101
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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: 47] [Impact Index Per Article: 6.7] [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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102
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Biology and Pathobiology of TDP-43 and Emergent Therapeutic Strategies. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a024554. [PMID: 27920024 DOI: 10.1101/cshperspect.a024554] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cytoplasmic TDP-43 mislocalization and aggregation is a pathological hallmark of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. TDP-43 is an RNA-binding protein (RBP) with a prion-like domain (PrLD) that promotes TDP-43 misfolding. PrLDs possess compositional similarity to canonical prion domains of various yeast proteins, including Sup35. Strikingly, disease-causing TDP-43 mutations reside almost exclusively in the PrLD and can enhance TDP-43 misfolding and toxicity. Another ∼70 human RBPs harbor PrLDs, including FUS, TAF15, EWSR1, hnRNPA1, and hnRNPA2, which have surfaced in the etiology of neurodegenerative diseases. Importantly, PrLDs enable RBP function and mediate phase transitions that partition functional ribonucleoprotein compartments. This PrLD activity, however, renders RBPs prone to populating deleterious oligomers or self-templating fibrils that might spread disease, and disease-linked PrLD mutations can exacerbate this risk. Several strategies have emerged to counter TDP-43 proteinopathies, including engineering enhanced protein disaggregases based on Hsp104.
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103
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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: 71] [Impact Index Per Article: 10.1] [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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104
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Mompeán M, Romano V, Pantoja-Uceda D, Stuani C, Baralle FE, Buratti E, Laurents DV. Point mutations in the N-terminal domain of transactive response DNA-binding protein 43 kDa (TDP-43) compromise its stability, dimerization, and functions. J Biol Chem 2017; 292:11992-12006. [PMID: 28566288 PMCID: PMC5512090 DOI: 10.1074/jbc.m117.775965] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/25/2017] [Indexed: 12/14/2022] Open
Abstract
Transactive response DNA-binding protein 43 (TDP-43) performs multiple tasks in mRNA processing, transport, and translational regulation, but it also forms aggregates implicated in amyotrophic lateral sclerosis. TDP-43's N-terminal domain (NTD) is important for these activities and dysfunctions; however, there is an open debate about whether or not it adopts a specifically folded, stable structure. Here, we studied NTD mutations designed to destabilize its structure utilizing NMR and fluorescence spectroscopies, analytical ultracentrifugation, splicing assays, and cell microscopy. The substitutions V31R and T32R abolished TDP-43 activity in splicing and aggregation processes, and even the rather mild L28A mutation severely destabilized the NTD, drastically reducing TDP-43's in vitro splicing activity and inducing aberrant localization and aggregation in cells. These findings strongly support the idea that a stably folded NTD is essential for correct TDP-43 function. The stably folded NTD also promotes dimerization, which is pertinent to the protein's activities and pathological aggregation, and we present an atomic-level structural model for the TDP-43 dimer based on NMR data. Leu-27 is evolutionarily well conserved even though it is exposed in the monomeric NTD. We found here that Leu-27 is buried in the dimer and that the L27A mutation promotes monomerization. In conclusion, our study sheds light on the structural and biological properties of the TDP-43 NTD, indicating that the NTD must be stably folded for TDP-43's physiological functions, and has implications for understanding the mechanisms promoting the pathological aggregation of this protein.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain
| | - Valentina Romano
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - David Pantoja-Uceda
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, I-34149 Trieste, Italy.
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, E-28006 Madrid, Spain.
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105
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Afroz T, Hock EM, Ernst P, Foglieni C, Jambeau M, Gilhespy LAB, Laferriere F, Maniecka Z, Plückthun A, Mittl P, Paganetti P, Allain FHT, Polymenidou M. Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation. Nat Commun 2017; 8:45. [PMID: 28663553 PMCID: PMC5491494 DOI: 10.1038/s41467-017-00062-0] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/02/2017] [Indexed: 01/28/2023] Open
Abstract
TDP-43 is a primarily nuclear RNA-binding protein, whose abnormal phosphorylation and cytoplasmic aggregation characterizes affected neurons in patients with amyotrophic lateral sclerosis and frontotemporal dementia. Here, we report that physiological nuclear TDP-43 in mouse and human brain forms homo-oligomers that are resistant to cellular stress. Physiological TDP-43 oligomerization is mediated by its N-terminal domain, which can adopt dynamic, solenoid-like structures, as revealed by a 2.1 Å crystal structure in combination with nuclear magnetic resonance spectroscopy and electron microscopy. These head-to-tail TDP-43 oligomers are unique among known RNA-binding proteins and represent the functional form of the protein in vivo, since their destabilization results in loss of alternative splicing regulation of known neuronal RNA targets. Our findings indicate that N-terminal domain-driven oligomerization spatially separates the adjoining highly aggregation-prone, C-terminal low-complexity domains of consecutive TDP-43 monomers, thereby preventing low-complexity domain inter-molecular interactions and antagonizing the formation of pathologic aggregates.TDP-43 aggregation is observed in amyotrophic lateral sclerosis. Here the authors combine X-ray crystallography, nuclear magnetic resonance and electron microscopy studies and show that physiological oligomerization of TDP-43 is mediated through its N-terminal domain, which forms functional and dynamic oligomers antagonizing pathologic aggregation.
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Affiliation(s)
- Tariq Afroz
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Eva-Maria Hock
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Chiara Foglieni
- Laboratory for Biomedical Neurosciences, Neurocenter of Southern Switzerland, Via Tesserete 46, CH-6900, Lugano, Switzerland
| | - Melanie Jambeau
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Larissa A B Gilhespy
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Florent Laferriere
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Zuzanna Maniecka
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Peer Mittl
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Paolo Paganetti
- Laboratory for Biomedical Neurosciences, Neurocenter of Southern Switzerland, Via Tesserete 46, CH-6900, Lugano, Switzerland
| | - Frédéric H T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Magdalini Polymenidou
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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106
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Hock EM, Polymenidou M. Prion-like propagation as a pathogenic principle in frontotemporal dementia. J Neurochem 2017; 138 Suppl 1:163-83. [PMID: 27502124 PMCID: PMC6680357 DOI: 10.1111/jnc.13668] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/22/2016] [Accepted: 05/11/2016] [Indexed: 12/12/2022]
Abstract
Frontotemporal dementia is a devastating neurodegenerative disease causing stark alterations in personality and language. Characterized by severe atrophy of the frontal and temporal brain lobes, frontotemporal dementia (FTD) shows extreme heterogeneity in clinical presentation, genetic causes, and pathological findings. Like most neurodegenerative diseases, the initial symptoms of FTD are subtle, but increase in severity over time, as the disease progresses. Clinical progression is paralleled by exacerbation of pathological findings and the involvement of broader brain regions, which currently lack mechanistic explanation. Yet, a flurry of studies indicate that protein aggregates accumulating in neurodegenerative diseases can act as propagating entities, amplifying their pathogenic conformation, in a way similar to infectious prions. In this prion‐centric view, FTD can be divided into three subtypes, TDP‐43 or FUS proteinopathy and tauopathy. Here, we review the current evidence that FTD‐linked pathology propagates in a prion‐like manner and discuss the implications of these findings for disease progression and heterogeneity.
Frontotemporal dementia (FTD) is a progressive neurodegenerative disease causing severe personality dysfunctions, characterized by profound heterogeneity. Accumulation of tau, TDP‐43 or FUS cytoplasmic aggregates characterize molecularly distinct and non‐overlapping FTD subtypes. Here, we discuss the current evidence suggesting that prion‐like propagation and cell‐to‐cell spread of each of these cytoplasmic aggregates may underlie disease progression and heterogeneity.
This article is part of the Frontotemporal Dementia special issue.
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Affiliation(s)
- Eva-Maria Hock
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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107
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Gu J, Chen F, Iqbal K, Gong CX, Wang X, Liu F. Transactive response DNA-binding protein 43 (TDP-43) regulates alternative splicing of tau exon 10: Implications for the pathogenesis of tauopathies. J Biol Chem 2017; 292:10600-10612. [PMID: 28487370 DOI: 10.1074/jbc.m117.783498] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/08/2017] [Indexed: 12/14/2022] Open
Abstract
Hyperphosphorylation and aggregation of the neuronal protein tau are responsible for neurodegenerative diseases called tauopathies. Dysregulation of the alternative splicing of tau exon 10 results in alterations of the ratio of two tau isoforms, 3R-tau and 4R-tau, which have been seen in several tauopathies. Transactive response DNA-binding protein of 43 kDa (TDP-43) is involved in the regulation of RNA processing, including splicing. Cytoplasmic aggregation of TDP-43 has been observed in the brains of individuals with chronic traumatic encephalopathy or Alzheimer's disease, diseases in which neurofibrillary tangles of hyperphosphorylated tau are hallmarks. Here, we investigated the role of TDP-43 in tau exon 10 splicing. We found that TDP-43 promoted tau exon 10 inclusion, which increased production of the 4R-tau isoform. Moreover, TDP-43 could bind to intron 9 of tau pre-mRNA. Deletion of the TDP-43 N or C terminus promoted its cytoplasmic aggregation and abolished or diminished TDP-43-promoted tau exon 10 inclusion. Several TDP-43 mutations associated with amyotrophic lateral sclerosis or frontotemporal lobar degeneration with ubiquitin inclusions promoted tau exon 10 inclusion more effectively than wild-type TDP-43 but did not affect TDP-43 cytoplasmic aggregation in cultured cells. The ratio of 3R-tau/4R-tau was decreased in transgenic mouse brains expressing human TDP-43 and increased in the brains expressing the disease-causing mutation TDP-43M337V, in which cytoplasmic TDP-43 was increased. These findings suggest that TDP-43 promotes tau exon 10 inclusion and 4R-tau expression and that disease-related changes of TDP-43, truncations and mutations, affect its function in tau exon 10 splicing, possibly because of TDP-43 mislocalization to the cytoplasm.
