1
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Liu L, Lucero B, Manriquez-Rodriguez C, Francisco KR, Teixeira TR, Yohannan DJ, Ballatore C, Myers SA, O’Donoghue AJ, Caffrey CR. Clickable Probes for Pathogen Proteasomes: Synthesis and Applications. ACS OMEGA 2024; 9:34829-34840. [PMID: 39157084 PMCID: PMC11325529 DOI: 10.1021/acsomega.4c04316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/20/2024]
Abstract
The 20S proteasome is a multimeric protease complex that is essential for proteostasis in the cell. Small molecule proteasome inhibitors are approved drugs for various cancers and are advancing clinically as antiparasitics. Although tools and technologies to study the 20S proteasome have advanced, only one probe is commercially available to image proteasome activity. This probe consists of a fluorescently labeled, peptidyl vinyl sulfone that binds to one or more of the catalytic proteasome subunits. Here, we synthesized two, active site-directed epoxyketone probes, LJL-1 and LJL-2, that were based on the peptidyl backbones of the anticancer drugs, carfilzomib and bortezomib, respectively. Each probe was conjugated, via click chemistry, to a bifunctional group comprising 5-carboxytetramethylrhodamine (TAMRA) and biotin to, respectively, visualize and enrich the 20S proteasome from protein extracts of two eukaryotic pathogens, Leishmania donovani and Trichomonas vaginalis. Depending on species, each probe generated a different subunit-binding profile by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), and the biotin tag enabled the enrichment of the bound subunits which were then formally identified by proteomics. Species differences in the order of electrophoretic migration by the β subunits were also noted. Finally, both probes reacted specifically with the 20S subunits in contrast to the commercial vinyl sulfone probe that cross reacted with cysteine proteases. LJL-1 and LJL-2 should find general utility in the identification and characterization of pathogen proteasomes, and serve as reagents to evaluate the specificity and mechanism of binding of new antiparasitic proteasome inhibitors.
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Affiliation(s)
- Lawrence
J. Liu
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Center
for Discovery and Innovation in Parasitic Diseases, Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Bobby Lucero
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Center
for Discovery and Innovation in Parasitic Diseases, Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Cindy Manriquez-Rodriguez
- Center
for Autoimmunity and Inflammation, La Jolla
Institute for Immunology, La Jolla, California 92037, United States
- Laboratory
for Immunochemical Circuits, La Jolla Institute
for Immunology, La Jolla, California 92037, United States
| | - Karol R. Francisco
- Center
for Discovery and Innovation in Parasitic Diseases, Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Thaiz R. Teixeira
- Center
for Discovery and Innovation in Parasitic Diseases, Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Darius J. Yohannan
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Center
for Discovery and Innovation in Parasitic Diseases, Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Carlo Ballatore
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Center
for Discovery and Innovation in Parasitic Diseases, Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Samuel A. Myers
- Center
for Autoimmunity and Inflammation, La Jolla
Institute for Immunology, La Jolla, California 92037, United States
- Laboratory
for Immunochemical Circuits, La Jolla Institute
for Immunology, La Jolla, California 92037, United States
| | - Anthony J. O’Donoghue
- Center
for Discovery and Innovation in Parasitic Diseases, Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Conor R. Caffrey
- Center
for Discovery and Innovation in Parasitic Diseases, Skaggs School
of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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2
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Mariner BL, Rodriguez AS, Heath OC, McCormick MA. Induction of proteasomal activity in mammalian cells by lifespan-extending tRNA synthetase inhibitors. GeroScience 2024; 46:1755-1773. [PMID: 37749371 PMCID: PMC10828360 DOI: 10.1007/s11357-023-00938-8] [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: 05/08/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
We have recently shown that multiple tRNA synthetase inhibitors can greatly increase lifespan in multiple models by acting through the conserved transcription factor ATF4. Here, we show that these compounds, and several others of the same class, can greatly upregulate mammalian ATF4 in cells in vitro, in a dose dependent manner. Further, RNASeq analysis of these cells pointed toward changes in protein turnover. In subsequent experiments here we show that multiple tRNA synthetase inhibitors can greatly upregulate activity of the ubiquitin proteasome system (UPS) in cells in an ATF4-dependent manner. The UPS plays an important role in the turnover of many damaged or dysfunctional proteins in an organism. Increasing UPS activity has been shown to enhance the survival of Huntington's disease cell models, but there are few known pharmacological enhancers of the UPS. Additionally, we see separate ATF4 dependent upregulation of macroautophagy upon treatment with tRNA synthetase inhibitors. Protein degradation is an essential cellular process linked to many important human diseases of aging such as Alzheimer's disease and Huntington's disease. These drugs' ability to enhance proteostasis more broadly could have wide-ranging implications in the treatment of important age-related neurodegenerative diseases.
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Affiliation(s)
- Blaise L Mariner
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA
| | - Antonio S Rodriguez
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Olivia C Heath
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, School of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA.
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, Albuquerque, NM, 87131, USA.
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3
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Pepelnjak M, Rogawski R, Arkind G, Leushkin Y, Fainer I, Ben-Nissan G, Picotti P, Sharon M. Systematic identification of 20S proteasome substrates. Mol Syst Biol 2024; 20:403-427. [PMID: 38287148 PMCID: PMC10987551 DOI: 10.1038/s44320-024-00015-y] [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: 09/13/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024] Open
Abstract
For years, proteasomal degradation was predominantly attributed to the ubiquitin-26S proteasome pathway. However, it is now evident that the core 20S proteasome can independently target proteins for degradation. With approximately half of the cellular proteasomes comprising free 20S complexes, this degradation mechanism is not rare. Identifying 20S-specific substrates is challenging due to the dual-targeting of some proteins to either 20S or 26S proteasomes and the non-specificity of proteasome inhibitors. Consequently, knowledge of 20S proteasome substrates relies on limited hypothesis-driven studies. To comprehensively explore 20S proteasome substrates, we employed advanced mass spectrometry, along with biochemical and cellular analyses. This systematic approach revealed hundreds of 20S proteasome substrates, including proteins undergoing specific N- or C-terminal cleavage, possibly for regulation. Notably, these substrates were enriched in RNA- and DNA-binding proteins with intrinsically disordered regions, often found in the nucleus and stress granules. Under cellular stress, we observed reduced proteolytic activity in oxidized proteasomes, with oxidized protein substrates exhibiting higher structural disorder compared to unmodified proteins. Overall, our study illuminates the nature of 20S substrates, offering crucial insights into 20S proteasome biology.
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Affiliation(s)
- Monika Pepelnjak
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yegor Leushkin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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4
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Soh WT, Roetschke HP, Cormican JA, Teo BF, Chiam NC, Raabe M, Pflanz R, Henneberg F, Becker S, Chari A, Liu H, Urlaub H, Liepe J, Mishto M. Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing. Nat Commun 2024; 15:1147. [PMID: 38326304 PMCID: PMC10850103 DOI: 10.1038/s41467-024-45339-3] [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: 01/17/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
If and how proteasomes catalyze not only peptide hydrolysis but also peptide splicing is an open question that has divided the scientific community. The debate has so far been based on immunopeptidomics, in vitro digestions of synthetic polypeptides as well as ex vivo and in vivo experiments, which could only indirectly describe proteasome-catalyzed peptide splicing of full-length proteins. Here we develop a workflow-and cognate software - to analyze proteasome-generated non-spliced and spliced peptides produced from entire proteins and apply it to in vitro digestions of 15 proteins, including well-known intrinsically disordered proteins such as human tau and α-Synuclein. The results confirm that 20S proteasomes produce a sizeable variety of cis-spliced peptides, whereas trans-spliced peptides are a minority. Both peptide hydrolysis and splicing produce peptides with well-defined characteristics, which hint toward an intricate regulation of both catalytic activities. At protein level, both non-spliced and spliced peptides are not randomly localized within protein sequences, but rather concentrated in hotspots of peptide products, in part driven by protein sequence motifs and proteasomal preferences. At sequence level, the different peptide sequence preference of peptide hydrolysis and peptide splicing suggests a competition between the two catalytic activities of 20S proteasomes during protein degradation.
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Affiliation(s)
- Wai Tuck Soh
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Hanna P Roetschke
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
| | - John A Cormican
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Bei Fang Teo
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Nyet Cheng Chiam
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Monika Raabe
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ralf Pflanz
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Fabian Henneberg
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Ashwin Chari
- Research Group of Structural Biochemistry and Mechanisms, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Haiyan Liu
- Immunology Programme, Life Sciences Institute; Immunology Translational Research Program and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Henning Urlaub
- Research Group of Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Juliane Liepe
- Research Group of Quantitative and Systems Biology, Max-Planck-Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany.
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL, London, UK.
- Research Group of Molecular Immunology, Francis Crick Institute, NW1 1AT, London, UK.
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5
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Fernandes PMP, Guedes RA, Victor BL, Salvador JAR, Guedes RC. Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome. Front Chem 2024; 11:1322628. [PMID: 38260042 PMCID: PMC10801056 DOI: 10.3389/fchem.2023.1322628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Acquired resistance to drugs that modulate specific protein functions, such as the human proteasome, presents a significant challenge in targeted therapies. This underscores the importance of devising new methodologies to predict drug binding and potential resistance due to specific protein mutations. In this work, we conducted an extensive computational analysis to ascertain the effects of selected mutations (Ala49Thr, Ala50Val, and Cys52Phe) within the active site of the human proteasome. Specifically, we sought to understand how these mutations might disrupt protein function either by altering protein stability or by impeding interactions with a clinical administered drug. Leveraging molecular dynamics simulations and molecular docking calculations, we assessed the effect of these mutations on protein stability and ligand affinity. Notably, our results indicate that the Cys52Phe mutation critically impacts protein-ligand binding, providing valuable insights into potential proteasome inhibitor resistance.
