1
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Fare CM, Rothstein JD. Nuclear pore dysfunction and disease: a complex opportunity. Nucleus 2024; 15:2314297. [PMID: 38383349 PMCID: PMC10883112 DOI: 10.1080/19491034.2024.2314297] [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: 11/27/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
The separation of genetic material from bulk cytoplasm has enabled the evolution of increasingly complex organisms, allowing for the development of sophisticated forms of life. However, this complexity has created new categories of dysfunction, including those related to the movement of material between cellular compartments. In eukaryotic cells, nucleocytoplasmic trafficking is a fundamental biological process, and cumulative disruptions to nuclear integrity and nucleocytoplasmic transport are detrimental to cell survival. This is particularly true in post-mitotic neurons, where nuclear pore injury and errors to nucleocytoplasmic trafficking are strongly associated with neurodegenerative disease. In this review, we summarize the current understanding of nuclear pore biology in physiological and pathological contexts and discuss potential therapeutic approaches for addressing nuclear pore injury and dysfunctional nucleocytoplasmic transport.
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Affiliation(s)
- Charlotte M Fare
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey D Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
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2
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Song J. Molecular Mechanisms of Phase Separation and Amyloidosis of ALS/FTD-linked FUS and TDP-43. Aging Dis 2024; 15:2084-2112. [PMID: 38029395 PMCID: PMC11346406 DOI: 10.14336/ad.2023.1118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023] Open
Abstract
FUS and TDP-43, two RNA-binding proteins from the heterogeneous nuclear ribonucleoprotein family, have gained significant attention in the field of neurodegenerative diseases due to their association with amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). They possess folded domains for binding ATP and various nucleic acids including DNA and RNA, as well as substantial intrinsically disordered regions (IDRs) including prion-like domains (PLDs) and RG-/RGG-rich regions. They play vital roles in various cellular processes, including transcription, splicing, microRNA maturation, RNA stability and transport and DNA repair. In particular, they are key components for forming ribonucleoprotein granules and stress granules (SGs) through homotypic or heterotypic liquid-liquid phase separation (LLPS). Strikingly, liquid-like droplets formed by FUS and TDP-43 may undergo aging to transform into less dynamic assemblies such as hydrogels, inclusions, and amyloid fibrils, which are the pathological hallmarks of ALS and FTD. This review aims to synthesize and consolidate the biophysical knowledge of the sequences, structures, stability, dynamics, and inter-domain interactions of FUS and TDP-43 domains, so as to shed light on the molecular mechanisms underlying their liquid-liquid phase separation (LLPS) and amyloidosis. The review further delves into the mechanisms through which ALS-causing mutants of the well-folded hPFN1 disrupt the dynamics of LLPS of FUS prion-like domain, providing key insights into a potential mechanism for misfolding/aggregation-prone proteins to cause neurodegenerative diseases and aging by gain of functions. With better understanding of different biophysical aspects of FUS and TDP-43, the ultimate goal is to develop drugs targeting LLPS and amyloidosis, which could mediate protein homeostasis within cells and lead to new treatments for currently intractable diseases, particularly neurodegenerative diseases such as ALS, FTD and aging. However, the study of membrane-less organelles and condensates is still in its infancy and therefore the review also highlights key questions that require future investigation.
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3
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Hayashi M, Girdhar A, Ko YH, Kim KM, DePierro JA, Buchler JR, Arunprakash N, Bajaj A, Cingolani G, Guo L. Engineered NLS-chimera downregulates expression of aggregation-prone endogenous FUS. Nat Commun 2024; 15:7887. [PMID: 39251571 PMCID: PMC11384663 DOI: 10.1038/s41467-024-52151-6] [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: 12/08/2023] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
Importin β-superfamily nuclear import receptors (NIRs) mitigate mislocalization and aggregation of RNA-binding proteins (RBPs), like FUS and TDP-43, which are implicated in neurodegenerative diseases. NIRs potently disaggregate RBPs by recognizing their nuclear localization signal (NLS). However, disease-causing mutations in NLS compromise NIR binding and activity. Here, we define features that characterize the anti-aggregation activity of NIR and NLS. We find that high binding affinity between NIR and NLS, and optimal NLS location relative to the aggregating domain plays a role in determining NIR disaggregation activity. A designed FUS chimera (FUSIBB), carrying the importin β binding (IBB) domain, is solubilized by importin β in vitro, translocated to the nucleus in cultured cells, and downregulates the expression of endogenous FUS. In this study, we posit that guiding the mutual recognition of NLSs and NIRs will aid the development of therapeutics, illustrated by the highly soluble FUSIBB replacing the aggregation-prone endogenous FUS.
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Affiliation(s)
- Miyuki Hayashi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Amandeep Girdhar
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ying-Hui Ko
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kevin M Kim
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jacquelyn A DePierro
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Joseph R Buchler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, USA
| | - Nikhita Arunprakash
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aditya Bajaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gino Cingolani
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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4
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Hu G, Song H, Chen X, Li J. Wet Conformation of Prion-Like Domain and Intimate Correlation of Hydration and Conformational Fluctuations. J Phys Chem Lett 2024; 15:8315-8325. [PMID: 39109535 DOI: 10.1021/acs.jpclett.4c01476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Proteins with prion-like domains (PLDs) are involved in neurodegeneration-associated aggregation and are prevalent in liquid-like membrane-less organelles. These PLDs contain amyloidogenic stretches but can maintain dynamic disordered conformations, even in the condensed phase. However, the molecular mechanism underlying such intricate conformational properties of PLDs remains elusive. Here we employed molecular dynamics simulations to investigate the conformational properties of a prototypical PLD system (i.e., FUS PLD). According to our simulation results, PLD adopts a wet collapsed conformation, wherein most residues maintain sufficient hydration with the abundance of internal water. These internal water molecules can rapidly exchange between the protein interior and the bulk, enabling intensive coupling of the entire protein with its hydration environment. The dynamic exchange of water molecules is intimately correlated to the overall conformational fluctuations of PLD. Furthermore, the abundance of dynamic internal water suppresses the formation of aggregation-prone ordered structures. These results collectively elucidate the crucial role of internal water in sustaining the dynamic disordered conformation of the PLD and inhibiting its aggregation propensity.
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Affiliation(s)
- Guorong Hu
- School of Physics, Zhejiang University, Hangzhou 310058, China
| | - Haoyu Song
- School of Physics, Zhejiang University, Hangzhou 310058, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Jingyuan Li
- School of Physics, Zhejiang University, Hangzhou 310058, China
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5
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Strong MJ, McLellan C, Kaplanis B, Droppelmann CA, Junop M. Phase Separation of SARS-CoV-2 Nucleocapsid Protein with TDP-43 Is Dependent on C-Terminus Domains. Int J Mol Sci 2024; 25:8779. [PMID: 39201466 PMCID: PMC11354357 DOI: 10.3390/ijms25168779] [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: 06/28/2024] [Revised: 08/01/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
The SARS-CoV-2 nucleocapsid protein (N protein) is critical in viral replication by undergoing liquid-liquid phase separation to seed the formation of a ribonucleoprotein (RNP) complex to drive viral genomic RNA (gRNA) translation and in suppressing both stress granules and processing bodies, which is postulated to increase uncoated gRNA availability. The N protein can also form biomolecular condensates with a broad range of host endogenous proteins including RNA binding proteins (RBPs). Amongst these RBPs are proteins that are associated with pathological, neuronal, and glial cytoplasmic inclusions across several adult-onset neurodegenerative disorders, including TAR DNA binding protein 43 kDa (TDP-43) which forms pathological inclusions in over 95% of amyotrophic lateral sclerosis cases. In this study, we demonstrate that the N protein can form biomolecular condensates with TDP-43 and that this is dependent on the N protein C-terminus domain (N-CTD) and the intrinsically disordered C-terminus domain of TDP-43. This process is markedly accelerated in the presence of RNA. In silico modeling suggests that the biomolecular condensate that forms in the presence of RNA is composed of an N protein quadriplex in which the intrinsically disordered TDP-43 C terminus domain is incorporated.
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Affiliation(s)
- Michael J. Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada; (C.M.); (C.A.D.)
- Department of Clinical Neurological Sciences, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
| | - Crystal McLellan
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada; (C.M.); (C.A.D.)
| | - Brianna Kaplanis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada; (B.K.); (M.J.)
| | - Cristian A. Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada; (C.M.); (C.A.D.)
| | - Murray Junop
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada; (B.K.); (M.J.)
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6
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Belur NR, Bustos BI, Lubbe SJ, Mazzulli JR. Nuclear aggregates of NONO/SFPQ and A-to-I-edited RNA in Parkinson's disease and dementia with Lewy bodies. Neuron 2024; 112:2558-2580.e13. [PMID: 38761794 PMCID: PMC11309915 DOI: 10.1016/j.neuron.2024.05.003] [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: 05/27/2023] [Revised: 03/06/2024] [Accepted: 05/01/2024] [Indexed: 05/20/2024]
Abstract
Neurodegenerative diseases are commonly classified as proteinopathies that are defined by the aggregation of a specific protein. Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are classified as synucleinopathies since α-synuclein (α-syn)-containing inclusions histopathologically define these diseases. Unbiased biochemical analysis of PD and DLB patient material unexpectedly revealed novel pathological inclusions in the nucleus comprising adenosine-to-inosine (A-to-I)-edited mRNAs and NONO and SFPQ proteins. These inclusions showed no colocalization with Lewy bodies and accumulated at levels comparable to α-syn. NONO and SFPQ aggregates reduced the expression of the editing inhibitor ADAR3, increasing A-to-I editing mainly within human-specific, Alu-repeat regions of axon, synaptic, and mitochondrial transcripts. Inosine-containing transcripts aberrantly accumulated in the nucleus, bound tighter to recombinant purified SFPQ in vitro, and potentiated SFPQ aggregation in human dopamine neurons, resulting in a self-propagating pathological state. Our data offer new insight into the inclusion composition and pathophysiology of PD and DLB.
