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Demongin C, Tranier S, Joshi V, Ceschi L, Desforges B, Pastré D, Hamon L. RNA and the RNA-binding protein FUS act in concert to prevent TDP-43 spatial segregation. J Biol Chem 2024; 300:105716. [PMID: 38311174 PMCID: PMC10912363 DOI: 10.1016/j.jbc.2024.105716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
FUS and TDP-43 are two self-adhesive aggregation-prone mRNA-binding proteins whose pathological mutations have been linked to neurodegeneration. While TDP-43 and FUS form reversible mRNA-rich compartments in the nucleus, pathological mutations promote their respective cytoplasmic aggregation in neurons with no apparent link between the two proteins except their intertwined function in mRNA processing. By combining analyses in cellular context and at high resolution in vitro, we unraveled that TDP-43 is specifically recruited in FUS assemblies to form TDP-43-rich subcompartments but without reciprocity. The presence of mRNA provides an additional scaffold to promote the mixing between TDP-43 and FUS. Accordingly, we also found that the pathological truncated form of TDP-43, TDP-25, which has an impaired RNA-binding ability, no longer mixes with FUS. Together, these results suggest that the binding of FUS along nascent mRNAs enables TDP-43, which is highly aggregation-prone, to mix with FUS phase to form mRNA-rich subcompartments. A functional link between FUS and TDP-43 may explain their common implication in amyotrophic lateral sclerosis.
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Affiliation(s)
- Clément Demongin
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Samuel Tranier
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Vandana Joshi
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Léa Ceschi
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | | | - David Pastré
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France.
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2
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Mehrabipour M, Jasemi NSK, Dvorsky R, Ahmadian MR. A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling. Cells 2023; 12:2054. [PMID: 37626864 PMCID: PMC10453029 DOI: 10.3390/cells12162054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
SRC homology 3 (SH3) domains are fundamental modules that enable the assembly of protein complexes through physical interactions with a pool of proline-rich/noncanonical motifs from partner proteins. They are widely studied modular building blocks across all five kingdoms of life and viruses, mediating various biological processes. The SH3 domains are also implicated in the development of human diseases, such as cancer, leukemia, osteoporosis, Alzheimer's disease, and various infections. A database search of the human proteome reveals the existence of 298 SH3 domains in 221 SH3 domain-containing proteins (SH3DCPs), ranging from 13 to 720 kilodaltons. A phylogenetic analysis of human SH3DCPs based on their multi-domain architecture seems to be the most practical way to classify them functionally, with regard to various physiological pathways. This review further summarizes the achievements made in the classification of SH3 domain functions, their binding specificity, and their significance for various diseases when exploiting SH3 protein modular interactions as drug targets.
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Affiliation(s)
- Mehrnaz Mehrabipour
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Neda S. Kazemein Jasemi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
| | - Radovan Dvorsky
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, 040 01 Košice, Slovakia
| | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.M.); (N.S.K.J.)
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Bertrand E, Demongin C, Dobra I, Rengifo-Gonzalez JC, Singatulina AS, Sukhanova MV, Lavrik OI, Pastré D, Hamon L. FUS fibrillation occurs through a nucleation-based process below the critical concentration required for liquid-liquid phase separation. Sci Rep 2023; 13:7772. [PMID: 37179431 PMCID: PMC10183042 DOI: 10.1038/s41598-023-34558-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
FUS is an RNA-binding protein involved in familiar forms of ALS and FTLD that also assembles into fibrillar cytoplasmic aggregates in some neurodegenerative diseases without genetic causes. The self-adhesive prion-like domain in FUS generates reversible condensates via the liquid-liquid phase separation process (LLPS) whose maturation can lead to the formation of insoluble fibrillar aggregates in vitro, consistent with the appearance of cytoplasmic inclusions in ageing neurons. Using a single-molecule imaging approach, we reveal that FUS can assemble into nanofibrils at concentrations in the nanomolar range. These results suggest that the formation of fibrillar aggregates of FUS could occur in the cytoplasm at low concentrations of FUS, below the critical ones required to trigger the liquid-like condensate formation. Such nanofibrils may serve as seeds for the formation of pathological inclusions. Interestingly, the fibrillation of FUS at low concentrations is inhibited by its binding to mRNA or after the phosphorylation of its prion-like domain, in agreement with previous models.
