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Talaia G, Bentley-DeSousa A, Ferguson SM. Lysosomal TBK1 Responds to Amino Acid Availability to Relieve Rab7-Dependent mTORC1 Inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.16.571979. [PMID: 38168426 PMCID: PMC10760094 DOI: 10.1101/2023.12.16.571979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Lysosomes play a pivotal role in coordinating macromolecule degradation and regulating cell growth and metabolism. Despite substantial progress in identifying lysosomal signaling proteins, understanding the pathways that synchronize lysosome functions with changing cellular demands remains incomplete. This study uncovers a role for TANK-binding kinase 1 (TBK1), well known for its role in innate immunity and organelle quality control, in modulating lysosomal responsiveness to nutrients. Specifically, we identify a pool of TBK1 that is recruited to lysosomes in response to elevated amino acid levels. At lysosomes, this TBK1 phosphorylates Rab7 on serine 72. This is critical for alleviating Rab7-mediated inhibition of amino acid-dependent mTORC1 activation. Furthermore, a TBK1 mutant (E696K) associated with amyotrophic lateral sclerosis and frontotemporal dementia constitutively accumulates at lysosomes, resulting in elevated Rab7 phosphorylation and increased mTORC1 activation. This data establishes the lysosome as a site of amino acid regulated TBK1 signaling that is crucial for efficient mTORC1 activation. This lysosomal pool of TBK1 has broader implications for lysosome homeostasis, and its dysregulation could contribute to the pathogenesis of ALS-FTD.
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Affiliation(s)
- Gabriel Talaia
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Wu Tsai Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Amanda Bentley-DeSousa
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Wu Tsai Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Shawn M. Ferguson
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Wu Tsai Institute, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
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Giménez-Bejarano A, Alegre-Cortés E, Yakhine-Diop SMS, Gómez-Suaga P, Fuentes JM. Mitochondrial Dysfunction in Repeat Expansion Diseases. Antioxidants (Basel) 2023; 12:1593. [PMID: 37627588 PMCID: PMC10451345 DOI: 10.3390/antiox12081593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/29/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Repeat expansion diseases are a group of neuromuscular and neurodegenerative disorders characterized by expansions of several successive repeated DNA sequences. Currently, more than 50 repeat expansion diseases have been described. These disorders involve diverse pathogenic mechanisms, including loss-of-function mechanisms, toxicity associated with repeat RNA, or repeat-associated non-ATG (RAN) products, resulting in impairments of cellular processes and damaged organelles. Mitochondria, double membrane organelles, play a crucial role in cell energy production, metabolic processes, calcium regulation, redox balance, and apoptosis regulation. Its dysfunction has been implicated in the pathogenesis of repeat expansion diseases. In this review, we provide an overview of the signaling pathways or proteins involved in mitochondrial functioning described in these disorders. The focus of this review will be on the analysis of published data related to three representative repeat expansion diseases: Huntington's disease, C9orf72-frontotemporal dementia/amyotrophic lateral sclerosis, and myotonic dystrophy type 1. We will discuss the common effects observed in all three repeat expansion disorders and their differences. Additionally, we will address the current gaps in knowledge and propose possible new lines of research. Importantly, this group of disorders exhibit alterations in mitochondrial dynamics and biogenesis, with specific proteins involved in these processes having been identified. Understanding the underlying mechanisms of mitochondrial alterations in these disorders can potentially lead to the development of neuroprotective strategies.
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Affiliation(s)
- Alberto Giménez-Bejarano
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Eva Alegre-Cortés
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Sokhna M. S. Yakhine-Diop
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Patricia Gómez-Suaga
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - José M. Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
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3
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Cui Z, Joiner AMN, Jansen RM, Hurley JH. Amino acid sensing and lysosomal signaling complexes. Curr Opin Struct Biol 2023; 79:102544. [PMID: 36804703 DOI: 10.1016/j.sbi.2023.102544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/18/2023]
Abstract
Amino acid pools in the cell are monitored by dedicated sensors, whose structures are now coming into view. The lysosomal Rag GTPases are central to this pathway, and the regulation of their GAP complexes, FLCN-FNIP and GATOR1, have been worked out in detail. For FLCN-FNIP, the entire chain of events from the arginine transporter SLC38A9 to substrate-specific mTORC1 activation has been visualized. The structure GATOR2 has been determined, hinting at an ordering of amino acid signaling across a larger size scale than anticipated. The centerpiece of lysosomal signaling, mTORC1, has been revealed to recognize its substrates by more nuanced and substrate-specific mechanisms than previous appreciated. Beyond the well-studied Rag GTPase and mTORC1 machinery, another lysosomal amino acid sensor/effector system, that of PQLC2 and the C9orf72-containing CSW complex, is coming into structural view. These developments hold promise for further insights into lysosomal physiology and lysosome-centric therapeutics.
