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Nedomova M, Haberecht-Müller S, Möller S, Venz S, Prochazkova M, Prochazka J, Sedlak F, Chawengsaksophak K, Hammer E, Kasparek P, Adamek M, Sedlacek R, Konvalinka J, Krüger E, Grantz Saskova K. DDI2 protease controls embryonic development and inflammation via TCF11/NRF1. iScience 2024; 27:110893. [PMID: 39328932 PMCID: PMC11424978 DOI: 10.1016/j.isci.2024.110893] [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: 03/14/2024] [Revised: 03/25/2024] [Accepted: 09/03/2024] [Indexed: 09/28/2024] Open
Abstract
DDI2 is an aspartic protease that cleaves polyubiquitinated substrates. Upon proteotoxic stress, DDI2 activates the transcription factor TCF11/NRF1 (NFE2L1), crucial for maintaining proteostasis in mammalian cells, enabling the expression of rescue factors, including proteasome subunits. Here, we describe the consequences of DDI2 ablation in vivo and in cells. DDI2 knock-out (KO) in mice caused embryonic lethality at E12.5 with severe developmental failure. Molecular characterization of embryos showed insufficient proteasome expression with proteotoxic stress, accumulation of high molecular weight ubiquitin conjugates and induction of the unfolded protein response (UPR) and cell death pathways. In DDI2 surrogate KO cells, proteotoxic stress activated the integrated stress response (ISR) and induced a type I interferon (IFN) signature and IFN-induced proliferative signaling, possibly ensuring survival. These results indicate an important role for DDI2 in the cell-tissue proteostasis network and in maintaining a balanced immune response.
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Affiliation(s)
- Monika Nedomova
- Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague, Czech Republic
- First Faculty of Medicine, Charles University in Prague, Katerinska 32, 121 08 Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 25242 Vestec, Czech Republic
| | - Stefanie Haberecht-Müller
- Institute of Medical Biochemistry and Molecular Biology, Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Klinikum DZ 7, 17475 Greifswald, Germany
| | - Sophie Möller
- Institute of Medical Biochemistry and Molecular Biology, Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Klinikum DZ 7, 17475 Greifswald, Germany
| | - Simone Venz
- Institute of Medical Biochemistry and Molecular Biology, Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Klinikum DZ 7, 17475 Greifswald, Germany
| | - Michaela Prochazkova
- Department of Functional Genomics, Universitätsmedizin Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Jan Prochazka
- Department of Functional Genomics, Universitätsmedizin Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Frantisek Sedlak
- Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague, Czech Republic
- First Faculty of Medicine, Charles University in Prague, Katerinska 32, 121 08 Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 25242 Vestec, Czech Republic
| | - Kallayanee Chawengsaksophak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, BIOCEV, 25242 Vestec, Czech Republic
| | - Elke Hammer
- Department of Functional Genomics, Universitätsmedizin Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Petr Kasparek
- Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, BIOCEV, 25242 Vestec, Czech Republic
| | - Michael Adamek
- Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 25242 Vestec, Czech Republic
| | - Radislav Sedlacek
- Institute of Molecular Genetics of the Czech Academy of Sciences, Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, BIOCEV, 25242 Vestec, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague, Czech Republic
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Klinikum DZ 7, 17475 Greifswald, Germany
| | - Klara Grantz Saskova
- Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 25242 Vestec, Czech Republic
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Salcedo-Tacuma D, Howells GD, McHose C, Gutierrez-Diaz A, Schupp J, Smith DM. ProEnd: a comprehensive database for identifying HbYX motif-containing proteins across the tree of life. BMC Genomics 2024; 25:951. [PMID: 39396964 DOI: 10.1186/s12864-024-10864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 10/03/2024] [Indexed: 10/15/2024] Open
Abstract
The proteasome plays a crucial role in cellular homeostasis by degrading misfolded, damaged, or unnecessary proteins. Understanding the regulatory mechanisms of proteasome activity is vital, particularly the interaction with activators containing the hydrophobic-tyrosine-any amino acid (HbYX) motif. Here, we present ProEnd, a comprehensive database designed to identify and catalog HbYX motif-containing proteins across the tree of life. Using a simple bioinformatics pipeline, we analyzed approximately 73 million proteins from 22,000 reference proteomes in the UniProt/SwissProt database. Our findings reveal the widespread presence of HbYX motifs in diverse organisms, highlighting their evolutionary conservation and functional significance. Notably, we observed an interesting prevalence of these motifs in viral proteomes, suggesting strategic interactions with the host proteasome. As validation two novel HbYX proteins found in this database were experimentally tested by pulldowns, confirming that they directly interact with the proteasome, with one of them directly activating it. ProEnd's extensive dataset and user-friendly interface enable researchers to explore the potential proteasomal regulator landscape, generating new hypotheses to advance proteasome biology. This resource is set to facilitate the discovery of novel therapeutic targets, enhancing our approach to treating diseases such as neurodegenerative disorders and cancer.
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Affiliation(s)
- David Salcedo-Tacuma
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Giovanni D Howells
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Coleman McHose
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Aimer Gutierrez-Diaz
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Jane Schupp
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - David M Smith
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA.
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, USA.
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3
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Wojtaszek JL, Williams RS. From the TOP: Formation, recognition and resolution of topoisomerase DNA protein crosslinks. DNA Repair (Amst) 2024; 142:103751. [PMID: 39180935 PMCID: PMC11404304 DOI: 10.1016/j.dnarep.2024.103751] [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: 04/22/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Since the report of "DNA untwisting" activity in 1972, ∼50 years of research has revealed seven topoisomerases in humans (TOP1, TOP1mt, TOP2α, TOP2β, TOP3α, TOP3β and Spo11). These conserved regulators of DNA topology catalyze controlled breakage to the DNA backbone to relieve the torsional stress that accumulates during essential DNA transactions including DNA replication, transcription, and DNA repair. Each topoisomerase-catalyzed reaction involves the formation of a topoisomerase cleavage complex (TOPcc), a covalent protein-DNA reaction intermediate formed between the DNA phosphodiester backbone and a topoisomerase catalytic tyrosine residue. A variety of perturbations to topoisomerase reaction cycles can trigger failure of the enzyme to re-ligate the broken DNA strand(s), thereby generating topoisomerase DNA-protein crosslinks (TOP-DPC). TOP-DPCs pose unique threats to genomic integrity. These complex lesions are comprised of structurally diverse protein components covalently linked to genomic DNA, which are bulky DNA adducts that can directly impact progression of the transcription and DNA replication apparatus. A variety of genome maintenance pathways have evolved to recognize and resolve TOP-DPCs. Eukaryotic cells harbor tyrosyl DNA phosphodiesterases (TDPs) that directly reverse 3'-phosphotyrosyl (TDP1) and 5'-phoshotyrosyl (TDP2) protein-DNA linkages. The broad specificity Mre11-Rad50-Nbs1 and APE2 nucleases are also critical for mitigating topoisomerase-generated DNA damage. These DNA-protein crosslink metabolizing enzymes are further enabled by proteolytic degradation, with the proteasome, Spartan, GCNA, Ddi2, and FAM111A proteases implicated thus far. Strategies to target, unfold, and degrade the protein component of TOP-DPCs have evolved as well. Here we survey mechanisms for addressing Topoisomerase 1 (TOP1) and Topoisomerase 2 (TOP2) DPCs, highlighting systems for which molecular structure information has illuminated function of these critical DNA damage response pathways.
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Affiliation(s)
- Jessica L Wojtaszek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, United States.
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4
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Adolf F, Du J, Goodall EA, Walsh RM, Rawson S, von Gronau S, Harper JW, Hanna J, Schulman BA. Visualizing chaperone-mediated multistep assembly of the human 20S proteasome. Nat Struct Mol Biol 2024; 31:1176-1188. [PMID: 38600324 PMCID: PMC11327110 DOI: 10.1038/s41594-024-01268-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Dedicated assembly factors orchestrate the stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here we report cryo-electron microscopy reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, as well as how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors and reveals conceptual principles underlying human proteasome biogenesis, thus providing an explanation for many previous biochemical and genetic observations.
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Affiliation(s)
- Frank Adolf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ellen A Goodall
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Richard M Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Wade Harper
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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5
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Zhou X, Xu R, Wu Y, Zhou L, Xiang T. The role of proteasomes in tumorigenesis. Genes Dis 2024; 11:101070. [PMID: 38523673 PMCID: PMC10958230 DOI: 10.1016/j.gendis.2023.06.037] [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: 02/22/2023] [Revised: 05/10/2023] [Accepted: 06/27/2023] [Indexed: 03/26/2024] Open
Abstract
Protein homeostasis is the basis of normal life activities, and the proteasome family plays an extremely important function in this process. The proteasome 20S is a concentric circle structure with two α rings and two β rings overlapped. The proteasome 20S can perform both ATP-dependent and non-ATP-dependent ubiquitination proteasome degradation by binding to various subunits (such as 19S, 11S, and 200 PA), which is performed by its active subunit β1, β2, and β5. The proteasome can degrade misfolded, excess proteins to maintain homeostasis. At the same time, it can be utilized by tumors to degrade over-proliferate and unwanted proteins to support their growth. Proteasomes can affect the development of tumors from several aspects including tumor signaling pathways such as NF-κB and p53, cell cycle, immune regulation, and drug resistance. Proteasome-encoding genes have been found to be overexpressed in a variety of tumors, providing a potential novel target for cancer therapy. In addition, proteasome inhibitors such as bortezomib, carfilzomib, and ixazomib have been put into clinical application as the first-line treatment of multiple myeloma. More and more studies have shown that it also has different therapeutic effects in other tumors such as hepatocellular carcinoma, non-small cell lung cancer, glioblastoma, and neuroblastoma. However, proteasome inhibitors are not much effective due to their tolerance and singleness in other tumors. Therefore, further studies on their mechanisms of action and drug interactions are needed to investigate their therapeutic potential.
