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Yu ZQ, Carmichael J, Collins GA, D'Agostino MD, Lessard M, Firth HV, Harijan P, Fry AE, Dean J, Zhang J, Kini U, Goldberg AL, Rubinsztein DC. PSMC5 insufficiency and P320R mutation impair proteasome function. Hum Mol Genet 2024:ddae085. [PMID: 38776958 DOI: 10.1093/hmg/ddae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The ubiquitin-proteasome system mediates the degradation of a wide variety of proteins. Proteasome dysfunction is associated with neurodegenerative diseases and neurodevelopmental disorders in humans. Here we identified mutations in PSMC5, an AAA ATPase subunit of the proteasome 19S regulatory particle, in individuals with neurodevelopmental disorders, which were initially considered as variants of unknown significance. We have now found heterozygotes with the following mutations: P320R (6 individuals), R325W, Q160A, and one nonsense mutation at Q69. We focused on understanding the functional consequence of PSMC5 insufficiency and the P320R mutation in cells and found that both impair proteasome function and activate apoptosis. Interestingly, the P320R mutation impairs proteasome function by weakening the association between the 19S regulatory particle and the 20S core particle. Our study supports that proteasome dysfunction is the pathogenic cause of neurodevelopmental disorders in individuals carrying PSMC5 variants.
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Affiliation(s)
- Zhong-Qiu Yu
- Cambridge Institute for Medical Research, The Keith Peters Building, Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
- UK Dementia Research Institute, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Jenny Carmichael
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Box 134, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Galen A Collins
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, 32 Creelman Street, Starkville MS 39762, United States
| | - Maria Daniela D'Agostino
- Division of Medical Genetics, Department of Specialised Medicine, McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada
- Care for Rare Canada Consortium, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, K1H 8L1, ON, Canada
| | - Mathieu Lessard
- Division of Medical Genetics, Department of Specialised Medicine, McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada
- Care for Rare Canada Consortium, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, K1H 8L1, ON, Canada
| | - Helen V Firth
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Box 134, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Pooja Harijan
- Department of Paediatric Neurosciences, Box 107, Child development centre, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Andrew E Fry
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, United Kingdom
- Division of Cancer and Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - John Dean
- The School of Medicine, Medical Sciences and Nutrition, Polwarth Building, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford & Radcliffe Department of Medicine, University of Oxford, Windmill Road, Oxford, OX3 7HE, United Kingdom
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
| | - David C Rubinsztein
- Cambridge Institute for Medical Research, The Keith Peters Building, Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
- UK Dementia Research Institute, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
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Aviner R, Lee TT, Masto VB, Li KH, Andino R, Frydman J. Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington's disease. Nat Cell Biol 2024:10.1038/s41556-024-01414-x. [PMID: 38741019 DOI: 10.1038/s41556-024-01414-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG trinucleotide repeat in the Huntingtin (HTT) gene, encoding a homopolymeric polyglutamine (polyQ) tract. Although mutant HTT (mHTT) protein is known to aggregate, the links between aggregation and neurotoxicity remain unclear. Here we show that both translation and aggregation of wild-type HTT and mHTT are regulated by a stress-responsive upstream open reading frame and that polyQ expansions cause abortive translation termination and release of truncated, aggregation-prone mHTT fragments. Notably, we find that mHTT depletes translation elongation factor eIF5A in brains of symptomatic HD mice and cultured HD cells, leading to pervasive ribosome pausing and collisions. Loss of eIF5A disrupts homeostatic controls and impairs recovery from acute stress. Importantly, drugs that inhibit translation initiation reduce premature termination and mitigate this escalating cascade of ribotoxic stress and dysfunction in HD.
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Affiliation(s)
- Ranen Aviner
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Ting-Ting Lee
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
| | - Vincent B Masto
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA.