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Affiliation(s)
- Zhicheng Cui
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Aaron M N Joiner
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Rachel M Jansen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA.
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Diab R, Pilotto F, Saxena S. Autophagy and neurodegeneration: Unraveling the role of C9ORF72 in the regulation of autophagy and its relationship to ALS-FTD pathology. Front Cell Neurosci 2023; 17:1086895. [PMID: 37006471 PMCID: PMC10060823 DOI: 10.3389/fncel.2023.1086895] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
The proper functioning of the cell clearance machinery is critical for neuronal health within the central nervous system (CNS). In normal physiological conditions, the cell clearance machinery is actively involved in the elimination of misfolded and toxic proteins throughout the lifetime of an organism. The highly conserved and regulated pathway of autophagy is one of the important processes involved in preventing and neutralizing pathogenic buildup of toxic proteins that could eventually lead to the development of neurodegenerative diseases (NDs) such as Alzheimer’s disease or Amyotrophic lateral sclerosis (ALS). The most common genetic cause of ALS and frontotemporal dementia (FTD) is a hexanucleotide expansion consisting of GGGGCC (G4C2) repeats in the chromosome 9 open reading frame 72 gene (C9ORF72). These abnormally expanded repeats have been implicated in leading to three main modes of disease pathology: loss of function of the C9ORF72 protein, the generation of RNA foci, and the production of dipeptide repeat proteins (DPRs). In this review, we discuss the normal physiological role of C9ORF72 in the autophagy-lysosome pathway (ALP), and present recent research deciphering how dysfunction of the ALP synergizes with C9ORF72 haploinsufficiency, which together with the gain of toxic mechanisms involving hexanucleotide repeat expansions and DPRs, drive the disease process. This review delves further into the interactions of C9ORF72 with RAB proteins involved in endosomal/lysosomal trafficking, and their role in regulating various steps in autophagy and lysosomal pathways. Lastly, the review aims to provide a framework for further investigations of neuronal autophagy in C9ORF72-linked ALS-FTD as well as other neurodegenerative diseases.
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Affiliation(s)
- Rim Diab
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Federica Pilotto
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Smita Saxena
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, Bern, Switzerland
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- *Correspondence: Smita Saxena,
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5
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Jansen RM, Hurley JH. Longin domain GAP complexes in nutrient signalling, membrane traffic and neurodegeneration. FEBS Lett 2023; 597:750-761. [PMID: 36367440 PMCID: PMC10050129 DOI: 10.1002/1873-3468.14538] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Small GTPases act as molecular switches and control numerous cellular processes by their binding and hydrolysis of guanosine triphosphate (GTP). The activity of small GTPases is coordinated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). Recent structural and functional studies have characterized a subset of GAPs whose catalytic units consist of longin domains. Longin domain containing GAPs regulate small GTPases that facilitate nutrient signalling, autophagy, vesicular trafficking and lysosome homeostasis. All known examples in this GAP family function as part of larger multiprotein complexes. The three characterized mammalian protein complexes in this class are FLCN:FNIP, GATOR1 and C9orf72:SMCR8. Each complex carries out a unique cellular function by regulating distinct small GTPases. In this article, we explore the roles of longin domain GAPs in nutrient sensing, membrane dynamic, vesicular trafficking and disease. Through a structural lens, we examine the mechanism of each longin domain GAP and highlight potential therapeutic applications.
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Affiliation(s)
- Rachel M. Jansen
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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6
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Xue B, Li R, Ma H, Rahaman A, Kumar V. Comprehensive mapping of mutations in the C9ORF72 that affect folding and binding to SMCR8 protein. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Houghton OH, Mizielinska S, Gomez-Suaga P. The Interplay Between Autophagy and RNA Homeostasis: Implications for Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Front Cell Dev Biol 2022; 10:838402. [PMID: 35573690 PMCID: PMC9096704 DOI: 10.3389/fcell.2022.838402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/14/2022] [Indexed: 01/18/2023] Open
Abstract
Amyotrophic lateral sclerosis and frontotemporal dementia are neurodegenerative disorders that lie on a disease spectrum, sharing genetic causes and pathology, and both without effective therapeutics. Two pathways that have been shown to play major roles in disease pathogenesis are autophagy and RNA homeostasis. Intriguingly, there is an increasing body of evidence suggesting a critical interplay between these pathways. Autophagy is a multi-stage process for bulk and selective clearance of malfunctional cellular components, with many layers of regulation. Although the majority of autophagy research focuses on protein degradation, it can also mediate RNA catabolism. ALS/FTD-associated proteins are involved in many stages of autophagy and autophagy-mediated RNA degradation, particularly converging on the clearance of persistent pathological stress granules. In this review, we will summarise the progress in understanding the autophagy-RNA homeostasis interplay and how that knowledge contributes to our understanding of the pathobiology of ALS/FTD.
