1
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Tsekrekou M, Giannakou M, Papanikolopoulou K, Skretas G. Protein aggregation and therapeutic strategies in SOD1- and TDP-43- linked ALS. Front Mol Biosci 2024; 11:1383453. [PMID: 38855322 PMCID: PMC11157337 DOI: 10.3389/fmolb.2024.1383453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with severe socio-economic impact. A hallmark of ALS pathology is the presence of aberrant cytoplasmic inclusions composed of misfolded and aggregated proteins, including both wild-type and mutant forms. This review highlights the critical role of misfolded protein species in ALS pathogenesis, particularly focusing on Cu/Zn superoxide dismutase (SOD1) and TAR DNA-binding protein 43 (TDP-43), and emphasizes the urgent need for innovative therapeutic strategies targeting these misfolded proteins directly. Despite significant advancements in understanding ALS mechanisms, the disease remains incurable, with current treatments offering limited clinical benefits. Through a comprehensive analysis, the review focuses on the direct modulation of the misfolded proteins and presents recent discoveries in small molecules and peptides that inhibit SOD1 and TDP-43 aggregation, underscoring their potential as effective treatments to modify disease progression and improve clinical outcomes.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Maria Giannakou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Katerina Papanikolopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
- Institute for Bio-innovation, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
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2
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Godoy-Corchuelo JM, Ali Z, Brito Armas JM, Martins-Bach AB, García-Toledo I, Fernández-Beltrán LC, López-Carbonero JI, Bascuñana P, Spring S, Jimenez-Coca I, Muñoz de Bustillo Alfaro RA, Sánchez-Barrena MJ, Nair RR, Nieman BJ, Lerch JP, Miller KL, Ozdinler HP, Fisher EMC, Cunningham TJ, Acevedo-Arozena A, Corrochano S. TDP-43-M323K causes abnormal brain development and progressive cognitive and motor deficits associated with mislocalised and increased levels of TDP-43. Neurobiol Dis 2024; 193:106437. [PMID: 38367882 PMCID: PMC10988218 DOI: 10.1016/j.nbd.2024.106437] [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: 12/15/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/19/2024] Open
Abstract
TDP-43 pathology is found in several neurodegenerative disorders, collectively referred to as "TDP-43 proteinopathies". Aggregates of TDP-43 are present in the brains and spinal cords of >97% of amyotrophic lateral sclerosis (ALS), and in brains of ∼50% of frontotemporal dementia (FTD) patients. While mutations in the TDP-43 gene (TARDBP) are usually associated with ALS, many clinical reports have linked these mutations to cognitive impairments and/or FTD, but also to other neurodegenerative disorders including Parkinsonism (PD) or progressive supranuclear palsy (PSP). TDP-43 is a ubiquitously expressed, highly conserved RNA-binding protein that is involved in many cellular processes, mainly RNA metabolism. To investigate systemic pathological mechanisms in TDP-43 proteinopathies, aiming to capture the pleiotropic effects of TDP-43 mutations, we have further characterised a mouse model carrying a point mutation (M323K) within the endogenous Tardbp gene. Homozygous mutant mice developed cognitive and behavioural deficits as early as 3 months of age. This was coupled with significant brain structural abnormalities, mainly in the cortex, hippocampus, and white matter fibres, together with progressive cortical interneuron degeneration and neuroinflammation. At the motor level, progressive phenotypes appeared around 6 months of age. Thus, cognitive phenotypes appeared to be of a developmental origin with a mild associated progressive neurodegeneration, while the motor and neuromuscular phenotypes seemed neurodegenerative, underlined by a progressive loss of upper and lower motor neurons as well as distal denervation. This is accompanied by progressive elevated TDP-43 protein and mRNA levels in cortex and spinal cord of homozygous mutant mice from 3 months of age, together with increased cytoplasmic TDP-43 mislocalisation in cortex, hippocampus, hypothalamus, and spinal cord at 12 months of age. In conclusion, we find that Tardbp M323K homozygous mutant mice model many aspects of human TDP-43 proteinopathies, evidencing a dual role for TDP-43 in brain morphogenesis as well as in the maintenance of the motor system, making them an ideal in vivo model system to study the complex biology of TDP-43.
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Affiliation(s)
- Juan M Godoy-Corchuelo
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Zeinab Ali
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain; MRC Harwell Institute, Oxfordshire, UK
| | - Jose M Brito Armas
- Unidad de Investigación, Hospital Universitario de Canarias, ITB-ULL and CIBERNED, La Laguna, Spain
| | | | - Irene García-Toledo
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Luis C Fernández-Beltrán
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain; Department of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan I López-Carbonero
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | - Pablo Bascuñana
- Brain Mapping Group, Hospital Clínico San Carlos, IdISSC, Madrid, Spain
| | - Shoshana Spring
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Irene Jimenez-Coca
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain
| | | | - Maria J Sánchez-Barrena
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Blas Cabrera", CSIC, Madrid, Spain
| | - Remya R Nair
- MRC Harwell Institute, Oxfordshire, UK; Nucleic Acid Therapy Accelerator (NATA), Harwell Campus, Oxfordshire, UK
| | - Brian J Nieman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jason P Lerch
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
| | - Karla L Miller
- Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, UK
| | - Hande P Ozdinler
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, and UCL Queen Square Motor Neuron Disease Centre, UCL, Institute of Neurology, London, UK
| | - Thomas J Cunningham
- MRC Harwell Institute, Oxfordshire, UK; MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, UK
| | - Abraham Acevedo-Arozena
- Unidad de Investigación, Hospital Universitario de Canarias, ITB-ULL and CIBERNED, La Laguna, Spain.
| | - Silvia Corrochano
- Neurological Disorders Group, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria Hospital Clínico San Carlos (IdiSSC), Madrid 28040, Spain; MRC Harwell Institute, Oxfordshire, UK.
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3
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Arnold FJ, Nguyen AD, Bedlack RS, Bennett CL, La Spada AR. Intercellular transmission of pathogenic proteins in ALS: Exploring the pathogenic wave. Neurobiol Dis 2023:106218. [PMID: 37394036 DOI: 10.1016/j.nbd.2023.106218] [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: 04/01/2023] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023] Open
Abstract
In patients with amyotrophic lateral sclerosis (ALS), disease symptoms and pathology typically spread in a predictable spatiotemporal pattern beginning at a focal site of onset and progressing along defined neuroanatomical tracts. Like other neurodegenerative diseases, ALS is characterized by the presence of protein aggregates in postmortem patient tissue. Cytoplasmic, ubiquitin-positive aggregates of TDP-43 are observed in approximately 97% of sporadic and familial ALS patients, while SOD1 inclusions are likely specific to cases of SOD1-ALS. Additionally, the most common subtype of familial ALS, caused by a hexanucleotide repeat expansion in the first intron of the C9orf72 gene (C9-ALS), is further characterized by the presence of aggregated dipeptide repeat proteins (DPRs). As we will describe, cell-to-cell propagation of these pathological proteins tightly correlates with the contiguous spread of disease. While TDP-43 and SOD1 are capable of seeding protein misfolding and aggregation in a prion-like manner, C9orf72 DPRs appear to induce (and transmit) a 'disease state' more generally. Multiple mechanisms of intercellular transport have been described for all of these proteins, including anterograde and retrograde axonal transport, extracellular vesicle secretion, and macropinocytosis. In addition to neuron-to-neuron transmission, transmission of pathological proteins occurs between neurons and glia. Given that the spread of ALS disease pathology corresponds with the spread of symptoms in patients, the various mechanisms by which ALS-associated protein aggregates propagate through the central nervous system should be closely examined.
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Affiliation(s)
- F J Arnold
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - A D Nguyen
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - R S Bedlack
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - C L Bennett
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - A R La Spada
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; Departments of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, University of California, Irvine, Irvine, CA, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
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4
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Li F, Chen Y, Tang Y, Liu X, Wei G. Dissecting the Effect of ALS Mutation G335D on the Early Aggregation of the TDP-43 Amyloidogenic Core Peptide: Helix-to-β-Sheet Transition and Conformational Shift. J Chem Inf Model 2023; 63:3579-3590. [PMID: 37218694 DOI: 10.1021/acs.jcim.3c00513] [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: 05/24/2023]
Abstract
The aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) into fibrillary deposits is associated with amyotrophic lateral sclerosis (ALS). The 311-360 fragment of TDP-43 (TDP-43311-360), the amyloidogenic core region, can spontaneously aggregate into fibrils, and the ALS-associated mutation G335D has an enhanced effect on TDP-43311-360 fibrillization. However, the molecular mechanism underlying G335D-enhanced aggregation at atomic level remains largely unknown. By utilizing all-atom molecular dynamics (MD) and replica exchange with solute tempering 2 (REST2) simulations, we investigated influences of G335D on the dimerization (the first step of aggregation) and conformational ensemble of the TDP-43311-360 peptide. Our simulations show that G335D mutation increases inter-peptide interactions, especially inter-peptide hydrogen-bonding interactions in which the mutant site has a relatively large contribution, and enhances the dimerization of TDP-43311-360 peptides. The α-helix regions in the NMR-resolved conformation of the TDP-43311-360 monomer (321-330 and 335-343) play an essential role in the formation of the dimer. G335D mutation induces helix unfolding and promotes α-to-β conversion. G335D mutation alters the conformational distribution of TDP-43311-360 dimers and causes population shift from helix-rich to β-sheet-rich conformations, which facilitates the fibrillization of the TDP-43311-360 peptide. Our MD and REST2 simulation results suggest that the 321-330 region is of paramount importance to α-to-β transition and could be the initiation site for TDP-43311-360 fibrillization. Our work reveals the mechanism underlying the enhanced aggregation propensity of the G335D TDP-43311-360 peptide, which provides atomistic insights into the G335D mutation-caused pathogenicity of TDP-43 protein.
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Affiliation(s)
- Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Xianshi Liu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
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5
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Kitamura A, Yuno S, Kawamura R, Kinjo M. Intracellular Conformation of Amyotrophic Lateral Sclerosis-Causative TDP-43. Int J Mol Sci 2023; 24:5513. [PMID: 36982587 PMCID: PMC10056606 DOI: 10.3390/ijms24065513] [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: 02/24/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023] Open
Abstract
Transactive response element DNA/RNA-binding protein 43 kDa (TDP-43) is the causative protein of amyotrophic lateral sclerosis (ALS); several ALS-associated mutants of TDP-43 have been identified. TDP-43 has several domains: an N-terminal domain, two RNA/DNA-recognition motifs, and a C-terminal intrinsically disordered region (IDR). Its structures have been partially determined, but the whole structure remains elusive. In this study, we investigate the possible end-to-end distance between the N- and C-termini of TDP-43, its alterations due to ALS-associated mutations in the IDR, and its apparent molecular shape in live cells using Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS). Furthermore, the interaction between ALS-associated TDP-43 and heteronuclear ribonucleoprotein A1 (hnRNP A1) is slightly stronger than that of wild-type TDP-43. Our findings provide insights into the structure of wild-type and ALS-associated mutants of TDP-43 in a cell.
