1
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Stuart S, Tarade D, Ohh M. Cathepsins L and B target HIF1α for oxygen-independent proteolytic cleavage. Sci Rep 2024; 14:14799. [PMID: 38926538 PMCID: PMC11208597 DOI: 10.1038/s41598-024-65537-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
The oxygen-labile transcription factor called hypoxia-inducible factor (HIF) is responsible for the cellular and organismal adaptive response to reduced oxygen availability. Deregulation of HIF is associated with the pathogenesis of major human diseases including cardiovascular disease and cancer. Under normoxia, the HIFα subunit is hydroxylated on conserved proline residues within the oxygen-dependent degradation domain (ODD) that labels HIFα for proteasome-mediated degradation. Despite similar oxygen-dependent degradation machinery acting on HIF1α and HIF2α, these two paralogs have been shown to exhibit unique kinetics under hypoxia, which suggests that other regulatory processes may be at play. Here, we characterize the protease activity found in rabbit reticulocytes that specifically cleaves the ODD of HIF1α but not HIF2α. Notably, the cleavage product is observed irrespective of the oxygen-dependent prolyl-hydroxylation potential of HIF1α, suggesting independence from oxygen. HIF1α M561T substitution, which mimics an evolutionary substitution that occurred during the duplication and divergence of HIF1α and HIF2α, diminished the cleavage of HIF1α. Protease inhibitor screening suggests that cysteine proteases cathepsins L and B preferentially cleave HIF1αODD, thereby revealing an additional layer of differential HIF regulation.
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Affiliation(s)
- Sarah Stuart
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Daniel Tarade
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Michael Ohh
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.
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2
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Arkinson C, Dong KC, Gee CL, Costello SM, Marqusee S, Martin A. Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598715. [PMID: 38915702 PMCID: PMC11195292 DOI: 10.1101/2024.06.12.598715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor Nub1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system and revealed that Nub1 utilizes FAT10's intrinsic instability to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin- and p97-independent manner. Through hydrogen-deuterium exchange, structural modeling, and site-directed mutagenesis, we identified the formation of a peculiar complex with FAT10 that activates Nub1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic Nub1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These studies thus identified a novel mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.
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Affiliation(s)
- Connor Arkinson
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Ken C. Dong
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Christine L. Gee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Shawn M. Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Susan Marqusee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Andreas Martin
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
- Lead contact
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3
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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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4
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Dabravolski SA, Isayenkov SV. The Role of Plant Ubiquitin-like Modifiers in the Formation of Salt Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1468. [PMID: 38891277 PMCID: PMC11174624 DOI: 10.3390/plants13111468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
The climate-driven challenges facing Earth necessitate a comprehensive understanding of the mechanisms facilitating plant resilience to environmental stressors. This review delves into the crucial role of ubiquitin-like modifiers, particularly focusing on ATG8-mediated autophagy, in bolstering plant tolerance to salt stress. Synthesising recent research, we unveil the multifaceted contributions of ATG8 to plant adaptation mechanisms amidst salt stress conditions, including stomatal regulation, photosynthetic efficiency, osmotic adjustment, and antioxidant defence. Furthermore, we elucidate the interconnectedness of autophagy with key phytohormone signalling pathways, advocating for further exploration into their molecular mechanisms. Our findings underscore the significance of understanding molecular mechanisms underlying ubiquitin-based protein degradation systems and autophagy in salt stress tolerance, offering valuable insights for designing innovative strategies to improve crop productivity and ensure global food security amidst increasing soil salinisation. By harnessing the potential of autophagy and other molecular mechanisms, we can foster sustainable agricultural practices and develop stress-tolerant crops resilient to salt stress.