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Affiliation(s)
- O H Houghton
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,UK Dementia Research Institute at King's College London, London, United Kingdom
| | - S Mizielinska
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,UK Dementia Research Institute at King's College London, London, United Kingdom
| | - P Gomez-Suaga
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom.,Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Cáceres, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, Spain
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Jiang L, Zhang T, Lu K, Qi S. The progress in C9orf72 research: ALS/FTD pathogenesis, functions and structure. Small GTPases 2022; 13:56-76. [PMID: 33663328 PMCID: PMC9707547 DOI: 10.1080/21541248.2021.1892443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The hexanucleotide repeat (GGGGCC) expansion in C9orf72 is accounted for a large proportion of the genetic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The hypotheses of how the massive G4C2 repeats in C9orf72 destroy the neurons and lead to ALS/FTD are raised and improving. As a multirole player, C9orf72 exerts critical roles in many cellular processes, including autophagy, membrane trafficking, immune response, and so on. Notably, the partners of C9orf72, through which C9orf72 participates in the cell activities, have been identified. Notably, the structures of the C9orf72-SMCR8-WDR41 complex shed light on its activity as GTPase activating proteins (GAP). In this manuscript, we reviewed the latest research progress in the C9orf72-mediated ALS/FTD, the physiological functions of C9orf72, and the putative function models of C9orf72/C9orf72-containing complex.
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Affiliation(s)
- Lan Jiang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tizhong Zhang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kefeng Lu
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China,CONTACT Shiqian Qi Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, Chengdu, China.
These authors contributed equally to this work.
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Nörpel J, Cavadini S, Schenk AD, Graff-Meyer A, Hess D, Seebacher J, Chao JA, Bhaskar V. Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture. PLoS Biol 2021; 19:e3001344. [PMID: 34297726 PMCID: PMC8336837 DOI: 10.1371/journal.pbio.3001344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 08/04/2021] [Accepted: 07/01/2021] [Indexed: 12/30/2022] Open
Abstract
A major cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) spectrum disorder is the hexanucleotide G4C2 repeat expansion in the first intron of the C9orf72 gene. Many underlying mechanisms lead to manifestation of disease that include toxic gain-of-function by repeat G4C2 RNAs, dipeptide repeat proteins, and a reduction of the C9orf72 gene product. The C9orf72 protein interacts with SMCR8 and WDR41 to form a trimeric complex and regulates multiple cellular pathways including autophagy. Here, we report the structure of the C9orf72-SMCR8 complex at 3.8 Å resolution using single-particle cryo-electron microscopy (cryo-EM). The structure reveals 2 distinct dimerization interfaces between C9orf72 and SMCR8 that involves an extensive network of interactions. Homology between C9orf72-SMCR8 and Folliculin-Folliculin Interacting Protein 2 (FLCN-FNIP2), a GTPase activating protein (GAP) complex, enabled identification of a key residue within the active site of SMCR8. Further structural analysis suggested that a coiled-coil region within the uDenn domain of SMCR8 could act as an interaction platform for other coiled-coil proteins, and its deletion reduced the interaction of the C9orf72-SMCR8 complex with FIP200 upon starvation. In summary, this study contributes toward our understanding of the biological function of the C9orf72-SMCR8 complex. Structural and biochemical characterisation of the C9orf72-SMCR8 complex sheds light on its overall architecture and highlights its role as a multi-functional scaffold for coordinating autophagy.
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Affiliation(s)
- Julia Nörpel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andreas D. Schenk
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jeffrey A. Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- * E-mail: (JAC); (VB)
| | - Varun Bhaskar
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- * E-mail: (JAC); (VB)
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10
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Kumar V. Molecular interactions between C9ORF72 and SMCR8: A local energetic frustration perspective. Biochem Biophys Res Commun 2021; 570:1-7. [PMID: 34256240 DOI: 10.1016/j.bbrc.2021.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 11/19/2022]
Abstract
The hexanucleotide repeat expansion in C9orf72 represents a major cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). C9orf72, together with SMCR8 and WDR41, can form a stable complex that regulates autophagy and membrane trafficking. Very recently, the cryo-EM structure of C9orf72-SMCR8-WDR41 helps in understanding the structure-function relationship of C9orf72. This protein complex is indispensable to several cellular processes and is strongly linked to familial ALS and FTD. Understanding the molecular basis of the C9orf72-SMCR8 protein-protein interaction is thus important to comprehend their function. To establish a basis for understanding the relationships between sequence, structure, and function of the C9orf72, this study reports a local frustration analysis on the C9orf72-SMCR8 complex structure. An analysis of local frustration profiles indicated that (1) the structural domains in C9orf72 are minimally-frustrated and relatively conserved, (2) high frustration patches on the protein-protein interface (3) increased frustration in the C-terminal helices involved in the dimerization of C9orf72 structures.