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Affiliation(s)
- Akira Kitamura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
- PRIME, The Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan
| | - Sachiko Yuno
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Rintaro Kawamura
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
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6
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Ohene-Nyako M, Nass SR, Richard HT, Lukande R, Nicol MR, McRae M, Knapp PE, Hauser KF. Casein Kinase 2 Mediates HIV- and Opioid-Induced Pathologic Phosphorylation of TAR DNA Binding Protein 43 in the Basal Ganglia. ASN Neuro 2023; 15:17590914231158218. [PMID: 36890725 PMCID: PMC9998424 DOI: 10.1177/17590914231158218] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
SUMMARY STATEMENT HIV/HIV-1 Tat and morphine independently increase pathologic phosphorylation of TAR DNA binding protein 43 in the striatum. HIV- and opioid-induced pathologic phosphorylation of TAR DNA binding protein 43 may involve enhanced CK2 activity and protein levels.
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Affiliation(s)
- Michael Ohene-Nyako
- Pharmacology and Toxicology, School of Medicine, 6886Virginia Commonwealth University, Richmond, VA, USA
| | - Sara R Nass
- Pharmacology and Toxicology, School of Medicine, 6886Virginia Commonwealth University, Richmond, VA, USA
| | - Hope T Richard
- Pathology, School of Medicine, 6886Virginia Commonwealth University, Richmond, VA, USA
| | - Robert Lukande
- Pathology, College of Health Sciences, 58589Makerere University, Kampala, Uganda
| | - Melanie R Nicol
- Experimental and Clinical Pharmacology, College of Pharmacy, 15515University of Minnesota, Minneapolis, MN, USA
| | - MaryPeace McRae
- Pharmacotherapy and Outcomes Science, School of Pharmacy, 15535Virginia Commonwealth University, Richmond, VA, USA
| | - Pamela E Knapp
- Pharmacology and Toxicology, School of Medicine, 6886Virginia Commonwealth University, Richmond, VA, USA.,Anatomy and Neurobiology, School of Medicine, 6886Virginia Commonwealth University, Richmond, VA, USA.,Institute for Drug and Alcohol Studies, 6886Virginia Commonwealth University, Richmond, VA, USA
| | - Kurt F Hauser
- Pharmacology and Toxicology, School of Medicine, 6886Virginia Commonwealth University, Richmond, VA, USA.,Anatomy and Neurobiology, School of Medicine, 6886Virginia Commonwealth University, Richmond, VA, USA.,Institute for Drug and Alcohol Studies, 6886Virginia Commonwealth University, Richmond, VA, USA
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7
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Tamaki Y, Urushitani M. Molecular Dissection of TDP-43 as a Leading Cause of ALS/FTLD. Int J Mol Sci 2022; 23:ijms232012508. [PMID: 36293362 PMCID: PMC9604209 DOI: 10.3390/ijms232012508] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
TAR DNA binding protein 43 (TDP-43) is a DNA/RNA binding protein involved in pivotal cellular functions, especially in RNA metabolism. Hyperphosphorylated and ubiquitinated TDP-43-positive neuronal cytoplasmic inclusions are identified in the brain and spinal cord in most cases of amyotrophic lateral sclerosis (ALS) and a substantial proportion of frontotemporal lobar degeneration (FTLD) cases. TDP-43 dysfunctions and cytoplasmic aggregation seem to be the central pathogenicity in ALS and FTLD. Therefore, unraveling both the physiological and pathological mechanisms of TDP-43 may enable the exploration of novel therapeutic strategies. This review highlights the current understanding of TDP-43 biology and pathology, describing the cellular processes involved in the pathogeneses of ALS and FTLD, such as post-translational modifications, RNA metabolism, liquid–liquid phase separation, proteolysis, and the potential prion-like propagation propensity of the TDP-43 inclusions.
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Affiliation(s)
- Yoshitaka Tamaki
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Makoto Urushitani
- Department of Neurology, Shiga University of Medical Science, Otsu 520-2192, Japan
- Correspondence:
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8
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Tran NN, Lee BH. Functional implication of ubiquitinating and deubiquitinating mechanisms in TDP-43 proteinopathies. Front Cell Dev Biol 2022; 10:931968. [PMID: 36158183 PMCID: PMC9500471 DOI: 10.3389/fcell.2022.931968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/23/2022] [Indexed: 11/15/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease in which motor neurons in spinal cord and motor cortex are progressively lost. About 15% cases of ALS also develop the frontotemporal dementia (FTD), in which the frontotemporal lobar degeneration (FTLD) occurs in the frontal and temporal lobes of the brain. Among the pathologic commonalities in ALS and FTD is ubiquitin-positive cytoplasmic aggregation of TDP-43 that may reflect both its loss-of-function and gain-of-toxicity from proteostasis impairment. Deep understanding of how protein quality control mechanisms regulate TDP-43 proteinopathies still remains elusive. Recently, a growing body of evidence indicates that ubiquitinating and deubiquitinating pathways are critically engaged in the fate decision of aberrant or pathological TDP-43 proteins. E3 ubiquitin ligases coupled with deubiquitinating enzymes may influence the TDP-43-associated proteotoxicity through diverse events, such as protein stability, translocation, and stress granule or inclusion formation. In this article, we recapitulate our current understanding of how ubiquitinating and deubiquitinating mechanisms can modulate TDP-43 protein quality and its pathogenic nature, thus shedding light on developing targeted therapies for ALS and FTD by harnessing protein degradation machinery.
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Affiliation(s)
- Non-Nuoc Tran
- Department of New Biology, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Byung-Hoon Lee
- Department of New Biology, Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
- Department of New Biology Research Center (NBRC), Daegu-Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
- *Correspondence: Byung-Hoon Lee,
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9
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Conversion of the Native N-Terminal Domain of TDP-43 into a Monomeric Alternative Fold with Lower Aggregation Propensity. Molecules 2022; 27:molecules27134309. [PMID: 35807552 PMCID: PMC9268139 DOI: 10.3390/molecules27134309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/30/2022] [Accepted: 07/02/2022] [Indexed: 11/17/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) forms intraneuronal cytoplasmic inclusions associated with amyotrophic lateral sclerosis and ubiquitin-positive frontotemporal lobar degeneration. Its N-terminal domain (NTD) can dimerise/oligomerise with the head-to-tail arrangement, which is essential for function but also favours liquid-liquid phase separation and inclusion formation of full-length TDP-43. Using various biophysical approaches, we identified an alternative conformational state of NTD in the presence of Sulfobetaine 3-10 (SB3-10), with higher content of α-helical structure and tryptophan solvent exposure. NMR shows a highly mobile structure, with partially folded regions and β-sheet content decrease, with a concomitant increase of α-helical structure. It is monomeric and reverts to native oligomeric NTD upon SB3-10 dilution. The equilibrium GdnHCl-induced denaturation shows a cooperative folding and a somewhat lower conformational stability. When the aggregation processes were compared with and without pre-incubation with SB3-10, but at the identical final SB3-10 concentration, a slower aggregation was found in the former case, despite the reversible attainment of the native conformation in both cases. This was attributed to protein monomerization and oligomeric seeds disruption by the conditions promoting the alternative conformation. Overall, the results show a high plasticity of TDP-43 NTD and identify strategies to monomerise TDP-43 NTD for methodological and biomedical applications.
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10
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Garg DK, Bhat R. Modulation of assembly of TDP-43 low-complexity domain by heparin: From droplets to amyloid fibrils. Biophys J 2022; 121:2568-2582. [PMID: 35644946 PMCID: PMC9300664 DOI: 10.1016/j.bpj.2022.05.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/03/2021] [Accepted: 05/25/2022] [Indexed: 11/02/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA-regulating protein that carries out many cellular functions through liquid-liquid phase separation (LLPS). The LLPS of TDP-43 is mediated by its C-terminal low-complexity domain (TDP43-LCD) corresponding to the region 267-414. In neurodegenerative disorders amyotrophic lateral sclerosis and frontotemporal dementia, pathological inclusions of the TDP-43 are found that are rich in the C-terminal fragments of ∼25 and ∼35 kDa, of which TDP43-LCD is a part. Thus, understanding the assembly process of TDP43-LCD is essential, given its involvement in the formation of both functional liquid-like assemblies and solid- or gel-like pathological aggregates. Here, we show that the solution pH and salt modulate TDP43-LCD LLPS. A gradual reduction in the pH below its isoelectric point of 9.8 results in a monotonic decrease of TDP43-LCD LLPS due to charge-charge repulsion between monomers, while at pH 6 and below no LLPS was observed. The addition of heparin to TDP43-LCD solution at pH 6, at a 1:2 heparin-to-TDP43-LCD molar ratio, promotes TDP43-LCD LLPS, while at higher concentration, it disrupts LLPS through a reentrant phase transition. Upon incubation at pH 6, TDP43-LCD undergoes gelation without phase separation. However, in the reentrant regime in the presence of a high heparin concentration, it forms thick amyloid aggregates that are significantly more SDS resistant than the gel. The results indicate that the material nature of the TDP43-LCD assembly products can be modulated by heparin which is significant in the context of liquid-to-solid phase transition observed in TDP-43 proteinopathies. Our findings are also crucial in relation to similar transitions that could occur due to alteration in the molecular level interactions among various multivalent biomolecules involving other LCDs and RNAs.