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Affiliation(s)
- Pedro M. P. Fernandes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Romina A. Guedes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Bruno L. Victor
- BioISI─Biosystems & Integrative Sciences Institute, Faculty of Sciences, Universidade de Lisboa, Lisboa, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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6
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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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7
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Guedes RA, Grilo JH, Carvalho AN, Fernandes PMP, Ressurreição AS, Brito V, Santos AO, Silvestre S, Gallerani E, Gama MJ, Gavioli R, Salvador JAR, Guedes RC. New Scaffolds of Proteasome Inhibitors: Boosting Anticancer Potential by Exploiting the Synergy of In Silico and In Vitro Methodologies. Pharmaceuticals (Basel) 2023; 16:1096. [PMID: 37631011 PMCID: PMC10458307 DOI: 10.3390/ph16081096] [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: 07/07/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer is a complex multifactorial disease whose pathophysiology involves multiple metabolic pathways, including the ubiquitin-proteasome system, for which several proteasome inhibitors have already been approved for clinical use. However, the resistance to existing therapies and the occurrence of severe adverse effects is still a concern. The purpose of this study was the discovery of novel scaffolds of proteasome inhibitors with anticancer activity, aiming to overcome the limitations of the existing proteasome inhibitors. Thus, a structure-based virtual screening protocol was developed using the structure of the human 20S proteasome, and 246 compounds from virtual databases were selected for in vitro evaluation, namely proteasome inhibition assays and cell viability assays. Compound 4 (JHG58) was shortlisted as the best hit compound based on its potential in terms of proteasome inhibitory activity and its ability to induce cell death (both with IC50 values in the low micromolar range). Molecular docking studies revealed that compound 4 interacts with key residues, namely with the catalytic Thr1, Ala20, Thr21, Lys33, and Asp125 at the chymotrypsin-like catalytic active site. The hit compound is a good candidate for additional optimization through a hit-to-lead campaign.
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Affiliation(s)
- Romina A. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Jorge H. Grilo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Andreia N. Carvalho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Pedro M. P. Fernandes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ana S. Ressurreição
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Vanessa Brito
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Adriana O. Santos
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Samuel Silvestre
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Eleonora Gallerani
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Maria João Gama
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Riccardo Gavioli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Jorge A. R. Salvador
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
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8
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Mamrosh JL, Sherman DJ, Cohen JR, Johnston JA, Joubert MK, Li J, Lipford JR, Lomenick B, Moradian A, Prabhu S, Sweredoski MJ, Vander Lugt B, Verma R, Deshaies RJ. Quantitative measurement of the requirement of diverse protein degradation pathways in MHC class I peptide presentation. SCIENCE ADVANCES 2023; 9:eade7890. [PMID: 37352349 PMCID: PMC10289651 DOI: 10.1126/sciadv.ade7890] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/17/2023] [Indexed: 06/25/2023]
Abstract
Peptides from degradation of intracellular proteins are continuously displayed by major histocompatibility complex (MHC) class I. To better understand origins of these peptides, we performed a comprehensive census of the class I peptide repertoire in the presence and absence of ubiquitin-proteasome system (UPS) activity upon developing optimized methodology to enrich for and quantify these peptides. Whereas most class I peptides are dependent on the UPS for their generation, a surprising 30%, enriched in peptides of mitochondrial origin, appears independent of the UPS. A further ~10% of peptides were found to be dependent on the proteasome but independent of ubiquitination for their generation. Notably, clinically achievable partial inhibition of the proteasome resulted in display of atypical peptides. Our results suggest that generation of MHC class I•peptide complexes is more complex than previously recognized, with UPS-dependent and UPS-independent components; paradoxically, alternative protein degradation pathways also generate class I peptides when canonical pathways are impaired.
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Affiliation(s)
- Jennifer L. Mamrosh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - David J. Sherman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - Joseph R. Cohen
- Process Development, Amgen Inc., Thousand Oaks, CA 91320, USA
| | | | | | - Jing Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | | | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Michael J. Sweredoski
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Rati Verma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
| | - Raymond J. Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Amgen Research, Thousand Oaks, CA 91320, USA
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9
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Deshmukh FK, Ben-Nissan G, Olshina MA, Füzesi-Levi MG, Polkinghorn C, Arkind G, Leushkin Y, Fainer I, Fleishman SJ, Tawfik D, Sharon M. Allosteric regulation of the 20S proteasome by the Catalytic Core Regulators (CCRs) family. Nat Commun 2023; 14:3126. [PMID: 37253751 DOI: 10.1038/s41467-023-38404-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/26/2023] [Indexed: 06/01/2023] Open
Abstract
Controlled degradation of proteins is necessary for ensuring their abundance and sustaining a healthy and accurately functioning proteome. One of the degradation routes involves the uncapped 20S proteasome, which cleaves proteins with a partially unfolded region, including those that are damaged or contain intrinsically disordered regions. This degradation route is tightly controlled by a recently discovered family of proteins named Catalytic Core Regulators (CCRs). Here, we show that CCRs function through an allosteric mechanism, coupling the physical binding of the PSMB4 β-subunit with attenuation of the complex's three proteolytic activities. In addition, by dissecting the structural properties that are required for CCR-like function, we could recapitulate this activity using a designed protein that is half the size of natural CCRs. These data uncover an allosteric path that does not involve the proteasome's enzymatic subunits but rather propagates through the non-catalytic subunit PSMB4. This way of 20S proteasome-specific attenuation opens avenues for decoupling the 20S and 26S proteasome degradation pathways as well as for developing selective 20S proteasome inhibitors.
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Affiliation(s)
- Fanindra Kumar Deshmukh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya A Olshina
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maria G Füzesi-Levi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Caley Polkinghorn
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yegor Leushkin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dan Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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10
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Kulbacka J, Rembiałkowska N, Szewczyk A, Rossowska J, Drąg-Zalesińska M, Kulbacki M, Choromańska A. Nanosecond PEF Induces Oxidative Stress and Apoptosis via Proteasomal Activity Inhibition in Gastric Adenocarcinoma Cells with Drug Resistance. Int J Mol Sci 2022; 23:12943. [PMID: 36361727 PMCID: PMC9657809 DOI: 10.3390/ijms232112943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/06/2022] [Accepted: 10/18/2022] [Indexed: 08/01/2023] Open
Abstract
Nanosecond (ns) pulsed electric field (PEF) is a technology in which the application of ultra-short electrical pulses can be used to disrupt the barrier function of cell plasma and internal membranes. Disruptions of the membrane integrity cause a substantial imbalance in cell homeostasis in which oxidative stress is a principal component. In the present study, nsPEF-induced oxidative stress was investigated in two gastric adenocarcinoma cell lines (EPG85-257P and EPG85-257RDB) which differ by their sensitivity to daunorubicin. Cells were exposed to 200 pulses of 10 ns duration, with the amplitude and pulse repetition frequency at 1 kHz, with electric field intensity varying from 12.5 to 50 kV/cm. The electroporation buffer contained either 1 mM or 2 mM calcium chloride. CellMask DeepRed visualized cell plasma permeabilization, Fluo-4 was used to visualize internal calcium ions content, and F-actin was labeled with AlexaFluor®488 for the cytoskeleton. The cellular viability was determined by MTT assay. An alkaline and neutral comet assay was employed to detect apoptotic and necrotic cell death. The luminescent method estimated the modifications in GSSG/GSH redox potential and the imbalance of proteasomal activity (chymotrypsin-, trypsin- and caspase-like). The reactive oxygen species (ROS) level was measured by flow cytometry using dihydroethidium (DHE) dye. Morphological visualization indicated cell shrinkage, affected cell membranes (characteristic bubbles and changed cell shape), and the reorganization of actin fibers with sites of its dense concentration; the effect was more intense with the increasing electric field strength. The most significant decrease in cell viability and GSSG/GSH redox potential was noted at the highest amplitude of 50 kV/cm, and calcium ions amplified this effect. nsPEF, particularly with calcium ions, inhibited proteasomal activities, resulting in increased protein degradation. nsPEF increased the percentage of apoptotic cells and ROS levels. The EPG85-257 RDB cell line, which is resistant to standard chemotherapy, was more sensitive to applied nsPEF protocols. The applied nsPEF method disrupted the metabolism of cancer cells and induced apoptotic cell death. The nsPEF ability to cause apoptosis, oxidative stress, and protein degradation make the nsPEF methodology a suitable alternative to current anticancer pharmacological methods.
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Affiliation(s)
- Julita Kulbacka
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211 A, 50-556 Wroclaw, Poland
| | - Nina Rembiałkowska
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211 A, 50-556 Wroclaw, Poland
| | - Anna Szewczyk
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211 A, 50-556 Wroclaw, Poland
- Department of Animal Developmental Biology, Faculty of Biological Sciences, University of Wroclaw, 50-335 Wroclaw, Poland
| | - Joanna Rossowska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 50-422 Wroclaw, Poland
| | - Małgorzata Drąg-Zalesińska
- Division of Histology and Embryology, Division of Human Morpholog and Embryology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland
| | - Marek Kulbacki
- Polish-Japanese Academy of Information Technology, 02-008 Warsaw, Poland
- DIVE IN AI, 53-307 Wroclaw, Poland
| | - Anna Choromańska
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211 A, 50-556 Wroclaw, Poland
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11
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West G, Turunen M, Aalto A, Virtanen L, Li SP, Heliö T, Meinander A, Taimen P. A heterozygous p.S143P mutation in LMNA associates with proteasome dysfunction and enhanced autophagy-mediated degradation of mutant lamins A and C. Front Cell Dev Biol 2022; 10:932983. [PMID: 36111332 PMCID: PMC9468711 DOI: 10.3389/fcell.2022.932983] [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: 04/30/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
Lamins A and C are nuclear intermediate filament proteins that form a proteinaceous meshwork called lamina beneath the inner nuclear membrane. Mutations in the LMNA gene encoding lamins A and C cause a heterogenous group of inherited degenerative diseases known as laminopathies. Previous studies have revealed altered cell signaling pathways in lamin-mutant patient cells, but little is known about the fate of mutant lamins A and C within the cells. Here, we analyzed the turnover of lamins A and C in cells derived from a dilated cardiomyopathy patient with a heterozygous p.S143P mutation in LMNA. We found that transcriptional activation and mRNA levels of LMNA are increased in the primary patient fibroblasts, but the protein levels of lamins A and C remain equal in control and patient cells because of a meticulous interplay between autophagy and the ubiquitin-proteasome system (UPS). Both endogenous and ectopic expression of p.S143P lamins A and C cause significantly reduced activity of UPS and an accumulation of K48-ubiquitin chains in the nucleus. Furthermore, K48-ubiquitinated lamins A and C are degraded by compensatory enhanced autophagy, as shown by increased autophagosome formation and binding of lamins A and C to microtubule-associated protein 1A/1B-light chain 3. Finally, chaperone 4-PBA augmented protein degradation by restoring UPS activity as well as autophagy in the patient cells. In summary, our results suggest that the p.S143P-mutant lamins A and C have overloading and deleterious effects on protein degradation machinery and pharmacological interventions with compounds enhancing protein degradation may be beneficial for cell homeostasis.