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Affiliation(s)
- Nandkishore R Belur
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bernabe I Bustos
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Steven J Lubbe
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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7
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Hu J, Dong H, Li Y, Gu J, Yang L, Si C, Zhang Y, Li T, Li D, Liu C. Hsp90α forms condensate engaging client proteins with RG motif repeats. Chem Sci 2024; 15:10508-10518. [PMID: 38994413 PMCID: PMC11234873 DOI: 10.1039/d4sc00267a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/28/2024] [Indexed: 07/13/2024] Open
Abstract
Hsp90α, a pivotal canonical chaperone, is renowned for its broad interaction with numerous protein clients to maintain protein homeostasis, chromatin remodeling, and cell growth. Recent studies indicate its role in modifying various components of membraneless organelles (MLOs) such as stress granules and processing bodies, suggesting its participation in the regulation of protein condensates. In this study, we found that Hsp90α possesses an inherent ability to form dynamic condensates in vitro. Utilizing LC-MS/MS, we further pinpointed proteins in cell lysates that preferentially integrate into Hsp90α condensates. Significantly, we observed a prevalence of RG motif repeats in client proteins of Hsp90α condensates, many of which are linked to various MLOs. Moreover, each of the three domains of Hsp90α was found to undergo phase separation, with numerous solvent-exposed negatively charged residues on these domains being crucial for driving Hsp90α condensation through multivalent weak electrostatic interactions. Additionally, various clients like TDP-43 and hnRNPA1, along with poly-GR and PR dipeptide repeats, exhibit varied impacts on the dynamic behavior of Hsp90α condensates. Our study spotlights various client proteins associated with Hsp90α condensates, illustrating its intricate adaptive nature in interacting with diverse clients and its functional adaptability across multiple MLOs.
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Affiliation(s)
- Jiaojiao Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 China
| | - Yichen Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University Shanghai 200240 China
| | - Jinge Gu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 China
| | - Liang Yang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center Beijing 100191 China
- Key Laboratory for Neuroscience, Ministry of Education, National Health Commission of China, Peking University Beijing 100191 China
| | - Chenfang Si
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center Beijing 100191 China
- Key Laboratory for Neuroscience, Ministry of Education, National Health Commission of China, Peking University Beijing 100191 China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University Shanghai 200240 China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University Shanghai 200240 China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 China
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8
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Morelli C, Faltova L, Capasso Palmiero U, Makasewicz K, Papp M, Jacquat RPB, Pinotsi D, Arosio P. RNA modulates hnRNPA1A amyloid formation mediated by biomolecular condensates. Nat Chem 2024; 16:1052-1061. [PMID: 38472406 PMCID: PMC11230912 DOI: 10.1038/s41557-024-01467-3] [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: 05/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Several RNA binding proteins involved in membraneless organelles can form pathological amyloids associated with neurodegenerative diseases, but the mechanisms of how this aggregation is modulated remain elusive. Here we investigate how heterotypic protein-RNA interactions modulate the condensation and the liquid to amyloid transition of hnRNPA1A, a protein involved in amyothropic lateral sclerosis. In the absence of RNA, formation of condensates promotes hnRNPA1A aggregation and fibrils are localized at the interface of the condensates. Addition of RNA modulates the soluble to amyloid transition of hnRNPA1A according to different pathways depending on RNA/protein stoichiometry. At low RNA concentrations, RNA promotes both condensation and amyloid formation, and the catalytic effect of RNA adds to the role of the interface between the dense and dilute phases. At higher RNA concentrations, condensation is suppressed according to re-entrant phase behaviour but formation of hnRNPA1A amyloids is observed over longer incubation times. Our findings show how heterotypic nucleic acid-protein interactions affect the kinetics and molecular pathways of amyloid formation.
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Affiliation(s)
- Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Raphaël P B Jacquat
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zürich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland.
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9
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Hong L, Zhang Z, Wang Z, Yu X, Zhang J. Phase separation provides a mechanism to drive phenotype switching. Phys Rev E 2024; 109:064414. [PMID: 39021038 DOI: 10.1103/physreve.109.064414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024]
Abstract
Phenotypic switching plays a crucial role in cell fate determination across various organisms. Recent experimental findings highlight the significance of protein compartmentalization via liquid-liquid phase separation in influencing such decisions. However, the precise mechanism through which phase separation regulates phenotypic switching remains elusive. To investigate this, we established a mathematical model that couples a phase separation process and a gene expression process with feedback. We used the chemical master equation theory and mean-field approximation to study the effects of phase separation on the gene expression products. We found that phase separation can cause bistability and bimodality. Furthermore, phase separation can control the bistable properties of the system, such as bifurcation points and bistable ranges. On the other hand, in stochastic dynamics, the droplet phase exhibits double peaks within a more extensive phase separation threshold range than the dilute phase, indicating the pivotal role of the droplet phase in cell fate decisions. These findings propose an alternative mechanism that influences cell fate decisions through the phase separation process. As phase separation is increasingly discovered in gene regulatory networks, related modeling research can help build biomolecular systems with desired properties and offer insights into explaining cell fate decisions.
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10
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Hu Y, Chen W, Wei C, Jiang S, Li S, Wang X, Xu R. Pathological mechanisms of amyotrophic lateral Sclerosis. Neural Regen Res 2024; 19:1036-1044. [PMID: 37862206 PMCID: PMC10749610 DOI: 10.4103/1673-5374.382985] [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: 02/11/2023] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 10/22/2023] Open
Abstract
Amyotrophic lateral sclerosis refers to a neurodegenerative disease involving the motor system, the cause of which remains unexplained despite several years of research. Thus, the journey to understanding or treating amyotrophic lateral sclerosis is still a long one. According to current research, amyotrophic lateral sclerosis is likely not due to a single factor but rather to a combination of mechanisms mediated by complex interactions between molecular and genetic pathways. The progression of the disease involves multiple cellular processes and the interaction between different complex mechanisms makes it difficult to identify the causative factors of amyotrophic lateral sclerosis. Here, we review the most common amyotrophic lateral sclerosis-associated pathogenic genes and the pathways involved in amyotrophic lateral sclerosis, as well as summarize currently proposed potential mechanisms responsible for amyotrophic lateral sclerosis disease and their evidence for involvement in amyotrophic lateral sclerosis. In addition, we discuss current emerging strategies for the treatment of amyotrophic lateral sclerosis. Studying the emergence of these new therapies may help to further our understanding of the pathogenic mechanisms of the disease.
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Affiliation(s)
- Yushu Hu
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Wenzhi Chen
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Caihui Wei
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Shishi Jiang
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Shu Li
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Xinxin Wang
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
| | - Renshi Xu
- Department of Clinical Medicine, Nanchang University, Nanchang, Jiangxi Province, China
- Department of Neurology, Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi Province, China
- Department of Neurology, The First Affiliated Hospital of Nanchang Medical College; The Clinical College of Nanchang Medical College, Nanchang, Jiangxi Province, China
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11
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Titus AR, Herron P, Streletzky KA, Madeira PP, Uversky VN, Zaslavsky BY. Effect of trimethylamine- N-oxide on the phase separation of aqueous polyethylene glycol-600-Dextran-75 two-phase systems. Phys Chem Chem Phys 2024; 26:10546-10556. [PMID: 38506647 DOI: 10.1039/d3cp06200g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The emergence of phase separation in both intracellular biomolecular condensates (membrane-less organelles) and in vitro aqueous two-phase systems (ATPS) relies on the formation of immiscible water-based phases/domains. The solvent properties and arrangement of hydrogen bonds within these domains have been shown to differ and can be modulated with the addition of various inorganic salts and osmolytes. The naturally occuring osmolyte, trimethylamine-N-oxide (TMAO), is well established as a biological condensate stabilizer whose presence results in enhanced phase separation of intracellular membrane-less compartments. Here, we show the unique effect of TMAO on the mechanism of phase separation in model PEG-600-Dextran-75 ATPS using dynamic and static light scattering in conjunction with ATR-FTIR and solvatochromic analysis. We observe that the presence of TMAO may enhance or destabilize phase separation depending on the concentration of phase forming components. Additionally, the behavior and density of mesoscopic polymer agglomerates, which arise prior to macroscopic phase separation, are altered by the presence and concentration of TMAO.
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Affiliation(s)
- Amber R Titus
- Cleveland Diagnostics, 3615 Superior Ave., Cleveland, OH 44114, USA.
| | - Patrick Herron
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, USA.
| | - Kiril A Streletzky
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, USA.
| | - Pedro P Madeira
- Centro de Investigacao em Materiais Ceramicos e Compositos, Department of Chemistry, 3810-193 Aveiro, Portugal.
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Boris Y Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Cleveland, OH 44114, USA.
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12
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Yu Q, Wang Z, Tu Y, Cao Y, Zhu H, Shao J, Zhuang R, Zhou Y, Zhang J. Proteasome activation: A novel strategy for targeting undruggable intrinsically disordered proteins. Bioorg Chem 2024; 145:107217. [PMID: 38368657 DOI: 10.1016/j.bioorg.2024.107217] [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: 11/03/2023] [Revised: 01/23/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by their inability to adopt well-defined tertiary structures under physiological conditions. Nonetheless, they often play pivotal roles in the progression of various diseases, including cancer, neurodegenerative disorders, and cardiovascular ailments. Owing to their inherent dynamism, conventional drug design approaches based on structural considerations encounter substantial challenges when applied to IDPs. Consequently, the pursuit of therapeutic interventions directed towards IDPs presents a complex endeavor. While there are indeed existing methodologies for targeting IDPs, they are encumbered by noteworthy constrains. Hence, there exists an imminent imperative to investigate more efficacious and universally applicable strategies for modulating IDPs. Here, we present an overview of the latest advancements in the research pertaining to IDPs, along with the indirect regulation approach involving the modulation of IDP degradation through proteasome. By comprehending these advancements in research, novel insights can be generated to facilitate the development of new drugs targeted at addressing the accumulation of IDPs in diverse pathological conditions.
