2020; 55:4-17. [PMID: 33007213 DOI: 10.1016/j.devcel.2020.09.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/28/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022]
Abstract
The animal germline is an immortal cell lineage that gives rise to eggs and/or sperm each generation. Fusion of an egg and sperm, or fertilization, sets off a cascade of developmental events capable of producing an array of different cell types and body plans. How germ cells develop, function, and eventually give rise to entirely new organisms is an important question in biology. A growing body of evidence suggests that phase separation events likely play a significant and multifaceted role in germ cells and development. Here, we discuss the organization, dynamics, and potential functions of phase-separated compartments in germ cells and examine the various ways in which phase separation might contribute to the development of multicellular organisms.
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Affiliation(s)
- Anne E Dodson
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
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59
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Jeon BJ, Nguyen DT, Saleh OA. Sequence-Controlled Adhesion and Microemulsification in a Two-Phase System of DNA Liquid Droplets. J Phys Chem B 2020; 124:8888-8895. [PMID: 32960601 DOI: 10.1021/acs.jpcb.0c06911] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Membrane-less organelles, the liquid droplets formed via liquid-liquid phase separation (LLPS) of biomolecules in cells, act to organize intracellular components into multiple compartments. As a model for this process, and as a potential vehicle for in vitro exploitation of its properties, we explore here a synthetic multiphase LLPS system consisting of a mixture of self-assembled DNA particles. The particles, termed "DNA nanostars" (NSs), consist of four double-stranded DNA arms that each terminate in a single-stranded overhang. NSs condense into droplets due to overhang hybridization. Using two types of NSs with orthogonal overhangs enables the creation of two types of immiscible DNA droplets. Adhesion between the droplets can be tuned by the addition of "cross-linker NSs" that have two overhang sequences of each type. We find that increasing the amount of the cross-linker NSs decreases the droplet/droplet surface tension until a microemulsion transition occurs. Controlled droplet adhesion can also be achieved, without cross-linkers, using overhangs that can weakly hybridize. Finally, we show that solutes can be specifically targeted to the DNA phases by labeling them with appropriate sticky-ends. Overall, our findings demonstrate the ability to create a multiphase LLPS system, and to control its mesoscale configuration, via sequence design of the component molecules.
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Affiliation(s)
- Byoung-Jin Jeon
- Materials Department, University of California, Santa Barbara, California 93110, United States
| | - Dan T Nguyen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93110, United States
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, California 93110, United States.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93110, United States
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60
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Gotor NL, Armaos A, Calloni G, Torrent Burgas M, Vabulas R, De Groot NS, Tartaglia GG. RNA-binding and prion domains: the Yin and Yang of phase separation. Nucleic Acids Res 2020; 48:9491-9504. [PMID: 32857852 PMCID: PMC7515694 DOI: 10.1093/nar/gkaa681] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/08/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Proteins and RNAs assemble in membrane-less organelles that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to form condensates is encoded in their sequences, yet it is unknown which domains drive the phase separation (PS) process and what are their specific roles. Here, we systematically investigated the human and yeast proteomes to find regions promoting condensation. Using advanced computational methods to predict the PS propensity of proteins, we designed a set of experiments to investigate the contributions of Prion-Like Domains (PrLDs) and RNA-binding domains (RBDs). We found that one PrLD is sufficient to drive PS, whereas multiple RBDs are needed to modulate the dynamics of the assemblies. In the case of stress granule protein Pub1 we show that the PrLD promotes sequestration of protein partners and the RBD confers liquid-like behaviour to the condensate. Our work sheds light on the fine interplay between RBDs and PrLD to regulate formation of membrane-less organelles, opening up the avenue for their manipulation.
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Affiliation(s)
- Nieves Lorenzo Gotor
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, RNA System Biology Lab, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main,60438, Germany
| | - Marc Torrent Burgas
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - R Martin Vabulas
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main,60438, Germany
- Charité – Universitätsmedizin Berlin, Institute of Biochemistry, 10117 Berlin, Germany
| | - Natalia Sanchez De Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, RNA System Biology Lab, Via Enrico Melen 83, 16152 Genoa, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
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61
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Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation. mBio 2020; 11:mBio.02052-20. [PMID: 32900808 PMCID: PMC7482068 DOI: 10.1128/mbio.02052-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
By employing biophysical and liquid-liquid phase separation concepts, this study revealed how a highly abundant extracellular protein enhances the key environmental and industrial bioprocess of anaerobic ammonium oxidation (anammox). Extracellular proteins of environmental biofilms are understudied and poorly annotated in public databases. Understanding the function of extracellular proteins is also increasingly important for improving bioprocesses and resource recovery. Here, protein functions were assessed based on theoretical predictions of intrinsically disordered domains, known to promote adhesion and liquid-liquid phase separation, and available surface layer protein properties. A model is thus proposed to explain how the protein promotes aggregation and biofilm formation by extracellular matrix remodeling and phase transitions. This work provides a strong foundation for functional investigations of extracellular proteins involved in biofilm development. This study describes the first direct functional assignment of a highly abundant extracellular protein from a key environmental and biotechnological biofilm performing an anaerobic ammonium oxidation (anammox) process. Expression levels of Brosi_A1236, belonging to a class of proteins previously suggested to be cell surface associated, were in the top one percentile of all genes in the “Candidatus Brocadia sinica”-enriched biofilm. The Brosi_A1236 structure was computationally predicted to consist of immunoglobulin-like anti-parallel β-strands, and circular dichroism conducted on the isolated surface protein indicated that β-strands are the dominant higher-order structure. The isolated protein was stained positively by the β-sheet-specific stain thioflavin T, along with cell surface- and matrix-associated regions of the biofilm. The surface protein has a large unstructured content, including two highly disordered domains at its C terminus. The disordered domains bound to the substratum and thereby facilitated the adhesion of negatively charged latex microspheres, which were used as a proxy for cells. The disordered domains and isolated whole surface protein also underwent liquid-liquid phase separation to form liquid droplets in suspension. Liquid droplets of disordered protein wet the surfaces of microspheres and bacterial cells and facilitated their coalescence. Furthermore, the surface layer protein formed gels as well as ordered crystalline structures. These observations suggest that biophysical remodeling through phase transitions promotes aggregation and biofilm formation.
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62
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Liquid-Liquid Phase Separation in Crowded Environments. Int J Mol Sci 2020; 21:ijms21165908. [PMID: 32824618 PMCID: PMC7460619 DOI: 10.3390/ijms21165908] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/13/2020] [Indexed: 12/23/2022] Open
Abstract
Biomolecular condensates play a key role in organizing cellular fluids such as the cytoplasm and nucleoplasm. Most of these non-membranous organelles show liquid-like properties both in cells and when studied in vitro through liquid–liquid phase separation (LLPS) of purified proteins. In general, LLPS of proteins is known to be sensitive to variations in pH, temperature and ionic strength, but the role of crowding remains underappreciated. Several decades of research have shown that macromolecular crowding can have profound effects on protein interactions, folding and aggregation, and it must, by extension, also impact LLPS. However, the precise role of crowding in LLPS is far from trivial, as most condensate components have a disordered nature and exhibit multiple weak attractive interactions. Here, we discuss which factors determine the scope of LLPS in crowded environments, and we review the evidence for the impact of macromolecular crowding on phase boundaries, partitioning behavior and condensate properties. Based on a comparison of both in vivo and in vitro LLPS studies, we propose that phase separation in cells does not solely rely on attractive interactions, but shows important similarities to segregative phase separation.