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Affiliation(s)
- Jianlan Gu
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration and.,Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, and.,Department of Biochemistry and Molecular Biology, School of Medicine, Nantong University, Nantong, Jiangsu 226001, China
| | - Feng Chen
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration and.,Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, and
| | - Khalid Iqbal
- Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, and
| | - Cheng-Xin Gong
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration and.,Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, and
| | - Xinglong Wang
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Fei Liu
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration and .,Department of Neurochemistry, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York 10314, and
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108
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Ishiguro T, Sato N, Ueyama M, Fujikake N, Sellier C, Kanegami A, Tokuda E, Zamiri B, Gall-Duncan T, Mirceta M, Furukawa Y, Yokota T, Wada K, Taylor JP, Pearson CE, Charlet-Berguerand N, Mizusawa H, Nagai Y, Ishikawa K. Regulatory Role of RNA Chaperone TDP-43 for RNA Misfolding and Repeat-Associated Translation in SCA31. Neuron 2017; 94:108-124.e7. [PMID: 28343865 PMCID: PMC5681996 DOI: 10.1016/j.neuron.2017.02.046] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/04/2016] [Accepted: 02/24/2017] [Indexed: 12/20/2022]
Abstract
Microsatellite expansion disorders are pathologically characterized by RNA foci formation and repeat-associated non-AUG (RAN) translation. However, their underlying pathomechanisms and regulation of RAN translation remain unknown. We report that expression of expanded UGGAA (UGGAAexp) repeats, responsible for spinocerebellar ataxia type 31 (SCA31) in Drosophila, causes neurodegeneration accompanied by accumulation of UGGAAexp RNA foci and translation of repeat-associated pentapeptide repeat (PPR) proteins, consistent with observations in SCA31 patient brains. We revealed that motor-neuron disease (MND)-linked RNA-binding proteins (RBPs), TDP-43, FUS, and hnRNPA2B1, bind to and induce structural alteration of UGGAAexp. These RBPs suppress UGGAAexp-mediated toxicity in Drosophila by functioning as RNA chaperones for proper UGGAAexp folding and regulation of PPR translation. Furthermore, nontoxic short UGGAA repeat RNA suppressed mutated RBP aggregation and toxicity in MND Drosophila models. Thus, functional crosstalk of the RNA/RBP network regulates their own quality and balance, suggesting convergence of pathomechanisms in microsatellite expansion disorders and RBP proteinopathies.
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Affiliation(s)
- Taro Ishiguro
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan; Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan; Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Nozomu Sato
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan; Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Morio Ueyama
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan; Department of Neurotherapeutics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobuhiro Fujikake
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Chantal Sellier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, University of Strasbourg, Illkirch 67400, France
| | - Akemi Kanegami
- Research Institute of Biomolecule Metrology, 807-133 Enokido, Tsukuba, Ibaraki 305-0853, Japan
| | - Eiichi Tokuda
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Yokohama, Kanagawa 223-8522, Japan
| | - Bita Zamiri
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; Department of Genetics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Terence Gall-Duncan
- Department of Genetics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Mila Mirceta
- Department of Genetics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Yoshiaki Furukawa
- Department of Chemistry, Keio University, 3-14-1 Hiyoshi, Yokohama, Kanagawa 223-8522, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan; Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Keiji Wada
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - J Paul Taylor
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher E Pearson
- Department of Genetics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, University of Strasbourg, Illkirch 67400, France
| | - Hidehiro Mizusawa
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan; Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan; Department of Neurotherapeutics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kinya Ishikawa
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan; Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan; Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8519, Japan.
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109
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Abstract
TDP-43 is a dimeric nuclear protein that plays a central role in RNA metabolism. In recent years, this protein has become a focal point of research in the amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD) disease spectrum, as pathognomonic inclusions within affected neurons contain post-translationally modified TDP-43. A key question in TDP-43 research involves determining the mechanisms and triggers that cause TDP-43 to form pathological aggregates. This review gives a brief overview of the physiological and pathological roles of TDP-43 and focuses on the structural features of its protein domains and how they may contribute to normal protein function and to disease. A special emphasis is placed on the C-terminal prion-like region thought to be implicated in pathology, as it is where nearly all ALS/FTD-associated mutations reside. Recent structural studies of this domain revealed its crucial role in the formation of phase-separated liquid droplets through a partially populated α-helix. This new discovery provides further support for the theory that liquid droplets such as stress granules may be precursors to pathological aggregates, linking environmental effects such as stress to the potential etiology of the disease. The transition of TDP-43 among soluble, droplet, and aggregate phases and the implications of these transitions for pathological aggregation are summarized and discussed.
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Affiliation(s)
- Yulong Sun
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G1L7, Canada
| | - Avijit Chakrabartty
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G1L7, Canada.,Department of Biochemistry, University of Toronto , Toronto, Ontario M5G1L7, Canada
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110
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Rossi S, Cozzolino M, Carrì MT. Old versus New Mechanisms in the Pathogenesis of ALS. Brain Pathol 2016; 26:276-86. [PMID: 26779612 DOI: 10.1111/bpa.12355] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/14/2016] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is recognized as a very complex disease. As we have learned in the past 20 years from studies in patients and in models based on the expression of mutant SOD1, ALS is not a purely motor neuron disease as previously thought. While undoubtedly motor neurons are lost in patients, a number of alterations in those cell-types that interact functionally with motor neurons (astrocytes, microglia, muscle fibers, oligodendrocytes) take place even long before onset of symptoms. At the same time, disturbance of several, only partly inter-related physiological functions play some role in the onset and progression of the disease. Traditionally, mitochondrial damage and oxidative stress, excitotoxicity, neuroinflammation, altered axonal transport, ER stress, protein aggregation and defective removal of toxic proteins have been considered as key factors in the pathogenesis of ALS, with the relatively recent addition of disturbances in RNA metabolism. This complexity makes the search for an effective treatment extremely difficult and prompts further studies to reveal other possible, previously unappreciated aspects of the pathogenesis of ALS. In this review, we focus on previous knowledge on ALS mechanisms as well as new facets emerging from studies on genetic ALS patients and models that may both provide precious information for a novel therapeutic approach.
