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Magrinelli F, Tesson C, Angelova PR, Salazar-Villacorta A, Rodriguez JA, Scardamaglia A, Chung BHY, Jaconelli M, Vona B, Esteras N, Kwong AKY, Courtin T, Maroofian R, Alavi S, Nirujogi R, Severino M, Lewis PA, Efthymiou S, O’Callaghan B, Buchert R, Sofan L, Lis P, Pinon C, Breedveld GJ, Chui MMC, Murphy D, Pitz V, Makarious MB, Cassar M, Hassan BA, Iftikhar S, Rocca C, Bauer P, Tinazzi M, Svetel M, Samanci B, Hanağası HA, Bilgiç B, Obeso JA, Kurtis MM, Cogan G, Başak AN, Kiziltan G, Gül T, Yalçın G, Elibol B, Barišić N, Ng EWS, Fan SS, Hershkovitz T, Weiss K, Raza Alvi J, Sultan T, Azmi Alkhawaja I, Froukh T, E Alrukban HA, Fauth C, Schatz UA, Zöggeler T, Zech M, Stals K, Varghese V, Gandhi S, Blauwendraat C, Hardy JA, Lesage S, Bonifati V, Haack TB, Bertoli-Avella AM, Steinfeld R, Alessi DR, Steller H, Brice A, Abramov AY, Bhatia KP, Houlden H. PSMF1 variants cause a phenotypic spectrum from early-onset Parkinson's disease to perinatal lethality by disrupting mitochondrial pathways. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.19.24308302. [PMID: 39148840 PMCID: PMC11326324 DOI: 10.1101/2024.06.19.24308302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Dissecting biological pathways highlighted by Mendelian gene discovery has provided critical insights into the pathogenesis of Parkinson's disease (PD) and neurodegeneration. This approach ultimately catalyzes the identification of potential biomarkers and therapeutic targets. Here, we identify PSMF1 as a new gene implicated in PD and childhood neurodegeneration. We find that biallelic PSMF1 missense and loss-of-function variants co-segregate with phenotypes from early-onset PD and parkinsonism to perinatal lethality with neurological manifestations across 15 unrelated pedigrees with 22 affected subjects, showing clear genotype-phenotype correlation. PSMF1 encodes the proteasome regulator PSMF1/PI31, a highly conserved, ubiquitously expressed partner of the 20S proteasome and neurodegeneration-associated F-box-O 7 and valosin-containing proteins. We demonstrate that PSMF1 variants impair mitochondrial membrane potential, dynamics and mitophagy in patient-derived fibroblasts. Additionally, we develop models of psmf1 knockdown Drosophila and Psmf1 conditional knockout mouse exhibiting age-dependent motor impairment, with diffuse gliosis in mice. These findings unequivocally link defective PSMF1 to early-onset PD and neurodegeneration and suggest mitochondrial dysfunction as a mechanistic contributor.
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Affiliation(s)
- Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Christelle Tesson
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Plamena R. Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Ainara Salazar-Villacorta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Jose A. Rodriguez
- Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Annarita Scardamaglia
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Hong Kong Genome Institute, Hong Kong SAR, China
| | - Matthew Jaconelli
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, Göttingen, Germany
| | - Noemi Esteras
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- Neurochemistry Research Institute, Department of Biochemistry and Molecular Biology, School of Medicine, Complutense University of Madrid, Madrid, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, Madrid, Spain
| | - Anna Ka-Yee Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Thomas Courtin
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Shahryar Alavi
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Raja Nirujogi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | | | - Patrick A. Lewis
- Royal Veterinary College, London, United Kingdom
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Benjamin O’Callaghan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Linda Sofan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Pawel Lis
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Chloé Pinon
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Guido J. Breedveld
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Martin Man-Chun Chui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Vanessa Pitz
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mary B. Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Marlene Cassar
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Bassem A. Hassan
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Sana Iftikhar
- Department of Real-World evidence studies, CENTOGENE GmbH, Rostock, Germany
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Peter Bauer
- Department of Medical Genetics, CENTOGENE GmbH, Rostock, Germany
| | - Michele Tinazzi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Marina Svetel
- Movement Disorders Department, Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Bedia Samanci
- Behavioral Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Haşmet A. Hanağası
- Behavioral Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Basar Bilgiç
- Behavioral Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - José A. Obeso
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, Madrid, Spain
- HM CINAC, Hospital Universitario HM Puerta del Sur, HM Hospitales, Madrid, Spain
- University CEU-San Pablo, Madrid, Spain
| | - Monica M. Kurtis
- Neurology Department, Hospital Ruber Internacional, Madrid, Spain
| | - Guillaume Cogan
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Ayşe Nazlı Başak
- Koç University, School of Medicine, Research Center for Translational Medicine KUTTAM-Neurodegeneration Research Laboratory NDAL, Istanbul, Turkey
| | - Güneş Kiziltan
- Department of Neurology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Tuğçe Gül
- Koç University, School of Medicine, Research Center for Translational Medicine KUTTAM-Neurodegeneration Research Laboratory NDAL, Istanbul, Turkey
| | - Gül Yalçın
- Department of Neurology, School of Medicine, Hacettepe University, Ankara, Turkey
| | - Bülent Elibol
- Department of Neurology, School of Medicine, Hacettepe University, Ankara, Turkey
| | - Nina Barišić
- Department of Pediatrics, University of Zagreb Medical School and University Hospital Center Zagreb, Zagreb, Croatia
| | - Earny Wei-Sen Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sze-Shing Fan
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Tova Hershkovitz
- The Genetics Institute, Galilee Medical Center, Nahariya, Israel
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Center, Haifa, Israel
- Ruth and Bruce Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Javeria Raza Alvi
- Department of Paediatric Neurology, The Children’s Hospital and the University of Child Health Sciences, Lahore, Punjab, Pakistan
| | - Tipu Sultan
- Department of Paediatric Neurology, The Children’s Hospital and the University of Child Health Sciences, Lahore, Punjab, Pakistan
| | - Issam Azmi Alkhawaja
- Pediatric Neurology Unit, Pediatric Department, Albashir Hospital, Amman, Jordan
| | - Tawfiq Froukh
- Department of Biotechnology and Genetics Engineering, Philadelphia University, Jordan
| | | | - Christine Fauth
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Ulrich A. Schatz
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
- Institute of Human Genetics, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Thomas Zöggeler
- Department of Pediatrics I, Medical University Innsbruck, Innsbruck, Austria
| | - Michael Zech
- Institute of Human Genetics, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum Munich, Munich, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Karen Stals
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Vinod Varghese
- All Wales Medical Genomics Service, Cardiff, United Kingdom
| | - Sonia Gandhi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - John A. Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Suzanne Lesage
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Vincenzo Bonifati
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Institute of Neurogenomics, Helmholtz Zentrum Munich, Munich, Germany
| | | | - Robert Steinfeld
- Department of Pediatrics and Pediatric Neurology, University of Göttingen, Göttingen, Germany
- Department of Pediatric Neurology, Charité University Medicine, Berlin, Germany
| | - Dario R. Alessi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hermann Steller
- Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Alexis Brice
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm, CNRS, Sorbonne Université, Paris, France
| | - Andrey Y. Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Kailash P. Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
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Al Rawi S, Simpson L, Agnarsdóttir G, McDonald NQ, Chernuha V, Elpeleg O, Zeviani M, Barker RA, Spiegel R, Laman H. Study of an FBXO7 patient mutation reveals Fbxo7 and PI31 co-regulate proteasomes and mitochondria. FEBS J 2024; 291:2565-2589. [PMID: 38466799 DOI: 10.1111/febs.17114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/18/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Mutations in FBXO7 have been discovered to be associated with an atypical parkinsonism. We report here a new homozygous missense mutation in a paediatric patient that causes an L250P substitution in the dimerisation domain of Fbxo7. This alteration selectively ablates the Fbxo7-PI31 interaction and causes a significant reduction in Fbxo7 and PI31 levels in patient cells. Consistent with their association with proteasomes, patient fibroblasts have reduced proteasome activity and proteasome subunits. We also show PI31 interacts with the MiD49/51 fission adaptor proteins, and unexpectedly, PI31 acts to facilitate SCFFbxo7-mediated ubiquitination of MiD49. The L250P mutation reduces the SCFFbxo7 ligase-mediated ubiquitination of a subset of its known substrates. Although MiD49/51 expression was reduced in patient cells, there was no effect on the mitochondrial network. However, patient cells show reduced levels of mitochondrial function and mitophagy, higher levels of ROS and are less viable under stress. Our study demonstrates that Fbxo7 and PI31 regulate proteasomes and mitochondria and reveals a new function for PI31 in enhancing the SCFFbxo7 E3 ubiquitin ligase activity.
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Affiliation(s)
- Sara Al Rawi
- Department of Pathology, University of Cambridge, UK
| | - Lorna Simpson
- Department of Pathology, University of Cambridge, UK
| | | | - Neil Q McDonald
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Biological Sciences, Institute of Structural and Molecular Biology, London, UK
| | - Veronika Chernuha
- Pediatric Neurology Institute, Dana-Dwek Children's Hospital, Tel Aviv Medical Centre and Sackler Faculty of Medicine, Israel
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Massimo Zeviani
- Mitochondrial Biology Unit, The MRC and University of Cambridge, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, UK
| | - Ronen Spiegel
- Pediatric Department, Emek Medical Center, Afula, Israel
| | - Heike Laman
- Department of Pathology, University of Cambridge, UK
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3
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Wang J, Kjellgren A, DeMartino GN. Differential Interactions of the Proteasome Inhibitor PI31 with Constitutive and Immuno-20S Proteasomes. Biochemistry 2024; 63:1000-1015. [PMID: 38577872 DOI: 10.1021/acs.biochem.3c00707] [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] [Indexed: 04/06/2024]
Abstract
PI31 (Proteasome Inhibitor of 31,000 Da) is a 20S proteasome binding protein originally identified as an in vitro inhibitor of 20S proteasome proteolytic activity. Recently reported cryo-electron microscopy structures of 20S-PI31 complexes have revealed that the natively disordered proline-rich C-terminus of PI31 enters the central chamber in the interior of the 20S proteasome and interacts directly with the proteasome's multiple catalytic threonine residues in a manner predicted to inhibit their enzymatic function while evading its own proteolysis. Higher eukaryotes express an alternative form of the 20S proteasome (termed "immuno-proteasome") that features genetically and functionally distinct catalytic subunits. The effect of PI31 on immuno-proteasome function is unknown. We examine the relative inhibitory effects of PI31 on purified constitutive (20Sc) and immuno-(20Si) 20S proteasomes in vitro and show that PI31 inhibits 20Si hydrolytic activity to a significantly lesser degree than that of 20Sc. Unlike 20Sc, 20Si hydrolyzes the carboxyl-terminus of PI31 and this effect contributes to the reduced inhibitory activity of PI31 toward 20Si. Conversely, loss of 20Sc inhibition by PI31 point mutants leads to PI31 degradation by 20Sc. These results demonstrate unexpected differential interactions of PI31 with 20Sc and 20Si and document their functional consequences.