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Affiliation(s)
- Xiangyi Zhou
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Ruqing Xu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yue Wu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Zhou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Tingxiu Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
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6
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Ott C. Mapping the interplay of immunoproteasome and autophagy in different heart failure phenotypes. Free Radic Biol Med 2024; 218:149-165. [PMID: 38570171 DOI: 10.1016/j.freeradbiomed.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/25/2024] [Accepted: 03/30/2024] [Indexed: 04/05/2024]
Abstract
Proper protein degradation is required for cellular protein homeostasis and organ function. Particularly, in post-mitotic cells, such as cardiomyocytes, unbalanced proteolysis due to inflammatory stimuli and oxidative stress contributes to organ dysfunction. To ensure appropriate protein turnover, eukaryotic cells exert two main degradation systems, the ubiquitin-proteasome-system and the autophagy-lysosome-pathway. It has been shown that proteasome activity affects the development of cardiac dysfunction differently, depending on the type of heart failure. Studies analyzing the inducible subtype of the proteasome, the immunoproteasome (i20S), demonstrated that the i20S plays a double role in diseased hearts. While i20S subunits are increased in cardiac hypertrophy, atrial fibrillation and partly in myocarditis, the opposite applies to diabetic cardiomyopathy and ischemia/reperfusion injury. In addition, the i20S appears to play a role in autophagy modulation depending on heart failure phenotype. This review summarizes the current literature on the i20S in different heart failure phenotypes, emphasizing the two faces of i20S in injured hearts. A selection of established i20S inhibitors is introduced and signaling pathways linking the i20S to autophagy are highlighted. Mapping the interplay of the i20S and autophagy in different types of heart failure offers potential approaches for developing treatment strategies against heart failure.
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Affiliation(s)
- Christiane Ott
- German Institute of Human Nutrition Potsdam-Rehbruecke, Department of Molecular Toxicology, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.
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7
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Cekała K, Trepczyk K, Witkowska J, Jankowska E, Wieczerzak E. Rpt5-Derived Analogs Stimulate Human Proteasome Activity in Cells and Degrade Proteins Forming Toxic Aggregates in Age-Related Diseases. Int J Mol Sci 2024; 25:4663. [PMID: 38731881 PMCID: PMC11082943 DOI: 10.3390/ijms25094663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Aging and age-related diseases are associated with a decline in the capacity of protein turnover. Intrinsically disordered proteins, as well as proteins misfolded and oxidatively damaged, prone to aggregation, are preferentially digested by the ubiquitin-independent proteasome system (UIPS), a major component of which is the 20S proteasome. Therefore, boosting 20S activity constitutes a promising strategy to counteract a decrease in total proteasome activity during aging. One way to enhance the proteolytic removal of unwanted proteins appears to be the use of peptide-based activators of the 20S. In this study, we synthesized a series of peptides and peptidomimetics based on the C-terminus of the Rpt5 subunit of the 19S regulatory particle. Some of them efficiently stimulated human 20S proteasome activity. The attachment of the cell-penetrating peptide TAT allowed them to penetrate the cell membrane and stimulate proteasome activity in HEK293T cells, which was demonstrated using a cell-permeable substrate of the proteasome, TAS3. Furthermore, the best activator enhanced the degradation of aggregation-prone α-synuclein and Tau-441. The obtained compounds may therefore have the potential to compensate for the unbalanced proteostasis found in aging and age-related diseases.
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Affiliation(s)
| | | | | | - Elżbieta Jankowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (K.C.)
| | - Ewa Wieczerzak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (K.C.)
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8
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Wang J, Kjellgren A, DeMartino GN. Differential Interactions of the Proteasome Inhibitor PI31 with Constitutive and Immuno-20S Proteasomes. Biochemistry 2024; 63:1000-1015. [PMID: 38577872 DOI: 10.1021/acs.biochem.3c00707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
PI31 (Proteasome Inhibitor of 31,000 Da) is a 20S proteasome binding protein originally identified as an in vitro inhibitor of 20S proteasome proteolytic activity. Recently reported cryo-electron microscopy structures of 20S-PI31 complexes have revealed that the natively disordered proline-rich C-terminus of PI31 enters the central chamber in the interior of the 20S proteasome and interacts directly with the proteasome's multiple catalytic threonine residues in a manner predicted to inhibit their enzymatic function while evading its own proteolysis. Higher eukaryotes express an alternative form of the 20S proteasome (termed "immuno-proteasome") that features genetically and functionally distinct catalytic subunits. The effect of PI31 on immuno-proteasome function is unknown. We examine the relative inhibitory effects of PI31 on purified constitutive (20Sc) and immuno-(20Si) 20S proteasomes in vitro and show that PI31 inhibits 20Si hydrolytic activity to a significantly lesser degree than that of 20Sc. Unlike 20Sc, 20Si hydrolyzes the carboxyl-terminus of PI31 and this effect contributes to the reduced inhibitory activity of PI31 toward 20Si. Conversely, loss of 20Sc inhibition by PI31 point mutants leads to PI31 degradation by 20Sc. These results demonstrate unexpected differential interactions of PI31 with 20Sc and 20Si and document their functional consequences.
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Affiliation(s)
- Jason Wang
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
| | - Abbey Kjellgren
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
| | - George N DeMartino
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
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9
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Adolf F, Du J, Goodall EA, Walsh RM, Rawson S, von Gronau S, Harper JW, Hanna J, Schulman BA. Visualizing chaperone-mediated multistep assembly of the human 20S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.27.577538. [PMID: 38328185 PMCID: PMC10849659 DOI: 10.1101/2024.01.27.577538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Dedicated assembly factors orchestrate stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here, we report cryo-EM reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, and how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates, and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. The structural findings reported here explain many previous biochemical and genetic observations. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors, and reveals conceptual principles underlying human proteasome biogenesis.
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Affiliation(s)
- Frank Adolf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Ellen A. Goodall
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard M. Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J. Wade Harper
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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10
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He T, Wen C, Yang G, Yang X. Targeted Protein Degradation: Principles, Strategies, and Applications. Adv Biol (Weinh) 2023; 7:e2300083. [PMID: 37518856 DOI: 10.1002/adbi.202300083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/11/2023] [Indexed: 08/01/2023]
Abstract
Protein degradation is a general process to maintain cell homeostasis. The intracellular protein quality control system mainly includes the ubiquitin-proteasome system and the lysosome pathway. Inspired by the physiological process, strategies to degrade specific proteins have developed, which emerge as potent and effective tools in biological research and drug discovery. This review focuses on recent advances in targeted protein degradation techniques, summarizing the principles, advantages, and challenges. Moreover, the potential applications and future direction in biological science and clinics are also discussed.
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Affiliation(s)
- Ting He
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Chenxi Wen
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Guodong Yang
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Xuekang Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
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11
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Thomas T, Salcedo-Tacuma D, Smith DM. Structure, Function, and Allosteric Regulation of the 20S Proteasome by the 11S/PA28 Family of Proteasome Activators. Biomolecules 2023; 13:1326. [PMID: 37759726 PMCID: PMC10526260 DOI: 10.3390/biom13091326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
The proteasome, a complex multi-catalytic protease machinery, orchestrates the protein degradation essential for maintaining cellular homeostasis, and its dysregulation also underlies many different types of diseases. Its function is regulated by many different mechanisms that encompass various factors such as proteasome activators (PAs), adaptor proteins, and post-translational modifications. This review highlights the unique characteristics of proteasomal regulation through the lens of a distinct family of regulators, the 11S, REGs, or PA26/PA28. This ATP-independent family, spanning from amoebas to mammals, exhibits a common architectural structure; yet, their cellular biology and criteria for protein degradation remain mostly elusive. We delve into their evolution and cellular biology, and contrast their structure and function comprehensively, emphasizing the unanswered questions regarding their regulatory mechanisms and broader roles in proteostasis. A deeper understanding of these processes will illuminate the roles of this regulatory family in biology and disease, thus contributing to the advancement of therapeutic strategies.
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Affiliation(s)
- Taylor Thomas
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Drive, Morgantown, WV 26506, USA
| | - David Salcedo-Tacuma
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Drive, Morgantown, WV 26506, USA
| | - David M. Smith
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, 64 Medical Center Drive, Morgantown, WV 26506, USA
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV 26506, USA
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12
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Chuah JJY, Rexroad MS, Smith DM. High resolution structures define divergent and convergent mechanisms of archaeal proteasome activation. Commun Biol 2023; 6:733. [PMID: 37454196 PMCID: PMC10349882 DOI: 10.1038/s42003-023-05123-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Considering the link between neurodegenerative diseases and impaired proteasome function, and the neuro-protective impact of enhanced proteasome activity in animal models, it's crucial to understand proteasome activation mechanisms. A hydrophobic-tyrosine-any residue (HbYX) motif on the C-termini of proteasome-activating complexes independently triggers gate-opening of the 20S core particle for protein degradation; however, the causal allosteric mechanism remains unclear. Our study employs a structurally irreducible dipeptide HbYX mimetic to investigate the allosteric mechanism of gate-opening in the archaeal proteasome. High-resolution cryo-EM structures pinpoint vital residues and conformational changes in the proteasome α-subunit implicated in HbYX-dependent activation. Using point mutations, we simulated the HbYX-bound state, providing support for our mechanistic model. We discerned four main mechanistic elements triggering gate-opening: 1) back-loop rearrangement adjacent to K66, 2) intra- and inter- α subunit conformational changes, 3) occupancy of the hydrophobic pocket, and 4) a highly conserved isoleucine-threonine pair in the 20S channel stabilizing the open and closed states, termed the "IT switch." Comparison of different complexes unveiled convergent and divergent mechanism of 20S gate-opening among HbYX-dependent and independent activators. This study delivers a detailed molecular model for HbYX-dependent 20S gate-opening, enabling the development of small molecule proteasome activators that hold promise to treat neurodegenerative diseases.
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Affiliation(s)
- Janelle J Y Chuah
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV, USA
| | - Matthew S Rexroad
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV, USA
| | - David M Smith
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV, USA.
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, USA.