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Affiliation(s)
- Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, UP, 201303, India.
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11
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Root J, Merino P, Nuckols A, Johnson M, Kukar T. Lysosome dysfunction as a cause of neurodegenerative diseases: Lessons from frontotemporal dementia and amyotrophic lateral sclerosis. Neurobiol Dis 2021; 154:105360. [PMID: 33812000 PMCID: PMC8113138 DOI: 10.1016/j.nbd.2021.105360] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 03/16/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are fatal neurodegenerative disorders that are thought to exist on a clinical and pathological spectrum. FTD and ALS are linked by shared genetic causes (e.g. C9orf72 hexanucleotide repeat expansions) and neuropathology, such as inclusions of ubiquitinated, misfolded proteins (e.g. TAR DNA-binding protein 43; TDP-43) in the CNS. Furthermore, some genes that cause FTD or ALS when mutated encode proteins that localize to the lysosome or modulate endosome-lysosome function, including lysosomal fusion, cargo trafficking, lysosomal acidification, autophagy, or TFEB activity. In this review, we summarize evidence that lysosomal dysfunction, caused by genetic mutations (e.g. C9orf72, GRN, MAPT, TMEM106B) or toxic-gain of function (e.g. aggregation of TDP-43 or tau), is an important pathogenic disease mechanism in FTD and ALS. Further studies into the normal function of many of these proteins are required and will help uncover the mechanisms that cause lysosomal dysfunction in FTD and ALS. Mutations or polymorphisms in genes that encode proteins important for endosome-lysosome function also occur in other age-dependent neurodegenerative diseases, including Alzheimer's (e.g. APOE, PSEN1, APP) and Parkinson's (e.g. GBA, LRRK2, ATP13A2) disease. A more complete understanding of the common and unique features of lysosome dysfunction across the spectrum of neurodegeneration will help guide the development of therapies for these devastating diseases.
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Affiliation(s)
- Jessica Root
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Paola Merino
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Austin Nuckols
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Michelle Johnson
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Thomas Kukar
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia; Department of Neurology, Emory University, School of Medicine, Atlanta 30322, Georgia.
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12
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Su MY, Fromm SA, Remis J, Toso DB, Hurley JH. Structural basis for the ARF GAP activity and specificity of the C9orf72 complex. Nat Commun 2021; 12:3786. [PMID: 34145292 PMCID: PMC8213707 DOI: 10.1038/s41467-021-24081-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/27/2021] [Indexed: 02/05/2023] Open
Abstract
Mutation of C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 forms a complex with SMCR8 and WDR41, which was reported to have GTPase activating protein activity toward ARF proteins, RAB8A, and RAB11A. We determined the cryo-EM structure of ARF1-GDP-BeF3- bound to C9orf72:SMCR8:WDR41. The SMCR8longin and C9orf72longin domains form the binding pocket for ARF1. One face of the C9orf72longin domain holds ARF1 in place, while the SMCR8longin positions the catalytic finger Arg147 in the ARF1 active site. Mutations in interfacial residues of ARF1 and C9orf72 reduced or eliminated GAP activity. RAB8A GAP required ~10-fold higher concentrations of the C9orf72 complex than for ARF1. These data support a specific function for the C9orf72 complex as an ARF GAP. The structure also provides a model for the active forms of the longin domain GAPs of FLCN and NPRL2 that regulate the Rag GTPases of the mTORC1 pathway.
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Affiliation(s)
- Ming-Yuan Su
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Simon A Fromm
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonathan Remis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Daniel B Toso
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
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13
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Chua JP, De Calbiac H, Kabashi E, Barmada SJ. Autophagy and ALS: mechanistic insights and therapeutic implications. Autophagy 2021; 18:254-282. [PMID: 34057020 PMCID: PMC8942428 DOI: 10.1080/15548627.2021.1926656] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mechanisms of protein homeostasis are crucial for overseeing the clearance of misfolded and toxic proteins over the lifetime of an organism, thereby ensuring the health of neurons and other cells of the central nervous system. The highly conserved pathway of autophagy is particularly necessary for preventing and counteracting pathogenic insults that may lead to neurodegeneration. In line with this, mutations in genes that encode essential autophagy factors result in impaired autophagy and lead to neurodegenerative conditions such as amyotrophic lateral sclerosis (ALS). However, the mechanistic details underlying the neuroprotective role of autophagy, neuronal resistance to autophagy induction, and the neuron-specific effects of autophagy-impairing mutations remain incompletely defined. Further, the manner and extent to which non-cell autonomous effects of autophagy dysfunction contribute to ALS pathogenesis are not fully understood. Here, we review the current understanding of the interplay between autophagy and ALS pathogenesis by providing an overview of critical steps in the autophagy pathway, with special focus on pivotal factors impaired by ALS-causing mutations, their physiologic effects on autophagy in disease models, and the cell type-specific mechanisms regulating autophagy in non-neuronal cells which, when impaired, can contribute to neurodegeneration. This review thereby provides a framework not only to guide further investigations of neuronal autophagy but also to refine therapeutic strategies for ALS and related neurodegenerative diseases.Abbreviations: ALS: amyotrophic lateral sclerosis; Atg: autophagy-related; CHMP2B: charged multivesicular body protein 2B; DPR: dipeptide repeat; FTD: frontotemporal dementia; iPSC: induced pluripotent stem cell; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; PINK1: PTEN induced kinase 1; RNP: ribonuclear protein; sALS: sporadic ALS; SPHK1: sphingosine kinase 1; TARDBP/TDP-43: TAR DNA binding protein; TBK1: TANK-binding kinase 1; TFEB: transcription factor EB; ULK: unc-51 like autophagy activating kinase; UPR: unfolded protein response; UPS: ubiquitin-proteasome system; VCP: valosin containing protein.
