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Cuinat S, Bézieau S, Deb W, Mercier S, Vignard V, Isidor B, Küry S, Ebstein F. Understanding neurodevelopmental proteasomopathies as new rare disease entities: A review of current concepts, molecular biomarkers, and perspectives. Genes Dis 2024; 11:101130. [PMID: 39220754 PMCID: PMC11364055 DOI: 10.1016/j.gendis.2023.101130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/30/2023] [Accepted: 08/19/2023] [Indexed: 09/04/2024] Open
Abstract
The recent advances in high throughput sequencing technology have drastically changed the practice of medical diagnosis, allowing for rapid identification of hundreds of genes causing human diseases. This unprecedented progress has made clear that most forms of intellectual disability that affect more than 3% of individuals worldwide are monogenic diseases. Strikingly, a substantial fraction of the mendelian forms of intellectual disability is associated with genes related to the ubiquitin-proteasome system, a highly conserved pathway made up of approximately 1200 genes involved in the regulation of protein homeostasis. Within this group is currently emerging a new class of neurodevelopmental disorders specifically caused by proteasome pathogenic variants which we propose to designate "neurodevelopmental proteasomopathies". Besides cognitive impairment, these diseases are typically associated with a series of syndromic clinical manifestations, among which facial dysmorphism, motor delay, and failure to thrive are the most prominent ones. While recent efforts have been made to uncover the effects exerted by proteasome variants on cell and tissue landscapes, the molecular pathogenesis of neurodevelopmental proteasomopathies remains ill-defined. In this review, we discuss the cellular changes typically induced by genomic alterations in proteasome genes and explore their relevance as biomarkers for the diagnosis, management, and potential treatment of these new rare disease entities.
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Affiliation(s)
- Silvestre Cuinat
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes F-44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France
| | - Stéphane Bézieau
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes F-44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France
| | - Wallid Deb
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes F-44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France
| | - Sandra Mercier
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes F-44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France
| | - Virginie Vignard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes F-44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes F-44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France
| | - Sébastien Küry
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes F-44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France
| | - Frédéric Ebstein
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes F-44000, France
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2
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Zhang H, Zhou C, Mohammad Z, Zhao J. Structural basis of human 20S proteasome biogenesis. Nat Commun 2024; 15:8184. [PMID: 39294158 PMCID: PMC11410832 DOI: 10.1038/s41467-024-52513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 09/11/2024] [Indexed: 09/20/2024] Open
Abstract
New proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the function of the five chaperones PAC1-4 and POMP. Here, to understand how these chaperones facilitate proteasome assembly, we tagged the endogenous chaperones using CRISPR/Cas gene editing and examined the chaperone-bound complexes by cryo-EM. We observe an early α-ring intermediate subcomplex that is stabilized by PAC1-4, which transitions to β-ring assembly upon dissociation of PAC3/PAC4 and rearrangement of the PAC1 N-terminal tail. Completion of the β-ring and dimerization of half-proteasomes repositions critical lysine K33 to trigger cleavage of the β pro-peptides, leading to the concerted dissociation of POMP and PAC1/PAC2 to yield mature 20S proteasomes. This study reveals structural insights into critical points along the assembly pathway of the human proteasome and provides a molecular blueprint for 20S biogenesis.
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Affiliation(s)
- Hanxiao Zhang
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA
| | - Chenyu Zhou
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA
| | - Zarith Mohammad
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA
| | - Jianhua Zhao
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA.
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3
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Zhang H, Zhou C, Mohammad Z, Zhao J. Structural basis of human 20S proteasome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607236. [PMID: 39211201 PMCID: PMC11361150 DOI: 10.1101/2024.08.08.607236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
New proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the function of the five chaperones PAC1-4 and POMP. To understand how these chaperones facilitate proteasome assembly, we tagged the endogenous chaperones using CRISPR/Cas gene editing and examined the chaperone-bound complexes by cryo-EM. We observed an early α-ring intermediate subcomplex that is stabilized by PAC1-4, which transitions to β-ring assembly upon dissociation of PAC3/PAC4 and rearrangement of the PAC1 N-terminal tail. Completion of the β-ring and dimerization of half-proteasomes repositions critical lysine K33 to trigger cleavage of the β pro-peptides, leading to the concerted dissociation of POMP and PAC1/PAC2 to yield mature 20S proteasomes. This study reveals structural insights into critical points along the assembly pathway of the human proteasome and provides a molecular blueprint for 20S biogenesis.