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13
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Chuah JJY, Thibaudeau TA, Smith DM. Minimal mechanistic component of HbYX-dependent proteasome activation that reverses impairment by neurodegenerative-associated oligomers. Commun Biol 2023; 6:725. [PMID: 37452144 PMCID: PMC10349142 DOI: 10.1038/s42003-023-05082-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023] Open
Abstract
The implication of reduced proteasomal function in neurodegenerative diseases combined with studies showing the protective effects of increasing proteasome activity in animal models highlight the need to understand the capacity for proteasome activation by small molecules. The C-terminal HbYX motif is present on many proteasome binding proteins and functions to tether activators to the 20S core particle. Previous studies have shown that peptides with a HbYX motif can autonomously activate 20S gate-opening to allow protein degradation. In this study, through an iterative process of peptide synthesis, we design a HbYX-like dipeptide mimetic that represents only the fundamental components of the HbYX motif. The mimetic robustly induces gate-opening in archaeal, yeast, and mammalian proteasomes. We identify multiple proteasome α subunit residues in the archaeal proteasome involved in HbYX-dependent activation. When stimulated by the mimetic, the mammalian 20S can degrade unfolded proteins such as tau. Findings using our peptide mimetic suggest the HbYX-dependent mechanism requires cooperative binding in at least two intersubunit pockets of the α ring. Most significantly, our peptide mimetic reverses proteasome impairment by neurodegenerative disease-associated oligomers. Collectively, these results validate HbYX-like molecules as having robust potential to stimulate proteasome function, which are potentially useful for treating neurodegenerative diseases.
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Affiliation(s)
- Janelle J Y Chuah
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV, USA
| | - Tiffany A Thibaudeau
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV, USA
| | - David M Smith
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV, USA.
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, USA.
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14
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Hsu HC, Wang J, Kjellgren A, Li H, DeMartino GN. Ηigh-resolution structure of mammalian PI31-20S proteasome complex reveals mechanism of proteasome inhibition. J Biol Chem 2023; 299:104862. [PMID: 37236357 PMCID: PMC10319324 DOI: 10.1016/j.jbc.2023.104862] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/08/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Proteasome-catalyzed protein degradation mediates and regulates critical aspects of many cellular functions and is an important element of proteostasis in health and disease. Proteasome function is determined in part by the types of proteasome holoenzymes formed between the 20S core particle that catalyzes peptide bond hydrolysis and any of multiple regulatory proteins to which it binds. One of these regulators, PI31, was previously identified as an in vitro 20S proteasome inhibitor, but neither the molecular mechanism nor the possible physiologic significance of PI31-mediated proteasome inhibition has been clear. Here we report a high-resolution cryo-EM structure of the mammalian 20S proteasome in complex with PI31. The structure shows that two copies of the intrinsically disordered carboxyl terminus of PI31 are present in the central cavity of the closed-gate conformation of the proteasome and interact with proteasome catalytic sites in a manner that blocks proteolysis of substrates but resists their own degradation. The two inhibitory polypeptide chains appear to originate from PI31 monomers that enter the catalytic chamber from opposite ends of the 20S cylinder. We present evidence that PI31 can inhibit proteasome activity in mammalian cells and may serve regulatory functions for the control of cellular proteostasis.
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Affiliation(s)
- Hao-Chi Hsu
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Jason Wang
- Department of Physiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Abbey Kjellgren
- Department of Physiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
| | - George N DeMartino
- Department of Physiology, UT Southwestern Medical Center, Dallas, Texas, USA.
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15
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Boon L, Belmondo T, Vulsteke JB, Wuyts G, Derua R, Hüe S, Bossuyt X. Anti-Ki/anti-PA28γ autoantibodies contribute to the HEp-2 indirect immunofluorescence nuclear speckled pattern. Clin Chem Lab Med 2023; 61:435-441. [PMID: 36445291 DOI: 10.1515/cclm-2022-0858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/16/2022] [Indexed: 12/02/2022]
Abstract
OBJECTIVES Antinuclear antibodies (ANAs) are associated with several autoimmune diseases. Indirect immunofluorescence (IIF) on human epithelial type 2 (HEp-2) cells is the golden standard for ANA detection in the clinic. In case of a positive HEp-2 IIF test result, follow-up tests are done to determine autoantibody specificity. For a fraction of the HEp-2 IIF-positive samples, the nature of the autoantigens remains uncharacterized. Our objective was to characterize autoantigens in such samples. METHODS To characterize autoantigens in an unbiased way, we combined protein immunoprecipitation with liquid chromatography (LC) tandem mass spectrometry (MS/MS) sequencing. RESULTS Using such approach we detected the Ki antigen, also referred to as PA28γ, in the immunoprecipitate of serum samples of three individuals with an autoimmune disease. The HEp-2 nuclear speckled IIF fluorescent signal of all three serum samples was abolished after pre-absorption of the serum with recombinant Ki antigen, confirming that autoantibodies against Ki underlie the HEp-2 IIF signal. CONCLUSIONS Our data suggest that anti-Ki autoantibodies can underlie a nuclear speckled HEp-2 IIF pattern.
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Affiliation(s)
- Lise Boon
- Clinical and Diagnostic Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Thibaut Belmondo
- Department of Laboratory Medicine, Henri Mondor Hospital, Créteil, France
| | - Jean-Baptiste Vulsteke
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Division of Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Greet Wuyts
- Clinical and Diagnostic Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Rita Derua
- Laboratory of Protein Phosphorylation and Proteomics, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sophie Hüe
- Department of Laboratory Medicine, Henri Mondor Hospital, Créteil, France
| | - Xavier Bossuyt
- Clinical and Diagnostic Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.,Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
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16
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Suzuki Y, Lutshumba J, Chen KC, Abdelaziz MH, Sa Q, Ochiai E. IFN-γ production by brain-resident cells activates cerebral mRNA expression of a wide spectrum of molecules critical for both innate and T cell-mediated protective immunity to control reactivation of chronic infection with Toxoplasma gondii. Front Cell Infect Microbiol 2023; 13:1110508. [PMID: 36875520 PMCID: PMC9975934 DOI: 10.3389/fcimb.2023.1110508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
We previously demonstrated that brain-resident cells produce IFN-γ in response to reactivation of cerebral infection with Toxoplasma gondii. To obtain an overall landscape view of the effects of IFN-γ from brain-resident cells on the cerebral protective immunity, in the present study we employed NanoString nCounter assay and quantified mRNA levels for 734 genes in myeloid immunity in the brains of T and B cell-deficient, bone marrow chimeric mice with and without IFN-γ production by brain-resident cells in response to reactivation of cerebral T. gondii infection. Our study revealed that IFN-γ produced by brain-resident cells amplified mRNA expression for the molecules to activate the protective innate immunity including 1) chemokines for recruitment of microglia and macrophages (CCL8 and CXCL12) and 2) the molecules for activating those phagocytes (IL-18, TLRs, NOD1, and CD40) for killing tachyzoites. Importantly, IFN-γ produced by brain-resident cells also upregulated cerebral expression of molecules for facilitating the protective T cell immunity, which include the molecules for 1) recruiting effector T cells (CXCL9, CXCL10, and CXCL11), 2) antigen processing (PA28αβ, LMP2, and LMP7), transporting the processed peptides (TAP1 and TAP2), assembling the transported peptides to the MHC class I molecules (Tapasin), and the MHC class I (H2-K1 and H2-D1) and Ib molecules (H2-Q1, H-2Q2, and H2-M3) for presenting antigens to activate the recruited CD8+ T cells, 3) MHC class II molecules (H2-Aa, H2-Ab1, H2-Eb1, H2-Ea-ps, H2-DMa, H2-Ob, and CD74) to present antigens for CD4+ T cell activation, 4) co-stimulatory molecules (ICOSL) for T cell activation, and 5) cytokines (IL-12, IL-15, and IL-18) facilitating IFN-γ production by NK and T cells. Notably, the present study also revealed that IFN-γ production by brain-resident cells also upregulates cerebral expressions of mRNA for the downregulatory molecules (IL-10, STAT3, SOCS1, CD274 [PD-L1], IL-27, and CD36), which can prevent overly stimulated IFN-γ-mediated pro-inflammatory responses and tissue damages. Thus, the present study uncovered the previously unrecognized the capability of IFN-γ production by brain-resident cells to upregulate expressions of a wide spectrum of molecules for coordinating both innate and T cell-mediated protective immunity with a fine-tuning regulation system to effectively control cerebral infection with T. gondii.
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Affiliation(s)
- Yasuhiro Suzuki
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, United States
- *Correspondence: Yasuhiro Suzuki,
| | - Jenny Lutshumba
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Kuey Chu Chen
- Department of Pharmacology and Nutritional Science, University of Kentucky College of Medicine, Lexington, KY, United States
- Genomics Core Laboratory, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Mohamed H. Abdelaziz
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Qila Sa
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Eri Ochiai
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, United States
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17
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Thomas TA, Smith DM. Proteasome activator 28γ (PA28γ) allosterically activates trypsin-like proteolysis by binding to the α-ring of the 20S proteasome. J Biol Chem 2022; 298:102140. [PMID: 35714770 PMCID: PMC9287138 DOI: 10.1016/j.jbc.2022.102140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Proteasome activator 28γ (PA28γ/REGγ) is a member of the 11S family of proteasomal regulators that is constitutively expressed in the nucleus and implicated in various diseases, including certain cancers and systemic lupus erythematosus. Despite years of investigation, how PA28γ functions to stimulate proteasomal protein degradation remains unclear. Alternative hypotheses have been proposed for the molecular mechanism of PA28γ, including the following: (1) substrate selection, (2) allosteric upregulation of the trypsin-like (T-L) site, (3) allosteric inhibition of the chymotrypsin-like (CT-L) and caspase-like (C-L) sites, (4) conversion of the CT-L or C-L sites to new T-L sites, and (5) gate opening alone or in combination with a previous hypothesis. Here, by mechanistically decoupling gating effects from active site effects, we unambiguously demonstrate that WT PA28γ allosterically activates the T-L site. We show PA28γ binding increases the Kcat/Km by 13-fold for T-L peptide substrates while having little-to-no effect on hydrolysis kinetics for CT-L or C-L substrates. Furthermore, mutagenesis and domain swaps of PA28γ reveal that it does not select for T-L peptide substrates through either the substrate entry pore or the distal intrinsically disordered region. We also show that a previously reported point mutation can functionally switch PA28γ from a T-L activating to a gate-opening activator in a mutually exclusive fashion. Finally, using cryogenic electron microscopy, we visualized the PA28γ-proteasome complex at 4.3 Å and confirmed its expected quaternary structure. The results of this study provide unambiguous evidence that PA28γ can function by binding the 20S proteasome to allosterically activate the T-L proteolytic site.