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Affiliation(s)
- Simona Rossi
- Institute of Translational Pharmacology, National Research Council (CNR), Rome, Italy
| | - Mauro Cozzolino
- Institute of Translational Pharmacology, National Research Council (CNR), Rome, Italy.,Lab of Neurochemistry, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Maria Teresa Carrì
- Lab of Neurochemistry, Fondazione Santa Lucia IRCCS, Rome, Italy.,Department of Biology, University of Rome Tor Vergata
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111
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Mompeán M, Baralle M, Buratti E, Laurents DV. An Amyloid-Like Pathological Conformation of TDP-43 Is Stabilized by Hypercooperative Hydrogen Bonds. Front Mol Neurosci 2016; 9:125. [PMID: 27909398 PMCID: PMC5112254 DOI: 10.3389/fnmol.2016.00125] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/04/2016] [Indexed: 12/14/2022] Open
Abstract
TDP-43 is an essential RNA-binding protein forming aggregates in almost all cases of sporadic amyotrophic lateral sclerosis (ALS) and many cases of frontotemporal lobar dementia (FTLD) and other neurodegenerative diseases. TDP-43 consists of a folded N-terminal domain with a singular structure, two RRM RNA-binding domains, and a long disordered C-terminal region which plays roles in functional RNA regulatory assemblies as well as pernicious aggregation. Evidence from pathological mutations and seeding experiments strongly suggest that TDP-43 aggregates are pathologically relevant through toxic gain-of-harmful-function and/or harmful loss-of-native-function mechanisms. Recent, but not early, microscopy studies and the ability of TDP-43 aggregates to resist harsh treatment and to seed new pathological aggregates in vitro and in cells strongly suggest that TDP-43 aggregates have a self-templating, amyloid-like structure. Based on the importance of the Gln/Asn-rich 341–367 residue segment for efficient aggregation of endogenous TDP-43 when presented as a 12X-repeat and extensive spectroscopic and computational experiments, we recently proposed that this segment adopts a beta-hairpin structure that assembles in a parallel with a beta-turn configuration to form an amyloid-like structure. Here, we propose that this conformer is stabilized by an especially strong class of hypercooperative hydrogen bonding unique to Gln and Asn sidechains. The clinical existence of this conformer is supported by very recent LC-MS/MS characterization of TDP-43 from ex vivo aggregates, which show that residues 341–367 were protected in vivo from Ser phosphorylation, Gln/Asn deamidation and Met oxidation. Its distinct pattern of SDS-PAGE bands allows us to link this conformer to the exceptionally stable seed of the Type A TDP-43 proteinopathy.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain
| | - Marco Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB) Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB) Trieste, Italy
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain
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112
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Puschmann A, Fiesel FC, Caulfield TR, Hudec R, Ando M, Truban D, Hou X, Ogaki K, Heckman MG, James ED, Swanberg M, Jimenez-Ferrer I, Hansson O, Opala G, Siuda J, Boczarska-Jedynak M, Friedman A, Koziorowski D, Rudzińska-Bar M, Aasly JO, Lynch T, Mellick GD, Mohan M, Silburn PA, Sanotsky Y, Vilariño-Güell C, Farrer MJ, Chen L, Dawson VL, Dawson TM, Wszolek ZK, Ross OA, Springer W. Heterozygous PINK1 p.G411S increases risk of Parkinson's disease via a dominant-negative mechanism. Brain 2016; 140:98-117. [PMID: 27807026 PMCID: PMC5379862 DOI: 10.1093/brain/aww261] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 01/31/2023] Open
Abstract
See Gandhi and Plun-Favreau (doi:10.1093/aww320) for a scientific commentary on this article. Heterozygous mutations in recessive Parkinson’s disease genes have been postulated to increase disease risk. Puschmann et al. report a genetic association between heterozygous PINK1 p.G411S and Parkinson’s disease. They provide structural and functional explanations for a partial dominant-negative effect of the mutant protein, which impairs wild-type PINK1 activity through hetero-dimerization. See Gandhi and Plun-Favreau (doi:10.1093/aww320) for a scientific commentary on this article. It has been postulated that heterozygous mutations in recessive Parkinson’s genes may increase the risk of developing the disease. In particular, the PTEN-induced putative kinase 1 (PINK1) p.G411S (c.1231G>A, rs45478900) mutation has been reported in families with dominant inheritance patterns of Parkinson’s disease, suggesting that it might confer a sizeable disease risk when present on only one allele. We examined families with PINK1 p.G411S and conducted a genetic association study with 2560 patients with Parkinson’s disease and 2145 control subjects. Heterozygous PINK1 p.G411S mutations markedly increased Parkinson’s disease risk (odds ratio = 2.92, P = 0.032); significance remained when supplementing with results from previous studies on 4437 additional subjects (odds ratio = 2.89, P = 0.027). We analysed primary human skin fibroblasts and induced neurons from heterozygous PINK1 p.G411S carriers compared to PINK1 p.Q456X heterozygotes and PINK1 wild-type controls under endogenous conditions. While cells from PINK1 p.Q456X heterozygotes showed reduced levels of PINK1 protein and decreased initial kinase activity upon mitochondrial damage, stress-response was largely unaffected over time, as expected for a recessive loss-of-function mutation. By contrast, PINK1 p.G411S heterozygotes showed no decrease of PINK1 protein levels but a sustained, significant reduction in kinase activity. Molecular modelling and dynamics simulations as well as multiple functional assays revealed that the p.G411S mutation interferes with ubiquitin phosphorylation by wild-type PINK1 in a heterodimeric complex. This impairs the protective functions of the PINK1/parkin-mediated mitochondrial quality control. Based on genetic and clinical evaluation as well as functional and structural characterization, we established p.G411S as a rare genetic risk factor with a relatively large effect size conferred by a partial dominant-negative function phenotype.
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Affiliation(s)
- Andreas Puschmann
- 1 Lund University, Department of Clinical Sciences Lund, Neurology, Sweden .,2 Department of Neurology, Skåne University Hospital, Sweden.,3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Fabienne C Fiesel
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Roman Hudec
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Maya Ando
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dominika Truban
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Xu Hou
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Kotaro Ogaki
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Michael G Heckman
- 4 Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Elle D James
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Maria Swanberg
- 5 Lund University, Department of Experimental Medical Science, Lund, Sweden
| | | | - Oskar Hansson
- 6 Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Sweden.,7 Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Grzegorz Opala
- 8 Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Joanna Siuda
- 8 Department of Neurology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | | | | | | | | | - Jan O Aasly
- 10 Department of Neurology, St. Olav's Hospital, and Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Timothy Lynch
- 11 Dublin Neurological Institute at the Mater Misericordiae University Hospital, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - George D Mellick
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Megha Mohan
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
| | - Peter A Silburn
- 12 Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.,13 University of Queensland, Asia-Pacific Centre for Neuromodulation, Centre for Clinical Research, Brisbane, Queensland, Australia
| | | | - Carles Vilariño-Güell
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,15 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Matthew J Farrer
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,15 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Li Chen
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Valina L Dawson
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,19 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,20 Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- 16 Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,17 Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,18 Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,19 Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,21 Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Owen A Ross
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,23 School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,24 Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Wolfdieter Springer
- 3 Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA .,24 Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, FL 32224, USA
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113
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Manghera M, Ferguson-Parry J, Douville RN. TDP-43 regulates endogenous retrovirus-K viral protein accumulation. Neurobiol Dis 2016; 94:226-36. [PMID: 27370226 DOI: 10.1016/j.nbd.2016.06.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 05/30/2016] [Accepted: 06/27/2016] [Indexed: 12/12/2022] Open
Abstract
The concomitant expression of neuronal TAR DNA binding protein 43 (TDP-43) and human endogenous retrovirus-K (ERVK) is a hallmark of ALS. Since the involvement of TDP-43 in retrovirus replication remains controversial, we sought to evaluate whether TDP-43 exerts an effect on ERVK expression. In this study, TDP-43 bound the ERVK promoter in the context of inflammation or proteasome inhibition, with no effect on ERVK transcription. However, over-expression of ALS-associated aggregating forms of TDP-43, but not wild-type TDP-43, significantly enhanced ERVK viral protein accumulation. Human astrocytes and neurons further demonstrated cell-type specific differences in their ability to express and clear ERVK proteins during inflammation and proteasome inhibition. Astrocytes, but not neurons, were able to clear excess ERVK proteins through stress granule formation and autophagy. In vitro findings were validated in autopsy motor cortex tissue from patients with ALS and neuro-normal controls. We further confirmed marked enhancement of ERVK in cortical neurons of patients with ALS. Despite evidence of enhanced stress granule and autophagic response in ALS cortical neurons, these cells failed to clear excess ERVK protein accumulation. This highlights how multiple cellular pathways, in conjunction with disease-associated mutations, can converge to modulate the expression and clearance of viral gene products from genomic elements such as ERVK. In ALS, ERVK protein aggregation is a novel aspect of TDP-43 misregulation contributing towards the pathology of this neurodegenerative disease.
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Affiliation(s)
- Mamneet Manghera
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, Manitoba R3B 2G3, Canada
| | - Jennifer Ferguson-Parry
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, Manitoba R3B 2G3, Canada
| | - Renée N Douville
- Department of Biology, University of Winnipeg, 599 Portage Avenue, Winnipeg, Manitoba R3B 2G3, Canada; Department of Immunology, University of Manitoba, 750 McDermot Avenue, Winnipeg, Manitoba R3E 0T5, Canada.
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114
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Bozzo F, Salvatori I, Iacovelli F, Mirra A, Rossi S, Cozzolino M, Falconi M, Valle C, Carrì MT. Structural insights into the multi-determinant aggregation of TDP-43 in motor neuron-like cells. Neurobiol Dis 2016; 94:63-72. [PMID: 27317832 DOI: 10.1016/j.nbd.2016.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/06/2016] [Accepted: 06/13/2016] [Indexed: 12/12/2022] Open
Abstract
TDP-43 is aggregated in patients with ALS and FLTD through mechanisms still incompletely understood. Since aggregation in the cytosol is most probably responsible for the delocalization and loss of proper RNA-binding function of TDP-43 in the nucleus, interception of the formation of aggregates may represent a useful therapeutic option. In this study, we investigated the relative importance of the N-terminal and C-terminal moieties of TDP-43 in the aggregation process and the weight of each of the six cysteine residues in determining unfolding and aggregation of the different domains. We report that cytoplasmic inclusions formed by WT and mutant TDP-43 in motor neuron-like NSC34 cells are redox-sensitive only in part, and contain at least two components, i.e. oligomers and large aggregates, that are made of different molecular species. The two N-terminal cysteine residues contribute to the seeding for the first step in oligomerization, which is then accomplished by mechanisms depending on the four cysteines in the RNA-recognition motifs. Cysteine-independent large aggregates contain unfolded isoforms of the protein, held together by unspecific hydrophobic interactions. Interestingly, truncated isoforms are entrapped exclusively in oligomers. Ab initio modeling of TDP-43 structure, molecular dynamics and molecular docking analysis indicate a differential accessibility of cysteine residues that contributes to aggregation propensity. We propose a model of TDP-43 aggregation involving cysteine-dependent and cysteine-independent stages that may constitute a starting point to devise strategies counteracting the formation of inclusions in TDP-43 proteinopathies.
