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Giudice J, Jiang H. Splicing regulation through biomolecular condensates and membraneless organelles. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00739-7. [PMID: 38773325 DOI: 10.1038/s41580-024-00739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Biomolecular condensates, sometimes also known as membraneless organelles (MLOs), can form through weak multivalent intermolecular interactions of proteins and nucleic acids, a process often associated with liquid-liquid phase separation. Biomolecular condensates are emerging as sites and regulatory platforms of vital cellular functions, including transcription and RNA processing. In the first part of this Review, we comprehensively discuss how alternative splicing regulates the formation and properties of condensates, and conversely the roles of biomolecular condensates in splicing regulation. In the second part, we focus on the spatial connection between splicing regulation and nuclear MLOs such as transcriptional condensates, splicing condensates and nuclear speckles. We then discuss key studies showing how splicing regulation through biomolecular condensates is implicated in human pathologies such as neurodegenerative diseases, different types of cancer, developmental disorders and cardiomyopathies, and conclude with a discussion of outstanding questions pertaining to the roles of condensates and MLOs in splicing regulation and how to experimentally study them.
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Affiliation(s)
- Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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2
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Yan Y, Luo A, Liu S, Cai M, Liu X, Zhang X, Zhang S, Liu Y, Zeng J, Xu X, Zhang N, Zhang Z, Xu Y, He J, Liu X. METTL3-Mediated LINC00475 Alternative Splicing Promotes Glioma Progression by Inducing Mitochondrial Fission. RESEARCH (WASHINGTON, D.C.) 2024; 7:0324. [PMID: 38405130 PMCID: PMC10886067 DOI: 10.34133/research.0324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Mitochondrial fission promotes glioma progression. The function and regulation mechanisms of lncRNAs in glioma mitochondrial fission are unclear. The expression of LINC00475 and its correlation with clinical parameters in glioma were analyzed using bioinformatics. Then, in vitro and in vivo assays were performed to explore the function of spliced variant LINC00475 (LINC00475-S) in gliomas. To explore the mechanisms, RNA-seq, MeRIP, RIP, pulldown-IP, dCas9-ALKBH5 editing system, LC/MS, and Western blotting were utilized. LINC00475 was confirmed to be overexpressed and with higher frequencies of AS events in gliomas compared to normal brain tissue and was associated with worse prognosis. In vitro and animal tumor formation experiments demonstrated that the effect of LINC00475-S on proliferation, metastasis, autophagy, and mitochondrial fission of glioma cells was significantly stronger than that of LINC00475. Mechanistically, METTL3 induced the generation of LINC00475-S by splicing LINC00475 through m6A modification and subsequently promotes mitochondrial fission in glioma cells by inhibiting the expression of MIF. Pull-down combined LC/MS and RIP assays identified that the m6A recognition protein HNRNPH1 bound to LINC00475 within GYR and GY domains and promoted LINC00475 splicing. METTL3 facilitated HNRNPH1 binding to LINC00475 in an m6A-dependent manner, thereby inducing generation of LINC00475-S. METTL3 facilitated HNRNPH1-mediated AS of LINC00475, which promoted glioma progression by inducing mitochondrial fission. Targeting AS of LINC00475 and m6A editing could serve as a therapeutic strategy against gliomas.
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Affiliation(s)
- Yaping Yan
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Ailing Luo
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Shanshan Liu
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Mansi Cai
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Xiaodan Liu
- Division of Birth Cohort Study, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Xiaohong Zhang
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Siyi Zhang
- Department of Anesthesiology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Yu Liu
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
| | - Jiamin Zeng
- Department of Anesthesiology,
The Second Affiliated Hospital of University of South China, Hengyang, Hunan Province 421001, China
| | - Xinke Xu
- Department of Neurosurgery, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Na Zhang
- Department of Anesthesiology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Zhuorong Zhang
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Yingyi Xu
- Department of Anesthesiology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangzhou 510623, China
| | - Xiaoping Liu
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center,
Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510623, China
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3
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McConnell BS, Parker MW. Protein intrinsically disordered regions have a non-random, modular architecture. Bioinformatics 2023; 39:btad732. [PMID: 38039154 PMCID: PMC10719218 DOI: 10.1093/bioinformatics/btad732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023] Open
Abstract
MOTIVATION Protein sequences can be broadly categorized into two classes: those which adopt stable secondary structure and fold into a domain (i.e. globular proteins), and those that do not. The sequences belonging to this latter class are conformationally heterogeneous and are described as being intrinsically disordered. Decades of investigation into the structure and function of globular proteins has resulted in a suite of computational tools that enable their sub-classification by domain type, an approach that has revolutionized how we understand and predict protein functionality. Conversely, it is unknown if sequences of disordered protein regions are subject to broadly generalizable organizational principles that would enable their sub-classification. RESULTS Here, we report the development of a statistical approach that quantifies linear variance in amino acid composition across a sequence. With multiple examples, we provide evidence that intrinsically disordered regions are organized into statistically non-random modules of unique compositional bias. Modularity is observed for both low and high-complexity sequences and, in some cases, we find that modules are organized in repetitive patterns. These data demonstrate that disordered sequences are non-randomly organized into modular architectures and motivate future experiments to comprehensively classify module types and to determine the degree to which modules constitute functionally separable units analogous to the domains of globular proteins. AVAILABILITY AND IMPLEMENTATION The source code, documentation, and data to reproduce all figures are freely available at https://github.com/MWPlabUTSW/Chi-Score-Analysis.git. The analysis is also available as a Google Colab Notebook (https://colab.research.google.com/github/MWPlabUTSW/Chi-Score-Analysis/blob/main/ChiScore_Analysis.ipynb).