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Affiliation(s)
- Taylor A Thomas
- Department of Biochemistry, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, USA
| | - David M Smith
- Department of Biochemistry, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, USA; Department of Neuroscience, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, USA; WVU Rockefeller Neuroscience Institute, Morgantown, West Virginia, USA; WVU Cancer Institute, Morgantown, West Virginia, USA.
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18
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Cekała K, Trepczyk K, Sowik D, Karpowicz P, Giełdoń A, Witkowska J, Giżyńska M, Jankowska E, Wieczerzak E. Peptidomimetics Based on C-Terminus of Blm10 Stimulate Human 20S Proteasome Activity and Promote Degradation of Proteins. Biomolecules 2022; 12:biom12060777. [PMID: 35740902 PMCID: PMC9221443 DOI: 10.3390/biom12060777] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/15/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Degradation of misfolded, redundant and oxidatively damaged proteins constitutes one of the cellular processes which are influenced by the 20S proteasome. However, its activity is generally thought to decrease with age which leads to the gradual accumulation of abnormal proteins in cells and their subsequent aggregation. Therefore, increasing proteasomal degradation constitutes a promising strategy to delay the onset of various age-related diseases, including neurodegenerative disorders. In this study we designed and obtained a series of peptidomimetic stimulators of 20S comprising in their sequences the C-terminal fragment of Blm10 activator. Some of the compounds were capable of enhancing the degradation of natively unfolded and oxidatively damaged proteins, such as α-synuclein and enolase, whose applicability as proteasome substrates was evaluated by microscale thermophoresis (MST). Furthermore, they increased the ChT-L activity of the proteasome in HEK293T cell extracts. Our studies indicate that the 20S proteasome-mediated protein substrates hydrolysis may be selectively increased by peptide-based stimulators acting in an allosteric manner. These compounds, after further optimization, may have the potential to counteract proteasome impairment in patients suffering from age-related diseases.
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19
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Modulation of the 20S Proteasome Activity by Porphyrin Derivatives Is Steered through Their Charge Distribution. Biomolecules 2022; 12:biom12060741. [PMID: 35740865 PMCID: PMC9220251 DOI: 10.3390/biom12060741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/15/2022] [Accepted: 05/20/2022] [Indexed: 11/20/2022] Open
Abstract
Cationic porphyrins exhibit an amazing variety of binding modes and inhibition mechanisms of 20S proteasome. Depending on the spatial distribution of their electrostatic charges, they can occupy different sites on α rings of 20S proteasome by exploiting the structural code responsible for the interaction with regulatory proteins. Indeed, they can act as competitive or allosteric inhibitors by binding at the substrate gate or at the grooves between the α subunits, respectively. Moreover, the substitution of a charged moiety in the peripheral arm with a hydrophobic moiety revealed a “new” 20S functional state with higher substrate affinity and catalytic efficiency. In the present study, we expand our structure–activity relationship (SAR) analysis in order to further explore the potential of this versatile class of 20S modulators. Therefore, we have extended the study to additional macrocyclic compounds, displaying different structural features, comparing their interaction behavior on the 20S proteasome with previously investigated compounds. In particular, in order to evaluate how the introduction of a peptidic chain can affect the affinity and the interacting mechanism of porphyrins, we investigate the MTPyApi, a porphyrin derivatized with an Arg–Pro-rich antimicrobial peptide. Moreover, to unveil the role played by the porphyrin core, this was replaced with a corrole scaffold, a “contracted” version of the tetrapyrrolic ring due to the lack of a methine bridge. The analysis has been undertaken by means of integrated kinetic, Nuclear Magnetic Resonance, and computational studies. Finally, in order to assess a potential pharmacological significance of this type of investigation, a preliminary attempt has been performed to evaluate the biological effect of these molecules on MCF7 breast cancer cells in dark conditions, envisaging that porphyrins may indeed represent a powerful tool for the modulation of cellular proteostasis.
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20
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Serrano-Aparicio N, Ferrer S, Świderek K. Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies. Pharmaceuticals (Basel) 2022; 15:ph15050531. [PMID: 35631358 PMCID: PMC9143130 DOI: 10.3390/ph15050531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
20S proteasome is a main player in the protein degradation pathway in the cytosol, thus intervening in multiple pivotal cellular processes. Over the years the proteasome has emerged as a crucial target for the treatment of many diseases such as neurodegenerative diseases, cancer, autoimmune diseases, developmental disorders, cystic fibrosis, diabetes, cardiac diseases, atherosclerosis, and aging. In this work, the mechanism of proteasome covalent inhibition with bisbenzyl-protected homobelactosin C (hBelC) was explored using quantum mechanics/molecular mechanics (QM/MM) methods. Molecular dynamic simulations were used to describe key interactions established between the hBelC and its unique binding mode in the primed site of the β5 subunit. The free energy surfaces were computed to characterize the kinetics and thermodynamics of the inhibition process. This study revealed that although the final inhibition product for hBelC is formed according to the same molecular mechanism as one described for hSalA, the free energy profile of the reaction pathway differs significantly from the one previously reported for γ-lactam-β-lactone containing inhibitors in terms of the height of the activation barrier as well as the stabilization of the final product. Moreover, it was proved that high stabilization of the covalent adduct formed between β5-subunit and hBelC, together with the presence of aminocarbonyl side chain in the structure of the inhibitor which prevents the hydrolysis of the ester bond from taking place, determines its irreversible character.
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21
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The YΦ motif defines the structure-activity relationships of human 20S proteasome activators. Nat Commun 2022; 13:1226. [PMID: 35264557 PMCID: PMC8907193 DOI: 10.1038/s41467-022-28864-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/11/2022] [Indexed: 11/08/2022] Open
Abstract
The 20S proteasome (20S) facilitates turnover of most eukaryotic proteins. Substrate entry into the 20S first requires opening of gating loops through binding of HbYX motifs that are present at the C-termini of certain proteasome activators (PAs). The HbYX motif has been predominantly characterized in the archaeal 20S, whereas little is known about the sequence preferences of the human 20S (h20S). Here, we synthesize and screen ~120 HbYX-like peptides, revealing unexpected differences from the archaeal system and defining the h20S recognition sequence as the Y-F/Y (YФ) motif. To gain further insight, we create a functional chimera of the optimized sequence, NLSYYT, fused to the model activator, PA26E102A. A cryo-EM structure of PA26E102A-h20S is used to identify key interactions, including non-canonical contacts and gate-opening mechanisms. Finally, we demonstrate that the YФ sequence preferences are tuned by valency, allowing multivalent PAs to sample greater sequence space. These results expand the model for termini-mediated gating and provide a template for the design of h20S activators. The proteasome complexes, composed of 20S core particles and one or two regulatory particles (proteasome activators), degrade most eukaryotic proteins. Here, the authors identify a sequence motif and resolve its interactions mediating the activation of the human 20S proteasome.
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22
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Hung KYS, Klumpe S, Eisele MR, Elsasser S, Tian G, Sun S, Moroco JA, Cheng TC, Joshi T, Seibel T, Van Dalen D, Feng XH, Lu Y, Ovaa H, Engen JR, Lee BH, Rudack T, Sakata E, Finley D. Allosteric control of Ubp6 and the proteasome via a bidirectional switch. Nat Commun 2022; 13:838. [PMID: 35149681 PMCID: PMC8837689 DOI: 10.1038/s41467-022-28186-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022] Open
Abstract
The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome.
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Affiliation(s)
| | - Sven Klumpe
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Markus R Eisele
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Suzanne Elsasser
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Shuangwu Sun
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Life Sciences Institute (LSI), Zhejiang University, Hangzhou, 310058, China
| | - Jamie A Moroco
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Tat Cheung Cheng
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Institute for Auditory Neuroscience, University Medical Center Göttingen, 37077, Göttingen, Germany
| | - Tapan Joshi
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Timo Seibel
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Duco Van Dalen
- Leiden University Medical Center, Einthovenweg 20, 2333, Leiden, ZC, the Netherlands
| | - Xin-Hua Feng
- Life Sciences Institute (LSI), Zhejiang University, Hangzhou, 310058, China
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Huib Ovaa
- Leiden University Medical Center, Einthovenweg 20, 2333, Leiden, ZC, the Netherlands
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | - Byung-Hoon Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea.
| | - Till Rudack
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, 44801, Bochum, Germany. .,Department of Biophysics, Ruhr University Bochum, 44801, Bochum, Germany.
| | - Eri Sakata
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany. .,Institute for Auditory Neuroscience, University Medical Center Göttingen, 37077, Göttingen, Germany. .,Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Goettingen, 37073, Göttingen, Germany.
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
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23
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Frayssinhes JYA, Cerruti F, Laulin J, Cattaneo A, Bachi A, Apcher S, Coux O, Cascio P. PA28γ-20S proteasome is a proteolytic complex committed to degrade unfolded proteins. Cell Mol Life Sci 2021; 79:45. [PMID: 34913092 PMCID: PMC11071804 DOI: 10.1007/s00018-021-04045-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023]
Abstract
PA28γ is a nuclear activator of the 20S proteasome that, unlike the 19S regulatory particle, stimulates hydrolysis of several substrates in an ATP- and ubiquitin-independent manner and whose exact biological functions and molecular mechanism of action still remain elusive. In an effort to shed light on these important issues, we investigated the stimulatory effect of PA28γ on the hydrolysis of different fluorogenic peptides and folded or denatured full-length proteins by the 20S proteasome. Importantly, PA28γ was found to dramatically enhance breakdown rates by 20S proteasomes of several naturally or artificially unstructured proteins, but not of their native, folded counterparts. Furthermore, these data were corroborated by experiments in cell lines with a nucleus-tagged myelin basic protein. Finally, mass spectrometry analysis of the products generated during proteasomal degradation of two proteins demonstrated that PA28γ does not increase, but rather decreases, the variability of peptides that are potentially suitable for MHC class I antigen presentation. These unexpected findings indicate that global stimulation of the degradation of unfolded proteins may represent a more general feature of PA28γ and suggests that this proteasomal activator might play a broader role in the pathway of protein degradation than previously believed.