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Affiliation(s)
- Jason P Chua
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
| | - Hortense De Calbiac
- Recherche translationnelle sur les maladies neurologiques, Institut Imagine, UMR-1163 INSERM et Université Paris Descartes, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Edor Kabashi
- Recherche translationnelle sur les maladies neurologiques, Institut Imagine, UMR-1163 INSERM et Université Paris Descartes, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
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14
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Rodrigo LM, Nyholt DR. Imputation and Reanalysis of ExomeChip Data Identifies Novel, Conditional and Joint Genetic Effects on Parkinson's Disease Risk. Genes (Basel) 2021; 12:genes12050689. [PMID: 34064523 PMCID: PMC8147919 DOI: 10.3390/genes12050689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/22/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Given that improved imputation software and high-coverage whole genome sequence (WGS)-based haplotype reference panels now enable inexpensive approximation of WGS genotype data, we hypothesised that WGS-based imputation and analysis of existing ExomeChip-based genome-wide association (GWA) data will identify novel intronic and intergenic single nucleotide polymorphism (SNP) effects associated with complex disease risk. In this study, we reanalysed a Parkinson’s disease (PD) dataset comprising 5540 cases and 5862 controls genotyped using the ExomeChip-based NeuroX array. After genotype imputation and extensive quality control, GWA analysis was performed using PLINK and a recently developed machine learning approach (GenEpi), to identify novel, conditional and joint genetic effects associated with PD. In addition to improved validation of previously reported loci, we identified five novel genome-wide significant loci associated with PD: three (rs137887044, rs78837976 and rs117672332) with 0.01 < MAF < 0.05, and two (rs187989831 and rs12100172) with MAF < 0.01. Conditional analysis within genome-wide significant loci revealed four loci (p < 1 × 10−5) with multiple independent risk variants, while GenEpi analysis identified SNP–SNP interactions in seven genes. In addition to identifying novel risk loci for PD, these results demonstrate that WGS-based imputation and analysis of existing exome genotype data can identify novel intronic and intergenic SNP effects associated with complex disease risk.
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15
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Creekmore BC, Chang YW, Lee EB. The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Proteostasis Factors. J Neuropathol Exp Neurol 2021; 80:494-513. [PMID: 33860329 DOI: 10.1093/jnen/nlab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins. This protein aggregation suggests that abnormal proteostasis contributes to aging-related neurodegeneration. A better fundamental understanding of proteins that regulate proteostasis may provide insight into the pathophysiology of neurodegenerative disease and may perhaps reveal novel therapeutic opportunities. The 26S proteasome is the key effector of the ubiquitin-proteasome system responsible for degrading polyubiquitinated proteins. However, additional factors, such as valosin-containing protein (VCP/p97/Cdc48) and C9orf72, play a role in regulation and trafficking of substrates through the normal proteostasis systems of a cell. Nonhuman AAA+ ATPases, such as the disaggregase Hsp104, also provide insights into the biochemical processes that regulate protein aggregation. X-ray crystallography and cryo-electron microscopy (cryo-EM) structures not bound to substrate have provided meaningful information about the 26S proteasome, VCP, and Hsp104. However, recent cryo-EM structures bound to substrate have provided new information about the function and mechanism of these proteostasis factors. Cryo-EM and cryo-electron tomography data combined with biochemical data have also increased the understanding of C9orf72 and its role in maintaining proteostasis. These structural insights provide a foundation for understanding proteostasis mechanisms with near-atomic resolution upon which insights can be gleaned regarding the pathophysiology of neurodegenerative diseases.
