1
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Kochen NN, Seaney D, Vasandani V, Murray M, Braun AR, Sachs JN. Post-translational modification sites are present in hydrophilic cavities of alpha-synuclein, tau, FUS, and TDP-43 fibrils: A molecular dynamics study. Proteins 2024; 92:854-864. [PMID: 38458997 PMCID: PMC11147710 DOI: 10.1002/prot.26679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/09/2024] [Accepted: 02/28/2024] [Indexed: 03/10/2024]
Abstract
Hydration plays a crucial role in the refolding of intrinsically disordered proteins into amyloid fibrils; however, the specific interactions between water and protein that may contribute to this process are still unknown. In our previous studies of alpha-synuclein (aSyn), we have shown that waters confined in fibril cavities are stabilizing features of this pathological fold; and that amino acids that hydrogen bond with these confined waters modulate primary and seeded aggregation. Here, we extend our aSyn molecular dynamics (MD) simulations with three new polymorphs and correlate MD trajectory information with known post-translational modifications (PTMs) and experimental data. We show that cavity residues are more evolutionarily conserved than non-cavity residues and are enriched with PTM sites. As expected, the confinement within hydrophilic cavities results in more stably hydrated amino acids. Interestingly, cavity PTM sites display the longest protein-water hydrogen bond lifetimes, three-fold greater than non-PTM cavity sites. Utilizing the deep mutational screen dataset by Newberry et al. and the Thioflavin T aggregation review by Pancoe et al. parsed using a fibril cavity/non-cavity definition, we show that hydrophobic changes to amino acids in cavities have a larger effect on fitness and aggregation rate than residues outside cavities, supporting our hypothesis that these sites are involved in the inhibition of aSyn toxic fibrillization. Finally, we expand our study to include analysis of fibril structures of tau, FUS, TDP-43, prion, and hnRNPA1; all of which contained hydrated cavities, with tau, FUS, and TDP-43 recapitulating our PTM results in aSyn fibril cavities.
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Affiliation(s)
- Noah Nathan Kochen
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Darren Seaney
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vivek Vasandani
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Marguerite Murray
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Anthony R Braun
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA
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2
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Chen Y, Pei X, Chen L, Chen L. A dynamic regulatory switch for phase separation of FUS protein: Zinc ions and zinc finger domain. Biochem Biophys Res Commun 2024; 710:149862. [PMID: 38593618 DOI: 10.1016/j.bbrc.2024.149862] [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: 02/27/2024] [Revised: 03/17/2024] [Accepted: 03/28/2024] [Indexed: 04/11/2024]
Abstract
Zinc is an important trace element in the human body, and its homeostasis is closely related to amyotrophic lateral sclerosis (ALS). Cytoplasmic FUS proteins from patients with ALS aggregate their important pathologic markers. Liquid-liquid phase separation (LLPS) of FUS can lead to its aggregation. However, whether and how zinc homeostasis affects the aggregation of disease-associated FUS proteins in the cytoplasm remains unclear. Here, we found that zinc ion enhances LLPS and promotes the aggregation in the cytoplasm for FUS protein. In the FUS, the cysteine of the zinc finger (ZnF), recognizes and binds to zinc ions, reducing droplet mobility and enhancing protein aggregation in the cytoplasm. The mutation of FUS cysteine disrupts the dynamic regulatory switch of zinc ions and ZnF, resulting in insensitivity to zinc ions. These results suggest that the dynamic regulation of LLPS by binding with zinc ions may be a widespread mechanism and provide a new understanding of neurological diseases such as ALS and other ZnF protein-related diseases.
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Affiliation(s)
- Yatao Chen
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoying Pei
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Long Chen
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Liming Chen
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China; Cancer Institute, School of Life Sciences, Nanjing Normal University, Nanjing, China.
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3
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Sundara Rajan S, Ebegboni VJ, Pichling P, Ludwig KR, Jones TL, Chari R, Tran A, Kruhlak MJ, Loncarek J, Caplen NJ. Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription. Mol Cell Biol 2024; 44:103-122. [PMID: 38506112 PMCID: PMC10986767 DOI: 10.1080/10985549.2024.2315425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 03/21/2024] Open
Abstract
EWSR1 is a member of the FET family of nucleic acid binding proteins that includes FUS and TAF15. Here, we report the systematic analysis of endogenous EWSR1's cellular organization in human cells. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vernon J. Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Patricio Pichling
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, Maryland, USA
| | - Andy Tran
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael J. Kruhlak
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jadranka Loncarek
- Centrosome Biology Section, Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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4
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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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5
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Yan X, Zhang M, Wang D. Interplay between posttranslational modifications and liquid‒liquid phase separation in tumors. Cancer Lett 2024; 584:216614. [PMID: 38246226 DOI: 10.1016/j.canlet.2024.216614] [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: 11/08/2023] [Revised: 12/22/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
Liquid‒liquid phase separation (LLPS) is a general phenomenon recently recognized to be critically involved in the regulation of a variety of cellular biological processes, such as transcriptional regulation, heterochromatin formation and signal transduction, through the compartmentalization of proteins or nucleic acids into droplet-like condensates. These processes are directly or indirectly related to tumor initiation and treatment. Posttranslational modifications (PTMs), which represent a rapid and reversible mechanism involved in the functional regulation of proteins, have emerged as key events in modulating LLPS under physiological or pathophysiological conditions, including tumorigenesis and antitumor therapy. In this review, we introduce the biological functions participated in cancer-associated LLPS, discuss the potential roles of LLPS during tumor onset or therapy, and emphasize the mechanistic characteristics of LLPS regulated by PTMs and its effects on tumor progression. We then provide a perspective on further studies on LLPS and its regulation by PTMs in cancer research. This review aims to broaden the understanding of the functions of LLPS and its regulation by PTMs under normal or aberrant cellular conditions.
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Affiliation(s)
- Xiaojun Yan
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Donglai Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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6
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Cóppola-Segovia V, Reggiori F. Molecular Insights into Aggrephagy: Their Cellular Functions in the Context of Neurodegenerative Diseases. J Mol Biol 2024:168493. [PMID: 38360089 DOI: 10.1016/j.jmb.2024.168493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Protein homeostasis or proteostasis is an equilibrium of biosynthetic production, folding and transport of proteins, and their timely and efficient degradation. Proteostasis is guaranteed by a network of protein quality control systems aimed at maintaining the proteome function and avoiding accumulation of potentially cytotoxic proteins. Terminal unfolded and dysfunctional proteins can be directly turned over by the ubiquitin-proteasome system (UPS) or first amassed into aggregates prior to degradation. Aggregates can also be disposed into lysosomes by a selective type of autophagy known as aggrephagy, which relies on a set of so-called selective autophagy receptors (SARs) and adaptor proteins. Failure in eliminating aggregates, also due to defects in aggrephagy, can have devastating effects as underscored by several neurodegenerative diseases or proteinopathies, which are characterized by the accumulation of aggregates mostly formed by a specific disease-associated, aggregate-prone protein depending on the clinical pathology. Despite its medical relevance, however, the process of aggrephagy is far from being understood. Here we review the findings that have helped in assigning a possible function to specific SARs and adaptor proteins in aggrephagy in the context of proteinopathies, and also highlight the interplay between aggrephagy and the pathogenesis of proteinopathies.
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Affiliation(s)
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark.
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7
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Garcia-Pardo J, Ventura S. Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies. Trends Biochem Sci 2024; 49:119-133. [PMID: 37926650 DOI: 10.1016/j.tibs.2023.10.005] [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: 07/26/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
Amyloids are implicated in neurodegenerative and systemic diseases, yet they serve important functional roles in numerous organisms. Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that control central events of RNA biogenesis in normal and diseased cellular conditions. Many of these proteins contain prion-like sequences of low complexity, which not only assemble into functional fibrils in response to cellular cues but can also lead to disease when missense mutations arise in their sequences. Recent advances in cryo-electron microscopy (cryo-EM) have provided unprecedented high-resolution structural insights into diverse amyloid assemblies formed by hnRNPs and structurally related RBPs, including TAR DNA-binding protein 43 (TDP-43), Fused in Sarcoma (FUS), Orb2, hnRNPA1, hnRNPA2, and hnRNPDL-2. This review provides a comprehensive overview of these structures and explores their functional and pathological implications.