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Affiliation(s)
- Gun West
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Minttu Turunen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Anna Aalto
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland,Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Laura Virtanen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Song-Ping Li
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Tiina Heliö
- Heart and Lung Center Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Annika Meinander
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland,Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Pekka Taimen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland,InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland,Department of Pathology, Laboratory Division, Turku University Hospital, Turku, Finland,*Correspondence: Pekka Taimen,
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12
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Kloetzel PM. Neo-Splicetopes in Tumor Therapy: A Lost Case? Front Immunol 2022; 13:849863. [PMID: 35265089 PMCID: PMC8898901 DOI: 10.3389/fimmu.2022.849863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Proteasome generates spliced peptides by ligating two distant cleavage products in a reverse proteolysis reaction. The observation that CD8+ T cells recognizing a spliced peptide induced T cell rejection in a melanoma patient following adoptive T cell transfer (ATT), raised some hopes with regard to the general therapeutic and immune relevance of spliced peptides. Concomitantly, the identification of spliced peptides was also the start of a controversy with respect to their frequency, abundancy and their therapeutic applicability. Here I review some of the recent evidence favoring or disfavoring an immune relevance of splicetopes and discuss from a theoretical point of view the potential usefulness of tumor specific splicetopes and why against all odds it still may seem worth trying to identify such tumor and patient-specific neosplicetopes for application in ATT.
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Affiliation(s)
- Peter M Kloetzel
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Biochemistry, Berlin, Germany
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13
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Alvarado ME, Chaparro-Gutiérrez JJ, Calvo EP, Prada LF, Wasserman M. Activity of the Giardia intestinalis proteasome during encystation and its connection with the expression of the cyst wall protein 1 (CWP1). Acta Trop 2022; 225:106183. [PMID: 34627761 DOI: 10.1016/j.actatropica.2021.106183] [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: 12/13/2020] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/01/2022]
Abstract
Giardia is a parasite whose life cycle is composed of two stages: replicative trophozoites, responsible for the symptoms of the disease, and infective cysts, resistant to adverse environments outside of hosts. Proteasomes are multicatalytic peptidase complexes responsible for the specific degradation of proteins in eukaryotic cells. This study assessed the proteasome activity in the trophozoite and during encystation. Strong activation of the proteasome was observed during the differentiation of trophozoites into cysts, reaching its maximum level 24 h after the stimulus. We also found that the Giardia proteasome presents unusual characteristics related to higher eukaryotic proteasomes, making it an eventual therapeutic target. Here we tested the effects on the synthesis of a cyst wall protein by chemical inactivation of the proteasome and by overexpression or partial inhibition of the deubiquitinating protein RPN11 in transfected cells. Moreover, an analysis of the intracellular localization of RPN11 (an integral part of the proteasome regulatory particle) revealed major changes associated with the differentiation of trophozoites into cysts. This evidence further supports the important role of the proteasome in Giardia encystation.
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14
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Kisselev AF. Site-Specific Proteasome Inhibitors. Biomolecules 2021; 12:54. [PMID: 35053202 PMCID: PMC8773591 DOI: 10.3390/biom12010054] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/14/2022] Open
Abstract
Proteasome is a multi-subunit protein degradation machine, which plays a key role in the maintenance of protein homeostasis and, through degradation of regulatory proteins, in the regulation of numerous cell functions. Proteasome inhibitors are essential tools for biomedical research. Three proteasome inhibitors, bortezomib, carfilzomib, and ixazomib are approved by the FDA for the treatment of multiple myeloma; another inhibitor, marizomib, is undergoing clinical trials. The proteolytic core of the proteasome has three pairs of active sites, β5, β2, and β1. All clinical inhibitors and inhibitors that are widely used as research tools (e.g., epoxomicin, MG-132) inhibit multiple active sites and have been extensively reviewed in the past. In the past decade, highly specific inhibitors of individual active sites and the distinct active sites of the lymphoid tissue-specific immunoproteasome have been developed. Here, we provide a comprehensive review of these site-specific inhibitors of mammalian proteasomes and describe their utilization in the studies of the biology of the active sites and their roles as drug targets for the treatment of different diseases.
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Affiliation(s)
- Alexei F Kisselev
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL 36849, USA
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15
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Vijayasimha K, Tran MV, Leestemaker-Palmer AL, Dolan BP. Direct Conjugation of NEDD8 to the N-Terminus of a Model Protein Can Induce Degradation. Cells 2021; 10:854. [PMID: 33918652 PMCID: PMC8069691 DOI: 10.3390/cells10040854] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/28/2022] Open
Abstract
While the role of ubiquitin in protein degradation is well established, the role of other ubiquitin-like proteins (UBLs) in protein degradation is less clear. Neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) is the UBL with the highest level of amino acids identified when compared to ubiquitin. Here we tested if the N-terminal addition of NEDD8 to a protein of interest could lead to degradation. Mutation of critical glycine residues required for normal NEDD8 processing resulted in a non-cleavable fusion protein that was rapidly degraded within the cells by both the proteasome and autophagy. Both degradation pathways were dependent on a functional ubiquitin-conjugation system as treatment with MLN7243 increased levels of non-cleavable NEDD8-GFP. The degradation of non-cleavable, N-terminal NEDD8-GFP was not due to a failure of GFP folding as different NEDD8-GFP constructs with differing abilities to fold and fluoresce were similarly degraded. Though the fusion of NEDD8 to a protein resulted in degradation, treatment of cells with MLN4924, an inhibitor of the E1 activating enzyme for NEDD8, failed to prevent degradation of other destabilized substrates. Taken together these data suggest that under certain conditions, such as the model system described here, the covalent linkage of NEDD8 to a protein substrate may result in the target proteins degradation.
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Affiliation(s)
| | | | | | - Brian P. Dolan
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA; (K.V.); (M.V.T.); (A.L.L.-P.)
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16
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Huai B, Bai M, Tong PP, He HJ, Liang MJ, Chen CY, Wu H. CgPBA1 may be involved in nuclear degradation during secretory cavity formation by programmed cell death in Citrus grandis 'Tomentosa' fruits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 160:306-314. [PMID: 33545608 DOI: 10.1016/j.plaphy.2021.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Caspase-3 is the crucial executor caspase of apoptosis in mammalian cells, which is essential for chromatin condensation and DNA fragmentation. Although plants have no caspase-3 homologs, PBA1 acts as a plant caspase-3-like enzyme in plant programmed cell death (PCD). PCD occurs during the formation of secretory cavities in Citrus fruits; hence, secretory cavities could be utilized as a new cell biology model for investigating the regulatory mechanisms of plant PCD. To further study the association between PBA1 and PCD during secretory cavity development in Citrus fruits, CgPBA1 was identified in the fruit of Citrus grandis 'Tomentosa'. The temporal and spatial expression of CgPBA1 during secretory cavity development were analyzed using quantitative real-time PCR and in situ hybridization, and the morphological changes in the apoptotic cell nuclei were observed using TUNEL assay and ultra-thin section technology. The results revealed that the full-length cDNA of CgPBA1 contains a 711 bp ORF that encodes a putative protein containing 236 amino acid with a proteasome-β-6 functional domain that belongs to the Ntn hydrolase super family. CgPBA1 was predominantly expressed in the secretory cavities; its expression changes coincided with the morphological changes and DNA fragmentation in apoptotic cell nuclei. The green fluorescent fusion protein of CgPBA1 is also located in the nucleus of tobacco epidermal cells. Based on previous research and the findings of the present study, we speculate that CgPBA1 is a highly functional conserved protein in plants, and it might be involved in nuclear degradation during PCD for secretory cavity formation in C. grandis 'Tomentosa' fruits.
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Affiliation(s)
- B Huai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - M Bai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry, South China Agricultural University, Guangzhou, 510642, China.
| | - P P Tong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - H J He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - M J Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - C Y Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - H Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry, South China Agricultural University, Guangzhou, 510642, China.
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17
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Cascio P. PA28γ: New Insights on an Ancient Proteasome Activator. Biomolecules 2021; 11:228. [PMID: 33562807 PMCID: PMC7915322 DOI: 10.3390/biom11020228] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
PA28 (also known as 11S, REG or PSME) is a family of proteasome regulators whose members are widely present in many of the eukaryotic supergroups. In jawed vertebrates they are represented by three paralogs, PA28α, PA28β, and PA28γ, which assemble as heptameric hetero (PA28αβ) or homo (PA28γ) rings on one or both extremities of the 20S proteasome cylindrical structure. While they share high sequence and structural similarities, the three isoforms significantly differ in terms of their biochemical and biological properties. In fact, PA28α and PA28β seem to have appeared more recently and to have evolved very rapidly to perform new functions that are specifically aimed at optimizing the process of MHC class I antigen presentation. In line with this, PA28αβ favors release of peptide products by proteasomes and is particularly suited to support adaptive immune responses without, however, affecting hydrolysis rates of protein substrates. On the contrary, PA28γ seems to be a slow-evolving gene that is most similar to the common ancestor of the PA28 activators family, and very likely retains its original functions. Notably, PA28γ has a prevalent nuclear localization and is involved in the regulation of several essential cellular processes including cell growth and proliferation, apoptosis, chromatin structure and organization, and response to DNA damage. In striking contrast with the activity of PA28αβ, most of these diverse biological functions of PA28γ seem to depend on its ability to markedly enhance degradation rates of regulatory protein by 20S proteasome. The present review will focus on the molecular mechanisms and biochemical properties of PA28γ, which are likely to account for its various and complex biological functions and highlight the common features with the PA28αβ paralog.
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Affiliation(s)
- Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy
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18
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Song Y, Du T, Ray A, Chauhan K, Samur M, Munshi N, Chauhan D, Anderson KC. Identification of novel anti-tumor therapeutic target via proteomic characterization of ubiquitin receptor ADRM1/Rpn13. Blood Cancer J 2021; 11:13. [PMID: 33441535 PMCID: PMC7806750 DOI: 10.1038/s41408-020-00398-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/28/2020] [Accepted: 12/09/2020] [Indexed: 02/08/2023] Open
Affiliation(s)
- Yan Song
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ting Du
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Arghya Ray
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Krishan Chauhan
- Department of Biomedical Engineering (BME), Wentworth Institute of Technology, Boston, MA, USA
| | - Mehmet Samur
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nikhil Munshi
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dharminder Chauhan
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Kenneth C Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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19
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Maurits E, Degeling CG, Kisselev AF, Florea BI, Overkleeft HS. Structure-Based Design of Fluorogenic Substrates Selective for Human Proteasome Subunits. Chembiochem 2020; 21:3220-3224. [PMID: 32598532 PMCID: PMC7754458 DOI: 10.1002/cbic.202000375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/29/2020] [Indexed: 11/07/2022]
Abstract
Proteasomes are established therapeutic targets for hematological cancers and promising targets for autoimmune diseases. In the past, we have designed and synthesized mechanism-based proteasome inhibitors that are selective for the individual catalytic activities of human constitutive proteasomes and immunoproteasomes: β1c, β1i, β2c, β2i, β5c and β5i. We show here that by taking the oligopeptide recognition element and substituting the electrophile for a fluorogenic leaving group, fluorogenic substrates are obtained that report on the proteasome catalytic activity also targeted by the parent inhibitor. Though not generally applicable (β5c and β2i substrates showing low activity), effective fluorogenic substrates reporting on the individual activity of β1c, β1i, β2c and β5i subunits in Raji (human B cell) lysates and purified 20S proteasome were identified in this manner. Our work thus adds to the expanding proteasome research toolbox through the identification of new and/or more effective subunit-selective fluorogenic substrates.