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Affiliation(s)
- Qian Yu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Zheng Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Yutong Tu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yu Cao
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China
| | - Huajian Zhu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Jiaan Shao
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China
| | - Rangxiao Zhuang
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China.
| | - Yubo Zhou
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Jiankang Zhang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310015, Zhejiang Province, China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang Province, China.
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13
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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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14
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Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [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] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
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Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
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15
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Davis RB, Supakar A, Ranganath AK, Moosa MM, Banerjee PR. Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex. Nat Commun 2024; 15:1168. [PMID: 38326345 PMCID: PMC10850361 DOI: 10.1038/s41467-024-44945-5] [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: 04/12/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
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Affiliation(s)
- Richoo B Davis
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA
| | - Anushka Supakar
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | | | - Priya R Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY, 14260, USA.
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16
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Sweeney KM, Chantarawong S, Barbieri EM, Cajka G, Liu M, Spruce L, Fazelinia H, Portz B, Copley K, Lapidot T, Duhamel L, Greenwald P, Saida N, Shalgi R, Shorter J, Shalem O. CRISPR screen for protein inclusion formation uncovers a role for SRRD in the regulation of intermediate filament dynamics and aggresome assembly. PLoS Genet 2024; 20:e1011138. [PMID: 38315730 PMCID: PMC10868785 DOI: 10.1371/journal.pgen.1011138] [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: 06/20/2023] [Revised: 02/15/2024] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Abstract
The presence of large protein inclusions is a hallmark of neurodegeneration, and yet the precise molecular factors that contribute to their formation remain poorly understood. Screens using aggregation-prone proteins have commonly relied on downstream toxicity as a readout rather than the direct formation of aggregates. Here, we combined a genome-wide CRISPR knockout screen with Pulse Shape Analysis, a FACS-based method for inclusion detection, to identify direct modifiers of TDP-43 aggregation in human cells. Our screen revealed both canonical and novel proteostasis genes, and unearthed SRRD, a poorly characterized protein, as a top regulator of protein inclusion formation. APEX biotin labeling reveals that SRRD resides in proximity to proteins that are involved in the formation and breakage of disulfide bonds and to intermediate filaments, suggesting a role in regulation of the spatial dynamics of the intermediate filament network. Indeed, loss of SRRD results in aberrant intermediate filament fibrils and the impaired formation of aggresomes, including blunted vimentin cage structure, during proteotoxic stress. Interestingly, SRRD also localizes to aggresomes and unfolded proteins, and rescues proteotoxicity in yeast whereby its N-terminal low complexity domain is sufficient to induce this affect. Altogether this suggests an unanticipated and broad role for SRRD in cytoskeletal organization and cellular proteostasis.
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Affiliation(s)
- Katelyn M. Sweeney
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sapanna Chantarawong
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Edward M. Barbieri
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Greg Cajka
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew Liu
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lynn Spruce
- Proteomics Core Facility, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Hossein Fazelinia
- Proteomics Core Facility, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Bede Portz
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katie Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tomer Lapidot
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lauren Duhamel
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Phoebe Greenwald
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Naseeb Saida
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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17
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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [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: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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18
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Khalil B, Linsenmeier M, Smith CL, Shorter J, Rossoll W. Nuclear-import receptors as gatekeepers of pathological phase transitions in ALS/FTD. Mol Neurodegener 2024; 19:8. [PMID: 38254150 PMCID: PMC10804745 DOI: 10.1186/s13024-023-00698-1] [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: 06/05/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders on a disease spectrum that are characterized by the cytoplasmic mislocalization and aberrant phase transitions of prion-like RNA-binding proteins (RBPs). The common accumulation of TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), and other nuclear RBPs in detergent-insoluble aggregates in the cytoplasm of degenerating neurons in ALS/FTD is connected to nuclear pore dysfunction and other defects in the nucleocytoplasmic transport machinery. Recent advances suggest that beyond their canonical role in the nuclear import of protein cargoes, nuclear-import receptors (NIRs) can prevent and reverse aberrant phase transitions of TDP-43, FUS, and related prion-like RBPs and restore their nuclear localization and function. Here, we showcase the NIR family and how they recognize cargo, drive nuclear import, and chaperone prion-like RBPs linked to ALS/FTD. We also discuss the promise of enhancing NIR levels and developing potentiated NIR variants as therapeutic strategies for ALS/FTD and related neurodegenerative proteinopathies.
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Affiliation(s)
- Bilal Khalil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - Miriam Linsenmeier
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A
| | - Courtney L Smith
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
- Mayo Clinic Graduate School of Biomedical Sciences, Neuroscience Track, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A..
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A..
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19
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Ray M, Zaborowsky J, Mahableshwarkar P, Vaidyanathan S, Shum J, Viswanathan R, Huang A, Wang SH, Johnson V, Wake N, Conard AM, Conicella AE, Puterbaugh R, Fawzi NL, Larschan E. Dual DNA/RNA-binding factor regulates dynamics of hnRNP splicing condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575216. [PMID: 38260450 PMCID: PMC10802580 DOI: 10.1101/2024.01.11.575216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Despite decades of research, mechanisms by which co-transcriptional alternative splicing events are targeted to the correct genomic locations to drive cell fate decisions remain unknown. By combining structural and molecular approaches, we define a new mechanism by which an essential transcription factor (TF) targets co-transcriptional splicing through physical and functional interaction with RNA and RNA binding proteins (RBPs). We show that an essential TF co-transcriptionally regulates sex-specific alternative splicing by directly interacting with a subset of target RNAs on chromatin and modulating the dynamics of hnRNPA2 homolog nuclear splicing condensates.
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20
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Isozumi N, Sugie K, Mori E. [Biological phase separation in neuromuscular diseases]. Rinsho Shinkeigaku 2023; 63:799-805. [PMID: 37989290 DOI: 10.5692/clinicalneurol.cn-001877] [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] [Indexed: 11/23/2023]
Abstract
Biological phase separation refers to the liquid-liquid phase separation of biomolecules such as proteins in cells. Phase separation is driven by low-complexity domains of phase-separating proteins and strictly controlled by regulatory factors. Phase separation has also been found to be disrupted by genetic abnormalities. Abnormal aggregates of causative proteins accumulate in many neuromuscular diseases. In recent years, it has become clear that phase separating proteins are associated with neuromuscular diseases, and that abnormalities in the regulation of phase separation leads to the formation of aggregates. Gains in our knowledge of biological phase separation is gradually elucidating the pathogenesis of neuromuscular diseases.
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Affiliation(s)
| | - Kazuma Sugie
- Department of Neurology, Nara Medical University
| | - Eiichiro Mori
- Department of Future Basic Medicine, Nara Medical University
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21
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Marshall AC, Cummins J, Kobelke S, Zhu T, Widagdo J, Anggono V, Hyman A, Fox AH, Bond CS, Lee M. Different Low-complexity Regions of SFPQ Play Distinct Roles in the Formation of Biomolecular Condensates. J Mol Biol 2023; 435:168364. [PMID: 37952770 DOI: 10.1016/j.jmb.2023.168364] [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: 08/30/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Demixing of proteins and nucleic acids into condensed liquid phases is rapidly emerging as a ubiquitous mechanism underlying the complex spatiotemporal organisation of molecules within the cell. Long disordered regions of low sequence complexity (LCRs) are a common feature of proteins that form liquid-like microscopic biomolecular condensates. In particular, RNA-binding proteins with prion-like regions have emerged as key drivers of liquid demixing to form condensates such as nucleoli, paraspeckles and stress granules. Splicing factor proline- and glutamine-rich (SFPQ) is an RNA- and DNA-binding protein essential for DNA repair and paraspeckle formation. SFPQ contains two LCRs of different length and composition. Here, we show that the shorter C-terminal LCR of SFPQ is the main region responsible for the condensation of SFPQ in vitro and in the cell nucleus. In contrast, we find that the longer N-terminal prion-like LCR of SFPQ attenuates condensation of the full-length protein, suggesting a more regulatory role in preventing aberrant condensate formation in the cell. The compositions of these respective LCRs are discussed with reference to current literature. Our data add nuance to the emerging understanding of biomolecular condensation, by providing the first example of a common multifunctional nucleic acid-binding protein with an extensive prion-like region that serves to regulate rather than drive condensate formation.
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Affiliation(s)
- Andrew C Marshall
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jerry Cummins
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Simon Kobelke
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Tianyi Zhu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jocelyn Widagdo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Victor Anggono
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Anthony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia.
| | - Mihwa Lee
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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22
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Sahin C, Leppert A, Landreh M. Advances in mass spectrometry to unravel the structure and function of protein condensates. Nat Protoc 2023; 18:3653-3661. [PMID: 37907762 DOI: 10.1038/s41596-023-00900-0] [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: 04/18/2023] [Accepted: 08/09/2023] [Indexed: 11/02/2023]
Abstract
Membrane-less organelles assemble through liquid-liquid phase separation (LLPS) of partially disordered proteins into highly specialized microenvironments. Currently, it is challenging to obtain a clear understanding of the relationship between the structure and function of phase-separated protein assemblies, owing to their size, dynamics and heterogeneity. In this Perspective, we discuss recent advances in mass spectrometry (MS) that offer several promising approaches for the study of protein LLPS. We survey MS tools that have provided valuable insights into other insoluble protein systems, such as amyloids, and describe how they can also be applied to study proteins that undergo LLPS. On the basis of these recent advances, we propose to integrate MS into the experimental workflow for LLPS studies. We identify specific challenges and future opportunities for the analysis of protein condensate structure and function by MS.
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Affiliation(s)
- Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden.
- Structural Biology and NMR laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Axel Leppert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet-Biomedicum, Solna, Sweden.