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Affiliation(s)
- Siarhei A. Dabravolski
- Department of Biotechnology Engineering, Braude Academic College of Engineering, Snunit 51, Karmiel 2161002, Israel;
| | - Stanislav V. Isayenkov
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Strasse 3, 06120 Halle, Germany
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics, The National Academy of Sciences of Ukraine, Baidi-Vyshneveckogo Str. 2a, 04123 Kyiv, Ukraine
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5
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Li H, Ji Z, Paulo JA, Gygi SP, Rapoport TA. Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation. Mol Cell 2024; 84:1290-1303.e7. [PMID: 38401542 DOI: 10.1016/j.molcel.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 12/12/2023] [Accepted: 01/31/2024] [Indexed: 02/26/2024]
Abstract
Most eukaryotic proteins are degraded by the 26S proteasome after modification with a polyubiquitin chain. Substrates lacking unstructured segments cannot be degraded directly and require prior unfolding by the Cdc48 ATPase (p97 or VCP in mammals) in complex with its ubiquitin-binding partner Ufd1-Npl4 (UN). Here, we use purified yeast components to reconstitute Cdc48-dependent degradation of well-folded model substrates by the proteasome. We show that a minimal system consists of the 26S proteasome, the Cdc48-UN ATPase complex, the proteasome cofactor Rad23, and the Cdc48 cofactors Ubx5 and Shp1. Rad23 and Ubx5 stimulate polyubiquitin binding to the 26S proteasome and the Cdc48-UN complex, respectively, allowing these machines to compete for substrates before and after their unfolding. Shp1 stimulates protein unfolding by the Cdc48-UN complex rather than substrate recruitment. Experiments in yeast cells confirm that many proteins undergo bidirectional substrate shuttling between the 26S proteasome and Cdc48 ATPase before being degraded.
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Affiliation(s)
- Hao Li
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Zhejian Ji
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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6
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Kim J, Byun I, Kim DY, Joh H, Kim HJ, Lee MJ. Targeted protein degradation directly engaging lysosomes or proteasomes. Chem Soc Rev 2024; 53:3253-3272. [PMID: 38369971 DOI: 10.1039/d3cs00344b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Targeted protein degradation (TPD) has been established as a viable alternative to attenuate the function of a specific protein of interest in both biological and clinical contexts. The unique TPD mode-of-action has allowed previously undruggable proteins to become feasible targets, expanding the landscape of "druggable" properties and "privileged" target proteins. As TPD continues to evolve, a range of innovative strategies, which do not depend on recruiting E3 ubiquitin ligases as in proteolysis-targeting chimeras (PROTACs), have emerged. Here, we present an overview of direct lysosome- and proteasome-engaging modalities and discuss their perspectives, advantages, and limitations. We outline the chemical composition, biochemical activity, and pharmaceutical characteristics of each degrader. These alternative TPD approaches not only complement the first generation of PROTACs for intracellular protein degradation but also offer unique strategies for targeting pathologic proteins located on the cell membrane and in the extracellular space.
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Affiliation(s)
- Jiseong Kim
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Do Young Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hyunhi Joh
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hak Joong Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Min Jae Lee
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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7
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Waite KA, Vontz G, Lee SY, Roelofs J. Proteasome condensate formation is driven by multivalent interactions with shuttle factors and ubiquitin chains. Proc Natl Acad Sci U S A 2024; 121:e2310756121. [PMID: 38408252 DOI: 10.1073/pnas.2310756121] [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: 06/26/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome condensates in yeast depends on ubiquitin chains together with the proteasome shuttle factors Rad23 and Dsk2. These shuttle factors colocalize to these condensates. Strains deleted for the third shuttle factor gene, DDI1, show proteasome condensates in the absence of cellular stress, consistent with the accumulation of substrates with long K48-linked ubiquitin chains that accumulate in this mutant. We propose a model where the long K48-linked ubiquitin chains function as a scaffold for the ubiquitin-binding domains of the shuttle factors and the proteasome, allowing for the multivalent interactions that further drive condensate formation. Indeed, we determined different intrinsic ubiquitin receptors of the proteasome-Rpn1, Rpn10, and Rpn13-and the Ubl domains of Rad23 and Dsk2 are critical under different condensate-inducing conditions. In all, our data support a model where the cellular accumulation of substrates with long ubiquitin chains, potentially due to reduced cellular energy, allows for proteasome condensate formation. This suggests that proteasome condensates are not simply for proteasome storage, but function to sequester soluble ubiquitinated substrates together with inactive proteasomes.