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Affiliation(s)
- F Bozzo
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy
| | - I Salvatori
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy
| | - F Iacovelli
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; Interuniversity Consortium, National Institute of Biostructure and Biosystem (INBB), Italy
| | - A Mirra
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy
| | - S Rossi
- Institute of Translational Pharmacology, CNR, 00133 Rome, Italy
| | - M Cozzolino
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; Institute of Translational Pharmacology, CNR, 00133 Rome, Italy
| | - M Falconi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; Interuniversity Consortium, National Institute of Biostructure and Biosystem (INBB), Italy
| | - C Valle
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; Institute for Cell Biology and Neurobiology, CNR, c/o CERC, 00143 Rome, Italy.
| | - M T Carrì
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy; Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy.
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115
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Sasaguri H, Chew J, Xu YF, Gendron TF, Garrett A, Lee CW, Jansen-West K, Bauer PO, Perkerson EA, Tong J, Stetler C, Zhang YJ. The extreme N-terminus of TDP-43 mediates the cytoplasmic aggregation of TDP-43 and associated toxicity in vivo. Brain Res 2016; 1647:57-64. [PMID: 27155453 DOI: 10.1016/j.brainres.2016.04.069] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 12/13/2022]
Abstract
Inclusions of Tar DNA- binding protein 43 (TDP-43) are a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43-positive inclusions (FTLD-TDP). Pathological TDP-43 exhibits the disease-specific biochemical signatures, which include its ubiquitination, phosphorylation and truncation. Recently, we demonstrated that the extreme N-terminus of TDP-43 regulates formation of abnormal cytoplasmic TDP-43 aggregation in cultured cells and primary neurons. However, it remained unclear whether this N-terminal domain mediates TDP-43 aggregation and the associated toxicity in vivo. To investigate this, we expressed a GFP-tagged TDP-43 with a nuclear localization signal mutation (GFP-TDP-43NLSm) and a truncated form without the extreme N-terminus (GFP-TDP-4310-414-NLSm) by adeno-associated viral (AAV) vectors in mouse primary cortical neurons and murine central nervous system. Compared to neurons containing GFP alone, expression of GFP-TDP-43NLSm resulted in the formation of ubiquitin-positive cytoplasmic inclusions and activation of caspase-3, an indicator of cell death. Moreover, mice expressing GFP-TDP-43NLSm proteins show reactive gliosis and develop neurological abnormalities. However, by deletion of TDP-43's extreme N-terminus, these pathological alterations can be abrogated. Together, our study provides further evidence confirming the critical role of the extreme N-terminus of TDP-43 in regulating protein structure as well as mediating toxicity associated with its aggregation. This article is part of a Special Issue entitled SI:RNA Metabolism in Disease.
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Affiliation(s)
- Hiroki Sasaguri
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Jeannie Chew
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Ya-Fei Xu
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Aliesha Garrett
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Chris W Lee
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Peter O Bauer
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Emilie A Perkerson
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Jimei Tong
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Caroline Stetler
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic Jacksonville, 4500 San Pablo Road, Jacksonville, FL 32224, USA.
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116
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Langellotti S, Romano V, Romano G, Klima R, Feiguin F, Cragnaz L, Romano M, Baralle FE. A novel Drosophila model of TDP-43 proteinopathies: N-terminal sequences combined with the Q/N domain induce protein functional loss and locomotion defects. Dis Model Mech 2016; 9:659-69. [PMID: 27101846 PMCID: PMC4920146 DOI: 10.1242/dmm.023382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 04/20/2016] [Indexed: 12/12/2022] Open
Abstract
Transactive response DNA-binding protein 43 kDa (TDP-43, also known as TBPH in Drosophila melanogaster and TARDBP in mammals) is the main protein component of the pathological inclusions observed in neurons of patients affected by different neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration (FTLD). The number of studies investigating the molecular mechanisms underlying neurodegeneration is constantly growing; however, the role played by TDP-43 in disease onset and progression is still unclear. A fundamental shortcoming that hampers progress is the lack of animal models showing aggregation of TDP-43 without overexpression. In this manuscript, we have extended our cellular model of aggregation to a transgenic Drosophila line. Our fly model is not based on the overexpression of a wild-type TDP-43 transgene. By contrast, we engineered a construct that includes only the specific TDP-43 amino acid sequences necessary to trigger aggregate formation and capable of trapping endogenous Drosophila TDP-43 into a non-functional insoluble form. Importantly, the resulting recombinant product lacks functional RNA recognition motifs (RRMs) and, thus, does not have specific TDP-43-physiological functions (i.e. splicing regulation ability) that might affect the animal phenotype per se. This novel Drosophila model exhibits an evident degenerative phenotype with reduced lifespan and early locomotion defects. Additionally, we show that important proteins involved in neuromuscular junction function, such as syntaxin (SYX), decrease their levels as a consequence of TDP-43 loss of function implying that the degenerative phenotype is a consequence of TDP-43 sequestration into the aggregates. Our data lend further support to the role of TDP-43 loss-of-function in the pathogenesis of neurodegenerative disorders. The novel transgenic Drosophila model presented in this study will help to gain further insight into the molecular mechanisms underlying neurodegeneration and will provide a valuable system to test potential therapeutic agents to counteract disease. Summary: An engineered TDP-43 construct can be used to induce TDP-43 aggregation in Drosophila, providing a model that could be useful for characterization of pathogenetic mechanisms and drug screening.
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Affiliation(s)
- Simona Langellotti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste I-34149, Italy
| | - Valentina Romano
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste I-34149, Italy
| | - Giulia Romano
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste I-34149, Italy
| | - Raffaella Klima
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste I-34149, Italy
| | - Fabian Feiguin
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste I-34149, Italy
| | - Lucia Cragnaz
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste I-34149, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, Trieste 34127, Italy
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste I-34149, Italy
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117
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Mompeán M, Romano V, Pantoja-Uceda D, Stuani C, Baralle FE, Buratti E, Laurents DV. The TDP-43 N-terminal domain structure at high resolution. FEBS J 2016; 283:1242-60. [DOI: 10.1111/febs.13651] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/18/2015] [Accepted: 01/08/2016] [Indexed: 02/06/2023]
Affiliation(s)
| | - Valentina Romano
- International Centre for Genetic Engineering and Biotechnology; Trieste Italy
| | | | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology; Trieste Italy
| | | | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology; Trieste Italy
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118
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Romano V, Quadri Z, Baralle FE, Buratti E. The structural integrity of TDP-43 N-terminus is required for efficient aggregate entrapment and consequent loss of protein function. Prion 2016; 9:1-9. [PMID: 25635624 DOI: 10.1080/19336896.2015.1011885] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nuclear factor TDP-43 has been shown to play a key role in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia, where TDP-43 aggregates accumulate in patient's affected neurons and this event can cause neuronal dysfunction. A major focus of today's research is to discover the critical factors that lead to TDP-43 aggregation and the consequences for neuronal metabolism. From a structural point of view, several lines of evidence point toward TDP-43 C-terminus as a key domain able to mediate this process. Regarding this region, we have recently described a novel cellular TDP-43 aggregation model based on 12 tandem repetitions of its 339-366 Q/N rich prion-like domain. In addition, we have shown and confirmed that a minimal TDP-43 construct constituted by the N and C-terminal regions, but lacking both RRM domains, induce aggregation of endogenous TDP-43 and leads to its total loss of function as seen by changes in the alternative splicing of endogenous genes. In this work, we further characterize this model and show the importance of the N-terminus structure in the loss of function process. In addition, from a biochemical point of view we report that, as shown in a previous version of this model (GFP 12 × Q/N), the endogenous TDP-43 trapped in the aggregates undergoes the 2 most important post-translational modifications seen in pathological TDP-43 inclusions: ubiquitination and hyperphosphorylation.