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4
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Adolf F, Du J, Goodall EA, Walsh RM, Rawson S, von Gronau S, Harper JW, Hanna J, Schulman BA. Visualizing chaperone-mediated multistep assembly of the human 20S proteasome. Nat Struct Mol Biol 2024; 31:1176-1188. [PMID: 38600324 PMCID: PMC11327110 DOI: 10.1038/s41594-024-01268-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Dedicated assembly factors orchestrate the stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here we report cryo-electron microscopy reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, as well as how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors and reveals conceptual principles underlying human proteasome biogenesis, thus providing an explanation for many previous biochemical and genetic observations.
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Affiliation(s)
- Frank Adolf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ellen A Goodall
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Richard M Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Wade Harper
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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5
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Nie Y, Ma Z, Zhang B, Sun M, Zhang D, Li HH, Song X. The role of the immunoproteasome in cardiovascular disease. Pharmacol Res 2024; 204:107215. [PMID: 38744399 DOI: 10.1016/j.phrs.2024.107215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
The ubiquitinproteasome system (UPS) is the main mechanism responsible for the intracellular degradation of misfolded or damaged proteins. Under inflammatory conditions, the immunoproteasome, an isoform of the proteasome, can be induced, enhancing the antigen-presenting function of the UPS. Furthermore, the immunoproteasome also serves nonimmune functions, such as maintaining protein homeostasis and regulating signalling pathways, and is involved in the pathophysiological processes of various cardiovascular diseases (CVDs). This review aims to provide a comprehensive summary of the current research on the involvement of the immunoproteasome in cardiovascular diseases, with the ultimate goal of identifying novel strategies for the treatment of these conditions.
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Affiliation(s)
- Yifei Nie
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China.
| | - Zhao Ma
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China.
| | - Baoen Zhang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China.
| | - Meichen Sun
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China.
| | - Dongfeng Zhang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China.
| | - Hui-Hua Li
- Department of Emergency Medicine, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China.
| | - Xiantao Song
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China.
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6
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Wen P, Sun Y, Jiang TX, Qiu XB. PA200-Mediated Proteasomal Protein Degradation and Regulation of Cellular Senescence. Int J Mol Sci 2024; 25:5637. [PMID: 38891826 PMCID: PMC11171664 DOI: 10.3390/ijms25115637] [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: 03/10/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 06/21/2024] Open
Abstract
Cellular senescence is closely related to DNA damage, proteasome inactivity, histone loss, epigenetic alterations, and tumorigenesis. The mammalian proteasome activator PA200 (also referred to as PSME4) or its yeast ortholog Blm10 promotes the acetylation-dependent degradation of the core histones during transcription, DNA repair, and spermatogenesis. According to recent studies, PA200 plays an important role in senescence, probably because of its role in promoting the degradation of the core histones. Loss of PA200 or Blm10 is a major cause of the decrease in proteasome activity during senescence. In this paper, recent research progress on the association of PA200 with cellular senescence is summarized, and the potential of PA200 to serve as a therapeutic target in age-related diseases is discussed.
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Affiliation(s)
- Pei Wen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
| | - Yan Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
| | - Tian-Xia Jiang
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Xiao-Bo Qiu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
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Cascio P. PA28γ, the ring that makes tumors invisible to the immune system? Biochimie 2024:S0300-9084(24)00078-6. [PMID: 38631454 DOI: 10.1016/j.biochi.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024]
Abstract
PA28γ is a proteasomal interactor whose main and most known function is to stimulate the hydrolytic activity of the 20 S proteasome independently of ubiquitin and ATP. Unlike its two paralogues, PA28α and PA28β, PA28γ is largely present in the nuclear compartment and plays pivotal functions in important pathways such as cellular division, apoptosis, neoplastic transformation, chromatin structure and organization, fertility, lipid metabolism, and DNA repair mechanisms. Although it is known that a substantial fraction of PA28γ is found in the cell in a free form (i.e. not associated with 20 S), almost all of the studies so far have focused on its ability to modulate proteasomal enzymatic activities. In this respect, the ability of PA28γ to strongly stimulate degradation of proteins, especially if intrinsically disordered and therefore devoid of three-dimensional tightly folded structure, appears to be the main molecular mechanism underlying its multiple biological effects. Initial studies, conducted more than 20 years ago, came to the conclusion that among the many biological functions of PA28γ, the immunological ones were rather limited and circumscribed. In this review, we focus on recent evidence showing that PA28γ fulfills significant functions in cell-mediated acquired immunity, with a particular role in attenuating MHC class I antigen presentation, especially in relation to neoplastic transformation and autoimmune diseases.