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Affiliation(s)
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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11
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Charif SE, Vassallu MF, Salvañal L, Igaz LM. Protein synthesis modulation as a therapeutic approach for amyotrophic lateral sclerosis and frontotemporal dementia. Neural Regen Res 2021; 17:1423-1430. [PMID: 34916412 PMCID: PMC8771112 DOI: 10.4103/1673-5374.330593] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Protein synthesis is essential for cells to perform life metabolic processes. Pathological alterations of protein content can lead to particular diseases. Cells have an intrinsic array of mechanisms and pathways that are activated when protein misfolding, accumulation, aggregation or mislocalization occur. Some of them (like the unfolded protein response) represent complex interactions between endoplasmic reticulum sensors and elongation factors that tend to increase expression of chaperone proteins and/or repress translation in order to restore protein homeostasis (also known as proteostasis). This is even more important in neurons, as they are very susceptible to harmful effects associated with protein overload and proteostatic mechanisms are less effective with age. Several neurodegenerative pathologies such as Alzheimer's, Parkinson's, and Huntington's diseases, amyotrophic lateral sclerosis and frontotemporal dementia exhibit a particular molecular signature of distinct, unbalanced protein overload. In amyotrophic lateral sclerosis and frontotemporal dementia, the majority of cases present intracellular inclusions of ubiquitinated transactive response DNA-binding protein of 43 kDa (TDP-43). TDP-43 is an RNA binding protein that participates in RNA metabolism, among other functions. Dysregulation of TDP-43 (e.g. aggregation and mislocalization) can dramatically affect neurons, and this has been linked to disease development. Expression of amyotrophic lateral sclerosis/frontotemporal dementia TDP-43-related mutations in cellular and animal models has been shown to recapitulate key features of the amyotrophic lateral sclerosis/frontotemporal dementia disease spectrum. These variants can be causative of degeneration onset and progression. Most neurodegenerative diseases (including amyotrophic lateral sclerosis and frontotemporal dementia) have no cure at the moment; however, modulating translation has recently emerged as an attractive approach that can be performed at several steps (i.e. regulating activation of initiation and elongation factors, inhibiting unfolded protein response activation or inducing chaperone expression and activity). This review focuses on the features of protein imbalance in neurodegenerative disorders and the relevance of developing therapeutical compounds aiming at restoring proteostasis. We strive to highlight the importance of research on drugs that, not only restore protein imbalance without compromising translational activity of cells, but are also as safe as possible for the patients.
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Affiliation(s)
- Santiago E Charif
- IFIBIO Houssay, Grupo de Neurociencia de Sistemas, Facultad de Medicina, Universidad de Buenos Aires -CONICET, Buenos Aires, Argentina
| | - M Florencia Vassallu
- IFIBIO Houssay, Grupo de Neurociencia de Sistemas, Facultad de Medicina, Universidad de Buenos Aires -CONICET, Buenos Aires, Argentina
| | - Lara Salvañal
- IFIBIO Houssay, Grupo de Neurociencia de Sistemas, Facultad de Medicina, Universidad de Buenos Aires -CONICET, Buenos Aires, Argentina
| | - Lionel M Igaz
- IFIBIO Houssay, Grupo de Neurociencia de Sistemas, Facultad de Medicina, Universidad de Buenos Aires -CONICET, Buenos Aires, Argentina
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12
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Gao J, Wang L, Ren X, Dunn JR, Peters A, Miyagi M, Fujioka H, Zhao F, Askwith C, Liang J, Wang X. Translational regulation in the brain by TDP-43 phase separation. J Cell Biol 2021; 220:e202101019. [PMID: 34427634 PMCID: PMC8404466 DOI: 10.1083/jcb.202101019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/03/2021] [Accepted: 07/22/2021] [Indexed: 01/08/2023] Open
Abstract
The in vivo physiological function of liquid-liquid phase separation (LLPS) that governs non-membrane-bound structures remains elusive. Among LLPS-prone proteins, TAR DNA-binding protein of 43 kD (TDP-43) is under intense investigation because of its close association with neurological disorders. Here, we generated mice expressing endogenous LLPS-deficient murine TDP-43. LLPS-deficient TDP-43 mice demonstrate impaired neuronal function and behavioral abnormalities specifically related to brain function. Brain neurons of these mice, however, did not show TDP-43 proteinopathy or neurodegeneration. Instead, the global rate of protein synthesis was found to be greatly enhanced by TDP-43 LLPS loss. Mechanistically, TDP-43 LLPS ablation increased its association with PABPC4, RPS6, RPL7, and other translational factors. The physical interactions between TDP-43 and translational factors relies on a motif, the deletion of which abolished the impact of LLPS-deficient TDP-43 on translation. Our findings show a specific physiological role for TDP-43 LLPS in the regulation of brain function and uncover an intriguing novel molecular mechanism of translational control by LLPS.
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Affiliation(s)
- Ju Gao
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Luwen Wang
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Xiaojia Ren
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Justin R. Dunn
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Ariele Peters
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
| | - Hisashi Fujioka
- Electron Microscopy Core Facility, Case Western Reserve University, Cleveland, OH
| | - Fangli Zhao
- Department of Neuroscience, The Ohio State University, Columbus, OH
| | - Candice Askwith
- Department of Neuroscience, The Ohio State University, Columbus, OH
| | - Jingjing Liang
- Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Xinglong Wang
- Department of Pharmacology and Experimental Neurosciences, University of Nebraska Medical Center, Omaha, NE
- Department of Pathology, Case Western Reserve University, Cleveland, OH
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13
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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14
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Strategies in the design and development of (TAR) DNA-binding protein 43 (TDP-43) binding ligands. Eur J Med Chem 2021; 225:113753. [PMID: 34388383 DOI: 10.1016/j.ejmech.2021.113753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/16/2021] [Accepted: 08/05/2021] [Indexed: 01/09/2023]
Abstract
The human transactive responsive (TAR) DNA-binding protein 43 (TDP-43) is involved in a number of physiological processes in the body. Its primary function involves RNA regulation. The TDP-43 protein is also involved in many diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease (AD), Parkinson's disease (PD) and even cancers. These TDP-43 mediated diseases are collectively called as TDP-43 proteinopathies. Intense research in the last decade has increased our understanding on TDP-43 structure and function in biology. The three-dimensional structures of TDP-43 domains such as N-terminal domain (NTD), RNA-recognition motif-1 (RRM1), RNA-recognition motif-2 (RRM2) and the C-terminal domain (CTD) or low-complexity domain (LCD) have been solved. These structures have yielded insights into novel binding sites and pockets at various TDP-43 domains, which can be targeted by designing a diverse library of ligands including small molecules, peptides and oligonucleotides as molecular tools to (i) study TDP-43 function, (ii) develop novel diagnostic agents and (iii) discover disease-modifying therapies to treat TDP-43 proteinopathies. This review provides a summary on recent progress in the development of TDP-43 binding ligands and uses the solved structures of various TDP-43 domains to investigate putative ligand binding regions that can be exploited to discover novel molecular probes to modulate TDP-43 structure and function.
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15
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Francois-Moutal L, Scott DD, Khanna M. Direct targeting of TDP-43, from small molecules to biologics: the therapeutic landscape. RSC Chem Biol 2021; 2:1158-1166. [PMID: 34458829 PMCID: PMC8341936 DOI: 10.1039/d1cb00110h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
Tar DNA binding (TDP)-43 proteinopathy, typically described as cytoplasmic accumulation of highly modified and misfolded TDP-43 molecules, is characteristic of several neurodegenerative diseases such as Amyotrophic Lateral Sclerosis (ALS) and limbic-predominant age-related TDP-43 encephalopathy (LATE). TDP-43 proposed proteinopathies include homeostatic imbalance between nuclear and cytoplasmic localization, aggregation of ubiquitinated and hyper-phosphorylated TDP-43, and an increase in protein truncation of cytoplasmic TDP-43. Given the therapeutic interest of targeting TDP-43, this review focuses on the current landscape of strategies, ranging from biologics to small molecules, that directly target TDP-43. Antibodies, peptides and compounds have been designed or found to recognize specific TDP-43 sequences but alleviate TDP-43 toxicity through different mechanisms. While two antibodies described here were able to induce degradation of pathological TDP-43, the peptides and small molecules were primarily designed to reduce aggregation of TDP-43. Furthermore, we discuss promising emerging therapeutic targets.
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Affiliation(s)
- Liberty Francois-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona 1501 North Campbell Drive, P.O. Box 245050 Tucson AZ 85724 USA +520-626-2204 +520-626-2147
- Center of Innovation in Brain Science Tucson AZ 85721 USA
| | - David Donald Scott
- Department of Pharmacology, College of Medicine, University of Arizona 1501 North Campbell Drive, P.O. Box 245050 Tucson AZ 85724 USA +520-626-2204 +520-626-2147
- Center of Innovation in Brain Science Tucson AZ 85721 USA
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona 1501 North Campbell Drive, P.O. Box 245050 Tucson AZ 85724 USA +520-626-2204 +520-626-2147
- Center of Innovation in Brain Science Tucson AZ 85721 USA
- Bio5 Institute, University of Arizona Tucson USA
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16
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Liu W, Li C, Shan J, Wang Y, Chen G. Insights into the aggregation mechanism of RNA recognition motif domains in TDP-43: a theoretical exploration. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210160. [PMID: 34457335 PMCID: PMC8371369 DOI: 10.1098/rsos.210160] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/19/2021] [Indexed: 05/10/2023]
Abstract
The transactive response DNA-binding protein 43 (TDP-43) is associated with several diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) due to pathogenic aggregations. In this work, we examined the dimer, tetramer and hexamer models built from the RRM domains of TDP-43 using molecular dynamics simulations in combination with the protein-protein docking. Our results showed that the formations of the dimer models are mainly achieved by the interactions of the RRM1 domains. The parallel β-sheet layers between the RRM1 domains provide most of the binding sites in these oligomer models, and thus play an important role in the aggregation process. The approaching of the parallel β-sheet layers from small oligomer models gradually expand to large ones through the allosteric communication between the α1/α2 helices of the RRM1 domains, which maintains the binding affinities and interactions in the larger oligomer models. Using the repeatable-superimposing method based on the tetramer models, we proposed a new aggregation mechanism of RRM domains in TDP-43, which could well characterize the formation of the large aggregation models with the repeated, helical and rope-like structures. These new insights help to understand the amyloid-like aggregation phenomena of TDP-43 protein in ALS and FTLD diseases.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Chaoqun Li
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan 056005, Hebei Province, People's Republic of China
| | - Jiankai Shan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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17
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Farina S, Esposito F, Battistoni M, Biamonti G, Francia S. Post-Translational Modifications Modulate Proteinopathies of TDP-43, FUS and hnRNP-A/B in Amyotrophic Lateral Sclerosis. Front Mol Biosci 2021; 8:693325. [PMID: 34291086 PMCID: PMC8287968 DOI: 10.3389/fmolb.2021.693325] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
It has been shown that protein low-sequence complexity domains (LCDs) induce liquid-liquid phase separation (LLPS), which is responsible for the formation of membrane-less organelles including P-granules, stress granules and Cajal bodies. Proteins harbouring LCDs are widely represented among RNA binding proteins often mutated in ALS. Indeed, LCDs predispose proteins to a prion-like behaviour due to their tendency to form amyloid-like structures typical of proteinopathies. Protein post-translational modifications (PTMs) can influence phase transition through two main events: i) destabilizing or augmenting multivalent interactions between phase-separating macromolecules; ii) recruiting or excluding other proteins and/or nucleic acids into/from the condensate. In this manuscript we summarize the existing evidence describing how PTM can modulate LLPS thus favouring or counteracting proteinopathies at the base of neurodegeneration in ALS.