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Affiliation(s)
- Valentina Romano
- a International Centre for Genetic Engineering and Biotechnology (ICGEB) ; Trieste , Italy
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119
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Lim L, Wei Y, Lu Y, Song J. ALS-Causing Mutations Significantly Perturb the Self-Assembly and Interaction with Nucleic Acid of the Intrinsically Disordered Prion-Like Domain of TDP-43. PLoS Biol 2016; 14:e1002338. [PMID: 26735904 PMCID: PMC4703307 DOI: 10.1371/journal.pbio.1002338] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022] Open
Abstract
TAR-DNA-binding protein-43 (TDP-43) C-terminus encodes a prion-like domain widely presented in RNA-binding proteins, which functions to form dynamic oligomers and also, amazingly, hosts most amyotrophic lateral sclerosis (ALS)-causing mutations. Here, as facilitated by our previous discovery, by circular dichroism (CD), fluorescence and nuclear magnetic resonance (NMR) spectroscopy, we have successfully determined conformations, dynamics, and self-associations of the full-length prion-like domains of the wild type and three ALS-causing mutants (A315E, Q331K, and M337V) in both aqueous solutions and membrane environments. The study decodes the following: (1) The TDP-43 prion-like domain is intrinsically disordered only with some nascent secondary structures in aqueous solutions, but owns the capacity to assemble into dynamic oligomers rich in β-sheet structures. By contrast, despite having highly similar conformations, three mutants gained the ability to form amyloid oligomers. The wild type and three mutants all formed amyloid fibrils after incubation as imaged by electron microscopy. (2) The interaction with nucleic acid enhances the self-assembly for the wild type but triggers quick aggregation for three mutants. (3) A membrane-interacting subdomain has been identified over residues Met311-Gln343 indispensable for TDP-43 neurotoxicity, which transforms into a well-folded Ω-loop-helix structure in membrane environments. Furthermore, despite having very similar membrane-embedded conformations, three mutants will undergo further self-association in the membrane environment. Our study implies that the TDP-43 prion-like domain appears to have an energy landscape, which allows the assembly of the wild-type sequence into dynamic oligomers only under very limited condition sets, and ALS-causing point mutations are sufficient to remodel it to more favor the amyloid formation or irreversible aggregation, thus supporting the emerging view that the pathologic aggregation may occur via the exaggeration of functionally important assemblies. Furthermore, the coupled capacity of TDP-43 in aggregation and membrane interaction may critically account for its high neurotoxicity, and therefore its decoupling may represent a promising therapeutic strategy to treat TDP-43 causing neurodegenerative diseases. The prion-like domain of TDP-43 appears to have an energy landscape that allows oligomerisation only under very limited conditions; however, TDP-43 mutations that cause amyotrophic lateral sclerosis are sufficient to remodel the protein in favor of amyloid formation. Amyotrophic lateral sclerosis (ALS) is the most prevalent fatal motor neuron disease. It was identified ~140 years ago, but the exact mechanism underlying the disease has still not been well defined. TAR-DNA-binding protein-43 (TDP-43) was identified as the major component of the proteinaceous inclusions present in ~97% ALS and ~45% frontotemporal dementia (FTD) patients, and has also been observed in an increasing spectrum of other neurodegenerative disorders, including Alzheimer disease. The TDP-43 C-terminus is a key domain—it encodes a prion-like domain and, crucially, hosts almost all ALS-causing mutations. Here we have successfully determined the conformations, dynamics, and self-associations of the prion-like domains of both wild type and three ALS-causing mutants in both aqueous solutions and membrane environments. The study suggests that the TDP-43 prion-like domain appears to have a unique energy landscape, which allows the assembly of the wild-type sequence into specific oligomers only under very limited conditions. Intriguingly, ALS-causing point mutations remodel the energy landscape to favor amyloid formation or irreversible aggregation, thus supporting the emerging view that pathologic aggregation may occur via the exaggeration of functionally important assemblies. Furthermore, the coupled capacity of TDP-43 in aggregation and membrane interaction may partly account for its high neurotoxicity; decoupling these may therefore represent a promising therapeutic strategy to treat TDP-43-mediated neurodegenerative diseases.
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Affiliation(s)
- Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Yuanyuan Wei
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Yimei Lu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- * E-mail:
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Abstract
The PINK1 (phosphatase and tensin homologue-induced putative kinase 1)/Parkin-dependent mitochondrial quality control pathway mediates the clearance of damaged organelles, but appears to be disrupted in Parkinson's disease (PD) [Springer and Kahle (2011) Autophagy 7, 266-278]. Upon mitochondrial stress, PINK1 activates the E3 ubiquitin (Ub) ligase Parkin through phosphorylation of the Ub-like (UBL) domain of Parkin and of the small modifier Ub itself at a conserved residue [Sauvé and Gehring (2014) Cell Res. 24, 1025-1026]. Recently resolved partial crystal structures of Parkin showed a 'closed', auto-inhibited conformation, consistent with its notoriously weak enzymatic activity at steady state [Wauer and Komander (2013) EMBO J. 32, 2099-2112; Riley et al. (2013) Nat. Commun. 4, 1982; Trempe et al. (2013) Science 340, 1451-1455; Spratt et al. (2013) Nat. Commun. 4, 1983]. It has thus become clear that Parkin must undergo major structural rearrangements in order to unleash its catalytic functions. Recent published findings derived from X-ray structures and molecular modelling present a complete structural model of human Parkin at an all-atom resolution [Caulfield et al. (2014) PLoS Comput. Biol. 10, e1003935]. The results of the combined in silico simulations-based and experimental assay-based study indicates that PINK1-dependent Ser65 phosphorylation of Parkin is required for its activation and triggering of 'opening' conformations. Indeed, the obtained structures showed a sequential release of Parkin's intertwined domains and allowed docking of an Ub-charged E2 coenzyme, which could enable its enzymatic activity. In addition, using cell-based screening, select E2 enzymes that redundantly, cooperatively or antagonistically regulate Parkin's activation and/or enzymatic functions at different stages of the mitochondrial autophagy (mitophagy) process were identified [Fiesel et al. (2014) J. Cell Sci. 127, 3488-3504]. Other work that aims to pin-point the particular pathogenic dysfunctions of Parkin mis-sense mutations have been recently disseminated (Fabienne C. Fiesel, Thomas R. Caulfield, Elisabeth L. Moussaud-Lamodiere, Daniel F.A.R. Dourado, Kotaro Ogaki, Owen A. Ross, Samuel C. Flores, and Wolfdieter Springer, submitted). Such a structure-function approach provides the basis for the dissection of Parkin's regulation and a targeted drug design to identify small-molecule activators of this neuroprotective E3 Ub ligase.
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Varghese DS, Chandran U, Soumya A, Pillai SM, Jayakrishnan K, Reddi PP, Kumar PG. Aberrant expression of TAR DNA binding protein-43 is associated with spermatogenic disorders in men. Reprod Fertil Dev 2016; 28:713-22. [DOI: 10.1071/rd14090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 08/12/2014] [Indexed: 12/21/2022] Open
Abstract
Loss of function of TAR DNA-binding protein (TDP-43) has been implicated in neurodegenerative disorders in both humans and animal models. TDP-43 has also been shown to be cis-acting transcriptional repressor of the acrosome vesicle (Acrv) gene in mice. In the present study, we investigated the expression of the TDP-43 transcript (TARDBP) and protein in germ cells from 11 fertile and 98 subfertile men to verify its potential association with poor seminograms. The expression profile of TDP-43 was characterised in immature germ cells and spermatozoa from semen from fertile and subfertile men using reverse transcription–polymerase chain reaction, western blotting and immunofluorescence. Although germ cells from subfertile men tested negative for TARDBP, the full-length message of the same was detected in fertile men. TDP-43 was detected in spermatozoa from fertile men using western blot analysis and immunofluorescence. The expression of this protein was negligible in spermatozoa from men with primary spermatogenic dysfunction. We conclude that a deficiency in the TDP-43 expression is associated with defective spermatogenesis and male infertility. We propose that TDP-43 could be used as a marker of male factor infertility.
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122
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Li Y, Collins M, Geiser R, Bakkar N, Riascos D, Bowser R. RBM45 homo-oligomerization mediates association with ALS-linked proteins and stress granules. Sci Rep 2015; 5:14262. [PMID: 26391765 PMCID: PMC4585734 DOI: 10.1038/srep14262] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/21/2015] [Indexed: 12/12/2022] Open
Abstract
The aggregation of RNA-binding proteins is a pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). RBM45 is an RNA-binding protein that forms cytoplasmic inclusions in neurons and glia in ALS and FTLD. To explore the role of RBM45 in ALS and FTLD, we examined the contribution of the protein’s domains to its function, subcellular localization, and interaction with itself and ALS-linked proteins. We find that RBM45 forms homo-oligomers and physically associates with the ALS-linked proteins TDP-43 and FUS in the nucleus. Nuclear localization of RBM45 is mediated by a bipartite nuclear-localization sequence (NLS) located at the C-terminus. RBM45 mutants that lack a functional NLS accumulate in the cytoplasm and form TDP-43 positive stress granules. Moreover, we identify a novel structural element, termed the homo-oligomer assembly (HOA) domain, that is highly conserved across species and promote homo-oligomerization of RBM45. RBM45 mutants that fail to form homo-oligomers exhibit significantly reduced association with ALS-linked proteins and inclusion into stress granules. These results show that RMB45 may function as a homo-oligomer and that its oligomerization contributes to ALS/FTLD RNA-binding protein aggregation.