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Affiliation(s)
- Brendan S McConnell
- Department of Biophysics, , University of Texas Southwestern Medical Center, Dallas, TX 75235, United States
| | - Matthew W Parker
- Department of Biophysics, , University of Texas Southwestern Medical Center, Dallas, TX 75235, United States
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4
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Yang Y, Lee GC, Nakagaki-Silva E, Huang Y, Peacey M, Partridge R, Gooding C, Smith CJ. Cell-type specific regulator RBPMS switches alternative splicing via higher-order oligomerization and heterotypic interactions with other splicing regulators. Nucleic Acids Res 2023; 51:9961-9982. [PMID: 37548402 PMCID: PMC10570038 DOI: 10.1093/nar/gkad652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/28/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
Alternative pre-mRNA splicing decisions are regulated by RNA binding proteins (RBPs) that can activate or repress regulated splice sites. Repressive RBPs typically harness multivalent interactions to bind stably to target RNAs. Multivalency can be achieved by homomeric oligomerization and heteromeric interactions with other RBPs, often mediated by intrinsically disordered regions (IDRs), and by possessing multiple RNA binding domains. Cell-specific splicing decisions often involve the action of widely expressed RBPs, which are able to bind multivalently around target exons, but without effect in the absence of a cell-specific regulator. To address how cell-specific regulators can collaborate with constitutive RBPs in alternative splicing regulation, we used the smooth-muscle specific regulator RBPMS. Recombinant RBPMS is sufficient to confer smooth muscle cell specific alternative splicing of Tpm1 exon 3 in cell-free assays by preventing assembly of ATP-dependent splicing complexes. This activity depends upon a C-terminal IDR that facilitates dynamic higher-order self-assembly, cooperative binding to multivalent RNA and interactions with widely expressed splicing co-regulators, including MBNL1 and RBFOX2, allowing cooperative assembly of stable cell-specific regulatory complexes.
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Affiliation(s)
- Yi Yang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Giselle C Lee
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | | | - Yuling Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Matthew Peacey
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ruth Partridge
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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Brownmiller T, Caplen NJ. The HNRNPF/H RNA binding proteins and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1788. [PMID: 37042074 PMCID: PMC10523889 DOI: 10.1002/wrna.1788] [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: 10/31/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 04/13/2023]
Abstract
The members of the HNRNPF/H family of heterogeneous nuclear RNA proteins-HNRNPF, HNRNPH1, HNRNPH2, HNRNPH3, and GRSF1, are critical regulators of RNA maturation. Documented functions of these proteins include regulating splicing, particularly alternative splicing, 5' capping and 3' polyadenylation of RNAs, and RNA export. The assignment of these proteins to the HNRNPF/H protein family members relates to differences in the amino acid composition of their RNA recognition motifs, which differ from those of other RNA binding proteins (RBPs). HNRNPF/H proteins typically bind RNA sequences enriched with guanine (G) residues, including sequences that, in the presence of a cation, have the potential to form higher-order G-quadruplex structures. The need to further investigate members of the HNRNPF/H family of RBPs has intensified with the recent descriptions of their involvement in several disease states, including the pediatric tumor Ewing sarcoma and the hematological malignancy mantle cell lymphoma; newly described groups of developmental syndromes; and neuronal-related disorders, including addictive behavior. Here, to foster the study of the HNRNPF/H family of RBPs, we discuss features of the genes encoding these proteins, their structures and functions, and emerging contributions to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Tayvia Brownmiller
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, Maryland, USA