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63
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Alshareedah I, Kaur T, Banerjee PR. Methods for characterizing the material properties of biomolecular condensates. Methods Enzymol 2020; 646:143-183. [PMID: 33453924 PMCID: PMC7849318 DOI: 10.1016/bs.mie.2020.06.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are membrane-less sub-cellular compartments that perform a plethora of important functions in signaling and storage. The material properties of biomolecular condensates such as viscosity, surface tension, viscoelasticity, and macromolecular diffusion play important roles in regulating their biological functions. Aberrations in these properties have been implicated in various neurodegenerative disorders and certain types of cancer. Unraveling the molecular driving forces that control the fluid structure and dynamics of biomolecular condensates across different length- and time-scales necessitates the application of innovative biophysical methodologies. In this chapter, we discuss major experimental techniques that are widely used to study the material states and dynamics of biomolecular condensates as well as their practical and conceptual limitations. We end this chapter with a discussion on more advanced tools that are currently emerging to address the complex fluid dynamics of these condensates.
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Affiliation(s)
| | - Taranpreet Kaur
- Department of Physics, University at Buffalo, Buffalo, NY, United States
| | - Priya R Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY, United States.
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64
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Klein IA, Boija A, Afeyan LK, Hawken SW, Fan M, Dall'Agnese A, Oksuz O, Henninger JE, Shrinivas K, Sabari BR, Sagi I, Clark VE, Platt JM, Kar M, McCall PM, Zamudio AV, Manteiga JC, Coffey EL, Li CH, Hannett NM, Guo YE, Decker TM, Lee TI, Zhang T, Weng JK, Taatjes DJ, Chakraborty A, Sharp PA, Chang YT, Hyman AA, Gray NS, Young RA. Partitioning of cancer therapeutics in nuclear condensates. Science 2020; 368:1386-1392. [PMID: 32554597 PMCID: PMC7735713 DOI: 10.1126/science.aaz4427] [Citation(s) in RCA: 337] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/24/2020] [Accepted: 04/29/2020] [Indexed: 12/21/2022]
Abstract
The nucleus contains diverse phase-separated condensates that compartmentalize and concentrate biomolecules with distinct physicochemical properties. Here, we investigated whether condensates concentrate small-molecule cancer therapeutics such that their pharmacodynamic properties are altered. We found that antineoplastic drugs become concentrated in specific protein condensates in vitro and that this occurs through physicochemical properties independent of the drug target. This behavior was also observed in tumor cells, where drug partitioning influenced drug activity. Altering the properties of the condensate was found to affect the concentration and activity of drugs. These results suggest that selective partitioning and concentration of small molecules within condensates contributes to drug pharmacodynamics and that further understanding of this phenomenon may facilitate advances in disease therapy.
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Affiliation(s)
- Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Susana Wilson Hawken
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mengyang Fan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Krishna Shrinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin R Sabari
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ido Sagi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Victoria E Clark
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jesse M Platt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Mrityunjoy Kar
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Patrick M McCall
- Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John C Manteiga
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yang Eric Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tim-Michael Decker
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Arup Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phillip A Sharp
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Young Tae Chang
- Department of Chemistry, Pohang University of Science and Technology, and Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01062 Dresden, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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65
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Mészáros B, Erdős G, Szabó B, Schád É, Tantos Á, Abukhairan R, Horváth T, Murvai N, Kovács OP, Kovács M, Tosatto SCE, Tompa P, Dosztányi Z, Pancsa R. PhaSePro: the database of proteins driving liquid-liquid phase separation. Nucleic Acids Res 2020; 48:D360-D367. [PMID: 31612960 PMCID: PMC7145634 DOI: 10.1093/nar/gkz848] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 11/13/2022] Open
Abstract
Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid-liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life. While numerous experimental studies report novel cases, the computational identification of LLPS drivers is lagging behind, and many open questions remain about the sequence determinants, composition, regulation and biological relevance of the resulting condensates. Our limited ability to overcome these issues is largely due to the lack of a dedicated LLPS database. Therefore, here we introduce PhaSePro (https://phasepro.elte.hu), an openly accessible, comprehensive, manually curated database of experimentally validated LLPS driver proteins/protein regions. It not only provides a wealth of information on such systems, but improves the standardization of data by introducing novel LLPS-specific controlled vocabularies. PhaSePro can be accessed through an appealing, user-friendly interface and thus has definite potential to become the central resource in this dynamically developing field.
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Affiliation(s)
- Bálint Mészáros
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Gábor Erdős
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Beáta Szabó
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Ágnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Rawan Abukhairan
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Orsolya P Kovács
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Márton Kovács
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova CNR Institute of Neuroscience, Padova, Italy
| | - Péter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Structural Biology (CSB), Brussels, Belgium; Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium
| | - Zsuzsanna Dosztányi
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
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66
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Kohata K, Miyoshi D. RNA phase separation-mediated direction of molecular trafficking under conditions of molecular crowding. Biophys Rev 2020; 12:669-676. [PMID: 32415614 DOI: 10.1007/s12551-020-00696-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022] Open
Abstract
Living cells are highly crowded with large and small biomolecules. The total concentration of biomolecules can reach 400 mg/ml, and 40% of the cell volume is occupied by biomolecules. Droplet formation in cells via liquid-liquid phase separation may play a role in controlling biochemical reactions in this complex molecular environment. Liquid-liquid phase separation generally involves nucleic acids and proteins as anionic and cationic components, respectively. Significant characteristics of droplets, which make them different from protein aggregation or fibril formation, are reversibility of formation and responsiveness to the molecular environment. In this review, we quantitatively describe the molecular environment inside cells and droplets that participate in controlling central dogma reactions. Finally, we discuss the importance of droplets under conditions of molecular crowding within living cells.
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Affiliation(s)
- Kazuki Kohata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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67
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Yoshizawa T, Nozawa RS, Jia TZ, Saio T, Mori E. Biological phase separation: cell biology meets biophysics. Biophys Rev 2020; 12:519-539. [PMID: 32189162 PMCID: PMC7242575 DOI: 10.1007/s12551-020-00680-x] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Progress in development of biophysical analytic approaches has recently crossed paths with macromolecule condensates in cells. These cell condensates, typically termed liquid-like droplets, are formed by liquid-liquid phase separation (LLPS). More and more cell biologists now recognize that many of the membrane-less organelles observed in cells are formed by LLPS caused by interactions between proteins and nucleic acids. However, the detailed biophysical processes within the cell that lead to these assemblies remain largely unexplored. In this review, we evaluate recent discoveries related to biological phase separation including stress granule formation, chromatin regulation, and processes in the origin and evolution of life. We also discuss the potential issues and technical advancements required to properly study biological phase separation.
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Affiliation(s)
- Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Ryu-Suke Nozawa
- Division of Experimental Pathology, Cancer Institute of the Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Tomohide Saio
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Eiichiro Mori
- Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan.
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68
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Erdel F. Biophysical mechanisms of chromatin patterning. Curr Opin Genet Dev 2020; 61:62-68. [DOI: 10.1016/j.gde.2020.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/08/2023]
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69
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Sehgal PB, Westley J, Lerea KM, DiSenso-Browne S, Etlinger JD. Biomolecular condensates in cell biology and virology: Phase-separated membraneless organelles (MLOs). Anal Biochem 2020; 597:113691. [PMID: 32194074 DOI: 10.1016/j.ab.2020.113691] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 12/12/2022]
Abstract
Membraneless organelles (MLOs) in the cytoplasm and nucleus in the form of 2D and 3D phase-separated biomolecular condensates are increasingly viewed as critical in regulating diverse cellular functions. These functions include cell signaling, immune synapse function, nuclear transcription, RNA splicing and processing, mRNA storage and translation, virus replication and maturation, antiviral mechanisms, DNA sensing, synaptic transmission, protein turnover and mitosis. Components comprising MLOs often associate with low affinity; thus cell integrity can be critical to the maintenance of the full complement of respective MLO components. Phase-separated condensates are typically metastable (shape-changing) and can undergo dramatic, rapid and reversible assembly and disassembly in response to cell signaling events, cell stress, during mitosis, and after changes in cytoplasmic "crowding" (as observed with condensates of the human myxovirus resistance protein MxA). Increasing evidence suggests that neuron-specific aberrations in phase-separation properties of RNA-binding proteins (e.g. FUS and TDP-43) and others (such as the microtubule-binding protein tau) contribute to the development of degenerative neurological diseases (e.g. amyotrophic lateral sclerosis, frontotemporal lobar degeneration, and Alzheimer's disease). Thus, studies of liquid-like phase separation (LLPS) and the formation, structure and function of MLOs are of considerable importance in understanding basic cell biology and the pathogenesis of human diseases.