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Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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8
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Sołtys K, Tarczewska A, Bystranowska D. Modulation of biomolecular phase behavior by metal ions. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119567. [PMID: 37582439 DOI: 10.1016/j.bbamcr.2023.119567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/17/2023]
Abstract
Liquid-liquid phase separation (LLPS) appears to be a newly appreciated aspect of the cellular organization of biomolecules that leads to the formation of membraneless organelles (MLOs). MLOs generate distinct microenvironments where particular biomolecules are highly concentrated compared to those in the surrounding environment. Their thermodynamically driven formation is reversible, and their liquid nature allows them to fuse with each other. Dysfunctional biomolecular condensation is associated with human diseases. Pathological states of MLOs may originate from the mutation of proteins or may be induced by other factors. In most aberrant MLOs, transient interactions are replaced by stronger and more rigid interactions, preventing their dissolution, and causing their uncontrolled growth and dysfunction. For these reasons, there is great interest in identifying factors that modulate LLPS. In this review, we discuss an enigmatic and mostly unexplored aspect of this process, namely, the regulatory effects of metal ions on the phase behavior of biomolecules.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Aneta Tarczewska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Dominika Bystranowska
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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9
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Dong H, Zhang H, Jalin J, He Z, Wang R, Huang L, Liu Z, Zhang S, Dai B, Li D. Nucleocapsid proteins from human coronaviruses possess phase separation capabilities and promote FUS pathological aggregation. Protein Sci 2023; 32:e4826. [PMID: 37906538 PMCID: PMC10659942 DOI: 10.1002/pro.4826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
The nucleocapsid (N) protein is an essential structural component necessary for genomic packaging and replication in various human coronaviruses (HCoVs), such as SARS-CoV-2 and MERS-CoV. Recent studies have revealed that the SARS-CoV-2 N protein exhibits a high capacity for liquid-liquid phase separation (LLPS), which plays multiple roles in viral infection and replication. In this study, we systematically investigate the LLPS capabilities of seven homologous N proteins from different HCoVs using a high-throughput protein phase separation assay. We found that LLPS is a shared intrinsic property among these N proteins. However, the phase separation profiles of the various N protein homologs differ, and they undergo phase separation under distinct in vitro conditions. Moreover, we demonstrate that N protein homologs can co-phase separate with FUS, a SG-containing protein, and accelerate its liquid-to-solid phase transition and amyloid aggregation, which is closely related to amyotrophic lateral sclerosis. Further study shows that N protein homologs can directly bind to the low complexity domain of FUS. Together, our work demonstrates that N proteins of different HCoVs possess phase separation capabilities, which may contribute to promoting pathological aggregation of host proteins and disrupting SG homeostasis during the infection and replication of various HCoVs.
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Affiliation(s)
- Hui Dong
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Present address:
Interdisciplinary Research Center on Biology and ChemistryShanghai Institute of Organic Chemistry, Chinese Academy of SciencesShanghaiChina
| | - Hong Zhang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Julie Jalin
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ziqi He
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
| | - Runhan Wang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Leqi Huang
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zibo Liu
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Shenqing Zhang
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Zhangjiang Institute for Advanced StudyShanghai Jiao Tong UniversityShanghaiChina
| | - Bin Dai
- School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Dan Li
- Bio‐X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of EducationShanghai Jiao Tong UniversityShanghaiChina
- Zhangjiang Institute for Advanced StudyShanghai Jiao Tong UniversityShanghaiChina
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10
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Blazquez S, Sanchez‐Burgos I, Ramirez J, Higginbotham T, Conde MM, Collepardo‐Guevara R, Tejedor AR, Espinosa JR. Location and Concentration of Aromatic-Rich Segments Dictates the Percolating Inter-Molecular Network and Viscoelastic Properties of Ageing Condensates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207742. [PMID: 37386790 PMCID: PMC10477902 DOI: 10.1002/advs.202207742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/03/2023] [Indexed: 07/01/2023]
Abstract
Maturation of functional liquid-like biomolecular condensates into solid-like aggregates has been linked to the onset of several neurodegenerative disorders. Low-complexity aromatic-rich kinked segments (LARKS) contained in numerous RNA-binding proteins can promote aggregation by forming inter-protein β-sheet fibrils that accumulate over time and ultimately drive the liquid-to-solid transition of the condensates. Here, atomistic molecular dynamics simulations are combined with sequence-dependent coarse-grained models of various resolutions to investigate the role of LARKS abundance and position within the amino acid sequence in the maturation of condensates. Remarkably, proteins with tail-located LARKS display much higher viscosity over time than those in which the LARKS are placed toward the center. Yet, at very long timescales, proteins with a single LARKS-independently of its location-can still relax and form high viscous liquid condensates. However, phase-separated condensates of proteins containing two or more LARKS become kinetically trapped due to the formation of percolated β-sheet networks that display gel-like behavior. Furthermore, as a work case example, they demonstrate how shifting the location of the LARKS-containing low-complexity domain of FUS protein toward its center effectively precludes the accumulation of β-sheet fibrils in FUS-RNA condensates, maintaining functional liquid-like behavior without ageing.
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Affiliation(s)
- Samuel Blazquez
- Department of Physical‐ChemistryUniversidad Complutense de MadridAv. Complutense s/nMadrid28040Spain
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Ignacio Sanchez‐Burgos
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Jorge Ramirez
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Tim Higginbotham
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Maria M. Conde
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Rosana Collepardo‐Guevara
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of GeneticsUniversity of CambridgeCambridgeCB2 3EH, UK
| | - Andres R. Tejedor
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Jorge R. Espinosa
- Department of Physical‐ChemistryUniversidad Complutense de MadridAv. Complutense s/nMadrid28040Spain
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
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11
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Rajan SS, Ebegboni VJ, Pichling P, Ludwig KR, Jones TL, Chari R, Tran A, Kruhlak MJ, Loncarek J, Caplen NJ. EWSR1's visual modalities are defined by its association with nucleic acids and RNA polymerase II. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553246. [PMID: 37645932 PMCID: PMC10462028 DOI: 10.1101/2023.08.16.553246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
We report systematic analysis of endogenous EWSR1's cellular organization. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Interestingly, EWSR1 and FUS, another FET protein, exhibit distinct spatial organizations. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Vernon J. Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Patricio Pichling
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program at the Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Andy Tran
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael J. Kruhlak
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jadranka Loncarek
- Centrosome Biology Section, Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
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12
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Tzeplaeff L, Wilfling S, Requardt MV, Herdick M. Current State and Future Directions in the Therapy of ALS. Cells 2023; 12:1523. [PMID: 37296644 PMCID: PMC10252394 DOI: 10.3390/cells12111523] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodegenerative disorder affecting upper and lower motor neurons, with death resulting mainly from respiratory failure three to five years after symptom onset. As the exact underlying causative pathological pathway is unclear and potentially diverse, finding a suitable therapy to slow down or possibly stop disease progression remains challenging. Varying by country Riluzole, Edaravone, and Sodium phenylbutyrate/Taurursodiol are the only drugs currently approved in ALS treatment for their moderate effect on disease progression. Even though curative treatment options, able to prevent or stop disease progression, are still unknown, recent breakthroughs, especially in the field of targeting genetic disease forms, raise hope for improved care and therapy for ALS patients. In this review, we aim to summarize the current state of ALS therapy, including medication as well as supportive therapy, and discuss the ongoing developments and prospects in the field. Furthermore, we highlight the rationale behind the intense research on biomarkers and genetic testing as a feasible way to improve the classification of ALS patients towards personalized medicine.
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Affiliation(s)
- Laura Tzeplaeff
- Department of Neurology, Rechts der Isar Hospital, Technical University of Munich, 81675 München, Germany
| | - Sibylle Wilfling
- Department of Neurology, University of Regensburg, 93053 Regensburg, Germany;
- Center for Human Genetics Regensburg, 93059 Regensburg, Germany
| | - Maria Viktoria Requardt
- Formerly: Department of Neurology with Institute of Translational Neurology, Münster University Hospital (UKM), 48149 Münster, Germany;
| | - Meret Herdick
- Precision Neurology, University of Lübeck, 23562 Luebeck, Germany
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13
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Ranganathan S, Dasmeh P, Furniss S, Shakhnovich E. Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates. Proc Natl Acad Sci U S A 2023; 120:e2215828120. [PMID: 37155880 PMCID: PMC10193986 DOI: 10.1073/pnas.2215828120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023] Open
Abstract
Assemblies of multivalent RNA-binding protein fused in sarcoma (FUS) can exist in the functional liquid-like state as well as less dynamic and potentially toxic amyloid- and hydrogel-like states. How could then cells form liquid-like condensates while avoiding their transformation to amyloids? Here, we show how posttranslational phosphorylation can provide a "handle" that prevents liquid-solid transition of intracellular condensates containing FUS. Using residue-specific coarse-grained simulations, for 85 different mammalian FUS sequences, we show how the number of phosphorylation sites and their spatial arrangement affect intracluster dynamics preventing conversion to amyloids. All atom simulations further confirm that phosphorylation can effectively reduce the β-sheet propensity in amyloid-prone fragments of FUS. A detailed evolutionary analysis shows that mammalian FUS PLDs are enriched in amyloid-prone stretches compared to control neutrally evolved sequences, suggesting that mammalian FUS proteins evolved to self-assemble. However, in stark contrast to proteins that do not phase-separate for their function, mammalian sequences have phosphosites in close proximity to these amyloid-prone regions. These results suggest that evolution uses amyloid-prone sequences in prion-like domains to enhance phase separation of condensate proteins while enriching phosphorylation sites in close proximity to safeguard against liquid-solid transitions.
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Affiliation(s)
- Srivastav Ranganathan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Pouria Dasmeh
- Center for Human Genetics, Marburg University, Marburg35033, Germany
| | - Seth Furniss
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, OxfordOX1 3QZ, United Kingdom
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
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14
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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] [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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15
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Che X, Wu J, Liu H, Su J, Chen X. Cellular liquid-liquid phase separation: Concept, functions, regulations, and detections. J Cell Physiol 2023; 238:847-865. [PMID: 36870067 DOI: 10.1002/jcp.30980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023]
Abstract
Liquid-liquid phase separation is a multicomponent system separated into phases with different compositions and structures. It has been identified and explored in organisms after being introduced from the thermodynamic field. Condensate, the product of phase separation, exists in different scales of cellular structures, such as nucleolus, stress granules, and other organelles in nuclei or cytoplasm. And also play critical roles in different cellular behaviors. Here, we review the concept, thermodynamical and biochemical principles of phase separation. We summarized the main functions including the adjustment of biochemical reaction rates, the regulation of macromolecule folding state, subcellular structural support, the mediation of subcellular location, and intimately linked to different kinds of diseases, such as cancer and neurodegeneration. Advanced detection methods to investigate phase separation are collected and analyzed. We conclude with the discussion of anxiety of phase separation, and thought about how progress can be made to develop precise detection methods and disclose the potential application of condensates.