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Affiliation(s)
- Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy.
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8
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Zhang L, Du Y, Qu Q, Zheng Q. Structure basis for recognition of plant Rpn10 by phytoplasma SAP05 in ubiquitin-independent protein degradation. iScience 2024; 27:108892. [PMID: 38322988 PMCID: PMC10844826 DOI: 10.1016/j.isci.2024.108892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/26/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Besides traditional ubiquitin-dependent proteasome degradation, thousands of eukaryotic proteins more than previously appreciated could undergo ubiquitin-independent proteasomal degradation (UbInPD). A pathogen-encoded effector protein SAP05 secreted by phytoplasma, could hijack hostage Rpn10 subunit of proteasome derived from Arabidopsis thaliana and target the degradation of GATA BINDING FACTOR (GATA) or SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors (TFs) without ubiquitin or additional proteasome shuttle factors. To explain how could SAP05 target the degradation bypassing the ubiquitin-dependent pathway, we have determined the crystal structure of the complex between Arabidopsis thaliana Rpn10 and Aster Yellows witches'-broom phytoplasma SAP05 or onion yellow phytoplasma SAP05, which showed a previously unknown recognition interface. Sequence alignment and structural biological evidence showed that this interaction is highly conserved in various SAP05 homologs, suggesting a general mode in plant infection. After docking the complex structure to the plant proteasome, SAP05 was near to the adenosine triphosphatase (ATPase) central pore and enough to submit substrate to degradation process, which suggested a molecular glue-like role to bridge TFs close to the ATPase central pore of proteasomes for the direct degradation.
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Affiliation(s)
- Liying Zhang
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yunxiang Du
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qian Qu
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingyun Zheng
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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9
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Li R, Yan L, Jiu J, Liu H, Li D, Li X, Zhang J, Li S, Fan Z, Lv Z, Zhu Y, Wang B. PSME2 offers value as a biomarker of M1 macrophage infiltration in pan-cancer and inhibits osteosarcoma malignant phenotypes. Int J Biol Sci 2024; 20:1452-1470. [PMID: 38385075 PMCID: PMC10878157 DOI: 10.7150/ijbs.90226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
A growing number of studies have revealed an association between proteasome activator complex subunit 2 (PSME2) and the progression of various forms of cancer. However, the effect of PSME2 on osteosarcoma progression is unknown. Pan-cancer analyses focused on the immunological activity and prognostic relevance of PSME2 have yet to be conducted. The Cancer Genome Atlas and Genome-Tissue Expression databases were leveraged to evaluate PSME2 expression and activity across 33 cancer types. Significant PSME2 dysregulation was noted in a wide range of cancer types and this gene was found to offer significant diagnostic and prognostic utility in most analyzed cancers. From a mechanistic perspective, PSME2 expression levels were correlated with DNA methylation, DNA repair, genomic instability, and TME scores in multiple cancer types. PSME2 was subsequently established as a pan-cancer biomarker of M1 macrophage infiltration based on a combination of bulk, single-cell, and spatial transcriptomic data and confirmatory fluorescent staining results. In osteosarcoma cells, overexpressing PSME2 significantly suppressed tumor proliferative, migratory, and invasive activity. Screening efforts also successfully identified the PSME2-activating drug irinotecan, which can synergistically promote the death of osteosarcoma cells when combined with the chemotherapeutic drug paclitaxel. As a biomarker of M1 macrophage infiltration, PSME2 expression levels may offer insight into tumor development and progression for a wide range of cancers including osteosarcoma, emphasizing its potential utility as a prognostic and therapeutic target worthy of further study.