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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23
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Davis RB, Supakar A, Ranganath AK, Moosa MM, Banerjee PR. Heterotypic interactions in the dilute phase can drive co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536623. [PMID: 37090622 PMCID: PMC10120661 DOI: 10.1101/2023.04.12.536623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous co-condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
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Affiliation(s)
- Richoo B. Davis
- Department of Physics, University at Buffalo, Buffalo NY 14260, USA
| | - Anushka Supakar
- Department of Biological Sciences, University at Buffalo, Buffalo NY 14260, USA
| | | | | | - Priya R. Banerjee
- Department of Physics, University at Buffalo, Buffalo NY 14260, USA
- Department of Biological Sciences, University at Buffalo, Buffalo NY 14260, USA
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo NY 14260, USA
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24
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Li A, Bouhss A, Clément MJ, Bauvais C, Taylor JP, Bollot G, Pastré D. Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives. Front Mol Biosci 2023; 10:1298441. [PMID: 38033386 PMCID: PMC10687564 DOI: 10.3389/fmolb.2023.1298441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
In recent years, RNA has gained traction both as a therapeutic molecule and as a therapeutic target in several human pathologies. In this review, we consider the approach of targeting RNA using small molecules for both research and therapeutic purposes. Given the primary challenge presented by the low structural diversity of RNA, we discuss the potential for targeting RNA: protein interactions to enhance the structural and sequence specificity of drug candidates. We review available tools and inherent challenges in this approach, ranging from adapted bioinformatics tools to in vitro and cellular high-throughput screening and functional analysis. We further consider two critical steps in targeting RNA/protein interactions: first, the integration of in silico and structural analyses to improve the efficacy of molecules by identifying scaffolds with high affinity, and second, increasing the likelihood of identifying on-target compounds in cells through a combination of high-throughput approaches and functional assays. We anticipate that the development of a new class of molecules targeting RNA: protein interactions to prevent physio-pathological mechanisms could significantly expand the arsenal of effective therapeutic compounds.
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Affiliation(s)
- Aixiao Li
- Synsight, Genopole Entreprises, Evry, France
| | - Ahmed Bouhss
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
| | - Marie-Jeanne Clément
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
| | | | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | | | - David Pastré
- Université Paris-Saclay, INSERM U1204, Université d’Évry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry, France
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25
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Pisciottani A, Croci L, Lauria F, Marullo C, Savino E, Ambrosi A, Podini P, Marchioretto M, Casoni F, Cremona O, Taverna S, Quattrini A, Cioni JM, Viero G, Codazzi F, Consalez GG. Neuronal models of TDP-43 proteinopathy display reduced axonal translation, increased oxidative stress, and defective exocytosis. Front Cell Neurosci 2023; 17:1253543. [PMID: 38026702 PMCID: PMC10679756 DOI: 10.3389/fncel.2023.1253543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, lethal neurodegenerative disease mostly affecting people around 50-60 years of age. TDP-43, an RNA-binding protein involved in pre-mRNA splicing and controlling mRNA stability and translation, forms neuronal cytoplasmic inclusions in an overwhelming majority of ALS patients, a phenomenon referred to as TDP-43 proteinopathy. These cytoplasmic aggregates disrupt mRNA transport and localization. The axon, like dendrites, is a site of mRNA translation, permitting the local synthesis of selected proteins. This is especially relevant in upper and lower motor neurons, whose axon spans long distances, likely accentuating their susceptibility to ALS-related noxae. In this work we have generated and characterized two cellular models, consisting of virtually pure populations of primary mouse cortical neurons expressing a human TDP-43 fusion protein, wt or carrying an ALS mutation. Both forms facilitate cytoplasmic aggregate formation, unlike the corresponding native proteins, giving rise to bona fide primary culture models of TDP-43 proteinopathy. Neurons expressing TDP-43 fusion proteins exhibit a global impairment in axonal protein synthesis, an increase in oxidative stress, and defects in presynaptic function and electrical activity. These changes correlate with deregulation of axonal levels of polysome-engaged mRNAs playing relevant roles in the same processes. Our data support the emerging notion that deregulation of mRNA metabolism and of axonal mRNA transport may trigger the dying-back neuropathy that initiates motor neuron degeneration in ALS.
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Affiliation(s)
- Alessandra Pisciottani
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Croci
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Chiara Marullo
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Savino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Ambrosi
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Podini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Filippo Casoni
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ottavio Cremona
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
| | - Stefano Taverna
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jean-Michel Cioni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Franca Codazzi
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - G. Giacomo Consalez
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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26
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Kang H, Park S, Jo A, Mao X, Kumar M, Park C, Ahn J, Lee Y, Choi J, Lee Y, Dawson VL, Dawson TM, Kam T, Shin J. PARIS undergoes liquid-liquid phase separation and poly(ADP-ribose)-mediated solidification. EMBO Rep 2023; 24:e56166. [PMID: 37870275 PMCID: PMC10626450 DOI: 10.15252/embr.202256166] [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: 09/20/2022] [Revised: 08/04/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
ZNF746 was identified as parkin-interacting substrate (PARIS). Investigating its pathophysiological properties, we find that PARIS undergoes liquid-liquid phase separation (LLPS) and amorphous solid formation. The N-terminal low complexity domain 1 (LCD1) of PARIS is required for LLPS, whereas the C-terminal prion-like domain (PrLD) drives the transition from liquid to solid phase. In addition, we observe that poly(ADP-ribose) (PAR) strongly binds to the C-terminus of PARIS near the PrLD, accelerating its LLPS and solidification. N-Methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced PAR formation leads to PARIS oligomerization in human iPSC-derived dopaminergic neurons that is prevented by the PARP inhibitor, ABT-888. Furthermore, SDS-resistant PARIS species are observed in the substantia nigra (SN) of aged mice overexpressing wild-type PARIS, but not with a PAR binding-deficient PARIS mutant. PARIS solidification is also found in the SN of mice injected with preformed fibrils of α-synuclein (α-syn PFF) and adult mice with a conditional knockout (KO) of parkin, but not if α-syn PFF is injected into mice deficient for PARP1. Herein, we demonstrate that PARIS undergoes LLPS and PAR-mediated solidification in models of Parkinson's disease.
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Affiliation(s)
- Hojin Kang
- Department of PharmacologySungkyunkwan University School of MedicineSuwonSouth Korea
- Neuroregeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
- Single Cell Network Research CenterSungkyunkwan University School of MedicineSuwonSouth Korea
| | - Soojeong Park
- Department of PharmacologySungkyunkwan University School of MedicineSuwonSouth Korea
| | - Areum Jo
- Department of PharmacologySungkyunkwan University School of MedicineSuwonSouth Korea
- Neuroregeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Xiaobo Mao
- Neuroregeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Manoj Kumar
- Neuroregeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Chi‐Hu Park
- Neurodegeneration Research InstituteYEP Bio Co., Ltd.AnyangSouth Korea
| | - Jee‐Yin Ahn
- Single Cell Network Research CenterSungkyunkwan University School of MedicineSuwonSouth Korea
- Samsung Biomedical Research Institute, Samsung Medical CenterSeoulSouth Korea
| | - Yunjong Lee
- Department of PharmacologySungkyunkwan University School of MedicineSuwonSouth Korea
- Samsung Biomedical Research Institute, Samsung Medical CenterSeoulSouth Korea
| | - Jeong‐Yun Choi
- Department of PharmacologySungkyunkwan University School of MedicineSuwonSouth Korea
- Samsung Biomedical Research Institute, Samsung Medical CenterSeoulSouth Korea
| | - Yun‐Song Lee
- Department of PharmacologySungkyunkwan University School of MedicineSuwonSouth Korea
- Samsung Biomedical Research Institute, Samsung Medical CenterSeoulSouth Korea
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of PhysiologyJohns Hopkins University School of MedicineBaltimoreMDUSA
- Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
- Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of Pharmacology and Molecular SciencesJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Tae‐In Kam
- Neuroregeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of Brain and Cognitive SciencesKorea Advanced Institute of Science and TechnologyDaejeonSouth Korea
| | - Joo‐Ho Shin
- Department of PharmacologySungkyunkwan University School of MedicineSuwonSouth Korea
- Neuroregeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMDUSA
- Single Cell Network Research CenterSungkyunkwan University School of MedicineSuwonSouth Korea
- Samsung Biomedical Research Institute, Samsung Medical CenterSeoulSouth Korea
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27
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Mamontova EM, Clément MJ, Sukhanova MV, Joshi V, Bouhss A, Rengifo-Gonzalez JC, Desforges B, Hamon L, Lavrik OI, Pastré D. FUS RRM regulates poly(ADP-ribose) levels after transcriptional arrest and PARP-1 activation on DNA damage. Cell Rep 2023; 42:113199. [PMID: 37804508 DOI: 10.1016/j.celrep.2023.113199] [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: 03/06/2023] [Revised: 07/08/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023] Open
Abstract
PARP-1 activation at DNA damage sites leads to the synthesis of long poly(ADP-ribose) (PAR) chains, which serve as a signal for DNA repair. Here we show that FUS, an RNA-binding protein, is specifically directed to PAR through its RNA recognition motif (RRM) to increase PAR synthesis by PARP-1 in HeLa cells after genotoxic stress. Using a structural approach, we also identify specific residues located in the FUS RRM, which can be PARylated by PARP-1 to control the level of PAR synthesis. Based on the results of this work, we propose a model in which, following a transcriptional arrest that releases FUS from nascent mRNA, FUS can be recruited by PARP-1 activated by DNA damage to stimulate PAR synthesis. We anticipate that this model offers new perspectives to understand the role of FET proteins in cancers and in certain neurodegenerative diseases such as amyotrophic lateral sclerosis.
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Affiliation(s)
- Evgeniya M Mamontova
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France; Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Marie-Jeanne Clément
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Vandana Joshi
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ahmed Bouhss
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | | | - Bénédicte Desforges
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Loic Hamon
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk 630090, Russia.
| | - David Pastré
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France.