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Affiliation(s)
- Benjamin C Creekmore
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yi-Wei Chang
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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16
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Beckers J, Tharkeshwar AK, Van Damme P. C9orf72 ALS-FTD: recent evidence for dysregulation of the autophagy-lysosome pathway at multiple levels. Autophagy 2021; 17:3306-3322. [PMID: 33632058 PMCID: PMC8632097 DOI: 10.1080/15548627.2021.1872189] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two clinically distinct classes of neurodegenerative disorders. Yet, they share a range of genetic, cellular, and molecular features. Hexanucleotide repeat expansions (HREs) in the C9orf72 gene and the accumulation of toxic protein aggregates in the nervous systems of the affected individuals are among such common features. Though the mechanisms by which HREs cause toxicity is not clear, the toxic gain of function due to transcribed HRE RNA or dipeptide repeat proteins (DPRs) produced by repeat-associated non-AUG translation together with a reduction in C9orf72 expression are proposed as the contributing factors for disease pathogenesis in ALS and FTD. In addition, several recent studies point toward alterations in protein homeostasis as one of the root causes of the disease pathogenesis. In this review, we discuss the effects of the C9orf72 HRE in the autophagy-lysosome pathway based on various recent findings. We suggest that dysfunction of the autophagy-lysosome pathway synergizes with toxicity from C9orf72 repeat RNA and DPRs to drive disease pathogenesis. Abbreviation: ALP: autophagy-lysosome pathway; ALS: amyotrophic lateral sclerosis; AMPK: AMP-activated protein kinase; ATG: autophagy-related; ASO: antisense oligonucleotide; C9orf72: C9orf72-SMCR8 complex subunit; DENN: differentially expressed in normal and neoplastic cells; DPR: dipeptide repeat protein; EIF2A/eIF2α: eukaryotic translation initiation factor 2A; ER: endoplasmic reticulum; FTD: frontotemporal dementia; GAP: GTPase-activating protein; GEF: guanine nucleotide exchange factor; HRE: hexanucleotide repeat expansion; iPSC: induced pluripotent stem cell; ISR: integrated stress response; M6PR: mannose-6-phosphate receptor, cation dependent; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MN: motor neuron; MTORC1: mechanistic target of rapamycin kinase complex 1; ND: neurodegenerative disorder; RAN: repeat-associated non-ATG; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SLC66A1/PQLC2: solute carrier family 66 member 1; SMCR8: SMCR8-C9orf72 complex subunit; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TARDBP/TDP-43: TAR DNA binding protein; TBK1: TANK binding kinase 1; TFEB: transcription factor EB; ULK1: unc-51 like autophagy activating kinase 1; UPS: ubiquitin-proteasome system; WDR41: WD repeat domain 41.
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Affiliation(s)
- Jimmy Beckers
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Arun Kumar Tharkeshwar
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, Leuven, Belgium
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17
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Talaia G, Amick J, Ferguson SM. Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids. Proc Natl Acad Sci U S A 2021; 118:e2014941118. [PMID: 33597295 PMCID: PMC7923529 DOI: 10.1073/pnas.2014941118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PQLC2, a lysosomal cationic amino acid transporter, also serves as a sensor that responds to scarcity of its substrates by recruiting a protein complex composed of C9orf72, SMCR8, and WDR41 to the surface of lysosomes. This protein complex controls multiple aspects of lysosome function. Although it is known that this response to changes in cationic amino acid availability depends on an interaction between PQLC2 and WDR41, the underlying mechanism for the regulated interaction is not known. In this study, we present evidence that the WDR41-PQLC2 interaction is mediated by a short peptide motif in a flexible loop that extends from the WDR41 β-propeller and inserts into a cavity presented by the inward-facing conformation of PQLC2. The data support a transceptor model wherein conformational changes in PQLC2 related to substrate transport regulate the availability of the WDR41-binding site on PQLC2 and mediate recruitment of the WDR41-SMCR8-C9orf72 complex to the surface of lysosomes.
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Affiliation(s)
- Gabriel Talaia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Joseph Amick
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Shawn M Ferguson
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510;
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
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18
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Su MY, Fromm SA, Zoncu R, Hurley JH. Structure of the C9orf72 ARF GAP complex that is haploinsufficient in ALS and FTD. Nature 2020; 585:251-255. [PMID: 32848248 PMCID: PMC8054479 DOI: 10.1038/s41586-020-2633-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 05/20/2020] [Indexed: 12/17/2022]
Abstract
Mutation of C9orf72 is the most prevalent defect associated with amyotrophic lateral sclerosis and frontotemporal degeneration1. Together with hexanucleotide-repeat expansion2,3, haploinsufficiency of C9orf72 contributes to neuronal dysfunction4-6. Here we determine the structure of the C9orf72-SMCR8-WDR41 complex by cryo-electron microscopy. C9orf72 and SMCR8 both contain longin and DENN (differentially expressed in normal and neoplastic cells) domains7, and WDR41 is a β-propeller protein that binds to SMCR8 such that the whole structure resembles an eye slip hook. Contacts between WDR41 and the DENN domain of SMCR8 drive the lysosomal localization of the complex in conditions of amino acid starvation. The structure suggested that C9orf72-SMCR8 is a GTPase-activating protein (GAP), and we found that C9orf72-SMCR8-WDR41 acts as a GAP for the ARF family of small GTPases. These data shed light on the function of C9orf72 in normal physiology, and in amyotrophic lateral sclerosis and frontotemporal degeneration.