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Affiliation(s)
- Pravin B Sehgal
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA; Department of Medicine, New York Medical College, Valhalla, NY, 10595, USA.
| | - Jenna Westley
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Kenneth M Lerea
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
| | - Susan DiSenso-Browne
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA; Department of Dental Medicine, Touro College of Dental Medicine, Hawthorne, NY, 10532, USA
| | - Joseph D Etlinger
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, 10595, USA
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70
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Lin YH, Brady JP, Chan HS, Ghosh K. A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes. J Chem Phys 2020; 152:045102. [PMID: 32007034 PMCID: PMC7043852 DOI: 10.1063/1.5139661] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/23/2019] [Indexed: 12/20/2022] Open
Abstract
The physical chemistry of liquid-liquid phase separation (LLPS) of polymer solutions bears directly on the assembly of biologically functional dropletlike bodies from proteins and nucleic acids. These biomolecular condensates include certain extracellular materials and intracellular compartments that are characterized as "membraneless organelles." Analytical theories are a valuable, computationally efficient tool for addressing general principles. LLPS of neutral homopolymers is quite well described by theory, but it has been a challenge to develop general theories for the LLPS of heteropolymers involving charge-charge interactions. Here, we present a theory that combines a random-phase-approximation treatment of polymer density fluctuations and an account of intrachain conformational heterogeneity based on renormalized Kuhn lengths to provide predictions of LLPS properties as a function of pH, salt, and charge patterning along the chain sequence. Advancing beyond more limited analytical approaches, our LLPS theory is applicable to a wide variety of charged sequences ranging from highly charged polyelectrolytes to neutral or nearly neutral polyampholytes. This theory should be useful in high-throughput screening of protein and other sequences for their LLPS propensities and can serve as a basis for more comprehensive theories that incorporate nonelectrostatic interactions. Experimental ramifications of our theory are discussed.
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Affiliation(s)
- Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jacob P Brady
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Colorado, Colorado 80208, USA
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71
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Chodasiewicz M, Sokolowska EM, Nelson-Dittrich AC, Masiuk A, Beltran JCM, Nelson ADL, Skirycz A. Identification and Characterization of the Heat-Induced Plastidial Stress Granules Reveal New Insight Into Arabidopsis Stress Response. FRONTIERS IN PLANT SCIENCE 2020; 11:595792. [PMID: 33224174 PMCID: PMC7674640 DOI: 10.3389/fpls.2020.595792] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/07/2020] [Indexed: 05/06/2023]
Abstract
Plants exhibit different physiological and molecular responses to adverse changes in their environment. One such molecular response is the sequestration of proteins, RNAs, and metabolites into cytoplasmic bodies called stress granules (cSGs). Here we report that, in addition to cSGs, heat stress also induces the formation of SG-like foci (cGs) in the chloroplasts of the model plant Arabidopsis thaliana. Similarly to the cSGs, (i) cpSG assemble rapidly in response to stress and disappear when the stress ceases, (ii) cpSG formation is inhibited by treatment with a translation inhibitor (lincomycin), and (iii) cpSG are composed of a stable core and a fluid outer shell. A previously published protocol for cSG extraction was successfully adapted to isolate cpSG, followed by protein, metabolite, and RNA analysis. Analogously to the cSGs, cpSG sequester proteins essential for SG formation, dynamics, and function, also including RNA-binding proteins with prion-like domain, ATPases and chaperones, and the amino acids proline and glutamic acid. However, the most intriguing observation relates to the cpSG localization of proteins, such as a complete magnesium chelatase complex, which is involved in photosynthetic acclimation to stress. These data suggest that cpSG have a role in plant stress tolerance.
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Affiliation(s)
- Monika Chodasiewicz
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Monika Chodasiewicz, ;
| | | | | | | | | | | | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- *Correspondence: Monika Chodasiewicz, ;
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72
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Uversky VN, Finkelstein AV. Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions. Biomolecules 2019; 9:E842. [PMID: 31817975 PMCID: PMC6995567 DOI: 10.3390/biom9120842] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Proteins, these evolutionarily-edited biological polymers, are able to undergo intramolecular and intermolecular phase transitions. Spontaneous intramolecular phase transitions define the folding of globular proteins, whereas binding-induced, intra- and inter- molecular phase transitions play a crucial role in the functionality of many intrinsically-disordered proteins. On the other hand, intermolecular phase transitions are the behind-the-scenes players in a diverse set of macrosystemic phenomena taking place in protein solutions, such as new phase nucleation in bulk, on the interface, and on the impurities, protein crystallization, protein aggregation, the formation of amyloid fibrils, and intermolecular liquid-liquid or liquid-gel phase transitions associated with the biogenesis of membraneless organelles in the cells. This review is dedicated to the systematic analysis of the phase behavior of protein molecules and their ensembles, and provides a description of the major physical principles governing intramolecular and intermolecular phase transitions in protein solutions.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow, Russia
| | - Alexei V. Finkelstein
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow, Russia
- Biology Department, Lomonosov Moscow State University, 119192 Moscow, Russia
- Bioltechnogy Department, Lomonosov Moscow State University, 142290 Pushchino, Moscow, Russia
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73
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Mountain GA, Keating CD. Formation of Multiphase Complex Coacervates and Partitioning of Biomolecules within them. Biomacromolecules 2019; 21:630-640. [PMID: 31743027 DOI: 10.1021/acs.biomac.9b01354] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biological systems employ liquid-liquid phase separation to localize macromolecules and processes. The properties of intracellular condensates that allow for multiple, distinct liquid compartments and the impact of their coexistence on phase composition and solute partitioning are not well understood. Here, we generate two and three coexisting macromolecule-rich liquid compartments by complex coacervation based on ion pairing in mixtures that contain two or three polyanions together with one, two, or three polycations. While in some systems polyelectrolyte order-of-addition was important to achieve coexisting liquid phases, for others it was not, suggesting that the observed multiphase droplet morphologies are energetically favorable. Polyelectrolytes were distributed across all coacervate phases, depending on the relative interactions between them, which in turn impacted partitioning of oligonucleotide and oligopeptide solutes. These results show the ease of generating multiphase coacervates and the ability to tune their partitioning properties via the polyelectrolyte sharing inherent to multiphase complex coacervate systems.
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Affiliation(s)
- Gregory A Mountain
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Christine D Keating
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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74
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Alberti S, Gladfelter A, Mittag T. Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates. Cell 2019; 176:419-434. [PMID: 30682370 DOI: 10.1016/j.cell.2018.12.035] [Citation(s) in RCA: 1744] [Impact Index Per Article: 290.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/05/2018] [Accepted: 12/19/2018] [Indexed: 12/20/2022]
Abstract
Evidence is now mounting that liquid-liquid phase separation (LLPS) underlies the formation of membraneless compartments in cells. This realization has motivated major efforts to delineate the function of such biomolecular condensates in normal cells and their roles in contexts ranging from development to age-related disease. There is great interest in understanding the underlying biophysical principles and the specific properties of biological condensates with the goal of bringing insights into a wide range of biological processes and systems. The explosion of physiological and pathological contexts involving LLPS requires clear standards for their study. Here, we propose guidelines for rigorous experimental characterization of LLPS processes in vitro and in cells, discuss the caveats of common experimental approaches, and point out experimental and theoretical gaps in the field.