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Affiliation(s)
- Xuanlin Che
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Jiajun Wu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Hua Liu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Changsha, Hunan, China.,Xiangya Clinical Research Center for Cancer Immunotherapy, Central South University, Changsha, Hunan, China
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16
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Assoni AF, Foijer F, Zatz M. Amyotrophic Lateral Sclerosis, FUS and Protein Synthesis Defects. Stem Cell Rev Rep 2022; 19:625-638. [PMID: 36515764 DOI: 10.1007/s12015-022-10489-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that mainly affects the motor system. It is a very heterogeneous disorder, so far more than 40 genes have been described as responsible for ALS. The cause of motor neuron degeneration is not yet fully understood, but there is consensus in the literature that it is the result of a complex interplay of several pathogenic processes, which include alterations in nucleocytoplasmic transport, defects in transcription and splicing, altered formation and/or disassembly of stress granules and impaired proteostasis. These defects result in protein aggregation, impaired DNA repair, mitochondrial dysfunction and oxidative stress, neuroinflammation, impaired axonal transport, impaired vesicular transport, excitotoxicity, as well as impaired calcium influx. We argue here that all the above functions ultimately lead to defects in protein synthesis. Fused in Sarcoma (FUS) is one of the genes associated with ALS. It causes ALS type 6 when mutated and is found mislocalized to the cytoplasm in the motor neurons of sporadic ALS patients (without FUS mutations). In addition, FUS plays a role in all cellular functions that are impaired in degenerating motor neurons. Moreover, ALS patients with FUS mutations present the first symptoms significantly earlier than in other forms of the disease. Therefore, the aim of this review is to further discuss ALS6, detail the cellular functions of FUS, and suggest that the localization of FUS, as well as protein synthesis rates, could be hallmarks of the ALS phenotype and thus good therapeutic targets.
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Affiliation(s)
- Amanda Faria Assoni
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, 055080-090, CidadeUniversitária, São Paulo, Brazil.,European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, 055080-090, CidadeUniversitária, São Paulo, Brazil.
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17
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Different states and the associated fates of biomolecular condensates. Essays Biochem 2022; 66:849-862. [PMID: 36350032 DOI: 10.1042/ebc20220054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/20/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
Abstract
Abstract
Biomolecular condensates are functional assemblies, which can enrich intrinsically disordered proteins (IDPs) and/or RNAs at concentrations that are orders of magnitude higher than the bulk. In their native functional state, these structures can exist in multiple physical states including liquid-droplet phase, hydrogels, and solid assemblies. On the other hand, an aberrant transition between these physical states can result in loss-of-function or a gain-of-toxic-function. A prime example of such an aberrant transition is droplet aging—a phenomenon where some condensates may progressively transition into less dynamic material states at biologically relevant timescales. In this essay, we review structural and viscoelastic roots of aberrant liquid–solid transitions. Also, we highlight the different checkpoints and experimentally tunable handles, both active (ATP-dependent enzymes, post-translational modifications) and passive (colocalization of RNA molecules), that could alter the material state of assemblies.
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18
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Ji Y, Li F, Qiao Y. Modulating liquid-liquid phase separation of FUS: mechanisms and strategies. J Mater Chem B 2022; 10:8616-8628. [PMID: 36268634 DOI: 10.1039/d2tb01688e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Liquid-liquid phase separation (LLPS) of biomolecules inspires the construction of protocells and drives the formation of cellular membraneless organelles. The resulting biomolecular condensates featuring dynamic assembly, disassembly, and phase transition play significant roles in a series of biological processes, including RNA metabolism, DNA damage response, signal transduction and neurodegenerative disease. Intensive investigations have been conducted for understanding and manipulating intracellular phase-separated disease-related proteins (e.g., FUS, tau and TDP-43). Herein, we review current studies on the regulation strategies of intracellular LLPS focusing on FUS, which are categorized into physical stimuli, biochemical modulators, and protein structural modifications, with summarized molecular mechanisms. This review is expected to provide a sketch of the modulation of FUS LLPS with its pros and cons, and an outlook for the potential clinical treatments of neurodegenerative diseases.
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Affiliation(s)
- Yanglimin Ji
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fen Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China
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19
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Tejedor AR, Sanchez-Burgos I, Estevez-Espinosa M, Garaizar A, Collepardo-Guevara R, Ramirez J, Espinosa JR. Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it. Nat Commun 2022; 13:5717. [PMID: 36175408 PMCID: PMC9522849 DOI: 10.1038/s41467-022-32874-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/18/2022] [Indexed: 12/03/2022] Open
Abstract
Biomolecular condensates, some of which are liquid-like during health, can age over time becoming gel-like pathological systems. One potential source of loss of liquid-like properties during ageing of RNA-binding protein condensates is the progressive formation of inter-protein β-sheets. To bridge microscopic understanding between accumulation of inter-protein β-sheets over time and the modulation of FUS and hnRNPA1 condensate viscoelasticity, we develop a multiscale simulation approach. Our method integrates atomistic simulations with sequence-dependent coarse-grained modelling of condensates that exhibit accumulation of inter-protein β-sheets over time. We reveal that inter-protein β-sheets notably increase condensate viscosity but does not transform the phase diagrams. Strikingly, the network of molecular connections within condensates is drastically altered, culminating in gelation when the network of strong β-sheets fully percolates. However, high concentrations of RNA decelerate the emergence of inter-protein β-sheets. Our study uncovers molecular and kinetic factors explaining how the accumulation of inter-protein β-sheets can trigger liquid-to-solid transitions in condensates, and suggests a potential mechanism to slow such transitions down. In this work the authors propose a multiscale computational approach, integrating atomistic and coarse-grained models simulations, to study the thermodynamic and kinetic factors playing a major role in the liquid-to-solid transition of biomolecular condensates. It is revealed how the gradual accumulation of inter-protein β-sheets increases the viscosity of functional liquid-like condensates, transforming them into gel-like pathological aggregates, and it is also shown how high concentrations of RNA can decelerate such transition.
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Affiliation(s)
- Andres R Tejedor
- Department of Chemical Engineering, Universidad Politécnica de Madrid, José Gutiérrez Abascal 2, 28006, Madrid, Spain.,Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Ignacio Sanchez-Burgos
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Maria Estevez-Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK.,Department of Biochemistry, University College London, Gower Street, London, WC1E 6BT, UK
| | - Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK.,Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Jorge Ramirez
- Department of Chemical Engineering, Universidad Politécnica de Madrid, José Gutiérrez Abascal 2, 28006, Madrid, Spain.
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK.
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20
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J Proteins Counteract Amyloid Propagation and Toxicity in Yeast. BIOLOGY 2022; 11:biology11091292. [PMID: 36138771 PMCID: PMC9495310 DOI: 10.3390/biology11091292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Dozens of diseases are associated with misfolded proteins that accumulate in highly ordered fibrous aggregates called amyloids. Protein quality control (PQC) factors keep cells healthy by helping maintain the integrity of the cell’s proteins and physiological processes. Yeast has been used widely for years to study how amyloids cause toxicity to cells and how PQC factors help protect cells from amyloid toxicity. The so-called J-domain proteins (JDPs) are PQC factors that are particularly effective at providing such protection. We discuss how PQC factors protect animals, human cells, and yeast from amyloid toxicity, focusing on yeast and human JDPs. Abstract The accumulation of misfolded proteins as amyloids is associated with pathology in dozens of debilitating human disorders, including diabetes, Alzheimer’s, Parkinson’s, and Huntington’s diseases. Expressing human amyloid-forming proteins in yeast is toxic, and yeast prions that propagate as infectious amyloid forms of cellular proteins are also harmful. The yeast system, which has been useful for studying amyloids and their toxic effects, has provided much insight into how amyloids affect cells and how cells respond to them. Given that an amyloid is a protein folding problem, it is unsurprising that the factors found to counteract the propagation or toxicity of amyloids in yeast involve protein quality control. Here, we discuss such factors with an emphasis on J-domain proteins (JDPs), which are the most highly abundant and diverse regulators of Hsp70 chaperones. The anti-amyloid effects of JDPs can be direct or require interaction with Hsp70.
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21
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Wu S, Yin Y, Du L. FUS aggregation following ischemic stroke favors brain astrocyte activation through inducing excessive autophagy. Exp Neurol 2022; 355:114144. [PMID: 35718207 DOI: 10.1016/j.expneurol.2022.114144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 11/04/2022]
Abstract
As is the case with neurodegenerative diseases, abnormal accumulation of aggregated proteins in neurons and glial are also known to implicate in the pathogenesis of ischemic stroke. However, the potential role of protein aggregates in brain ischemia remains largely unknown. Fused in Sarcoma (FUS) protein has a vital role in RNA metabolism and regulating cellular homeostasis. FUS pathology has been demonstrated in the formation of toxic aggregates and critically affecting cell viability in neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), but whether this also applies to neurological injury following cerebral ischemia is unclear. Herein, we demonstrated a critical role of aggregated FUS in astrocyte activation caused by cerebral ischemia and a possible underlying molecular mechanism. Cerebral ischemic injury significantly induced the formation of cytoplasmic FUS aggregates in reactive astrocytes and injured neurons, thereby aggravating neurofunctional damages and worsening stroke outcomes. Further analysis revealed that extranuclear aggregation of FUS in astrocytes was involved in the induction of excessive autophagy, which contributes to autophagic cell injury or death. In conclusion, our results reveal the important contribution of FUS aggregates in promoting astrocyte activation in stroke pathology independent of its transcriptional regulation activity. We thus propose that aggregation of FUS is an important pathological process in ischemic stroke and targeting FUS aggregates might be of unique therapeutic value in the development of future treatment strategies for ischemic stroke.
