1
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Sahoo MP, Lavy T, Cohen N, Sahu I, Kleifeld O. Activity-Guided Proteomic Profiling of Proteasomes Uncovers a Variety of Active (and Inactive) Proteasome Species. Mol Cell Proteomics 2024; 23:100728. [PMID: 38296025 PMCID: PMC10907802 DOI: 10.1016/j.mcpro.2024.100728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/11/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
Proteasomes are multisubunit, multicatalytic protein complexes present in eukaryotic cells that degrade misfolded, damaged, or unstructured proteins. In this study, we used an activity-guided proteomic methodology based on a fluorogenic peptide substrate to characterize the composition of proteasome complexes in WT yeast and the changes these complexes undergo upon the deletion of Pre9 (Δα3) or of Sem1 (ΔSem1). A comparison of whole-cell proteomic analysis to activity-guided proteasome profiling indicates that the amounts of proteasomal proteins and proteasome interacting proteins in the assembled active proteasomes differ significantly from their total amounts in the cell as a whole. Using this activity-guided profiling approach, we characterized the changes in the abundance of subunits of various active proteasome species in different strains, quantified the relative abundance of active proteasomes across these strains, and charted the overall distribution of different proteasome species within each strain. The distributions obtained by our mass spectrometry-based quantification were markedly higher for some proteasome species than those obtained by activity-based quantification alone, suggesting that the activity of some of these species is impaired. The impaired activity appeared mostly among 20SBlm10 proteasome species which account for 20% of the active proteasomes in WT. To identify the factors behind this impaired activity, we mapped and quantified known proteasome-interacting proteins. Our results suggested that some of the reduced activity might be due to the association of the proteasome inhibitor Fub1. Additionally, we provide novel evidence for the presence of nonmature and therefore inactive proteasomal protease subunits β2 and β5 in the fully assembled proteasomes.
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Affiliation(s)
| | - Tali Lavy
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, Israel
| | - Noam Cohen
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, Israel
| | - Indrajit Sahu
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, Israel.
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2
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Betancourt D, Lawal T, Tomko RJ. Wiggle and Shake: Managing and Exploiting Conformational Dynamics during Proteasome Biogenesis. Biomolecules 2023; 13:1223. [PMID: 37627288 PMCID: PMC10452565 DOI: 10.3390/biom13081223] [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: 07/04/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
The 26S proteasome is the largest and most complicated protease known, and changes to proteasome assembly or function contribute to numerous human diseases. Assembly of the 26S proteasome from its ~66 individual polypeptide subunits is a highly orchestrated process requiring the concerted actions of both intrinsic elements of proteasome subunits, as well as assistance by extrinsic, dedicated proteasome assembly chaperones. With the advent of near-atomic resolution cryo-electron microscopy, it has become evident that the proteasome is a highly dynamic machine, undergoing numerous conformational changes in response to ligand binding and during the proteolytic cycle. In contrast, an appreciation of the role of conformational dynamics during the biogenesis of the proteasome has only recently begun to emerge. Herein, we review our current knowledge of proteasome assembly, with a particular focus on how conformational dynamics guide particular proteasome biogenesis events. Furthermore, we highlight key emerging questions in this rapidly expanding area.
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Affiliation(s)
| | | | - Robert J. Tomko
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA; (D.B.); (T.L.)