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Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Technische Universität Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Biotechnology Center, 01307 Dresden, Germany.
| | - Amy Gladfelter
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Tanja Mittag
- Department for Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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75
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Mudogo CN, Falke S, Brognaro H, Duszenko M, Betzel C. Protein phase separation and determinants of in cell crystallization. Traffic 2019; 21:220-230. [DOI: 10.1111/tra.12711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Celestin N. Mudogo
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
- Department of Basic Sciences, School of MedicineUniversity of Kinshasa Kinshasa Democratic Republic of Congo
| | - Sven Falke
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
| | - Hévila Brognaro
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
- Centre for Free‐Electron‐Laser Science Hamburg Germany
| | - Michael Duszenko
- Institute of Neurophysiology, University of Tübingen Tübingen Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
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76
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Pushpalatha KV, Besse F. Local Translation in Axons: When Membraneless RNP Granules Meet Membrane-Bound Organelles. Front Mol Biosci 2019; 6:129. [PMID: 31824961 PMCID: PMC6882739 DOI: 10.3389/fmolb.2019.00129] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cell compartmentalization relies on long-known membrane-delimited organelles, as well as on more recently discovered membraneless macromolecular condensates. How these two types of organelles interact to regulate cellular functions is still largely unclear. In this review, we highlight how membraneless ribonucleoprotein (RNP) organelles, enriched in RNAs and associated regulatory proteins, cooperate with membrane-bound organelles for tight spatio-temporal control of gene expression in the axons of neuronal cells. Specifically, we present recent evidence that motile membrane-bound organelles are used as vehicles by RNP cargoes, promoting the long-range transport of mRNA molecules to distal axons. As demonstrated by recent work, membrane-bound organelles also promote local protein synthesis, by serving as platforms for the local translation of mRNAs recruited to their outer surface. Furthermore, dynamic and specific association between RNP cargoes and membrane-bound organelles is mediated by bi-partite adapter molecules that interact with both types of organelles selectively, in a regulated-manner. Maintaining such a dynamic interplay is critical, as alterations in this process are linked to neurodegenerative diseases. Together, emerging studies thus point to the coordination of membrane-bound and membraneless organelles as an organizing principle underlying local cellular responses.
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Affiliation(s)
| | - Florence Besse
- Université Côte d'Azur, CNRS, Inserm, Institut de Biology Valrose, Nice, France
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77
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Human Antiviral Protein MxA Forms Novel Metastable Membraneless Cytoplasmic Condensates Exhibiting Rapid Reversible Tonicity-Driven Phase Transitions. J Virol 2019; 93:JVI.01014-19. [PMID: 31484749 DOI: 10.1128/jvi.01014-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/28/2019] [Indexed: 12/13/2022] Open
Abstract
Phase-separated biomolecular condensates of proteins and nucleic acids form functional membrane-less organelles (e.g., stress granules and P-bodies) in the mammalian cell cytoplasm and nucleus. In contrast to the long-standing belief that interferon (IFN)-inducible human myxovirus resistance protein A (MxA) associated with the endoplasmic reticulum (ER) and Golgi apparatus, we report that MxA formed membraneless metastable (shape-changing) condensates in the cytoplasm. In our studies, we used the same cell lines and methods as those used by previous investigators but concluded that wild-type MxA formed variably sized spherical or irregular bodies, filaments, and even a reticulum distinct from that of ER/Golgi membranes. Moreover, in Huh7 cells, MxA structures associated with a novel cytoplasmic reticular meshwork of intermediate filaments. In live-cell assays, 1,6-hexanediol treatment led to rapid disassembly of green fluorescent protein (GFP)-MxA structures; FRAP revealed a relative stiffness with a mobile fraction of 0.24 ± 0.02 within condensates, consistent with a higher-order MxA network structure. Remarkably, in intact cells, GFP-MxA condensates reversibly disassembled/reassembled within minutes of sequential decrease/increase, respectively, in tonicity of extracellular medium, even in low-salt buffers adjusted only with sucrose. Condensates formed from IFN-α-induced endogenous MxA also displayed tonicity-driven disassembly/reassembly. In vesicular stomatitis virus (VSV)-infected Huh7 cells, the nucleocapsid (N) protein, which participates in forming phase-separated viral structures, associated with spherical GFP-MxA condensates in cells showing an antiviral effect. These observations prompt comparisons with the extensive literature on interactions between viruses and stress granules/P-bodies. Overall, the new data correct a long-standing misinterpretation in the MxA literature and provide evidence for membraneless MxA biomolecular condensates in the uninfected cell cytoplasm.IMPORTANCE There is a long-standing belief that interferon (IFN)-inducible human myxovirus resistance protein A (MxA), which displays antiviral activity against several RNA and DNA viruses, associates with the endoplasmic reticulum (ER) and Golgi apparatus. We provide data to correct this misinterpretation and further report that MxA forms membraneless metastable (shape-changing) condensates in the cytoplasm consisting of variably sized spherical or irregular bodies, filaments, and even a reticulum. Remarkably, MxA condensates showed the unique property of rapid (within 1 to 3 min) reversible disassembly and reassembly in intact cells exposed sequentially to hypotonic and isotonic conditions. Moreover, GFP-MxA condensates included the VSV nucleocapsid (N) protein, a protein previously shown to form liquid-like condensates. Since intracellular edema and ionic changes are hallmarks of cytopathic effects of a viral infection, the tonicity-driven regulation of MxA condensates may reflect a mechanism for modulation of MxA function during viral infection.
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78
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Schmidt HB, Barreau A, Rohatgi R. Phase separation-deficient TDP43 remains functional in splicing. Nat Commun 2019; 10:4890. [PMID: 31653829 PMCID: PMC6814767 DOI: 10.1038/s41467-019-12740-2] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022] Open
Abstract
Intrinsically disordered regions (IDRs) are often fast-evolving protein domains of low sequence complexity that can drive phase transitions and are commonly found in many proteins associated with neurodegenerative diseases, including the RNA processing factor TDP43. Yet, how phase separation contributes to the physiological functions of TDP43 in cells remains enigmatic. Here, we combine systematic mutagenesis guided by evolutionary sequence analysis with a live-cell reporter assay of TDP43 phase dynamics to identify regularly-spaced hydrophobic motifs separated by flexible, hydrophilic segments in the IDR as a key determinant of TDP43 phase properties. This heuristic framework allows customization of the material properties of TDP43 condensates to determine effects on splicing function. Remarkably, even a mutant that fails to phase-separate at physiological concentrations can still efficiently mediate the splicing of a quantitative, single-cell splicing reporter and endogenous targets. This suggests that the ability of TDP43 to phase-separate is not essential for its splicing function.
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Affiliation(s)
| | - Ariana Barreau
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Rajat Rohatgi
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA, 94305, USA.
- Department of Medicine, Stanford School of Medicine, Stanford, CA, 94305, USA.
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79
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Supramolecular Fuzziness of Intracellular Liquid Droplets: Liquid-Liquid Phase Transitions, Membrane-Less Organelles, and Intrinsic Disorder. Molecules 2019; 24:molecules24183265. [PMID: 31500307 PMCID: PMC6767272 DOI: 10.3390/molecules24183265] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/29/2019] [Accepted: 09/06/2019] [Indexed: 12/14/2022] Open
Abstract
Cells are inhomogeneously crowded, possessing a wide range of intracellular liquid droplets abundantly present in the cytoplasm of eukaryotic and bacterial cells, in the mitochondrial matrix and nucleoplasm of eukaryotes, and in the chloroplast’s stroma of plant cells. These proteinaceous membrane-less organelles (PMLOs) not only represent a natural method of intracellular compartmentalization, which is crucial for successful execution of various biological functions, but also serve as important means for the processing of local information and rapid response to the fluctuations in environmental conditions. Since PMLOs, being complex macromolecular assemblages, possess many characteristic features of liquids, they represent highly dynamic (or fuzzy) protein–protein and/or protein–nucleic acid complexes. The biogenesis of PMLOs is controlled by specific intrinsically disordered proteins (IDPs) and hybrid proteins with ordered domains and intrinsically disordered protein regions (IDPRs), which, due to their highly dynamic structures and ability to facilitate multivalent interactions, serve as indispensable drivers of the biological liquid–liquid phase transitions (LLPTs) giving rise to PMLOs. In this article, the importance of the disorder-based supramolecular fuzziness for LLPTs and PMLO biogenesis is discussed.