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Affiliation(s)
- Shusheng Wu
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yuye Yin
- Department of Immunology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Longfei Du
- Department of Laboratory Medicine, Affiliated Hospital of Yangzhou University, Yangzhou, Jiangsu, China.
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22
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Ranganathan S, Shakhnovich E. The physics of liquid-to-solid transitions in multi-domain protein condensates. Biophys J 2022; 121:2751-2766. [PMID: 35702028 DOI: 10.1016/j.bpj.2022.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/21/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
Many RNA-binding proteins (RBPs) that assemble into membraneless organelles have a common architecture including disordered prion-like domain (PLD) and folded RNA-binding domain (RBD). An enrichment of PLD within the condensed phase gives rise to formation, on longer time scales, of amyloid-like fibrils (aging). In this study, we employ coarse-grained Langevin dynamics simulations to explore the physical basis for the structural diversity in condensed phases of multi-domain RBPs. We discovered a highly cooperative first-order transition between disordered structures and an ordered phase whereby chains of PLD organize in fibrils with high nematic orientational order. An interplay between homodomain (PLD-PLD) and heterodomain (PLD-RBD) interactions results in variety of structures with distinct spatial architectures. Interestingly, the different structural phases also exhibit vastly different intracluster dynamics of proteins, with diffusion coefficients 5 times (disordered structures) to 50 times (ordered structures) lower than that of the dilute phase. Cooperativity of this liquid-solid transition makes fibril formation highly malleable to mutations or post-translational modifications. Our results provide a mechanistic understanding of how multi-domain RBPs could form assemblies with distinct structural and material properties.
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Affiliation(s)
- Srivastav Ranganathan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
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23
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Krause LJ, Herrera MG, Winklhofer KF. The Role of Ubiquitin in Regulating Stress Granule Dynamics. Front Physiol 2022; 13:910759. [PMID: 35694405 PMCID: PMC9174786 DOI: 10.3389/fphys.2022.910759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Stress granules (SGs) are dynamic, reversible biomolecular condensates, which assemble in the cytoplasm of eukaryotic cells under various stress conditions. Formation of SGs typically occurs upon stress-induced translational arrest and polysome disassembly. The increase in cytoplasmic mRNAs triggers the formation of a protein-RNA network that undergoes liquid-liquid phase separation when a critical interaction threshold has been reached. This adaptive stress response allows a transient shutdown of several cellular processes until the stress is removed. During the recovery from stress, SGs disassemble to re-establish cellular activities. Persistent stress and disease-related mutations in SG components favor the formation of aberrant SGs that are impaired in disassembly and prone to aggregation. Recently, posttranslational modifications of SG components have been identified as major regulators of SG dynamics. Here, we summarize new insights into the role of ubiquitination in affecting SG dynamics and clearance and discuss implications for neurodegenerative diseases linked to aberrant SG formation.
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Affiliation(s)
- Laura J. Krause
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Maria G. Herrera
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F. Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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24
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Phase-Separated Subcellular Compartmentation and Related Human Diseases. Int J Mol Sci 2022; 23:ijms23105491. [PMID: 35628304 PMCID: PMC9141834 DOI: 10.3390/ijms23105491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/06/2023] Open
Abstract
In live cells, proteins and nucleic acids can associate together through multivalent interactions, and form relatively isolated phases that undertake designated biological functions and activities. In the past decade, liquid–liquid phase separation (LLPS) has gradually been recognized as a general mechanism for the intracellular organization of biomolecules. LLPS regulates the assembly and composition of dozens of membraneless organelles and condensates in cells. Due to the altered physiological conditions or genetic mutations, phase-separated condensates may undergo aberrant formation, maturation or gelation that contributes to the onset and progression of various diseases, including neurodegenerative disorders and cancers. In this review, we summarize the properties of different membraneless organelles and condensates, and discuss multiple phase separation-regulated biological processes. Based on the dysregulation and mutations of several key regulatory proteins and signaling pathways, we also exemplify how aberrantly regulated LLPS may contribute to human diseases.
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25
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Li J, Zhang M, Ma W, Yang B, Lu H, Zhou F, Zhang L. Post-translational modifications in liquid-liquid phase separation: a comprehensive review. MOLECULAR BIOMEDICINE 2022; 3:13. [PMID: 35543798 PMCID: PMC9092326 DOI: 10.1186/s43556-022-00075-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/25/2022] [Indexed: 11/23/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) has received significant attention in recent biological studies. It refers to a phenomenon that biomolecule exceeds the solubility, condensates and separates itself from solution in liquid like droplets formation. Our understanding of it has also changed from memebraneless organelles to compartmentalization, muti-functional crucibles, and reaction regulators. Although this phenomenon has been employed for a variety of biological processes, recent studies mainly focus on its physiological significance, and the comprehensive research of the underlying physical mechanism is limited. The characteristics of side chains of amino acids and the interaction tendency of proteins function importantly in regulating LLPS thus should be pay more attention on. In addition, the importance of post-translational modifications (PTMs) has been underestimated, despite their abundance and crucial functions in maintaining the electrostatic balance. In this review, we first introduce the driving forces and protein secondary structures involved in LLPS and their different physical functions in cell life processes. Subsequently, we summarize the existing reports on PTM regulation related to LLPS and analyze the underlying basic principles, hoping to find some common relations between LLPS and PTM. Finally, we speculate several unreported PTMs that may have a significant impact on phase separation basing on the findings.
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Affiliation(s)
- Jingxian Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Mengdi Zhang
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, Zhejiang, China
| | - Weirui Ma
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Bing Yang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Huasong Lu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, P. R. China.
| | - Long Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
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26
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Carey JL, Guo L. Liquid-Liquid Phase Separation of TDP-43 and FUS in Physiology and Pathology of Neurodegenerative Diseases. Front Mol Biosci 2022; 9:826719. [PMID: 35187086 PMCID: PMC8847598 DOI: 10.3389/fmolb.2022.826719] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid-liquid phase separation of RNA-binding proteins mediates the formation of numerous membraneless organelles with essential cellular function. However, aberrant phase transition of these proteins leads to the formation of insoluble protein aggregates, which are pathological hallmarks of neurodegenerative diseases including ALS and FTD. TDP-43 and FUS are two such RNA-binding proteins that mislocalize and aggregate in patients of ALS and FTD. They have similar domain structures that provide multivalent interactions driving their phase separation in vitro and in the cellular environment. In this article, we review the factors that mediate and regulate phase separation of TDP-43 and FUS. We also review evidences that connect the phase separation property of TDP-43 and FUS to their functional roles in cells. Aberrant phase transition of TDP-43 and FUS leads to protein aggregation and disrupts their regular cell function. Therefore, restoration of functional protein phase of TDP-43 and FUS could be beneficial for neuronal cells. We discuss possible mechanisms for TDP-43 and FUS aberrant phase transition and aggregation while reviewing the methods that are currently being explored as potential therapeutic strategies to mitigate aberrant phase transition and aggregation of TDP-43 and FUS.
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27
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Sanchez-Burgos I, Espinosa JR, Joseph JA, Collepardo-Guevara R. RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins. PLoS Comput Biol 2022; 18:e1009810. [PMID: 35108264 PMCID: PMC8896709 DOI: 10.1371/journal.pcbi.1009810] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/04/2022] [Accepted: 01/06/2022] [Indexed: 12/29/2022] Open
Abstract
Biomolecular condensates formed via liquid-liquid phase separation (LLPS) play a crucial role in the spatiotemporal organization of the cell material. Nucleic acids can act as critical modulators in the stability of these protein condensates. To unveil the role of RNA length in regulating the stability of RNA binding protein (RBP) condensates, we present a multiscale computational strategy that exploits the advantages of a sequence-dependent coarse-grained representation of proteins and a minimal coarse-grained model wherein proteins are described as patchy colloids. We find that for a constant nucleotide/protein ratio, the protein fused in sarcoma (FUS), which can phase separate on its own-i.e., via homotypic interactions-only exhibits a mild dependency on the RNA strand length. In contrast, the 25-repeat proline-arginine peptide (PR25), which does not undergo LLPS on its own at physiological conditions but instead exhibits complex coacervation with RNA-i.e., via heterotypic interactions-shows a strong dependence on the length of the RNA strands. Our minimal patchy particle simulations suggest that the strikingly different effect of RNA length on homotypic LLPS versus RBP-RNA complex coacervation is general. Phase separation is RNA-length dependent whenever the relative contribution of heterotypic interactions sustaining LLPS is comparable or higher than those stemming from protein homotypic interactions. Taken together, our results contribute to illuminate the intricate physicochemical mechanisms that influence the stability of RBP condensates through RNA inclusion.