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3
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Galka D, Ali TT, Bast A, Niederleithinger M, Gerhardt E, Motosugi R, Sakata E, Knop M, Outeiro TF, Popova B, Braus GH. Inhibition of 26S proteasome activity by α-synuclein is mediated by the proteasomal chaperone Rpn14/PAAF1. Aging Cell 2024; 23:e14128. [PMID: 38415292 PMCID: PMC11113265 DOI: 10.1111/acel.14128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/01/2024] [Accepted: 02/11/2024] [Indexed: 02/29/2024] Open
Abstract
Parkinson's disease (PD) is characterized by aggregation of α-synuclein (α-syn) into protein inclusions in degenerating brains. Increasing amounts of aggregated α-syn species indicate significant perturbation of cellular proteostasis. Altered proteostasis depends on α-syn protein levels and the impact of α-syn on other components of the proteostasis network. Budding yeast Saccharomyces cerevisiae was used as eukaryotic reference organism to study the consequences of α-syn expression on protein dynamics. To address this, we investigated the impact of overexpression of α-syn and S129A variant on the abundance and stability of most yeast proteins using a genome-wide yeast library and a tandem fluorescent protein timer (tFT) reporter as a measure for protein stability. This revealed that the stability of in total 377 cellular proteins was altered by α-syn expression, and that the impact on protein stability was significantly enhanced by phosphorylation at Ser129 (pS129). The proteasome assembly chaperone Rpn14 was identified as one of the top candidates for increased protein stability by expression of pS129 α-syn. Elevated levels of Rpn14 enhanced the growth inhibition by α-syn and the accumulation of ubiquitin conjugates in the cell. We found that Rpn14 interacts physically with α-syn and stabilizes pS129 α-syn. The expression of α-syn along with elevated levels of Rpn14 or its human counterpart PAAF1 reduced the proteasome activity in yeast and in human cells, supporting that pS129 α-syn negatively affects the 26S proteasome through Rpn14. This comprehensive study into the alternations of protein homeostasis highlights the critical role of the Rpn14/PAAF1 in α-syn-mediated proteasome dysfunction.
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Affiliation(s)
- Dajana Galka
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and GeneticsUniversity of GöttingenGöttingenGermany
| | - Tariq T. Ali
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and GeneticsUniversity of GöttingenGöttingenGermany
| | - Alexander Bast
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and GeneticsUniversity of GöttingenGöttingenGermany
| | - Marie Niederleithinger
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and GeneticsUniversity of GöttingenGöttingenGermany
| | - Ellen Gerhardt
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of NeurodegenerationUniversity Medical Center GöttingenGöttingenGermany
| | - Ryo Motosugi
- Institute for Auditory NeuroscienceUniversity Medical Center GöttingenGöttingenGermany
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC)University of GöttingenGöttingenGermany
| | - Eri Sakata
- Institute for Auditory NeuroscienceUniversity Medical Center GöttingenGöttingenGermany
- Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC)University of GöttingenGöttingenGermany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ‐ZMBH AllianceHeidelberg UniversityHeidelbergGermany
| | - Tiago F. Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of NeurodegenerationUniversity Medical Center GöttingenGöttingenGermany
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)GöttingenGermany
| | - Blagovesta Popova
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and GeneticsUniversity of GöttingenGöttingenGermany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and GeneticsUniversity of GöttingenGöttingenGermany
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4
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Ikeda T, Yamazaki K, Okumura F, Kamura T, Nakatsukasa K. Role of the San1 ubiquitin ligase in the heat stress-induced degradation of nonnative Nup1 in the nuclear pore complex. Genetics 2024; 226:iyae017. [PMID: 38302116 DOI: 10.1093/genetics/iyae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 11/21/2022] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
The nuclear pore complex (NPC) mediates the selective exchange of macromolecules between the nucleus and the cytoplasm. Neurodegenerative diseases such as amyotrophic lateral sclerosis are characterized by mislocalization of nucleoporins (Nups), transport receptors, and Ras-related nuclear proteins into nucleoplasmic or cytosolic aggregates, underscoring the importance of precise assembly of the NPC. The assembly state of large protein complexes is strictly monitored by the protein quality control system. The ubiquitin-proteasome system may eliminate aberrant, misfolded, and/or orphan components; however, the involvement of the ubiquitin-proteasome system in the degradation of nonnative Nups in the NPC remains unclear. Here, we show that in Saccharomyces cerevisiae, although Nup1 (the FG-Nup component of the central core of the NPC) was stable, C-terminally green fluorescent protein-tagged Nup1, which had been incorporated into the NPC, was degraded by the proteasome especially under heat stress conditions. The degradation was dependent on the San1 ubiquitin ligase and Cdc48/p97, as well as its cofactor Doa1. We also demonstrate that San1 weakly but certainly contributes to the degradation of nontagged endogenous Nup1 in cells defective in NPC biogenesis by the deletion of NUP120. In addition, the overexpression of SAN1 exacerbated the growth defect phenotype of nup120Δ cells, which may be caused by excess degradation of defective Nups due to the deletion of NUP120. These biochemical and genetic data suggest that San1 is involved in the degradation of nonnative Nups generated by genetic mutation or when NPC biogenesis is impaired.