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Affiliation(s)
- Elmer Maurits
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Christian G. Degeling
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Alexei F. Kisselev
- Department of Drug Discovery and DevelopmentHarrison School of PharmacyAuburn UniversityAuburnAL 36849USA
| | - Bogdan I. Florea
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Herman S. Overkleeft
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
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20
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Dokanehiifard S, Soltani BM, Ghiasi P, Baharvand H, Reza Ganjali M, Hosseinkhani S. hsa-miR-766-5p as a new regulator of mitochondrial apoptosis pathway for discriminating of cell death from cardiac differentiation. Gene 2020; 736:144448. [DOI: 10.1016/j.gene.2020.144448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/26/2020] [Accepted: 02/04/2020] [Indexed: 12/19/2022]
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21
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Chemical Patterns of Proteasome Inhibitors: Lessons Learned from Two Decades of Drug Design. Int J Mol Sci 2019; 20:ijms20215326. [PMID: 31731563 PMCID: PMC6862029 DOI: 10.3390/ijms20215326] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/23/2022] Open
Abstract
Drug discovery now faces a new challenge, where the availability of experimental data is no longer the limiting step, and instead, making sense of the data has gained a new level of importance, propelled by the extensive incorporation of cheminformatics and bioinformatics methodologies into the drug discovery and development pipeline. These enable, for example, the inference of structure-activity relationships that can be useful in the discovery of new drug candidates. One of the therapeutic applications that could benefit from this type of data mining is proteasome inhibition, given that multiple compounds have been designed and tested for the last 20 years, and this collection of data is yet to be subjected to such type of assessment. This study presents a retrospective overview of two decades of proteasome inhibitors development (680 compounds), in order to gather what could be learned from them and apply this knowledge to any future drug discovery on this subject. Our analysis focused on how different chemical descriptors coupled with statistical tools can be used to extract interesting patterns of activity. Multiple instances of the structure-activity relationship were observed in this dataset, either for isolated molecular descriptors (e.g., molecular refractivity and topological polar surface area) as well as scaffold similarity or chemical space overlap. Building a decision tree allowed the identification of two meaningful decision rules that describe the chemical parameters associated with high activity. Additionally, a characterization of the prevalence of key functional groups gives insight into global patterns followed in drug discovery projects, and highlights some systematically underexplored parts of the chemical space. The various chemical patterns identified provided useful insight that can be applied in future drug discovery projects, and give an overview of what has been done so far.
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Bibo-Verdugo B, Wang SC, Almaliti J, Ta AP, Jiang Z, Wong DA, Lietz CB, Suzuki BM, El-Sakkary N, Hook V, Salvesen GS, Gerwick WH, Caffrey CR, O’Donoghue AJ. The Proteasome as a Drug Target in the Metazoan Pathogen, Schistosoma mansoni. ACS Infect Dis 2019; 5:1802-1812. [PMID: 31355632 DOI: 10.1021/acsinfecdis.9b00237] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Proteases are fundamental to successful parasitism, including that of the schistosome flatworm parasite, which causes the disease schistosomiasis in 200 million people worldwide. The proteasome is receiving attention as a potential drug target for treatment of a variety of infectious parasitic diseases, but it has been understudied in the schistosome. Adult Schistosoma mansoni were incubated with 1 μM concentrations of the proteasome inhibitors bortezomib, carfilzomib, and MG132. After 24 h, bortezomib and carfilzomib decreased worm motility by more than 85% and endogenous proteasome activity by >75%, and after 72 h, they increased caspase activity by >4.5-fold. The association between the engagement of the proteasome target and the phenotypic and biochemical effects recorded encouraged the chromatographic enrichment of the S. mansoni proteasome (Sm20S). Activity assays with fluorogenic proteasome substrates revealed that Sm20S contains caspase-type (β1), trypsin-type (β2), and chymotrypsin-type (β5) activities. Sm20S was screened with 11 peptide epoxyketone inhibitors derived from the marine natural product carmaphycin B. Analogue 17 was 27.4-fold less cytotoxic to HepG2 cells than carmaphycin B and showed equal potency for the β5 subunits of Sm20S, human constitutive proteasome, and human immunoproteasome. However, this analogue was 13.2-fold more potent at targeting Sm20S β2 than it was at targeting the equivalent subunits of the human enzymes. Furthermore, 1 μM 17 decreased both worm motility and endogenous Sm20S activity by more than 90% after 24 h. We provide direct evidence of the proteasome's importance to schistosome viability and identify a lead for which future studies will aim to improve the potency, selectivity, and safety.
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Affiliation(s)
- Betsaida Bibo-Verdugo
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Steven C Wang
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jehad Almaliti
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Anh P. Ta
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Derek A. Wong
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Christopher B. Lietz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian M. Suzuki
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Nelly El-Sakkary
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Guy S. Salvesen
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - William H. Gerwick
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Anthony J. O’Donoghue
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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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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24
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Snigirevskaya ES, Komissarchik YY. Ultrastructural traits of apoptosis. Cell Biol Int 2019; 43:728-738. [DOI: 10.1002/cbin.11148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/03/2019] [Accepted: 04/07/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Ekaterina S. Snigirevskaya
- Group of Cell Membrane Ultrastructure, Institute of CytologyRussian Academy of Sciences4 Tikhoretsky Ave 194064 St. Petersburg Russia
| | - Yan Y. Komissarchik
- Group of Cell Membrane Ultrastructure, Institute of CytologyRussian Academy of Sciences4 Tikhoretsky Ave 194064 St. Petersburg Russia
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25
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Kim HT, Collins GA, Goldberg AL. Measurement of the Multiple Activities of 26S Proteasomes. Methods Mol Biol 2019; 1844:289-308. [PMID: 30242717 DOI: 10.1007/978-1-4939-8706-1_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because proteasomes catalyze most of the protein degradation in mammalian cells, and their functioning is essential for cellular homeostasis, proteasome structure, biochemical mechanisms, and regulation in normal and disease states are now widely studied and are of major importance. In addition, inhibitors of the proteasome's peptidase activity have proven to be very valuable as research tools and in the treatment of hematologic malignancies, and a number of newer pharmacological agents that alter proteasome function are being developed. The rapid degradation of ubiquitinated proteins by the 26S proteasome involves multiple enzymatic and non-enzymatic steps, including the binding of ubiquitinated substrates to the 19S particle (Subheading 3.2), opening the gated substrate entry channel into the 20S particle (Subheading 3.3), disassembly of the Ub chain (Subheading 3.4), ATP hydrolysis (Subheading 3.5), substrate unfolding and translocation, and proteolysis within the 20S particle (Subheadings 3.3 and 3.7). Assaying each of these processes is important if we are to fully understand the physiological regulation of proteasome function and the effects of disease or drugs. Here, we describe several methods that we have found useful to measure many of these individual activities using purified proteasomes. Studies using these approaches have already provided valuable new insights into the effects of post-synthetic modifications to 26S subunits, the physiological regulation of the ubiquitin-proteasome system, and the impairment of proteasome activity in neurodegenerative disease. These advances would not have been possible if only the standard assays of peptidase activity were used.
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Affiliation(s)
- Hyoung Tae Kim
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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26
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UBL domain of Usp14 and other proteins stimulates proteasome activities and protein degradation in cells. Proc Natl Acad Sci U S A 2018; 115:E11642-E11650. [PMID: 30487212 DOI: 10.1073/pnas.1808731115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The best-known function of ubiquitin-like (UBL) domains in proteins is to enable their binding to 26S proteasomes. The proteasome-associated deubiquitinating enzyme Usp14/UBP6 contains an N-terminal UBL domain and is an important regulator of proteasomal activity. Usp14 by itself represses multiple proteasomal activities but, upon binding a ubiquitin chain, Usp14 stimulates these activities and promotes ubiquitin-conjugate degradation. Here, we demonstrate that Usp14's UBL domain alone mimics this activation of proteasomes by ubiquitin chains. Addition of this UBL domain to purified 26S proteasomes stimulated the same activities inhibited by Usp14: peptide entry and hydrolysis, protein-dependent ATP hydrolysis, deubiquitination by Rpn11, and the degradation of ubiquitinated and nonubiquitinated proteins. Thus, the binding of Usp14's UBL (apparently to Rpn1's T2 site) seems to mediate the activation of proteasomes by ubiquitinated substrates. However, the stimulation of these various activities was greater in proteasomes lacking Usp14 than in wild-type particles and thus is a general response that does not involve some displacement of Usp14. Furthermore, the UBL domains from hHR23 and hPLIC1/UBQLN1 also stimulated peptide hydrolysis, and the expression of hHR23A's UBL domain in HeLa cells stimulated overall protein degradation. Therefore, many UBL-containing proteins that bind to proteasomes may also enhance allosterically its proteolytic activity.
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27
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Seth-Pasricha M, Senn S, Sanman LE, Bogyo M, Nanda V, Bidle KA, Bidle KD. Catalytic linkage between caspase activity and proteostasis in Archaea. Environ Microbiol 2018; 21:286-298. [PMID: 30370585 DOI: 10.1111/1462-2920.14456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 11/29/2022]
Abstract
The model haloarchaeon, Haloferax volcanii possess an extremely high, and highly specific, basal caspase activity in exponentially growing cells that closely resembles caspase-4. This activity is specifically inhibited by the pan-caspase inhibitor, z-VAD-FMK, and has no cross-reactivity with other known protease families. Although it is one of the dominant cellular proteolytic activities in exponentially growing H. volcanii cells, the interactive cellular roles remain unknown and the protein(s) responsible for this activity remain elusive. Here, biochemical purification and in situ trapping with caspase targeted covalent inhibitors combined with genome-enabled proteomics, structural analysis, targeted gene knockouts and treatment with canavanine demonstrated a catalytic linkage between caspase activity and thermosomes, proteasomes and cdc48b, a cell division protein and proteasomal degradation facilitating ATPase, as part of an 'interactase' of stress-related protein complexes with an established link to the unfolded protein response (UPR). Our findings provide novel cellular and biochemical context for the observed caspase activity in Archaea and add new insight to understanding the role of this activity, implicating their possible role in the establishment of protein stress and ER associated degradation pathways in Eukarya.