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80
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Alshareedah I, Kaur T, Ngo J, Seppala H, Kounatse LAD, Wang W, Moosa MM, Banerjee PR. Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes. J Am Chem Soc 2019; 141:14593-14602. [PMID: 31437398 DOI: 10.1021/jacs.9b03689] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In eukaryotic cells, ribonucleoproteins (RNPs) form mesoscale condensates by liquid-liquid phase separation that play essential roles in subcellular dynamic compartmentalization. The formation and dissolution of many RNP condensates are finely dependent on the RNA-to-RNP ratio, giving rise to a windowlike phase separation behavior. This is commonly referred to as reentrant liquid condensation (RLC). Here, using ribonucleoprotein-inspired polypeptides with low-complexity RNA-binding sequences as well as an archetypal disordered RNP, fused in sarcoma, as model systems, we investigate the molecular driving forces underlying this nonmonotonous phase transition. We show that an interplay between short-range cation-π attractions and long-range electrostatic forces governs the heterotypic RLC behavior of RNP-RNA complexes. Short-range attractions, which can be encoded by both polypeptide chain primary sequence and nucleic acid base sequence, control the two-phase coexistence regime, regulate material properties of polypeptide-RNA condensates, and oppose condensate reentrant dissolution. In the presence of excess RNA, a competition between short-range attraction and long-range electrostatic repulsion drives the formation of a colloidlike cluster phase. With increasing short-range attraction, the fluid dynamics of the cluster phase is arrested, leading to the formation of a colloidal gel. Our results reveal that phase behavior, supramolecular organization, and material states of RNP-RNA assemblies are controlled by a dynamic interplay between molecular interactions at different length scales.
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Affiliation(s)
- Ibraheem Alshareedah
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Taranpreet Kaur
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Jason Ngo
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Hannah Seppala
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | | | - Wei Wang
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Mahdi Muhammad Moosa
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
| | - Priya R Banerjee
- Department of Physics , University at Buffalo , Buffalo , New York 14260 , United States
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81
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Zhang C, Rabouille C. Membrane-Bound Meet Membraneless in Health and Disease. Cells 2019; 8:cells8091000. [PMID: 31470564 PMCID: PMC6770257 DOI: 10.3390/cells8091000] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022] Open
Abstract
Membraneless organelles (MLOs) are defined as cellular structures that are not sealed by a lipidic membrane and are shown to form by phase separation. They exist in both the nucleus and the cytoplasm that is also heavily populated by numerous membrane-bound organelles. Even though the name membraneless suggests that MLOs are free of membrane, both membrane and factors regulating membrane trafficking steps are emerging as important components of MLO formation and function. As a result, we name them biocondensates. In this review, we examine the relationships between biocondensates and membrane. First, inhibition of membrane trafficking in the early secretory pathway leads to the formation of biocondensates (P-bodies and Sec bodies). In the same vein, stress granules have a complex relationship with the cyto-nuclear transport machinery. Second, membrane contributes to the regulated formation of phase separation in the cells and we will present examples including clustering at the plasma membrane and at the synapse. Finally, the whole cell appears to transit from an interphase phase-separated state to a mitotic diffuse state in a DYRK3 dependent manner. This firmly establishes a crosstalk between the two types of cell organization that will need to be further explored.
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Affiliation(s)
- Chujun Zhang
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
- Department of Biomedical Science of Cells and Systems, University Medical Center Groningen, 9713 AV Groningen, The Netherlands.
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82
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Martin N. Dynamic Synthetic Cells Based on Liquid-Liquid Phase Separation. Chembiochem 2019; 20:2553-2568. [PMID: 31039282 DOI: 10.1002/cbic.201900183] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Indexed: 12/16/2022]
Abstract
Living cells have long been a source of inspiration for chemists. Their capacity of performing complex tasks relies on the spatiotemporal coordination of matter and energy fluxes. Recent years have witnessed growing interest in the bottom-up construction of cell-like models capable of reproducing aspects of such dynamic organisation. Liquid-liquid phase-separation (LLPS) processes in water are increasingly recognised as representing a viable compartmentalisation strategy through which to produce dynamic synthetic cells. Herein, we highlight examples of the dynamic properties of LLPS used to assemble synthetic cells, including their biocatalytic activity, reversible condensation and dissolution, growth and division, and recent directions towards the design of higher-order structures and behaviour.
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Affiliation(s)
- Nicolas Martin
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, 115 Avenue du Dr. Albert Schweitzer, 33600, Pessac, France
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83
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Vijayakumar J, Perrois C, Heim M, Bousset L, Alberti S, Besse F. The prion-like domain of Drosophila Imp promotes axonal transport of RNP granules in vivo. Nat Commun 2019; 10:2593. [PMID: 31197139 PMCID: PMC6565635 DOI: 10.1038/s41467-019-10554-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 05/15/2019] [Indexed: 01/29/2023] Open
Abstract
Prion-like domains (PLDs), defined by their low sequence complexity and intrinsic disorder, are present in hundreds of human proteins. Although gain-of-function mutations in the PLDs of neuronal RNA-binding proteins have been linked to neurodegenerative disease progression, the physiological role of PLDs and their range of molecular functions are still largely unknown. Here, we show that the PLD of Drosophila Imp, a conserved component of neuronal ribonucleoprotein (RNP) granules, is essential for the developmentally-controlled localization of Imp RNP granules to axons and regulates in vivo axonal remodeling. Furthermore, we demonstrate that Imp PLD restricts, rather than promotes, granule assembly, revealing a novel modulatory function for PLDs in RNP granule homeostasis. Swapping the position of Imp PLD compromises RNP granule dynamic assembly but not transport, suggesting that these two functions are uncoupled. Together, our study uncovers a physiological function for PLDs in the spatio-temporal control of neuronal RNP assemblies. The physiological role of prion-like domains (PLDs) within RNA-binding proteins is not well understood. Here, authors show in Drosophila that the PLD in the protein Imp is required for localization of ribonucleoprotein granules to axons and axonal remodelling.
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Affiliation(s)
| | | | - Marjorie Heim
- University Côte d'Azur, CNRS, Inserm, iBV, Nice, 06100, France
| | - Luc Bousset
- Paris-Saclay Institute of Neuroscience, Orsay, 91505, France
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Center for Molecular and Cellular Bioengineering (CMCB), Biotechnology Center, Technische Universität Dresden, Dresden, 01307, Germany
| | - Florence Besse
- University Côte d'Azur, CNRS, Inserm, iBV, Nice, 06100, France.
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84
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Intrinsic Disorder-Based Emergence in Cellular Biology: Physiological and Pathological Liquid-Liquid Phase Transitions in Cells. Polymers (Basel) 2019; 11:polym11060990. [PMID: 31167414 PMCID: PMC6631845 DOI: 10.3390/polym11060990] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
The visible outcome of liquid-liquid phase transitions (LLPTs) in cells is the formation and disintegration of various proteinaceous membrane-less organelles (PMLOs). Although LLPTs and related PMLOs have been observed in living cells for over 200 years, the physiological functions of these transitions (also known as liquid-liquid phase separation, LLPS) are just starting to be understood. While unveiling the functionality of these transitions is important, they have come into light more recently due to the association of abnormal LLPTs with various pathological conditions. In fact, several maladies, such as various cancers, different neurodegenerative diseases, and cardiovascular diseases, are known to be associated with either aberrant LLPTs or some pathological transformations within the resultant PMLOs. Here, we will highlight both the physiological functions of cellular liquid-liquid phase transitions as well as the pathological consequences produced through both dysregulated biogenesis of PMLOs and the loss of their dynamics. We will also discuss the potential downstream toxic effects of proteins that are involved in pathological formations.