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Affiliation(s)
- Takanari Ikeda
- Graduate School of Science, Nagoya City University, Nagoya, Aichi 467-8501, Japan
| | - Kenji Yamazaki
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Fukuoka 813-8529, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Nagoya, Aichi 467-8501, Japan
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5
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Kandel R, Jung J, Neal S. Proteotoxic stress and the ubiquitin proteasome system. Semin Cell Dev Biol 2024; 156:107-120. [PMID: 37734998 PMCID: PMC10807858 DOI: 10.1016/j.semcdb.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/01/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
The ubiquitin proteasome system maintains protein homeostasis by regulating the breakdown of misfolded proteins, thereby preventing misfolded protein aggregates. The efficient elimination is vital for preventing damage to the cell by misfolded proteins, known as proteotoxic stress. Proteotoxic stress can lead to the collapse of protein homeostasis and can alter the function of the ubiquitin proteasome system. Conversely, impairment of the ubiquitin proteasome system can also cause proteotoxic stress and disrupt protein homeostasis. This review examines two impacts of proteotoxic stress, 1) disruptions to ubiquitin homeostasis (ubiquitin stress) and 2) disruptions to proteasome homeostasis (proteasome stress). Here, we provide a mechanistic description of the relationship between proteotoxic stress and the ubiquitin proteasome system. This relationship is illustrated by findings from several protein misfolding diseases, mainly neurodegenerative diseases, as well as from basic biology discoveries from yeast to mammals. In addition, we explore the importance of the ubiquitin proteasome system in endoplasmic reticulum quality control, and how proteotoxic stress at this organelle is alleviated. Finally, we highlight how cells utilize the ubiquitin proteasome system to adapt to proteotoxic stress and how the ubiquitin proteasome system can be genetically and pharmacologically manipulated to maintain protein homeostasis.
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Affiliation(s)
- Rachel Kandel
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Jasmine Jung
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Sonya Neal
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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6
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Du H, Dardas Z, Jolly A, Grochowski CM, Jhangiani SN, Li H, Muzny D, Fatih JM, Yesil G, Elçioglu NH, Gezdirici A, Marafi D, Pehlivan D, Calame DG, Carvalho CMB, Posey JE, Gambin T, Coban-Akdemir Z, Lupski JR. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. Nucleic Acids Res 2024; 52:e18. [PMID: 38153174 PMCID: PMC10899794 DOI: 10.1093/nar/gkad1223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/18/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Homozygous duplications contribute to genetic disease by altering gene dosage or disrupting gene regulation and can be more deleterious to organismal biology than heterozygous duplications. Intragenic exonic duplications can result in loss-of-function (LoF) or gain-of-function (GoF) alleles that when homozygosed, i.e. brought to homozygous state at a locus by identity by descent or state, could potentially result in autosomal recessive (AR) rare disease traits. However, the detection and functional interpretation of homozygous duplications from exome sequencing data remains a challenge. We developed a framework algorithm, HMZDupFinder, that is designed to detect exonic homozygous duplications from exome sequencing (ES) data. The HMZDupFinder algorithm can efficiently process large datasets and accurately identifies small intragenic duplications, including those associated with rare disease traits. HMZDupFinder called 965 homozygous duplications with three or less exons from 8,707 ES with a recall rate of 70.9% and a precision of 16.1%. We experimentally confirmed 8/10 rare homozygous duplications. Pathogenicity assessment of these copy number variant alleles allowed clinical genomics contextualization for three homozygous duplications alleles, including two affecting known OMIM disease genes EDAR (MIM# 224900), TNNT1(MIM# 605355), and one variant in a novel candidate disease gene: PAAF1.
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Affiliation(s)
- Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gozde Yesil
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul 34093, Turkey
| | - Nursel H Elçioglu
- Department of Pediatric Genetics, Marmara University Medical Faculty, Istanbul and Eastern Mediterranean University Faculty of Medicine, Mersin 10, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, University of Health Sciences, Basaksehir Cam and Sakura City Hospital, 34480 Istanbul, Turkey
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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7
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Münch C, Kirstein J. Protein quality control: from molecular mechanisms to therapeutic intervention-EMBO workshop, May 21-26 2023, Srebreno, Croatia. Cell Stress Chaperones 2023; 28:631-640. [PMID: 37731161 PMCID: PMC10746685 DOI: 10.1007/s12192-023-01383-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
Protein quality control pathways ensure a functional proteome and rely on a complex proteostasis network (PN) that is composed of molecular chaperones and proteases. Failures in the PN can lead to a broad spectrum of diseases, including neurodegenerative disorders like Alzheimer's, Parkinson's, and a range of motor neuron diseases. The EMBO workshop "Protein quality control: from molecular mechanisms to therapeutic intervention" covered all aspects of protein quality control from underlying molecular mechanisms of chaperones and proteases to stress signaling pathways and medical implications. This report summarizes the workshop and highlights selected presentations.
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Affiliation(s)
- Christian Münch
- Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Janine Kirstein
- Friedrich-Schiller-Universität Jena, Jena, Germany.
- Leibniz-Institute on Aging/Fritz-Lipmann Institute, Jena, Germany.