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Affiliation(s)
- Yang Li
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Mahlon Collins
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Rachel Geiser
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Nadine Bakkar
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - David Riascos
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA
| | - Robert Bowser
- Divisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona 85013, USA.,University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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123
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Ling JP, Pletnikova O, Troncoso JC, Wong PC. TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD. Science 2015; 349:650-5. [PMID: 26250685 DOI: 10.1126/science.aab0983] [Citation(s) in RCA: 366] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytoplasmic aggregation of TDP-43, accompanied by its nuclear clearance, is a key common pathological hallmark of amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). However, a limited understanding of this RNA-binding protein (RBP) impedes the clarification of pathogenic mechanisms underlying TDP-43 proteinopathy. In contrast to RBPs that regulate splicing of conserved exons, we found that TDP-43 repressed the splicing of nonconserved cryptic exons, maintaining intron integrity. When TDP-43 was depleted from mouse embryonic stem cells, these cryptic exons were spliced into messenger RNAs, often disrupting their translation and promoting nonsense-mediated decay. Moreover, enforced repression of cryptic exons prevented cell death in TDP-43-deficient cells. Furthermore, repression of cryptic exons was impaired in ALS-FTD cases, suggesting that this splicing defect could potentially underlie TDP-43 proteinopathy.
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Affiliation(s)
- Jonathan P Ling
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA. Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205-2196, USA.
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124
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Fiesel FC, Ando M, Hudec R, Hill AR, Castanedes-Casey M, Caulfield TR, Moussaud-Lamodière EL, Stankowski JN, Bauer PO, Lorenzo-Betancor O, Ferrer I, Arbelo JM, Siuda J, Chen L, Dawson VL, Dawson TM, Wszolek ZK, Ross OA, Dickson DW, Springer W. (Patho-)physiological relevance of PINK1-dependent ubiquitin phosphorylation. EMBO Rep 2015; 16:1114-30. [PMID: 26162776 DOI: 10.15252/embr.201540514] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/25/2015] [Indexed: 11/09/2022] Open
Abstract
Mutations in PINK1 and PARKIN cause recessive, early-onset Parkinson's disease (PD). Together, these two proteins orchestrate a protective mitophagic response that ensures the safe disposal of damaged mitochondria. The kinase PINK1 phosphorylates ubiquitin (Ub) at the conserved residue S65, in addition to modifying the E3 ubiquitin ligase Parkin. The structural and functional consequences of Ub phosphorylation (pS65-Ub) have already been suggested from in vitro experiments, but its (patho-)physiological significance remains unknown. We have generated novel antibodies and assessed pS65-Ub signals in vitro and in cells, including primary neurons, under endogenous conditions. pS65-Ub is dependent on PINK1 kinase activity as confirmed in patient fibroblasts and postmortem brain samples harboring pathogenic mutations. We show that pS65-Ub is reversible and barely detectable under basal conditions, but rapidly induced upon mitochondrial stress in cells and amplified in the presence of functional Parkin. pS65-Ub accumulates in human brain during aging and disease in the form of cytoplasmic granules that partially overlap with mitochondrial, lysosomal, and total Ub markers. Additional studies are now warranted to further elucidate pS65-Ub functions and fully explore its potential for biomarker or therapeutic development.
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Affiliation(s)
| | - Maya Ando
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Roman Hudec
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | | | | | | | - Peter O Bauer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Isidre Ferrer
- Institut de Neuropatologia, Servei d'Anatomia Patològica Hospital Universitari de Bellvitge, Hospitalet del Llobregat, Spain CIBERNED, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Barcelona, Spain
| | - José M Arbelo
- Department of Neurology, Parkinson's and Movement Disorders Unit, Hospital Universitario Insular de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Joanna Siuda
- Department of Neurology, School of Medicine in Katowice Medical University of Silesia, Katowice, Poland
| | - Li Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA Neurobiology of Disease, Mayo Graduate School, Jacksonville, FL, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA Neurobiology of Disease, Mayo Graduate School, Jacksonville, FL, USA
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA Neurobiology of Disease, Mayo Graduate School, Jacksonville, FL, USA
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125
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Abstract
The transactive response DNA binding protein (TDP-43) has long been characterized as a main hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U, also known as FTLD-TDP). Several studies have indicated TDP-43 deposits in Alzheimer's disease (AD) brains and have robust connection with AD clinical phenotype. FTLD-U, which was symptomatically connected with AD, may be predictable for the comprehension of the role TDP-43 in AD. TDP-43 may contribute to AD through both β-amyloid (Aβ)-dependent and Aβ-independent pathways. In this article, we summarize the latest studies concerning the role of TDP-43 in AD and explore TDP-43 modulation as a potential therapeutic strategy for AD. However, to date, little of pieces of the research on TDP-43 have been performed to investigate the role in AD; more investigations need to be confirmed in the future.
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126
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TDP-43 as a possible biomarker for frontotemporal lobar degeneration: a systematic review of existing antibodies. Acta Neuropathol Commun 2015; 3:15. [PMID: 25853864 PMCID: PMC4380254 DOI: 10.1186/s40478-015-0195-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/05/2015] [Indexed: 12/12/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) is one of the leading causes of dementia after Alzheimer’s disease. A high-ranking candidate to become a diagnostic marker for a major pathological subtype of FTLD is the transactive response DNA binding protein of 43 kDa (TDP-43). The main objective is to elucidate which antibodies are specific for pathological TDP-43, with special interest in its modified isoforms. Indeed, TDP-43 has been shown to be hyperphosphorylated and truncated in disease. A secondary objective is to review existing immunoassays that quantify TDP-43 in biofluids. A systematic review of literature was performed by searching PubMed and Web of Science using predefined keywords. Of considered research papers the methods section was reviewed to select publications that enabled us to answer our learning objective. After quality assessment, antibody characteristics and related outcomes were extracted. We identified a series of well-characterized antibodies based on a scoring system that assessed the ability of each antibody to detect TDP-43 pathology. A selection of 29 unique antibodies was made comprising 10 high-ranking antibodies which were reported multiple times to detect TDP-43 pathology in both immunostaining and immunoblotting experiments and 19 additional antibodies which detected TDP-43 pathology but were only scored once. This systematic review provides an overview of antibodies that are reported to detect pathological TDP-43. These antibodies can be used in future studies of TDP-43 proteinopathies. Additionally, selected antibodies hold the potential to be used in the development of novel immunoassays for the quantification of TDP-43 in biofluids, as a possible biomarker for FTLD-TDP.
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127
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Maniecka Z, Polymenidou M. From nucleation to widespread propagation: A prion-like concept for ALS. Virus Res 2015; 207:94-105. [PMID: 25656065 DOI: 10.1016/j.virusres.2014.12.032] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/12/2014] [Accepted: 12/29/2014] [Indexed: 12/12/2022]
Abstract
Propagation of pathological protein assemblies via a prion-like mechanism has been suggested to drive neurodegenerative diseases, such as Parkinson's and Alzheimer's. Recently, amyotrophic lateral sclerosis (ALS)-linked proteins, such as SOD1, TDP-43 and FUS were shown to follow self-perpetuating seeded aggregation, thereby adding ALS to the group of prion-like disorders. The cell-to-cell spread of these pathological protein assemblies and their pathogenic mechanism is poorly understood. However, as ALS is a non-cell autonomous disease and pathology in glial cells was shown to contribute to motor neuron damage, spreading mechanisms are likely to underlie disease progression via the interplay between affected neurons and their neighboring glial cells.
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Affiliation(s)
- Zuzanna Maniecka
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Magdalini Polymenidou
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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128
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Buratti E. Functional Significance of TDP-43 Mutations in Disease. ADVANCES IN GENETICS 2015; 91:1-53. [DOI: 10.1016/bs.adgen.2015.07.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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129
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TDP-43 N terminus encodes a novel ubiquitin-like fold and its unfolded form in equilibrium that can be shifted by binding to ssDNA. Proc Natl Acad Sci U S A 2014; 111:18619-24. [PMID: 25503365 DOI: 10.1073/pnas.1413994112] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Transactivation response element (TAR) DNA-binding protein 43 (TDP-43) is the principal component of ubiquitinated inclusions characteristic of most forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia-frontotemporal lobar degeneration with TDP-43-positive inclusions (FTLD-TDP), as well as an increasing spectrum of other neurodegenerative diseases. Previous structural and functional studies on TDP-43 have been mostly focused on its recognized domains. Very recently, however, its extreme N terminus was identified to be a double-edged sword indispensable for both physiology and proteinopathy, but thus far its structure remains unknown due to the severe aggregation. Here as facilitated by our previous discovery that protein aggregation can be significantly minimized by reducing salt concentrations, by circular dichroism and NMR spectroscopy we revealed that the TDP-43 N terminus encodes a well-folded structure in concentration-dependent equilibrium with its unfolded form. Despite previous failure in detecting any sequence homology to ubiquitin, the folded state was determined to adopt a novel ubiquitin-like fold by the CS-Rosetta program with NMR chemical shifts and 78 unambiguous long-range nuclear Overhauser effect (NOE) constraints. Remarkably, this ubiquitin-like fold could bind ssDNA, and the binding shifted the conformational equilibrium toward reducing the unfolded population. To the best of our knowledge, the TDP-43 N terminus represents the first ubiquitin-like fold capable of directly binding nucleic acid. Our results provide a molecular mechanism rationalizing the functional dichotomy of TDP-43 and might also shed light on the formation and dynamics of cellular ribonucleoprotein granules, which have been recently linked to ALS pathogenesis. As a consequence, one therapeutic strategy for TDP-43-causing diseases might be to stabilize its ubiquitin-like fold by ssDNA or designed molecules.