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3
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Tundo GR, Sbardella D, Santoro AM, Coletta A, Oddone F, Grasso G, Milardi D, Lacal PM, Marini S, Purrello R, Graziani G, Coletta M. The proteasome as a druggable target with multiple therapeutic potentialities: Cutting and non-cutting edges. Pharmacol Ther 2020; 213:107579. [PMID: 32442437 PMCID: PMC7236745 DOI: 10.1016/j.pharmthera.2020.107579] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 01/10/2023]
Abstract
Ubiquitin Proteasome System (UPS) is an adaptable and finely tuned system that sustains proteostasis network under a large variety of physiopathological conditions. Its dysregulation is often associated with the onset and progression of human diseases; hence, UPS modulation has emerged as a promising new avenue for the development of treatments of several relevant pathologies, such as cancer and neurodegeneration. The clinical interest in proteasome inhibition has considerably increased after the FDA approval in 2003 of bortezomib for relapsed/refractory multiple myeloma, which is now used in the front-line setting. Thereafter, two other proteasome inhibitors (carfilzomib and ixazomib), designed to overcome resistance to bortezomib, have been approved for treatment-experienced patients, and a variety of novel inhibitors are currently under preclinical and clinical investigation not only for haematological malignancies but also for solid tumours. However, since UPS collapse leads to toxic misfolded proteins accumulation, proteasome is attracting even more interest as a target for the care of neurodegenerative diseases, which are sustained by UPS impairment. Thus, conceptually, proteasome activation represents an innovative and largely unexplored target for drug development. According to a multidisciplinary approach, spanning from chemistry, biochemistry, molecular biology to pharmacology, this review will summarize the most recent available literature regarding different aspects of proteasome biology, focusing on structure, function and regulation of proteasome in physiological and pathological processes, mostly cancer and neurodegenerative diseases, connecting biochemical features and clinical studies of proteasome targeting drugs.
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Affiliation(s)
- G R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
| | | | - A M Santoro
- CNR, Institute of Crystallography, Catania, Italy
| | - A Coletta
- Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - F Oddone
- IRCCS-Fondazione Bietti, Rome, Italy
| | - G Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - D Milardi
- CNR, Institute of Crystallography, Catania, Italy
| | - P M Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, Rome, Italy
| | - S Marini
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - R Purrello
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - G Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - M Coletta
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
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4
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Quinet G, Gonzalez-Santamarta M, Louche C, Rodriguez MS. Mechanisms Regulating the UPS-ALS Crosstalk: The Role of Proteaphagy. Molecules 2020; 25:E2352. [PMID: 32443527 PMCID: PMC7288101 DOI: 10.3390/molecules25102352] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 12/18/2022] Open
Abstract
Protein degradation is tightly regulated inside cells because of its utmost importance for protein homeostasis (proteostasis). The two major intracellular proteolytic pathways are the ubiquitin-proteasome and the autophagy-lysosome systems which ensure the fate of proteins when modified by various members of the ubiquitin family. These pathways are tightly interconnected by receptors and cofactors that recognize distinct chain architectures to connect with either the proteasome or autophagy under distinct physiologic and pathologic situations. The degradation of proteasome by autophagy, known as proteaphagy, plays an important role in this crosstalk since it favours the activity of autophagy in the absence of fully active proteasomes. Recently described in several biological models, proteaphagy appears to help the cell to survive when proteostasis is broken by the absence of nutrients or the excess of proteins accumulated under various stress conditions. Emerging evidence indicates that proteaphagy could be permanently activated in some types of cancer or when chemoresistance is observed in patients.
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Affiliation(s)
| | | | | | - Manuel S. Rodriguez
- ITAV-CNRS USR 3505 IPBS-UPS, 1 Place Pierre Potier, 31106 Toulouse, France; (G.Q.); (M.G.-S.); (C.L.)
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5
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The Proteasome Lid Triggers COP9 Signalosome Activity during the Transition of Saccharomyces cerevisiae Cells into Quiescence. Biomolecules 2019; 9:biom9090449. [PMID: 31487956 PMCID: PMC6770237 DOI: 10.3390/biom9090449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
The class of Cullin-RING E3 ligases (CRLs) selectively ubiquitinate a large portion of proteins targeted for proteolysis by the 26S proteasome. Before degradation, ubiquitin molecules are removed from their conjugated proteins by deubiquitinating enzymes, a handful of which are associated with the proteasome. The CRL activity is triggered by modification of the Cullin subunit with the ubiquitin-like protein, NEDD8 (also known as Rub1 in Saccharomyces cerevisiae). Cullin modification is then reversed by hydrolytic action of the COP9 signalosome (CSN). As the NEDD8-Rub1 catalytic cycle is not essential for the viability of S. cerevisiae, this organism is a useful model system to study the alteration of Rub1-CRL conjugation patterns. In this study, we describe two distinct mutants of Rpn11, a proteasome-associated deubiquitinating enzyme, both of which exhibit a biochemical phenotype characterized by high accumulation of Rub1-modified Cdc53-Cullin1 (yCul1) upon entry into quiescence in S. cerevisiae. Further characterization revealed proteasome 19S-lid-associated deubiquitination activity that authorizes the hydrolysis of Rub1 from yCul1 by the CSN complex. Thus, our results suggest a negative feedback mechanism via proteasome capacity on upstream ubiquitinating enzymes.