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8
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Yagita Y, Zavodszky E, Peak-Chew SY, Hegde RS. Mechanism of orphan subunit recognition during assembly quality control. Cell 2023; 186:3443-3459.e24. [PMID: 37480851 PMCID: PMC10501995 DOI: 10.1016/j.cell.2023.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 05/16/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
Cells contain numerous abundant molecular machines assembled from multiple subunits. Imbalances in subunit production and failed assembly generate orphan subunits that are eliminated by poorly defined pathways. Here, we determined how orphan subunits of the cytosolic chaperonin CCT are recognized. Several unassembled CCT subunits recruited the E3 ubiquitin ligase HERC2 using ZNRD2 as an adaptor. Both factors were necessary for orphan CCT subunit degradation in cells, sufficient for CCT subunit ubiquitination with purified factors, and necessary for optimal cell fitness. Domain mapping and structure prediction defined the molecular features of a minimal HERC2-ZNRD2-CCT module. The structural model, whose key elements were validated in cells using point mutants, shows why ZNRD2 selectively recognizes multiple orphaned CCT subunits without engaging assembled CCT. Our findings reveal how failures during CCT assembly are monitored and provide a paradigm for the molecular recognition of orphan subunits, the largest source of quality control substrates in cells.
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Affiliation(s)
- Yuichi Yagita
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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9
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Liu K, Zhang S, Gong Y, Zhu P, Shen W, Zhang Q. PSMC4 promotes prostate carcinoma progression by regulating the CBX3-EGFR-PI3K-AKT-mTOR pathway. J Cell Mol Med 2023; 27:2437-2447. [PMID: 37436074 PMCID: PMC10424298 DOI: 10.1111/jcmm.17832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/15/2023] [Accepted: 06/24/2023] [Indexed: 07/13/2023] Open
Abstract
Proteasome 26S subunit ATPase 4 (PSMC4) could regulate cancer progression. However, the function of PSMC4 in prostate carcinoma (PCa) progression requires further clarification. In the study, PSMC4 and chromobox 3 (CBX3) levels were verified by TCGA data and tissue microarrays. Cell counting kit-8, cell apoptosis, cell cycle, wound healing, transwell and xenograft tumour model assays were performed to verify biological functions of PSMC4 in PCa. RNA-seq, PCR, western blotting and co-IP assays were performed to verify the mechanism of PSMC4. Results showed that PSMC4 level was significantly increased in PCa tissues, and patients with PCa with a high PSMC4 level exhibited shorter overall survival. PSMC4 knockdown markedly inhibited cell proliferation, cell cycle and migration in vitro and in vivo, and significantly promoted cell apoptosis. Then further study revealed that CBX3 was a downstream target of PSMC4. PSMC4 knockdown markedly reduced CBX3 level, and inhibited PI3K-AKT-mTOR signalling. CBX3 overexpression markedly promoted epidermal growth factor receptor (EGFR) level. Finally, PSMC4 overexpression showed reverse effect in DU145 cells, and the effects of PSMC4 overexpression on cell proliferation, migration and clonal formation were rescued by the CBX3 knockdown, and regulated EGFR-PI3K-AKT-mTOR signalling. In conclusion, PSMC4 could regulate the PCa progression by mediating the CBX3-EGFR-PI3K-AKT-mTOR pathway. These findings provided a new target for PCa treatment.
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Affiliation(s)
- Kaifeng Liu
- Department of AndrologyNorthern Jiangsu People's Hospital Affiliated to Yangzhou UniversityYangzhouChina
- Department of Andrology, Northern Jiangsu People's HospitalAffiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Shengmin Zhang
- Department of AndrologyNorthern Jiangsu People's Hospital Affiliated to Yangzhou UniversityYangzhouChina
- Department of Andrology, Northern Jiangsu People's HospitalAffiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Yongzhan Gong
- Department of AndrologyNorthern Jiangsu People's Hospital Affiliated to Yangzhou UniversityYangzhouChina
- Department of Andrology, Northern Jiangsu People's HospitalAffiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Panyan Zhu
- Department of AndrologyNorthern Jiangsu People's Hospital Affiliated to Yangzhou UniversityYangzhouChina
- Department of Andrology, Northern Jiangsu People's HospitalAffiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Weigan Shen
- Department of AndrologyNorthern Jiangsu People's Hospital Affiliated to Yangzhou UniversityYangzhouChina
- Yangzhou University Medical CollegeYangzhouChina
| | - Qi Zhang
- Department of UrologyZhejiang Provincial People's HospitalHangzhouChina
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10
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Sun C, Desch K, Nassim-Assir B, Giandomenico SL, Nemcova P, Langer JD, Schuman EM. An abundance of free regulatory (19 S) proteasome particles regulates neuronal synapses. Science 2023; 380:eadf2018. [PMID: 37228199 DOI: 10.1126/science.adf2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/04/2023] [Indexed: 05/27/2023]
Abstract
The proteasome, the major protein-degradation machine in cells, regulates neuronal synapses and long-term information storage. Here, using super-resolution microscopy, we found that the two essential subcomplexes of the proteasome, the regulatory (19S) and catalytic (20S) particles, are differentially distributed within individual rat cortical neurons. We discovered an unexpected abundance of free 19S particles near synapses. The free neuronal 19S particles bind and deubiquitylate lysine 63-ubiquitin (Lys63-ub), a non-proteasome-targeting ubiquitin linkage. Pull-down assays revealed a significant overrepresentation of synaptic molecules as Lys63-ub interactors. Inhibition of the 19S deubiquitylase activity significantly altered excitatory synaptic transmission and reduced the synaptic availability of AMPA receptors at multiple trafficking points in a proteasome-independent manner. Together, these results reveal a moonlighting function of the regulatory proteasomal subcomplex near synapses.