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Affiliation(s)
- Kenrick A Waite
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Gabrielle Vontz
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Stella Y Lee
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
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8
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Ali EMH, Loy CA, Trader DJ. ByeTAC: Bypassing an E3 Ligase for Targeted Protein Degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576376. [PMID: 38293213 PMCID: PMC10827187 DOI: 10.1101/2024.01.20.576376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Targeted protein degradation utilizing a bifunctional molecule to initiate ubiquitination and subsequent degradation by the 26S proteasome has been shown to be a powerful therapeutic intervention. Many bifunctional molecules, including covalent and non-covalent ligands to proteins of interest, have been developed. The traditional target protein degradation methodology targets the protein of interest in both healthy and diseased cell populations, and a therapeutic window is obtained based on the overexpression of the targeted protein. We report here a series of bifunctional degraders that do not rely on interacting with an E3 ligase, but rather a 26S proteasome subunit, which we have named ByeTACs: Bypassing E3 Targeting Chimeras. Rpn-13 is a non-essential ubiquitin receptor for the 26S proteasome. Cells under significant stress or require significant ubiquitin-dependent degradation of proteins for survival, incorporate Rpn-13 in the 26S to increase protein degradation rates. The targeted protein degraders reported here are bifunctional molecules that include a ligand to Rpn-13 and BRD4, the protein of interest we wish to degrade. We synthesized a suite of degraders with varying PEG chain lengths and showed that bifunctional molecules that incorporate a Rpn-13 binder (TCL1) and a BRD4 binder (JQ1) with a PEG linker of 3 or 4 units are the most effective to induce BRD4 degradation. We also demonstrate that our new targeted protein degraders are dependent upon proteasome activity and Rpn-13 expression levels. This establishes a new mechanism of action for our ByeTACs that can be employed for the targeted degradation of a wide variety of protein substrates.
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9
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Li H, Ji Z, Paulo JA, Gygi SP, Rapoport TA. Bidirectional substrate shuttling between the 26S proteasome and the Cdc48 ATPase promotes protein degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572403. [PMID: 38187576 PMCID: PMC10769200 DOI: 10.1101/2023.12.20.572403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Most eukaryotic proteins are degraded by the 26S proteasome after modification with a polyubiquitin chain. Substrates lacking unstructured segments cannot be degraded directly and require prior unfolding by the Cdc48 ATPase (p97 or VCP in mammals) in complex with its ubiquitin-binding partner Ufd1-Npl4 (UN). Here, we use purified yeast components to reconstitute Cdc48-dependent degradation of well-folded model substrates by the proteasome. We show that a minimal system consists of the 26S proteasome, the Cdc48-UN ATPase complex, the proteasome cofactor Rad23, and the Cdc48 cofactors Ubx5 and Shp1. Rad23 and Ubx5 stimulate polyubiquitin binding to the 26S proteasome and the Cdc48-UN complex, respectively, allowing these machines to compete for substrates before and after their unfolding. Shp1 stimulates protein unfolding by the Cdc48-UN complex, rather than substrate recruitment. In vivo experiments confirm that many proteins undergo bidirectional substrate shuttling between the 26S proteasome and Cdc48 ATPase before being degraded.
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10
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Mebratu YA, Jones JT, Liu C, Negasi ZH, Rahman M, Rojas-Quintero J, O’Connor GT, Gao W, Dupuis J, Cho MH, Litonjua AA, Randell S, Tesfaigzi Y. Bik promotes proteasomal degradation to control low-grade inflammation. J Clin Invest 2023; 134:e170594. [PMID: 38113109 PMCID: PMC10866658 DOI: 10.1172/jci170594] [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: 03/20/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023] Open
Abstract
Although chronic low-grade inflammation does not cause immediate clinical symptoms, over the longer term, it can enhance other insults or age-dependent damage to organ systems and thereby contribute to age-related disorders, such as respiratory disorders, heart disease, metabolic disorders, autoimmunity, and cancer. However, the molecular mechanisms governing low-level inflammation are largely unknown. We discovered that Bcl-2-interacting killer (Bik) deficiency causes low-level inflammation even at baseline and the development of spontaneous emphysema in female but not male mice. Similarly, a single nucleotide polymorphism that reduced Bik levels was associated with increased inflammation and enhanced decline in lung function in humans. Transgenic expression of Bik in the airways of Bik-deficient mice inhibited allergen- or LPS-induced lung inflammation and reversed emphysema in female mice. Bik deficiency increased nuclear but not cytosolic p65 levels because Bik, by modifying the BH4 domain of Bcl-2, interacted with regulatory particle non-ATPase 1 (RPN1) and RPN2 and enhanced proteasomal degradation of nuclear proteins. Bik deficiency increased inflammation primarily in females because Bcl-2 and Bik levels were reduced in lung tissues and airway cells of female compared with male mice. Therefore, controlling low-grade inflammation by modifying the unappreciated role of Bik and Bcl-2 in facilitating proteasomal degradation of nuclear proteins may be crucial in treating chronic age-related diseases.
