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Van Lindt J, Lazar T, Pakravan D, Demulder M, Meszaros A, Van Den Bosch L, Maes D, Tompa P. F/YGG-motif is an intrinsically disordered nucleic-acid binding motif. RNA Biol 2022; 19:622-635. [PMID: 35491929 PMCID: PMC9067507 DOI: 10.1080/15476286.2022.2066336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNP) function in RNA processing, have RNA-recognition motifs (RRMs) and intrinsically disordered, low-complexity domains (LCDs). While RRMs are drivers of RNA binding, there is only limited knowledge about the RNA interaction by the LCD of some hnRNPs. Here, we show that the LCD of hnRNPA2 interacts with RNA via an embedded Tyr/Gly-rich region which is a disordered RNA-binding motif. RNA binding is maintained upon mutating tyrosine residues to phenylalanines, but abrogated by mutating to alanines, thus we term the RNA-binding region ‘F/YGG motif’. The F/YGG motif can bind a broad range of structured (e.g. tRNA) and disordered (e.g. polyA) RNAs, but not rRNA. As the F/YGG otif can also interact with DNA, we consider it a general nucleic acid-binding motif. hnRNPA2 LCD can form dense droplets, by liquid–liquid phase separation (LLPS). Their formation is inhibited by RNA binding, which is mitigated by salt and 1,6-hexanediol, suggesting that both electrostatic and hydrophobic interactions feature in the F/YGG motif. The D290V mutant also binds RNA, which interferes with both LLPS and aggregation thereof. We found homologous regions in a broad range of RNA- and DNA-binding proteins in the human proteome, suggesting that the F/YGG motif is a general nucleic acid-interaction motif.
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Affiliation(s)
- Joris Van Lindt
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tamas Lazar
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Donya Pakravan
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Leuven, Belgium
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Manon Demulder
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Attila Meszaros
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ludo Van Den Bosch
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Leuven, Belgium
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Tompa
- Center for Structural Biology, VIBVIB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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Pakravan D, Michiels E, Bratek-Skicki A, De Decker M, Van Lindt J, Alsteens D, Derclaye S, Van Damme P, Schymkowitz J, Rousseau F, Tompa P, Van Den Bosch L. Liquid-Liquid Phase Separation Enhances TDP-43 LCD Aggregation but Delays Seeded Aggregation. Biomolecules 2021; 11:548. [PMID: 33917983 PMCID: PMC8068378 DOI: 10.3390/biom11040548] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
Aggregates of TAR DNA-binding protein (TDP-43) are a hallmark of several neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). Although TDP-43 aggregates are an undisputed pathological species at the end stage of these diseases, the molecular changes underlying the initiation of aggregation are not fully understood. The aim of this study was to investigate how phase separation affects self-aggregation and aggregation seeded by pre-formed aggregates of either the low-complexity domain (LCD) or its short aggregation-promoting regions (APRs). By systematically varying the physicochemical conditions, we observed that liquid-liquid phase separation (LLPS) promotes spontaneous aggregation. However, we noticed less efficient seeded aggregation in phase separating conditions. By analyzing a broad range of conditions using the Hofmeister series of buffers, we confirmed that stabilizing hydrophobic interactions prevail over destabilizing electrostatic forces. RNA affected the cooperativity between LLPS and aggregation in a "reentrant" fashion, having the strongest positive effect at intermediate concentrations. Altogether, we conclude that conditions which favor LLPS enhance the subsequent aggregation of the TDP-43 LCD with complex dependence, but also negatively affect seeding kinetics.
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Affiliation(s)
- Donya Pakravan
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000 Leuven, Belgium; (D.P.); (M.D.D.); (P.V.D.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Emiel Michiels
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; (E.M.); (J.S.); (F.R.)
| | - Anna Bratek-Skicki
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (A.B.-S.); (J.V.L.); (P.T.)
| | - Mathias De Decker
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000 Leuven, Belgium; (D.P.); (M.D.D.); (P.V.D.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Joris Van Lindt
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (A.B.-S.); (J.V.L.); (P.T.)
| | - David Alsteens
- Institute of Life Sciences, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; (D.A.); (S.D.)
| | - Sylvie Derclaye
- Institute of Life Sciences, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; (D.A.); (S.D.)
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000 Leuven, Belgium; (D.P.); (M.D.D.); (P.V.D.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; (E.M.); (J.S.); (F.R.)
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; (E.M.); (J.S.); (F.R.)
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, 1050 Brussels, Belgium; (A.B.-S.); (J.V.L.); (P.T.)
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, 3000 Leuven, Belgium; (D.P.); (M.D.D.); (P.V.D.)