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Affiliation(s)
- Chao Sun
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | - Kristina Desch
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | | | | | - Paulina Nemcova
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
- Max Planck Institute for Biophysics, 60438 Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
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11
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Li H, Xu Y, Li W, Zhang L, Zhang X, Li B, Chen Y, Wang X, Zhu C. Novel insights into the immune cell landscape and gene signatures in autism spectrum disorder by bioinformatics and clinical analysis. Front Immunol 2023; 13:1082950. [PMID: 36761165 PMCID: PMC9905846 DOI: 10.3389/fimmu.2022.1082950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023] Open
Abstract
The pathogenesis of autism spectrum disorder (ASD) is not well understood, especially in terms of immunity and inflammation, and there are currently no early diagnostic or treatment methods. In this study, we obtained six existing Gene Expression Omnibus transcriptome datasets from the blood of ASD patients. We performed functional enrichment analysis, PPI analysis, CIBERSORT algorithm, and Spearman correlation analysis, with a focus on expression profiling in hub genes and immune cells. We validated that monocytes and nonclassical monocytes were upregulated in the ASD group using peripheral blood (30 children with ASD and 30 age and sex-matched typically developing children) using flow cytometry. The receiver operating characteristic curves (PSMC4 and ALAS2) and analysis stratified by ASD severity (LIlRB1 and CD69) showed that they had predictive value using the "training" and verification groups. Three immune cell types - monocytes, M2 macrophages, and activated dendritic cells - had different degrees of correlation with 15 identified hub genes. In addition, we analyzed the miRNA-mRNA network and agents-gene interactions using miRNA databases (starBase and miRDB) and the DSigDB database. Two miRNAs (miR-342-3p and miR-1321) and 23 agents were linked with ASD. These findings suggest that dysregulation of the immune system may contribute to ASD development, especially dysregulation of monocytes and monocyte-derived cells. ASD-related hub genes may serve as potential predictors for ASD, and the potential ASD-related miRNAs and agents identified here may open up new strategies for the prevention and treatment of ASD.
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Affiliation(s)
- Hongwei Li
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China,National Health Council (NHC) Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Wenhua Li
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lingling Zhang
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bingbing Li
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiwen Chen
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoyang Wang
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Centre of Perinatal Medicine and Health, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden,*Correspondence: Changlian Zhu, ;;
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12
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Pérez-Villegas EM, Ruiz R, Bachiller S, Ventura F, Armengol JA, Rosa JL. The HERC proteins and the nervous system. Semin Cell Dev Biol 2022; 132:5-15. [PMID: 34848147 DOI: 10.1016/j.semcdb.2021.11.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022]
Abstract
The HERC protein family is one of three subfamilies of Homologous to E6AP C-terminus (HECT) E3 ubiquitin ligases. Six HERC genes have been described in humans, two of which encode Large HERC proteins -HERC1 and HERC2- with molecular weights above 520 kDa that are constitutively expressed in the brain. There is a large body of evidence that mutations in these Large HERC genes produce clinical syndromes in which key neurodevelopmental events are altered, resulting in intellectual disability and other neurological disorders like epileptic seizures, dementia and/or signs of autism. In line with these consequences in humans, two mice carrying mutations in the Large HERC genes have been studied quite intensely: the tambaleante mutant for Herc1 and the Herc2+/530 mutant for Herc2. In both these mutant mice there are clear signs that autophagy is dysregulated, eliciting cerebellar Purkinje cell death and impairing motor control. The tambaleante mouse was the first of these mice to appear and is the best studied, in which the Herc1 mutation elicits: (i) delayed neural transmission in the peripheral nervous system; (ii) impaired learning, memory and motor control; and (iii) altered presynaptic membrane dynamics. In this review, we discuss the information currently available on HERC proteins in the nervous system and their biological activity, the dysregulation of which could explain certain neurodevelopmental syndromes and/or neurodegenerative diseases.