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85
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Abstract
Cells under stress must adjust their physiology, metabolism, and architecture to adapt to the new conditions. Most importantly, they must down-regulate general gene expression, but at the same time induce synthesis of stress-protective factors, such as molecular chaperones. Here, we investigate how the process of phase separation is used by cells to ensure adaptation to stress. We summarize recent findings and propose that the solubility of important translation factors is specifically affected by changes in physical-chemical parameters such temperature or pH and modulated by intrinsically disordered prion-like domains. These stress-triggered changes in protein solubility induce phase separation into condensates that regulate the activity of the translation factors and promote cellular fitness. Prion-like domains play important roles in this process as environmentally regulated stress sensors and modifier sequences that determine protein solubility and phase behavior. We propose that protein phase separation is an evolutionary conserved feature of proteins that cells harness to regulate adaptive stress responses and ensure survival in extreme environmental conditions.
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Affiliation(s)
- Titus M Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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86
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Turoverov KK, Kuznetsova IM, Fonin AV, Darling AL, Zaslavsky BY, Uversky VN. Stochasticity of Biological Soft Matter: Emerging Concepts in Intrinsically Disordered Proteins and Biological Phase Separation. Trends Biochem Sci 2019; 44:716-728. [PMID: 31023505 DOI: 10.1016/j.tibs.2019.03.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/14/2019] [Accepted: 03/22/2019] [Indexed: 12/19/2022]
Abstract
At the turn of this century, cardinal changes took place in the perceptions of the structure and function of proteins, as well as in the organizational principles of membrane-less organelles. As a result, the model of the organization of living matter is changing to one described by highly dynamic biological soft matter positioned at the edge of chaos. Intrinsically disordered proteins (IDPs) and membrane-less organelles are key examples of this new outlook and may represent a critical foundation of life, defining its complexity and the evolution of living things.
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Affiliation(s)
- Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia; Peter the Great St. Petersburg Polytechnic University, Department of Biophysics, Polytechnicheskaya Av. 29, St. Petersburg 195251, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - April L Darling
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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87
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Nakashima KK, Vibhute MA, Spruijt E. Biomolecular Chemistry in Liquid Phase Separated Compartments. Front Mol Biosci 2019; 6:21. [PMID: 31001538 PMCID: PMC6456709 DOI: 10.3389/fmolb.2019.00021] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/11/2019] [Indexed: 12/11/2022] Open
Abstract
Biochemical processes inside the cell take place in a complex environment that is highly crowded, heterogeneous, and replete with interfaces. The recently recognized importance of biomolecular condensates in cellular organization has added new elements of complexity to our understanding of chemistry in the cell. Many of these condensates are formed by liquid-liquid phase separation (LLPS) and behave like liquid droplets. Such droplet organelles can be reproduced and studied in vitro by using coacervates and have some remarkable features, including regulated assembly, differential partitioning of macromolecules, permeability to small molecules, and a uniquely crowded environment. Here, we review the main principles of biochemical organization in model membraneless compartments. We focus on some promising in vitro coacervate model systems that aptly mimic part of the compartmentalized cellular environment. We address the physicochemical characteristics of these liquid phase separated compartments, and their impact on biomolecular chemistry and assembly. These model systems enable a systematic investigation of the role of spatiotemporal organization of biomolecules in controlling biochemical processes in the cell, and they provide crucial insights for the development of functional artificial organelles and cells.
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Affiliation(s)
| | | | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, Netherlands
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88
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Pancsa R, Schad E, Tantos A, Tompa P. Emergent functions of proteins in non-stoichiometric supramolecular assemblies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:970-979. [PMID: 30826453 DOI: 10.1016/j.bbapap.2019.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 12/12/2022]
Abstract
Proteins are the basic functional units of the cell, carrying out myriads of functions essential for life. There are countless reports in molecular cell biology addressing the functioning of proteins under physiological and pathological conditions, aiming to understand life at the atomistic-molecular level and thereby being able to develop remedies against diseases. The central theme in most of these studies is that the functional unit under study is the protein itself. Recent rapid progress has radically challenged and extended this protein-function paradigm, by demonstrating that novel function(s) may emerge when proteins form dynamic and non-stoichiometric supramolecular assemblies. There is an increasing number of cases for such collective functions, such as targeting, localization, protection/shielding and filtering effects, as exemplified by signaling complexes and prions, biominerals and mucus, amphibian adhesions and bacterial biofilms, and a broad range of membraneless organelles (bio-condensates) formed by liquid-liquid phase separation in the cell. In this short review, we show that such non-stoichiometric organization may derive from the heterogeneity of the system, a mismatch in valency and/or geometry of the partners, and/or intrinsic structural disorder and multivalency of the component proteins. Either way, the resulting functional features cannot be simply described by, or predicted from, the properties of the isolated single protein(s), as they belong to the collection of proteins.
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Affiliation(s)
- Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary; VIB Center for Structural Biology (CSB), Brussels, Belgium; Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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89
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Sehgal PB. Biomolecular condensates in cancer cell biology: interleukin-6-induced cytoplasmic and nuclear STAT3/PY-STAT3 condensates in hepatoma cells. Contemp Oncol (Pozn) 2019; 23:16-22. [PMID: 31061632 PMCID: PMC6500392 DOI: 10.5114/wo.2019.83018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 01/21/2019] [Indexed: 11/17/2022] Open
Abstract
We highlight previous incompletely understood cell biology data in the STAT3 signaling field with respect to interleukin-6 (IL-6)-induced activation of this transcription factor in hepatoma cells to generate cytoplasmic and nuclear STAT3 bodies. We provide a novel re-interpretation of the previous observations. We show that IL-6-induced GFP-STAT3/PY-STAT3 cytoplas-mic and nuclear bodies represent phase-separated biomolecular condensates. These structures represent examples of a cytokine-induced phase transition which occurs within 10-15 min of exposure to the cytokine, and which was Tyr phosphorylation dependent. Evidence that these IL-6-induced cytoplasmic and nuclear GFP-STAT3 bodies in live cells represented phase-separated condensates came from the observation that 1,6-hexanediol caused their disassembly within 30-60 seconds. Moreover, these STAT3 condensates also showed rapid tonicity-driven phase transitions - disassembly under hypotonic conditions and reassembly when cells were returned to isotonic medium. That STAT3 condensates were rapidly disassembled in hypotonic buffer commonly used for cell fractionation points to a limitation of studies of STAT3 biochemistry using hypotonic swelling and mechanical breakage. Overall, the new data help reinterpret IL-6-induced cytoplasmic and nuclear STAT3 bodies as phase-separated biomolecular condensates, and bring the concept of membrane-less organelles to the cytokine-induced STAT transcription factor field and cancer cell biology.
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Affiliation(s)
- Pravin B Sehgal
- Department of Cell Biology & Anatomy, New York Medical College, Valhalla, New York, USADepartment of Medicine, New York Medical College, Valhalla, New York, USA
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90
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Identification and characterization of a factor Va-binding site on human prothrombin fragment 2. Sci Rep 2019; 9:2436. [PMID: 30792421 PMCID: PMC6385242 DOI: 10.1038/s41598-019-38857-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/11/2019] [Indexed: 11/18/2022] Open
Abstract
The fragment 2 domain (F2) of prothrombin and its interaction with factor (F) Va is known to contribute significantly to prothrombinase-catalyzed activation of prothrombin. The extent to which the F2-FVa interaction affects the overall thrombin generation, however, is uncertain. To study this interaction, nuclear magnetic resonance spectroscopy of recombinant F2 was used to identify seven residues within F2 that are significantly responsive to FVa binding. The functional role of this region in interacting with FVa during prothrombin activation was verified by the FVa-dependent inhibition of thrombin generation using peptides that mimic the same region of F2. Because six of the seven residues were within a 9-residue span, these were mutated to generate a prothrombin derivative (PT6). These mutations led to a decreased affinity for FVa as determined by surface plasmon resonance. When thrombin generation by an array of FXa containing prothrombinase components was monitored, a 54% decrease in thrombin generation was observed with PT6 compared with the wild-type, only when FVa was present. The functional significance of the specific low-affinity binding between F2 and FVa is discussed within the context of a dynamic model of molecular interactions between prothrombin and FVa engaging multiple contact sites.