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Affiliation(s)
- Stefania Farina
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy.,University School for Advanced Studies IUSS, Pavia, Italy
| | - Francesca Esposito
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy.,Università Degli Studi di Pavia, Pavia, Italy
| | | | - Giuseppe Biamonti
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - Consiglio Nazionale delle Ricerce (CNR), Pavia, Italy
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18
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Carter GC, Hsiung CH, Simpson L, Yang H, Zhang X. N-terminal Domain of TDP43 Enhances Liquid-Liquid Phase Separation of Globular Proteins. J Mol Biol 2021; 433:166948. [PMID: 33744316 DOI: 10.1016/j.jmb.2021.166948] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/24/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
Liquid-liquid phase separation (LLPS) of proteins is involved in a growing number of cellular processes. Most proteins with LLPS harbor intrinsically disordered regions (IDR), which serve as a guideline to search for cellular proteins that potentially phase separate. Herein, we reveal that oligomerization lowers the barriers for LLPS and could act as a general mechanism to enhance LLPS of proteins domains independent of IDR. Using TDP43 as a model system, we found that deleting its IDR resulted in LLPS that was dependent on the oligomerization of the N-terminal domain (NTD). Replacing TDP43's NTD with other oligomerization domains enhanced the LLPS proportionately to the state of oligomerization. In addition to TDP43, fusing NTD to other globular proteins without known LLPS behavior also drove their phase separation in a manner dependent on oligomerization. Finally, we demonstrate that heterooligomers composed of NTD-fused proteins can be driven into droplets through NTD interactions. Our results potentiate a new paradigm for using oligomerization domains as a signature to systematically identify cellular proteins with LLPS behavior, thus broadening the scope of this exciting research field.
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Affiliation(s)
- G Campbell Carter
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Chia-Heng Hsiung
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
| | - Leman Simpson
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Haopeng Yang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States.
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19
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Advani VM, Ivanov P. Stress granule subtypes: an emerging link to neurodegeneration. Cell Mol Life Sci 2020; 77:4827-4845. [PMID: 32500266 PMCID: PMC7668291 DOI: 10.1007/s00018-020-03565-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022]
Abstract
Stress Granules (SGs) are membraneless cytoplasmic RNA granules, which contain translationally stalled mRNAs, associated translation initiation factors and multiple RNA-binding proteins (RBPs). They are formed in response to various stresses and contribute to reprogramming of cellular metabolism to aid cell survival. Because of their cytoprotective nature, association with translation regulation and cell signaling, SGs are an essential component of the integrated stress response pathway, a complex adaptive program central to stress management. Recent advances in SG biology unambiguously demonstrate that SGs are heterogeneous in their RNA and protein content leading to the idea that various SG subtypes exist. These SG variants are formed in cell type- and stress-specific manners and differ in their composition, dynamics of assembly and disassembly, and contribution to cell viability. As aberrant SG dynamics contribute to the formation of pathological persistent SGs that are implicated in neurodegenerative diseases, the biology of different SG subtypes may be directly implicated in neurodegeneration. Here, we will discuss mechanisms of SG formation, their subtypes, and potential contribution to health and disease.
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Affiliation(s)
- Vivek M Advani
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Harvard Initiative for RNA Medicine, Boston, MA, USA.
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20
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de Boer EMJ, Orie VK, Williams T, Baker MR, De Oliveira HM, Polvikoski T, Silsby M, Menon P, van den Bos M, Halliday GM, van den Berg LH, Van Den Bosch L, van Damme P, Kiernan MC, van Es MA, Vucic S. TDP-43 proteinopathies: a new wave of neurodegenerative diseases. J Neurol Neurosurg Psychiatry 2020; 92:jnnp-2020-322983. [PMID: 33177049 PMCID: PMC7803890 DOI: 10.1136/jnnp-2020-322983] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/28/2020] [Accepted: 09/13/2020] [Indexed: 12/31/2022]
Abstract
Inclusions of pathogenic deposits containing TAR DNA-binding protein 43 (TDP-43) are evident in the brain and spinal cord of patients that present across a spectrum of neurodegenerative diseases. For instance, the majority of patients with sporadic amyotrophic lateral sclerosis (up to 97%) and a substantial proportion of patients with frontotemporal lobar degeneration (~45%) exhibit TDP-43 positive neuronal inclusions, suggesting a role for this protein in disease pathogenesis. In addition, TDP-43 inclusions are evident in familial ALS phenotypes linked to multiple gene mutations including the TDP-43 gene coding (TARDBP) and unrelated genes (eg, C9orf72). While TDP-43 is an essential RNA/DNA binding protein critical for RNA-related metabolism, determining the pathophysiological mechanisms through which TDP-43 mediates neurodegeneration appears complex, and unravelling these molecular processes seems critical for the development of effective therapies. This review highlights the key physiological functions of the TDP-43 protein, while considering an expanding spectrum of neurodegenerative diseases associated with pathogenic TDP-43 deposition, and dissecting key molecular pathways through which TDP-43 may mediate neurodegeneration.
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Affiliation(s)
- Eva Maria Johanna de Boer
- Department of Neurology, Brain Centre Rudolf Magnus, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Viyanti K Orie
- Department of Neurology, Brain Centre Rudolf Magnus, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Timothy Williams
- Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Mark R Baker
- Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Clinical Neurophysiology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Hugo M De Oliveira
- Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tuomo Polvikoski
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Neuropathology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Matthew Silsby
- Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Parvathi Menon
- Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Mehdi van den Bos
- Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Glenda M Halliday
- Brain and Mind Center, University of Sydney, Sydney, New South Wales, Australia
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Leonard H van den Berg
- Department of Neurology, Brain Centre Rudolf Magnus, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Leuven, Belgium
| | - Philip van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), University of Leuven, Leuven, Belgium
- Center for Brain & Disease Research, Laboratory of Neurobiology, VIB, Leuven, Belgium
- Department of Neurology, University Hospital Leuven, Leuven, Belgium
| | - Matthew C Kiernan
- Brain and Mind Center, University of Sydney, Sydney, New South Wales, Australia
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Michael A van Es
- Department of Neurology, Brain Centre Rudolf Magnus, Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Steve Vucic
- Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
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21
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McAlary L, Chew YL, Lum JS, Geraghty NJ, Yerbury JJ, Cashman NR. Amyotrophic Lateral Sclerosis: Proteins, Proteostasis, Prions, and Promises. Front Cell Neurosci 2020; 14:581907. [PMID: 33328890 PMCID: PMC7671971 DOI: 10.3389/fncel.2020.581907] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of the motor neurons that innervate muscle, resulting in gradual paralysis and culminating in the inability to breathe or swallow. This neuronal degeneration occurs in a spatiotemporal manner from a point of onset in the central nervous system (CNS), suggesting that there is a molecule that spreads from cell-to-cell. There is strong evidence that the onset and progression of ALS pathology is a consequence of protein misfolding and aggregation. In line with this, a hallmark pathology of ALS is protein deposition and inclusion formation within motor neurons and surrounding glia of the proteins TAR DNA-binding protein 43, superoxide dismutase-1, or fused in sarcoma. Collectively, the observed protein aggregation, in conjunction with the spatiotemporal spread of symptoms, strongly suggests a prion-like propagation of protein aggregation occurs in ALS. In this review, we discuss the role of protein aggregation in ALS concerning protein homeostasis (proteostasis) mechanisms and prion-like propagation. Furthermore, we examine the experimental models used to investigate these processes, including in vitro assays, cultured cells, invertebrate models, and murine models. Finally, we evaluate the therapeutics that may best prevent the onset or spread of pathology in ALS and discuss what lies on the horizon for treating this currently incurable disease.
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Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Yee Lian Chew
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Jeremy Stephen Lum
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Nicholas John Geraghty
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Justin John Yerbury
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Neil R. Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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22
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Gotor NL, Armaos A, Calloni G, Torrent Burgas M, Vabulas R, De Groot NS, Tartaglia GG. RNA-binding and prion domains: the Yin and Yang of phase separation. Nucleic Acids Res 2020; 48:9491-9504. [PMID: 32857852 PMCID: PMC7515694 DOI: 10.1093/nar/gkaa681] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/08/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Proteins and RNAs assemble in membrane-less organelles that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to form condensates is encoded in their sequences, yet it is unknown which domains drive the phase separation (PS) process and what are their specific roles. Here, we systematically investigated the human and yeast proteomes to find regions promoting condensation. Using advanced computational methods to predict the PS propensity of proteins, we designed a set of experiments to investigate the contributions of Prion-Like Domains (PrLDs) and RNA-binding domains (RBDs). We found that one PrLD is sufficient to drive PS, whereas multiple RBDs are needed to modulate the dynamics of the assemblies. In the case of stress granule protein Pub1 we show that the PrLD promotes sequestration of protein partners and the RBD confers liquid-like behaviour to the condensate. Our work sheds light on the fine interplay between RBDs and PrLD to regulate formation of membrane-less organelles, opening up the avenue for their manipulation.
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Affiliation(s)
- Nieves Lorenzo Gotor
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alexandros Armaos
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, RNA System Biology Lab, Via Enrico Melen 83, 16152 Genoa, Italy
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main,60438, Germany
| | - Marc Torrent Burgas
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - R Martin Vabulas
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main,60438, Germany
- Charité – Universitätsmedizin Berlin, Institute of Biochemistry, 10117 Berlin, Germany
| | - Natalia Sanchez De Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Center for Human Technologies, Istituto Italiano di Tecnologia, RNA System Biology Lab, Via Enrico Melen 83, 16152 Genoa, Italy
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluis Companys, 08010 Barcelona, Spain
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
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23
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Floare ML, Allen SP. Why TDP-43? Why Not? Mechanisms of Metabolic Dysfunction in Amyotrophic Lateral Sclerosis. Neurosci Insights 2020; 15:2633105520957302. [PMID: 32995749 PMCID: PMC7503004 DOI: 10.1177/2633105520957302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disorder for which there is no effective curative treatment available and minimal palliative care. Mutations in the gene encoding the TAR DNA-binding protein 43 (TDP-43) are a well-recognized genetic cause of ALS, and an imbalance in energy homeostasis correlates closely to disease susceptibility and progression. Considering previous research supporting a plethora of downstream cellular impairments originating in the histopathological signature of TDP-43, and the solid evidence around metabolic dysfunction in ALS, a causal association between TDP-43 pathology and metabolic dysfunction cannot be ruled out. Here we discuss how TDP-43 contributes on a molecular level to these impairments in energy homeostasis, and whether the protein's pathological effects on cellular metabolism differ from those of other genetic risk factors associated with ALS such as superoxide dismutase 1 (SOD1), chromosome 9 open reading frame 72 (C9orf72) and fused in sarcoma (FUS).