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
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Van Lindt J, Bratek-Skicki A, Nguyen PN, Pakravan D, Durán-Armenta LF, Tantos A, Pancsa R, Van Den Bosch L, Maes D, Tompa P. A generic approach to study the kinetics of liquid-liquid phase separation under near-native conditions. Commun Biol 2021; 4:77. [PMID: 33469149 PMCID: PMC7815728 DOI: 10.1038/s42003-020-01596-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/30/2020] [Indexed: 11/09/2022] Open
Abstract
Understanding the kinetics, thermodynamics, and molecular mechanisms of liquid-liquid phase separation (LLPS) is of paramount importance in cell biology, requiring reproducible methods for studying often severely aggregation-prone proteins. Frequently applied approaches for inducing LLPS, such as dilution of the protein from an urea-containing solution or cleavage of its fused solubility tag, often lead to very different kinetic behaviors. Here we demonstrate that at carefully selected pH values proteins such as the low-complexity domain of hnRNPA2, TDP-43, and NUP98, or the stress protein ERD14, can be kept in solution and their LLPS can then be induced by a jump to native pH. This approach represents a generic method for studying the full kinetic trajectory of LLPS under near native conditions that can be easily controlled, providing a platform for the characterization of physiologically relevant phase-separation behavior of diverse proteins.
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Affiliation(s)
- Joris Van Lindt
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Anna Bratek-Skicki
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium. .,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Phuong N Nguyen
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Biology, College of Natural Sciences, Cantho University, Can Tho, Vietnam
| | - Donya Pakravan
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,KU Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium
| | - Luis F Durán-Armenta
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ludo Van Den Bosch
- VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,KU Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium. .,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
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Bratek-Skicki A, Pancsa R, Meszaros B, Van Lindt J, Tompa P. A guide to regulation of the formation of biomolecular condensates. FEBS J 2020; 287:1924-1935. [PMID: 32080961 DOI: 10.1111/febs.15254] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 12/18/2022]
Abstract
Cellular organelles that lack a surrounding lipid bilayer, such as the nucleolus and stress granule, represent a newly recognized, general paradigm of cellular organization. The formation of such biomolecular condensates that include 'membraneless organelles' (MLOs) by liquid-liquid phase separation (LLPS) has been in the focus of a surge of recent studies. Through a combination of in vitro and in vivo approaches, thousands of potential phase-separating proteins have been identified, and it was found that different cellular MLOs share many common components. These perplexing observations raise the question of how cells regulate the timing and specificity of LLPS, and ensure that different MLOs form and disperse at the right moment and cellular location and can preserve their identity and physical separation. This guide gives an overview of basic regulatory mechanisms, which manifest through the action of intrinsic regulatory elements, alternative splicing, post-translational modifications, and a broad range of phase-separating partners. We also elaborate on the cellular integration of these different mechanisms and highlight how complex regulation can orchestrate the parallel functioning of a dozen or so different MLOs in the cell.
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Affiliation(s)
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Balint Meszaros
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Joris Van Lindt
- VIB-VUB Center for Structural Biology (CSB), Brussels, Belgium
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Brussels, Belgium.,Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
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5
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Boeynaems S, Holehouse AS, Weinhardt V, Kovacs D, Van Lindt J, Larabell C, Van Den Bosch L, Das R, Tompa PS, Pappu RV, Gitler AD. Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. Proc Natl Acad Sci U S A 2019; 116:7889-7898. [PMID: 30926670 PMCID: PMC6475405 DOI: 10.1073/pnas.1821038116] [Citation(s) in RCA: 268] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phase separation of multivalent protein and RNA molecules underlies the biogenesis of biomolecular condensates such as membraneless organelles. In vivo, these condensates encompass hundreds of distinct types of molecules that typically organize into multilayered structures supporting the differential partitioning of molecules into distinct regions with distinct material properties. The interplay between driven (active) versus spontaneous (passive) processes that are required for enabling the formation of condensates with coexisting layers of distinct material properties remains unclear. Here, we deploy systematic experiments and simulations based on coarse-grained models to show that the collective interactions among the simplest, biologically relevant proteins and archetypal RNA molecules are sufficient for driving the spontaneous emergence of multilayered condensates with distinct material properties. These studies yield a set of rules regarding homotypic and heterotypic interactions that are likely to be relevant for understanding the interplay between active and passive processes that control the formation of functional biomolecular condensates.
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Affiliation(s)
- Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;
| | - Alex S Holehouse
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130
- Center for Science & Engineering of Living Systems, Washington University, St. Louis, MO 63130
| | - Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Anatomy, University of California, San Francisco, CA 94143
| | - Denes Kovacs
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Joris Van Lindt
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Anatomy, University of California, San Francisco, CA 94143
| | - Ludo Van Den Bosch
- Laboratory of Neurobiology, Center for Brain & Disease Research, Vlaams Instituut voor Biotechnologie, 3000 Leuven, Belgium
- Experimental Neurology, Department of Neurosciences, KU Leuven, 3001 Leuven, Belgium
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA 94305
- Department of Physics, Stanford University, Stanford, CA 94305
| | - Peter S Tompa
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63130;
- Center for Science & Engineering of Living Systems, Washington University, St. Louis, MO 63130
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;
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