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Affiliation(s)
- Ming-Yuan Su
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Simon A Fromm
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA. .,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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19
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Amick J, Tharkeshwar AK, Talaia G, Ferguson SM. PQLC2 recruits the C9orf72 complex to lysosomes in response to cationic amino acid starvation. J Cell Biol 2020; 219:132798. [PMID: 31851326 PMCID: PMC7039192 DOI: 10.1083/jcb.201906076] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/07/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022] Open
Abstract
This study reveals that PQLC2, a lysosomal transporter of cationic amino acids, coordinates cellular responses to cationic amino acid availability via the regulated recruitment of a heterotrimeric protein complex containing C9orf72, SMCR8, and WDR41 to the surface of lysosomes. The C9orf72 protein is required for normal lysosome function. In support of such functions, C9orf72 forms a heterotrimeric complex with SMCR8 and WDR41 that is recruited to lysosomes when amino acids are scarce. These properties raise questions about the identity of the lysosomal binding partner of the C9orf72 complex and the amino acid–sensing mechanism that regulates C9orf72 complex abundance on lysosomes. We now demonstrate that an interaction with the lysosomal cationic amino acid transporter PQLC2 mediates C9orf72 complex recruitment to lysosomes. This is achieved through an interaction between PQLC2 and WDR41. The interaction between PQLC2 and the C9orf72 complex is negatively regulated by arginine, lysine, and histidine, the amino acids that PQLC2 transports across the membrane of lysosomes. These results define a new role for PQLC2 in the regulated recruitment of the C9orf72 complex to lysosomes and reveal a novel mechanism that allows cells to sense and respond to changes in the availability of cationic amino acids within lysosomes.
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Affiliation(s)
- Joseph Amick
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
| | - Arun Kumar Tharkeshwar
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
| | - Gabriel Talaia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
| | - Shawn M Ferguson
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT.,Department of Neuroscience, Yale University School of Medicine, New Haven, CT.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
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20
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Goodier JL, Soares AO, Pereira GC, DeVine LR, Sanchez L, Cole RN, García-Pérez JL. C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease. Acta Neuropathol Commun 2020; 8:110. [PMID: 32678027 PMCID: PMC7364817 DOI: 10.1186/s40478-020-00982-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023] Open
Abstract
A pathogenic GGGCCC hexanucleotide expansion in the first intron/promoter region of the C9orf72 gene is the most common mutation associated with amyotrophic lateral sclerosis (ALS). The C9orf72 gene product forms a complex with SMCR8 (Smith-Magenis Syndrome Chromosome Region, Candidate 8) and WDR41 (WD Repeat domain 41) proteins. Recent studies have indicated roles for the complex in autophagy regulation, vesicle trafficking, and immune response in transgenic mice, however a direct connection with ALS etiology remains unclear. With the aim of increasing understanding of the multi-functional C9orf72-SMCR8-WDR41 complex, we determined by mass spectrometry analysis the proteins that directly associate with SMCR8. SMCR8 protein binds many components of the ubiquitin-proteasome system, and we demonstrate its poly-ubiquitination without obvious degradation. Evidence is also presented for localization of endogenous SMCR8 protein to cytoplasmic stress granules. However, in several cell lines we failed to reproduce previous observations that C9orf72 protein enters these granules. SMCR8 protein associates with many products of genes associated with various Mendelian neurological disorders in addition to ALS, implicating SMCR8-containing complexes in a range of neuropathologies. We reinforce previous observations that SMCR8 and C9orf72 protein levels are positively linked, and now show in vivo that SMCR8 protein levels are greatly reduced in brain tissues of C9orf72 gene expansion carrier individuals. While further study is required, these data suggest that SMCR8 protein level might prove a useful biomarker for the C9orf72 expansion in ALS.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Alisha O. Soares
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Gavin C. Pereira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Lauren R. DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Robert N. Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
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21
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Thimiri Govinda Raj DB, Khan NA, Venkatachalam S, Arumugam S. Efficient Nanobiotechnology Method for Magnetic Lysosome Enrichment Using DMSA-SPMNP 2.0. BIONANOSCIENCE 2020. [DOI: 10.1007/s12668-020-00736-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Cali CP, Patino M, Tai YK, Ho WY, McLean CA, Morris CM, Seeley WW, Miller BL, Gaig C, Vonsattel JPG, White CL, Roeber S, Kretzschmar H, Troncoso JC, Troakes C, Gearing M, Ghetti B, Van Deerlin VM, Lee VMY, Trojanowski JQ, Mok KY, Ling H, Dickson DW, Schellenberg GD, Ling SC, Lee EB. C9orf72 intermediate repeats are associated with corticobasal degeneration, increased C9orf72 expression and disruption of autophagy. Acta Neuropathol 2019; 138:795-811. [PMID: 31327044 PMCID: PMC6802287 DOI: 10.1007/s00401-019-02045-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022]