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Affiliation(s)
- Emilie Bertrand
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Clément Demongin
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Ioana Dobra
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | | | - Anastasia S Singatulina
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France.
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Dionne U, Percival LJ, Chartier FJM, Landry CR, Bisson N. SRC homology 3 domains: multifaceted binding modules. Trends Biochem Sci 2022; 47:772-784. [PMID: 35562294 DOI: 10.1016/j.tibs.2022.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
The assembly of complexes following the detection of extracellular signals is often controlled by signaling proteins comprising multiple peptide binding modules. The SRC homology (SH)3 family represents the archetypical modular protein interaction module, with ~300 annotated SH3 domains in humans that regulate an impressive array of signaling processes. We review recent findings regarding the allosteric contributions of SH3 domains host protein context, their phosphoregulation, and their roles in phase separation that challenge the simple model in which SH3s are considered to be portable domains binding to specific proline-rich peptide motifs.
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Affiliation(s)
- Ugo Dionne
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Lily J Percival
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Manchester, UK
| | - François J M Chartier
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada
| | - Christian R Landry
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Institute of Integrative and Systems Biology, Université Laval, Quebec, QC, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec, QC, Canada; Department of Biology, Université Laval, Quebec, QC, Canada.
| | - Nicolas Bisson
- Centre de recherche sur le cancer et Centre de recherche du CHU de Québec - Université Laval, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, QC, Canada.
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Spegg V, Altmeyer M. Biomolecular condensates at sites of DNA damage: More than just a phase. DNA Repair (Amst) 2021; 106:103179. [PMID: 34311273 PMCID: PMC7612016 DOI: 10.1016/j.dnarep.2021.103179] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022]
Abstract
Protein recruitment to DNA break sites is an integral part of the DNA damage response (DDR). Elucidation of the hierarchy and temporal order with which DNA damage sensors as well as repair and signaling factors assemble around chromosome breaks has painted a complex picture of tightly regulated macromolecular interactions that build specialized compartments to facilitate repair and maintenance of genome integrity. While many of the underlying interactions, e.g. between repair factors and damage-induced histone marks, can be explained by lock-and-key or induced fit binding models assuming fixed stoichiometries, structurally less well defined interactions, such as the highly dynamic multivalent interactions implicated in phase separation, also participate in the formation of multi-protein assemblies in response to genotoxic stress. Although much remains to be learned about these types of cooperative and highly dynamic interactions and their functional roles, the rapidly growing interest in material properties of biomolecular condensates and in concepts from polymer chemistry and soft matter physics to understand biological processes at different scales holds great promises. Here, we discuss nuclear condensates in the context of genome integrity maintenance, highlighting the cooperative potential between clustered stoichiometric binding and phase separation. Rather than viewing them as opposing scenarios, their combined effects can balance structural specificity with favorable physicochemical properties relevant for the regulation and function of multilayered nuclear condensates.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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Rengifo-Gonzalez JC, El Hage K, Clément MJ, Steiner E, Joshi V, Craveur P, Durand D, Pastré D, Bouhss A. The cooperative binding of TDP-43 to GU-rich RNA repeats antagonizes TDP-43 aggregation. eLife 2021; 10:67605. [PMID: 34490845 PMCID: PMC8523171 DOI: 10.7554/elife.67605] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
TDP-43 is a nuclear RNA-binding protein that forms neuronal cytoplasmic inclusions in two major neurodegenerative diseases, ALS and FTLD. While the self-assembly of TDP-43 by its structured N-terminal and intrinsically disordered C-terminal domains has been widely studied, the mechanism by which mRNA preserves TDP-43 solubility in the nucleus has not been addressed. Here, we demonstrate that tandem RNA recognition motifs of TDP-43 bind to long GU-repeats in a cooperative manner through intermolecular interactions. Moreover, using mutants whose cooperativity is impaired, we found that the cooperative binding of TDP-43 to mRNA may be critical to maintain the solubility of TDP-43 in the nucleus and the miscibility of TDP-43 in cytoplasmic stress granules. We anticipate that the knowledge of a higher order assembly of TDP-43 on mRNA may clarify its role in intron processing and provide a means of interfering with the cytoplasmic aggregation of TDP-43.
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Affiliation(s)
- Juan Carlos Rengifo-Gonzalez
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Krystel El Hage
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Marie-Jeanne Clément
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Emilie Steiner
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Vandana Joshi
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | | | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - David Pastré
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Ahmed Bouhss
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
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