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28
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Qian H, Ding WX. SQSTM1/p62 and Hepatic Mallory-Denk Body Formation in Alcohol-Associated Liver Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1415-1426. [PMID: 36906265 PMCID: PMC10642158 DOI: 10.1016/j.ajpath.2023.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/12/2023]
Abstract
Sequestosome 1 (SQSTM1/p62; hereafter p62) is an autophagy receptor protein for selective autophagy primarily due to its direct interaction with the microtubule light chain 3 protein that specifically localizes on autophagosome membranes. As a result, impaired autophagy leads to the accumulation of p62. p62 is also a common component of many human liver disease-related cellular inclusion bodies, such as Mallory-Denk bodies, intracytoplasmic hyaline bodies, α1-antitrypsin aggregates, as well as p62 bodies and condensates. p62 also acts as an intracellular signaling hub, and it involves multiple signaling pathways, including nuclear factor erythroid 2-related factor 2, NF-κB, and the mechanistic target of rapamycin, which are critical for oxidative stress, inflammation, cell survival, metabolism, and liver tumorigenesis. This review discusses the recent insights of p62 in protein quality control, including the role of p62 in the formation and degradation of p62 stress granules and protein aggregates as well as regulation of multiple signaling pathways in the pathogenesis of alcohol-associated liver disease.
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Affiliation(s)
- Hui Qian
- Department of Pharmacology, Toxicology, and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology, and Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas; Department of Internal Medicine, The University of Kansas Medical Center, Kansas City, Kansas.
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29
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Sharma K, Banerjee S, Savran D, Rajes C, Wiese S, Girdhar A, Schwierz N, Lee C, Shorter J, Schmidt M, Guo L, Fändrich M. Cryo-EM Structure of the Full-length hnRNPA1 Amyloid Fibril. J Mol Biol 2023; 435:168211. [PMID: 37481159 PMCID: PMC10530274 DOI: 10.1016/j.jmb.2023.168211] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) is a multifunctional RNA-binding protein that is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis and multisystem proteinopathy. In this study, we have used cryo-electron microscopy to investigate the three-dimensional structure of amyloid fibrils from full-length hnRNPA1 protein. We find that the fibril core is formed by a 45-residue segment of the prion-like low-complexity domain of the protein, whereas the remaining parts of the protein (275 residues) form a fuzzy coat around the fibril core. The fibril consists of two fibril protein stacks that are arranged into a pseudo-21 screw symmetry. The ordered core harbors several of the positions that are known to be affected by disease-associated mutations, but does not encompass the most aggregation-prone segments of the protein. These data indicate that the structures of amyloid fibrils from full-length proteins may be more complex than anticipated by current theories on protein misfolding.
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Affiliation(s)
- Kartikay Sharma
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany.
| | - Sambhasan Banerjee
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany. https://twitter.com/@SAMBHASANBANERJ
| | - Dilan Savran
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Cedric Rajes
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Amandeep Girdhar
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, 86159 Augsburg, Germany
| | - Christopher Lee
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. https://twitter.com/@shorterlab
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Lin Guo
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
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30
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Guo L, Mann JR, Mauna JC, Copley KE, Wang H, Rubien JD, Odeh HM, Lin J, Lee BL, Ganser L, Robinson E, Kim KM, Murthy AC, Paul T, Portz B, Gleixner AM, Diaz Z, Carey JL, Smirnov A, Padilla G, Lavorando E, Espy C, Shang Y, Huang EJ, Chesi A, Fawzi NL, Myong S, Donnelly CJ, Shorter J. Defining RNA oligonucleotides that reverse deleterious phase transitions of RNA-binding proteins with prion-like domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.555754. [PMID: 37732211 PMCID: PMC10508739 DOI: 10.1101/2023.09.04.555754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
RNA-binding proteins with prion-like domains, such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs (24-48 nucleotides) that prevent FUS fibrillization by promoting liquid phases, and distinct short RNAs that prevent and, remarkably, reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. Importantly, we define a short RNA that dissolves aberrant cytoplasmic FUS condensates, restores nuclear FUS, and mitigates FUS proteotoxicity in optogenetic models and human motor neurons. Another short RNA dissolves aberrant cytoplasmic TDP-43 condensates, restores nuclear TDP-43, and mitigates TDP-43 proteotoxicity. Since short RNAs can be effectively delivered to the human brain, these oligonucleotides could have therapeutic utility for ALS/FTD and related disorders.
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31
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Xu C, Li C, Chen J, Xiong Y, Qiao Z, Fan P, Li C, Ma S, Liu J, Song A, Tao B, Xu T, Xu W, Chi Y, Xue J, Wang P, Ye D, Gu H, Zhang P, Wang Q, Xiao R, Cheng J, Zheng H, Yu X, Zhang Z, Wu J, Liang K, Liu YJ, Lu H, Chen FX. R-loop-dependent promoter-proximal termination ensures genome stability. Nature 2023; 621:610-619. [PMID: 37557913 PMCID: PMC10511320 DOI: 10.1038/s41586-023-06515-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 08/03/2023] [Indexed: 08/11/2023]
Abstract
The proper regulation of transcription is essential for maintaining genome integrity and executing other downstream cellular functions1,2. Here we identify a stable association between the genome-stability regulator sensor of single-stranded DNA (SOSS)3 and the transcription regulator Integrator-PP2A (INTAC)4-6. Through SSB1-mediated recognition of single-stranded DNA, SOSS-INTAC stimulates promoter-proximal termination of transcription and attenuates R-loops associated with paused RNA polymerase II to prevent R-loop-induced genome instability. SOSS-INTAC-dependent attenuation of R-loops is enhanced by the ability of SSB1 to form liquid-like condensates. Deletion of NABP2 (encoding SSB1) or introduction of cancer-associated mutations into its intrinsically disordered region leads to a pervasive accumulation of R-loops, highlighting a genome surveillance function of SOSS-INTAC that enables timely termination of transcription at promoters to constrain R-loop accumulation and ensure genome stability.
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Affiliation(s)
- Congling Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Chengyu Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jiwei Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yan Xiong
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhibin Qiao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Pengyu Fan
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Shuangyu Ma
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Aixia Song
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Bolin Tao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Wei Xu
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yayun Chi
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jingyan Xue
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Pu Wang
- Huashan Hospital, Fudan University, Shanghai Key Laboratory of Medical Epigenetics, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Dan Ye
- Huashan Hospital, Fudan University, Shanghai Key Laboratory of Medical Epigenetics, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiong Wang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruijing Xiao
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jingdong Cheng
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Hai Zheng
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaoli Yu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhen Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jiong Wu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yan-Jun Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China.
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.
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32
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Nag S, Schneider JA. Limbic-predominant age-related TDP43 encephalopathy (LATE) neuropathological change in neurodegenerative diseases. Nat Rev Neurol 2023; 19:525-541. [PMID: 37563264 PMCID: PMC10964248 DOI: 10.1038/s41582-023-00846-7] [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] [Accepted: 06/26/2023] [Indexed: 08/12/2023]
Abstract
TAR DNA-binding protein 43 (TDP43) is a focus of research in late-onset dementias. TDP43 pathology in the brain was initially identified in amyotrophic lateral sclerosis and frontotemporal lobar degeneration, and later in Alzheimer disease (AD), other neurodegenerative diseases and ageing. Limbic-predominant age-related TDP43 encephalopathy (LATE), recognized as a clinical entity in 2019, is characterized by amnestic dementia resembling AD dementia and occurring most commonly in adults over 80 years of age. Neuropathological findings in LATE, referred to as LATE neuropathological change (LATE-NC), consist of neuronal and glial cytoplasmic TDP43 localized predominantly in limbic areas with or without coexisting hippocampal sclerosis and/or AD neuropathological change and without frontotemporal lobar degeneration or amyotrophic lateral sclerosis pathology. LATE-NC is frequently associated with one or more coexisting pathologies, mainly AD neuropathological change. The focus of this Review is the pathology, genetic risk factors and nature of the cognitive impairments and dementia in pure LATE-NC and in LATE-NC associated with coexisting pathologies. As the clinical and cognitive profile of LATE is currently not easily distinguishable from AD dementia, it is important to develop biomarkers to aid in the diagnosis of this condition in the clinic. The pathogenesis of LATE-NC should be a focus of future research to form the basis for the development of preventive and therapeutic strategies.
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Affiliation(s)
- Sukriti Nag
- Rush Alzheimer's Disease Center, Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, IL, USA.
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, IL, USA.
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Zajkowski T, Lee MD, Sharma S, Vallota-Eastman A, Kuska M, Malczewska M, Rothschild LJ. Conserved functions of prion candidates suggest a primeval role of protein self-templating. Proteins 2023; 91:1298-1315. [PMID: 37519023 DOI: 10.1002/prot.26558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Amyloid-based prions have simple structures, a wide phylogenetic distribution, and a plethora of functions in contemporary organisms, suggesting they may be an ancient phenomenon. However, this hypothesis has yet to be addressed with a systematic, computational, and experimental approach. Here we present a framework to help guide future experimental verification of candidate prions with conserved functions to understand their role in the early stages of evolution and potentially in the origins of life. We identified candidate prions in all high-quality proteomes available in UniProt computationally, assessed their phylogenomic distributions, and analyzed candidate-prion functional annotations. Of the 27 980 560 proteins scanned, 228 561 were identified as candidate prions (~0.82%). Among these candidates, there were 84 Gene Ontology (GO) terms conserved across the three domains of life. We found that candidate prions with a possible role in adaptation were particularly well-represented within this group. We discuss unifying features of candidate prions to elucidate the primeval roles of prions and their associated functions. Candidate prions annotated as transcription factors, DNA binding, and kinases are particularly well suited to generating diverse responses to changes in their environment and could allow for adaptation and population expansion into more diverse environments. We hypothesized that a relationship between these functions and candidate prions could be evolutionarily ancient, even if individual prion domains themselves are not evolutionarily conserved. Candidate prions annotated with these universally occurring functions potentially represent the oldest extant prions on Earth and are therefore excellent experimental targets.