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Affiliation(s)
- Mara-Luciana Floare
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Scott P. Allen
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
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24
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Insight into the Folding and Dimerization Mechanisms of the N-Terminal Domain from Human TDP-43. Int J Mol Sci 2020; 21:ijms21176259. [PMID: 32872449 PMCID: PMC7504384 DOI: 10.3390/ijms21176259] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a 414-residue long nuclear protein whose deposition into intraneuronal insoluble inclusions has been associated with the onset of amyotrophic lateral sclerosis (ALS) and other diseases. This protein is physiologically a homodimer, and dimerization occurs through the N-terminal domain (NTD), with a mechanism on which a full consensus has not yet been reached. Furthermore, it has been proposed that this domain is able to affect the formation of higher molecular weight assemblies. Here, we purified this domain and carried out an unprecedented characterization of its folding/dimerization processes in solution. Exploiting a battery of biophysical approaches, ranging from FRET to folding kinetics, we identified a head-to-tail arrangement of the monomers within the dimer. We found that folding of NTD proceeds through the formation of a number of conformational states and two parallel pathways, while a subset of molecules refold slower, due to proline isomerism. The folded state appears to be inherently prone to form high molecular weight assemblies. Taken together, our results indicate that NTD is inherently plastic and prone to populate different conformations and dimeric/multimeric states, a structural feature that may enable this domain to control the assembly state of TDP-43.
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25
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Dhanwani R, Pham J, Premlal ALR, Frazier A, Kumar A, Pero ME, Bartolini F, Dutra JR, Marder KS, Peters B, Sulzer D, Sette A, Lindestam Arlehamn CS. T Cell Responses to Neural Autoantigens Are Similar in Alzheimer's Disease Patients and Age-Matched Healthy Controls. Front Neurosci 2020; 14:874. [PMID: 32982670 PMCID: PMC7481378 DOI: 10.3389/fnins.2020.00874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/27/2020] [Indexed: 01/03/2023] Open
Abstract
Alzheimer's disease (AD), a chronic multifactorial and complex neurodegenerative disorder is a leading cause of dementia. Recently, neuroinflammation has been hypothesized as a contributing factor to AD pathogenesis. The role of adaptive immune responses against neuronal antigens, which can either confer protection or induce damage in AD, has not been fully characterized. Here, we measured T cell responses to several potential antigens of neural origin including amyloid precursor protein (APP), amyloid beta (Aβ), tau, α-synuclein, and transactive response DNA binding protein (TDP-43) in patients with AD and age-matched healthy controls (HC). Antigen-specific T cell reactivity was detected for all tested antigens, and response to tau-derived epitopes was particularly strong, but no significant differences between individuals with AD and age-matched HC were identified. We also did not observe any correlation between the antigen-specific T cell responses and clinical variables including age, gender, years since diagnosis and cognitive score. Additionally, further characterization did not reveal any differences in the relative frequency of major Peripheral Blood Mononuclear Cells (PBMC) subsets, or in the expression of genes between AD patients and HC. These observations have not identified a key role of neuronal antigen-specific T cell responses in AD.
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Affiliation(s)
- Rekha Dhanwani
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Atul Kumar
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Maria Elena Pero
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States.,Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Juliana Rezende Dutra
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
| | - Karen S Marder
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - David Sulzer
- Department of Neurology, New York State Psychiatric Institute, Columbia University, New York, NY, United States.,Department of Psychiatry and Pharmacology, New York State Psychiatric Institute, Columbia University, New York, NY, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California, San Diego, La Jolla, CA, United States
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26
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Srinivasan E, Rajasekaran R. A Systematic and Comprehensive Review on Disease-Causing Genes in Amyotrophic Lateral Sclerosis. J Mol Neurosci 2020; 70:1742-1770. [PMID: 32415434 DOI: 10.1007/s12031-020-01569-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and is characterized by degeneration and axon loss from the upper motor neuron, that descends from the lower motor neuron in the brain. Over the period, assorted outcomes from medical findings, molecular pathogenesis, and structural and biophysical studies have abetted in providing thoughtful insights underlying the importance of disease-causing genes in ALS. Consequently, numerous mechanisms were proposed for the pathogenesis of ALS, considering protein mutations, aggregation, and misfolding. Besides, the answers to the majority of ALS cases that happen to be sporadic still remain obscure. The application in discovering susceptibility factors in ALS contemplating the genetic factors is to be further dissevered in the future years with innovation in research studies. Hence, this review targets in revisiting the breakthroughs on the disease-causing genes related with ALS.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (deemed to be university), Vellore, Tamil Nadu, 632014, India
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (deemed to be university), Vellore, Tamil Nadu, 632014, India.
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27
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Chernoff YO, Grizel AV, Rubel AA, Zelinsky AA, Chandramowlishwaran P, Chernova TA. Application of yeast to studying amyloid and prion diseases. ADVANCES IN GENETICS 2020; 105:293-380. [PMID: 32560789 PMCID: PMC7527210 DOI: 10.1016/bs.adgen.2020.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyloids are fibrous cross-β protein aggregates that are capable of proliferation via nucleated polymerization. Amyloid conformation likely represents an ancient protein fold and is linked to various biological or pathological manifestations. Self-perpetuating amyloid-based protein conformers provide a molecular basis for transmissible (infectious or heritable) protein isoforms, termed prions. Amyloids and prions, as well as other types of misfolded aggregated proteins are associated with a variety of devastating mammalian and human diseases, such as Alzheimer's, Parkinson's and Huntington's diseases, transmissible spongiform encephalopathies (TSEs), amyotrophic lateral sclerosis (ALS) and transthyretinopathies. In yeast and fungi, amyloid-based prions control phenotypically detectable heritable traits. Simplicity of cultivation requirements and availability of powerful genetic approaches makes yeast Saccharomyces cerevisiae an excellent model system for studying molecular and cellular mechanisms governing amyloid formation and propagation. Genetic techniques allowing for the expression of mammalian or human amyloidogenic and prionogenic proteins in yeast enable researchers to capitalize on yeast advantages for characterization of the properties of disease-related proteins. Chimeric constructs employing mammalian and human aggregation-prone proteins or domains, fused to fluorophores or to endogenous yeast proteins allow for cytological or phenotypic detection of disease-related protein aggregation in yeast cells. Yeast systems are amenable to high-throughput screening for antagonists of amyloid formation, propagation and/or toxicity. This review summarizes up to date achievements of yeast assays in application to studying mammalian and human disease-related aggregating proteins, and discusses both limitations and further perspectives of yeast-based strategies.
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Affiliation(s)
- Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia.
| | - Anastasia V Grizel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Aleksandr A Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia; Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Sirius University of Science and Technology, Sochi, Russia
| | - Andrew A Zelinsky
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | | | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
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28
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Zhuo XF, Wang J, Zhang J, Jiang LL, Hu HY, Lu JX. Solid-State NMR Reveals the Structural Transformation of the TDP-43 Amyloidogenic Region upon Fibrillation. J Am Chem Soc 2020; 142:3412-3421. [PMID: 32003979 DOI: 10.1021/jacs.9b10736] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
TDP-43 is a primary pathological hallmark protein of amyotrophic lateral sclerosis and frontotemporal lobar degeneration, which may exist in the form of amyloid inclusions in the cells of patients. In addition to serving as a biomarker for these diseases, TDP-43 can also directly trigger neurodegeneration. We previously determined the amyloidogenic core region of TDP-43 (residues 311-360) and showed by solution NMR that this region includes two α-helices [(321-330) and (335-343)] in solution. We suggested that the helix-to-sheet structural transformation initiates TDP-43 aggregation. In the present study, X-ray diffraction shows that TDP-43 (311-360) aggregates adopt a cross-β structure. Thioredoxin (Trx)-fused TDP-43 (311-360) can undergo liquid-liquid phase separation (LLPS) before fibrillation, suggesting that phase separation is an intermediate step before amyloid formation. Solid-state NMR (SSNMR), carried out to elucidate the structural changes of TDP-43 (311-360) at the atomic level, indicates five β-strands of the amyloids formed, with the major two β-strands contributed by the first helical region in the solution structure. The NMR evidence is also in support of the fibril having a parallel in-register conformation, implying a mechanism in which the helix-helix interactions in LLPS are converted into β-strand parallel lateral association upon fibrillation. Our studies have assigned many key interresidue interactions that contribute to the stability of the fibril, including F316 with I318 and Q327 and W334 with A325, A326, A329, and S332. SSNMR with 1H detection reveals a unique close interaction between the indole Nε1-Hε1 of W334 and the side-chain carbonyl of Q343. This interaction could be a very important factor in initiating TDP-43 (311-360) folding/misfolding in LLPS.
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Affiliation(s)
- Xiao-Feng Zhuo
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Jian Wang
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China
| | - Jing Zhang
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031 , People's Republic of China
| | - Jun-Xia Lu
- School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , People's Republic of China
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29
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Shenoy J, El Mammeri N, Dutour A, Berbon M, Saad A, Lends A, Morvan E, Grélard A, Lecomte S, Kauffmann B, Theillet FX, Habenstein B, Loquet A. Structural dissection of amyloid aggregates of TDP-43 and its C-terminal fragments TDP-35 and TDP-16. FEBS J 2019; 287:2449-2467. [PMID: 31782904 DOI: 10.1111/febs.15159] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 10/17/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
Abstract
The TAR DNA-binding protein (TDP-43) self-assembles into prion-like aggregates considered to be the structural hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. Here, we use a combination of electron microscopy, X-ray fiber diffraction, Fourier-transform infrared spectroscopy analysis, and solid-state NMR spectroscopy to investigate the molecular organization of different TDP constructs, namely the full-length TDP-43 (1-414), two C-terminal fragments [TDP-35 (90-414) and TDP-16 (267-414)], and a C-terminal truncated fragment (TDP-43 ∆GaroS2), in their fibrillar state. Although the different protein constructs exhibit similar fibril morphology and a typical cross-β signature by X-ray diffraction, solid-state NMR indicates that TDP-43 and TDP-35 share the same polymorphic molecular structure, while TDP-16 encompasses a well-ordered amyloid core. We identified several residues in the so-called C-terminal GaroS2 (368-414) domain that participates in the rigid core of TDP-16 fibrils, underlining its importance during the aggregation process. Our findings demonstrate that C-terminal fragments can adopt a different molecular conformation in isolation or in the context of the full-length assembly, suggesting that the N-terminal domain and RRM domains play an important role in the TDP-43 amyloid transition.