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Affiliation(s)
| | - Fulvia Cerruti
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Justine Laulin
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie Des Tumeurs et Immunothérapie, Villejuif, France
| | | | - Angela Bachi
- The FIRC Institute of Molecular Oncology (IFOM), 20139, Milan, Italy
| | - Sebastien Apcher
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie Des Tumeurs et Immunothérapie, Villejuif, France
| | - Olivier Coux
- Centre de Recherche de Biologie Cellulaire de Montpellier (CRBM), CNRS UMR 5237, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy.
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24
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Reboud-Ravaux M. [The proteasome - structural aspects and inhibitors: a second life for a validated drug target]. Biol Aujourdhui 2021; 215:1-23. [PMID: 34397372 DOI: 10.1051/jbio/2021005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 02/06/2023]
Abstract
The proteasome is the central component of the adaptable ubiquitin proteasome system (UPS) discovered in the 1980's. It sustains protein homeostasis (proteostasis) under a large variety of physiological and pathological conditions. Its dysregulation has been often associated to various human diseases. Its potential regulation by modulators has emerged as promising avenue to develop treatments of various pathologies. The FDA approval in 2003 of the proteasome inhibitor bortezomib to treat multiple myeloma, then mantle lymphoma in 2006, has considerably increased the clinical interest of proteasome inhibition. Second-generation proteasome inhibitors (carfilzomib and ixazomib) have been approved to overcome bortezomib resistance and improved toxicity profile and route of administration. Selective inhibition of immunoproteasome is a promising approach towards the development of immunomodulatory drugs. The design of these drugs relies greatly on the elucidation of high-resolution structures of the targeted proteasomes. The ATPase-dependent 26S proteasome (2.4 MDa) consists of a 20S proteolytic core and one or two 19S regulatory particles. The 20S core contains three types of catalytic sites. In recent years, due to technical advances especially in atomic cryo-electron microscopy, significant progress has been made in the understanding of 26S proteasome structure and its dynamics. Stepwise conformational changes of the 19S particle induced by ATP hydrolysis lead to substrate translocation, 20S pore opening and processive protein degradation by the 20S proteolytic subunits (2β1, 2β2 and 2β5). A large variety of structurally different inhibitors, both natural products or synthetic compounds targeting immuno- and constitutive proteasomes, has been discovered. The latest advances in this drug discovery are presented. Knowledge about structures, inhibition mechanism and detailed biological regulations of proteasomes can guide strategies for the development of next-generation inhibitors to treat human diseases, especially cancers, immune disorders and pathogen infections. Proteasome activators are also potentially applicable to the reduction of proteotoxic stresses in neurodegeneration and aging.
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Affiliation(s)
- Michèle Reboud-Ravaux
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
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25
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Domnauer M, Zheng F, Li L, Zhang Y, Chang CE, Unruh JR, Conkright-Fincham J, McCroskey S, Florens L, Zhang Y, Seidel C, Fong B, Schilling B, Sharma R, Ramanathan A, Si K, Zhou C. Proteome plasticity in response to persistent environmental change. Mol Cell 2021; 81:3294-3309.e12. [PMID: 34293321 DOI: 10.1016/j.molcel.2021.06.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/28/2021] [Accepted: 06/22/2021] [Indexed: 01/17/2023]
Abstract
Temperature is a variable component of the environment, and all organisms must deal with or adapt to temperature change. Acute temperature change activates cellular stress responses, resulting in refolding or removal of damaged proteins. However, how organisms adapt to long-term temperature change remains largely unexplored. Here we report that budding yeast responds to long-term high temperature challenge by switching from chaperone induction to reduction of temperature-sensitive proteins and re-localizing a portion of its proteome. Surprisingly, we also find that many proteins adopt an alternative conformation. Using Fet3p as an example, we find that the temperature-dependent conformational difference is accompanied by distinct thermostability, subcellular localization, and, importantly, cellular functions. We postulate that, in addition to the known mechanisms of adaptation, conformational plasticity allows some polypeptides to acquire new biophysical properties and functions when environmental change endures.
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Affiliation(s)
- Matthew Domnauer
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA
| | - Fan Zheng
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Liying Li
- UCSF, 1550 Fourth St, RH490 San Francisco, CA 94158, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Catherine E Chang
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | | | - Scott McCroskey
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Christopher Seidel
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Benjamin Fong
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA
| | - Rishi Sharma
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA
| | - Arvind Ramanathan
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; Institute for Stem Cell Science and Regenerative Medicine GKVK, Bengaluru, Karnataka 560065, India
| | - Kausik Si
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Chuankai Zhou
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA 94945, USA; USC Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave., Los Angeles, CA 90191, USA.
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T-Type Ca 2+ Enhancer SAK3 Activates CaMKII and Proteasome Activities in Lewy Body Dementia Mice Model. Int J Mol Sci 2021; 22:ijms22126185. [PMID: 34201181 PMCID: PMC8228122 DOI: 10.3390/ijms22126185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/28/2022] Open
Abstract
Lewy bodies are pathological characteristics of Lewy body dementia (LBD) and are composed of α-synuclein (α-Syn), which is mostly degraded via the ubiquitin–proteasome system. More importantly, 26S proteasomal activity decreases in the brain of LBD patients. We recently introduced a T-type calcium channel enhancer SAK3 (ethyl-8-methyl-2,4-dioxo-2-(piperidin-1-yl)- 2H-spiro[cyclopentane-1,3-imidazo [1,2-a]pyridin]-2-ene-3-carboxylate) for Alzheimer’s disease therapeutics. SAK3 enhanced the proteasome activity via CaMKII activation in amyloid precursor protein knock-in mice, promoting the degradation of amyloid-β plaques to improve cognition. At this point, we addressed whether SAK3 promotes the degradation of misfolded α-Syn and the aggregates in α-Syn preformed fibril (PFF)-injected mice. The mice were injected with α-Syn PFF in the dorsal striatum, and SAK3 (0.5 or 1.0 mg/kg) was administered orally for three months, either immediately or during the last month after injection. SAK3 significantly inhibited the accumulation of fibrilized phosphorylated-α-Syn in the substantia nigra. Accordingly, SAK3 significantly recovered mesencephalic dopamine neurons from cell death. Decreased α-Syn accumulation was closely associated with increased proteasome activity. Elevated CaMKII/Rpt-6 signaling possibly mediates the enhanced proteasome activity after SAK3 administration in the cortex and hippocampus. CaMKII/Rpt-6 activation also accounted for improved memory and cognition in α-Syn PFF-injected mice. These findings indicate that CaMKII/Rpt-6-dependent proteasomal activation by SAK3 recovers from α-Syn pathology in LBD.
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27
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Mendes ML, Dittmar G. Analysis of the Dynamic Proteasome Structure by Cross-Linking Mass Spectrometry. Biomolecules 2021; 11:biom11040505. [PMID: 33801594 PMCID: PMC8067131 DOI: 10.3390/biom11040505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
The 26S proteasome is a macromolecular complex that degrades proteins maintaining cell homeostasis; thus, determining its structure is a priority to understand its function. Although the 20S proteasome's structure has been known for some years, the highly dynamic nature of the 19S regulatory particle has presented a challenge to structural biologists. Advances in cryo-electron microscopy (cryo-EM) made it possible to determine the structure of the 19S regulatory particle and showed at least seven different conformational states of the proteasome. However, there are still many questions to be answered. Cross-linking mass spectrometry (CLMS) is now routinely used in integrative structural biology studies, and it promises to take integrative structural biology to the next level, answering some of these questions.
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Bijlmakers MJ. Ubiquitination and the Proteasome as Drug Targets in Trypanosomatid Diseases. Front Chem 2021; 8:630888. [PMID: 33732684 PMCID: PMC7958763 DOI: 10.3389/fchem.2020.630888] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/29/2020] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic pathogens Trypanosoma brucei, Trypanosoma cruzi and Leishmania are responsible for debilitating diseases that affect millions of people worldwide. The numbers of drugs available to treat these diseases, Human African Trypanosomiasis, Chagas' disease and Leishmaniasis are very limited and existing treatments have substantial shortcomings in delivery method, efficacy and safety. The identification and validation of novel drug targets opens up new opportunities for the discovery of therapeutic drugs with better efficacy and safety profiles. Here, the potential of targeting the ubiquitin-proteasome system in these parasites is reviewed. Ubiquitination is the posttranslational attachment of one or more ubiquitin proteins to substrates, an essential eukaryotic mechanism that regulates a wide variety of cellular processes in many different ways. The best studied of these is the delivery of ubiquitinated substrates for degradation to the proteasome, the major cellular protease. However, ubiquitination can also regulate substrates in proteasome-independent ways, and proteasomes can degrade proteins to some extent in ubiquitin-independent ways. Because of these widespread roles, both ubiquitination and proteasomal degradation are essential for the viability of eukaryotes and the proteins that mediate these processes are therefore attractive drug targets in trypanosomatids. Here, the current understanding of these processes in trypanosomatids is reviewed. Furthermore, significant recent progress in the development of trypanosomatid-selective proteasome inhibitors that cure mouse models of trypanosomatid infections is presented. In addition, the targeting of the key enzyme in ubiquitination, the ubiquitin E1 UBA1, is discussed as an alternative strategy. Important differences between human and trypanosomatid UBA1s in susceptibility to inhibitors predicts that the selective targeting of these enzymes in trypanosomatids may also be feasible. Finally, it is proposed that activating enzymes of the ubiquitin-like proteins SUMO and NEDD8 may represent drug targets in these trypanosomatids as well.
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29
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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30
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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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31
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Cryo-EM of mammalian PA28αβ-iCP immunoproteasome reveals a distinct mechanism of proteasome activation by PA28αβ. Nat Commun 2021; 12:739. [PMID: 33531497 PMCID: PMC7854634 DOI: 10.1038/s41467-021-21028-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
The proteasome activator PA28αβ affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αβ-iCP structure, how PA28αβ regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28αβ-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determine the spatial arrangement between PA28αβ and iCP through XL-MS. Our structures reveal a slight leaning of PA28αβ towards the α3-α4 side of iCP, disturbing the allosteric network of the gatekeeper α2/3/4 subunits, resulting in a partial open iCP gate. We find that the binding and activation mechanism of iCP by PA28αβ is distinct from those of constitutive CP by the homoheptameric TbPA26 or PfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28αβ-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response. The proteasome activator PA28αβ affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). Cryo-EM structures of the mammalian PA28αβ -iCP immunoproteasome and free iCP, combined with cross-linking data, reveal the complex architecture and suggest a distinct immunoproteasome activation mechanism.