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Affiliation(s)
- Eva M Pérez-Villegas
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Seville, Spain
| | - Rocío Ruiz
- Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Seville, Seville, Spain
| | - Sara Bachiller
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Sevilla, Virgen del Rocío University Hospital, CSIC, University of Sevilla, Sevilla, Spain
| | - Francesc Ventura
- Departament de Ciències Fisiològiques, IBIDELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose A Armengol
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, Seville, Spain.
| | - Jose Luis Rosa
- Departament de Ciències Fisiològiques, IBIDELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.
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13
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Sun C, Schuman EM. Logistics of neuronal protein turnover: Numbers and mechanisms. Mol Cell Neurosci 2022; 123:103793. [PMID: 36396040 DOI: 10.1016/j.mcn.2022.103793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Research in the past twenty years or so has revealed that neurons synthesize and degrade proteins at their synapses to enable synaptic proteome remodelling on demand and in real-time. Here we provide a quantitative overview of the decentralized neuronal protein-turnover logistics. We first analyse the huge neuronal protein turnover demand that arises from subcellular compartments outside the cell body, followed by an overview of key quantities and modulation strategies in neuronal protein turnover logistics. In the end, we briefly review recent progress in neuronal local protein synthesis and summarize diverse protein-degradation mechanisms that are found near synapses.
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Affiliation(s)
- Chao Sun
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany.
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14
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Wang G, Lei J, Wang Y, Yu J, He Y, Zhao W, Hu Z, Xu Z, Jin Y, Gu Y, Guo X, Yang B, Gao Z, Wang Z. The ZSWIM8 ubiquitin ligase regulates neurodevelopment by guarding the protein quality of intrinsically disordered Dab1. Cereb Cortex 2022; 33:3866-3881. [PMID: 35989311 DOI: 10.1093/cercor/bhac313] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/15/2022] Open
Abstract
Protein quality control (PQC) is essential for maintaining protein homeostasis and guarding the accuracy of neurodevelopment. Previously, we found that a conserved EBAX-type CRL regulates the protein quality of SAX-3/ROBO guidance receptors in Caenorhabditis elegans. Here, we report that ZSWIM8, the mammalian homolog of EBAX-1, is essential for developmental stability of mammalian brains. Conditional deletion of Zswim8 in the embryonic nervous system causes global cellular stress, partial perinatal lethality and defective migration of neural progenitor cells. CRISPR-mediated knockout of ZSWIM8 impairs spine formation and synaptogenesis in hippocampal neurons. Mechanistic studies reveal that ZSWIM8 controls protein quality of Disabled 1 (Dab1), a key signal molecule for brain development, thus protecting the signaling strength of Dab1. As a ubiquitin ligase enriched with intrinsically disordered regions (IDRs), ZSWIM8 specifically recognizes IDRs of Dab1 through a "disorder targets misorder" mechanism and eliminates misfolded Dab1 that cannot be properly phosphorylated. Adult survivors of ZSWIM8 CKO show permanent hippocampal abnormality and display severely impaired learning and memory behaviors. Altogether, our results demonstrate that ZSWIM8-mediated PQC is critical for the stability of mammalian brain development.
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Affiliation(s)
- Guan Wang
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Jing Lei
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Yifeng Wang
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Jiahui Yu
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
- Chu Kochen Honors College of Zhejiang University, Hangzhou 310058, China
| | - Yinghui He
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Weiqi Zhao
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Zhechun Hu
- Center of Stem Cell and Regenerative Medicine, and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhenzhong Xu
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Yishi Jin
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yan Gu
- Center of Stem Cell and Regenerative Medicine, and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xing Guo
- The Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Bing Yang
- The Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhihua Gao
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Zhiping Wang
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China; The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
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15
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Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. Cells 2022; 11:cells11132067. [PMID: 35805150 PMCID: PMC9265785 DOI: 10.3390/cells11132067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/01/2023] Open
Abstract
The AAA-ATPases Pex1 and Pex6 are required for the formation and maintenance of peroxisomes, membrane-bound organelles that harbor enzymes for specialized metabolism. Together, Pex1 and Pex6 form a heterohexameric AAA-ATPase capable of unfolding substrate proteins via processive threading through a central pore. Here, we review the proposed roles for Pex1/Pex6 in peroxisome biogenesis and degradation, discussing how the unfolding of potential substrates contributes to peroxisome homeostasis. We also consider how advances in cryo-EM, computational structure prediction, and mechanisms of related ATPases are improving our understanding of how Pex1/Pex6 converts ATP hydrolysis into mechanical force. Since mutations in PEX1 and PEX6 cause the majority of known cases of peroxisome biogenesis disorders such as Zellweger syndrome, insights into Pex1/Pex6 structure and function are important for understanding peroxisomes in human health and disease.