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Affiliation(s)
- Jason Wang
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
| | - Abbey Kjellgren
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
| | - George N DeMartino
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
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4
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Velez B, Razi A, Hubbard RD, Walsh R, Rawson S, Tian G, Finley D, Hanna J. Rational design of proteasome inhibitors based on the structure of the endogenous inhibitor PI31/Fub1. Proc Natl Acad Sci U S A 2023; 120:e2308417120. [PMID: 38091293 PMCID: PMC10743371 DOI: 10.1073/pnas.2308417120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Proteasome inhibitors are widely used anticancer drugs. The three clinically approved agents are modified small peptides that preferentially target one of the proteasome's three active sites (β5) at physiologic concentrations. In addition to these drugs, there is also an endogenous proteasome inhibitor, PI31/Fub1, that enters the proteasome's interior to simultaneously yet specifically inhibit all three active sites. Here, we have used PI31's evolutionarily optimized inhibitory mechanisms to develop a suite of potent and specific β2 inhibitors. The lead compound strongly inhibited growth of multiple myeloma cells as a standalone agent, indicating the compound's cell permeability and establishing β2 as a potential therapeutic target in multiple myeloma. The lead compound also showed strong synergy with the existing β5 inhibitor bortezomib; such combination therapies might help with existing challenges of resistance and severe side effects. These results represent an effective method for rational structure-guided development of proteasome inhibitors.
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Affiliation(s)
- Benjamin Velez
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
| | - Aida Razi
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
| | | | - Richard Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology,Harvard Medical School,Boston, MA02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology,Harvard Medical School,Boston, MA02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
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5
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Sagathia V, Patel C, Beladiya J, Patel S, Sheth D, Shah G. Tankyrase: a promising therapeutic target with pleiotropic action. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2023; 396:3363-3374. [PMID: 37338576 DOI: 10.1007/s00210-023-02576-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
Tankyrase 1 (TNKS1) and tankyrase 2 (TNKS2) enzymes belong to the poly (ADP-ribose) polymerase (PARP) family participates in process of poly-ADP-ribosylation of different target proteins which leads to ubiquitin-mediated proteasomal degradation. Tankyrases are also involved in the pathophysiology of many diseases, especially cancer. Their functions include cell cycle homeostasis (primarily in mitosis), telomere maintenance, Wnt signaling pathway regulation, and insulin signaling (particularly GLUT4 translocation). Studies have implicated that genetic changes, mutations in the tankyrase coding sequence, or up regulation and down regulation of tankyrase are reflected in the numerous disease conditions. Investigations are pursued to develop putative molecules that target tankyrase in various diseases such as cancer, obesity, osteoarthritis, fibrosis, cherubism, and diabetes, thereby providing a new therapeutic treatment option. In the present review, we described the structure and function of tankyrase along with its role in different disease conditions. Furthermore, we also presented cumulative experimental evidences of different drugs acting on tankyrase.
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Affiliation(s)
- Vrunda Sagathia
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, 380009, Gujarat, India
| | - Chirag Patel
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, 380009, Gujarat, India.
| | - Jayesh Beladiya
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, 380009, Gujarat, India
| | - Sandip Patel
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, 380009, Gujarat, India
| | - Devang Sheth
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, 380009, Gujarat, India
| | - Gaurang Shah
- Department of Pharmacology, L. M. College of Pharmacy, Ahmedabad, 380009, Gujarat, India
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6
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Kim Y, Kim EK, Chey Y, Song MJ, Jang HH. Targeted Protein Degradation: Principles and Applications of the Proteasome. Cells 2023; 12:1846. [PMID: 37508510 PMCID: PMC10378610 DOI: 10.3390/cells12141846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The proteasome is a multi-catalytic protease complex that is involved in protein quality control via three proteolytic activities (i.e., caspase-, trypsin-, and chymotrypsin-like activities). Most cellular proteins are selectively degraded by the proteasome via ubiquitination. Moreover, the ubiquitin-proteasome system is a critical process for maintaining protein homeostasis. Here, we briefly summarize the structure of the proteasome, its regulatory mechanisms, proteins that regulate proteasome activity, and alterations to proteasome activity found in diverse diseases, chemoresistant cells, and cancer stem cells. Finally, we describe potential therapeutic modalities that use the ubiquitin-proteasome system.
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Affiliation(s)
- Yosup Kim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Eun-Kyung Kim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Yoona Chey
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Min-Jeong Song
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Ho Hee Jang
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
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7
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Hsu HC, Wang J, Kjellgren A, Li H, DeMartino GN. Ηigh-resolution structure of mammalian PI31-20S proteasome complex reveals mechanism of proteasome inhibition. J Biol Chem 2023; 299:104862. [PMID: 37236357 PMCID: PMC10319324 DOI: 10.1016/j.jbc.2023.104862] [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: 04/06/2023] [Revised: 05/08/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Proteasome-catalyzed protein degradation mediates and regulates critical aspects of many cellular functions and is an important element of proteostasis in health and disease. Proteasome function is determined in part by the types of proteasome holoenzymes formed between the 20S core particle that catalyzes peptide bond hydrolysis and any of multiple regulatory proteins to which it binds. One of these regulators, PI31, was previously identified as an in vitro 20S proteasome inhibitor, but neither the molecular mechanism nor the possible physiologic significance of PI31-mediated proteasome inhibition has been clear. Here we report a high-resolution cryo-EM structure of the mammalian 20S proteasome in complex with PI31. The structure shows that two copies of the intrinsically disordered carboxyl terminus of PI31 are present in the central cavity of the closed-gate conformation of the proteasome and interact with proteasome catalytic sites in a manner that blocks proteolysis of substrates but resists their own degradation. The two inhibitory polypeptide chains appear to originate from PI31 monomers that enter the catalytic chamber from opposite ends of the 20S cylinder. We present evidence that PI31 can inhibit proteasome activity in mammalian cells and may serve regulatory functions for the control of cellular proteostasis.
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Affiliation(s)
- Hao-Chi Hsu
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Jason Wang
- Department of Physiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Abbey Kjellgren
- Department of Physiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
| | - George N DeMartino
- Department of Physiology, UT Southwestern Medical Center, Dallas, Texas, USA.
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8
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Hsu HC, Wang J, Kjellgren A, Li H, DeMartino GN. High-resolution structure of mammalian PI31â€"20S proteasome complex reveals mechanism of proteasome inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535455. [PMID: 37066326 PMCID: PMC10103979 DOI: 10.1101/2023.04.03.535455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proteasome-catalyzed protein degradation mediates and regulates critical aspects of many cellular functions and is an important element of proteostasis in health and disease. Proteasome function is determined in part by the types of proteasome holoenzymes formed between the 20S core particle that catalyzes peptide bond hydrolysis and any of multiple regulatory proteins to which it binds. One of these regulators, PI31, was previously identified as an in vitro 20S proteasome inhibitor, but neither the molecular mechanism nor the possible physiologic significance of PI31-mediated proteasome inhibition has been clear. Here we report a high- resolution cryo-EM structure of the mammalian 20S proteasome in complex with PI31. The structure shows that two copies of the intrinsically-disordered carboxyl-terminus of PI31 are present in the central cavity of the closed-gate conformation of the proteasome and interact with proteasome catalytic sites in a manner that blocks proteolysis of substrates but resists their own degradation. The two inhibitory polypeptide chains appear to originate from PI31 monomers that enter the catalytic chamber from opposite ends of the 20S cylinder. We present evidence that PI31 can inhibit proteasome activity in mammalian cells and may serve regulatory functions for the control of cellular proteostasis.
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Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores. Nat Commun 2022; 13:6962. [PMID: 36379934 PMCID: PMC9666519 DOI: 10.1038/s41467-022-34691-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/02/2022] [Indexed: 11/17/2022] Open
Abstract
Proteasomes play an essential role in the life cycle of intracellular pathogens with extracellular stages by ensuring proteostasis in environments with limited resources. In microsporidia, divergent parasites with extraordinarily streamlined genomes, the proteasome complexity and structure are unknown, which limits our understanding of how these unique pathogens adapt and compact essential eukaryotic complexes. We present cryo-electron microscopy structures of the microsporidian 20S and 26S proteasome isolated from dormant or germinated Vairimorpha necatrix spores. The discovery of PI31-like peptides, known to inhibit proteasome activity, bound simultaneously to all six active sites within the central cavity of the dormant spore proteasome, suggests reduced activity in the environmental stage. In contrast, the absence of the PI31-like peptides and the existence of 26S particles post-germination in the presence of ATP indicates that proteasomes are reactivated in nutrient-rich conditions. Structural and phylogenetic analyses reveal that microsporidian proteasomes have undergone extensive reductive evolution, lost at least two regulatory proteins, and compacted nearly every subunit. The highly derived structure of the microsporidian proteasome, and the minimized version of PI31 presented here, reinforce the feasibility of the development of specific inhibitors and provide insight into the unique evolution and biology of these medically and economically important pathogens.
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10
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Yeast PI31 inhibits the proteasome by a direct multisite mechanism. Nat Struct Mol Biol 2022; 29:791-800. [PMID: 35927584 PMCID: PMC9399903 DOI: 10.1038/s41594-022-00808-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023]
Abstract
Proteasome inhibitors are widely used as therapeutics and research tools, and typically target one of the three active sites, each present twice in the proteasome complex. An endogeneous proteasome inhibitor, PI31, was identified 30 years ago, but its inhibitory mechanism has remained unclear. Here, we identify the mechanism of Saccharomyces cerevisiae PI31, also known as Fub1. Using cryo-electron microscopy (cryo-EM), we show that the conserved carboxy-terminal domain of Fub1 is present inside the proteasome's barrel-shaped core particle (CP), where it simultaneously interacts with all six active sites. Targeted mutations of Fub1 disrupt proteasome inhibition at one active site, while leaving the other sites unaffected. Fub1 itself evades degradation through distinct mechanisms at each active site. The gate that allows substrates to access the CP is constitutively closed, and Fub1 is enriched in mutant CPs with an abnormally open gate, suggesting that Fub1 may function to neutralize aberrant proteasomes, thereby ensuring the fidelity of proteasome-mediated protein degradation.