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Affiliation(s)
- Ignacio Sanchez-Burgos
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, United Kingdom
| | - Jorge R. Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, United Kingdom
| | - Jerelle A. Joseph
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, United Kingdom
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, United Kingdom
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, United Kingdom
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, United Kingdom
- * E-mail:
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28
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Salem A, Wilson CJ, Rutledge BS, Dilliott A, Farhan S, Choy WY, Duennwald ML. Matrin3: Disorder and ALS Pathogenesis. Front Mol Biosci 2022; 8:794646. [PMID: 35083279 PMCID: PMC8784776 DOI: 10.3389/fmolb.2021.794646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the degeneration of both upper and lower motor neurons in the brain and spinal cord. ALS is associated with protein misfolding and inclusion formation involving RNA-binding proteins, including TAR DNA-binding protein (TDP-43) and fused in sarcoma (FUS). The 125-kDa Matrin3 is a highly conserved nuclear DNA/RNA-binding protein that is implicated in many cellular processes, including binding and stabilizing mRNA, regulating mRNA nuclear export, modulating alternative splicing, and managing chromosomal distribution. Mutations in MATR3, the gene encoding Matrin3, have been identified as causal in familial ALS (fALS). Matrin3 lacks a prion-like domain that characterizes many other ALS-associated RNA-binding proteins, including TDP-43 and FUS, however, our bioinformatics analyses and preliminary studies document that Matrin3 contains long intrinsically disordered regions that may facilitate promiscuous interactions with many proteins and may contribute to its misfolding. In addition, these disordered regions in Matrin3 undergo numerous post-translational modifications, including phosphorylation, ubiquitination and acetylation that modulate the function and misfolding of the protein. Here we discuss the disordered nature of Matrin3 and review the factors that may promote its misfolding and aggregation, two elements that might explain its role in ALS pathogenesis.
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Affiliation(s)
- Ahmed Salem
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Carter J. Wilson
- Department of Applied Mathematics, Western University, London, ON, Canada
| | - Benjamin S. Rutledge
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Allison Dilliott
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
| | - Sali Farhan
- Department of Neurology and Neurosurgery, McGill Universty, Montreal, QC, Canada
- Department of Human Genetics, McGill Universty, Montreal, QC, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Martin L. Duennwald
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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29
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Deubiquitinating enzymes (DUBs): decipher underlying basis of neurodegenerative diseases. Mol Psychiatry 2022; 27:259-268. [PMID: 34285347 DOI: 10.1038/s41380-021-01233-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Neurodegenerative diseases (NDs) are characterized by the aggregation of neurotoxic proteins in the central nervous system. Aberrant protein accumulation in NDs is largely caused by the dysfunction of the two principal protein catabolism pathways, the ubiquitin-proteasome system (UPS), and the autophagy-lysosomal pathway (ALP). The two protein quality control pathways are bridged by ubiquitination, a post-translational modification that can induce protein degradation via both the UPS and the ALP. Perturbed ubiquitination leads to the formation of toxic aggregates and inclusion bodies that are deleterious to neurons. Ubiquitination is promoted by a cascade of ubiquitinating enzymes and counter-regulated by deubiquitinating enzymes (DUBs). As fine-tuning regulators of ubiquitination and protein degradation, DUBs modulate the stability of ND-associated pathogenic proteins including amyloid β protein, Tau, and α-synuclein. Besides, DUBs also influence ND-associated mitophagy, protein secretion, and neuroinflammation. Given the various and critical functions of DUBs in NDs, DUBs may become potential therapeutic targets for NDs.
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30
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Tejedor AR, Garaizar A, Ramírez J, Espinosa JR. 'RNA modulation of transport properties and stability in phase-separated condensates. Biophys J 2021; 120:5169-5186. [PMID: 34762868 DOI: 10.1101/2021.03.05.434111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/03/2021] [Accepted: 10/03/2021] [Indexed: 05/25/2023] Open
Abstract
One of the key mechanisms employed by cells to control their spatiotemporal organization is the formation and dissolution of phase-separated condensates. The balance between condensate assembly and disassembly can be critically regulated by the presence of RNA. In this work, we use a chemically-accurate sequence-dependent coarse-grained model for proteins and RNA to unravel the impact of RNA in modulating the transport properties and stability of biomolecular condensates. We explore the phase behavior of several RNA-binding proteins such as FUS, hnRNPA1, and TDP-43 proteins along with that of their corresponding prion-like domains and RNA recognition motifs from absence to moderately high RNA concentration. By characterizing the phase diagram, key molecular interactions, surface tension, and transport properties of the condensates, we report a dual RNA-induced behavior: on the one hand, RNA enhances phase separation at low concentration as long as the RNA radius of gyration is comparable to that of the proteins, whereas at high concentration, it inhibits the ability of proteins to self-assemble independently of its length. On the other hand, along with the stability modulation, the viscosity of the condensates can be considerably reduced at high RNA concentration as long as the length of the RNA chains is shorter than that of the proteins. Conversely, long RNA strands increase viscosity even at high concentration, but barely modify protein self-diffusion which mainly depends on RNA concentration and on the effect RNA has on droplet density. On the whole, our work rationalizes the different routes by which RNA can regulate phase separation and condensate dynamics, as well as the subsequent aberrant rigidification implicated in the emergence of various neuropathologies and age-related diseases.
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Affiliation(s)
- Andrés R Tejedor
- Department of Chemical Engineering, Universidad Politécnica de Madrid, Madrid, Spain
| | - Adiran Garaizar
- Cavendish Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Jorge Ramírez
- Department of Chemical Engineering, Universidad Politécnica de Madrid, Madrid, Spain.
| | - Jorge R Espinosa
- Cavendish Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge, United Kingdom.
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31
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Tejedor AR, Garaizar A, Ramírez J, Espinosa JR. 'RNA modulation of transport properties and stability in phase-separated condensates. Biophys J 2021; 120:5169-5186. [PMID: 34762868 PMCID: PMC8715277 DOI: 10.1016/j.bpj.2021.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/03/2021] [Accepted: 10/03/2021] [Indexed: 12/29/2022] Open
Abstract
One of the key mechanisms employed by cells to control their spatiotemporal organization is the formation and dissolution of phase-separated condensates. The balance between condensate assembly and disassembly can be critically regulated by the presence of RNA. In this work, we use a chemically-accurate sequence-dependent coarse-grained model for proteins and RNA to unravel the impact of RNA in modulating the transport properties and stability of biomolecular condensates. We explore the phase behavior of several RNA-binding proteins such as FUS, hnRNPA1, and TDP-43 proteins along with that of their corresponding prion-like domains and RNA recognition motifs from absence to moderately high RNA concentration. By characterizing the phase diagram, key molecular interactions, surface tension, and transport properties of the condensates, we report a dual RNA-induced behavior: on the one hand, RNA enhances phase separation at low concentration as long as the RNA radius of gyration is comparable to that of the proteins, whereas at high concentration, it inhibits the ability of proteins to self-assemble independently of its length. On the other hand, along with the stability modulation, the viscosity of the condensates can be considerably reduced at high RNA concentration as long as the length of the RNA chains is shorter than that of the proteins. Conversely, long RNA strands increase viscosity even at high concentration, but barely modify protein self-diffusion which mainly depends on RNA concentration and on the effect RNA has on droplet density. On the whole, our work rationalizes the different routes by which RNA can regulate phase separation and condensate dynamics, as well as the subsequent aberrant rigidification implicated in the emergence of various neuropathologies and age-related diseases.
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Affiliation(s)
- Andrés R Tejedor
- Department of Chemical Engineering, Universidad Politécnica de Madrid, Madrid, Spain
| | - Adiran Garaizar
- Cavendish Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Jorge Ramírez
- Department of Chemical Engineering, Universidad Politécnica de Madrid, Madrid, Spain.
| | - Jorge R Espinosa
- Cavendish Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge, United Kingdom.