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Affiliation(s)
- Tomasz Zajkowski
- Universities Space Research Association at NASA Ames Research Center, Mountain View, California, USA
- Polish Astrobiology Society, Warsaw, Poland
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michael D Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- KBR, NASA Ames Research Center, Mountain View, California, USA
| | - Siddhant Sharma
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Alec Vallota-Eastman
- Department of Earth Science, University of California, Santa Barbara, California, USA
| | - Mikołaj Kuska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Małgorzata Malczewska
- Polish Astrobiology Society, Warsaw, Poland
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Lynn J Rothschild
- Space Science and Astrobiology Division, NASA Ames Research Center, Mountain View, California, USA
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Mohanty P, Shenoy J, Rizuan A, Mercado-Ortiz JF, Fawzi NL, Mittal J. A synergy between site-specific and transient interactions drives the phase separation of a disordered, low-complexity domain. Proc Natl Acad Sci U S A 2023; 120:e2305625120. [PMID: 37579155 PMCID: PMC10450430 DOI: 10.1073/pnas.2305625120] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is involved in key processes in RNA metabolism and is frequently implicated in many neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia. The prion-like, disordered C-terminal domain (CTD) of TDP-43 is aggregation-prone, can undergo liquid-liquid phase separation (LLPS) in isolation, and is critical for phase separation (PS) of the full-length protein under physiological conditions. While a short conserved helical region (CR, spanning residues 319-341) promotes oligomerization and is essential for LLPS, aromatic residues in the flanking disordered regions (QN-rich, IDR1/2) are also found to play a critical role in PS and aggregation. Compared with other phase-separating proteins, TDP-43 CTD has a notably distinct sequence composition including many aliphatic residues such as methionine and leucine. Aliphatic residues were previously suggested to modulate the apparent viscosity of the resulting phases, but their direct contribution toward CTD phase separation has been relatively ignored. Using multiscale simulations coupled with in vitro saturation concentration (csat) measurements, we identified the importance of aromatic residues while also suggesting an essential role for aliphatic methionine residues in promoting single-chain compaction and LLPS. Surprisingly, NMR experiments showed that transient interactions involving phenylalanine and methionine residues in the disordered flanking regions can directly enhance site-specific, CR-mediated intermolecular association. Overall, our work highlights an underappreciated mode of biomolecular recognition, wherein both transient and site-specific hydrophobic interactions act synergistically to drive the oligomerization and phase separation of a disordered, low-complexity domain.
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Affiliation(s)
- Priyesh Mohanty
- Artie McFerrinDepartment of Chemical Engineering, Texas A&M University, College Station, TX77843
| | - Jayakrishna Shenoy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI02912
| | - Azamat Rizuan
- Artie McFerrinDepartment of Chemical Engineering, Texas A&M University, College Station, TX77843
| | - José F. Mercado-Ortiz
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI02912
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI02912
| | - Jeetain Mittal
- Artie McFerrinDepartment of Chemical Engineering, Texas A&M University, College Station, TX77843
- Department of Chemistry, Texas A&M University, College Station, TX77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX77843
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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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Zelenka T, Papamatheakis DA, Tzerpos P, Panagopoulos G, Tsolis KC, Papadakis VM, Mariatos Metaxas D, Papadogkonas G, Mores E, Kapsetaki M, Papamatheakis J, Stanek D, Spilianakis C. A novel SATB1 protein isoform with different biophysical properties. Front Cell Dev Biol 2023; 11:1242481. [PMID: 37635874 PMCID: PMC10457122 DOI: 10.3389/fcell.2023.1242481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Intra-thymic T cell development is coordinated by the regulatory actions of SATB1 genome organizer. In this report, we show that SATB1 is involved in the regulation of transcription and splicing, both of which displayed deregulation in Satb1 knockout murine thymocytes. More importantly, we characterized a novel SATB1 protein isoform and described its distinct biophysical behavior, implicating potential functional differences compared to the commonly studied isoform. SATB1 utilized its prion-like domains to transition through liquid-like states to aggregated structures. This behavior was dependent on protein concentration as well as phosphorylation and interaction with nuclear RNA. Notably, the long SATB1 isoform was more prone to aggregate following phase separation. Thus, the tight regulation of SATB1 isoforms expression levels alongside with protein post-translational modifications, are imperative for SATB1's mode of action in T cell development. Our data indicate that deregulation of these processes may also be linked to disorders such as cancer.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Petros Tzerpos
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | | | - Konstantinos C. Tsolis
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Vassilis M. Papadakis
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | | | - George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Eleftherios Mores
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Joseph Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - David Stanek
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
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Beckwith SL, Nomberg EJ, Newman AC, Taylor JV, Guerrero-Ferreira RC, Garfinkel DJ. An interchangeable prion-like domain is required for Ty1 retrotransposition. Proc Natl Acad Sci U S A 2023; 120:e2303358120. [PMID: 37459521 PMCID: PMC10372613 DOI: 10.1073/pnas.2303358120] [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: 03/02/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Retrotransposons and retroviruses shape genome evolution and can negatively impact genome function. Saccharomyces cerevisiae and its close relatives harbor several families of LTR-retrotransposons, the most abundant being Ty1 in several laboratory strains. The cytosolic foci that nucleate Ty1 virus-like particle (VLP) assembly are not well understood. These foci, termed retrosomes or T-bodies, contain Ty1 Gag and likely Gag-Pol and the Ty1 mRNA destined for reverse transcription. Here, we report an intrinsically disordered N-terminal prion-like domain (PrLD) within Gag that is required for transposition. This domain contains amino acid composition similar to known yeast prions and is sufficient to nucleate prionogenesis in an established cell-based prion reporter system. Deleting the Ty1 PrLD results in dramatic VLP assembly and retrotransposition defects but does not affect Gag protein level. Ty1 Gag chimeras in which the PrLD is replaced with other sequences, including yeast and mammalian prionogenic domains, display a range of retrotransposition phenotypes from wild type to null. We examine these chimeras throughout the Ty1 replication cycle and find that some support retrosome formation, VLP assembly, and retrotransposition, including the yeast Sup35 prion and the mouse PrP prion. Our interchangeable Ty1 system provides a useful, genetically tractable in vivo platform for studying PrLDs, complete with a suite of robust and sensitive assays. Our work also invites study into the prevalence of PrLDs in additional mobile elements.
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Affiliation(s)
- Sean L. Beckwith
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
| | - Emily J. Nomberg
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
| | - Abigail C. Newman
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
| | - Jeannette V. Taylor
- Robert P. Apkarian Integrated Electron Microscopy Core at Emory University, Atlanta, GA30322
| | | | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA30602
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Guo G, Wang X, Zhang Y, Li T. Sequence variations of phase-separating proteins and resources for studying biomolecular condensates. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1119-1132. [PMID: 37464880 PMCID: PMC10423696 DOI: 10.3724/abbs.2023131] [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: 04/13/2023] [Accepted: 06/06/2023] [Indexed: 07/20/2023] Open
Abstract
Phase separation (PS) is an important mechanism underlying the formation of biomolecular condensates. Physiological condensates are associated with numerous biological processes, such as transcription, immunity, signaling, and synaptic transmission. Changes in particular amino acids or segments can disturb the protein's phase behavior and interactions with other biomolecules in condensates. It is thus presumed that variations in the phase-separating-prone domains can significantly impact the properties and functions of condensates. The dysfunction of condensates contributes to a number of pathological processes. Pharmacological perturbation of these condensates is proposed as a promising way to restore physiological states. In this review, we characterize the variations observed in PS proteins that lead to aberrant biomolecular compartmentalization. We also showcase recent advancements in bioinformatics of membraneless organelles (MLOs), focusing on available databases useful for screening PS proteins and describing endogenous condensates, guiding researchers to seek the underlying pathogenic mechanisms of biomolecular condensates.
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Affiliation(s)
- Gaigai Guo
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Xinxin Wang
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Yi Zhang
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
| | - Tingting Li
- Department of Biomedical InformaticsSchool of Basic Medical SciencesPeking University Health Science CenterBeijing100191China
- Key Laboratory for NeuroscienceMinistry of Education/National Health Commission of ChinaPeking UniversityBeijing100191China
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39
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Acosta-Galeana I, Hernández-Martínez R, Reyes-Cruz T, Chiquete E, Aceves-Buendia JDJ. RNA-binding proteins as a common ground for neurodegeneration and inflammation in amyotrophic lateral sclerosis and multiple sclerosis. Front Mol Neurosci 2023; 16:1193636. [PMID: 37475885 PMCID: PMC10355071 DOI: 10.3389/fnmol.2023.1193636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/14/2023] [Indexed: 07/22/2023] Open
Abstract
The neurodegenerative and inflammatory illnesses of amyotrophic lateral sclerosis and multiple sclerosis were once thought to be completely distinct entities that did not share any remarkable features, but new research is beginning to reveal more information about their similarities and differences. Here, we review some of the pathophysiological features of both diseases and their experimental models: RNA-binding proteins, energy balance, protein transportation, and protein degradation at the molecular level. We make a thorough analysis on TDP-43 and hnRNP A1 dysfunction, as a possible common ground in both pathologies, establishing a potential link between neurodegeneration and pathological immunity. Furthermore, we highlight the putative variations that diverge from a common ground in an atemporal course that proposes three phases for all relevant molecular events.
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Affiliation(s)
| | | | - Tania Reyes-Cruz
- Laboratorio de Biología Molecular, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Erwin Chiquete
- Departamento de Neurología y Psiquiatría, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jose de Jesus Aceves-Buendia
- Departamento de Neurología y Psiquiatría, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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40
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Kumar A, Daripa P, Maiti S, Jain N. Interaction of hnRNPB1 with Helix-12 of hHOTAIR Reveals the Distinctive Mode of RNA Recognition That Enables the Structural Rearrangement by LCD. Biochemistry 2023; 62:2041-2054. [PMID: 37307069 DOI: 10.1021/acs.biochem.3c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The lncRNA human Hox transcript antisense intergenic RNA (hHOTAIR) regulates gene expression by recruiting chromatin modifiers. The prevailing model suggests that hHOTAIR recruits hnRNPB1 to facilitate intermolecular RNA-RNA interactions between the lncRNA HOTAIR and its target gene transcripts. This B1-mediated RNA-RNA interaction modulates the structure of hHOTAIR, attenuates its inhibitory effect on polycomb repression complex 2, and enhances its methyl transferase activity. However, the molecular details by which the nuclear hnRNPB1 protein assembles on the lncRNA HOTAIR have not yet been described. Here, we investigate the molecular interactions between hnRNPB1 and Helix-12 (hHOTAIR). We show that the low-complexity domain segment (LCD) of hnRNPB1 interacts with a strong affinity for Helix-12. Our studies revealed that unbound Helix-12 folds into a specific base-pairing pattern and contains an internal loop that, as determined by thermal melting and NMR studies, exhibits hydrogen bonding between strands and forms the recognition site for the LCD segment. In addition, mutation studies show that the secondary structure of Helix-12 makes an important contribution by acting as a landing pad for hnRNPB1. The secondary structure of Helix-12 is involved in specific interactions with different domains of hnRNPB1. Finally, we show that the LCD unwinds Helix-12 locally, indicating its importance in the hHOTAIR restructuring mechanism.