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6
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Synthetic ubiquitinated proteins meet the proteasome: Distinct roles of ubiquitin in a chain. Proc Natl Acad Sci U S A 2019; 116:7614-7616. [PMID: 30926663 DOI: 10.1073/pnas.1903405116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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7
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Bramasole L, Sinha A, Gurevich S, Radzinski M, Klein Y, Panat N, Gefen E, Rinaldi T, Jimenez-Morales D, Johnson J, Krogan NJ, Reis N, Reichmann D, Glickman MH, Pick E. Proteasome lid bridges mitochondrial stress with Cdc53/Cullin1 NEDDylation status. Redox Biol 2019; 20:533-543. [PMID: 30508698 PMCID: PMC6279957 DOI: 10.1016/j.redox.2018.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
Cycles of Cdc53/Cullin1 rubylation (a.k.a NEDDylation) protect ubiquitin-E3 SCF (Skp1-Cullin1-F-box protein) complexes from self-destruction and play an important role in mediating the ubiquitination of key protein substrates involved in cell cycle progression, development, and survival. Cul1 rubylation is balanced by the COP9 signalosome (CSN), a multi-subunit derubylase that shows 1:1 paralogy to the 26S proteasome lid. The turnover of SCF substrates and their relevance to various diseases is well studied, yet, the extent by which environmental perturbations influence Cul1 rubylation/derubylation cycles per se is still unclear. In this study, we show that the level of cellular oxidation serves as a molecular switch, determining Cullin1 rubylation/derubylation ratio. We describe a mutant of the proteasome lid subunit, Rpn11 that exhibits accumulated levels of Cullin1-Rub1 conjugates, a characteristic phenotype of csn mutants. By dissecting between distinct phenotypes of rpn11 mutants, proteasome and mitochondria dysfunction, we were able to recognize the high reactive oxygen species (ROS) production during the transition of cells into mitochondrial respiration, as a checkpoint of Cullin1 rubylation in a reversible manner. Thus, the study adds the rubylation cascade to the list of cellular pathways regulated by redox homeostasis.
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Affiliation(s)
- L Bramasole
- Department of Human Biology, The Faculty of Natural Sciences, University of Haifa, Haifa 3190500, Israel; Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - A Sinha
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - S Gurevich
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - M Radzinski
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - Y Klein
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - N Panat
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - E Gefen
- Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel
| | - T Rinaldi
- Department of Biology and Biotechnology, University of Rome ''La Sapienza'', Rome 00185, Italy
| | - D Jimenez-Morales
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - J Johnson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - N J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - N Reis
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - D Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 9190400, Israel
| | - M H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 3200000 Haifa, Israel
| | - E Pick
- Department of Human Biology, The Faculty of Natural Sciences, University of Haifa, Haifa 3190500, Israel; Department of Biology and Environment, The Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 3600600, Israel.
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8
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Budenholzer L, Cheng CL, Li Y, Hochstrasser M. Proteasome Structure and Assembly. J Mol Biol 2017; 429:3500-3524. [PMID: 28583440 DOI: 10.1016/j.jmb.2017.05.027] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
Abstract
The eukaryotic 26S proteasome is a large multisubunit complex that degrades the majority of proteins in the cell under normal conditions. The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle and the 20S core particle. Most substrates are first covalently modified by ubiquitin, which then directs them to the proteasome. The function of the regulatory particle is to recognize, unfold, deubiquitylate, and translocate substrates into the core particle, which contains the proteolytic sites of the proteasome. Given the abundance and subunit complexity of the proteasome, the assembly of this ~2.5MDa complex must be carefully orchestrated to ensure its correct formation. In recent years, significant progress has been made in the understanding of proteasome assembly, structure, and function. Technical advances in cryo-electron microscopy have resulted in a series of atomic cryo-electron microscopy structures of both human and yeast 26S proteasomes. These structures have illuminated new intricacies and dynamics of the proteasome. In this review, we focus on the mechanisms of proteasome assembly, particularly in light of recent structural information.