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11
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Liu J, Jia J, Wang S, Zhang J, Xian S, Zheng Z, Deng L, Feng Y, Zhang Y, Zhang J. Prognostic Ability of Enhancer RNAs in Metastasis of Non-Small Cell Lung Cancer. Molecules 2022; 27:molecules27134108. [PMID: 35807355 PMCID: PMC9268450 DOI: 10.3390/molecules27134108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 02/01/2023] Open
Abstract
(1) Background: Non-small cell lung cancer (NSCLC) is the most common lung cancer. Enhancer RNA (eRNA) has potential utility in the diagnosis, prognosis and treatment of cancer, but the role of eRNAs in NSCLC metastasis is not clear; (2) Methods: Differentially expressed transcription factors (DETFs), enhancer RNAs (DEEs), and target genes (DETGs) between primary NSCLC and metastatic NSCLC were identified. Prognostic DEEs (PDEEs) were screened by Cox regression analyses and a predicting model for metastatic NSCLC was constructed. We identified DEE interactions with DETFs, DETGs, reverse phase protein arrays (RPPA) protein chips, immunocytes, and pathways to construct a regulation network using Pearson correlation. Finally, the mechanisms and clinical significance were explained using multi-dimensional validation unambiguously; (3) Results: A total of 255 DEEs were identified, and 24 PDEEs were selected into the multivariate Cox regression model (AUC = 0.699). Additionally, the NSCLC metastasis-specific regulation network was constructed, and six key PDEEs were defined (ANXA8L1, CASTOR2, CYP4B1, GTF2H2C, PSMF1 and TNS4); (4) Conclusions: This study focused on the exploration of the prognostic value of eRNAs in the metastasis of NSCLC. Finally, six eRNAs were identified as potential markers for the prediction of metastasis of NSCLC.
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Affiliation(s)
- Jun Liu
- Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; (J.L.); (J.J.)
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Jingyi Jia
- Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; (J.L.); (J.J.)
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
- Shanghai Clinical Research Center for Infectious Diseases (Tuberculosis), Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Siqiao Wang
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Junfang Zhang
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Shuyuan Xian
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Zixuan Zheng
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
| | - Lin Deng
- Normal College, Qingdao University, Qingdao 266071, China;
| | - Yonghong Feng
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
- Shanghai Clinical Research Center for Infectious Diseases (Tuberculosis), Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
- Correspondence: (Y.F.); (Y.Z.); (J.Z.)
| | - Yuan Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
- Correspondence: (Y.F.); (Y.Z.); (J.Z.)
| | - Jie Zhang
- Department of Anesthesiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; (J.L.); (J.J.)
- School of Medicine, Tongji University, Shanghai 200092, China; (S.W.); (J.Z.); (S.X.); (Z.Z.)
- Correspondence: (Y.F.); (Y.Z.); (J.Z.)
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12
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Yang S, Tang D, Zhao YC, Liu H, Luo S, Stinchcombe TE, Glass C, Su L, Shen S, Christiani DC, Wang Q, Wei Q. Potentially functional variants of ERAP1, PSMF1 and NCF2 in the MHC-I-related pathway predict non-small cell lung cancer survival. Cancer Immunol Immunother 2021; 70:2819-2833. [PMID: 33651148 DOI: 10.1007/s00262-021-02877-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/01/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND Cellular immunity against tumor cells is highly dependent on antigen presentation by major histocompatibility complex class I (MHC-I) molecules. However, few published studies have investigated associations between functional variants of MHC-I-related genes and clinical outcomes of lung cancer patients. METHODS We performed a two-phase Cox proportional hazards regression analysis by using two previously published genome-wide association studies to evaluate associations between genetic variants in the MHC-I-related gene set and the survival of non-small cell lung cancer (NSCLC) patients, followed by expression quantitative trait loci analysis. RESULTS Of the 7811 single-nucleotide polymorphisms (SNPs) in 89 genes of 1185 NSCLC patients in the discovery dataset of the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial, 24 SNPs remained statistically significant after validation in additional 984 NSCLC patients from the Harvard Lung Cancer Susceptibility Study. In a multivariate stepwise Cox model, three independent functional SNPs (ERAP1 rs469783 T > C, PSMF1 rs13040574 C > A and NCF2 rs36071574 G > A) remained significant with an adjusted hazards ratio (HR) of 0.83 [95% confidence interval (CI) = 0.77-0.89, P = 8.0 × 10-7], 0.86 (0.80-0.93, P = 9.4 × 10-5) and 1.31 (1.11-1.54, P = 0.001) for overall survival (OS), respectively. Further combined genotypes revealed a poor survival in a dose-response manner in association with the number of unfavorable genotypes (Ptrend < 0.0001 and 0.0002 for OS and disease-specific survival, respectively). Also, ERAP1 rs469783C and PSMF1 rs13040574A alleles were associated with higher mRNA expression levels of their genes. CONCLUSION These potentially functional SNPs of the MHC-I-related genes may be biomarkers for NSCLC survival, possibly through modulating the expression of corresponding genes.
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Affiliation(s)
- Sen Yang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Dongfang Tang
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yu Chen Zhao
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Hongliang Liu
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Thomas E Stinchcombe
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Carolyn Glass
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Pathology, Duke ©University School of Medicine, Durham, NC, 27710, USA
| | - Li Su
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Sipeng Shen
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - David C Christiani
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.
| | - Qingyi Wei
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA.
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
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13
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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Wu J, Peled-Zehavi H, Galili G. The m 6 A reader ECT2 post-transcriptionally regulates proteasome activity in Arabidopsis. THE NEW PHYTOLOGIST 2020; 228:151-162. [PMID: 32416015 DOI: 10.1111/nph.16660] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/29/2020] [Indexed: 05/23/2023]
Abstract
Methylation of internal adenosine at nitrogen-6 position (m6 A) is the most abundant post-transcriptional modification in eukaryotic RNAs. These modifications are recognized by m6 A-binding proteins ('readers') that affect downstream functions. In plants, the scope of gene expression regulation by reader proteins is not clear. Here, overexpression and loss-of-function mutants were used to characterize the role of the Arabidopsis m6 A reader ECT2 in proteasome regulation. ECT2 regulates the mRNA levels of the proteasome regulator PTRE1 and of several 20S proteasome subunits, resulting in enhanced 26S proteasome activity. This regulation is dependent on ECT2 m6 A binding function. Interestingly, though ECT2 positively regulates proteasome activity in both young and mature plants, PTRE1 has different regulatory effects in different developmental stages. In mature plants, PTRE1 inhibits 26S proteasome activity, while in seedlings PTRE1 knockout mutants have reduced 26S proteasome activity. Taken together, our results suggest a novel epitranscriptomic mechanism of proteasome regulation by ECT2 that is used to fine tune proteasome activity by affecting the expression of PTRE1 and 20S proteasome subunits.
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Affiliation(s)
- Jian Wu
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Hadas Peled-Zehavi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gad Galili
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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15
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Damale MG, Pathan SK, Shinde DB, Patil RH, Arote RB, Sangshetti JN. Insights of tankyrases: A novel target for drug discovery. Eur J Med Chem 2020; 207:112712. [PMID: 32877803 DOI: 10.1016/j.ejmech.2020.112712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/24/2022]
Abstract
Tankyrases are the group of enzymes belonging to a class of Poly (ADP-ribose) polymerase (PARP) recently named ADP-ribosyltransferase (ARTD). The two isoforms of tankyrase i.e. tankyrase1 (TNKS1) and tankyrase2 (TNKS2) were abundantly expressed in various biological functions in telomere regulation, Wnt/β-catenin signaling pathway, viral replication, endogenous hormone regulation, glucose transport, cherubism disease, erectile dysfunction, and apoptosis. The structural analysis, mechanistic information, in vitro and in vivo studies led identification and development of several classes of tankyrase inhibitors under clinical phases. In the nutshell, this review will drive future research on tankyrase as it enlighten the structural and functional features of TNKS 1 and TNKS 2, different classes of inhibitors with their structure-activity relationship studies, molecular modeling studies, as well as past, current and future perspective of the different class of tankyrase inhibitors.
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Affiliation(s)
- Manoj G Damale
- Department of Pharmaceutical Medicinal Chemistry, Srinath College of Pharmacy, Aurangabad, 431136, MS, India
| | - Shahebaaz K Pathan
- Y.B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, MS, 431001, India
| | | | - Rajendra H Patil
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, M.S, India
| | - Rohidas B Arote
- Department of Molecular Genetics, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Jaiprakash N Sangshetti
- Y.B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, MS, 431001, India.
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16
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Wang X, Meul T, Meiners S. Exploring the proteasome system: A novel concept of proteasome inhibition and regulation. Pharmacol Ther 2020; 211:107526. [PMID: 32173559 DOI: 10.1016/j.pharmthera.2020.107526] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/08/2020] [Indexed: 12/13/2022]
Abstract
The proteasome is a well-identified therapeutic target for cancer treatment. It acts as the main protein degradation system in the cell and degrades key mediators of cell growth, survival and function. The term "proteasome" embraces a whole family of distinct complexes, which share a common proteolytic core, the 20S proteasome, but differ by their attached proteasome activators. Each of these proteasome complexes plays specific roles in the control of cellular function. In addition, distinct proteasome interacting proteins regulate proteasome activity in subcellular compartments and in response to cellular signals. Proteasome activators and regulators may thus serve as building blocks to fine-tune proteasome function in the cell according to cellular needs. Inhibitors of the proteasome, e.g. the FDA approved drugs Velcade™, Kyprolis™, Ninlaro™, inactivate the catalytic 20S core and effectively block protein degradation of all proteasome complexes in the cell resulting in inhibition of cell growth and induction of apoptosis. Efficacy of these inhibitors, however, is hampered by their pronounced cytotoxic side-effects as well as by the emerging development of resistance to catalytic proteasome inhibitors. Targeted inhibition of distinct buiding blocks of the proteasome system, i.e. proteasome activators or regulators, represents an alternative strategy to overcome these limitations. In this review, we stress the importance of the diversity of the proteasome complexes constituting an entire proteasome system. Our building block concept provides a rationale for the defined targeting of distinct proteasome super-complexes in disease. We thereby aim to stimulate the development of innovative therapeutic approaches beyond broad catalytic proteasome inhibition.
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Affiliation(s)
- Xinyuan Wang
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Thomas Meul
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany.
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17
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Kondo H, Matsumura T, Kaneko M, Inoue K, Kosako H, Ikawa M, Takahama Y, Ohigashi I. PITHD1 is a proteasome-interacting protein essential for male fertilization. J Biol Chem 2020; 295:1658-1672. [PMID: 31915251 PMCID: PMC7008373 DOI: 10.1074/jbc.ra119.011144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/23/2019] [Indexed: 11/06/2022] Open
Abstract
The proteasome is a protein-degrading molecular complex that is necessary for protein homeostasis and various biological functions, including cell cycle regulation, signal transduction, and immune response. Proteasome activity is finely regulated by a variety of proteasome-interacting molecules. PITHD1 is a recently described molecule that has a domain putatively capable of interacting with the proteasome. However, it is unknown whether PITHD1 can actually bind to proteasomes and what it does in vivo Here we report that PITHD1 is detected specifically in the spermatids in the testis and the cortical thymic epithelium in the thymus. Interestingly, PITHD1 associates with immunoproteasomes in the testis, but not with thymoproteasomes in the thymus. Mice deficient in PITHD1 exhibit severe male infertility accompanied with morphological abnormalities and impaired motility of spermatozoa. Furthermore, PITHD1 deficiency reduces proteasome activity in the testis and alters the amount of proteins that are important for fertilization capability by the sperm. However, the PITHD1-deficient mice demonstrate no detectable defects in the thymus, including T cell development. Collectively, our results identify PITHD1 as a proteasome-interacting protein that plays a nonredundant role in the male reproductive system.