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Affiliation(s)
- Ajit Kumar
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Purba Daripa
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Souvik Maiti
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Niyati Jain
- CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India
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Hnath B, Chen J, Reynolds J, Choi E, Wang J, Zhang D, Sha CM, Dokholyan NV. Big versus small: The impact of aggregate size in disease. Protein Sci 2023; 32:e4686. [PMID: 37243896 PMCID: PMC10273386 DOI: 10.1002/pro.4686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Protein aggregation results in an array of different size soluble oligomers and larger insoluble fibrils. Insoluble fibrils were originally thought to cause neuronal cell deaths in neurodegenerative diseases due to their prevalence in tissue samples and disease models. Despite recent studies demonstrating the toxicity associated with soluble oligomers, many therapeutic strategies still focus on fibrils or consider all types of aggregates as one group. Oligomers and fibrils require different modeling and therapeutic strategies, targeting the toxic species is crucial for successful study and therapeutic development. Here, we review the role of different-size aggregates in disease, and how factors contributing to aggregation (mutations, metals, post-translational modifications, and lipid interactions) may promote oligomers opposed to fibrils. We review two different computational modeling strategies (molecular dynamics and kinetic modeling) and how they are used to model both oligomers and fibrils. Finally, we outline the current therapeutic strategies targeting aggregating proteins and their strengths and weaknesses for targeting oligomers versus fibrils. Altogether, we aim to highlight the importance of distinguishing the difference between oligomers and fibrils and determining which species is toxic when modeling and creating therapeutics for protein aggregation in disease.
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Affiliation(s)
- Brianna Hnath
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Jiaxing Chen
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Joshua Reynolds
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Esther Choi
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Medical Scientist Training ProgramPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Jian Wang
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Dongyan Zhang
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - Congzhou M. Sha
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Medical Scientist Training ProgramPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of Engineering Science and MechanicsPenn State UniversityUniversity ParkPennsylvaniaUSA
| | - Nikolay V. Dokholyan
- Department of Biomedical EngineeringPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of PharmacologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of Engineering Science and MechanicsPenn State UniversityUniversity ParkPennsylvaniaUSA
- Department of Biochemistry & Molecular BiologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Department of ChemistryPenn State UniversityUniversity ParkPennsylvaniaUSA
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Que Z, Yang K, Wang N, Li S, Li T. Functional Role of RBP in Osteosarcoma: Regulatory Mechanism and Clinical Therapy. Anal Cell Pathol (Amst) 2023; 2023:9849719. [PMID: 37426488 PMCID: PMC10328736 DOI: 10.1155/2023/9849719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023] Open
Abstract
Malignant bone neoplasms can be represented by osteosarcoma (OS), which accounts for 36% of all sarcomas. To reduce tumor malignancy, extensive efforts have been devoted to find an ideal target from numerous candidates, among which RNA-binding proteins (RBPs) have shown their unparalleled competitiveness. With the special structure of RNA-binding domains, RBPs have the potential to establish relationships with RNAs or small molecules and are considered regulators of different sections of RNA processes, including splicing, transport, translation, and degradation of RNAs. RBPs have considerable significant roles in various cancers, and experiments revealed that there was a strong association of RBPs with tumorigenesis and tumor cell progression. Regarding OS, RBPs are a new orientation, but achievements in hand are noteworthy. Higher or lower expression of RBPs was first found in tumor cells compared to normal tissue. By binding to different molecules, RBPs are capable of influencing tumor cell phenotypes through different signaling pathways or other axes, and researches on medical treatment have been largely inspired. Exploring the prognostic and therapeutic values of RBPs in OS is a hotspot where diverse avenues on regulating RBPs have achieved dramatical effects. In this review, we briefly summarize the contribution of RBPs and their binding molecules to OS oncogenicity and generally introduce distinctive RBPs as samples. Moreover, we focus on the attempts to differentiate RBP's opposite functions in predicting prognosis and collect possible strategies for treatment. Our review provides forwards insight into improving the understanding of OS and suggests RBPs as potential biomarkers for therapies.
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Affiliation(s)
- Ziyuan Que
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Kang Yang
- Department of Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Nan Wang
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Shuying Li
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Tao Li
- Department of Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
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Padmanabhan S, Manjithaya R. Leaderless secretory proteins of the neurodegenerative diseases via TNTs: a structure-function perspective. Front Mol Neurosci 2023; 16:983108. [PMID: 37396786 PMCID: PMC10308029 DOI: 10.3389/fnmol.2023.983108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Neurodegenerative disease-causing proteins such as alpha-synuclein, tau, and huntingtin are known to traverse across cells via exosomes, extracellular vesicles and tunneling nanotubes (TNTs). There seems to be good synergy between exosomes and TNTs in intercellular communication. Interestingly, many of the known major neurodegenerative proteins/proteolytic products are leaderless and are also reported to be secreted out of the cell via unconventional protein secretion. Such classes contain intrinsically disordered proteins and regions (IDRs) within them. The dynamic behavior of these proteins is due to their heterogenic conformations that is exhibited owing to various factors that occur inside the cells. The amino acid sequence along with the chemical modifications has implications on the functional roles of IDRs inside the cells. Proteins that form aggregates resulting in neurodegeneration become resistant to degradation by the processes of autophagy and proteasome system thus leading to Tunneling nanotubes, TNT formation. The proteins that traverse across TNTs may or may not be dependent on the autophagy machinery. It is not yet clear whether the conformation of the protein plays a crucial role in its transport from one cell to another without getting degraded. Although there is some experimental data, there are many grey areas which need to be revisited. This review provides a different perspective on the structural and functional aspects of these leaderless proteins that get secreted outside the cell. In this review, attention has been focused on the characteristic features that lead to aggregation of leaderless secretory proteins (from structural-functional aspect) with special emphasis on TNTs.
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Ervilha Pereira P, Schuermans N, Meylemans A, LeBlanc P, Versluys L, Copley KE, Rubien JD, Altheimer C, Peetermans M, Debackere E, Vanakker O, Janssens S, Baets J, Verhoeven K, Lammens M, Symoens S, De Paepe B, Barmada SJ, Shorter J, De Bleecker JL, Bogaert E, Dermaut B. C-terminal frameshift variant of TDP-43 with pronounced aggregation-propensity causes rimmed vacuole myopathy but not ALS/FTD. Acta Neuropathol 2023; 145:793-814. [PMID: 37000196 PMCID: PMC10175433 DOI: 10.1007/s00401-023-02565-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/01/2023]
Abstract
Neuronal TDP-43-positive inclusions are neuropathological hallmark lesions in frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Pathogenic missense variants in TARDBP, the gene encoding TDP-43, can cause ALS and cluster in the C-terminal prion-like domain (PrLD), where they modulate the liquid condensation and aggregation properties of the protein. TDP-43-positive inclusions are also found in rimmed vacuole myopathies, including sporadic inclusion body myositis, but myopathy-causing TDP-43 variants have not been reported. Using genome-wide linkage analysis and whole exome sequencing in an extended five-generation family with an autosomal dominant rimmed vacuole myopathy, we identified a conclusively linked frameshift mutation in TDP-43 producing a C-terminally altered PrLD (TDP-43p.Trp385IlefsTer10) (maximum multipoint LOD-score 3.61). Patient-derived muscle biopsies showed TDP-43-positive sarcoplasmic inclusions, accumulation of autophagosomes and transcriptomes with abnormally spliced sarcomeric genes (including TTN and NEB) and increased expression of muscle regeneration genes. In vitro phase separation assays demonstrated that TDP-43Trp385IlefsTer10 does not form liquid-like condensates and readily forms solid-like fibrils indicating increased aggregation propensity compared to wild-type TDP-43. In Drosophila TDP-43p.Trp385IlefsTer10 behaved as a partial loss-of-function allele as it was able to rescue the TBPH (fly ortholog of TARDBP) neurodevelopmental lethal null phenotype while showing strongly reduced toxic gain-of-function properties upon overexpression. Accordingly, TDP-43p.Trp385IlefsTer10 showed reduced toxicity in a primary rat neuron disease model. Together, these genetic, pathological, in vitro and in vivo results demonstrate that TDP-43p.Trp385IlefsTer10 is an aggregation-prone partial loss-of-function variant that causes autosomal dominant vacuolar myopathy but not ALS/FTD. Our study genetically links TDP-43 proteinopathy to myodegeneration, and reveals a tissue-specific role of the PrLD in directing pathology.