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Affiliation(s)
- Lauren Budenholzer
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Chin Leng Cheng
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Yanjie Li
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
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9
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Chojnacki M, Mansour W, Hameed DS, Singh RK, El Oualid F, Rosenzweig R, Nakasone MA, Yu Z, Glaser F, Kay LE, Fushman D, Ovaa H, Glickman MH. Polyubiquitin-Photoactivatable Crosslinking Reagents for Mapping Ubiquitin Interactome Identify Rpn1 as a Proteasome Ubiquitin-Associating Subunit. Cell Chem Biol 2017; 24:443-457.e6. [PMID: 28330605 DOI: 10.1016/j.chembiol.2017.02.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 12/29/2016] [Accepted: 02/23/2017] [Indexed: 01/05/2023]
Abstract
Ubiquitin (Ub) signaling is a diverse group of processes controlled by covalent attachment of small protein Ub and polyUb chains to a range of cellular protein targets. The best documented Ub signaling pathway is the one that delivers polyUb proteins to the 26S proteasome for degradation. However, studies of molecular interactions involved in this process have been hampered by the transient and hydrophobic nature of these interactions and the lack of tools to study them. Here, we develop Ub-phototrap (UbPT), a synthetic Ub variant containing a photoactivatable crosslinking side chain. Enzymatic polymerization into chains of defined lengths and linkage types provided a set of reagents that led to identification of Rpn1 as a third proteasome ubiquitin-associating subunit that coordinates docking of substrate shuttles, unloading of substrates, and anchoring of polyUb conjugates. Our work demonstrates the value of UbPT, and we expect that its future uses will help define and investigate the ubiquitin interactome.
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Affiliation(s)
- Michal Chojnacki
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel; Department of Medical Biochemistry, Medical University of Łódź, Łódź, Poland
| | - Wissam Mansour
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Dharjath S Hameed
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Rajesh K Singh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Farid El Oualid
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Rina Rosenzweig
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mark A Nakasone
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Zanlin Yu
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Fabian Glaser
- The Technion Bioinformatics Knowledge Unit (BKU) of the Lorry Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
| | - Huib Ovaa
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel.
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10
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Howell LA, Tomko RJ, Kusmierczyk AR. Putting it all together: intrinsic and extrinsic mechanisms governing proteasome biogenesis. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s11515-017-1439-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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11
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Singh SK, Sahu I, Mali SM, Hemantha HP, Kleifeld O, Glickman MH, Brik A. Synthetic Uncleavable Ubiquitinated Proteins Dissect Proteasome Deubiquitination and Degradation, and Highlight Distinctive Fate of Tetraubiquitin. J Am Chem Soc 2016; 138:16004-16015. [PMID: 27960333 DOI: 10.1021/jacs.6b09611] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various hypotheses have been proposed regarding how chain length, linkage type, position on substrate, and susceptibility to deubiquitinases (DUBs) affect processing of different substrates by proteasome. Here we report a new strategy for the chemical synthesis of ubiquitinated proteins to generate a set of well-defined conjugates bearing an oxime bond between the chain and the substrate. We confirmed that this isopeptide replacement is resistant to DUBs and to shaving by proteasome. Analyzing products generated by proteasomes ranked how chain length governed degradation outcome. Our results support that (1) the cleavage of the proximal isopeptide bond is not a prerequisite for proteasomal degradation, (2) by overcoming trimming at the proteasome, tetraUb is a fundamentally different signal than shorter chains, and (3) the tetra-ubiquitin chain can be degraded with the substrate. Together these results highlight the usefulness of chemistry to dissect the contribution of proteasome-associated DUBs and the complexity of the degradation process.