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32
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Lenard AJ, Hutten S, Zhou Q, Usluer S, Zhang F, Bourgeois BMR, Dormann D, Madl T. Phosphorylation Regulates CIRBP Arginine Methylation, Transportin-1 Binding and Liquid-Liquid Phase Separation. Front Mol Biosci 2021; 8:689687. [PMID: 34738012 PMCID: PMC8562343 DOI: 10.3389/fmolb.2021.689687] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/01/2021] [Indexed: 12/20/2022] Open
Abstract
Arginine-glycine(-glycine) (RG/RGG) regions are highly abundant in RNA-binding proteins and involved in numerous physiological processes. Aberrant liquid-liquid phase separation (LLPS) and stress granule (SGs) association of RG/RGG regions in the cytoplasm have been implicated in several neurodegenerative disorders. LLPS and SG association of these proteins is regulated by the interaction with nuclear import receptors, such as transportin-1 (TNPO1), and by post-translational arginine methylation. Strikingly, many RG/RGG proteins harbour potential phosphorylation sites within or close to their arginine methylated regions, indicating a regulatory role. Here, we studied the role of phosphorylation within RG/RGG regions on arginine methylation, TNPO1-binding and LLPS using the cold-inducible RNA-binding protein (CIRBP) as a paradigm. We show that the RG/RGG region of CIRBP is in vitro phosphorylated by serine-arginine protein kinase 1 (SRPK1), and discovered two novel phosphorylation sites in CIRBP. SRPK1-mediated phosphorylation of the CIRBP RG/RGG region impairs LLPS and binding to TNPO1 in vitro and interferes with SG association in cells. Furthermore, we uncovered that arginine methylation of the CIRBP RG/RGG region regulates in vitro phosphorylation by SRPK1. In conclusion, our findings indicate that LLPS and TNPO1-mediated chaperoning of RG/RGG proteins is regulated through an intricate interplay of post-translational modifications.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Saskia Hutten
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany.,BioMedical Center, Cell Biology, Ludwig-Maximilians-Universität (LMU) München, Martinsried, Germany
| | - Qishun Zhou
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Sinem Usluer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Fangrong Zhang
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Benjamin M R Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dorothee Dormann
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany.,BioMedical Center, Cell Biology, Ludwig-Maximilians-Universität (LMU) München, Martinsried, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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33
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Garaizar A, Espinosa JR. Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions. J Chem Phys 2021; 155:125103. [PMID: 34598583 DOI: 10.1063/5.0062687] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Multivalent proteins and nucleic acids can self-assemble into biomolecular condensates that contribute to compartmentalize the cell interior. Computer simulations offer a unique view to elucidate the mechanisms and key intermolecular interactions behind the dynamic formation and dissolution of these condensates. In this work, we present a novel approach to include explicit water and salt in sequence-dependent coarse-grained (CG) models for proteins and RNA, enabling the study of biomolecular condensate formation in a salt-dependent manner. Our framework combines a reparameterized version of the HPS protein force field with the monoatomic mW water model and the mW-ion potential for NaCl. We show how our CG model qualitatively captures the experimental radius of the gyration trend of a subset of intrinsically disordered proteins and reproduces the experimental protein concentration and water percentage of the human fused in sarcoma (FUS) low-complexity-domain droplets at physiological salt concentration. Moreover, we perform seeding simulations as a function of salt concentration for two antagonist systems: the engineered peptide PR25 and poly-uridine/poly-arginine mixtures, finding good agreement with their reported in vitro phase behavior with salt concentration in both cases. Taken together, our work represents a step forward towards extending sequence-dependent CG models to include water and salt, and to consider their key role in biomolecular condensate self-assembly.
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Affiliation(s)
- Adiran Garaizar
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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34
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Tejido C, Pakravan D, Bosch LVD. Potential Therapeutic Role of HDAC Inhibitors in FUS-ALS. Front Mol Neurosci 2021; 14:686995. [PMID: 34434087 PMCID: PMC8380926 DOI: 10.3389/fnmol.2021.686995] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/29/2021] [Indexed: 01/05/2023] Open
Abstract
Mutations in the FUS gene cause amyotrophic lateral sclerosis (ALS-FUS). However, the exact pathogenic mechanism of mutant fused in sarcoma (FUS) protein is not completely understood. FUS is an RNA binding protein (RBP) localized predominantly in the nucleus, but ALS-linked FUS mutations can affect its nuclear localization signal impairing its import into the nucleus. This mislocalization to the cytoplasm facilitates FUS aggregation in cytoplasmic inclusions. Therapies targeting post translational modifications are rising as new treatments for ALS, in particular acetylation which could have a role in the dynamics of RBPs. Research using histone deacetylase (HDAC) inhibitors in FUS-ALS models showed that HDACs can influence cytoplasmic FUS localization. Inhibition of HDACs could promote acetylation of the FUS RNA binding domain (RRM) and altering its RNA interactions resulting in FUS maintenance in the nucleus. In addition, acetylation of FUS RRMs might also favor or disfavor its incorporation into pathological inclusions. In this review, we summarize and discuss the evidence for the potential role of HDACs in the context of FUS-ALS and we propose a new hypothesis based on this overview.
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Affiliation(s)
- Clara Tejido
- Vlaams Instituut voor Biotechnologie (VIB), Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Donya Pakravan
- Vlaams Instituut voor Biotechnologie (VIB), Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,Department of Neurosciences, Experimental Neurology, Leuven Brain Institute, Katholieke Universiteit Leuven (KU Leuven)-University of Leuven, Leuven, Belgium
| | - Ludo Van Den Bosch
- Vlaams Instituut voor Biotechnologie (VIB), Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,Department of Neurosciences, Experimental Neurology, Leuven Brain Institute, Katholieke Universiteit Leuven (KU Leuven)-University of Leuven, Leuven, Belgium
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35
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Chen M, Foster JP, Lock IC, Leisenring NH, Daniel AR, Floyd W, Xu E, Davis IJ, Kirsch DG. Radiation-induced phosphorylation of a prion-like domain regulates transformation by FUS-CHOP. Cancer Res 2021; 81:4939-4948. [PMID: 34385184 DOI: 10.1158/0008-5472.can-20-1497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/01/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022]
Abstract
Chromosomal translocations generate oncogenic fusion proteins in approximately one-third of sarcomas, but how these proteins promote tumorigenesis is not well understood. Interestingly, some translocation-driven cancers exhibit dramatic clinical responses to therapy, such as radiotherapy, though the precise mechanism has not been elucidated. Here we reveal a molecular mechanism by which the fusion oncoprotein FUS-CHOP promotes tumor maintenance that also explains the remarkable sensitivity of myxoid liposarcomas to radiation therapy. FUS-CHOP interacted with chromatin remodeling complexes to regulate sarcoma cell proliferation. One of these chromatin remodelers, SNF2H, co-localized with FUS-CHOP genome-wide at active enhancers. Following ionizing radiation, DNA damage response kinases phosphorylated the prion-like domain of FUS-CHOP to impede these protein-protein interactions, which are required for transformation. Therefore, the DNA damage response after irradiation disrupted oncogenic targeting of chromatin remodelers required for FUS-CHOP-driven sarcomagenesis. This mechanism of disruption links phosphorylation of the prion-like domain of an oncogenic fusion protein to DNA damage after ionizing radiation and reveals that a dependence on oncogenic chromatin remodeling underlies sensitivity to radiation therapy in myxoid liposarcoma.
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Affiliation(s)
- Mark Chen
- Radiation Oncology, Duke Medical Center
| | | | | | | | | | - Warren Floyd
- Department of Pharmacology and Molecular Cancer Biology, Duke University School of Medicine
| | - Eric Xu
- Radiation Oncology, Duke Medical Center
| | - Ian J Davis
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill
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36
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Farina S, Esposito F, Battistoni M, Biamonti G, Francia S. Post-Translational Modifications Modulate Proteinopathies of TDP-43, FUS and hnRNP-A/B in Amyotrophic Lateral Sclerosis. Front Mol Biosci 2021; 8:693325. [PMID: 34291086 PMCID: PMC8287968 DOI: 10.3389/fmolb.2021.693325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
It has been shown that protein low-sequence complexity domains (LCDs) induce liquid-liquid phase separation (LLPS), which is responsible for the formation of membrane-less organelles including P-granules, stress granules and Cajal bodies. Proteins harbouring LCDs are widely represented among RNA binding proteins often mutated in ALS. Indeed, LCDs predispose proteins to a prion-like behaviour due to their tendency to form amyloid-like structures typical of proteinopathies. Protein post-translational modifications (PTMs) can influence phase transition through two main events: i) destabilizing or augmenting multivalent interactions between phase-separating macromolecules; ii) recruiting or excluding other proteins and/or nucleic acids into/from the condensate. In this manuscript we summarize the existing evidence describing how PTM can modulate LLPS thus favouring or counteracting proteinopathies at the base of neurodegeneration in ALS.
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Affiliation(s)
- Stefania Farina
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy.,University School for Advanced Studies IUSS, Pavia, Italy
| | - Francesca Esposito
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy.,Università Degli Studi di Pavia, Pavia, Italy
| | | | - Giuseppe Biamonti
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy
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37
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Portz B, Lee BL, Shorter J. FUS and TDP-43 Phases in Health and Disease. Trends Biochem Sci 2021; 46:550-563. [PMID: 33446423 PMCID: PMC8195841 DOI: 10.1016/j.tibs.2020.12.005] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/24/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022]
Abstract
The distinct prion-like domains (PrLDs) of FUS and TDP-43, modulate phase transitions that result in condensates with a range of material states. These assemblies are implicated in both health and disease. In this review, we examine how sequence, structure, post-translational modifications, and RNA can affect the self-assembly of these RNA-binding proteins (RBPs). We discuss how our emerging understanding of FUS and TDP-43 liquid-liquid phase separation (LLPS) and aggregation, could be leveraged to design new therapies for neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and limbic-predominant age-related TDP-43 encephalopathy (LATE).
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Affiliation(s)
- Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bo Lim Lee
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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38
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Gupta R, Sahu M, Srivastava D, Tiwari S, Ambasta RK, Kumar P. Post-translational modifications: Regulators of neurodegenerative proteinopathies. Ageing Res Rev 2021; 68:101336. [PMID: 33775891 DOI: 10.1016/j.arr.2021.101336] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/10/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
One of the hallmark features in the neurodegenerative disorders (NDDs) is the accumulation of aggregated and/or non-functional protein in the cellular milieu. Post-translational modifications (PTMs) are an essential regulator of non-functional protein aggregation in the pathogenesis of NDDs. Any alteration in the post-translational mechanism and the protein quality control system, for instance, molecular chaperone, ubiquitin-proteasome system, autophagy-lysosomal degradation pathway, enhances the accumulation of misfolded protein, which causes neuronal dysfunction. Post-translational modification plays many roles in protein turnover rate, accumulation of aggregate and can also help in the degradation of disease-causing toxic metabolites. PTMs such as acetylation, glycosylation, phosphorylation, ubiquitination, palmitoylation, SUMOylation, nitration, oxidation, and many others regulate protein homeostasis, which includes protein structure, functions and aggregation propensity. Different studies demonstrated the involvement of PTMs in the regulation of signaling cascades such as PI3K/Akt/GSK3β, MAPK cascade, AMPK pathway, and Wnt signaling pathway in the pathogenesis of NDDs. Further, mounting evidence suggests that targeting different PTMs with small chemical molecules, which acts as an inhibitor or activator, reverse misfolded protein accumulation and thus enhances the neuroprotection. Herein, we briefly discuss the protein aggregation and various domain structures of different proteins involved in the NDDs, indicating critical amino acid residues where PTMs occur. We also describe the implementation and involvement of various PTMs on signaling cascade and cellular processes in NDDs. Lastly, we implement our current understanding of the therapeutic importance of PTMs in neurodegeneration, along with emerging techniques targeting various PTMs.