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Affiliation(s)
- Hiroyuki Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Takafumi Matsumura
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Laboratory of Biopharmaceutical and Regenerative Sciences, Institute of Molecular Medicine and Life Science, Yokohama City University Association of Medical Science, Yokohama 236-0004, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Kenichi Inoue
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan.
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18
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Rathje CC, Randle SJ, Al Rawi S, Skinner BM, Nelson DE, Majumdar A, Johnson EEP, Bacon J, Vlazaki M, Affara NA, Ellis PJ, Laman H. A Conserved Requirement for Fbxo7 During Male Germ Cell Cytoplasmic Remodeling. Front Physiol 2019; 10:1278. [PMID: 31649556 PMCID: PMC6795710 DOI: 10.3389/fphys.2019.01278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Fbxo7 is the substrate-recognition subunit of an SCF-type ubiquitin E3 ligase complex. It has physiologically important functions in regulating mitophagy, proteasome activity and the cell cycle in multiple cell types, like neurons, lymphocytes and erythrocytes. Here, we show that in addition to the previously known Parkinsonian and hematopoietic phenotypes, male mice with reduced Fbxo7 expression are sterile. In these males, despite successful meiosis, nuclear elongation and eviction of histones from chromatin, the developing spermatids are phagocytosed by Sertoli cells during late spermiogenesis, as the spermatids undergo cytoplasmic remodeling. Surprisingly, despite the loss of all germ cells, there was no evidence of the symplast formation and cell sloughing that is typically associated with spermatid death in other mouse sterility models, suggesting that novel cell death and/or cell disposal mechanisms may be engaged in Fbxo7 mutant males. Mutation of the Drosophila Fbxo7 ortholog, nutcracker (ntc) also leads to sterility with germ cell death during cytoplasmic remodeling, indicating that the requirement for Fbxo7 at this stage is conserved. The ntc phenotype was attributed to decreased levels of the proteasome regulator, DmPI31 and reduced proteasome activity. Consistent with the fly model, we observe a reduction in PI31 levels in mutant mice; however, there is no alteration in proteasome activity in whole mouse testes. Our results are consistent with findings that Fbxo7 regulates PI31 protein levels, and indicates that a defect at the late stages of spermiogenesis, possibly due to faulty spatial dynamics of proteasomes during cytoplasmic remodeling, may underlie the fertility phenotype in mice.
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Affiliation(s)
- Claudia C Rathje
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Suzanne J Randle
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Sara Al Rawi
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin M Skinner
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - David E Nelson
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Antara Majumdar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Emma E P Johnson
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Joanne Bacon
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Myrto Vlazaki
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nabeel A Affara
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Peter J Ellis
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Heike Laman
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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19
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Xu FQ, Xue HW. The ubiquitin-proteasome system in plant responses to environments. PLANT, CELL & ENVIRONMENT 2019; 42:2931-2944. [PMID: 31364170 DOI: 10.1111/pce.13633] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 05/12/2023]
Abstract
The ubiquitin-proteasome system (UPS) is a rapid regulatory mechanism for selective protein degradation in plants and plays crucial roles in growth and development. There is increasing evidence that the UPS is also an integral part of plant adaptation to environmental stress, such as drought, salinity, cold, nutrient deprivation and pathogens. This review focuses on recent studies illustrating the important functions of the UPS components E2s, E3s and subunits of the proteasome and describes the regulation of proteasome activity during plant responses to environment stimuli. The future research hotspots and the potential for utilization of the UPS to improve plant tolerance to stress are discussed.
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Affiliation(s)
- Fa-Qing Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
- Shanghai College of Life Science, University of Chinese Academy of Sciences, 200032, Shanghai, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
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20
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Liu K, Jones S, Minis A, Rodriguez J, Molina H, Steller H. PI31 Is an Adaptor Protein for Proteasome Transport in Axons and Required for Synaptic Development. Dev Cell 2019; 50:509-524.e10. [PMID: 31327739 DOI: 10.1016/j.devcel.2019.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/18/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022]
Abstract
Protein degradation by the ubiquitin-proteasome system is critical for neuronal function. Neurons utilize microtubule-dependent molecular motors to allocate proteasomes to synapses, but how proteasomes are coupled to motors and how this is regulated to meet changing demand for protein breakdown remain largely unknown. We show that the conserved proteasome-binding protein PI31 serves as an adaptor to couple proteasomes with dynein light chain proteins (DYNLL1/2). The inactivation of PI31 inhibited proteasome motility in axons and disrupted synaptic proteostasis, structure, and function. Moreover, phosphorylation of PI31 by p38 MAPK enhanced binding to DYNLL1/2 and promoted the directional movement of proteasomes in axons, suggesting a mechanism to regulate loading of proteasomes onto motors. Inactivation of PI31 in mouse neurons attenuated proteasome movement in axons, indicating this process is conserved. Because mutations affecting PI31 activity are associated with human neurodegenerative diseases, impairment of PI31-mediated axonal transport of proteasomes may contribute to these disorders.
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Affiliation(s)
- Kai Liu
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sandra Jones
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Adi Minis
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jose Rodriguez
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Hermann Steller
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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21
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Kudriaeva AA, Belogurov AA. Proteasome: a Nanomachinery of Creative Destruction. BIOCHEMISTRY (MOSCOW) 2019; 84:S159-S192. [PMID: 31213201 DOI: 10.1134/s0006297919140104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the middle of the 20th century, it was postulated that degradation of intracellular proteins is a stochastic process. More than fifty years of intense studies have finally proven that protein degradation is a very complex and tightly regulated in time and space process that plays an incredibly important role in the vast majority of metabolic pathways. Degradation of more than a half of intracellular proteins is controlled by a hierarchically aligned and evolutionarily perfect system consisting of many components, the main ones being ubiquitin ligases and proteasomes, together referred to as the ubiquitin-proteasome system (UPS). The UPS includes more than 1000 individual components, and most of them are critical for the cell functioning and survival. In addition to the well-known signaling functions of ubiquitination, such as modification of substrates for proteasomal degradation and DNA repair, polyubiquitin (polyUb) chains are involved in other important cellular processes, e.g., cell cycle regulation, immunity, protein degradation in mitochondria, and even mRNA stability. This incredible variety of ubiquitination functions is related to the ubiquitin ability to form branching chains through the ε-amino group of any of seven lysine residues in its sequence. Deubiquitination is accomplished by proteins of the deubiquitinating enzyme family. The second main component of the UPS is proteasome, a multisubunit proteinase complex that, in addition to the degradation of functionally exhausted and damaged proteins, regulates many important cellular processes through controlled degradation of substrates, for example, transcription factors and cyclins. In addition to the ubiquitin-dependent-mediated degradation, there is also ubiquitin-independent degradation, when the proteolytic signal is either an intrinsic protein sequence or shuttle molecule. Protein hydrolysis is a critically important cellular function; therefore, any abnormalities in this process lead to systemic impairments further transforming into serious diseases, such as diabetes, malignant transformation, and neurodegenerative disorders (multiple sclerosis, Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease and Huntington's disease). In this review, we discuss the mechanisms that orchestrate all components of the UPS, as well as the plurality of the fine-tuning pathways of proteasomal degradation.
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Affiliation(s)
- A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia. .,Lomonosov Moscow State University, Moscow, 119991, Russia
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22
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Marshall RS, Vierstra RD. Dynamic Regulation of the 26S Proteasome: From Synthesis to Degradation. Front Mol Biosci 2019; 6:40. [PMID: 31231659 PMCID: PMC6568242 DOI: 10.3389/fmolb.2019.00040] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/09/2019] [Indexed: 01/12/2023] Open
Abstract
All eukaryotes rely on selective proteolysis to control the abundance of key regulatory proteins and maintain a healthy and properly functioning proteome. Most of this turnover is catalyzed by the 26S proteasome, an intricate, multi-subunit proteolytic machine. Proteasomes recognize and degrade proteins first marked with one or more chains of poly-ubiquitin, the addition of which is actuated by hundreds of ligases that individually identify appropriate substrates for ubiquitylation. Subsequent proteasomal digestion is essential and influences a myriad of cellular processes in species as diverse as plants, fungi and humans. Importantly, dysfunction of 26S proteasomes is associated with numerous human pathologies and profoundly impacts crop performance, thus making an understanding of proteasome dynamics critically relevant to almost all facets of human health and nutrition. Given this widespread significance, it is not surprising that sophisticated mechanisms have evolved to tightly regulate 26S proteasome assembly, abundance and activity in response to demand, organismal development and stress. These include controls on transcription and chaperone-mediated assembly, influences on proteasome localization and activity by an assortment of binding proteins and post-translational modifications, and ultimately the removal of excess or damaged particles via autophagy. Intriguingly, the autophagic clearance of damaged 26S proteasomes first involves their modification with ubiquitin, thus connecting ubiquitylation and autophagy as key regulatory events in proteasome quality control. This turnover is also influenced by two distinct biomolecular condensates that coalesce in the cytoplasm, one attracting damaged proteasomes for autophagy, and the other reversibly storing proteasomes during carbon starvation to protect them from autophagic clearance. In this review, we describe the current state of knowledge regarding the dynamic regulation of 26S proteasomes at all stages of their life cycle, illustrating how protein degradation through this proteolytic machine is tightly controlled to ensure optimal growth, development and longevity.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
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23
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Hemming ML, Lawlor MA, Andersen JL, Hagan T, Chipashvili O, Scott TG, Raut CP, Sicinska E, Armstrong SA, Demetri GD, Bradner JE, Ganz PA, Tomlinson G, Olopade OI, Couch FJ, Wang X, Lindor NM, Pankratz VS, Radice P, Manoukian S, Peissel B, Zaffaroni D, Barile M, Viel A, Allavena A, Dall'Olio V, Peterlongo P, Szabo CI, Zikan M, Claes K, Poppe B, Foretova L, Mai PL, Greene MH, Rennert G, Lejbkowicz F, Glendon G, Ozcelik H, Andrulis IL, Thomassen M, Gerdes AM, Sunde L, Cruger D, Birk Jensen U, Caligo M, Friedman E, Kaufman B, Laitman Y, Milgrom R, Dubrovsky M, Cohen S, Borg A, Jernström H, Lindblom A, Rantala J, Stenmark-Askmalm M, Melin B, Nathanson K, Domchek S, Jakubowska A, Lubinski J, Huzarski T, Osorio A, Lasa A, Durán M, Tejada MI, Godino J, Benitez J, Hamann U, Kriege M, Hoogerbrugge N, van der Luijt RB, van Asperen CJ, Devilee P, Meijers-Heijboer EJ, Blok MJ, Aalfs CM, Hogervorst F, Rookus M, Cook M, Oliver C, Frost D, Conroy D, Evans DG, Lalloo F, Pichert G, Davidson R, Cole T, Cook J, Paterson J, Hodgson S, Morrison PJ, Porteous ME, Walker L, Kennedy MJ, Dorkins H, Peock S, Godwin AK, Stoppa-Lyonnet D, de Pauw A, Mazoyer S, Bonadona V, Lasset C, Dreyfus H, Leroux D, Hardouin A, Berthet P, Faivre L, Loustalot C, Noguchi T, Sobol H, Rouleau E, Nogues C, Frénay M, Vénat-Bouvet L, Hopper JL, Daly MB, Terry MB, John EM, Buys SS, Yassin Y, Miron A, Goldgar D, Singer CF, Dressler AC, Gschwantler-Kaulich D, Pfeiler G, Hansen TVO, Jønson L, Agnarsson BA, Kirchhoff T, Offit K, Devlin V, Dutra-Clarke A, Piedmonte M, Rodriguez GC, Wakeley K, Boggess JF, Basil J, Schwartz PE, Blank SV, Toland AE, Montagna M, Casella C, Imyanitov E, Tihomirova L, Blanco I, Lazaro C, Ramus SJ, Sucheston L, Karlan BY, Gross J, Schmutzler R, Wappenschmidt B, Engel C, Meindl A, Lochmann M, Arnold N, Heidemann S, Varon-Mateeva R, Niederacher D, Sutter C, Deissler H, Gadzicki D, Preisler-Adams S, Kast K, Schönbuchner I, Caldes T, de la Hoya M, Aittomäki K, Nevanlinna H, Simard J, Spurdle AB, Holland H, Chen X, Platte R, Chenevix-Trench G, Easton DF. Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and Are Targetable by BET Bromodomain Inhibition. Cancer Res 2019. [PMID: 18483246 DOI: 10.1158/0008-5472] [Citation(s) in RCA: 680] [Impact Index Per Article: 136.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT and PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, resulting in high expression levels of the oncogene required for tumor growth. Although kinase inhibition is an effective therapy for many patients with GIST, disease progression from kinase-resistant mutations is common and no other effective classes of systemic therapy exist. In this study, we identify regulatory regions of the KIT enhancer essential for KIT gene expression and GIST cell viability. Given the dependence of GIST upon enhancer-driven expression of RTKs, we hypothesized that the enhancer domains could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell-cycle arrest, apoptosis, and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to superior cytotoxic effects in vitro and in vivo, with BBI preventing tumor growth in TKI-resistant xenografts. Resistance to select BBI in GIST was attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST. SIGNIFICANCE: Expression and activity of mutant KIT is essential for driving the majority of GIST neoplasms, which can be therapeutically targeted using BET bromodomain inhibitors.