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Affiliation(s)
- Jayakrishna Shenoy
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Nadia El Mammeri
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Antoine Dutour
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Mélanie Berbon
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Ahmad Saad
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Alons Lends
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Estelle Morvan
- Université de Bordeaux, CNRS, INSERM, UMS3033, Institut Européen de Chimie et Biologie (IECB), Pessac, France
| | - Axelle Grélard
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Sophie Lecomte
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Brice Kauffmann
- Université de Bordeaux, CNRS, INSERM, UMS3033, Institut Européen de Chimie et Biologie (IECB), Pessac, France
| | - François-Xavier Theillet
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Birgit Habenstein
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Antoine Loquet
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
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30
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François-Moutal L, Perez-Miller S, Scott DD, Miranda VG, Mollasalehi N, Khanna M. Structural Insights Into TDP-43 and Effects of Post-translational Modifications. Front Mol Neurosci 2019; 12:301. [PMID: 31920533 PMCID: PMC6934062 DOI: 10.3389/fnmol.2019.00301] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Transactive response DNA binding protein (TDP-43) is a key player in neurodegenerative diseases. In this review, we have gathered and presented structural information on the different regions of TDP-43 with high resolution structures available. A thorough understanding of TDP-43 structure, effect of modifications, aggregation and sites of localization is necessary as we develop therapeutic strategies targeting TDP-43 for neurodegenerative diseases. We discuss how different domains as well as post-translational modification may influence TDP-43 overall structure, aggregation and droplet formation. The primary aim of the review is to utilize structural insights as we develop an understanding of the deleterious behavior of TDP-43 and highlight locations of established and proposed post-translation modifications. TDP-43 structure and effect on localization is paralleled by many RNA-binding proteins and this review serves as an example of how structure may be modulated by numerous compounding elements.
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Affiliation(s)
- Liberty François-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Samantha Perez-Miller
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - David D Scott
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Victor G Miranda
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
| | - Niloufar Mollasalehi
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States.,Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, United States.,Center for Innovation in Brain Science, Tucson, AZ, United States
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31
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McAlary L, Plotkin SS, Yerbury JJ, Cashman NR. Prion-Like Propagation of Protein Misfolding and Aggregation in Amyotrophic Lateral Sclerosis. Front Mol Neurosci 2019; 12:262. [PMID: 31736708 PMCID: PMC6838634 DOI: 10.3389/fnmol.2019.00262] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/14/2019] [Indexed: 01/26/2023] Open
Abstract
The discovery that prion protein can misfold into a pathological conformation that encodes structural information capable of both propagation and inducing severe neuropathology has revolutionized our understanding of neurodegenerative disease. Many neurodegenerative diseases with a protein misfolding component are now classified as “prion-like” owing to the propagation of both symptoms and protein aggregation pathology in affected individuals. The neuromuscular disorder amyotrophic lateral sclerosis (ALS) is characterized by protein inclusions formed by either TAR DNA-binding protein of 43 kDa (TDP-43), Cu/Zn superoxide dismutase (SOD1), or fused in sarcoma (FUS), in both upper and lower motor neurons. Evidence from in vitro, cell culture, and in vivo studies has provided strong evidence to support the involvement of a prion-like mechanism in ALS. In this article, we review the evidence suggesting that prion-like propagation of protein aggregation is a primary pathomechanism in ALS, focusing on the key proteins and genes involved in disease (TDP-43, SOD1, FUS, and C9orf72). In each case, we discuss the evidence ranging from biophysical studies to in vivo examinations of prion-like spreading. We suggest that the idiopathic nature of ALS may stem from its prion-like nature and that elucidation of the specific propagating protein assemblies is paramount to developing effective therapies.
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Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada.,Genome Sciences and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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32
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Role of physical nucleation theory in understanding conformational conversion between pathogenic and nonpathogenic aggregates of low-complexity amyloid peptides. RESEARCH ON CHEMICAL INTERMEDIATES 2019. [DOI: 10.1007/s11164-019-03974-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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François-Moutal L, Felemban R, Scott DD, Sayegh MR, Miranda VG, Perez-Miller S, Khanna R, Gokhale V, Zarnescu DC, Khanna M. Small Molecule Targeting TDP-43's RNA Recognition Motifs Reduces Locomotor Defects in a Drosophila Model of Amyotrophic Lateral Sclerosis (ALS). ACS Chem Biol 2019; 14:2006-2013. [PMID: 31241884 DOI: 10.1021/acschembio.9b00481] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RNA dysregulation likely contributes to disease pathogenesis of amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. A pathological form of the transactive response (TAR) DNA binding protein (TDP-43) binds to RNA in stress granules and forms membraneless, amyloid-like TDP-43 aggregates in the cytoplasm of ALS motor neurons. In this study, we hypothesized that by targeting the RNA recognition motif (RRM) domains of TDP-43 that confer a pathogenic interaction between TDP-43 and RNA, motor neuron toxicity could be reduced. In silico docking of 50000 compounds to the RRM domains of TDP-43 identified a small molecule (rTRD01) that (i) bound to TDP-43's RRM1 and RRM2 domains, (ii) partially disrupted TDP-43's interaction with the hexanucleotide RNA repeat of the disease-linked c9orf72 gene, but not with (UG)6 canonical binding sequence of TDP-43, and (iii) improved larval turning, an assay measuring neuromuscular coordination and strength, in an ALS fly model based on the overexpression of mutant TDP-43. Our findings provide an instructive example of a chemical biology approach pivoted to discover small molecules targeting RNA-protein interactions in neurodegenerative diseases.
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Affiliation(s)
- Liberty François-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center for Innovation in Brain Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Razaz Felemban
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center for Innovation in Brain Science, University of Arizona, Tucson, Arizona 85721, United States
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard, Jeddah, Kingdom of Saudi Arabia
| | - David D. Scott
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center for Innovation in Brain Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Melissa R. Sayegh
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
- Department of Neuroscience, University of Arizona, Tucson, Arizona 85721, United States
- Department of Neurology, University of Arizona, Tucson Arizona 85721, United States
| | - Victor G. Miranda
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center for Innovation in Brain Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Samantha Perez-Miller
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center for Innovation in Brain Science, University of Arizona, Tucson, Arizona 85721, United States
| | - Rajesh Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
| | - Vijay Gokhale
- Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Daniela C. Zarnescu
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
- Department of Neuroscience, University of Arizona, Tucson, Arizona 85721, United States
- Department of Neurology, University of Arizona, Tucson Arizona 85721, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center for Innovation in Brain Science, University of Arizona, Tucson, Arizona 85721, United States
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34
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Bolognesi B, Faure AJ, Seuma M, Schmiedel JM, Tartaglia GG, Lehner B. The mutational landscape of a prion-like domain. Nat Commun 2019; 10:4162. [PMID: 31519910 PMCID: PMC6744496 DOI: 10.1038/s41467-019-12101-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/15/2019] [Indexed: 12/11/2022] Open
Abstract
Insoluble protein aggregates are the hallmarks of many neurodegenerative diseases. For example, aggregates of TDP-43 occur in nearly all cases of amyotrophic lateral sclerosis (ALS). However, whether aggregates cause cellular toxicity is still not clear, even in simpler cellular systems. We reasoned that deep mutagenesis might be a powerful approach to disentangle the relationship between aggregation and toxicity. We generated >50,000 mutations in the prion-like domain (PRD) of TDP-43 and quantified their toxicity in yeast cells. Surprisingly, mutations that increase hydrophobicity and aggregation strongly decrease toxicity. In contrast, toxic variants promote the formation of dynamic liquid-like condensates. Mutations have their strongest effects in a hotspot that genetic interactions reveal to be structured in vivo, illustrating how mutagenesis can probe the in vivo structures of unstructured proteins. Our results show that aggregation of TDP-43 is not harmful but protects cells, most likely by titrating the protein away from a toxic liquid-like phase. TDP43 aggregates are a hallmark of amyotrophic lateral sclerosis. By using deep mutagenesis to measure the toxicity of more than 50,000 mutations in the prion domain of TDP43, the authors conclude that mutations that increase toxicity promote formation of liquid-like condensates, while aggregation of TDP43 is protective for the cell.
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Affiliation(s)
- Benedetta Bolognesi
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003, Barcelona, Spain. .,Institute of Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Andre J Faure
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Mireia Seuma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003, Barcelona, Spain.,Institute of Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jörn M Schmiedel
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003, Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010, Barcelona, Spain.,Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy
| | - Ben Lehner
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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35
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Vega MV, Nigro A, Luti S, Capitini C, Fani G, Gonnelli L, Boscaro F, Chiti F. Isolation and characterization of soluble human full‐length TDP‐43 associated with neurodegeneration. FASEB J 2019; 33:10780-10793. [DOI: 10.1096/fj.201900474r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mirella Vivoli Vega
- Department of Experimental and Clinical Biomedical SciencesUniversity of FlorenceFlorenceItaly
| | - Alessia Nigro
- Department of Experimental and Clinical Biomedical SciencesUniversity of FlorenceFlorenceItaly
| | - Simone Luti
- Department of Experimental and Clinical Biomedical SciencesUniversity of FlorenceFlorenceItaly
| | - Claudia Capitini
- Department of Experimental and Clinical Biomedical SciencesUniversity of FlorenceFlorenceItaly
| | - Giulia Fani
- Department of Experimental and Clinical Biomedical SciencesUniversity of FlorenceFlorenceItaly
| | - Leonardo Gonnelli
- Centro di Ricerca di Risonanze Magnetiche (CERM)University of FlorenceFlorenceItaly
| | | | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical SciencesUniversity of FlorenceFlorenceItaly
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36
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Hong JY, Wang DD, Xue W, Yue HW, Yang H, Jiang LL, Wang WN, Hu HY. Structural and dynamic studies reveal that the Ala-rich region of ataxin-7 initiates α-helix formation of the polyQ tract but suppresses its aggregation. Sci Rep 2019; 9:7481. [PMID: 31097749 PMCID: PMC6522498 DOI: 10.1038/s41598-019-43926-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/04/2019] [Indexed: 11/26/2022] Open
Abstract
Ataxin-7 (Atx7) is a disease-related protein associated with the pathogenesis of spinocerebellar ataxia 7, while its polyglutamine (polyQ) tract in N-terminus is the causative source of aggregation and proteinopathy. We investigated the structure, dynamics and aggregation properties of the N-terminal 62-residue fragment of Atx7 (Atx7-N) by biochemical and biophysical approaches. The results showed that the normal Atx7-N with a tract of 10 glutamines (10Q) overall adopts a flexible and disordered structure, but it may contain a short or small population of helical structure in solution. PolyQ expansion increases the α-helical propensity of the polyQ tract and consequently enhances its transformation into β-sheet structures during amyloid aggregation. An alanine-rich region (ARR) just ahead of the polyQ tract forms a local and relatively stable α-helix. The ARR α-helix can initiate and stabilize helical formation of the following polyQ tract, but it may suppress aggregation of the polyQ-expanded Atx7-N both in vitro and in cell. Thus, the preceding ARR segment in Atx7-N may influence the dynamic structure and aggregation property of the polyQ tract and even determine the threshold of the pathogenic polyQ lengths. This study may gain structural and dynamic insights into amyloid aggregation of Atx7 and help us further understand the Atx7 proteinopathy based on polyQ expansion.