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Affiliation(s)
- Mansha Seth-Pasricha
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Stefan Senn
- Abteilung für Chemie und Bioanalytik, Universität Salzburg, Salzburg, Austria
| | - Laura E Sanman
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Kelly A Bidle
- Department of Biology, Behavioral Neuroscience, and Health Sciences, Rider University, Lawrenceville, NJ, USA
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
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28
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Lubos M, Dębowski D, Barcińska E, Meid A, Inkielewicz‐Stepniak I, Burster T, Rolka K. Inhibition of human constitutive 20S proteasome and 20S immunoproteasome with novel
N
‐terminally modified peptide aldehydes and their antitumor activity. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Marta Lubos
- Department of Molecular Biochemistry, Faculty of ChemistryUniversity of Gdansk Gdansk Poland
| | - Dawid Dębowski
- Department of Molecular Biochemistry, Faculty of ChemistryUniversity of Gdansk Gdansk Poland
| | - Ewelina Barcińska
- Department of Medical ChemistryMedical University of Gdansk Gdansk Poland
| | - Annika Meid
- Department of Neurosurgery, Surgery CenterUlm University Medical Center Ulm Germany
| | | | - Timo Burster
- Department of BiologySchool of Science and Technology, Nazarbayev University Astana Kazakhstan Republic
| | - Krzysztof Rolka
- Department of Molecular Biochemistry, Faculty of ChemistryUniversity of Gdansk Gdansk Poland
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29
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Rut W, Poręba M, Kasperkiewicz P, Snipas SJ, Drąg M. Selective Substrates and Activity-Based Probes for Imaging of the Human Constitutive 20S Proteasome in Cells and Blood Samples. J Med Chem 2018; 61:5222-5234. [DOI: 10.1021/acs.jmedchem.8b00026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marcin Poręba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Scott J. Snipas
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Marcin Drąg
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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30
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Ravichandran M, Priebe S, Grigolon G, Rozanov L, Groth M, Laube B, Guthke R, Platzer M, Zarse K, Ristow M. Impairing L-Threonine Catabolism Promotes Healthspan through Methylglyoxal-Mediated Proteohormesis. Cell Metab 2018; 27:914-925.e5. [PMID: 29551589 DOI: 10.1016/j.cmet.2018.02.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 07/23/2017] [Accepted: 02/06/2018] [Indexed: 12/22/2022]
Abstract
Whether and how regulation of genes and pathways contributes to physiological aging is topic of intense scientific debate. By performing an RNA expression-based screen for genes downregulated during aging of three different species, we identified glycine-C-acetyltransferase (GCAT, EC 2.3.1.29). Impairing gcat expression promotes the lifespan of C. elegans by interfering with threonine catabolism to promote methylglyoxal (MGO; CAS 78-98-8) formation in an amine oxidase-dependent manner. MGO is a reactive dicarbonyl inducing diabetic complications in mammals by causing oxidative stress and damaging cellular components, including proteins. While high concentrations of MGO consistently exert toxicity in nematodes, we unexpectedly find that low-dose MGO promotes lifespan, resembling key mediators of gcat impairment. These were executed by the ubiquitin-proteasome system, namely PBS-3 and RPN-6.1 subunits, regulated by the stress-responsive transcriptional regulators SKN-1/NRF2 and HSF-1. Taken together, GCAT acts as an evolutionary conserved aging-related gene by orchestrating an unexpected nonlinear impact of proteotoxic MGO on longevity.
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Affiliation(s)
- Meenakshi Ravichandran
- Energy Metabolism Laboratory, Institute of Translational Medicine, D-HEST, Swiss Federal Institute of Technology (ETH) Zürich, Schwerzenbach 8603, Switzerland; Life Sciences Zürich Graduate School, Molecular and Translational Biomedicine Program, Zurich 8044, Switzerland
| | - Steffen Priebe
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena 07745, Germany
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, D-HEST, Swiss Federal Institute of Technology (ETH) Zürich, Schwerzenbach 8603, Switzerland
| | - Leonid Rozanov
- Energy Metabolism Laboratory, Institute of Translational Medicine, D-HEST, Swiss Federal Institute of Technology (ETH) Zürich, Schwerzenbach 8603, Switzerland; Life Sciences Zürich Graduate School, Molecular and Translational Biomedicine Program, Zurich 8044, Switzerland
| | - Marco Groth
- Genome Analysis Group, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena 07745, Germany
| | - Beate Laube
- Energy Metabolism Laboratory, Institute of Translational Medicine, D-HEST, Swiss Federal Institute of Technology (ETH) Zürich, Schwerzenbach 8603, Switzerland
| | - Reinhard Guthke
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena 07745, Germany
| | - Matthias Platzer
- Genome Analysis Group, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena 07745, Germany
| | - Kim Zarse
- Energy Metabolism Laboratory, Institute of Translational Medicine, D-HEST, Swiss Federal Institute of Technology (ETH) Zürich, Schwerzenbach 8603, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, D-HEST, Swiss Federal Institute of Technology (ETH) Zürich, Schwerzenbach 8603, Switzerland.
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31
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Cerruti F, Jocollè G, Salio C, Oliva L, Paglietti L, Alessandria B, Mioletti S, Donati G, Numico G, Cenci S, Cascio P. Proteasome stress sensitizes malignant pleural mesothelioma cells to bortezomib-induced apoptosis. Sci Rep 2017; 7:17626. [PMID: 29247244 PMCID: PMC5732203 DOI: 10.1038/s41598-017-17977-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/04/2017] [Indexed: 12/11/2022] Open
Abstract
Based on promising results in preclinical models, clinical trials have been performed to evaluate the efficacy of the first-in-class proteasome inhibitor bortezomib towards malignant pleural mesothelioma (MPM), an aggressive cancer arising from the mesothelium of the serous cavities following exposure to asbestos. Unexpectedly, only minimal therapeutic benefits were observed, thus implicating that MPM harbors inherent resistance mechanisms. Identifying the molecular bases of this primary resistance is crucial to develop novel pharmacologic strategies aimed at increasing the vulnerability of MPM to bortezomib. Therefore, we assessed a panel of four human MPM lines with different sensitivity to bortezomib, for functional proteasome activity and levels of free and polymerized ubiquitin. We found that highly sensitive MPM lines display lower proteasome activity than more bortezomib-resistant clones, suggesting that reduced proteasomal capacity might contribute to the intrinsic susceptibility of mesothelioma cells to proteasome inhibitors-induced apoptosis. Moreover, MPM equipped with fewer active proteasomes accumulated polyubiquitinated proteins, at the expense of free ubiquitin, a condition known as proteasome stress, which lowers the cellular apoptotic threshold and sensitizes mesothelioma cells to bortezomib-induced toxicity as shown herein. Taken together, our data suggest that an unfavorable load-versus-capacity balance represents a critical determinant of primary apoptotic sensitivity to bortezomib in MPM.
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Affiliation(s)
- Fulvia Cerruti
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Genny Jocollè
- Medical Oncology Unit, Ospedale U. Parini, Viale Ginevra 3, 11100, Aosta, Italy
| | - Chiara Salio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Laura Oliva
- San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Via Olgettina 60, 20132, Milan, Italy
| | - Luca Paglietti
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Beatrice Alessandria
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Silvia Mioletti
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Giovanni Donati
- Thoracic Surgery Unit, Ospedale U. Parini, Viale Ginevra 3, 11100, Aosta, Italy
| | - Gianmauro Numico
- Medical Oncology, Azienda Ospedaliera SS Antonio e Biagio e C Arrigo, Via Venezia 16, 15121, Alessandria, Italy
| | - Simone Cenci
- San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Via Olgettina 60, 20132, Milan, Italy
| | - Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy.
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32
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Rut W, Drag M. Human 20S proteasome activity towards fluorogenic peptides of various chain lengths. Biol Chem 2017; 397:921-6. [PMID: 27176742 DOI: 10.1515/hsz-2016-0176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 11/15/2022]
Abstract
The proteasome is a multicatalytic protease responsible for the degradation of misfolded proteins. We have synthesized fluorogenic substrates in which the peptide chain was systematically elongated from two to six amino acids and evaluated the effect of peptide length on all three catalytic activities of human 20S proteasome. In the cases of five- and six-membered peptides, we have also synthesized libraries of fluorogenic substrates. Kinetic analysis revealed that six-amino-acid substrates are significantly better for chymotrypsin-like and caspase-like activity than shorter peptidic substrates. In the case of trypsin-like activity, a five-amino-acid substrate was optimal.