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39
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Dasmeh P, Wagner A. Natural Selection on the Phase-Separation Properties of FUS during 160 My of Mammalian Evolution. Mol Biol Evol 2021; 38:940-951. [PMID: 33022038 PMCID: PMC7947763 DOI: 10.1093/molbev/msaa258] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein phase separation can help explain the formation of many nonmembranous organelles. However, we know little about its ability to change in evolution. Here we studied the evolution of the mammalian RNA-binding protein Fused in Sarcoma (FUS), a protein whose prion-like domain (PLD) contributes to the formation of stress granules through liquid–liquid phase separation. Although the PLD evolves three times as rapidly as the remainder of FUS, it harbors absolutely conserved tyrosine residues that are crucial for phase separation. Ancestral reconstruction shows that the phosphorylation sites within the PLD are subject to stabilizing selection. They toggle among a small number of amino acid states. One exception to this pattern is primates, where the number of such phosphosites has increased through positive selection. In addition, we find frequent glutamine to proline changes that help maintain the unstructured state of FUS that is necessary for phase separation. Our work provides evidence that natural selection has stabilized the liquid forming potential of FUS and minimized the propensity of cytotoxic liquid-to-solid phase transitions during 160 My of mammalian evolution.
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Affiliation(s)
- Pouria Dasmeh
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Andreas Wagner
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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40
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Nargeh H, Aliabadi F, Ajami M, Pazoki-Toroudi H. Role of Polyphenols on Gut Microbiota and the Ubiquitin-Proteasome System in Neurodegenerative Diseases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6119-6144. [PMID: 34038102 DOI: 10.1021/acs.jafc.1c00923] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Today, neurodegenerative diseases have become a remarkable public health challenge due to their direct relation with aging. Accordingly, understanding the molecular and cellular mechanisms occurring in the pathogenesis of them is essential. Both protein aggregations as a result of the ubiquitin-proteasome system (UPS) inefficiency and gut microbiota alternation are the main pathogenic hallmarks. Polyphenols upregulating this system may decrease the developing rate of neurodegenerative diseases. Most of the dietary intake of polyphenols is converted into other microbial metabolites, which have completely different biological properties from the original polyphenols and should be thoroughly investigated. Herein, several prevalent neurodegenerative diseases are pinpointed to explain the role of gut microbiota alternations and the role of molecular changes, especially UPS down-regulation in their pathogenesis. Some of the most important polyphenols found in our diet are explained along with their microbial metabolites in the body.
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Affiliation(s)
- Hanieh Nargeh
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1417466191, Iran
| | - Fatemeh Aliabadi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
| | - Marjan Ajami
- Faculty of Nutrition Sciences & Food Technology, Shahid Beheshti University of Medical Sciences, 7th Floor, Bldg No. 2 SBUMS, Arabi Avenue, Daneshjoo Boulevard, Velenjak, Tehran 19839-63113, Iran
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
- Department of Physiology and Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran
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41
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Guo Q, Shi X, Wang X. RNA and liquid-liquid phase separation. Noncoding RNA Res 2021; 6:92-99. [PMID: 33997539 PMCID: PMC8111091 DOI: 10.1016/j.ncrna.2021.04.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/09/2023] Open
Abstract
Liquid-Liquid Phase Separation (LLPS) is a biological phenomenon that refers to the components of similar properties form droplets condensate in cells. These droplets play an important role in maintaining the stability of order in cells. In the studies of phase separation, weak multivalent interactions between proteins have always been the focus of attentions. With the deepening research of phase separation, more and more evidences show that RNA, especially long noncoding RNA (lncRNA), also plays an important regulatory role in the phase separation. We summarized recent researches between phase separation and RNA, and focused on the function of non-coding RNA (ncRNA) in the process of phase separation. In fact, phase separation and RNA have a two-way regulation relationship. Noncoding RNA usually recruits proteins as molecular scaffolds to drive phase separation. On the other hand, phase separation is also involved in RNA transcription, transport, metabolism and other processes.
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Affiliation(s)
- Qi Guo
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Xiangmin Shi
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Xiangting Wang
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
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42
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Jin Y, Vadukul DM, Gialama D, Ge Y, Thrush R, White JT, Aprile FA. The Diagnostic Potential of Amyloidogenic Proteins. Int J Mol Sci 2021; 22:4128. [PMID: 33923609 PMCID: PMC8074075 DOI: 10.3390/ijms22084128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative disorders are a highly prevalent class of diseases, whose pathological mechanisms start before the appearance of any clear symptoms. This fact has prompted scientists to search for biomarkers that could aid early treatment. These currently incurable pathologies share the presence of aberrant aggregates called amyloids in the nervous system, which are composed of specific proteins. In this review, we discuss how these proteins, their conformations and modifications could be exploited as biomarkers for diagnostic purposes. We focus on proteins that are associated with the most prevalent neurodegenerative disorders, including Alzheimer's and Parkinson's diseases, amyotrophic lateral sclerosis, and frontotemporal dementia. We also describe current challenges in detection, the most recent techniques with diagnostic potentials and possible future developments in diagnosis.
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Affiliation(s)
| | | | | | | | | | | | - Francesco Antonio Aprile
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; (Y.J.); (D.M.V.); (D.G.); (Y.G.); (R.T.); (J.T.W.)
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43
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Schisa JA, Elaswad MT. An Emerging Role for Post-translational Modifications in Regulating RNP Condensates in the Germ Line. Front Mol Biosci 2021; 8:658020. [PMID: 33898525 PMCID: PMC8060454 DOI: 10.3389/fmolb.2021.658020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins undergo regulated phase transitions in an array of cell types. The phase separation of RNA-binding proteins, and subsequent formation of RNP condensates or granules, occurs during physiological conditions and can also be induced by stress. Some RNP granules have roles in post-transcriptionally regulating mRNAs, and mutations that prevent the condensation of RNA-binding proteins can reduce an organism's fitness. The reversible and multivalent interactions among RNP granule components can result in RNP complexes that transition among diffuse and condensed states, the latter of which can be pathological; for example, in neurons solid RNP aggregates contribute to disease states such as amyotrophic lateral sclerosis (ALS), and the dysregulation of RNP granules in human germ cells may be involved in Fragile X-associated primary ovarian insufficiency. Thus, regulating the assembly of mRNAs and RNA-binding proteins into discrete granules appears to provide important functions at both cellular and physiological levels. Here we review our current understanding of the role of post-translational modifications (PTMs) in regulating the condensation of RNA-binding proteins in the germ line. We compare and contrast the in vitro evidence that methylation inhibits phase separation of RNA binding proteins, with the extent to which these results apply to the in vivo germ line environment of several model systems. We also focus on the role of phosphorylation in modulating the dynamics of RNP granules in the germ line. Finally, we consider the gaps that exist in our understanding of the role of PTMs in regulating germ line RNP granules.
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Affiliation(s)
- Jennifer A Schisa
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | - Mohamed T Elaswad
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
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44
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Hosoya Y, Ohkanda J. Intrinsically Disordered Proteins as Regulators of Transient Biological Processes and as Untapped Drug Targets. Molecules 2021; 26:2118. [PMID: 33917117 PMCID: PMC8067799 DOI: 10.3390/molecules26082118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are critical players in the dynamic control of diverse cellular processes, and provide potential new drug targets because their dysregulation is closely related to many diseases. This review focuses on several medicinal studies that have identified low-molecular-weight inhibitors of IDPs. In addition, clinically relevant liquid-liquid phase separations-which critically involve both intermolecular interactions between IDPs and their posttranslational modification-are analyzed to understand the potential of IDPs as new drug targets.
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Affiliation(s)
| | - Junko Ohkanda
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano 399-4598, Japan;
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45
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Harley J, Clarke BE, Patani R. The Interplay of RNA Binding Proteins, Oxidative Stress and Mitochondrial Dysfunction in ALS. Antioxidants (Basel) 2021; 10:antiox10040552. [PMID: 33918215 PMCID: PMC8066094 DOI: 10.3390/antiox10040552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
RNA binding proteins fulfil a wide number of roles in gene expression. Multiple mechanisms of RNA binding protein dysregulation have been implicated in the pathomechanisms of several neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Oxidative stress and mitochondrial dysfunction also play important roles in these diseases. In this review, we highlight the mechanistic interplay between RNA binding protein dysregulation, oxidative stress and mitochondrial dysfunction in ALS. We also discuss different potential therapeutic strategies targeting these pathways.
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Affiliation(s)
- Jasmine Harley
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK;
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin E. Clarke
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK;
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Correspondence: (B.E.C.); (R.P.)
| | - Rickie Patani
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK;
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- National Hospital for Neurology and Neurosurgery, University College London NHS, London WC1N 3BG, UK
- Correspondence: (B.E.C.); (R.P.)