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Vital T, Wali A, Butler KV, Xiong Y, Foster JP, Marcel SS, McFadden AW, Nguyen VU, Bailey BM, Lamb KN, James LI, Frye SV, Mosely AL, Jin J, Pattenden SG, Davis IJ. MS0621, a novel small-molecule modulator of Ewing sarcoma chromatin accessibility, interacts with an RNA-associated macromolecular complex and influences RNA splicing. Front Oncol 2023; 13:1099550. [PMID: 36793594 PMCID: PMC9924231 DOI: 10.3389/fonc.2023.1099550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Ewing sarcoma is a cancer of children and young adults characterized by the critical translocation-associated fusion oncoprotein EWSR1::FLI1. EWSR1::FLI1 targets characteristic genetic loci where it mediates aberrant chromatin and the establishment of de novo enhancers. Ewing sarcoma thus provides a model to interrogate mechanisms underlying chromatin dysregulation in tumorigenesis. Previously, we developed a high-throughput chromatin-based screening platform based on the de novo enhancers and demonstrated its utility in identifying small molecules capable of altering chromatin accessibility. Here, we report the identification of MS0621, a molecule with previously uncharacterized mechanism of action, as a small molecule modulator of chromatin state at sites of aberrant chromatin accessibility at EWSR1::FLI1-bound loci. MS0621 suppresses cellular proliferation of Ewing sarcoma cell lines by cell cycle arrest. Proteomic studies demonstrate that MS0621 associates with EWSR1::FLI1, RNA binding and splicing proteins, as well as chromatin regulatory proteins. Surprisingly, interactions with chromatin and many RNA-binding proteins, including EWSR1::FLI1 and its known interactors, were RNA-independent. Our findings suggest that MS0621 affects EWSR1::FLI1-mediated chromatin activity by interacting with and altering the activity of RNA splicing machinery and chromatin modulating factors. Genetic modulation of these proteins similarly inhibits proliferation and alters chromatin in Ewing sarcoma cells. The use of an oncogene-associated chromatin signature as a target allows for a direct approach to screen for unrecognized modulators of epigenetic machinery and provides a framework for using chromatin-based assays for future therapeutic discovery efforts.
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Affiliation(s)
- Tamara Vital
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Aminah Wali
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kyle V. Butler
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Joseph P. Foster
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Shelsa S. Marcel
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Andrew W. McFadden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Valerie U. Nguyen
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benton M. Bailey
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lindsey I. James
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stephen V. Frye
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amber L. Mosely
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Samantha G. Pattenden
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ian J. Davis
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Liquid-liquid Phase Separation of α-Synuclein: A New Mechanistic Insight for α-Synuclein Aggregation Associated with Parkinson's Disease Pathogenesis. J Mol Biol 2023; 435:167713. [PMID: 35787838 DOI: 10.1016/j.jmb.2022.167713] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023]
Abstract
Aberrant aggregation of the misfolded presynaptic protein, α-Synuclein (α-Syn) into Lewy body (LB) and Lewy neuritis (LN) is a major pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. Numerous studies have suggested that prefibrillar and fibrillar species of the misfolded α-Syn aggregates are responsible for cell death in PD pathogenesis. However, the precise molecular events during α-Syn aggregation, especially in the early stages, remain elusive. Emerging evidence has demonstrated that liquid-liquid phase separation (LLPS) of α-Syn occurs in the nucleation step of α-Syn aggregation, which offers an alternate non-canonical aggregation pathway in the crowded microenvironment. The liquid-like α-Syn droplets gradually undergo an irreversible liquid-to-solid phase transition into amyloid-like hydrogel entrapping oligomers and fibrils. This new mechanism of α-Syn LLPS and gel formation might represent the molecular basis of cellular toxicity associated with PD. This review aims to demonstrate the recent development of α-Syn LLPS, the underlying mechanism along with the microscopic events of aberrant phase transition. This review further discusses how several intrinsic and extrinsic factors regulate the thermodynamics and kinetics of α-Syn LLPS and co-LLPS with other proteins, which might explain the pathophysiology of α-Syn in various neurodegenerative diseases.