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16
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Nahar A, Sokolova V, Sekaran S, Orth JD, Park S. Assembly checkpoint of the proteasome regulatory particle is activated by coordinated actions of proteasomal ATPase chaperones. Cell Rep 2022; 39:110918. [PMID: 35675778 PMCID: PMC9214829 DOI: 10.1016/j.celrep.2022.110918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 11/26/2022] Open
Abstract
The proteasome holoenzyme regulates the cellular proteome via degrading most proteins. In its 19-subunit regulatory particle (RP), a heterohexameric ATPase enables protein degradation by injecting protein substrates into the core peptidase. RP assembly utilizes “checkpoints,” where multiple dedicated chaperones bind to specific ATPase subunits and control the addition of other subunits. Here, we find that the RP assembly checkpoint relies on two common features of the chaperones. Individual chaperones can distinguish an RP, in which their cognate ATPase persists in the ATP-bound state. Chaperones then together modulate ATPase activity to facilitate RP subunit rearrangements for switching to an active, substrate-processing state in the resulting proteasome holoenzyme. Thus, chaperones may sense ATP binding and hydrolysis as a readout for the quality of the RP complex to generate a functional proteasome holoenzyme. Our findings provide a basis to potentially exploit the assembly checkpoints in situations with known deregulation of proteasomal ATPase chaperones. Nahar et al. report that cells build functional proteasomes by utilizing an assembly checkpoint, which is activated by a common feature of multiple dedicated chaperones; they can distinguish the nucleotide state of proteasomal ATPases and help facilitate proper subunit rearrangement to ensure efficient protein degradation by the proteasome.
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Affiliation(s)
- Asrafun Nahar
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, 1945 Colorado Avenue, Boulder, CO 80309, USA
| | - Vladyslava Sokolova
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, 1945 Colorado Avenue, Boulder, CO 80309, USA
| | - Suganya Sekaran
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, 1945 Colorado Avenue, Boulder, CO 80309, USA
| | - James D Orth
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, 1945 Colorado Avenue, Boulder, CO 80309, USA
| | - Soyeon Park
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, 1945 Colorado Avenue, Boulder, CO 80309, USA.
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17
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Zhao S, Zhang C, Xu J, Liu S, Yu L, Chen S, Wen H, Li Z, Liu N. Dppa3 facilitates self-renewal of embryonic stem cells by stabilization of pluripotent factors. Stem Cell Res Ther 2022; 13:169. [PMID: 35477484 PMCID: PMC9044575 DOI: 10.1186/s13287-022-02846-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Developmental pluripotency-associated 3 (Dppa3, also called Stella or PGC7) is a principal maternal protein specially expressed in pre-implantation embryos, embryonic stem cells (ES cells) and primordial germ cells (PGCs). It plays critical role in the regulating of DNA methylation in zygotes and oocytes. However, the effect of Dppa3 in ES cells on the stability of proteins is still unclear. METHODS In this study, we first identified the potential interacting proteins with Dppa3 using immunoprecipitation-mass spectrometry (IP-MS). After GO analysis, we further constructed Dppa3-silenced ES cells and ES cell lines overexpressing with different lengths of Dppa3 to explore the mechanisms of Dppa3 on protein stability. RESULTS IP-MS results showed that Dppa3 interacted with quite a few subunits of 26S proteasome. Full length of Dppa3 stabilized Uhrf1 and Nanog by inhibiting its degradation. Silencing Dppa3 promoted degradation of Nanog protein. CONCLUSIONS Our results indicated that Dppa3 safeguard the stability of Uhrf1 and Nanog by inhibiting proteasome-associated degradation in ES cells. These findings shed light on new function of Dppa3 in maintaining stability of proteins and provides a valuable resource for understanding the roles of Dppa3 in embryonic stem cells.
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Affiliation(s)
- Shuang Zhao
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China.,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Chuanyu Zhang
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Jia Xu
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Siying Liu
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Lu Yu
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Shang Chen
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Hang Wen
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China
| | - Zongjin Li
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China.,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Na Liu
- School of Medicine, Nankai University, 94# Weijin Road, Tianjin, 300071, China. .,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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18
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Pla-Prats C, Thomä NH. Quality control of protein complex assembly by the ubiquitin-proteasome system. Trends Cell Biol 2022; 32:696-706. [PMID: 35300891 DOI: 10.1016/j.tcb.2022.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
The majority of human proteins operate as multimeric complexes with defined compositions and distinct architectures. How the assembly of these complexes is surveyed and how defective complexes are recognized is just beginning to emerge. In eukaryotes, over 600 E3 ubiquitin ligases form part of the ubiquitin-proteasome system (UPS) which detects structural characteristics in its target proteins and selectively induces their degradation. The UPS has recently been shown to oversee key quality control steps during the assembly of protein complexes. We review recent findings on how E3 ubiquitin ligases regulate protein complex assembly and highlight unanswered questions relating to their mechanism of action.