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33
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Capolupo A, Tosco A, Mozzicafreddo M, Tringali C, Cardullo N, Monti MC, Casapullo A. Proteasome as a New Target for Bio-Inspired Benzo[k
,l
]xanthene Lignans. Chemistry 2017; 23:8371-8374. [DOI: 10.1002/chem.201701095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Angela Capolupo
- Dipartimento di Farmacia; Università degli Studi di Salerno; via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Alessandra Tosco
- Dipartimento di Farmacia; Università degli Studi di Salerno; via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Matteo Mozzicafreddo
- Scuola di Bioscienze e Medicina Veterinaria; Università degli Studi di Camerino; Piazza Cavour 19/f 62032 Camerino Italy
| | - Corrado Tringali
- Dipartimento di Scienze Chimiche; Università degli Studi di Catania; Viale Andrea Doria 6 95131 Catania Italy
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche; Università degli Studi di Catania; Viale Andrea Doria 6 95131 Catania Italy
| | - Maria Chiara Monti
- Dipartimento di Farmacia; Università degli Studi di Salerno; via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Agostino Casapullo
- Dipartimento di Farmacia; Università degli Studi di Salerno; via Giovanni Paolo II 132 84084 Fisciano Italy
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Kim HT, Goldberg AL. The deubiquitinating enzyme Usp14 allosterically inhibits multiple proteasomal activities and ubiquitin-independent proteolysis. J Biol Chem 2017; 292:9830-9839. [PMID: 28416611 DOI: 10.1074/jbc.m116.763128] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
The proteasome-associated deubiquitinating enzyme Usp14/Ubp6 inhibits protein degradation by catalyzing substrate deubiquitination and by poorly understood allosteric actions. However, upon binding a ubiquitin chain, Usp14 enhances proteasomal degradation by stimulating ATP and peptide degradation. These studies were undertaken to clarify these seemingly opposite regulatory roles of Usp14 and their importance. To learn how the presence of Usp14 on 26S proteasomes influences its different activities, we compared enzymatic and regulatory properties of 26S proteasomes purified from wild-type mouse embryonic fibroblast cells and those lacking Usp14. The proteasomes lacking Usp14 had higher basal peptidase activity than WT 26S, and this activity was stimulated to a greater extent by adenosine 5'-O-(thiotriphosphate) (ATPγS) than with WT particles. These differences were clear even though Usp14 is present on only a minor fraction (30-40%) of the 26S in WT mouse embryonic fibroblast cells. Addition of purified Usp14 to the WT and Usp14-defficient proteasomes reduced both their basal peptidase activity and the stimulation by ATPγS. Usp14 inhibits these processes allosterically because a catalytically inactive Usp14 mutant also inhibited them. Proteasomes lacking Usp14 also exhibited greater deubiquitinating activity by Rpn11 and greater basal ATPase activity than WT particles. ATP hydrolysis by WT proteasomes is activated if they bind a ubiquitinated protein, which is loosely folded. Surprisingly, proteasomes lacking Usp14 could be activated by such proteins even without a ubiquitin chain present. Furthermore, proteasomes lacking Usp14 are much more active in degrading non-ubiquitinated proteins (e.g. Sic1) than WT particles. Thus, without a ubiquitinated substrate present, Usp14 suppresses multiple proteasomal activities, especially basal ATP consumption and degradation of non-ubiquitinated proteins. These allosteric effects thus reduce ATP hydrolysis by inactive proteasomes and nonspecific proteolysis and enhance proteasomal specificity for ubiquitinated proteins.
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Affiliation(s)
- Hyoung Tae Kim
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Alfred L Goldberg
- From the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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35
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Hewings DS, Flygare JA, Wertz IE, Bogyo M. Activity-based probes for the multicatalytic proteasome. FEBS J 2017; 284:1540-1554. [PMID: 28107776 DOI: 10.1111/febs.14016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/22/2016] [Accepted: 01/16/2017] [Indexed: 12/17/2022]
Abstract
Proteasomes are multisubunit protease complexes responsible for degrading most intracellular proteins. In addition to removing damaged proteins, they regulate many important cellular processes through the controlled degradation of transcription factors, cell cycle regulators, and enzymes. Eukaryotic proteasomes have three catalytic subunits, β1, β2, and β5, that each has different substrate specificities. Additionally, although we know that diverse cell types express proteasome variants with distinct activity and specificity profiles, the functions of these different pools of proteasomes are not fully understood. Covalent inhibitors of the protease activity of the proteasome have been developed as drugs for hematological malignancies and are currently under investigation for other diseases. Therefore, there is a need for tools that allow direct monitoring of proteasome activity in live cells and tissues. Activity-based probes have proven valuable for biochemical and cell biological studies of the role of individual proteasome subunits, and for evaluating the efficacy and selectivity of proteasome inhibitors. These probes react covalently with the protease active sites, and contain a reporter tag to identify the probe-labeled proteasome subunits. This review will describe the development of broad-spectrum and subunit-specific proteasome activity-based probes, and discuss how these probes have contributed to our understanding of proteasome biology, and to the development of proteasome inhibitors.
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Affiliation(s)
- David S Hewings
- Discovery Chemistry, Genentech, South San Francisco, CA, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - John A Flygare
- Discovery Chemistry, Genentech, South San Francisco, CA, USA
| | - Ingrid E Wertz
- Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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36
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Vriend J, Marzban H. The ubiquitin-proteasome system and chromosome 17 in cerebellar granule cells and medulloblastoma subgroups. Cell Mol Life Sci 2017; 74:449-467. [PMID: 27592301 PMCID: PMC11107675 DOI: 10.1007/s00018-016-2354-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/17/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022]
Abstract
Chromosome 17 abnormalities are often observed in medulloblastomas (MBs), particularly those classified in the consensus Groups 3 and 4. Herein we review MB signature genes associated with chromosome 17 and the relationship of these signature genes to the ubiquitin-proteasome system. While clinical investigators have not focused on the ubiquitin-proteasome system in relation to MB, a substantial amount of data on the topic has been hidden in the form of supplemental datasets of gene expression. A supplemental dataset associated with the Thompson classification of MBs shows that a subgroup of MB with 17p deletions is characterized by reduced expression of genes for several core particle subunits of the beta ring of the proteasome (β1, β4, β5, β7). One of these genes (PSMB6, the gene for the β1 subunit) is located on chromosome 17, near the telomeric end of 17p. By comparison, in the WNT group of MBs only one core proteasome subunit, β6, associated with loss of a gene (PSMB1) on chromosome 6, was down-regulated in this dataset. The MB subgroups with the worst prognosis have a significant association with chromosome 17 abnormalities and irregularities of APC/C cyclosome genes. We conclude that the expression of proteasome subunit genes and genes for ubiquitin ligases can contribute to prognostic classification of MBs. The therapeutic value of targeting proteasome subunits and ubiquitin ligases in the various subgroups of MB remains to be determined separately for each classification of MB.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Rm134, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
| | - Hassan Marzban
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Rm134, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
- Children's Hospital Research Institute of Manitoba (CHRIM), Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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37
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Lip PZY, Demasi M, Bonatto D. The role of the ubiquitin proteasome system in the memory process. Neurochem Int 2016; 102:57-65. [PMID: 27916542 DOI: 10.1016/j.neuint.2016.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/27/2016] [Accepted: 11/29/2016] [Indexed: 01/20/2023]
Abstract
Quite intuitive is the notion that memory formation and consolidation is orchestrated by protein synthesis because of the synaptic plasticity necessary for those processes. Nevertheless, recent advances have begun accumulating evidences of a high requirement for protein degradation on the molecular mechanisms of the memory process in the mammalian brain. Because degradation determines protein half-life, degradation has been increasingly recognized as an important intracellular regulatory mechanism. The proteasome is the main player in the degradation of intracellular proteins. Proteasomal substrates are mainly degraded after a post-translational modification by a poly-ubiquitin chain. Latter process, namely poly-ubiquitination, is highly regulated at the step of the ubiquitin molecule transferring to the protein substrate mediated by a set of proteins whose genes represent almost 2% of the human genome. Understanding the role of polyubiquitin-mediated protein degradation has challenging researchers in many fields of investigation as a new source of targets for therapeutic intervention, e.g. E3 ligases that transfer ubiquitin moieties to the substrate. The goal of present work was to uncover mechanisms underlying memory processes regarding the role of the ubiquitin-proteasome system (UPS). For that purpose, preceded of a short review on UPS and memory processes a top-down systems biology approach was applied to establish central proteins involved in memory formation and consolidation highlighting their cross-talking with the UPS. According to that approach, the pattern of expression of several elements of the UPS were found overexpressed in regions of the brain involved in processing cortical inputs.
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Affiliation(s)
- Philomena Z Y Lip
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, SP, Brazil; Medical Sciences Division, University of Oxford, Oxford, UK
| | - Marilene Demasi
- Medical Sciences Division, University of Oxford, Oxford, UK.
| | - Diego Bonatto
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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38
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Hakim V, Cohen LD, Zuchman R, Ziv T, Ziv NE. The effects of proteasomal inhibition on synaptic proteostasis. EMBO J 2016; 35:2238-2262. [PMID: 27613546 PMCID: PMC5069550 DOI: 10.15252/embj.201593594] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/08/2016] [Indexed: 01/03/2023] Open
Abstract
Synaptic function crucially depends on uninterrupted synthesis and degradation of synaptic proteins. While much has been learned on synaptic protein synthesis, little is known on the routes by which synaptic proteins are degraded. Here we systematically studied how inhibition of the ubiquitin-proteasome system (UPS) affects the degradation rates of thousands of neuronal and synaptic proteins. We identified a group of proteins, including several proteins related to glutamate receptor trafficking, whose degradation rates were significantly slowed by UPS inhibition. Unexpectedly, however, degradation rates of most synaptic proteins were not significantly affected. Interestingly, many of the differential effects of UPS inhibition were readily explained by a quantitative framework that considered known metabolic turnover rates for the same proteins. In contrast to the limited effects on protein degradation, UPS inhibition profoundly and preferentially suppressed the synthesis of a large number of synaptic proteins. Our findings point to the importance of the UPS in the degradation of certain synaptic proteins, yet indicate that under basal conditions most synaptic proteins might be degraded through alternative pathways.
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Affiliation(s)
- Vicky Hakim
- The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel.,Network Biology Research Laboratories, Technion - Israel Institute of Technology, Haifa, Israel
| | - Laurie D Cohen
- The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel.,Network Biology Research Laboratories, Technion - Israel Institute of Technology, Haifa, Israel
| | - Rina Zuchman
- Smoler Proteomics Center, Faculty of Biology, Technion, Haifa, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Faculty of Biology, Technion, Haifa, Israel
| | - Noam E Ziv
- The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel .,Network Biology Research Laboratories, Technion - Israel Institute of Technology, Haifa, Israel
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39
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Computational Approaches for the Discovery of Human Proteasome Inhibitors: An Overview. Molecules 2016; 21:molecules21070927. [PMID: 27438821 PMCID: PMC6274525 DOI: 10.3390/molecules21070927] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 01/10/2023] Open
Abstract
Proteasome emerged as an important target in recent pharmacological research due to its pivotal role in degrading proteins in the cytoplasm and nucleus of eukaryotic cells, regulating a wide variety of cellular pathways, including cell growth and proliferation, apoptosis, DNA repair, transcription, immune response, and signaling processes. The last two decades witnessed intensive efforts to discover 20S proteasome inhibitors with significant chemical diversity and efficacy. To date, the US FDA approved to market three proteasome inhibitors: bortezomib, carfilzomib, and ixazomib. However new, safer and more efficient drugs are still required. Computer-aided drug discovery has long being used in drug discovery campaigns targeting the human proteasome. The aim of this review is to illustrate selected in silico methods like homology modeling, molecular docking, pharmacophore modeling, virtual screening, and combined methods that have been used in proteasome inhibitors discovery. Applications of these methods to proteasome inhibitors discovery will also be presented and discussed to raise improvements in this particular field.