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Phase separation and other forms of α-Synuclein self-assemblies. Essays Biochem 2022; 66:987-1000. [DOI: 10.1042/ebc20220055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
Abstract
α-Synuclein (α-Syn) is a natively unstructured protein, which self-assembles into higher-order aggregates possessing serious pathophysiological implications. α-Syn aberrantly self-assembles into protein aggregates, which have been widely implicated in Parkinson’s disease (PD) pathogenesis and other synucleinopathies. The self-assembly of α-Syn involves the structural conversion of soluble monomeric protein into oligomeric intermediates and eventually fibrillar aggregates of amyloids with cross-β-sheet rich conformation. These aggregated α-Syn species majorly constitute the intraneuronal inclusions, which is a hallmark of PD neuropathology. Self-assembly/aggregation of α-Syn is not a single-state conversion process as unfolded protein can access multiple conformational states through the formation of metastable, transient pre-fibrillar intermediate species. Recent studies have indicated that soluble oligomers are the potential neurotoxic species responsible for cell death in PD pathogenesis. The heterogeneous and transient nature of oligomers formed during the early stage of aggregation pathway limit their detailed study in understanding the structure–toxicity relationship. Moreover, the precise molecular events occurring in the early stage of α-Syn aggregation process majorly remain unsolved. Recently, liquid–liquid phase separation (LLPS) of α-Syn has been designated as an alternate nucleation mechanism, which occurs in the early lag phase of the aggregation pathway leading to the formation of dynamic supramolecular assemblies. The stronger self-association among the protein molecules triggers the irreversible liquid-to-solid transition of these supramolecular assemblies into the amyloid-like hydrogel, which may serve as a reservoir entrapping toxic oligomeric intermediates and fibrils. This review strives to provide insights into different modes of α-Syn self-assemblies including LLPS-mediated self-assembly and its recent advancements.
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Lee J, Cho H, Kwon I. Phase separation of low-complexity domains in cellular function and disease. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1412-1422. [PMID: 36175485 PMCID: PMC9534829 DOI: 10.1038/s12276-022-00857-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
In this review, we discuss the ways in which recent studies of low-complexity (LC) domains have challenged our understanding of the mechanisms underlying cellular organization. LC sequences, long believed to function in the absence of a molecular structure, are abundant in the proteomes of all eukaryotic organisms. Over the past decade, the phase separation of LC domains has emerged as a fundamental mechanism driving dynamic multivalent interactions of many cellular processes. We review the key evidence showing the role of phase separation of individual proteins in organizing cellular assemblies and facilitating biological function while implicating the dynamics of phase separation as a key to biological validity and functional utility. We also highlight the evidence showing that pathogenic LC proteins alter various phase separation-dependent interactions to elicit debilitating human diseases, including cancer and neurodegenerative diseases. Progress in understanding the biology of phase separation may offer useful hints toward possible therapeutic interventions to combat the toxicity of pathogenic proteins.
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Affiliation(s)
- Jiwon Lee
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Hana Cho
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
| | - Ilmin Kwon
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
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10
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Kim CG, Hwang DE, Kumar R, Chung M, Eom YG, Kim H, Koo DH, Choi JM. Recent trends in studies of biomolecular phase separation. BMB Rep 2022. [PMID: 35880435 PMCID: PMC9442351 DOI: 10.5483/bmbrep.2022.55.8.101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biomolecular phase separation has recently attracted broad in-terest, due to its role in the spatiotemporal compartmentalization of living cells. It governs the formation, regulation, and dissociation of biomolecular condensates, which play multiple roles in vivo, from activating specific biochemical reactions to organizing chromatin. Interestingly, biomolecular phase separation seems to be a mainly passive process, which can be ex-plained by relatively simple physical principles and reproduced in vitro with a minimal set of components. This Mini review focuses on our current understanding of the fundamental principles of biomolecular phase separation and the recent progress in the research on this topic.
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Affiliation(s)
- Chan-Geun Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Rajeev Kumar
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Min Chung
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Hyunji Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Hyun Koo
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
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11
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Kim CG, Hwang DE, Kumar R, Chung M, Eom YG, Kim H, Koo DH, Choi JM. Recent trends in studies of biomolecular phase separation. BMB Rep 2022; 55:363-369. [PMID: 35880435 PMCID: PMC9442351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 03/08/2024] Open
Abstract
Biomolecular phase separation has recently attracted broad interest, due to its role in the spatiotemporal compartmentalization of living cells. It governs the formation, regulation, and dissociation of biomolecular condensates, which play multiple roles in vivo, from activating specific biochemical reactions to organizing chromatin. Interestingly, biomolecular phase separation seems to be a mainly passive process, which can be explained by relatively simple physical principles and reproduced in vitro with a minimal set of components. This Mini review focuses on our current understanding of the fundamental principles of biomolecular phase separation and the recent progress in the research on this topic. [BMB Reports 2022; 55(8): 363-369].
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Affiliation(s)
- Chan-Geun Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Eun Hwang
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Rajeev Kumar
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Min Chung
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Yu-Gon Eom
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Hyunji Kim
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Da-Hyun Koo
- Department of Chemistry, Pusan National University, Busan 46241, Korea
| | - Jeong-Mo Choi
- Department of Chemistry, Pusan National University, Busan 46241, Korea
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