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Affiliation(s)
- Jun-Ye Hong
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Dong-Dong Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Wei Xue
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Hong-Wei Yue
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Hui Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China
| | - Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China
| | - Wen-Ning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, P.R. China.
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37
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Babinchak WM, Haider R, Dumm BK, Sarkar P, Surewicz K, Choi JK, Surewicz WK. The role of liquid-liquid phase separation in aggregation of the TDP-43 low-complexity domain. J Biol Chem 2019; 294:6306-6317. [PMID: 30814253 PMCID: PMC6484124 DOI: 10.1074/jbc.ra118.007222] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Pathological aggregation of the transactive response DNA-binding protein of 43 kDa (TDP-43) is associated with several neurodegenerative disorders, including ALS, frontotemporal dementia, chronic traumatic encephalopathy, and Alzheimer's disease. TDP-43 aggregation appears to be largely driven by its low-complexity domain (LCD), which also has a high propensity to undergo liquid-liquid phase separation (LLPS). However, the mechanism of TDP-43 LCD pathological aggregation and, most importantly, the relationship between the aggregation process and LLPS remains largely unknown. Here, we show that amyloid formation by the LCD is controlled by electrostatic repulsion. We also demonstrate that the liquid droplet environment strongly accelerates LCD fibrillation and that its aggregation under LLPS conditions involves several distinct events, culminating in rapid assembly of fibrillar aggregates that emanate from within mature liquid droplets. These combined results strongly suggest that LLPS may play a major role in pathological TDP-43 aggregation, contributing to pathogenesis in neurodegenerative diseases.
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Affiliation(s)
- W Michael Babinchak
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Raza Haider
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Benjamin K Dumm
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Prottusha Sarkar
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Krystyna Surewicz
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Jin-Kyu Choi
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Witold K Surewicz
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
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38
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Scott DD, Francois-Moutal L, Kumirov VK, Khanna M. 1H, 15N and 13C backbone assignment of apo TDP-43 RNA recognition motifs. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:163-167. [PMID: 30694439 DOI: 10.1007/s12104-018-09870-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/28/2018] [Indexed: 06/09/2023]
Abstract
TAR DNA-binding protein 43 (TDP-43) is a ubiquitously expressed nuclear protein that influences diverse cellular processes by regulating alternative splicing of RNA and microRNA biogenesis. It is also a pathological protein found in sporadic ALS and in the most common subtype of frontotemporal lobar degeneration with ubiquitinated inclusions (FLTD-U). TDP-43 has two tandem RNA-binding domains, RRM1 and RRM2. The NMR structure of TDP-43 was solved in the presence of UG-rich RNA sequences bound to the RRM1 and RRM2 domains. Here we report the backbone assignment of apo TDP-43. The chemical shift (HN, N, C, Cα and Cβ) analysis shows the predicted regions of secondary structure are in good agreement with those observed for TDP-43 in complex with RNA. However, our data show that the apo structure of TPD-43 has increased flexibility in the regions that would normally have been used to anchor the RNA bases. The backbone chemical shifts assignments will prove useful in the study of TDP-43 interaction with non-canonical RNA and RRM-binding proteins.
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Affiliation(s)
- David D Scott
- Department of Pharmacology, College of Medicine, University of Arizona, 1501 North Campbell Drive, P.O. Box 245050, Tucson, AZ, 85724, USA
- Center of Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Liberty Francois-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, 1501 North Campbell Drive, P.O. Box 245050, Tucson, AZ, 85724, USA
- Center of Innovation in Brain Science, Tucson, AZ, 85721, USA
| | - Vlad K Kumirov
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd, Tucson, AZ, 85721, USA.
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, 1501 North Campbell Drive, P.O. Box 245050, Tucson, AZ, 85724, USA.
- Center of Innovation in Brain Science, Tucson, AZ, 85721, USA.
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39
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Prasad A, Bharathi V, Sivalingam V, Girdhar A, Patel BK. Molecular Mechanisms of TDP-43 Misfolding and Pathology in Amyotrophic Lateral Sclerosis. Front Mol Neurosci 2019; 12:25. [PMID: 30837838 PMCID: PMC6382748 DOI: 10.3389/fnmol.2019.00025] [Citation(s) in RCA: 428] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/21/2019] [Indexed: 12/11/2022] Open
Abstract
TAR DNA binding protein 43 (TDP-43) is a versatile RNA/DNA binding protein involved in RNA-related metabolism. Hyper-phosphorylated and ubiquitinated TDP-43 deposits act as inclusion bodies in the brain and spinal cord of patients with the motor neuron diseases: amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). While the majority of ALS cases (90-95%) are sporadic (sALS), among familial ALS cases 5-10% involve the inheritance of mutations in the TARDBP gene and the remaining (90-95%) are due to mutations in other genes such as: C9ORF72, SOD1, FUS, and NEK1 etc. Strikingly however, the majority of sporadic ALS patients (up to 97%) also contain the TDP-43 protein deposited in the neuronal inclusions, which suggests of its pivotal role in the ALS pathology. Thus, unraveling the molecular mechanisms of the TDP-43 pathology seems central to the ALS therapeutics, hence, we comprehensively review the current understanding of the TDP-43's pathology in ALS. We discuss the roles of TDP-43's mutations, its cytoplasmic mis-localization and aberrant post-translational modifications in ALS. Also, we evaluate TDP-43's amyloid-like in vitro aggregation, its physiological vs. pathological oligomerization in vivo, liquid-liquid phase separation (LLPS), and potential prion-like propagation propensity of the TDP-43 inclusions. Finally, we describe the various evolving TDP-43-induced toxicity mechanisms, such as the impairment of endocytosis and mitotoxicity etc. and also discuss the emerging strategies toward TDP-43 disaggregation and ALS therapeutics.
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Affiliation(s)
| | | | | | | | - Basant K. Patel
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, India
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40
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Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation. Nat Struct Mol Biol 2018; 25:463-471. [PMID: 29786080 PMCID: PMC5990464 DOI: 10.1038/s41594-018-0064-2] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 04/09/2018] [Indexed: 12/14/2022]
Abstract
The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation.
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41
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Zhang K, Coyne AN, Lloyd TE. Drosophila models of amyotrophic lateral sclerosis with defects in RNA metabolism. Brain Res 2018; 1693:109-120. [PMID: 29752901 DOI: 10.1016/j.brainres.2018.04.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022]
Abstract
The fruit fly Drosophila Melanogaster has been widely used to study neurodegenerative diseases. The conservation of nervous system biology coupled with the rapid life cycle and powerful genetic tools in the fly have enabled the identification of novel therapeutic targets that have been validated in vertebrate model systems and human patients. A recent example is in the study of the devastating motor neuron degenerative disease amyotrophic lateral sclerosis (ALS). Mutations in genes that regulate RNA metabolism are a major cause of inherited ALS, and functional analysis of these genes in the fly nervous system has shed light on how mutations cause disease. Importantly, unbiased genetic screens have identified key pathways that contribute to ALS pathogenesis such as nucleocytoplasmic transport and stress granule assembly. In this review, we will discuss the utilization of Drosophila models of ALS with defects in RNA metabolism.
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Affiliation(s)
- Ke Zhang
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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42
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Guenther EL, Ge P, Trinh H, Sawaya MR, Cascio D, Boyer DR, Gonen T, Zhou ZH, Eisenberg DS. Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2. Nat Struct Mol Biol 2018. [PMID: 29531287 DOI: 10.1038/s41594-018-0045-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that the 247DLIIKGISVHI257 segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. Additionally, we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.
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Affiliation(s)
- Elizabeth L Guenther
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peng Ge
- Electron Imaging Center for Nanomachines, California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hamilton Trinh
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - Michael R Sawaya
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Duilio Cascio
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - David R Boyer
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Z Hong Zhou
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Electron Imaging Center for Nanomachines, California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - David S Eisenberg
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA. .,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, CA, USA. .,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.
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43
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Bräuer S, Zimyanin V, Hermann A. Prion-like properties of disease-relevant proteins in amyotrophic lateral sclerosis. J Neural Transm (Vienna) 2018; 125:591-613. [PMID: 29417336 DOI: 10.1007/s00702-018-1851-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/30/2018] [Indexed: 02/07/2023]
Abstract
The hallmark of age-related neurodegenerative diseases is the appearance of cellular protein deposits and spreading of this pathology throughout the central nervous system. Growing evidence has shown the involvement and critical role of proteins with prion-like properties in the formation of these characteristic cellular aggregates. Prion-like domains of such proteins with their proposed function in the organization of membraneless organelles are prone for misfolding and promoting further aggregation. Spreading of these toxic aggregates between cells and across tissues can explain the progression of clinical phenotypes and pathology in a stereotypical manner, characteristic for almost every neurodegenerative disease. Here, we want to review the current evidence for the role of prion-like mechanisms in classical neurodegenerative diseases and ALS in particular. We will also discuss an intriguingly central role of the protein TDP-43 in the majority of cases of this devastating disease.
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Affiliation(s)
- S Bräuer
- Department of Neurology, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
- Department of Neurology, Städtisches Klinikum Dresden, 01129, Dresden, Germany
| | - V Zimyanin
- Department of Neurology, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - A Hermann
- Department of Neurology, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden and German Center for Neurodegenerative Diseases (DZNE), 01307, Dresden, Germany.
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44
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Li HR, Chen TC, Hsiao CL, Shi L, Chou CY, Huang JR. The physical forces mediating self-association and phase-separation in the C-terminal domain of TDP-43. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:214-223. [PMID: 28988034 DOI: 10.1016/j.bbapap.2017.10.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/22/2017] [Accepted: 10/02/2017] [Indexed: 12/14/2022]
Abstract
The TAR DNA-binding protein of 43kDa (TDP-43) has been identified as the main component of amyotrophic lateral sclerosis (ALS) cytoplasmic inclusions. The link between this proteinopathy and TDP-43's intrinsically disordered C-terminal domain is well known, but recently also, this domain has been shown to be involved in the formation of the membraneless organelles that mediate TDP-43's functions. The mechanisms that underpin the liquid-liquid phase separation (LLPS) of these membraneless organelles undergo remain elusive. Crucially though, these factors may be the key to understanding the delicate balance between TDP-43's physiological and pathological functions. In this study, we used nuclear magnetic resonance spectroscopy and optical methods to demonstrate that an α-helical component in the centre (residues 320-340) of the C-terminal domain is related to the protein's self-association and LLPS. Systematically analysing ALS-related TDP-43 mutants (G298S, M337V, and Q331K) in different buffer conditions at different temperatures, we prove that this phase separation is driven by hydrophobic interactions but is inhibited by electrostatic repulsion. Based on these findings, we rationally introduced a mutant, W334G, and demonstrate that this mutant disrupts LLPS without disturbing this α-helical propensity. This tryptophan may serve as a key residue in this protein's LLPS.