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32
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Molecular and cellular dynamics of the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140583. [PMID: 33321258 DOI: 10.1016/j.bbapap.2020.140583] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/16/2023]
Abstract
In eukaryotic cells, the ubiquitin-proteasome system serves to remove proteins that are either dysfunctional or no longer needed. The 26S proteasome is a 2.5 MDa multisubunit complex comprising the 20S core particle, where degradation is executed, and one or two regulatory particles which prepare substrates for degradation. Whereas the 20S core particles of several species had been studied extensively by X-ray crystallography, the 26S holocomplex structure had remained elusive for a long time. Recent advances in single-particle cryo-electron microscopy have changed the situation and provided atomic resolution models of this intriguing molecular machine and its dynamics. Besides, cryo-electron tomography enables structural studies in situ, providing molecular resolution images of macromolecules inside pristinely preserved cellular environments. This has greatly contributed to our understanding of proteasome dynamics in the context of cells.
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Lesne J, Locard-Paulet M, Parra J, Zivković D, Menneteau T, Bousquet MP, Burlet-Schiltz O, Marcoux J. Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks. Nat Commun 2020; 11:6140. [PMID: 33262340 PMCID: PMC7708635 DOI: 10.1038/s41467-020-19934-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/06/2020] [Indexed: 01/17/2023] Open
Abstract
Hydrogen-Deuterium eXchange coupled to Mass Spectrometry (HDX-MS) is now common practice in structural biology. However, it is most of the time applied to rather small oligomeric complexes. Here, we report on the use of HDX-MS to investigate conformational differences between the human standard 20S (std20S) and immuno 20S (i20s) proteasomes alone or in complex with PA28αβ or PA28γ activators. Their solvent accessibility is analyzed through a dedicated bioinformatic pipeline including stringent statistical analysis and 3D visualization. These data confirm the existence of allosteric differences between the std20S and i20S at the surface of the α-ring triggered from inside the catalytic β-ring. Additionally, binding of the PA28 regulators to the 20S proteasomes modify solvent accessibility due to conformational changes of the β-rings. This work is not only a proof-of-concept that HDX-MS can be used to get structural insights on large multi-protein complexes in solution, it also demonstrates that the binding of the std20S or i20S subtype to any of its PA28 activator triggers allosteric changes that are specific to this 20S/PA28 pair.
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Affiliation(s)
- Jean Lesne
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- Centre de Biologie Structurale, CNRS, Université de Montpellier, INSERM, 34090, Montpellier, France
| | - Marie Locard-Paulet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Julien Parra
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Dušan Zivković
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Thomas Menneteau
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Marie-Pierre Bousquet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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34
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Santoro AM, D’Urso A, Cunsolo A, Milardi D, Purrello R, Sbardella D, Tundo GR, Diana D, Fattorusso R, Dato AD, Paladino A, Persico M, Coletta M, Fattorusso C. Cooperative Binding of the Cationic Porphyrin Tris-T4 Enhances Catalytic Activity of 20S Proteasome Unveiling a Complex Distribution of Functional States. Int J Mol Sci 2020; 21:ijms21197190. [PMID: 33003385 PMCID: PMC7582714 DOI: 10.3390/ijms21197190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/13/2020] [Accepted: 09/23/2020] [Indexed: 12/17/2022] Open
Abstract
The present study provides new evidence that cationic porphyrins may be considered as tunable platforms to interfere with the structural “key code” present on the 20S proteasome α-rings and, by consequence, with its catalytic activity. Here, we describe the functional and conformational effects on the 20S proteasome induced by the cooperative binding of the tri-cationic 5-(phenyl)-10,15,20-(tri N-methyl-4-pyridyl) porphyrin (Tris-T4). Our integrated kinetic, NMR, and in silico analysis allowed us to disclose a complex effect on the 20S catalytic activity depending on substrate/porphyrin concentration. The analysis of the kinetic data shows that Tris-T4 shifts the relative populations of the multiple interconverting 20S proteasome conformations leading to an increase in substrate hydrolysis by an allosteric pathway. Based on our Tris-T4/h20S interaction model, Tris-T4 is able to affect gating dynamics and substrate hydrolysis by binding to an array of negatively charged and hydrophobic residues present on the protein surface involved in the 20S molecular activation by the regulatory proteins (RPs). Accordingly, despite the fact that Tris-T4 also binds to the α3ΔN mutant, allosteric modulation is not observed since the molecular mechanism connecting gate dynamics with substrate hydrolysis is impaired. We envisage that the dynamic view of the 20S conformational equilibria, activated through cooperative Tris-T4 binding, may work as a simplified model for a better understanding of the intricate network of 20S conformational/functional states that may be mobilized by exogenous ligands, paving the way for the development of a new generation of proteasome allosteric modulators.
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Affiliation(s)
- Anna Maria Santoro
- Istituto di Cristallografia—CNR Sede Secondaria di Catania, Via P. Gaifami 9/18, 95126 Catania, Italy; (A.M.S.); (D.M.)
| | - Alessandro D’Urso
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
| | - Alessandra Cunsolo
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
- Department of Molecular Medicine, The University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78245, USA
| | - Danilo Milardi
- Istituto di Cristallografia—CNR Sede Secondaria di Catania, Via P. Gaifami 9/18, 95126 Catania, Italy; (A.M.S.); (D.M.)
| | - Roberto Purrello
- Dipartimento di Scienze Chimiche, Università Degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy; (A.D.); (A.C.); (R.P.)
| | - Diego Sbardella
- IRCCS-Fondazione Bietti, 00198 Rome, Italy; (D.S.); (G.R.T.)
| | - Grazia R. Tundo
- IRCCS-Fondazione Bietti, 00198 Rome, Italy; (D.S.); (G.R.T.)
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy;
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli” Via Vivaldi 43, 81100 Caserta, Italy;
| | - Antonio Di Dato
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
| | - Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via M. Bianco 9, 20131 Milano, Italy;
| | - Marco Persico
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
- Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, 80131 Napoli, Italy
| | - Massimo Coletta
- Dipartimento di Scienze Cliniche e Medicina Traslazionale, Università di Roma Tor Vergata, Via Montpellier 1, 00133 Roma, Italy
- Correspondence: (M.C.); (C.F.); Tel.: +39-06-72596365 (M.C.); +39-081-678544 (C.F.)
| | - Caterina Fattorusso
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy; (A.D.D.); (M.P.)
- Centro Interuniversitario di Ricerca sulla Malaria/Italian Malaria Network, 80131 Napoli, Italy
- Correspondence: (M.C.); (C.F.); Tel.: +39-06-72596365 (M.C.); +39-081-678544 (C.F.)
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35
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Boulpicante M, Darrigrand R, Pierson A, Salgues V, Rouillon M, Gaudineau B, Khaled M, Cattaneo A, Bachi A, Cascio P, Apcher S. Tumors escape immunosurveillance by overexpressing the proteasome activator PSME3. Oncoimmunology 2020; 9:1761205. [PMID: 32923122 PMCID: PMC7458623 DOI: 10.1080/2162402x.2020.1761205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/03/2020] [Indexed: 11/09/2022] Open
Abstract
The success of CD8+ T cell-based cancer immunotherapy emphasizes the importance of understanding the mechanisms of generation of MHC-I peptide ligands and the possible pathways of tumor cell escape from immunosurveillance. Recently, we showed that peptides generated in the nucleus during a pioneer round of mRNA translation (pioneer translation products, or PTPs) are an important source of tumor specific peptides which correlates with the aberrant splicing and transcription events associated with oncogenesis. Here we show that up-regulation of PSME3 proteasome activator in cancer cells results in increased destruction of PTP-derived peptides in the nucleus thus enabling cancer cell to subvert immunosurveillance. These findings unveil a previously unexpected role for PSME3 in antigen processing and identify PSME3 as a druggable target to improve the efficacy of cancer immunotherapy.
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Affiliation(s)
- Mathilde Boulpicante
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Romain Darrigrand
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Alison Pierson
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Valérie Salgues
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Marine Rouillon
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Benoit Gaudineau
- Dynamique des Cellules Tumorales, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Mehdi Khaled
- Dynamique des Cellules Tumorales, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
| | - Angela Cattaneo
- IFOM, The FIRC Institute of Molecular Oncology, Milano, Italy
| | - Angela Bachi
- IFOM, The FIRC Institute of Molecular Oncology, Milano, Italy
| | - Paolo Cascio
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco, Turin, Italy
| | - Sébastien Apcher
- Immunologie des Tumeurs et Immunothérapie, Université Paris-Saclay, Institut Gustave Roussy, Inserm, Villejuif, France
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36
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Osmulski PA, Karpowicz P, Jankowska E, Bohmann J, Pickering AM, Gaczyńska M. New Peptide-Based Pharmacophore Activates 20S Proteasome. Molecules 2020; 25:E1439. [PMID: 32235805 PMCID: PMC7145288 DOI: 10.3390/molecules25061439] [Citation(s) in RCA: 12] [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: 01/07/2020] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 02/01/2023] Open
Abstract
The proteasome is a pivotal element of controlled proteolysis, responsible for the catabolic arm of proteostasis. By inducing apoptosis, small molecule inhibitors of proteasome peptidolytic activities are successfully utilized in treatment of blood cancers. However, the clinical potential of proteasome activation remains relatively unexplored. In this work, we introduce short TAT peptides derived from HIV-1 Tat protein and modified with synthetic turn-stabilizing residues as proteasome agonists. Molecular docking and biochemical studies point to the α1/α2 pocket of the core proteasome α ring as the binding site of TAT peptides. We postulate that the TATs' pharmacophore consists of an N-terminal basic pocket-docking "activation anchor" connected via a β turn inducer to a C-terminal "specificity clamp" that binds on the proteasome α surface. By allosteric effects-including destabilization of the proteasomal gate-the compounds substantially augment activity of the core proteasome in vitro. Significantly, this activation is preserved in the lysates of cultured cells treated with the compounds. We propose that the proteasome-stimulating TAT pharmacophore provides an attractive lead for future clinical use.