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Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Matthew A Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jessica L Andersen
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Timothy Hagan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Otari Chipashvili
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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24
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Forget A, Martignetti L, Puget S, Calzone L, Brabetz S, Picard D, Montagud A, Liva S, Sta A, Dingli F, Arras G, Rivera J, Loew D, Besnard A, Lacombe J, Pagès M, Varlet P, Dufour C, Yu H, Mercier AL, Indersie E, Chivet A, Leboucher S, Sieber L, Beccaria K, Gombert M, Meyer FD, Qin N, Bartl J, Chavez L, Okonechnikov K, Sharma T, Thatikonda V, Bourdeaut F, Pouponnot C, Ramaswamy V, Korshunov A, Borkhardt A, Reifenberger G, Poullet P, Taylor MD, Kool M, Pfister SM, Kawauchi D, Barillot E, Remke M, Ayrault O. Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling. Cancer Cell 2018; 34:379-395.e7. [PMID: 30205043 DOI: 10.1016/j.ccell.2018.08.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/12/2018] [Accepted: 08/03/2018] [Indexed: 12/20/2022]
Abstract
The current consensus recognizes four main medulloblastoma subgroups (wingless, Sonic hedgehog, group 3 and group 4). While medulloblastoma subgroups have been characterized extensively at the (epi-)genomic and transcriptomic levels, the proteome and phosphoproteome landscape remain to be comprehensively elucidated. Using quantitative (phospho)-proteomics in primary human medulloblastomas, we unravel distinct posttranscriptional regulation leading to highly divergent oncogenic signaling and kinase activity profiles in groups 3 and 4 medulloblastomas. Specifically, proteomic and phosphoproteomic analyses identify aberrant ERBB4-SRC signaling in group 4. Hence, enforced expression of an activated SRC combined with p53 inactivation induces murine tumors that resemble group 4 medulloblastoma. Therefore, our integrative proteogenomics approach unveils an oncogenic pathway and potential therapeutic vulnerability in the most common medulloblastoma subgroup.
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Affiliation(s)
- Antoine Forget
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France.
| | - Loredana Martignetti
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Stéphanie Puget
- Department of Pediatric Neurosurgery, Necker University Hospital, University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Laurence Calzone
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Sebastian Brabetz
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Picard
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany
| | - Arnau Montagud
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Stéphane Liva
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Alexandre Sta
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Florent Dingli
- Proteomics and Mass Spectrometry Laboratory, Institut Curie, PSL Research University, 75005 Paris, France
| | - Guillaume Arras
- Proteomics and Mass Spectrometry Laboratory, Institut Curie, PSL Research University, 75005 Paris, France
| | - Jaime Rivera
- Proteomics and Mass Spectrometry Laboratory, Institut Curie, PSL Research University, 75005 Paris, France
| | - Damarys Loew
- Proteomics and Mass Spectrometry Laboratory, Institut Curie, PSL Research University, 75005 Paris, France
| | - Aurore Besnard
- Department of Neuropathology, Sainte-Anne Hospital, 75014 Paris, France; University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Joëlle Lacombe
- Department of Neuropathology, Sainte-Anne Hospital, 75014 Paris, France; University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Mélanie Pagès
- Department of Neuropathology, Sainte-Anne Hospital, 75014 Paris, France; University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Pascale Varlet
- Department of Neuropathology, Sainte-Anne Hospital, 75014 Paris, France; University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Christelle Dufour
- Department of Pediatric and Adolescent Oncology, Gustave Roussy, Rue Edouard Vaillant, 94805 Villejuif, France
| | - Hua Yu
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Audrey L Mercier
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Emilie Indersie
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Anaïs Chivet
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Sophie Leboucher
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Institut Curie, Centre de Recherche, Plateforme d'Histologie, Orsay 91405, France
| | - Laura Sieber
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kevin Beccaria
- Department of Pediatric Neurosurgery, Necker University Hospital, University Paris Descartes, Sorbonne Paris Cité, 75015 Paris, France
| | - Michael Gombert
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Frauke D Meyer
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany
| | - Nan Qin
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany
| | - Jasmin Bartl
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany
| | - Lukas Chavez
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Tanvi Sharma
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Venu Thatikonda
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Franck Bourdeaut
- Paris-Sciences-Lettres Research University, Institut Curie Research Center, SiRIC, Laboratory of Translational Research in Pediatric Oncology, Paris 75005, France; Paris-Sciences-Lettres Research University, Institut Curie Research Center, INSERM U830, Laboratory of Biology and Genetics of Cancers, Paris 75005, France
| | - Celio Pouponnot
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, Hospital for Sick Children and Department of Paediatrics, Hospital for Sick Children, Toronto, ON, Canada
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center (DKFZ), and Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Patrick Poullet
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada; Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada; Departments of Surgery, Laboratory Medicine and Pathobiology, and Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Marcel Kool
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daisuke Kawauchi
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Emmanuel Barillot
- Institut Curie, 26 rue d'Ulm, 75005 Paris, France; PSL Research University, 75005 Paris, France; Inserm, U900, 75005 Paris, France; Mines Paris Tech, 77305 cedex Fontainebleau, France.
| | - Marc Remke
- Department of Pediatric Neuro-Oncogenomics, DKFZ, Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany; Institute of Neuropathology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; DKTK, Partner Site, Essen/Düsseldorf, Germany.
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France.
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Joseph S, Schulz JB, Stegmüller J. Mechanistic contributions of FBXO7 to Parkinson disease. J Neurochem 2017; 144:118-127. [DOI: 10.1111/jnc.14253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Sabitha Joseph
- Department of Neurology; RWTH University Hospital; Aachen Germany
| | - Jörg Bernhard Schulz
- Department of Neurology; RWTH University Hospital; Aachen Germany
- Jülich Aachen Research Alliance (JARA) - JARA-Institute Molecular Neuroscience and Neuroimaging; FZ Jülich and RWTH University; Aachen Germany
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Gaczynska M, Osmulski PA. Targeting Protein-Protein Interactions in the Ubiquitin-Proteasome Pathway. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 110:123-165. [PMID: 29412995 DOI: 10.1016/bs.apcsb.2017.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ubiquitin-proteasome pathway (UPP) is a major venue for controlled intracellular protein degradation in Eukaryota. The machinery of several hundred proteins is involved in recognizing, tagging, transporting, and cleaving proteins, all in a highly regulated manner. Short-lived transcription factors, misfolded translation products, stress-damaged polypeptides, or worn-out long-lived proteins, all can be found among the substrates of UPP. Carefully choreographed protein-protein interactions (PPI) are involved in each step of the pathway. For many of the steps small-molecule inhibitors have been identified and often they directly or indirectly target PPI. The inhibitors may destabilize intracellular proteostasis and trigger apoptosis. So far this is the most explored option used as an anticancer strategy. Alternatively, substrate-specific polyubiquitination may be regulated for a precise intervention aimed at a particular metabolic pathway. This very attractive opportunity is moving close to clinical application. The best known drug target in UPP is the proteasome: the end point of the journey of a protein destined for degradation. The proteasome alone is a perfect object to study the mechanisms and roles of PPI on many levels. This giant protease is built from multisubunit modules and additionally utilizes a service from transient protein ligands, for example, delivering substrates. An elaborate set of PPI within the highest-order proteasome assembly is involved in substrate recognition and processing. Below we will outline PPI involved in the UPP and discuss the growing prospects for their utilization in pharmacological interventions.
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Affiliation(s)
- Maria Gaczynska
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.
| | - Pawel A Osmulski
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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Ubiquitin and Parkinson's disease through the looking glass of genetics. Biochem J 2017; 474:1439-1451. [PMID: 28408429 PMCID: PMC5390927 DOI: 10.1042/bcj20160498] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/20/2017] [Accepted: 02/20/2017] [Indexed: 12/12/2022]
Abstract
Biochemical alterations found in the brains of Parkinson's disease (PD) patients indicate that cellular stress is a major driver of dopaminergic neuronal loss. Oxidative stress, mitochondrial dysfunction, and ER stress lead to impairment of the homeostatic regulation of protein quality control pathways with a consequent increase in protein misfolding and aggregation and failure of the protein degradation machinery. Ubiquitin signalling plays a central role in protein quality control; however, prior to genetic advances, the detailed mechanisms of how impairment in the ubiquitin system was linked to PD remained mysterious. The discovery of mutations in the α-synuclein gene, which encodes the main protein misfolded in PD aggregates, together with mutations in genes encoding ubiquitin regulatory molecules, including PTEN-induced kinase 1 (PINK1), Parkin, and FBX07, has provided an opportunity to dissect out the molecular basis of ubiquitin signalling disruption in PD, and this knowledge will be critical for developing novel therapeutic strategies in PD that target the ubiquitin system.