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Affiliation(s)
- Carlos Pla-Prats
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Science, University of Basel, Petersplatz 1, 4001 Basel, Switzerland
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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19
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Padovani C, Jevtić P, Rapé M. Quality control of protein complex composition. Mol Cell 2022; 82:1439-1450. [PMID: 35316660 DOI: 10.1016/j.molcel.2022.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/26/2022] [Accepted: 02/21/2022] [Indexed: 12/13/2022]
Abstract
Eukaryotic cells possess hundreds of protein complexes that contain multiple subunits and must be formed at the correct time and place during development. Despite specific assembly pathways, cells frequently encounter complexes with missing or aberrant subunits that can disrupt important signaling events. Cells, therefore, employ several ubiquitin-dependent quality control pathways that can prevent, correct, or degrade flawed complexes. In this review, we will discuss our emerging understanding of such quality control of protein complex composition.
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Affiliation(s)
- Chris Padovani
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Predrag Jevtić
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA.
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20
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Structure of human glycosylphosphatidylinositol transamidase. Nat Struct Mol Biol 2022; 29:203-209. [DOI: 10.1038/s41594-022-00726-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/11/2022] [Indexed: 01/31/2023]
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21
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Guo X. Localized Proteasomal Degradation: From the Nucleus to Cell Periphery. Biomolecules 2022; 12:biom12020229. [PMID: 35204730 PMCID: PMC8961600 DOI: 10.3390/biom12020229] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/31/2022] Open
Abstract
The proteasome is responsible for selective degradation of most cellular proteins. Abundantly present in the cell, proteasomes not only diffuse in the cytoplasm and the nucleus but also associate with the chromatin, cytoskeleton, various membranes and membraneless organelles/condensates. How and why the proteasome gets to these specific subcellular compartments remains poorly understood, although increasing evidence supports the hypothesis that intracellular localization may have profound impacts on the activity, substrate accessibility and stability/integrity of the proteasome. In this short review, I summarize recent advances on the functions, regulations and targeting mechanisms of proteasomes, especially those localized to the nuclear condensates and membrane structures of the cell, and I discuss the biological significance thereof in mediating compartmentalized protein degradation.
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Affiliation(s)
- Xing Guo
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Hangzhou 310058, China
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22
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Duan J, Li W, Shu X, Yang B, He X, Guo X. Conserved Mitotic Phosphorylation of a Proteasome Subunit Regulates Cell Proliferation. Cells 2021; 10:3075. [PMID: 34831298 PMCID: PMC8620773 DOI: 10.3390/cells10113075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 11/17/2022] Open
Abstract
Reversible phosphorylation has emerged as an important mechanism for regulating proteasome function in various physiological processes. Essentially all proteasome phosphorylations characterized thus far occur on proteasome holoenzyme or subcomplexes to regulate substrate degradation. Here, we report a highly conserved phosphorylation that only exists on the unassembled α5 subunit of the proteasome. The modified residue, α5-Ser16, is within a SP motif typically recognized by cyclin-dependent kinases (CDKs). Using a phospho-specific antibody generated against this site, we found that α5-S16 phosphorylation is mitosis-specific in both yeast and mammalian cells. Blocking this site with a S16A mutation caused growth defect and G2/M arrest of the cell cycle. α5-S16 phosphorylation depends on CDK1 activity and is highly abundant in some but not all mitotic cells. Immunoprecipitation and mass spectrometry (IP-MS) studies identified numerous proteins that could interact with phosphorylated α5, including PLK1, a key regulator of mitosis. α5-PLK1 interaction increased upon mitosis and could be facilitated by S16 phosphorylation. CDK1 activation downstream of PLK1 activity was delayed in S16A mutant cells, suggesting an important role of α5-S16 phosphorylation in regulating PLK1 and mitosis. These data have revealed an unappreciated function of "exo-proteasome" phosphorylation of a proteasome subunit and may bring new insights to our understanding of cell cycle control.
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Affiliation(s)
- Jinyuan Duan
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (J.D.); (W.L.); (X.S.); (B.Y.); (X.H.)
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Hangzhou 310058, China
| | - Wenzhu Li
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (J.D.); (W.L.); (X.S.); (B.Y.); (X.H.)
| | - Xin Shu
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (J.D.); (W.L.); (X.S.); (B.Y.); (X.H.)
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Hangzhou 310058, China
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (J.D.); (W.L.); (X.S.); (B.Y.); (X.H.)
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Hangzhou 310058, China
| | - Xiangwei He
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (J.D.); (W.L.); (X.S.); (B.Y.); (X.H.)
| | - Xing Guo
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (J.D.); (W.L.); (X.S.); (B.Y.); (X.H.)
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Hangzhou 310058, China
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