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Affiliation(s)
- Paweł A. Osmulski
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
| | - Przemysław Karpowicz
- Department of Organic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Elżbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Jonathan Bohmann
- Southwest Research Institute, San Antonio, Texas, TX 78238, USA;
| | - Andrew M. Pickering
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
- The Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases, UT Health San Antonio, TX 78229, USA
| | - Maria Gaczyńska
- Department of Molecular Medicine, UT Health San Antonio, Texas, TX 78245, USA;
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, Texas, TX 78245, USA
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37
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Wang X, Meul T, Meiners S. Exploring the proteasome system: A novel concept of proteasome inhibition and regulation. Pharmacol Ther 2020; 211:107526. [PMID: 32173559 DOI: 10.1016/j.pharmthera.2020.107526] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/08/2020] [Indexed: 12/13/2022]
Abstract
The proteasome is a well-identified therapeutic target for cancer treatment. It acts as the main protein degradation system in the cell and degrades key mediators of cell growth, survival and function. The term "proteasome" embraces a whole family of distinct complexes, which share a common proteolytic core, the 20S proteasome, but differ by their attached proteasome activators. Each of these proteasome complexes plays specific roles in the control of cellular function. In addition, distinct proteasome interacting proteins regulate proteasome activity in subcellular compartments and in response to cellular signals. Proteasome activators and regulators may thus serve as building blocks to fine-tune proteasome function in the cell according to cellular needs. Inhibitors of the proteasome, e.g. the FDA approved drugs Velcade™, Kyprolis™, Ninlaro™, inactivate the catalytic 20S core and effectively block protein degradation of all proteasome complexes in the cell resulting in inhibition of cell growth and induction of apoptosis. Efficacy of these inhibitors, however, is hampered by their pronounced cytotoxic side-effects as well as by the emerging development of resistance to catalytic proteasome inhibitors. Targeted inhibition of distinct buiding blocks of the proteasome system, i.e. proteasome activators or regulators, represents an alternative strategy to overcome these limitations. In this review, we stress the importance of the diversity of the proteasome complexes constituting an entire proteasome system. Our building block concept provides a rationale for the defined targeting of distinct proteasome super-complexes in disease. We thereby aim to stimulate the development of innovative therapeutic approaches beyond broad catalytic proteasome inhibition.
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Affiliation(s)
- Xinyuan Wang
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Thomas Meul
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians-University (LMU) and Helmholtz Zentrum München, German Center for Lung Research (DZL), 81377 Munich, Germany.
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38
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Cryo-EM structures of the human PA200 and PA200-20S complex reveal regulation of proteasome gate opening and two PA200 apertures. PLoS Biol 2020; 18:e3000654. [PMID: 32134919 PMCID: PMC7077846 DOI: 10.1371/journal.pbio.3000654] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/17/2020] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Proteasomes are highly abundant and conserved protease complexes that eliminate unwanted proteins in the cells. As a single-chain ATP-independent nuclear proteasome activator, proteasome activator 200 (PA200) associates with 20S core particle to form proteasome complex that catalyzes polyubiquitin-independent degradation of acetylated histones, thus playing a pivotal role in DNA repair and spermatogenesis. Here, we present cryo–electron microscopy (cryo-EM) structures of the human PA200-20S complex and PA200 at 2.72 Å and 3.75 Å, respectively. PA200 exhibits a dome-like architecture that caps 20S and uses its C-terminal YYA (Tyr-Tyr-Ala) to induce the α-ring rearrangements and partial opening of the 20S gate. Our structural data also indicate that PA200 has two openings formed by numerous positively charged residues that respectively bind (5,6)-bisdiphosphoinositol tetrakisphosphate (5,6[PP]2-InsP4) and inositol hexakisphosphate (InsP6) and are likely to be the gates that lead unfolded proteins through PA200 and into the 20S. Besides, our structural analysis of PA200 found that the bromodomain (BRD)-like (BRDL) domain of PA200 shows considerable sequence variation in comparison to other human BRDs, as it contains only 82 residues because of a short ZA loop, and cannot be classified into any of the eight typical human BRD families. Taken together, the results obtained from this study provide important insights into human PA200-induced 20S gate opening for substrate degradation and the opportunities to explore the mechanism for its recognition of H4 histone in acetylation-mediated proteasomal degradation. Proteasomes are highly abundant and conserved protease complexes that eliminate unwanted proteins in the cells. The cryo-EM structures of PA200 and the PA200-20S proteasome complex reveal two openings on PA200 which bind inositol phosphates as cofactors, and novel insights into PA200-induced gate-opening of 20S.
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39
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Exploring long-range cooperativity in the 20S proteasome core particle from Thermoplasma acidophilum using methyl-TROSY-based NMR. Proc Natl Acad Sci U S A 2020; 117:5298-5309. [PMID: 32094174 DOI: 10.1073/pnas.1920770117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The 20S core particle (CP) proteasome is a molecular assembly catalyzing the degradation of misfolded proteins or proteins no longer required for function. It is composed of four stacked heptameric rings that form a barrel-like structure, sequestering proteolytic sites inside its lumen. Proteasome function is regulated by gates derived from the termini of α-rings and through binding of regulatory particles (RPs) to one or both ends of the barrel. The CP is dynamic, with an extensive allosteric pathway extending from one end of the molecule to catalytic sites in its center. Here, using methyl-transverse relaxation optimized spectroscopy (TROSY)-based NMR optimized for studies of high-molecular-weight complexes, we evaluate whether the pathway extends over the entire 150-Å length of the molecule. By exploiting a number of different labeling schemes, the two halves of the molecule can be distinguished, so that the effects of 11S RP binding, or the introduction of gate or allosteric pathway mutations at one end of the barrel can be evaluated at the distal end. Our results establish that while 11S binding and the introduction of key mutations affect each half of the CP allosterically, they do not further couple opposite ends of the molecule. This may have implications for the function of so-called "hybrid" proteasomes where each end of the CP is bound with a different regulator, allowing the CP to be responsive to both RPs simultaneously. The methodology presented introduces a general NMR strategy for dissecting pathways of communication in homo-oligomeric molecular machines.
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40
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Proteasome Inhibitors: Harnessing Proteostasis to Combat Disease. Molecules 2020; 25:molecules25030671. [PMID: 32033280 PMCID: PMC7037493 DOI: 10.3390/molecules25030671] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
The proteasome is the central component of the main cellular protein degradation pathway. During the past four decades, the critical function of the proteasome in numerous physiological processes has been revealed, and proteasome activity has been linked to various human diseases. The proteasome prevents the accumulation of misfolded proteins, controls the cell cycle, and regulates the immune response, to name a few important roles for this macromolecular "machine." As a therapeutic target, proteasome inhibitors have been approved for the treatment of multiple myeloma and mantle cell lymphoma. However, inability to sufficiently inhibit proteasome activity at tolerated doses has hampered efforts to expand the scope of proteasome inhibitor-based therapies. With emerging new modalities in myeloma, it might seem challenging to develop additional proteasome-based therapies. However, the constant development of new applications for proteasome inhibitors and deeper insights into the intricacies of protein homeostasis suggest that proteasome inhibitors might have novel therapeutic applications. Herein, we summarize the latest advances in proteasome inhibitor development and discuss the future of proteasome inhibitors and other proteasome-based therapies in combating human diseases.
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41
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Finley D, Prado MA. The Proteasome and Its Network: Engineering for Adaptability. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033985. [PMID: 30833452 DOI: 10.1101/cshperspect.a033985] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteasome, the most complex protease known, degrades proteins that have been conjugated to ubiquitin. It faces the unique challenge of acting enzymatically on hundreds and perhaps thousands of structurally diverse substrates, mechanically unfolding them from their native state and translocating them vectorially from one specialized compartment of the enzyme to another. Moreover, substrates are modified by ubiquitin in myriad configurations of chains. The many unusual design features of the proteasome may have evolved in part to endow this enzyme with a robust ability to process substrates regardless of their identity. The proteasome plays a major role in preserving protein homeostasis in the cell, which requires adaptation to a wide variety of stress conditions. Modulation of proteasome function is achieved through a large network of proteins that interact with it dynamically, modify it enzymatically, or fine-tune its levels. The resulting adaptability of the proteasome, which is unique among proteases, enables cells to control the output of the ubiquitin-proteasome pathway on a global scale.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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42
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Coux O, Zieba BA, Meiners S. The Proteasome System in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:55-100. [DOI: 10.1007/978-3-030-38266-7_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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43
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Eisele MR, Reed RG, Rudack T, Schweitzer A, Beck F, Nagy I, Pfeifer G, Plitzko JM, Baumeister W, Tomko RJ, Sakata E. Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating. Cell Rep 2019; 24:1301-1315.e5. [PMID: 30067984 PMCID: PMC6140342 DOI: 10.1016/j.celrep.2018.07.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/08/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022] Open
Abstract
The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive the unfolding and translocation of substrates into the proteolytic 20S core particle for degradation. Here, we combine genetic and biochemical approaches with cryo-electron microscopy and integrative modeling to dissect the relationship between individual nucleotide binding events and proteasome conformational dynamics. We demonstrate unique impacts of ATP binding by individual ATPases on the proteasome conformational distribution and report two conformational states of the proteasome suggestive of a rotary ATP hydrolysis mechanism. These structures, coupled with functional analyses, reveal key roles for the ATPases Rpt1 and Rpt6 in gating substrate entry into the core particle. This deepened knowledge of proteasome conformational dynamics reveals key elements of intersubunit communication within the proteasome and clarifies the regulation of substrate entry into the proteolytic chamber.