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An H, Yang L, Wang C, Gan Z, Gu H, Zhang T, Huang X, Liu Y, Li Y, Chang SJ, Lai J, Li YB, Chen S, Sun FL. Interactome Analysis Reveals a Novel Role for RAD6 in the Regulation of Proteasome Activity and Localization in Response to DNA Damage. Mol Cell Biol 2017; 37:e00419-16. [PMID: 28031328 PMCID: PMC5335506 DOI: 10.1128/mcb.00419-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/01/2016] [Accepted: 12/04/2016] [Indexed: 01/25/2023] Open
Abstract
RAD6, an E2 ubiquitin-conjugating enzyme, is a key node for determining different DNA damage repair pathways, controlling both the error-prone and the error-free DNA damage repair pathways through differential regulation of the ubiquitination of the proliferating cell nuclear antigen (PCNA) protein. However, whether other pathways are involved in the RAD6-mediated regulation of DNA damage repair is still unclear. To deeply understand the molecular mechanisms of RAD6 in DNA damage repair, we performed a proteomic analysis and identified the changes of the protein-protein interaction (PPI) networks of RAD6 before and after X-ray irradiation. Furthermore, our study indicated that a proteasome-related event is likely involved in the DNA damage repair process. Moreover, we found that RAD6 promotes proteasome activity and nuclear translocation by enhancing the degradation of PSMF1 and the lamin B receptor (LBR). Therefore, we provide a novel pathway that is employed by RAD6 in response to DNA damage.
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Affiliation(s)
- Hongli An
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Lu Yang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Chen Wang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Zhixue Gan
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Haihui Gu
- Department of Transfusion Medicine, Changhai Hospital, Second Military Medical University, Shanghai, Shanghai, People's Republic of China
| | - Tao Zhang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Xin Huang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Yan Liu
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Yufeng Li
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Shing-Jyh Chang
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan, Republic of China
| | - Jianghua Lai
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Ya-Bin Li
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Su Chen
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Fang-Lin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
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The life cycle of the 26S proteasome: from birth, through regulation and function, and onto its death. Cell Res 2016; 26:869-85. [PMID: 27444871 PMCID: PMC4973335 DOI: 10.1038/cr.2016.86] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The 26S proteasome is a large, ∼2.5 MDa, multi-catalytic ATP-dependent protease complex that serves as the degrading arm of the ubiquitin system, which is the major pathway for regulated degradation of cytosolic, nuclear and membrane proteins in all eukaryotic organisms.
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Yang BJ, Han XX, Yin LL, Xing MQ, Xu ZH, Xue HW. Arabidopsis PROTEASOME REGULATOR1 is required for auxin-mediated suppression of proteasome activity and regulates auxin signalling. Nat Commun 2016; 7:11388. [PMID: 27109828 PMCID: PMC4848511 DOI: 10.1038/ncomms11388] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 03/21/2016] [Indexed: 01/14/2023] Open
Abstract
The plant hormone auxin is perceived by the nuclear F-box protein TIR1 receptor family and regulates gene expression through degradation of Aux/IAA transcriptional repressors. Several studies have revealed the importance of the proteasome in auxin signalling, but details on how the proteolytic machinery is regulated and how this relates to degradation of Aux/IAA proteins remains unclear. Here we show that an Arabidopsis homologue of the proteasome inhibitor PI31, which we name PROTEASOME REGULATOR1 (PTRE1), is a positive regulator of the 26S proteasome. Loss-of-function ptre1 mutants are insensitive to auxin-mediated suppression of proteasome activity, show diminished auxin-induced degradation of Aux/IAA proteins and display auxin-related phenotypes. We found that auxin alters the subcellular localization of PTRE1, suggesting this may be part of the mechanism by which it reduces proteasome activity. Based on these results, we propose that auxin regulates proteasome activity via PTRE1 to fine-tune the homoeostasis of Aux/IAA repressor proteins thus modifying auxin activity. Plant responses to auxin require proteasome-mediated degradation of Aux/IAA transcriptional repressor proteins. Here, Yang et al. show that auxin suppresses proteasome activity in a manner dependent on the proteasome regulator PTRE1 and propose a mechanism for fine tuning Aux/IAA homoeostasis.
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Affiliation(s)
- Bao-Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences, Shanghai 200032, People's Republic of China
| | - Xin-Xin Han
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences, Shanghai 200032, People's Republic of China
| | - Lin-Lin Yin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences, Shanghai 200032, People's Republic of China
| | - Mei-Qing Xing
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences, Shanghai 200032, People's Republic of China
| | - Zhi-Hong Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences, Shanghai 200032, People's Republic of China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences, Shanghai 200032, People's Republic of China
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Chondrogianni N, Voutetakis K, Kapetanou M, Delitsikou V, Papaevgeniou N, Sakellari M, Lefaki M, Filippopoulou K, Gonos ES. Proteasome activation: An innovative promising approach for delaying aging and retarding age-related diseases. Ageing Res Rev 2015; 23:37-55. [PMID: 25540941 DOI: 10.1016/j.arr.2014.12.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/09/2014] [Accepted: 12/15/2014] [Indexed: 11/16/2022]
Abstract
Aging is a natural process accompanied by a progressive accumulation of damage in all constituent macromolecules (nucleic acids, lipids and proteins). Accumulation of damage in proteins leads to failure of proteostasis (or vice versa) due to increased levels of unfolded, misfolded or aggregated proteins and, in turn, to aging and/or age-related diseases. The major cellular proteolytic machineries, namely the proteasome and the lysosome, have been shown to dysfunction during aging and age-related diseases. Regarding the proteasome, it is well established that it can be activated either through genetic manipulation or through treatment with natural or chemical compounds that eventually result to extension of lifespan or deceleration of the progression of age-related diseases. This review article focuses on proteasome activation studies in several species and cellular models and their effects on aging and longevity. Moreover, it summarizes findings regarding proteasome activation in the major age-related diseases as well as in progeroid syndromes.
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Affiliation(s)
- Niki Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece.
| | - Konstantinos Voutetakis
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Marianna Kapetanou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Vasiliki Delitsikou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Nikoletta Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Marianthi Sakellari
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece; Örebro University, Medical School, Örebro, Sweden
| | - Maria Lefaki
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Konstantina Filippopoulou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece; Örebro University, Medical School, Örebro, Sweden.
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32
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Clemen CS, Marko M, Strucksberg KH, Behrens J, Wittig I, Gärtner L, Winter L, Chevessier F, Matthias J, Türk M, Tangavelou K, Schütz J, Arhzaouy K, Klopffleisch K, Hanisch FG, Rottbauer W, Blümcke I, Just S, Eichinger L, Hofmann A, Schröder R. VCP and PSMF1: Antagonistic regulators of proteasome activity. Biochem Biophys Res Commun 2015; 463:1210-7. [DOI: 10.1016/j.bbrc.2015.06.086] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 06/12/2015] [Indexed: 11/25/2022]
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Meiners S, Keller IE, Semren N, Caniard A. Regulation of the proteasome: evaluating the lung proteasome as a new therapeutic target. Antioxid Redox Signal 2014; 21:2364-82. [PMID: 24437504 DOI: 10.1089/ars.2013.5798] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE Lung diseases are on the second rank worldwide with respect to morbidity and mortality. For most respiratory diseases, no effective therapies exist. Whereas the proteasome has been successfully evaluated as a novel target for therapeutic interventions in cancer, neurodegenerative, and cardiac disorders, there is a profound lack of knowledge on the regulation of proteasome activity in chronic and acute lung diseases. RECENT ADVANCES There are various means of how the amount of active proteasome complexes in the cell can be regulated such as transcriptional regulation of proteasomal subunit expression, association with different regulators, assembly and half-life of proteasomes and regulatory complexes, as well as post-translational modifications. It also becomes increasingly evident that proteasome activity is fine-tuned and depends on the state of the cell. We propose here that 20S proteasomes and their regulators can be regarded as dynamic building blocks, which assemble or disassemble in response to cellular needs. The composition of proteasome complexes in a cell may vary depending on tissue, cell type and compartment, stage of development, or pathological context. CRITICAL ISSUES AND FUTURE DIRECTIONS Dissecting the expression and regulation of the various catalytic forms of 20S proteasomes, such as constitutive, immuno-, and mixed proteasomes, together with their associated regulatory complexes will not only greatly enhance our understanding of proteasome function in lung pathogenesis but will also pave the way to develop new classes of drugs that inhibit or activate proteasome function in a defined setting for treatment of lung diseases.
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Affiliation(s)
- Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital , Ludwig-Maximilians University, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
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Gaczynska M, Osmulski PA. Harnessing proteasome dynamics and allostery in drug design. Antioxid Redox Signal 2014; 21:2286-301. [PMID: 24410482 PMCID: PMC4241894 DOI: 10.1089/ars.2013.5816] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 01/12/2014] [Indexed: 12/14/2022]
Abstract
SIGNIFICANCE The proteasome is the essential protease that is responsible for regulated cleavage of the bulk of intracellular proteins. Its central role in cellular physiology has been exploited in therapies against aggressive cancers where proteasome-specific competitive inhibitors that block proteasome active centers are very effectively used. However, drugs regulating this essential protease are likely to have broader clinical usefulness. The non-catalytic sites of the proteasome emerge as an attractive alternative target in search of highly specific and diverse proteasome regulators. RECENT ADVANCES Crystallographic models of the proteasome leave the false impression of fixed structures with minimal molecular dynamics lacking long-distance allosteric signaling. However, accumulating biochemical and structural observations strongly support the notion that the proteasome is regulated by precise allosteric interactions arising from protein dynamics, encouraging the active search for allosteric regulators. Here, we discuss properties of several promising compounds that affect substrate gating and processing in antechambers, and interactions of the catalytic core with regulatory proteins. CRITICAL ISSUES Given the structural complexity of proteasome assemblies, it is a painstaking process to better understand their allosteric regulation and molecular dynamics. Here, we discuss the challenges and achievements in this field. We place special emphasis on the role of atomic force microscopy imaging in probing the allostery and dynamics of the proteasome, and in dissecting the mechanisms involving small-molecule allosteric regulators. FUTURE DIRECTIONS New small-molecule allosteric regulators may become a next generation of drugs targeting the proteasome, which is critical to the development of new therapies in cancers and other diseases.
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Affiliation(s)
- Maria Gaczynska
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
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Gu ZC, Enenkel C. Proteasome assembly. Cell Mol Life Sci 2014; 71:4729-45. [PMID: 25107634 PMCID: PMC11113775 DOI: 10.1007/s00018-014-1699-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
Abstract
In eukaryotic cells, proteasomes are highly conserved protease complexes and eliminate unwanted proteins which are marked by poly-ubiquitin chains for degradation. The 26S proteasome consists of the proteolytic core particle, the 20S proteasome, and the 19S regulatory particle, which are composed of 14 and 19 different subunits, respectively. Proteasomes are the second-most abundant protein complexes and are continuously assembled from inactive precursor complexes in proliferating cells. The modular concept of proteasome assembly was recognized in prokaryotic ancestors and applies to eukaryotic successors. The efficiency and fidelity of eukaryotic proteasome assembly is achieved by several proteasome-dedicated chaperones that initiate subunit incorporation and control the quality of proteasome assemblies by transiently interacting with proteasome precursors. It is important to understand the mechanism of proteasome assembly as the proteasome has key functions in the turnover of short-lived proteins regulating diverse biological processes.