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Affiliation(s)
- Hao-Ru Li
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Tsai-Chen Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Chih-Lun Hsiao
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Lin Shi
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Chi-Yuan Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan.
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45
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Tsoi PS, Choi K, Leonard PG, Sizovs A, Moosa MM, MacKenzie KR, Ferreon JC, Ferreon ACM. The N‐Terminal Domain of ALS‐Linked TDP‐43 Assembles without Misfolding. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Phoebe S. Tsoi
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Kyoung‐Jae Choi
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Paul G. Leonard
- Department of Genomic Medicine and Core for Biomolecular Structure and Function University of Texas MD Anderson Cancer Center Houston TX USA
| | - Antons Sizovs
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Kevin R. MacKenzie
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
- Department of Pathology and Immunology Baylor College of Medicine Houston TX USA
| | - Josephine C. Ferreon
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Allan Chris M. Ferreon
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
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46
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Tsoi PS, Choi KJ, Leonard PG, Sizovs A, Moosa MM, MacKenzie KR, Ferreon JC, Ferreon ACM. The N-Terminal Domain of ALS-Linked TDP-43 Assembles without Misfolding. Angew Chem Int Ed Engl 2017; 56:12590-12593. [PMID: 28833982 DOI: 10.1002/anie.201706769] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/08/2017] [Indexed: 12/28/2022]
Abstract
Transactivation response element (TAR) DNA-binding protein 43 (TDP-43) misfolding is implicated in several neurodegenerative diseases characterized by aggregated protein inclusions. Misfolding is believed to be mediated by both the N- and C-terminus of TDP-43; however, the mechanistic basis of the contribution of individual domains in the process remained elusive. Here, using single-molecule fluorescence and ensemble biophysical techniques, and a wide range of pH and temperature conditions, we show that TDP-43NTD is thermodynamically stable, well-folded and undergoes reversible oligomerization. We propose that, in full-length TDP-43, association between folded N-terminal domains enhances the propensity of the intrinsically unfolded C-terminal domains to drive pathological aggregation.
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Affiliation(s)
- Phoebe S Tsoi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kyoung-Jae Choi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Paul G Leonard
- Department of Genomic Medicine and Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Antons Sizovs
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin R MacKenzie
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
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47
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Coyne AN, Zaepfel BL, Zarnescu DC. Failure to Deliver and Translate-New Insights into RNA Dysregulation in ALS. Front Cell Neurosci 2017; 11:243. [PMID: 28860970 PMCID: PMC5562674 DOI: 10.3389/fncel.2017.00243] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/31/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive and fatal neurodegenerative disease affecting both upper and lower motor neurons. The molecular mechanisms underlying disease pathogenesis remain largely unknown. Multiple genetic loci including genes involved in proteostasis and ribostasis have been linked to ALS providing key insights into the molecular mechanisms underlying disease. In particular, the identification of the RNA binding proteins TDP-43 and fused in sarcoma (FUS) as causative factors of ALS resulted in a paradigm shift centered on the study of RNA dysregulation as a major mechanism of disease. With wild-type TDP-43 pathology being found in ~97% of ALS cases and the identification of disease causing mutations within its sequence, TDP-43 has emerged as a prominent player in ALS. More recently, studies of the newly discovered C9orf72 repeat expansion are lending further support to the notion of defects in RNA metabolism as a key factor underlying ALS. RNA binding proteins are involved in all aspects of RNA metabolism ranging from splicing, transcription, transport, storage into RNA/protein granules, and translation. How these processes are affected by disease-associated mutations is just beginning to be understood. Considerable work has gone into the identification of splicing and transcription defects resulting from mutations in RNA binding proteins associated with disease. More recently, defects in RNA transport and translation have been shown to be involved in the pathomechanism of ALS. A central hypothesis in the field is that disease causing mutations lead to the persistence of RNA/protein complexes known as stress granules. Under times of prolonged cellular stress these granules sequester specific mRNAs preventing them from translation, and are thought to evolve into pathological aggregates. Here we will review recent efforts directed at understanding how altered RNA metabolism contributes to ALS pathogenesis.
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Affiliation(s)
- Alyssa N Coyne
- Department of Molecular and Cellular Biology, University of ArizonaTucson, AZ, United States.,Department of Neuroscience, University of ArizonaTucson, AZ, United States
| | - Benjamin L Zaepfel
- Department of Molecular and Cellular Biology, University of ArizonaTucson, AZ, United States
| | - Daniela C Zarnescu
- Department of Molecular and Cellular Biology, University of ArizonaTucson, AZ, United States.,Department of Neuroscience, University of ArizonaTucson, AZ, United States.,Department of Neurology, University of ArizonaTucson, AZ, United States
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48
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An Introduction to Infinite HMMs for Single-Molecule Data Analysis. Biophys J 2017; 112:2021-2029. [PMID: 28538142 DOI: 10.1016/j.bpj.2017.04.027] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/01/2017] [Accepted: 04/20/2017] [Indexed: 12/19/2022] Open
Abstract
The hidden Markov model (HMM) has been a workhorse of single-molecule data analysis and is now commonly used as a stand-alone tool in time series analysis or in conjunction with other analysis methods such as tracking. Here, we provide a conceptual introduction to an important generalization of the HMM, which is poised to have a deep impact across the field of biophysics: the infinite HMM (iHMM). As a modeling tool, iHMMs can analyze sequential data without a priori setting a specific number of states as required for the traditional (finite) HMM. Although the current literature on the iHMM is primarily intended for audiences in statistics, the idea is powerful and the iHMM's breadth in applicability outside machine learning and data science warrants a careful exposition. Here, we explain the key ideas underlying the iHMM, with a special emphasis on implementation, and provide a description of a code we are making freely available. In a companion article, we provide an important extension of the iHMM to accommodate complications such as drift.
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49
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Garnier C, Devred F, Byrne D, Puppo R, Roman AY, Malesinski S, Golovin AV, Lebrun R, Ninkina NN, Tsvetkov PO. Zinc binding to RNA recognition motif of TDP-43 induces the formation of amyloid-like aggregates. Sci Rep 2017; 7:6812. [PMID: 28754988 PMCID: PMC5533730 DOI: 10.1038/s41598-017-07215-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/23/2017] [Indexed: 12/12/2022] Open
Abstract
Aggregation of TDP-43 (transactive response DNA binding protein 43 kDa) is a hallmark of certain forms of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Moreover, intracellular TDP-43-positive inclusions are often found in other neurodegenerative diseases. Recently it was shown that zinc ions can provoke the aggregation of endogenous TDP-43 in cells, allowing to assume a direct interaction of TDP-43 with zinc ions. In this work, we investigated zinc binding to the 102-269 TDP-43 fragment, which comprise the two RNA recognition motifs. Using isothermal titration calorimetry, mass spectrometry, and differential scanning fluorimetry, we showed that zinc binds to this TDP-43 domain with a dissociation constant in the micromolar range and modifies its tertiary structure leading to a decrease of its thermostability. Moreover, the study by dynamic light scattering and negative stain electron microscopy demonstrated that zinc ions induce auto-association process of this TDP-43 fragment into rope-like structures. These structures are thioflavin-T-positive allowing to hypothesize the direct implication of zinc ions in pathological aggregation of TDP-43.
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Affiliation(s)
- Cyrille Garnier
- Mécanismes Moléculaires dans les Démences Neurodégénératives, Université de Montpellier, EPHE, INSERM, U1198, F-34095, Montpellier, France
- Université de Rennes 1, Campus de Beaulieu, 35042, Rennes cedex, France
| | - François Devred
- Aix-Marseille Univ, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
| | - Deborah Byrne
- Institut de Microbiologie de la Méditerranée, CNRS, FR3479, Aix-Marseille Université, Marseille, France
| | - Rémy Puppo
- Institut de Microbiologie de la Méditerranée, CNRS, FR3479, Aix-Marseille Université, Marseille, France
| | - Andrei Yu Roman
- Aix-Marseille Univ, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
- Institute of Physiologically Active Compounds, RAS, 142432, Chernogolovka, Russian Federation
| | - Soazig Malesinski
- Aix-Marseille Univ, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France
| | - Andrey V Golovin
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Régine Lebrun
- Institut de Microbiologie de la Méditerranée, CNRS, FR3479, Aix-Marseille Université, Marseille, France
| | - Natalia N Ninkina
- Institute of Physiologically Active Compounds, RAS, 142432, Chernogolovka, Russian Federation.
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Philipp O Tsvetkov
- Aix-Marseille Univ, Inserm, CRO2 UMR_S 911, Faculté de Pharmacie, 13385, Marseille, France.
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50
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Jiang LL, Xue W, Hong JY, Zhang JT, Li MJ, Yu SN, He JH, Hu HY. The N-terminal dimerization is required for TDP-43 splicing activity. Sci Rep 2017; 7:6196. [PMID: 28733604 PMCID: PMC5522446 DOI: 10.1038/s41598-017-06263-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/08/2017] [Indexed: 12/12/2022] Open
Abstract
TDP-43 is a nuclear factor that functions in promoting pre-mRNA splicing. Deletion of the N-terminal domain (NTD) and nuclear localization signal (NLS) (i.e., TDP-35) results in mislocalization to cytoplasm and formation of inclusions. However, how the NTD functions in TDP-43 activity and proteinopathy remains largely unknown. Here, we studied the structure and function of the NTD in inclusion formation and pre-mRNA splicing of TDP-43 by using biochemical and biophysical approaches. We found that TDP-43 NTD forms a homodimer in solution in a concentration-dependent manner, and formation of intermolecular disulfide results in further tetramerization. Based on the NMR structure of TDP-43 NTD, the dimerization interface centered on Leu71 and Val72 around the β7-strand was defined by mutagenesis and size-exclusion chromatography. Cell experiments revealed that the N-terminal dimerization plays roles in protecting TDP-43 against formation of cytoplasmic inclusions and enhancing pre-mRNA splicing activity of TDP-43 in nucleus. This study may provide mechanistic insights into the physiological function of TDP-43 and its related proteinopathies.
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Affiliation(s)
- Lei-Lei Jiang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R. China
| | - Wei Xue
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R. China
| | - Jun-Ye Hong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R. China
| | - Jun-Ting Zhang
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
| | - Min-Jun Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai, 201204, P.R. China
| | - Shao-Ning Yu
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai, 201204, P.R. China
| | - Hong-Yu Hu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, P.R. China.
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