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Affiliation(s)
- Sumeet K Singh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Indrajit Sahu
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Sachitanand M Mali
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Hosahalli P Hemantha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Oded Kleifeld
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Michael H Glickman
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
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12
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Abstract
Protein complexes form the critical foundation for a wide range of biological process, however understanding the intricate details of their activities is often challenging. In this review we describe how mass spectrometry plays a key role in the analysis of protein assemblies and the cellular pathways which they are involved in. Specifically, we discuss how the versatility of mass spectrometric approaches provides unprecedented information on multiple levels. We demonstrate this on the ubiquitin-proteasome proteolytic pathway, a process that is responsible for protein turnover. We follow the various steps of this degradation route and illustrate the different mass spectrometry workflows that were applied for elucidating molecular information. Overall, this review aims to stimulate the integrated use of multiple mass spectrometry approaches for analyzing complex biological systems.
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13
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Yedidi RS, Fatehi AK, Enenkel C. Proteasome dynamics between proliferation and quiescence stages of Saccharomyces cerevisiae. Crit Rev Biochem Mol Biol 2016; 51:497-512. [PMID: 27677933 DOI: 10.1080/10409238.2016.1230087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays a critical role in cellular protein homeostasis and is required for the turnover of short-lived and unwanted proteins, which are targeted by poly-ubiquitination for degradation. Proteasome is the key protease of UPS and consists of multiple subunits, which are organized into a catalytic core particle (CP) and a regulatory particle (RP). In Saccharomyces cerevisiae, proteasome holo-enzymes are engaged in degrading poly-ubiquitinated substrates and are mostly localized in the nucleus during cell proliferation. While in quiescence, the RP and CP are sequestered into motile and reversible storage granules in the cytoplasm, called proteasome storage granules (PSGs). The reversible nature of PSGs allows the proteasomes to be transported back into the nucleus upon exit from quiescence. Nuclear import of RP and CP through nuclear pores occurs via the canonical pathway that includes the importin-αβ heterodimer and takes advantage of the Ran-GTP gradient across the nuclear membrane. Dependent on the growth stage, either inactive precursor complexes or mature holo-enzymes are imported into the nucleus. The present review discusses the dynamics of proteasomes including their assembly, nucleo-cytoplasmic transport during proliferation and the sequestration of proteasomes into PSGs during quiescence. [Formula: see text].
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Affiliation(s)
| | | | - Cordula Enenkel
- a Department of Biochemistry , University of Toronto , Toronto , Canada
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14
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Mayor T, Sharon M, Glickman MH. Tuning the proteasome to brighten the end of the journey. Am J Physiol Cell Physiol 2016; 311:C793-C804. [PMID: 27605452 DOI: 10.1152/ajpcell.00198.2016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/04/2016] [Indexed: 02/07/2023]
Abstract
Degradation by the proteasome is the fate for a large portion of cellular proteins, and it plays a major role in maintaining protein homeostasis, as well as in regulating many cellular processes like cell cycle progression. A decrease in proteasome activity has been linked to aging and several age-related neurodegenerative pathologies and highlights the importance of the ubiquitin proteasome system regulation. While the proteasome has been traditionally viewed as a constitutive element of proteolysis, major studies have highlighted how different regulatory mechanisms can impact its activity. Importantly, alterations of proteasomal activity may have major impacts for its function and in therapeutics. On one hand, increasing proteasome activity could be beneficial to prevent the age-related downfall of protein homeostasis, whereas inhibiting or reducing its activity can prevent the proliferation of cancer cells.
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Affiliation(s)
- Thibault Mayor
- Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, Canada;
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel; and
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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15
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Castañeda CA, Dixon EK, Walker O, Chaturvedi A, Nakasone MA, Curtis JE, Reed MR, Krueger S, Cropp TA, Fushman D. Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins. Structure 2016; 24:423-36. [PMID: 26876099 DOI: 10.1016/j.str.2016.01.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/18/2015] [Accepted: 01/05/2016] [Indexed: 12/20/2022]
Abstract
Polyubiquitination, a critical protein post-translational modification, signals for a diverse set of cellular events via the different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the ɛ-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. We assembled di-ubiquitins (Ub2) comprising every lysine linkage and examined them biochemically and structurally. Of these, K27-Ub2 is unique as it is not cleaved by most deubiquitinases. As this remains the only structurally uncharacterized lysine linkage, we comprehensively examined the structures and dynamics of K27-Ub2 using nuclear magnetic resonance, small-angle neutron scattering, and in silico ensemble modeling. Our structural data provide insights into the functional properties of K27-Ub2, in particular that K27-Ub2 may be specifically recognized by K48-selective receptor UBA2 domain from proteasomal shuttle protein hHR23a. Binding studies and mutagenesis confirmed this prediction, further highlighting structural/recognition versatility of polyubiquitins and the potential power of determining function from elucidation of conformational ensembles.