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Affiliation(s)
- Pedro Ervilha Pereira
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Nika Schuermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Antoon Meylemans
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
- Department of Head and Skin, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Pontus LeBlanc
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Lauren Versluys
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jack D Rubien
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Myra Peetermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Debackere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jonathan Baets
- Department of Neurology, Neuromuscular Reference Centre, Antwerp University Hospital, Antwerp, Belgium
- Faculty of Medicine and Health Sciences, Translational Neurosciences, University of Antwerp, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Kristof Verhoeven
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
- Department of Neurology, Sint-Jan Hospital Bruges, Brugge, Belgium
| | - Martin Lammens
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Sofie Symoens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Boel De Paepe
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
- Department of Head and Skin, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jan L De Bleecker
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
- Department of Head and Skin, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
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45
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Bauer KE, de Queiroz BR, Kiebler MA, Besse F. RNA granules in neuronal plasticity and disease. Trends Neurosci 2023:S0166-2236(23)00104-2. [PMID: 37202301 DOI: 10.1016/j.tins.2023.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/16/2023] [Indexed: 05/20/2023]
Abstract
RNA granules are dynamic entities controlling the spatiotemporal distribution and translation of RNA molecules. In neurons, a variety of RNA granules exist both in the soma and in cellular processes. They contain transcripts encoding signaling and synaptic proteins as well as RNA-binding proteins causally linked to several neurological disorders. In this review, we highlight that neuronal RNA granules exhibit properties of biomolecular condensates that are regulated upon maturation and physiological aging and how they are reversibly remodeled in response to neuronal activity to control local protein synthesis and ultimately synaptic plasticity. Moreover, we propose a framework of how neuronal RNA granules mature over time in healthy conditions and how they transition into pathological inclusions in the context of late-onset neurodegenerative diseases.
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Affiliation(s)
- Karl E Bauer
- Biomedical Center (BMC), Department of Anatomy and Cell Biology, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Bruna R de Queiroz
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France
| | - Michael A Kiebler
- Biomedical Center (BMC), Department of Anatomy and Cell Biology, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany.
| | - Florence Besse
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, France.
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46
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Bertrand E, Demongin C, Dobra I, Rengifo-Gonzalez JC, Singatulina AS, Sukhanova MV, Lavrik OI, Pastré D, Hamon L. FUS fibrillation occurs through a nucleation-based process below the critical concentration required for liquid-liquid phase separation. Sci Rep 2023; 13:7772. [PMID: 37179431 PMCID: PMC10183042 DOI: 10.1038/s41598-023-34558-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
FUS is an RNA-binding protein involved in familiar forms of ALS and FTLD that also assembles into fibrillar cytoplasmic aggregates in some neurodegenerative diseases without genetic causes. The self-adhesive prion-like domain in FUS generates reversible condensates via the liquid-liquid phase separation process (LLPS) whose maturation can lead to the formation of insoluble fibrillar aggregates in vitro, consistent with the appearance of cytoplasmic inclusions in ageing neurons. Using a single-molecule imaging approach, we reveal that FUS can assemble into nanofibrils at concentrations in the nanomolar range. These results suggest that the formation of fibrillar aggregates of FUS could occur in the cytoplasm at low concentrations of FUS, below the critical ones required to trigger the liquid-like condensate formation. Such nanofibrils may serve as seeds for the formation of pathological inclusions. Interestingly, the fibrillation of FUS at low concentrations is inhibited by its binding to mRNA or after the phosphorylation of its prion-like domain, in agreement with previous models.
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Affiliation(s)
- Emilie Bertrand
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Clément Demongin
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Ioana Dobra
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | | | - Anastasia S Singatulina
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia, 630090
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France.
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47
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Dall'Agnese G, Dall'Agnese A, Banani SF, Codrich M, Malfatti MC, Antoniali G, Tell G. Role of condensates in modulating DNA repair pathways and its implication for chemoresistance. J Biol Chem 2023:104800. [PMID: 37164156 DOI: 10.1016/j.jbc.2023.104800] [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: 11/22/2022] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
For cells, it is important to repair DNA damage, such as double strand and single strand DNA breaks, because unrepaired DNA can compromise genetic integrity, potentially leading to cell death or cancer. Cells have multiple DNA damage repair pathways that have been the subject of detailed genetic, biochemical, and structural studies. Recently, the scientific community has started to gain evidence that the repair of DNA double strand breaks may occur within biomolecular condensates and that condensates may also contribute to DNA damage through concentrating genotoxic agents used to treat various cancers. Here, we summarize key features of biomolecular condensates and note where they have been implicated in the repair of DNA double strand breaks. We also describe evidence suggesting that condensates may be involved in the repair of other types of DNA damage, including single strand DNA breaks, nucleotide modifications (e.g., mismatch and oxidized bases) and bulky lesions, among others. Finally, we discuss old and new mysteries that could now be addressed considering the properties of condensates, including chemoresistance mechanisms.
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Affiliation(s)
- Giuseppe Dall'Agnese
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy; Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | | | - Salman F Banani
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, 33100 Udine, Italy.
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48
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Sahin C, Motso A, Gu X, Feyrer H, Lama D, Arndt T, Rising A, Gese GV, Hällberg BM, Marklund EG, Schafer NP, Petzold K, Teilum K, Wolynes PG, Landreh M. Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. J Am Chem Soc 2023; 145:10659-10668. [PMID: 37145883 DOI: 10.1021/jacs.3c00932] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Liquid-liquid phase separation (LLPS) of heterogeneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information about their assembled states is still lacking. Here, we address this challenge through a combination of protein engineering, native ion mobility mass spectrometry, and molecular dynamics simulations. We used an LLPS-compatible spider silk domain and pH changes to control the self-assembly of the hnRNPs FUS, TDP-43, and hCPEB3, which are implicated in neurodegeneration, cancer, and memory storage. By releasing the proteins inside the mass spectrometer from their native assemblies, we could monitor conformational changes associated with liquid-liquid phase separation. We find that FUS monomers undergo an unfolded-to-globular transition, whereas TDP-43 oligomerizes into partially disordered dimers and trimers. hCPEB3, on the other hand, remains fully disordered with a preference for fibrillar aggregation over LLPS. The divergent assembly mechanisms revealed by ion mobility mass spectrometry of soluble protein species that exist under LLPS conditions suggest structurally distinct complexes inside liquid droplets that may impact RNA processing and translation depending on biological context.
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Affiliation(s)
- Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Aikaterini Motso
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Xinyu Gu
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Hannes Feyrer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Tina Arndt
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 57 Huddinge, Sweden
| | - Anna Rising
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 57 Huddinge, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, S-750 07 Uppsala, Sweden
| | - Genis Valentin Gese
- Department of Cell and Molecular Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 171 65 Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 171 65 Stockholm, Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 24 Uppsala, Sweden
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Department of Cell- and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden
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49
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Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS. Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils. Nat Commun 2023; 14:2379. [PMID: 37185252 PMCID: PMC10127185 DOI: 10.1038/s41467-023-37865-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
The self-assembly of the Nucleocapsid protein (NCAP) of SARS-CoV-2 is crucial for its function. Computational analysis of the amino acid sequence of NCAP reveals low-complexity domains (LCDs) akin to LCDs in other proteins known to self-assemble as phase separation droplets and amyloid fibrils. Previous reports have described NCAP's propensity to phase-separate. Here we show that the central LCD of NCAP is capable of both, phase separation and amyloid formation. Within this central LCD we identified three adhesive segments and determined the atomic structure of the fibrils formed by each. Those structures guided the design of G12, a peptide that interferes with the self-assembly of NCAP and demonstrates antiviral activity in SARS-CoV-2 infected cells. Our work, therefore, demonstrates the amyloid form of the central LCD of NCAP and suggests that amyloidogenic segments of NCAP could be targeted for drug development.
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Affiliation(s)
- Einav Tayeb-Fligelman
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Jeannette T Bowler
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Christen E Tai
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Michael R Sawaya
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Yi Xiao Jiang
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
| | - Sarah L Griner
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Xinyi Cheng
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Lukasz Salwinski
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Liisa Lutter
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Paul M Seidler
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California School of Pharmacy, Los Angeles, CA, 90089-9121, USA
| | - Jiahui Lu
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Gregory M Rosenberg
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Ke Hou
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Romany Abskharon
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Hope Pan
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Chih-Te Zee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - David R Boyer
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Yan Li
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Daniel H Anderson
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Kevin A Murray
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA
| | - Genesis Falcon
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
| | - Lorena Saelices
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- Department of Bioengineering, UCLA, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
| | - Feng Guo
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - David S Eisenberg
- Department of Biological Chemistry, UCLA, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA.
- Howard Hughes Medical Institute, Los Angeles, CA, 90095, USA.
- UCLA-DOE Institute of Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, UCLA, Los Angeles, CA, 90095, USA.
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Jung KH, Sun J, Hsiung CH, Lance Lian X, Liu Y, Zhang X. Nuclear bodies protect phase separated proteins from degradation in stressed proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537522. [PMID: 37131610 PMCID: PMC10153235 DOI: 10.1101/2023.04.19.537522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
RNA-binding proteins (RBPs) containing intrinsically disordered domains undergo liquid-liquid phase separation to form nuclear bodies under stress conditions. This process is also connected to the misfolding and aggregation of RBPs, which are associated with a series of neurodegenerative diseases. However, it remains elusive how folding states of RBPs changes upon the formation and maturation of nuclear bodies. Here, we describe SNAP-tag based imaging methods to visualize the folding states of RBPs in live cells via time-resolved quantitative microscopic analyses of their micropolarity and microviscosity. Using these imaging methods in conjunction with immunofluorescence imaging, we demonstrate that RBPs, represented by TDP-43, initially enters the PML nuclear bodies in its native state upon transient proteostasis stress, albeit it begins to misfolded during prolonged stress. Furthermore, we show that heat shock protein 70 co-enters the PML nuclear bodies to prevent the degradation of TDP-43 from the proteotoxic stress, thus revealing a previously unappreciated protective role of the PML nuclear bodies in the prevention of stress-induced degradation of TDP-43. In summary, our imaging methods described in the manuscript, for the first time, reveal the folding states of RBPs, which were previously challenging to study with conventional methods in nuclear bodies of live cells. This study uncovers the mechanistic correlations between the folding states of a protein and functions of nuclear bodies, in particular PML bodies. We envision that the imaging methods can be generally applied to elucidating the structural aspects of other proteins that exhibit granular structures under biological stimulus.
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Affiliation(s)
- Kwan Ho Jung
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Jiarui Sun
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Chia-Heng Hsiung
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Present address: Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
| | - Yu Liu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, China
| | - Xin Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
- Present address: Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine; 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Department of Biomedical Engineering, The Huck Institute of Life Sciences, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States
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