Abstract
Microsatellite repeat expansion disease loci can exhibit pleiotropic clinical and biological effects depending on repeat length. Large expansions in C9orf72 (100s-1000s of units) are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). However, whether intermediate expansions also contribute to neurodegenerative disease is not well understood. Several studies have identified intermediate repeats in Parkinson's disease patients, but the association was not found in autopsy-confirmed cases. We hypothesized that intermediate C9orf72 repeats are a genetic risk factor for corticobasal degeneration (CBD), a neurodegenerative disease that can be clinically similar to Parkinson's but has distinct tau protein pathology. Indeed, intermediate C9orf72 repeats were significantly enriched in autopsy-proven CBD (n = 354 cases, odds ratio = 3.59, p = 0.00024). While large C9orf72 repeat expansions are known to decrease C9orf72 expression, intermediate C9orf72 repeats result in increased C9orf72 expression in human brain tissue and CRISPR/cas9 knockin iPSC-derived neural progenitor cells. In contrast to cases of FTD/ALS with large C9orf72 expansions, CBD with intermediate C9orf72 repeats was not associated with pathologic RNA foci or dipeptide repeat protein aggregates. Knock-in cells with intermediate repeats exhibit numerous changes in gene expression pathways relating to vesicle trafficking and autophagy. Additionally, overexpression of C9orf72 without the repeat expansion leads to defects in autophagy under nutrient starvation conditions. These results raise the possibility that therapeutic strategies to reduce C9orf72 expression may be beneficial for the treatment of CBD.
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Affiliation(s)
- Christopher P Cali
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Maribel Patino
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Yee Kit Tai
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Wan Yun Ho
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Catriona A McLean
- Department of Anatomical Pathology, Alfred Health and Victorian Brain Bank, Florey Neurosciences, Parkville, VIC, Australia
| | - Christopher M Morris
- Newcastle Brain Tissue Resource, Edwardson Building, Newcastle University, Newcastle upon Tyne, NE4 5PL, UK
| | - William W Seeley
- Department of Neurology, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Bruce L Miller
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Carles Gaig
- Universitat de Barcelona Hospital Clínic and Banc de Teixits Neurològics, Barcelona, Spain
| | | | - Charles L White
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sigrun Roeber
- Institute for Neuropathology and Prion Research and Brain Net Germany, Ludwig-Maximilians-Universität, Munich, Germany
| | - Hans Kretzschmar
- Institute for Neuropathology and Prion Research and Brain Net Germany, Ludwig-Maximilians-Universität, Munich, Germany
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Marla Gearing
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vivianna M Van Deerlin
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia M-Y Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kin Y Mok
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK
- Division of Life Science, State Key Laboratory of Molecular Neuroscience and Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Helen Ling
- Reta Lila Weston Institute of Neurological Studies, University College London Institute of Neurology, London, UK
| | | | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shuo-Chien Ling
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
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Angarola B, Ferguson SM. Weak membrane interactions allow Rheb to activate mTORC1 signaling without major lysosome enrichment. Mol Biol Cell 2019; 30:2750-2760. [PMID: 31532697 PMCID: PMC6789162 DOI: 10.1091/mbc.e19-03-0146] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Stable localization of the Rheb GTPase to lysosomes is thought to be required for activation of mTOR complex 1 (mTORC1) signaling. However, the lysosome targeting mechanisms for Rheb remain unclear. We therefore investigated the relationship between Rheb subcellular localization and mTORC1 activation. Surprisingly, we found that Rheb was undetectable at lysosomes. Nonetheless, functional assays in knockout human cells revealed that farnesylation of the C-terminal CaaX motif on Rheb was essential for Rheb-dependent mTORC1 activation. Although farnesylated Rheb exhibited partial endoplasmic reticulum (ER) localization, constitutively targeting Rheb to ER membranes did not support mTORC1 activation. Further systematic analysis of Rheb lipidation revealed that weak, nonselective, membrane interactions support Rheb-dependent mTORC1 activation without the need for a specific lysosome targeting motif. Collectively, these results argue against stable interactions of Rheb with lysosomes and instead that transient membrane interactions optimally allow Rheb to activate mTORC1 signaling.
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Affiliation(s)
- Brittany Angarola
- Departments of Cell Biology and Neuroscience, Yale University School of Medicine, New Haven, CT 06510
| | - Shawn M Ferguson
- Departments of Cell Biology and Neuroscience, Yale University School of Medicine, New Haven, CT 06510
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