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Affiliation(s)
- Carlos A Castañeda
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA; Departments of Biology & Chemistry, Syracuse University, Syracuse, NY 13244, USA.
| | - Emma K Dixon
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Olivier Walker
- Institut des Sciences Analytiques, UMR5280-Université de Lyon, 69100 Villeurbanne, France
| | - Apurva Chaturvedi
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Mark A Nakasone
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562, USA
| | - Megan R Reed
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899-8562, USA
| | - T Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
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Tomko RJ, Taylor DW, Chen ZA, Wang HW, Rappsilber J, Hochstrasser M. A Single α Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly. Cell 2016; 163:432-44. [PMID: 26451487 PMCID: PMC4601081 DOI: 10.1016/j.cell.2015.09.022] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/19/2015] [Accepted: 08/19/2015] [Indexed: 11/11/2022]
Abstract
Most short-lived eukaryotic proteins are degraded by the proteasome. A proteolytic core particle (CP) capped by regulatory particles (RPs) constitutes the 26S proteasome complex. RP biogenesis culminates with the joining of two large subcomplexes, the lid and base. In yeast and mammals, the lid appears to assemble completely before attaching to the base, but how this hierarchical assembly is enforced has remained unclear. Using biochemical reconstitutions, quantitative cross-linking/mass spectrometry, and electron microscopy, we resolve the mechanistic basis for the linkage between lid biogenesis and lid-base joining. Assimilation of the final lid subunit, Rpn12, triggers a large-scale conformational remodeling of the nascent lid that drives RP assembly, in part by relieving steric clash with the base. Surprisingly, this remodeling is triggered by a single Rpn12 α helix. Such assembly-coupled conformational switching is reminiscent of viral particle maturation and may represent a commonly used mechanism to enforce hierarchical assembly in multisubunit complexes. First in vitro reconstitution of RP assembly with completely recombinant components Electron microscopy and cross-linking reveal massive remodeling of a lid precursor Remodeling of the lid relieves steric clash with the RP base to promote RP assembly Lid remodeling can be triggered by a single C-terminal α helix in the Rpn12 subunit
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Affiliation(s)
- Robert J Tomko
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - David W Taylor
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Zhuo A Chen
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Mayfield Road, Edinburgh EH9 3BF, Scotland
| | - Hong-Wei Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, PRC
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Mayfield Road, Edinburgh EH9 3BF, Scotland; Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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17
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Alpha-ring Independent Assembly of the 20S Proteasome. Sci Rep 2015; 5:13130. [PMID: 26286114 PMCID: PMC4541365 DOI: 10.1038/srep13130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/20/2015] [Indexed: 12/17/2022] Open
Abstract
Archaeal proteasomes share many features with their eukaryotic counterparts and serve as important models for assembly. Proteasomes are also found in certain bacterial lineages yet their assembly mechanism is thought to be fundamentally different. Here we investigate α-ring formation using recombinant proteasomes from the archaeon Methanococcus maripaludis. Through an engineered disulfide cross-linking strategy, we demonstrate that double α-rings are structurally analogous to half-proteasomes and can form independently of single α-rings. More importantly, via targeted mutagenesis, we show that single α-rings are not required for the efficient assembly of 20S proteasomes. Our data support updating the currently held "α-ring first" view of assembly, initially proposed in studies of archaeal proteasomes, and present a way to reconcile the seemingly separate bacterial assembly mechanism with the rest of the proteasome realm. We suggest that a common assembly network underpins the absolutely conserved architecture of proteasomes across all domains of life.
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