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91
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Kaur T, Alshareedah I, Wang W, Ngo J, Moosa MM, Banerjee PR. Molecular Crowding Tunes Material States of Ribonucleoprotein Condensates. Biomolecules 2019; 9:biom9020071. [PMID: 30791483 PMCID: PMC6406554 DOI: 10.3390/biom9020071] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 12/19/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membraneless liquid condensates that dynamically form, dissolve, and mature into a gel-like state in response to a changing cellular environment. RNP condensation is largely governed by promiscuous attractive inter-chain interactions mediated by low-complexity domains (LCDs). Using an archetypal disordered RNP, fused in sarcoma (FUS), here we study how molecular crowding impacts the RNP liquid condensation. We observe that the liquid–liquid coexistence boundary of FUS is lowered by polymer crowders, consistent with an excluded volume model. With increasing bulk crowder concentration, the RNP partition increases and the diffusion rate decreases in the condensed phase. Furthermore, we show that RNP condensates undergo substantial hardening wherein protein-dense droplets transition from viscous fluid to viscoelastic gel-like states in a crowder concentration-dependent manner. Utilizing two distinct LCDs that broadly represent commonly occurring sequence motifs driving RNP phase transitions, we reveal that the impact of crowding is largely independent of LCD charge and sequence patterns. These results are consistent with a thermodynamic model of crowder-mediated depletion interaction, which suggests that inter-RNP attraction is enhanced by molecular crowding. The depletion force is likely to play a key role in tuning the physical properties of RNP condensates within the crowded cellular space.
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Affiliation(s)
- Taranpreet Kaur
- Department of Physics, University at Buffalo, SUNY, NY 14260, USA.
| | | | - Wei Wang
- Department of Physics, University at Buffalo, SUNY, NY 14260, USA.
| | - Jason Ngo
- Department of Physics, University at Buffalo, SUNY, NY 14260, USA.
| | - Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Priya R Banerjee
- Department of Physics, University at Buffalo, SUNY, NY 14260, USA.
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92
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Kojima T, Lin CC, Takayama S, Fan SK. Determination of Aqueous Two-Phase System Binodals and Tie-Lines by Electrowetting-on-Dielectric Droplet Manipulation. Chembiochem 2019; 20:270-275. [PMID: 30394637 PMCID: PMC6452887 DOI: 10.1002/cbic.201800553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Indexed: 01/12/2023]
Abstract
Handling the aqueous two-phase systems (ATPSs) formed by liquid-liquid phase separation (LLPS) relies on the accurate construction of binodal curves and tie-lines, which delineate the polymer concentrations required for phase separation and depict the properties of the resulting phases, respectively. Various techniques to determine the binodal curves and tie-lines of ATPSs exist, but most rely on manually pipetting relatively large volumes of fluids in a slow and tedious manner. We describe a method to determine ATPS binodals and tie-lines that overcomes these disadvantages: microscale droplet manipulation by electrowetting-on-dielectric (EWOD). EWOD enables automated handling of droplets in an optically transparent platform that allows for in situ droplet observation. Separated phases are clearly visible, and the volumes of each phase are readily determined. Additionally, in considering the molecular crowding present in living cells, this work examines the role of a macromolecule in prompting LLPS. These results show that EWOD-driven droplet manipulation effectively interrogates the phase dynamics of ATPSs and macromolecular crowding in LLPS.
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Affiliation(s)
- Taisuke Kojima
- The Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, 950 Atlantic Drive NW, Atalanta 30332 (USA)
| | - Chu-Chi Lin
- Department of Mechanical Engineering, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 10617 (Taiwan)
| | - Shuichi Takayama
- The Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, 950 Atlantic Drive NW, Atalanta 30332 (USA)
| | - Shih-Kang Fan
- Department of Mechanical Engineering, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 10617 (Taiwan)
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93
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Boija A, Klein IA, Sabari BR, Dall'Agnese A, Coffey EL, Zamudio AV, Li CH, Shrinivas K, Manteiga JC, Hannett NM, Abraham BJ, Afeyan LK, Guo YE, Rimel JK, Fant CB, Schuijers J, Lee TI, Taatjes DJ, Young RA. Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains. Cell 2018; 175:1842-1855.e16. [PMID: 30449618 PMCID: PMC6295254 DOI: 10.1016/j.cell.2018.10.042] [Citation(s) in RCA: 1180] [Impact Index Per Article: 168.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/20/2018] [Accepted: 10/16/2018] [Indexed: 01/19/2023]
Abstract
Gene expression is controlled by transcription factors (TFs) that consist of DNA-binding domains (DBDs) and activation domains (ADs). The DBDs have been well characterized, but little is known about the mechanisms by which ADs effect gene activation. Here, we report that diverse ADs form phase-separated condensates with the Mediator coactivator. For the OCT4 and GCN4 TFs, we show that the ability to form phase-separated droplets with Mediator in vitro and the ability to activate genes in vivo are dependent on the same amino acid residues. For the estrogen receptor (ER), a ligand-dependent activator, we show that estrogen enhances phase separation with Mediator, again linking phase separation with gene activation. These results suggest that diverse TFs can interact with Mediator through the phase-separating capacity of their ADs and that formation of condensates with Mediator is involved in gene activation.
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Affiliation(s)
- Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Benjamin R Sabari
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Eliot L Coffey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Krishna Shrinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John C Manteiga
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Lena K Afeyan
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yang E Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Jenna K Rimel
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Charli B Fant
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Jurian Schuijers
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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94
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Monterroso B, Zorrilla S, Sobrinos-Sanguino M, Robles-Ramos MA, López-Álvarez M, Margolin W, Keating CD, Rivas G. Bacterial FtsZ protein forms phase-separated condensates with its nucleoid-associated inhibitor SlmA. EMBO Rep 2018; 20:embr.201845946. [PMID: 30523075 DOI: 10.15252/embr.201845946] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 11/09/2022] Open
Abstract
Macromolecular condensation resulting from biologically regulated liquid-liquid phase separation is emerging as a mechanism to organize intracellular space in eukaryotes, with broad implications for cell physiology and pathology. Despite their small size, bacterial cells are also organized by proteins such as FtsZ, a tubulin homolog that assembles into a ring structure precisely at the cell midpoint and is required for cytokinesis. Here, we demonstrate that FtsZ can form crowding-induced condensates, reminiscent of those observed for eukaryotic proteins. Formation of these FtsZ-rich droplets occurs when FtsZ is bound to SlmA, a spatial regulator of FtsZ that antagonizes polymerization, while also binding to specific sites on chromosomal DNA. The resulting condensates are dynamic, allowing FtsZ to undergo GTP-driven assembly to form protein fibers. They are sensitive to compartmentalization and to the presence of a membrane boundary in cell mimetic systems. This is a novel example of a bacterial nucleoprotein complex exhibiting condensation into liquid droplets, suggesting that phase separation may also play a functional role in the spatiotemporal organization of essential bacterial processes.
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Affiliation(s)
- Begoña Monterroso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Silvia Zorrilla
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Marta Sobrinos-Sanguino
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Miguel A Robles-Ramos
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Marina López-Álvarez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston, TX, USA
| | - Christine D Keating
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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95
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Vural A, Fadillioglu E, Kelesoglu F, Ma D, Lanier SM. Role of G-proteins and phosphorylation in the distribution of AGS3 to cell puncta. J Cell Sci 2018; 131:jcs.216507. [PMID: 30404823 DOI: 10.1242/jcs.216507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/02/2018] [Indexed: 12/20/2022] Open
Abstract
Activator of G-protein signaling 3 (AGS3, also known as GPSM1) exhibits broad functional diversity and oscillates among different subcellular compartments in a regulated manner. AGS3 consists of a tetratricopeptide repeat (TPR) domain and a G-protein regulatory (GPR) domain. Here, we tested the hypothesis that phosphorylation of the AGS3 GPR domain regulates its subcellular distribution and functionality. In contrast to the cortical and/or diffuse non-homogeneous distribution of wild-type (WT) AGS3, an AGS3 construct lacking all 24 potential phosphorylation sites in the GPR domain localized to cytosolic puncta. This change in localization was revealed to be dependent upon phosphorylation of a single threonine amino acid (T602). The punctate distribution of AGS3-T602A was rescued by co-expression of Gαi and Gαo but not Gαs or Gαq Following treatment with alkaline phosphatase, both AGS3-T602A and WT AGS3 exhibited a gel shift in SDS-PAGE as compared to untreated WT AGS3, consistent with a loss of protein phosphorylation. The punctate distribution of AGS3-T602A was lost in an AGS3-A602T conversion mutant, but was still present upon T602 mutation to glutamate or aspartate. These results implicate dynamic phosphorylation as a discrete mechanism to regulate the subcellular distribution of AGS3 and associated functionality.