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40
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Zhang J, Lu W, Chen Y, Jiang Q, Yang K, Li M, Wang Z, Duan X, Xu L, Tang H, Sun D, Wang J. Bortezomib alleviates experimental pulmonary hypertension by regulating intracellular calcium homeostasis in PASMCs. Am J Physiol Cell Physiol 2016; 311:C482-97. [PMID: 27413173 PMCID: PMC5129762 DOI: 10.1152/ajpcell.00324.2015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 06/27/2016] [Indexed: 01/18/2023]
Abstract
The ubiquitin-proteasome system is considered to be the key regulator of protein degradation. Bortezomib (BTZ) is the first proteasome inhibitor approved by the US Food and Drug Administration for treatment of relapsed multiple myeloma and mantle cell lymphoma. Recently, BTZ treatment was reported to inhibit right ventricular hypertrophy and vascular remodeling in hypoxia-exposed and monocrotaline-injected rats. However, the underlying mechanisms remain poorly understood. We previously confirmed that hypoxia-elevated basal intracellular Ca(2+) concentration ([Ca(2+)]i) and store-operated Ca(2+) entry (SOCE) in pulmonary artery smooth muscle cells (PASMCs) are involved in pulmonary vascular remodeling. In this study we aim to determine whether BTZ attenuates the hypoxia-induced elevation of [Ca(2+)] in PASMCs and the signaling pathway involved in this mechanism. Our results showed that 1) in hypoxia- and monocrotaline-induced rat pulmonary hypertension (PH) models, BTZ markedly attenuated the development and progression of PH, 2) BTZ inhibited the hypoxia-induced increase in cell proliferation, basal [Ca(2+)]i, and SOCE in PASMCs, and 3) BTZ significantly normalized the hypoxia-upregulated expression of hypoxia-inducible factor-1α, bone morphogenetic protein 4, canonical transient receptor potential isoforms 1 and 6, and the hypoxia-downregulated expression of peroxisome proliferator-activated receptor-γ in rat distal pulmonary arteries and PASMCs. These results indicate that BTZ exerts its protective role in the development of PH potentially by inhibiting the canonical transient receptor potential-SOCE-[Ca(2+)]i signaling axis in PASMCs.
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenju Lu
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yuqin Chen
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qian Jiang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Kai Yang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Meichan Li
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ziyi Wang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin Duan
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; and
| | - Lei Xu
- Division of Pulmonary and Critical Care Medicine, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia, China
| | - Haiyang Tang
- Division of Translational and Regenerative Medicine, Department of Medicine, The University of Arizona, Tucson, Arizona
| | - Dejun Sun
- Division of Pulmonary Medicine, The People's Hospital of Inner Mongolia, Hohhot, Inner Mongolia, China
| | - Jian Wang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Division of Translational and Regenerative Medicine, Department of Medicine, The University of Arizona, Tucson, Arizona; Division of Pulmonary Medicine, The People's Hospital of Inner Mongolia, Hohhot, Inner Mongolia, China;
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41
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Salvesen GS, Hempel A, Coll NS. Protease signaling in animal and plant-regulated cell death. FEBS J 2016; 283:2577-98. [PMID: 26648190 PMCID: PMC5606204 DOI: 10.1111/febs.13616] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/23/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022]
Abstract
This review aims to highlight the proteases required for regulated cell death mechanisms in animals and plants. The aim is to be incisive, and not inclusive of all the animal proteases that have been implicated in various publications. The review also aims to focus on instances when several publications from disparate groups have demonstrated the involvement of an animal protease, and also when there is substantial biochemical, mechanistic and genetic evidence. In doing so, the literature can be culled to a handful of proteases, covering most of the known regulated cell death mechanisms: apoptosis, regulated necrosis, necroptosis, pyroptosis and NETosis in animals. In plants, the literature is younger and not as extensive as for mammals, although the molecular drivers of vacuolar death, necrosis and the hypersensitive response in plants are becoming clearer. Each of these death mechanisms has at least one proteolytic component that plays a major role in controlling the pathway, and sometimes they combine in networks to regulate cell death/survival decision nodes. Some similarities are found among animal and plant cell death proteases but, overall, the pathways that they govern are kingdom-specific with very little overlap.
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Affiliation(s)
- Guy S. Salvesen
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anne Hempel
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nuria Sanchez Coll
- Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra 08193, Barcelona, Spain
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42
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Levin N, Spencer A, Harrison SJ, Chauhan D, Burrows FJ, Anderson KC, Reich SD, Richardson PG, Trikha M. Marizomib irreversibly inhibits proteasome to overcome compensatory hyperactivation in multiple myeloma and solid tumour patients. Br J Haematol 2016; 174:711-20. [PMID: 27161872 PMCID: PMC5084787 DOI: 10.1111/bjh.14113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/15/2016] [Indexed: 11/30/2022]
Abstract
Proteasome inhibitors (PIs) are highly active in multiple myeloma (MM) but resistance is commonly observed. All clinical stage PIs effectively inhibit chymotrypsin‐like (CT‐L) activity; one possible mechanism of resistance is compensatory hyperactivation of caspase‐like (C‐L) and trypsin‐like (T‐L) subunits, in response to CT‐L blockade. Marizomib (MRZ), an irreversible PI that potently inhibits all three 20S proteasome subunits with a specificity distinct from other PIs, is currently in development for treatment of MM and malignant glioma. The pan‐proteasome pharmacodynamic activity in packed whole blood and peripheral blood mononuclear cells was measured in two studies in patients with advanced solid tumours and haematological malignancies. Functional inhibition of all proteasome subunits was achieved with once‐ or twice‐weekly MRZ dosing; 100% inhibition of CT‐L was frequently achieved within one cycle at therapeutic doses. Concomitantly, C‐L and T‐L activities were either unaffected or increased, suggesting compensatory hyperactivation of these subunits. Importantly, this response was overcome by continued administration of MRZ, with robust inhibition of T‐L and C‐L (up to 80% and 50%, respectively) by the end of Cycle 2 and maintained thereafter. This enhanced proteasome inhibition was independent of tumour type and may underlie the clinical activity of MRZ in patients resistant to other PIs.
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Gene therapy by proteasome activator, PA28γ, improves motor coordination and proteasome function in Huntington's disease YAC128 mice. Neuroscience 2016; 324:20-8. [PMID: 26944602 DOI: 10.1016/j.neuroscience.2016.02.054] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 02/23/2016] [Accepted: 02/23/2016] [Indexed: 12/21/2022]
Abstract
Huntington's disease (HD) is neurologically characterized by involuntary movements, associated with degeneration of the medium-sized spiny neurons (MSNs) and ubiquitin-positive neuronal intranuclear inclusions (NIIs). It has been reported that the proteolytic activities of the ubiquitin-proteasome system (UPS) are generally inhibited in HD patient's brain. We previously discovered that a proteasome activator (PA), PA28γ enhances proteasome activities and cell survival in in vitro HD model. In this study, we aimed to find whether PA28γ gene transfer improves the proteasome activities and pathological symptoms in in vivo HD model. We stereotaxically injected lenti-PA28γ virus into the striatum of mutant (MT) YAC128 HD mice and littermate (LM) controls at 14-18months of age, and validated their behavioral and biochemical changes at 12weeks after the injection. YAC128 mice showed a significant increase in their peptidyl-glutamyl preferring hydrolytic (PGPH) proteasome activity and the mRNA or protein levels of brain-derived neurotrophic factor (BDNF) and pro-BDNF after lenti-PA28γ injection. The number of ubiquitin-positive inclusion bodies was reduced in the striatum of YAC128 mice after lenti-PA28γ injection. YAC128 mice showed significant improvement of latency to fall on the rota-rod test after lenti-PA28γ injection. These data demonstrate that the gene therapy with PA, PA28γ can improve UPS function as well as behavioral abnormalities in HD model mice.
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44
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Textoris-Taube K, Keller C, Liepe J, Henklein P, Sidney J, Sette A, Kloetzel PM, Mishto M. The T210M Substitution in the HLA-a*02:01 gp100 Epitope Strongly Affects Overall Proteasomal Cleavage Site Usage and Antigen Processing. J Biol Chem 2015; 290:30417-28. [PMID: 26507656 DOI: 10.1074/jbc.m115.695189] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 01/01/2023] Open
Abstract
MHC class I-restricted epitopes, which carry a tumor-specific mutation resulting in improved MHC binding affinity, are preferred T cell receptor targets in innovative adoptive T cell therapies. However, T cell therapy requires efficient generation of the selected epitope. How such mutations may affect proteasome-mediated antigen processing has so far not been studied. Therefore, we analyzed by in vitro experiments the effect on antigen processing and recognition of a T210M exchange, which previously had been introduced into the melanoma gp100209-217 tumor epitope to improve the HLA-A*02:01 binding and its immunogenicity. A quantitative analysis of the main steps of antigen processing shows that the T210M exchange affects proteasomal cleavage site usage within the mutgp100201-230 polypeptide, leading to the generation of an unique set of cleavage products. The T210M substitution qualitatively affects the proteasome-catalyzed generation of spliced and non-spliced peptides predicted to bind HLA-A or -B complexes. The T210M substitution also induces an enhanced production of the mutgp100209-217 epitope and its N-terminally extended peptides. The T210M exchange revealed no effect on ERAP1-mediated N-terminal trimming of the precursor peptides. However, mutant N-terminally extended peptides exhibited significantly increased HLA-A*02:01 binding affinity and elicited CD8(+) T cell stimulation in vitro similar to the wtgp100209-217 epitope. Thus, our experiments demonstrate that amino acid exchanges within an epitope can result in the generation of an altered peptide pool with new antigenic peptides and in a wider CD8(+) T cell response also towards N-terminally extended versions of the minimal epitope.
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Affiliation(s)
- Kathrin Textoris-Taube
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christin Keller
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Juliane Liepe
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom, and
| | - Petra Henklein
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Peter M Kloetzel
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany,
| | - Michele Mishto
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany,
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45
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Proteomics in Traditional Chinese Medicine with an Emphasis on Alzheimer's Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 2015:393510. [PMID: 26557146 PMCID: PMC4628675 DOI: 10.1155/2015/393510] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/27/2015] [Indexed: 12/12/2022]
Abstract
In recent years, there has been an increasing worldwide interest in traditional Chinese medicine (TCM). This increasing demand for TCM needs to be accompanied by a deeper understanding of the mechanisms of action of TCM-based therapy. However, TCM is often described as a concept of Chinese philosophy, which is incomprehensible for Western medical society, thereby creating a gap between TCM and Western medicine (WM). In order to meet this challenge, TCM research has applied proteomics technologies for exploring the mechanisms of action of TCM treatment. Proteomics enables TCM researchers to oversee various pathways that are affected by treatment, as well as the dynamics of their interactions with one another. This review discusses the utility of comparative proteomics to better understand how TCM treatment may be used as a complementary therapy for Alzheimer's disease (AD). Additionally, we review the data from comparative AD-related TCM proteomics studies and establish the relevance of the data with available AD hypotheses, most notably regarding the ubiquitin proteasome system (UPS).