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Affiliation(s)
- Ruoqi Li
- Department of Orthopaedic Surgery, The First Affliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, Shanxi, China
| | - Lei Yan
- Department of orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key laboratory of Bone and Soft Tissue injury repair, 382 Wuyi Road, Taiyuan, Shanxi, China
| | - Jingwei Jiu
- Department of orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key laboratory of Bone and Soft Tissue injury repair, 382 Wuyi Road, Taiyuan, Shanxi, China
| | - Haifeng Liu
- Department of orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key laboratory of Bone and Soft Tissue injury repair, 382 Wuyi Road, Taiyuan, Shanxi, China
| | - Dijun Li
- Department of orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key laboratory of Bone and Soft Tissue injury repair, 382 Wuyi Road, Taiyuan, Shanxi, China
| | - Xiaoke Li
- Department of orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key laboratory of Bone and Soft Tissue injury repair, 382 Wuyi Road, Taiyuan, Shanxi, China
| | - Jing Zhang
- Department of Emergency, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550001, China
- Clinical College of Medicine, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Songyan Li
- Department of Orthopaedic Surgery, The First Affliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zijuan Fan
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Shanxi, China
| | - Zhi Lv
- Department of orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key laboratory of Bone and Soft Tissue injury repair, 382 Wuyi Road, Taiyuan, Shanxi, China
| | - Yuanyuan Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bin Wang
- Department of Orthopaedic Surgery, The First Affliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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10
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Bhardwaj S, Roy KK. ClpP Peptidase as a Plausible Target for the Discovery of Novel Antibiotics. Curr Drug Targets 2024; 25:108-120. [PMID: 38151841 DOI: 10.2174/0113894501274958231220053714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/16/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Antimicrobial resistance (AMR) to currently available antibiotics/drugs is a global threat. It is desirable to develop new drugs that work through a novel target(s) to avoid drug resistance. This review discusses the potential of the caseinolytic protease P (ClpP) peptidase complex as a novel target for finding novel antibiotics, emphasising the ClpP's structure and function. ClpP contributes to the survival of bacteria via its ability to destroy misfolded or aggregated proteins. In consequence, its inhibition may lead to microbial death. Drugs inhibiting ClpP activity are currently being tested, but no drug against this target has been approved yet. It was demonstrated that Nblocked dipeptides are essential for activating ClpP's proteolytic activity. Hence, compounds mimicking these dipeptides could act as inhibitors of the formation of an active ClpP complex. Drugs, including Bortezomib, Cisplatin, Cefmetazole, and Ixazomib, inhibit ClpP activation. However, they were not approved as drugs against the target because of their high toxicity, likely due to the presence of strong electrophiles in their warheads. The modifications of these warheads could be a good strategy to reduce the toxicity of these molecules. For instance, a boronate warhead was replaced by a chloromethyl ketone, and this new molecule was shown to exhibit selectivity for prokaryotic ClpP. A better understanding of the structure and function of the ClpP complex would benefit the search for compounds mimicking N-blocked dipeptides that would inhibit ClpP complex activity and cause bacterial death.
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Affiliation(s)
- Smriti Bhardwaj
- School of Health Sciences and Technology, UPES, Dehradun - 248007, Uttarakhand, India
| | - Kuldeep K Roy
- School of Health Sciences and Technology, UPES, Dehradun - 248007, Uttarakhand, India
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11
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Thomas T, Salcedo-Tacuma D, Smith DM. Structure, Function, and Allosteric Regulation of the 20S Proteasome by the 11S/PA28 Family of Proteasome Activators. Biomolecules 2023; 13:1326. [PMID: 37759726 PMCID: PMC10526260 DOI: 10.3390/biom13091326] [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: 07/17/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
The proteasome, a complex multi-catalytic protease machinery, orchestrates the protein degradation essential for maintaining cellular homeostasis, and its dysregulation also underlies many different types of diseases. Its function is regulated by many different mechanisms that encompass various factors such as proteasome activators (PAs), adaptor proteins, and post-translational modifications. This review highlights the unique characteristics of proteasomal regulation through the lens of a distinct family of regulators, the 11S, REGs, or PA26/PA28. This ATP-independent family, spanning from amoebas to mammals, exhibits a common architectural structure; yet, their cellular biology and criteria for protein degradation remain mostly elusive. We delve into their evolution and cellular biology, and contrast their structure and function comprehensively, emphasizing the unanswered questions regarding their regulatory mechanisms and broader roles in proteostasis. A deeper understanding of these processes will illuminate the roles of this regulatory family in biology and disease, thus contributing to the advancement of therapeutic strategies.