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46
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Darling AL, Shorter J. Combating deleterious phase transitions in neurodegenerative disease. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118984. [PMID: 33549703 PMCID: PMC7965345 DOI: 10.1016/j.bbamcr.2021.118984] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/11/2022]
Abstract
Protein aggregation is a hallmark of neurodegenerative diseases. However, the mechanism that induces pathogenic aggregation is not well understood. Recently, it has emerged that several of the pathological proteins found in an aggregated or mislocalized state in neurodegenerative diseases are also able to undergo liquid-liquid phase separation (LLPS) under physiological conditions. Although these phase transitions are likely important for various physiological functions, neurodegenerative disease-related mutations and conditions can alter the LLPS behavior of these proteins, which can elicit toxicity. Therefore, therapeutics that antagonize aberrant LLPS may be able to mitigate toxicity and aggregation that is ubiquitous in neurodegenerative disease. Here, we discuss the mechanisms by which aberrant protein phase transitions may contribute to neurodegenerative disease. We also outline potential therapeutic strategies to counter deleterious phases. State without borders: Membrane-less organelles and liquid-liquid phase transitions edited by Vladimir N Uversky.
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Affiliation(s)
- April L Darling
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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47
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Bock AS, Murthy AC, Tang WS, Jovic N, Shewmaker F, Mittal J, Fawzi NL. N-terminal acetylation modestly enhances phase separation and reduces aggregation of the low-complexity domain of RNA-binding protein fused in sarcoma. Protein Sci 2021; 30:1337-1349. [PMID: 33547841 DOI: 10.1002/pro.4029] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/22/2022]
Abstract
The RNA-binding protein fused in sarcoma (FUS) assembles via liquid-liquid phase separation (LLPS) into functional RNA granules and aggregates in amyotrophic lateral sclerosis associated neuronal inclusions. Several studies have demonstrated that posttranslational modification (PTM) can significantly alter FUS phase separation and aggregation, particularly charge-altering phosphorylation of the nearly uncharged N-terminal low complexity domain of FUS (FUS LC). However, the occurrence and impact of N-terminal acetylation on FUS phase separation remains unexplored, even though N-terminal acetylation is the most common PTM in mammals and changes the charge at the N-terminus. First, we find that FUS is predominantly acetylated in two human cell types and stress conditions. Next, we show that recombinant FUS LC can be acetylated when co-expressed with the NatA complex in Escherichia coli. Using NMR spectroscopy, we find that N-terminal acetylated FUS LC (FUS LC Nt-Ac) does not notably alter monomeric FUS LC structure or motions. Despite no difference in structure, Nt-Ac-FUS LC phase separates more avidly than unmodified FUS LC. More importantly, N-terminal acetylation of FUS LC reduces aggregation. Our findings highlight the importance of N-terminal acetylation of proteins that undergo physiological LLPS and pathological aggregation.
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Affiliation(s)
- Anna S Bock
- Graduate Program in Biotechnology, Brown University, Providence, Rhode Island, USA
| | - Anastasia C Murthy
- Graduate Program in Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Wai Shing Tang
- Graduate Program in Physics, Brown University, Providence, Rhode Island, USA
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Frank Shewmaker
- Department of Biochemistry, Uniformed Services University, Bethesda, Maryland, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Nicolas L Fawzi
- The Robert J and Nancy D Carney Institute for Brain Science & Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA
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48
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Perdikari TM, Jovic N, Dignon GL, Kim YC, Fawzi NL, Mittal J. A predictive coarse-grained model for position-specific effects of post-translational modifications. Biophys J 2021; 120:1187-1197. [PMID: 33582133 DOI: 10.1016/j.bpj.2021.01.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
Biomolecules undergo liquid-liquid phase separation (LLPS), resulting in the formation of multicomponent protein-RNA membraneless organelles in cells. However, the physiological and pathological role of post-translational modifications (PTMs) on the biophysics of phase behavior is only beginning to be probed. To study the effect of PTMs on LLPS in silico, we extend our transferable coarse-grained model of intrinsically disordered proteins to include phosphorylated and acetylated amino acids. Using the parameters for modified amino acids available for fixed-charge atomistic force fields, we parameterize the size and atomistic hydropathy of the coarse-grained-modified amino acid beads and, hence, the interactions between the modified and natural amino acids. We then elucidate how the number and position of phosphorylated and acetylated residues alter the protein's single-chain compactness and its propensity to phase separate. We show that both the number and the position of phosphorylated threonines/serines or acetylated lysines can serve as a molecular on/off switch for phase separation in the well-studied disordered regions of Fused in Sarcoma (FUS) and DDX3X, respectively. We also compare modified residues to their commonly used PTM mimics for their impact on chain properties. Importantly, we show that the model can predict and capture experimentally measured differences in the phase behavior for position-specific modifications, showing that the position of modifications can dictate phase separation. In sum, this model will be useful for studying LLPS of post-translationally modified intrinsically disordered proteins and predicting how modifications control phase behavior with position-specific resolution.
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Affiliation(s)
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Young C Kim
- Center for Materials Physics and Technology, U.S. Naval Research Laboratory, Washington D.C
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology; Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, Rhode Island.
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania.
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49
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Layalle S, They L, Ourghani S, Raoul C, Soustelle L. Amyotrophic Lateral Sclerosis Genes in Drosophila melanogaster. Int J Mol Sci 2021; 22:ijms22020904. [PMID: 33477509 PMCID: PMC7831090 DOI: 10.3390/ijms22020904] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating adult-onset neurodegenerative disease characterized by the progressive degeneration of upper and lower motoneurons. Most ALS cases are sporadic but approximately 10% of ALS cases are due to inherited mutations in identified genes. ALS-causing mutations were identified in over 30 genes with superoxide dismutase-1 (SOD1), chromosome 9 open reading frame 72 (C9orf72), fused in sarcoma (FUS), and TAR DNA-binding protein (TARDBP, encoding TDP-43) being the most frequent. In the last few decades, Drosophila melanogaster emerged as a versatile model for studying neurodegenerative diseases, including ALS. In this review, we describe the different Drosophila ALS models that have been successfully used to decipher the cellular and molecular pathways associated with SOD1, C9orf72, FUS, and TDP-43. The study of the known fruit fly orthologs of these ALS-related genes yielded significant insights into cellular mechanisms and physiological functions. Moreover, genetic screening in tissue-specific gain-of-function mutants that mimic ALS-associated phenotypes identified disease-modifying genes. Here, we propose a comprehensive review on the Drosophila research focused on four ALS-linked genes that has revealed novel pathogenic mechanisms and identified potential therapeutic targets for future therapy.
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Affiliation(s)
- Sophie Layalle
- The Neuroscience Institute of Montpellier, INSERM, University of Montpellier, 34091 Montpellier, France; (S.L.); (L.T.); (S.O.)
| | - Laetitia They
- The Neuroscience Institute of Montpellier, INSERM, University of Montpellier, 34091 Montpellier, France; (S.L.); (L.T.); (S.O.)
| | - Sarah Ourghani
- The Neuroscience Institute of Montpellier, INSERM, University of Montpellier, 34091 Montpellier, France; (S.L.); (L.T.); (S.O.)
| | - Cédric Raoul
- The Neuroscience Institute of Montpellier, INSERM, University of Montpellier, 34091 Montpellier, France; (S.L.); (L.T.); (S.O.)
- Laboratory of Neurobiology, Kazan Federal University, 420008 Kazan, Russia
- Correspondence: (C.R.); (L.S.)
| | - Laurent Soustelle
- The Neuroscience Institute of Montpellier, INSERM, University of Montpellier, 34091 Montpellier, France; (S.L.); (L.T.); (S.O.)
- Correspondence: (C.R.); (L.S.)
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50
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Kawahara D, Suzuki T, Nakaya T. Cytoplasmic granule formation by FUS-R495X is attributable to arginine methylation in all Gly-rich, RGG1 and RGG2 domains. Genes Cells 2021; 26:190-197. [PMID: 33411976 DOI: 10.1111/gtc.12827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/23/2020] [Accepted: 01/03/2021] [Indexed: 11/28/2022]
Abstract
Many mutations in the fused in sarcoma (FUS) gene have been identified as genetic causative factors of amyotrophic lateral sclerosis (ALS). As a certain number of mutants form aberrant cytoplasmic granules under specific conditions, granule forming ability of FUS is believed to be linked to the pathogenesis of ALS. However, molecular mechanisms underlying this property remain unclear. An ALS-linked FUS mutant, R495X, shows extensive cytoplasmic localization and forms granules in neurons. In the present study, using R495X domain deletion constructs, we showed that deletion of any of Gly-rich, RGG1 or RGG2 significantly suppressed granule formation. Furthermore, when neurons expressing EGFP-R495X were treated with an arginine methylation inhibitor, the number of cells displaying R495X granules was significantly reduced. When FLAG-tagged arginine N-methyltransferase 8 (PRMT8) was co-expressed with EGFP-R495X to facilitate its methylation, the number of cells with granules was significantly increased. Collectively, these findings suggest that cytoplasmic granule formation by R495X is attributable to the arginine methylation in all Gly-rich, RGG1 and RGG2 domains.
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Affiliation(s)
- Daiki Kawahara
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Toshiharu Suzuki
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Tadashi Nakaya
- School of Pharmacy at Fukuoka, International University of Health and Welfare, Fukuoka, Japan
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