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46
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Das DS, Ray A, Song Y, Richardson P, Trikha M, Chauhan D, Anderson KC. Synergistic anti-myeloma activity of the proteasome inhibitor marizomib and the IMiD immunomodulatory drug pomalidomide. Br J Haematol 2015; 171:798-812. [PMID: 26456076 DOI: 10.1111/bjh.13780] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/13/2015] [Indexed: 12/22/2022]
Abstract
The proteasome inhibitor bortezomib is an effective therapy for the treatment of relapsed and refractory multiple myeloma (RRMM); however, prolonged treatment can be associated with toxicity, peripheral neuropathy and drug resistance. Our earlier studies showed that the novel proteasome inhibitor marizomib is distinct from bortezomib in its chemical structure, mechanisms of action and effects on proteasomal activities, and that it can overcome bortezomib resistance. Pomalidomide, like lenalidomide, has potent immunomodulatory activity and has been approved by the US Food and Drug Administration for the treatment of RRMM. Here, we demonstrate that combining low concentrations of marizomib with pomalidomide induces synergistic anti-MM activity. Marizomib plus pomalidomide-induced apoptosis is associated with: (i) activation of caspase-8, caspase-9, caspase-3 and PARP cleavage, (ii) downregulation of cereblon (CRBN), IRF4, MYC and MCL1, and (iii) suppression of chymotrypsin-like, caspase-like, and trypsin-like proteasome activities. CRBN-siRNA attenuates marizomib plus pomalidomide-induced MM cells death. Furthermore, marizomib plus pomalidomide inhibits the migration of MM cells and tumour-associated angiogenesis, as well as overcomes cytoprotective effects of bone marrow microenvironment. In human MM xenograft model studies, the combination of marizomib and pomalidomide is well tolerated, inhibits tumour growth and prolongs survival. These preclinical studies provide the rationale for on-going clinical trials of combined marizomib and pomalidomide to improve outcome in patients with RRMM.
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Affiliation(s)
- Deepika S Das
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Arghya Ray
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yan Song
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Paul Richardson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Dharminder Chauhan
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kenneth C Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Pakavathkumar P, Sharma G, Kaushal V, Foveau B, LeBlanc AC. Methylene Blue Inhibits Caspases by Oxidation of the Catalytic Cysteine. Sci Rep 2015; 5:13730. [PMID: 26400108 PMCID: PMC4585840 DOI: 10.1038/srep13730] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/03/2015] [Indexed: 12/20/2022] Open
Abstract
Methylene blue, currently in phase 3 clinical trials against Alzheimer Disease, disaggregates the Tau protein of neurofibrillary tangles by oxidizing specific cysteine residues. Here, we investigated if methylene blue can inhibit caspases via the oxidation of their active site cysteine. Methylene blue, and derivatives, azure A and azure B competitively inhibited recombinant Caspase-6 (Casp6), and inhibited Casp6 activity in transfected human colon carcinoma cells and in serum-deprived primary human neuron cultures. Methylene blue also inhibited recombinant Casp1 and Casp3. Furthermore, methylene blue inhibited Casp3 activity in an acute mouse model of liver toxicity. Mass spectrometry confirmed methylene blue and azure B oxidation of the catalytic Cys163 cysteine of Casp6. Together, these results show a novel inhibitory mechanism of caspases via sulfenation of the active site cysteine. These results indicate that methylene blue or its derivatives could (1) have an additional effect against Alzheimer Disease by inhibiting brain caspase activity, (2) be used as a drug to prevent caspase activation in other conditions, and (3) predispose chronically treated individuals to cancer via the inhibition of caspases.
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Affiliation(s)
- Prateep Pakavathkumar
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Gyanesh Sharma
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Vikas Kaushal
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Bénédicte Foveau
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Andrea C. LeBlanc
- Bloomfield Center for Research in Aging, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
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Liepe J, Holzhütter HG, Bellavista E, Kloetzel PM, Stumpf MPH, Mishto M. Quantitative time-resolved analysis reveals intricate, differential regulation of standard- and immuno-proteasomes. eLife 2015; 4:e07545. [PMID: 26393687 PMCID: PMC4611054 DOI: 10.7554/elife.07545] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/18/2015] [Indexed: 12/15/2022] Open
Abstract
Proteasomal protein degradation is a key determinant of protein half-life and hence of cellular processes ranging from basic metabolism to a host of immunological processes. Despite its importance the mechanisms regulating proteasome activity are only incompletely understood. Here we use an iterative and tightly integrated experimental and modelling approach to develop, explore and validate mechanistic models of proteasomal peptide-hydrolysis dynamics. The 20S proteasome is a dynamic enzyme and its activity varies over time because of interactions between substrates and products and the proteolytic and regulatory sites; the locations of these sites and the interactions between them are predicted by the model, and experimentally supported. The analysis suggests that the rate-limiting step of hydrolysis is the transport of the substrates into the proteasome. The transport efficiency varies between human standard- and immuno-proteasomes thereby impinging upon total degradation rate and substrate cleavage-site usage. DOI:http://dx.doi.org/10.7554/eLife.07545.001 Cells have to be able to reliably destroy or remove molecules from their interior that they no longer need. Structures called proteasomes play a central part in this complex process by cutting up and digesting proteins. Mammals have several different types of proteasomes, each made up of several protein ‘subunits’. For example, when a cell experiences inflammation some proteasomes change some of their subunits and form an immuno-proteasome. These immuno-proteasomes tend to break down proteins more quickly than ‘standard’ proteasomes, but it was not clear how they are able to do so. Liepe et al. have now combined experiments and mathematical modelling to construct a detailed model of proteasome activity. The model shows that protein transport into and out of the proteasome chamber are the steps that limit how quickly the proteasomes can break down proteins. Furthermore, these transport processes are also to a large extent responsible for the different rates at which standard and immuno-proteasomes process proteins. Liepe et al. were also able to confirm the existence of regulatory sites within the proteasome, and describe how these are arranged. Problems that alter the rate at which proteasomes break down proteins have been linked to tumors and neurological and autoimmune diseases. Liepe et al.'s model opens up the ability to study how the proteasome's activity is affected by drugs and therefore makes it easier to investigate ways of interfering with this activity for therapeutic purposes. DOI:http://dx.doi.org/10.7554/eLife.07545.002
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Affiliation(s)
- Juliane Liepe
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Elena Bellavista
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Peter M Kloetzel
- Institut für Biochemie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael P H Stumpf
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Michele Mishto
- Institut für Biochemie, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Luigi Galvani, Alma Mater Studiorum, University of Bologna, Bologna, Italy
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Grigoreva TA, Tribulovich VG, Garabadzhiu AV, Melino G, Barlev NA. The 26S proteasome is a multifaceted target for anti-cancer therapies. Oncotarget 2015; 6:24733-49. [PMID: 26295307 PMCID: PMC4694792 DOI: 10.18632/oncotarget.4619] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 07/10/2015] [Indexed: 12/30/2022] Open
Abstract
Proteasomes play a critical role in the fate of proteins that are involved in major cellular processes, including signal transduction, gene expression, cell cycle, replication, differentiation, immune response, cellular response to stress, etc. In contrast to non-specific degradation by lysosomes, proteasomes are highly selective and destroy only the proteins that are covalently labelled with small proteins, called ubiquitins. Importantly, many diseases, including neurodegenerative diseases and cancers, are intimately connected to the activity of proteasomes making them an important pharmacological target. Currently, the vast majority of inhibitors are aimed at blunting the proteolytic activities of proteasomes. However, recent achievements in solving structures of proteasomes at very high resolution provided opportunities to design new classes of small molecules that target other physiologically-important enzymatic activities of proteasomes, including the de-ubiquitinating one. This review attempts to catalog the information available to date about novel classes of proteasome inhibitors that may have important pharmacological ramifications.
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Affiliation(s)
- Tatyana A Grigoreva
- St. Petersburg State Technological Institute (Technical University), St. Petersburng, Russia
| | | | | | - Gerry Melino
- St. Petersburg State Technological Institute (Technical University), St. Petersburng, Russia
- University of Rome Tor Vergata, Roma, Italy
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O'Brien MA, Moravec RA, Riss TL, Bulleit RF. Homogeneous, bioluminescent proteasome assays. Methods Mol Biol 2015; 1219:95-114. [PMID: 25308265 DOI: 10.1007/978-1-4939-1661-0_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Protein degradation is mediated predominantly through the ubiquitin-proteasome pathway. The importance of the proteasome in regulating degradation of proteins involved in cell-cycle control, apoptosis, and angiogenesis led to the recognition of the proteasome as a therapeutic target for cancer. The proteasome is also essential for degrading misfolded and aberrant proteins, and impaired proteasome function has been implicated in neurodegerative and cardiovascular diseases. Robust, sensitive assays are essential for monitoring proteasome activity and for developing inhibitors of the proteasome. Peptide-conjugated fluorophores are widely used as substrates for monitoring proteasome activity, but fluorogenic substrates can exhibit significant background and can be problematic for screening because of cellular autofluorescence or interference from fluorescent library compounds. Furthermore, fluorescent proteasome assays require column-purified 20S or 26S proteasome (typically obtained from erythrocytes), or proteasome extracts from whole cells, as their samples. To provide assays more amenable to high-throughput screening, we developed a homogeneous, bioluminescent method that combines peptide-conjugated aminoluciferin substrates and a stabilized luciferase. Using substrates for the chymotrypsin-like, trypsin-like, and caspase-like proteasome activities in combination with a selective membrane permeabilization step, we developed single-step, cell-based assays to measure each of the proteasome catalytic activities. The homogeneous method eliminates the need to prepare individual cell extracts as samples and has adequate sensitivity for 96- and 384-well plates. The simple "add and read" format enables sensitive and rapid proteasome assays ideal for inhibitor screening.
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Affiliation(s)
- Martha A O'Brien
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA,
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