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Affiliation(s)
- Ali Vural
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Ersin Fadillioglu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Fatih Kelesoglu
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular, and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stephen M Lanier
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA .,Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
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96
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Krishnakumar P, Riemer S, Perera R, Lingner T, Goloborodko A, Khalifa H, Bontems F, Kaufholz F, El-Brolosy MA, Dosch R. Functional equivalence of germ plasm organizers. PLoS Genet 2018; 14:e1007696. [PMID: 30399145 PMCID: PMC6219760 DOI: 10.1371/journal.pgen.1007696] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/16/2018] [Indexed: 11/18/2022] Open
Abstract
The proteins Oskar (Osk) in Drosophila and Bucky ball (Buc) in zebrafish act as germ plasm organizers. Both proteins recapitulate germ plasm activities but seem to be unique to their animal groups. Here, we discover that Osk and Buc show similar activities during germ cell specification. Drosophila Osk induces additional PGCs in zebrafish. Surprisingly, Osk and Buc do not show homologous protein motifs that would explain their related function. Nonetheless, we detect that both proteins contain stretches of intrinsically disordered regions (IDRs), which seem to be involved in protein aggregation. IDRs are known to rapidly change their sequence during evolution, which might obscure biochemical interaction motifs. Indeed, we show that Buc binds to the known Oskar interactors Vasa protein and nanos mRNA indicating conserved biochemical activities. These data provide a molecular framework for two proteins with unrelated sequence but with equivalent function to assemble a conserved core-complex nucleating germ plasm. Multicellular organisms use gametes for their propagation. Gametes are formed from germ cells, which are specified during embryogenesis in some animals by the inheritance of RNP granules known as germ plasm. Transplantation of germ plasm induces extra germ cells, whereas germ plasm ablation leads to the loss of gametes and sterility. Therefore, germ plasm is key for germ cell formation and reproduction. However, the molecular mechanisms of germ cell specification by germ plasm in the vertebrate embryo remain an unsolved question. Proteins, which assemble the germ plasm, are known as germ plasm organizers. Here, we show that the two germ plasm organizers Oskar from the fly and Bucky ball from the fish show similar functions by using a cross species approach. Both are intrinsically disordered proteins, which rapidly changed their sequence during evolution. Moreover, both proteins still interact with conserved components of the germ cell specification pathway. These data might provide a first example of two proteins with the same biological role, but distinct sequence.
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Affiliation(s)
- Pritesh Krishnakumar
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Stephan Riemer
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Roshan Perera
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Thomas Lingner
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Alexander Goloborodko
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Hazem Khalifa
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Franck Bontems
- Laboratory of Metabolism, Department of Internal Medicine Specialties, Faculty of Medicine, University of Geneva, Switzerland
| | - Felix Kaufholz
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Mohamed A. El-Brolosy
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Roland Dosch
- Institute for Developmental Biochemistry, University Medical Center, Göttingen, Germany
- Institute of Human Genetics, University Medical Center, Göttingen, Germany
- * E-mail:
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97
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Enzymatic complexes across scales. Essays Biochem 2018; 62:501-514. [PMID: 30315098 PMCID: PMC6204551 DOI: 10.1042/ebc20180008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023]
Abstract
An unprecedented opportunity to integrate ~100 years of meticulous in vitro biomolecular research is currently provided in the light of recent advances in methods to visualize closer-to-native architectures of biomolecular machines, and metabolic enzymes in particular. Traditional views of enzymes, namely biomolecular machines, only partially explain their role, organization and kinetics in the cellular milieu. Enzymes self- or hetero-associate, form fibers, may bind to membranes or cytoskeletal elements, have regulatory roles, associate into higher order assemblies (metabolons) or even actively participate in phase-separated membraneless organelles, and all the above in a transient, temporal and spatial manner in response to environmental changes or structural/functional changes of their assemblies. Here, we focus on traditional and emerging concepts in cellular biochemistry and discuss new opportunities in bridging structural, molecular and cellular analyses for metabolic pathways, accumulated over the years, highlighting functional aspects of enzymatic complexes discussed across different levels of spatial resolution.
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98
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Zagrovic B, Bartonek L, Polyansky AA. RNA-protein interactions in an unstructured context. FEBS Lett 2018; 592:2901-2916. [PMID: 29851074 PMCID: PMC6175095 DOI: 10.1002/1873-3468.13116] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/12/2018] [Accepted: 05/13/2018] [Indexed: 02/02/2023]
Abstract
Despite their importance, our understanding of noncovalent RNA-protein interactions is incomplete. This especially concerns the binding between RNA and unstructured protein regions, a widespread class of such interactions. Here, we review the recent experimental and computational work on RNA-protein interactions in an unstructured context with a particular focus on how such interactions may be shaped by the intrinsic interaction affinities between individual nucleobases and protein side chains. Specifically, we articulate the claim that the universal genetic code reflects the binding specificity between nucleobases and protein side chains and that, in turn, the code may be seen as the Rosetta stone for understanding RNA-protein interactions in general.
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Affiliation(s)
- Bojan Zagrovic
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria
| | - Lukas Bartonek
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria
| | - Anton A. Polyansky
- Department of Structural and Computational BiologyMax F. Perutz LaboratoriesUniversity of ViennaAustria,MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
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99
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Reconstituted Postsynaptic Density as a Molecular Platform for Understanding Synapse Formation and Plasticity. Cell 2018; 174:1172-1187.e16. [PMID: 30078712 DOI: 10.1016/j.cell.2018.06.047] [Citation(s) in RCA: 282] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/17/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022]
Abstract
Synapses are semi-membraneless, protein-dense, sub-micron chemical reaction compartments responsible for signal processing in each and every neuron. Proper formation and dynamic responses to stimulations of synapses, both during development and in adult, are fundamental to functions of mammalian brains, although the molecular basis governing formation and modulation of compartmentalized synaptic assemblies is unclear. Here, we used a biochemical reconstitution approach to show that, both in solution and on supported membrane bilayers, multivalent interaction networks formed by major excitatory postsynaptic density (PSD) scaffold proteins led to formation of PSD-like assemblies via phase separation. The reconstituted PSD-like assemblies can cluster receptors, selectively concentrate enzymes, promote actin bundle formation, and expel inhibitory postsynaptic proteins. Additionally, the condensed phase PSD assemblies have features that are distinct from those in homogeneous solutions and fit for synaptic functions. Thus, we have built a molecular platform for understanding how neuronal synapses are formed and dynamically regulated.
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100
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Bondarev SA, Antonets KS, Kajava AV, Nizhnikov AA, Zhouravleva GA. Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification. Int J Mol Sci 2018; 19:ijms19082292. [PMID: 30081572 PMCID: PMC6121665 DOI: 10.3390/ijms19082292] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023] Open
Abstract
Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.
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Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
| | - Kirill S Antonets
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France.
- Institut de Biologie Computationnelle (IBC), 34095 Montpellier, France.
- University ITMO, Institute of Bioengineering, Kronverksky Pr. 49, St. Petersburg 197101, Russia.
| | - Anton A Nizhnikov
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh., 3, Pushkin, St. Petersburg 196608, Russia.
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
- Laboratory of Amyloid Biology, St. Petersburg State University, Russia, Universitetskaya nab., 7/9, St. Petersburg 199034, Russia.
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