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Affiliation(s)
- Zhu Chao Gu
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8 Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8 Canada
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N-terminal α7 deletion of the proteasome 20S core particle substitutes for yeast PI31 function. Mol Cell Biol 2014; 35:141-52. [PMID: 25332237 DOI: 10.1128/mcb.00582-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The proteasome core particle (CP) is a conserved protease complex that is formed by the stacking of two outer α-rings and two inner β-rings. The α-ring is a heteroheptameric ring of subunits α1 to α7 and acts as a gate that restricts entry of substrate proteins into the catalytic cavity formed by the two abutting β-rings. The 31-kDa proteasome inhibitor (PI31) was originally identified as a protein that binds to the CP and inhibits CP activity in vitro, but accumulating evidence indicates that PI31 is required for physiological proteasome activity. To clarify the in vivo role of PI31, we examined the Saccharomyces cerevisiae PI31 ortholog Fub1. Fub1 was essential in a situation where the CP assembly chaperone Pba4 was deleted. The lethality of Δfub1 Δpba4 was suppressed by deletion of the N terminus of α7 (α7ΔN), which led to the partial activation of the CP. However, deletion of the N terminus of α3, which activates the CP more efficiently than α7ΔN by gate opening, did not suppress Δfub1 Δpba4 lethality. These results suggest that the α7 N terminus has a role in CP activation different from that of the α3 N terminus and that the role of Fub1 antagonizes a specific function of the α7 N terminus.
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Chondrogianni N, Sakellari M, Lefaki M, Papaevgeniou N, Gonos ES. Proteasome activation delays aging in vitro and in vivo. Free Radic Biol Med 2014; 71:303-320. [PMID: 24681338 DOI: 10.1016/j.freeradbiomed.2014.03.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/18/2014] [Accepted: 03/18/2014] [Indexed: 02/02/2023]
Abstract
Aging is a natural biological process that is characterized by a progressive accumulation of macromolecular damage. In the proteome, aging is accompanied by decreased protein homeostasis and function of the major cellular proteolytic systems, leading to the accumulation of unfolded, misfolded, or aggregated proteins. In particular, the proteasome is responsible for the removal of normal as well as damaged or misfolded proteins. Extensive work during the past several years has clearly demonstrated that proteasome activation by either genetic means or use of compounds significantly retards aging. Importantly, this represents a common feature across evolution, thereby suggesting proteasome activation to be an evolutionarily conserved mechanism of aging and longevity regulation. This review article reports on the means of function of these proteasome activators and how they regulate aging in various species.
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Affiliation(s)
- Niki Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece.
| | - Marianthi Sakellari
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece; Örebro University Medical School, Örebro, Sweden
| | - Maria Lefaki
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece
| | - Nikoletta Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece; Örebro University Medical School, Örebro, Sweden
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Shang J, Wang G, Yang Y, Huang X, Du Z. Structure of the FP domain of Fbxo7 reveals a novel mode of protein-protein interaction. ACTA ACUST UNITED AC 2013; 70:155-64. [PMID: 24419388 DOI: 10.1107/s1399004713025820] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/18/2013] [Indexed: 01/17/2023]
Abstract
The FP (Fbxo7/PI31) domains found in the F-box protein Fbxo7 and the proteasome inhibitor PI31 mediate the homodimerization and heterodimerization of Fbxo7 and PI31. Fbxo7 is the substrate-recognition subunit of the SCF(Fbxo7) (Skp1-Cul1-F-box protein) E3 ubiquitin ligase that catalyzes the ubiquitination of hepatoma up-regulated protein (HURP) and inhibitor of apoptosis protein (IAP). Fbxo7 also interacts with proteins that are not substrates of the ubiquitin proteasome system, such as Cdk6 and PI31. Here, the crystal structure of the Fbxo7 FP domain is reported at 2.0 Å resolution. The Fbxo7 FP domain adopts an α/β-fold similar to that of the PI31 FP domain. However, an α-helix and three β-strands in the Fbxo7 FP domain are longer than their counterparts in the PI31 FP domain. The differences in these secondary-structural elements are spatially clustered to define a more structured and extended C-terminal end of the Fbxo7 FP domain. The two FP domains also differ substantially in the length and conformation of the longest connecting loop. More importantly, structural differences between the two FP domains lead to drastically different modes of inter-domain protein-protein interaction. The inter-domain interface of the Fbxo7 FP domain is defined by the α-helical surface in one protomer and the β-sheet surface in the other protomer, whereas for the PI31 domain it is defined by either the α-helical surfaces or the β-sheet surfaces in both protomers. The inter-domain interaction of the Fbxo7 FP domain is much more extensive, featuring a larger contact surface area, better shape complementarity and more hydrophobic and hydrogen-bonding interactions. The Fbxo7 FP domain also has the potential to bind two protein partners simultaneously using the α-helical and β-sheet surfaces. The results of this structural study provide critical insights into how Fbxo7 may dimerize (or multimerize) and interact with other regulatory proteins via the FP domain.
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Affiliation(s)
- Jinsai Shang
- Chemistry and Biochemistry, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Guan Wang
- Chemistry and Biochemistry, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Yang Yang
- Chemistry and Biochemistry, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Xiaolan Huang
- Computer Science, Southern Illinois University, 1000 Faner Drive, Carbondale, IL 62901, USA
| | - Zhihua Du
- Chemistry and Biochemistry, Southern Illinois University, 1245 Lincoln Drive, Carbondale, IL 62901, USA
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Gomes AV. Genetics of proteasome diseases. SCIENTIFICA 2013; 2013:637629. [PMID: 24490108 PMCID: PMC3892944 DOI: 10.1155/2013/637629] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 11/18/2013] [Indexed: 05/28/2023]
Abstract
The proteasome is a large, multiple subunit complex that is capable of degrading most intracellular proteins. Polymorphisms in proteasome subunits are associated with cardiovascular diseases, diabetes, neurological diseases, and cancer. One polymorphism in the proteasome gene PSMA6 (-8C/G) is associated with three different diseases: type 2 diabetes, myocardial infarction, and coronary artery disease. One type of proteasome, the immunoproteasome, which contains inducible catalytic subunits, is adapted to generate peptides for antigen presentation. It has recently been shown that mutations and polymorphisms in the immunoproteasome catalytic subunit PSMB8 are associated with several inflammatory and autoinflammatory diseases including Nakajo-Nishimura syndrome, CANDLE syndrome, and intestinal M. tuberculosis infection. This comprehensive review describes the disease-related polymorphisms in proteasome genes associated with human diseases and the physiological modulation of proteasome function by these polymorphisms. Given the large number of subunits and the central importance of the proteasome in human physiology as well as the fast pace of detection of proteasome polymorphisms associated with human diseases, it is likely that other polymorphisms in proteasome genes associated with diseases will be detected in the near future. While disease-associated polymorphisms are now readily discovered, the challenge will be to use this genetic information for clinical benefit.
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Affiliation(s)
- Aldrin V. Gomes
- Department of Neurobiology, Physiology, and Behavior, University of California, Davis, CA 95616, USA
- Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, USA
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Nelson DE, Randle SJ, Laman H. Beyond ubiquitination: the atypical functions of Fbxo7 and other F-box proteins. Open Biol 2013; 3:130131. [PMID: 24107298 PMCID: PMC3814724 DOI: 10.1098/rsob.130131] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
F-box proteins (FBPs) are substrate-recruiting subunits of Skp1-cullin1-FBP (SCF)-type E3 ubiquitin ligases. To date, 69 FBPs have been identified in humans, but ubiquitinated substrates have only been identified for a few, with the majority of FBPs remaining ‘orphans’. In recent years, a growing body of work has identified non-canonical, SCF-independent roles for about 12% of the human FBPs. These atypical FBPs affect processes as diverse as transcription, cell cycle regulation, mitochondrial dynamics and intracellular trafficking. Here, we provide a general review of FBPs, with a particular emphasis on these expanded functions. We review Fbxo7 as an exemplar of this special group as it has well-defined roles in both SCF and non-SCF complexes. We review its function as a cell cycle regulator, via its ability to stabilize p27 protein and Cdk6 complexes, and as a proteasome regulator, owing to its high affinity binding to PI31. We also highlight recent advances in our understanding of Fbxo7 function in Parkinson's disease, where it functions in the regulation of mitophagy with PINK1 and Parkin. We postulate that a few extraordinary FBPs act as platforms that seamlessly segue their canonical and non-canonical functions to integrate different cellular pathways and link their regulation.
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Affiliation(s)
- David E Nelson
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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Schmidt M, Finley D. Regulation of proteasome activity in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:13-25. [PMID: 23994620 DOI: 10.1016/j.bbamcr.2013.08.012] [Citation(s) in RCA: 328] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 12/13/2022]
Abstract
The ubiquitin-proteasome system (UPS) is the primary selective degradation system in the nuclei and cytoplasm of eukaryotic cells, required for the turnover of myriad soluble proteins. The hundreds of factors that comprise the UPS include an enzymatic cascade that tags proteins for degradation via the covalent attachment of a poly-ubiquitin chain, and a large multimeric enzyme that degrades ubiquitinated proteins, the proteasome. Protein degradation by the UPS regulates many pathways and is a crucial component of the cellular proteostasis network. Dysfunction of the ubiquitination machinery or the proteolytic activity of the proteasome is associated with numerous human diseases. In this review we discuss the contributions of the proteasome to human pathology, describe mechanisms that regulate the proteolytic capacity of the proteasome, and discuss strategies to modulate proteasome function as a therapeutic approach to ameliorate diseases associated with altered UPS function. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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Affiliation(s)
- Marion Schmidt
- Albert Einstein College of Medicine, Department of Biochemistry, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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Leone P, Shin EC, Perosa F, Vacca A, Dammacco F, Racanelli V. MHC class I antigen processing and presenting machinery: organization, function, and defects in tumor cells. J Natl Cancer Inst 2013; 105:1172-87. [PMID: 23852952 DOI: 10.1093/jnci/djt184] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The surface presentation of peptides by major histocompatibility complex (MHC) class I molecules is critical to all CD8(+) T-cell adaptive immune responses, including those against tumors. The generation of peptides and their loading on MHC class I molecules is a multistep process involving multiple molecular species that constitute the so-called antigen processing and presenting machinery (APM). The majority of class I peptides begin as proteasome degradation products of cytosolic proteins. Once transported into the endoplasmic reticulum by TAP (transporter associated with antigen processing), peptides are not bound randomly by class I molecules but are chosen by length and sequence, with peptidases editing the raw peptide pool. Aberrations in APM genes and proteins have frequently been observed in human tumors and found to correlate with relevant clinical variables, including tumor grade, tumor stage, disease recurrence, and survival. These findings support the idea that APM defects are immune escape mechanisms that disrupt the tumor cells' ability to be recognized and killed by tumor antigen-specific cytotoxic CD8(+) T cells. Detailed knowledge of APM is crucial for the optimization of T cell-based immunotherapy protocols.