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130
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Chitta K, Paulus A, Caulfield TR, Akhtar S, Blake MKK, Ailawadhi S, Knight J, Heckman MG, Pinkerton A, Chanan-Khan A. Nimbolide targets BCL2 and induces apoptosis in preclinical models of Waldenströms macroglobulinemia. Blood Cancer J 2014; 4:e260. [PMID: 25382610 PMCID: PMC5424099 DOI: 10.1038/bcj.2014.74] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/15/2014] [Accepted: 09/18/2014] [Indexed: 12/31/2022] Open
Abstract
Neem leaf extract (NLE) has medicinal properties, which have been attributed to its limonoid content. We identified the NLE tetranorterpenoid, nimbolide, as being the key limonoid responsible for the cytotoxicity of NLE in various preclinical models of human B-lymphocyte cancer. Of the models tested, Waldenströms macroglobulinemia (WM) cells were most sensitive to nimbolide, undergoing significant mitochondrial mediated apoptosis. Notably, nimbolide toxicity was also observed in drug-resistant (bortezomib or ibrutinib) WM cells. To identify putative targets of nimbolide, relevant in WM, we used chemoinformatics-based approaches comprised of virtual in silico screening, molecular modeling and target–ligand reverse docking. In silico analysis revealed the antiapoptotic protein BCL2 was the preferential binding partner of nimbolide. The significance of this finding was further tested in vitro in RS4;11 (BCL2-dependent) tumor cells, in which nimbolide induced significantly more apoptosis compared with BCL2 mutated (Jurkat BCL2Ser70-Ala) cells. Lastly, intraperitoneal administration of nimbolide in WM tumor xenografted mice, significantly reduced tumor growth and IgM secretion in vivo, while modulating the expression of several proteins as seen on immunohistochemistry. Overall, our data demonstrate that nimbolide is highly active in WM cells, as well as other B-cell cancers, and engages BCL2 to exert its cytotoxic activity.
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Affiliation(s)
- K Chitta
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - A Paulus
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - T R Caulfield
- Department of Molecular Neuroscience, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - S Akhtar
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - M-K K Blake
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - S Ailawadhi
- Division of Hematology and Oncology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - J Knight
- Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - M G Heckman
- Department of Health Science Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
| | - A Pinkerton
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
| | - A Chanan-Khan
- Division of Hematology and Oncology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, USA
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131
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Suzuki H, Shibagaki Y, Hattori S, Matsuoka M. Nuclear TDP-43 causes neuronal toxicity by escaping from the inhibitory regulation by hnRNPs. Hum Mol Genet 2014; 24:1513-27. [DOI: 10.1093/hmg/ddu563] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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132
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Caulfield TR, Fiesel FC, Moussaud-Lamodière EL, Dourado DFAR, Flores SC, Springer W. Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin. PLoS Comput Biol 2014; 10:e1003935. [PMID: 25375667 PMCID: PMC4222639 DOI: 10.1371/journal.pcbi.1003935] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/25/2014] [Indexed: 11/19/2022] Open
Abstract
Loss-of-function mutations in PINK1 or PARKIN are the most common causes of autosomal recessive Parkinson's disease. Both gene products, the Ser/Thr kinase PINK1 and the E3 Ubiquitin ligase Parkin, functionally cooperate in a mitochondrial quality control pathway. Upon stress, PINK1 activates Parkin and enables its translocation to and ubiquitination of damaged mitochondria to facilitate their clearance from the cell. Though PINK1-dependent phosphorylation of Ser65 is an important initial step, the molecular mechanisms underlying the activation of Parkin's enzymatic functions remain unclear. Using molecular modeling, we generated a complete structural model of human Parkin at all atom resolution. At steady state, the Ub ligase is maintained inactive in a closed, auto-inhibited conformation that results from intra-molecular interactions. Evidently, Parkin has to undergo major structural rearrangements in order to unleash its catalytic activity. As a spark, we have modeled PINK1-dependent Ser65 phosphorylation in silico and provide the first molecular dynamics simulation of Parkin conformations along a sequential unfolding pathway that could release its intertwined domains and enable its catalytic activity. We combined free (unbiased) molecular dynamics simulation, Monte Carlo algorithms, and minimal-biasing methods with cell-based high content imaging and biochemical assays. Phosphorylation of Ser65 results in widening of a newly defined cleft and dissociation of the regulatory N-terminal UBL domain. This motion propagates through further opening conformations that allow binding of an Ub-loaded E2 co-enzyme. Subsequent spatial reorientation of the catalytic centers of both enzymes might facilitate the transfer of the Ub moiety to charge Parkin. Our structure-function study provides the basis to elucidate regulatory mechanisms and activity of the neuroprotective Parkin. This may open up new avenues for the development of small molecule Parkin activators through targeted drug design. Parkinson's disease (PD) is a devastating neurological condition caused by the selective and progressive degeneration of dopaminergic neurons in the brain. Loss-of-function mutations in the PINK1 or PARKIN genes are the most common causes of recessively inherited PD. Together the encoded proteins coordinate a protective cellular quality control pathway that allows elimination of impaired mitochondria in order to prevent further cellular damage and ultimately death. Although it is known that the kinase PINK1 operates upstream and activates the E3 Ubiquitin ligase Parkin, the molecular mechanisms remain elusive. Here, we combined state-of-the art computational and functional biological methods to demonstrate that Parkin is sequentially activated through PINK1-dependent phosphorylation and subsequent structural rearrangement. The induced motions result in release of Parkin's closed, auto-inhibited conformation to liberate its enzymatic functions. We provide for the first time a complete protein structure of Parkin at an all atom resolution and a comprehensive molecular dynamics simulation of its activation and opening conformations. The generated models will allow uncovering the exact mechanisms of regulation and enzymatic activity of Parkin and potentially the development of novel therapeutics through a structure-function-based drug design.
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Affiliation(s)
- Thomas R. Caulfield
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
- * E-mail: (TRC); (WS)
| | - Fabienne C. Fiesel
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
| | | | - Daniel F. A. R. Dourado
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Samuel C. Flores
- Department of Cell & Molecular Biology, Computational & Systems Biology, Uppsala University, Uppsala, Sweden
| | - Wolfdieter Springer
- Department of Neuroscience, Mayo Clinic Jacksonville, Florida, United States of America
- Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida, United States of America
- * E-mail: (TRC); (WS)
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133
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Zhang YJ, Jansen-West K, Xu YF, Gendron TF, Bieniek KF, Lin WL, Sasaguri H, Caulfield T, Hubbard J, Daughrity L, Chew J, Belzil VV, Prudencio M, Stankowski JN, Castanedes-Casey M, Whitelaw E, Ash PEA, DeTure M, Rademakers R, Boylan KB, Dickson DW, Petrucelli L. Aggregation-prone c9FTD/ALS poly(GA) RAN-translated proteins cause neurotoxicity by inducing ER stress. Acta Neuropathol 2014; 128:505-24. [PMID: 25173361 PMCID: PMC4159567 DOI: 10.1007/s00401-014-1336-5] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 08/20/2014] [Accepted: 08/20/2014] [Indexed: 12/13/2022]
Abstract
The occurrence of repeat-associated non-ATG (RAN) translation, an atypical form of translation of expanded repeats that results in the synthesis of homopolymeric expansion proteins, is becoming more widely appreciated among microsatellite expansion disorders. Such disorders include amyotrophic lateral sclerosis and frontotemporal dementia caused by a hexanucleotide repeat expansion in the C9ORF72 gene (c9FTD/ALS). We and others have recently shown that this bidirectionally transcribed repeat is RAN translated, and the "c9RAN proteins" thusly produced form neuronal inclusions throughout the central nervous system of c9FTD/ALS patients. Nonetheless, the potential contribution of c9RAN proteins to disease pathogenesis remains poorly understood. In the present study, we demonstrate that poly(GA) c9RAN proteins are neurotoxic and may be implicated in the neurodegenerative processes of c9FTD/ALS. Specifically, we show that expression of poly(GA) proteins in cultured cells and primary neurons leads to the formation of soluble and insoluble high molecular weight species, as well as inclusions composed of filaments similar to those observed in c9FTD/ALS brain tissues. The expression of poly(GA) proteins is accompanied by caspase-3 activation, impaired neurite outgrowth, inhibition of proteasome activity, and evidence of endoplasmic reticulum (ER) stress. Of importance, ER stress inhibitors, salubrinal and TUDCA, provide protection against poly(GA)-induced toxicity. Taken together, our data provide compelling evidence towards establishing RAN translation as a pathogenic mechanism of c9FTD/ALS, and suggest that targeting the ER using small molecules may be a promising therapeutic approach for these devastating diseases.