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Affiliation(s)
- Taylor Thomas
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Drive, Morgantown, WV 26506, USA
| | - David Salcedo-Tacuma
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Drive, Morgantown, WV 26506, USA
| | - David M. Smith
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Drive, Morgantown, WV 26506, USA
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV 26506, USA
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12
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Choi W, Wu H, Yserentant K, Huang B, Cheng Y. Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM. Proc Natl Acad Sci U S A 2023; 120:e2302471120. [PMID: 37487103 PMCID: PMC10401002 DOI: 10.1073/pnas.2302471120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/21/2023] [Indexed: 07/26/2023] Open
Abstract
CRISPR/Cas9-based genome engineering has revolutionized our ability to manipulate biological systems, particularly in higher organisms. Here, we designed a set of homology-directed repair donor templates that enable efficient tagging of endogenous proteins with affinity tags by transient transfection and selection of genome-edited cells in various human cell lines. Combined with technological advancements in single-particle cryogenic electron microscopy, this strategy allows efficient structural studies of endogenous proteins captured in their native cellular environment and during different cellular processes. We demonstrated this strategy by tagging six different human proteins in both HEK293T and Jurkat cells. Moreover, analysis of endogenous glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in HEK293T cells allowed us to follow its behavior spatially and temporally in response to prolonged oxidative stress, correlating the increased number of oxidation-induced inactive catalytic sites in GAPDH with its translocation from cytosol to nucleus.
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Affiliation(s)
- Wooyoung Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Hao Wu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
| | - Klaus Yserentant
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA94143
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA94158
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94143
- HHMI, University of California, San Francisco, CA94143
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13
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Negi H, Osei-Amponsa V, Ibrahim B, Evans CN, Sullenberger C, Loncarek J, Chari R, Walters KJ. An engineered cell line with a hRpn1-attached handle to isolate proteasomes. J Biol Chem 2023; 299:104948. [PMID: 37354974 PMCID: PMC10372910 DOI: 10.1016/j.jbc.2023.104948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
Regulated protein degradation in eukaryotes is performed by the 26S proteasome, which contains a 19-subunit regulatory particle (RP) that binds, processes, and translocates substrates to a 28-subunit hollow core particle (CP) where proteolysis occurs. In addition to its intrinsic subunits, myriad proteins interact with the proteasome transiently, including factors that assist and/or regulate its degradative activities. Efforts to identify proteasome-interacting components and/or to solve its structure have relied on over-expression of a tagged plasmid, establishing stable cell lines, or laborious purification protocols to isolate native proteasomes from cells. Here, we describe an engineered human cell line, derived from colon cancer HCT116 cells, with a biotin handle on the RP subunit hRpn1/PSMD2 (proteasome 26S subunit, non-ATPase 2) for purification of 26S proteasomes. A 75-residue sequence from Propionibacterium shermanii that is biotinylated in mammalian cells was added following a tobacco etch virus protease cut site at the C terminus of hRpn1. We tested and found that 26S proteasomes can be isolated from this modified HCT116 cell line by using a simple purification protocol. More specifically, biotinylated proteasomes were purified from the cell lysates by using neutravidin agarose resin and released from the resin following incubation with tobacco etch virus protease. The purified proteasomes had equivalent activity in degrading a model ubiquitinated substrate, namely ubiquitinated p53, compared to commercially available bovine proteasomes that were purified by fractionation. In conclusion, advantages of this approach to obtain 26S proteasomes over others is the simple purification protocol and that all cellular proteins, including the tagged hRpn1 subunit, remain at endogenous stoichiometry.
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Affiliation(s)
- Hitendra Negi
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Vasty Osei-Amponsa
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Bishoy Ibrahim
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Christine N Evans
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Catherine Sullenberger
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Jadranka Loncarek
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.
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14
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Targeting immunoproteasome in neurodegeneration: A glance to the future. Pharmacol Ther 2023; 241:108329. [PMID: 36526014 DOI: 10.1016/j.pharmthera.2022.108329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
The immunoproteasome is a specialized form of proteasome equipped with modified catalytic subunits that was initially discovered to play a pivotal role in MHC class I antigen processing and immune system modulation. However, over the last years, this proteolytic complex has been uncovered to serve additional functions unrelated to antigen presentation. Accordingly, it has been proposed that immunoproteasome synergizes with canonical proteasome in different cell types of the nervous system, regulating neurotransmission, metabolic pathways and adaptation of the cells to redox or inflammatory insults. Hence, studying the alterations of immunoproteasome expression and activity is gaining research interest to define the dynamics of neuroinflammation as well as the early and late molecular events that are likely involved in the pathogenesis of a variety of neurological disorders. Furthermore, these novel functions foster the perspective of immunoproteasome as a potential therapeutic target for neurodegeneration. In this review, we provide a brain and retina-wide overview, trying to correlate present knowledge on structure-function relationships of immunoproteasome with the variety of observed neuro-modulatory functions.
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15
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QnAs with Yifan Cheng. Proc Natl Acad Sci U S A 2022; 119:e2213436119. [PMID: 36037335 PMCID: PMC9457311 DOI: 10.1073/pnas.2213436119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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