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Affiliation(s)
- Patrizia Leone
- Department of Internal Medicine and Clinical Oncology, University of Bari Medical School, Bari, Italy
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43
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Proteasome regulation by ADP-ribosylation. Cell 2013; 153:614-27. [PMID: 23622245 DOI: 10.1016/j.cell.2013.03.040] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/21/2013] [Accepted: 03/25/2013] [Indexed: 12/11/2022]
Abstract
Protein degradation by the ubiquitin-proteasome system is central to cell homeostasis and survival. Defects in this process are associated with diseases such as cancer and neurodegenerative disorders. The 26S proteasome is a large protease complex that degrades ubiquitinated proteins. Here, we show that ADP-ribosylation promotes 26S proteasome activity in both Drosophila and human cells. We identify the ADP-ribosyltransferase tankyrase (TNKS) and the 19S assembly chaperones dp27 and dS5b as direct binding partners of the proteasome regulator PI31. TNKS-mediated ADP-ribosylation of PI31 drastically reduces its affinity for 20S proteasome α subunits to relieve 20S repression by PI31. Additionally, PI31 modification increases binding to and sequestration of dp27 and dS5b from 19S regulatory particles, promoting 26S assembly. Inhibition of TNKS by either RNAi or a small-molecule inhibitor, XAV939, blocks this process to reduce 26S assembly. These results unravel a mechanism of proteasome regulation that can be targeted with existing small-molecule inhibitors.
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44
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Hatanaka A, Chen B, Sun JQ, Mano Y, Funakoshi M, Kobayashi H, Ju Y, Mizutani T, Shinmyozu K, Nakayama JI, Miyamoto K, Uchida H, Oki M. Fub1p, a novel protein isolated by boundary screening, binds the proteasome complex. Genes Genet Syst 2012; 86:305-14. [PMID: 22362029 DOI: 10.1266/ggs.86.305] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Silenced chromatin domains are restricted to specific regions. Eukaryotic chromosomes are organized into discrete domains delimited by domain boundaries. From approximately 6,000 genes in Saccharomyces cerevisiae, we previously isolated 55 boundary genes. In this study, we focus on the molecular function of one of boundary genes, YCR076C/FUB1 (function of boundary), whose function has not been clearly defined in vivo. Biochemical analysis of Fub1p revealed that it interacted with multiple subunits of the 20S proteasome core particle (20S CP). To further clarify the functional link between Fub1p and proteasome, several proteasome mutants were analyzed. Although only 20S CP subunits were isolated as Fub1p interactors, a genetic interaction was also observed for component of 19S regulatory particle (19S RP) suggesting involvement of Fub1p with the whole proteasome. We also analyzed the mechanism of boundary establishment by using proteasome composition factor-deficient strains. Deletion of pre9 and ump1, whose products have effects on the 20S CP, resulted in a decrease in boundary function. Domain analyses of Fub1p identified a minimum functional domain in the C terminus that was essential for boundary establishment and showed a limited sequence homology to the human PSMF1, which is known to inhibit proteasome activity. Finally, boundary assay showed that human PSMF1 also exhibited boundary establishment activity in yeast. Our results defined the functional correlation between Fub1p and PSMF1.
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Affiliation(s)
- Akira Hatanaka
- Department of Applied Chemistry & Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
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Zheng J, Dasgupta A, Bizzozero OA. Changes in 20S subunit composition are largely responsible for altered proteasomal activities in experimental autoimmune encephalomyelitis. J Neurochem 2012; 121:486-94. [PMID: 22353035 DOI: 10.1111/j.1471-4159.2012.07699.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We recently reported that the proteasomal peptidase activities are altered in the cerebellum of mice with myelin oligodendrocyte glycoprotein (MOG) peptide-induced experimental autoimmune encephalomyelitis (EAE). To determine whether these fluctuations are caused by proteasome activation/inactivation and/or changes in the levels of individual β subunits, we characterized the proteasome subunit composition by western blotting. The results show that the rise in proteasomal peptidase activity in acute EAE correlates with an augmented expression of inducible β subunits whereas the decline in activity in chronic EAE correlates with a reduction in the amount of standard β subunits. Using pure standard (s) and immuno (i) 20S particles for calibration, we determined that the changes in the levels of catalytic subunits account for all of the fluctuations in peptidase activities in EAE. The i-20S and s-20S proteasome were found to degrade carbonylated β-actin with similar efficiency, suggesting that the amount of protein carbonyls in EAE may be controlled by the activity of both core particles. We also found an increase in proteasome activator 11S regulatory particle and a decrease in inhibitor proteasome inhibitor with molecular mass of 31 kDa levels in acute EAE, reflecting a response to inflammation. Elevated levels of 19S regulatory particle and 11S regulatory particle in chronic EAE, however, may occur in response to diminished proteasomal activity in this phase. These findings are central towards understanding the altered proteasomal physiology in inflammatory demyelinating disorders.
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Affiliation(s)
- Jianzheng Zheng
- Department of Cell Biology and Physiology, University of New Mexico-Health Sciences Center, Albuquerque, NM, USA
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Abstract
The ubiquitin-proteasomal system is an essential element of the protein quality control machinery in cells. The central part of this system is the 20S proteasome. The proteasome is a barrel-shaped multienzyme complex, containing several active centers hidden at the inner surface of the hollow cylinder. So, the regulation of the substrate entry toward the inner proteasomal surface is a key control mechanism of the activity of this protease. This chapter outlines the knowledge on the structure of the subunits of the 20S proteasome, the binding and structure of some proteasomal regulators and inducible proteasomal subunits. Therefore, this chapter imparts the knowledge on proteasomal structure which is required for the understanding of the following chapters.
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Scruggs SB, Ping P, Zong C. Heterogeneous cardiac proteasomes: mandated by diverse substrates? Physiology (Bethesda) 2011; 26:106-14. [PMID: 21487029 DOI: 10.1152/physiol.00039.2010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Proteasome biology has taken central stage in cardiac physiology and pathophysiology. The molecular heterogeneity of proteasome subpopulations supports the specificity of proteasome function to degrade diverse substrate repertoires. Unveiling the dynamics of proteasome function should inspire new therapeutic strategies for combating cardiac disease.
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Affiliation(s)
- Sarah B Scruggs
- Departments of Physiology and Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Bader M, Benjamin S, Wapinski OL, Smith DM, Goldberg AL, Steller H. A conserved F box regulatory complex controls proteasome activity in Drosophila. Cell 2011; 145:371-82. [PMID: 21529711 DOI: 10.1016/j.cell.2011.03.021] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 11/04/2010] [Accepted: 03/14/2011] [Indexed: 11/29/2022]
Abstract
The ubiquitin-proteasome system catalyzes the degradation of intracellular proteins. Although ubiquitination of proteins determines their stabilities, there is growing evidence that proteasome function is also regulated. We report the functional characterization of a conserved proteasomal regulatory complex. We identified DmPI31 as a binding partner of the F box protein Nutcracker, a component of an SCF ubiquitin ligase (E3) required for caspase activation during sperm differentiation in Drosophila. DmPI31 binds Nutcracker via a conserved mechanism that is also used by mammalian FBXO7 and PI31. Nutcracker promotes DmPI31 stability, which is necessary for caspase activation, proteasome function, and sperm differentiation. DmPI31 can activate 26S proteasomes in vitro, and increasing DmPI31 levels suppresses defects caused by diminished proteasome activity in vivo. Furthermore, loss of DmPI31 function causes lethality, cell-cycle abnormalities, and defects in protein degradation, demonstrating that DmPI31 is physiologically required for normal proteasome activity.
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Affiliation(s)
- Maya Bader
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA
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A conserved 20S proteasome assembly factor requires a C-terminal HbYX motif for proteasomal precursor binding. Nat Struct Mol Biol 2011; 18:622-9. [PMID: 21499243 PMCID: PMC3087856 DOI: 10.1038/nsmb.2027] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 02/07/2011] [Indexed: 02/06/2023]
Abstract
Dedicated chaperones facilitate eukaryotic proteasome assembly, yet how they function remains largely unknown. Here we demonstrate that a yeast 20S proteasome assembly factor, Pba1–Pba2, requires a previously overlooked C-terminal HbYX (hydrophobic-tyrosine-X) motif for function. HbYX motifs in proteasome activators open the 20S proteasome entry pore, but Pba1–Pba2 instead binds inactive proteasomal precursors. We discovered an archaeal ortholog of this factor, here named PbaA, that also binds preferentially to proteasomal precursors in a HbYX-dependent fashion using the same proteasomal α-ring surface pockets bound by activators. Remarkably, PbaA and the related PbaB protein can be induced to bind mature 20S proteasomes if the active sites in the central chamber are occupied by inhibitors. Our data suggest an allosteric mechanism in which proteasome active-site maturation determines assembly chaperone binding, potentially shielding assembly intermediates or misassembled complexes from non-productive associations until assembly is complete.
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50
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Savulescu AF, Glickman MH. Proteasome activator 200: the heat is on... Mol Cell Proteomics 2011; 10:R110.006890. [PMID: 21389348 DOI: 10.1074/mcp.r110.006890] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Proteasomes play a key regulatory role in all eukaryotic cells by removing proteins in a timely manner. There are two predominant forms: The 20S core particle (CP) can hydrolyze peptides and certain unstructured proteins, and the 26S holoenzyme is able to proteolyse most proteins conjugated to ubiquitin. The 26S complex consists of a CP barrel with a 19S regulatory particle (RP; a.k.a PA700) attached to its outer surface. Several studies purified another proteasome activator with a MW of 200 kDa (PA200) that attaches to the same outer ring of the CP. A role for PA200 has been demonstrated in spermatogenesis, in response to DNA repair and in maintenance of mitochondrial inheritance. Enhanced levels of PA200-CP complexes are observed under conditions in which either activated or disrupted CP prevail, suggesting it participates in regulating overall proteolytic activity. PA200, or its yeast ortholog Blm10, may also incorporate into 26S proteasomes yielding PA200-CP-RP hybrids. A three-dimensional molecular structure determined by x-ray crystallography of Blm10-CP provides a model for activation. The carboxy terminus of Blm10 inserts into a dedicated pocket in the outer ring of the CP surface, whereas multiple HEAT-like repeats fold into an asymmetric solenoid wrapping around the central pore to stabilize a partially open conformation. The resulting hollow domelike structure caps the entire CP surface. This asymmetric structure may provide insight as to how the 19S RP, with two HEAT repeatlike subunits (Rpn1, Rpn2) alongside six ATPases (Rpt1-6), attaches to the same surface of the CP ring, and likewise, induces pore opening.
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