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Affiliation(s)
- Markus R Eisele
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Randi G Reed
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306-4300, USA
| | - Till Rudack
- Department of Biophysics, Ruhr University Bochum, 44801 Bochum, Germany
| | - Andreas Schweitzer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Beck
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Istvan Nagy
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Günter Pfeifer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Robert J Tomko
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306-4300, USA.
| | - Eri Sakata
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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44
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Li S, Dai X, Gong K, Song K, Tai F, Shi J. PA28α/β Promote Breast Cancer Cell Invasion and Metastasis via Down-Regulation of CDK15. Front Oncol 2019; 9:1283. [PMID: 31824858 PMCID: PMC6883405 DOI: 10.3389/fonc.2019.01283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 11/05/2019] [Indexed: 12/22/2022] Open
Abstract
PA28α/β activated immunoproteasome frequently participates in MHC class I antigen processing, however, whether it is involved in breast tumor progression remains largely unclear. Here, our evidences show that PA28α/β proteins are responsible for breast cancer cell migration, invasion, and metastasis. Knockdown of immunoproteasome core subunit β5i also robustly suppresses the tumor cell migration and invasion. Interestingly, silencing of PA28α/β and β5i up-regulates the protein expression of cyclin-dependent kinase 15 (CDK15). Our data further indicate that the loss of CDK15 is important for breast tumor cell invasion and metastasis. Taken together, this study implicates that targeting of PA28α/β represents a potential way for treatment of metastatic breast cancer.
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Affiliation(s)
- Shengnan Li
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
| | - Xiaoqin Dai
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China.,Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Kunxiang Gong
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
| | - Kai Song
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
| | - Fang Tai
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
| | - Jian Shi
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
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45
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Toste Rêgo A, da Fonseca PCA. Characterization of Fully Recombinant Human 20S and 20S-PA200 Proteasome Complexes. Mol Cell 2019; 76:138-147.e5. [PMID: 31473102 PMCID: PMC6863390 DOI: 10.1016/j.molcel.2019.07.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/27/2019] [Accepted: 07/10/2019] [Indexed: 12/31/2022]
Abstract
Proteasomes are essential in all eukaryotic cells. However, their function and regulation remain considerably elusive, particularly those of less abundant variants. We demonstrate the human 20S proteasome recombinant assembly and confirmed the recombinant complex integrity biochemically and with a 2.6 Å resolution cryo-EM map. To assess its competence to form higher-order assemblies, we prepared and analyzed recombinant human 20S-PA200, a poorly characterized nuclear complex. Its 3.0 Å resolution cryo-EM structure reveals the PA200 unique architecture; the details of its intricate interactions with the proteasome, resulting in unparalleled proteasome α ring rearrangements; and the molecular basis for PA200 allosteric modulation of the proteasome active sites. Non-protein cryo-EM densities could be assigned to PA200-bound inositol phosphates, and we speculate regarding their functional role. Here we open extensive opportunities to study the fundamental properties of the diverse and distinct eukaryotic proteasome variants and to improve proteasome targeting under different therapeutic conditions. Recombinant human 20S proteasomes and 20S-PA200 complexes are characterized Cryo-EM reveals intricate 20S-PA200 interactions and PA200-bound cofactors PA200 binding is allosterically communicated to the proteolytic active sites Basis to fully characterize the function and regulation of proteasome variants
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Affiliation(s)
- Ana Toste Rêgo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Paula C A da Fonseca
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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46
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Morozov AV, Karpov VL. Proteasomes and Several Aspects of Their Heterogeneity Relevant to Cancer. Front Oncol 2019; 9:761. [PMID: 31456945 PMCID: PMC6700291 DOI: 10.3389/fonc.2019.00761] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/29/2019] [Indexed: 01/19/2023] Open
Abstract
The life of every organism is dependent on the fine-tuned mechanisms of protein synthesis and breakdown. The degradation of most intracellular proteins is performed by the ubiquitin proteasome system (UPS). Proteasomes are central elements of the UPS and represent large multisubunit protein complexes directly responsible for the protein degradation. Accumulating data indicate that there is an intriguing diversity of cellular proteasomes. Different proteasome forms, containing different subunits and attached regulators have been described. In addition, proteasomes specific for a particular tissue were identified. Cancer cells are highly dependent on the proper functioning of the UPS in general, and proteasomes in particular. At the same time, the information regarding the role of different proteasome forms in cancer is limited. This review describes the functional and structural heterogeneity of proteasomes, their association with cancer as well as several established and novel proteasome-directed therapeutic strategies.
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Affiliation(s)
- Alexey V. Morozov
- Laboratory of Regulation of Intracellular Proteolysis, W.A. Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
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47
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Proteasome Activation to Combat Proteotoxicity. Molecules 2019; 24:molecules24152841. [PMID: 31387243 PMCID: PMC6696185 DOI: 10.3390/molecules24152841] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Loss of proteome fidelity leads to the accumulation of non-native protein aggregates and oxidatively damaged species: hallmarks of an aged cell. These misfolded and aggregated species are often found, and suggested to be the culpable party, in numerous neurodegenerative diseases including Huntington's, Parkinson's, Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Diseases (AD). Many strategies for therapeutic intervention in proteotoxic pathologies have been put forth; one of the most promising is bolstering the efficacy of the proteasome to restore normal proteostasis. This strategy is ideal as monomeric precursors and oxidatively damaged proteins, so called "intrinsically disordered proteins" (IDPs), are targeted by the proteasome. This review will provide an overview of disorders in proteins, both intrinsic and acquired, with a focus on susceptibility to proteasomal degradation. We will then examine the proteasome with emphasis on newly published structural data and summarize current known small molecule proteasome activators.
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48
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Xie SC, Metcalfe RD, Hanssen E, Yang T, Gillett DL, Leis AP, Morton CJ, Kuiper MJ, Parker MW, Spillman NJ, Wong W, Tsu C, Dick LR, Griffin MDW, Tilley L. The structure of the PA28-20S proteasome complex from Plasmodium falciparum and implications for proteostasis. Nat Microbiol 2019; 4:1990-2000. [PMID: 31384003 DOI: 10.1038/s41564-019-0524-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 06/25/2019] [Indexed: 11/09/2022]
Abstract
The activity of the proteasome 20S catalytic core is regulated by protein complexes that bind to one or both ends. The PA28 regulator stimulates 20S proteasome peptidase activity in vitro, but its role in vivo remains unclear. Here, we show that genetic deletion of the PA28 regulator from Plasmodium falciparum (Pf) renders malaria parasites more sensitive to the antimalarial drug dihydroartemisinin, indicating that PA28 may play a role in protection against proteotoxic stress. The crystal structure of PfPA28 reveals a bell-shaped molecule with an inner pore that has a strong segregation of charges. Small-angle X-ray scattering shows that disordered loops, which are not resolved in the crystal structure, extend from the PfPA28 heptamer and surround the pore. Using single particle cryo-electron microscopy, we solved the structure of Pf20S in complex with one and two regulatory PfPA28 caps at resolutions of 3.9 and 3.8 Å, respectively. PfPA28 binds Pf20S asymmetrically, strongly engaging subunits on only one side of the core. PfPA28 undergoes rigid body motions relative to Pf20S. Molecular dynamics simulations support conformational flexibility and a leaky interface. We propose lateral transfer of short peptides through the dynamic interface as a mechanism facilitating the release of proteasome degradation products.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Riley D Metcalfe
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eric Hanssen
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.,Advanced Microscopy Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tuo Yang
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - David L Gillett
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew P Leis
- Advanced Microscopy Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Craig J Morton
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.,Australian Cancer Research Foundation Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Natalie J Spillman
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wilson Wong
- Infection and Immunity Division, The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Christopher Tsu
- Oncology Clinical R&D, Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Lawrence R Dick
- Oncology Clinical R&D, Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia.
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49
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Abstract
Proteasomes are multienzyme complexes that maintain protein homeostasis (proteostasis) and important cellular functions through the degradation of misfolded, redundant, and damaged proteins. It is well established that aging is associated with the accumulation of damaged and misfolded proteins. This phenomenon is paralleled by declined proteasome activity. When the accumulation of redundant proteins exceed degradation, undesirable signaling and/or aggregation occurs and are the hallmarks of neurodegenerative diseases and many cancers. Thus, increasing proteasome activity has been recognized as a new approach to delay the onset or ameliorate the symptoms of neurodegenerative and other proteotoxic disorders. Enhancement of proteasome activity has many therapeutic potentials but is still a relatively unexplored field. In this perspective, we review current approaches, genetic manipulation, posttranslational modification, and small molecule proteasome agonists used to increase proteasome activity, challenges facing the field, and applications beyond aging and neurodegenerative diseases.
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Affiliation(s)
- Evert Njomen
- Department of Chemistry, and Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jetze J. Tepe
- Department of Chemistry, and Pharmacology & Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
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50
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Buneeva OA, Medvedev AE. [Ubiquitin-independent protein degradation in proteasomes]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2019; 64:134-148. [PMID: 29723144 DOI: 10.18097/pbmc20186402134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proteasomes are large supramolecular protein complexes present in all prokaryotic and eukaryotic cells, where they perform targeted degradation of intracellular proteins. Until recently, it was generally accepted that prior proteolytic degradation in proteasomes the proteins had to be targeted by ubiquitination: the ATP-dependent addition of (typically four sequential) residues of the low-molecular ubiquitin protein, involving the ubiquitin-activating enzyme, ubiquitin-conjugating enzyme and ubiquitin ligase. The cytoplasm and nucleoplasm proteins labeled in this way are then digested in 26S proteasomes. However, in recent years it has become increasingly clear that using this route the cell eliminates only a part of unwanted proteins. Many proteins can be cleaved by the 20S proteasome in an ATP-independent manner and without previous ubiquitination. Ubiquitin-independent protein degradation in proteasomes is a relatively new area of studies of the role of the ubiquitin-proteasome system. However, recent data obtained in this direction already correct existing concepts about proteasomal degradation of proteins and its regulation. Ubiquitin-independent proteasome degradation needs the main structural precondition in proteins: the presence of unstructured regions in the amino acid sequences that provide interaction with the proteasome. Taking into consideration that in humans almost half of all genes encode proteins that contain a certain proportion of intrinsically disordered regions, it appears that the list of proteins undergoing ubiquitin-independent degradation will demonstrate further increase. Since 26S of proteasomes account for only 30% of the total proteasome content in mammalian cells, most of the proteasomes exist in the form of 20S complexes. The latter suggests that ubiquitin-independent proteolysis performed by the 20S proteasome is a natural process of removing damaged proteins from the cell and maintaining a constant level of intrinsically disordered proteins. In this case, the functional overload of proteasomes in aging and/or other types of pathological processes, if it is not accompanied by triggering more radical mechanisms for the elimination of damaged proteins, organelles and whole cells, has the most serious consequences for the whole organism.
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Affiliation(s)
- O A Buneeva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
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