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Affiliation(s)
- Yong-Jie Zhang
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Ya-Fei Xu
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Tania F. Gendron
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Kevin F. Bieniek
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
- Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905 USA
| | - Wen-Lang Lin
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Hiroki Sasaguri
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Thomas Caulfield
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Jaime Hubbard
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Lillian Daughrity
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Jeannie Chew
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
- Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905 USA
| | | | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | | | | | - Ena Whitelaw
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Peter E. A. Ash
- Department of Pharmacology, Boston University School of Medicine, Boston, MA 02118 USA
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Kevin B. Boylan
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL 32224 USA
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134
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Budini M, Romano V, Quadri Z, Buratti E, Baralle FE. TDP-43 loss of cellular function through aggregation requires additional structural determinants beyond its C-terminal Q/N prion-like domain. Hum Mol Genet 2014; 24:9-20. [PMID: 25122661 PMCID: PMC4262490 DOI: 10.1093/hmg/ddu415] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
TDP-43 aggregates are the neurohistological landmark of diseases like amyotrophic lateral sclerosis and frontotemporal dementia. Their role in the pathogenesis of these conditions is not yet clear mainly due to the lack of proper models of aggregation that may allow the study of the mechanism of formation, their interactions with other cellular components and their effect on the cell metabolism. In this work, we have used tandem repeats of the prion like Q/N-rich region of TAR DNA-binding protein (TDP-43) fused to additional TDP-43 protein sequences to trigger aggregate formation in neuronal and non-neuronal cell lines. At the functional level, these aggregates are able to sequester endogenous TDP-43 depleting its nuclear levels and inducing loss of function at the pre-mRNA splicing level. No apparent direct cellular toxicity of the aggregates seems to be present beyond the lack of functional TDP-43. To our knowledge, this is the only system that achieves full functional TDP 43 depletion with effects similar to RNAi depletion or gene deletion. As a result, this model will prove useful to investigate the loss-of-function effects mediated by TDP-43 aggregation within cells without affecting the expression of the endogenous gene. We have identified the N-terminus sequence of TDP-43 as the domain that enhances its interaction with the aggregates and its insolubilization. These data show for the first time that cellular TDP-43 aggregation can lead to total loss of function and to defective splicing of TDP-43-dependent splicing events in endogenous genes.
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Affiliation(s)
- Mauricio Budini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | - Valentina Romano
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | - Zainuddin Quadri
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34012 Trieste, Italy
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135
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Budini M, Baralle FE, Buratti E. Targeting TDP-43 in neurodegenerative diseases. Expert Opin Ther Targets 2014; 18:617-32. [DOI: 10.1517/14728222.2014.896905] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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136
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Kuo PH, Chiang CH, Wang YT, Doudeva LG, Yuan HS. The crystal structure of TDP-43 RRM1-DNA complex reveals the specific recognition for UG- and TG-rich nucleic acids. Nucleic Acids Res 2014; 42:4712-22. [PMID: 24464995 PMCID: PMC3985631 DOI: 10.1093/nar/gkt1407] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TDP-43 is an important pathological protein that aggregates in the diseased neuronal cells and is linked to various neurodegenerative disorders. In normal cells, TDP-43 is primarily an RNA-binding protein; however, how the dimeric TDP-43 binds RNA via its two RNA recognition motifs, RRM1 and RRM2, is not clear. Here we report the crystal structure of human TDP-43 RRM1 in complex with a single-stranded DNA showing that RRM1 binds the nucleic acid extensively not only by the conserved β-sheet residues but also by the loop residues. Mutational and biochemical assays further reveal that both RRMs in TDP-43 dimers participate in binding of UG-rich RNA or TG-rich DNA with RRM1 playing a dominant role and RRM2 playing a supporting role. Moreover, RRM1 of the amyotrophic lateral sclerosis-linked mutant D169G binds DNA as efficiently as the wild type; nevertheless, it is more resistant to thermal denaturation, suggesting that the resistance to degradation is likely linked to TDP-43 proteinopathies. Taken together all the data, we suggest a model showing that the two RRMs in each protomer of TDP-43 homodimer work together in RNA binding and thus the dimeric TDP-43 recognizes long clusters of UG-rich RNA to achieve high affinity and specificity.
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Affiliation(s)
- Pan-Hsien Kuo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu, Taiwan and Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei 10048, Taiwan
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137
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Mompeán M, Buratti E, Guarnaccia C, Brito RMM, Chakrabartty A, Baralle FE, Laurents DV. "Structural characterization of the minimal segment of TDP-43 competent for aggregation". Arch Biochem Biophys 2014; 545:53-62. [PMID: 24440310 DOI: 10.1016/j.abb.2014.01.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/13/2013] [Accepted: 01/07/2014] [Indexed: 12/13/2022]
Abstract
TDP-43 is a nuclear protein whose abnormal aggregates are implicated in ALS and FTLD. Recently, an Asn/Gln rich C-terminal segment of TDP-43 has been shown to produce aggregation in vitro and reproduce most of the protein's pathological hallmarks in cells, but little is known about this segment's structure. Here, CD and 2D heteronuclear NMR spectroscopies provide evidence that peptides corresponding to the wild type and mutated sequences of this segment adopt chiefly disordered conformations that, in the case of the wild type sequence, spontaneously forms a β-sheet rich oligomer. Moreover, MD simulation provides evidence for a structure consisting of two β-strands and a well-defined, yet non-canonical structural element. Furthermore, MD simulations of four pathological mutations (Q343R, N345K, G348V and N352S) occurring in this segment predict that all of them could affect this region's structure. In particular, the Q343R variant tends to stabilize disordered conformers, N345K permits the formation of longer, more stable β-strands, and G348V tends to shorten and destabilize them. Finally, N352S acts to alter the β-stand register and when S352 is phosphorylated, it induces partial unfolding. Our results provide a better understanding of TDP-43 aggregation process and will be useful to design effectors capable to modulate its progression.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano" CSIC, Serrano 119, E-28006 Madrid, Spain
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, I-34149 Trieste, Italy
| | - Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, I-34149 Trieste, Italy
| | - Rui M M Brito
- Chemistry Dept., Faculty of Science and Technology & Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Avijit Chakrabartty
- Dept. of Biochemistry, University of Toronto, Toronto Medical Discovery Tower 4-305, MaRS Centre, 101 College St., Toronto, ON M5G 1L7, Canada
| | - Francisco E Baralle
- International Centre for Genetic Engineering and Biotechnology, I-34149 Trieste, Italy.
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano" CSIC, Serrano 119, E-28006 Madrid, Spain.
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138
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Janssens J, Van Broeckhoven C. Pathological mechanisms underlying TDP-43 driven neurodegeneration in FTLD-ALS spectrum disorders. Hum Mol Genet 2013; 22:R77-87. [PMID: 23900071 PMCID: PMC3782069 DOI: 10.1093/hmg/ddt349] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 07/07/2013] [Accepted: 07/21/2013] [Indexed: 01/09/2023] Open
Abstract
Aggregation of misfolded TAR DNA-binding protein 43 (TDP-43) is a striking hallmark of neurodegenerative processes that are observed in several neurological disorders, and in particular in most patients diagnosed with frontotemporal lobar degeneration (FTLD) or amyotrophic lateral sclerosis (ALS). A direct causal link with TDP-43 brain proteinopathy was provided by the identification of pathogenic mutations in TARDBP, the gene encoding TDP-43, in ALS families. However, TDP-43 proteinopathy has also been observed in carriers of mutations in several other genes associated with both ALS and FTLD demonstrating a key role for TDP-43 in neurodegeneration. To date, and despite substantial research into the biology of TDP-43, its functioning in normal brain and in neurodegeneration processes remains largely elusive. Nonetheless, breakthroughs using cellular and animal models have provided valuable insights into ALS and FTLD pathogenesis. Accumulating evidence has redirected the research focus towards a major role for impaired RNA metabolism and protein homeostasis. At the same time, the concept that toxic TDP-43 protein aggregates promote neurodegeneration is losing its credibility. This review aims at highlighting and discussing the current knowledge on TDP-43 driven pathomechanisms leading to neurodegeneration as observed in TDP-43 proteinopathies. Based on the complexity of the associated neurological diseases, a clear understanding of the essential pathological modifications will be crucial for further therapeutic interventions.
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Affiliation(s)
- Jonathan Janssens
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
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