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Affiliation(s)
- Yohannes A. Mebratu
- Brigham and Women’s Hospital, Division of Pulmonary and Critical Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jane T. Jones
- University Geisel School of Medicine, Department of Microbiology and Immunology, Dartmouth, Hanover, New Hampshire, USA
| | - Congjian Liu
- Brigham and Women’s Hospital, Division of Pulmonary and Critical Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Zerihun H. Negasi
- Brigham and Women’s Hospital, Division of Pulmonary and Critical Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Mizanur Rahman
- Brigham and Women’s Hospital, Division of Pulmonary and Critical Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Joselyn Rojas-Quintero
- Brigham and Women’s Hospital, Division of Pulmonary and Critical Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - George T. O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
- National Heart, Lung, and Blood Institute’s (NHLBI’s) Framingham Heart Study, Framingham, Massachusetts, USA
| | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Canada
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Augusto A. Litonjua
- Division of Pediatric Pulmonary Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Scott Randell
- Marsico Lung Institute, UNC School of Medicine, Chapel Hill, North Carolina, USA
| | - Yohannes Tesfaigzi
- Brigham and Women’s Hospital, Division of Pulmonary and Critical Medicine, Harvard Medical School, Boston, Massachusetts, USA
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Zhang R, Pan S, Zheng S, Liao Q, Jiang Z, Wang D, Li X, Hu A, Li X, Zhu Y, Shen X, Lei J, Zhong S, Zhang X, Huang L, Wang X, Huang L, Shen L, Song BL, Zhao JW, Wang Z, Yang B, Guo X. Lipid-anchored proteasomes control membrane protein homeostasis. SCIENCE ADVANCES 2023; 9:eadj4605. [PMID: 38019907 PMCID: PMC10686573 DOI: 10.1126/sciadv.adj4605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Protein degradation in eukaryotic cells is mainly carried out by the 26S proteasome, a macromolecular complex not only present in the cytosol and nucleus but also associated with various membranes. How proteasomes are anchored to the membrane and the biological meaning thereof have been largely unknown in higher organisms. Here, we show that N-myristoylation of the Rpt2 subunit is a general mechanism for proteasome-membrane interaction. Loss of this modification in the Rpt2-G2A mutant cells leads to profound changes in the membrane-associated proteome, perturbs the endomembrane system, and undermines critical cellular processes such as cell adhesion, endoplasmic reticulum-associated degradation and membrane protein trafficking. Rpt2G2A/G2A homozygous mutation is embryonic lethal in mice and is sufficient to abolish tumor growth in a nude mice xenograft model. These findings have defined an evolutionarily conserved mechanism for maintaining membrane protein homeostasis and underscored the significance of compartmentalized protein degradation by myristoyl-anchored proteasomes in health and disease.
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Affiliation(s)
- Ruizhu Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shuxian Pan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Suya Zheng
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qingqing Liao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhaodi Jiang
- National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Dixian Wang
- Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Cryo-Electron Microscopy Center, Zhejiang University, Hangzhou 310058, China
| | - Xuemei Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ao Hu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Wuhan University, Wuhan 430072, China
| | - Xinran Li
- Zhejiang University-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Yezhang Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaoqi Shen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jing Lei
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
- The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Siming Zhong
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining 314400, China
- Deanery of Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Xiaomei Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Lingyun Huang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California-Irvine, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA 92697, USA
| | - Li Shen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Bao-Liang Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Taikang Center for Life and Medical Sciences, Taikang Medical School, Wuhan University, Wuhan 430072, China
| | - Jing-Wei Zhao
- Department of Human Anatomy, Histology and Embryology, System Medicine Research Center, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Cryo-Electron Microscopy Center, Zhejiang University, Hangzhou 310058, China
| | - Zhiping Wang
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
- The MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Brain Science and Brain Medicine, Hangzhou 310058, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xing Guo
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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12
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Lee H, Kim S, Lee D. The versatility of the proteasome in gene expression and silencing: Unraveling proteolytic and non-proteolytic functions. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194978. [PMID: 37633648 DOI: 10.1016/j.bbagrm.2023.194978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
The 26S proteasome consists of a 20S core particle and a 19S regulatory particle and critically regulates gene expression and silencing through both proteolytic and non-proteolytic functions. The 20S core particle mediates proteolysis, while the 19S regulatory particle performs non-proteolytic functions. The proteasome plays a role in regulating gene expression in euchromatin by modifying histones, activating transcription, initiating and terminating transcription, mRNA export, and maintaining transcriptome integrity. In gene silencing, the proteasome modulates the heterochromatin formation, spreading, and subtelomere silencing by degrading specific proteins and interacting with anti-silencing factors such as Epe1, Mst2, and Leo1. This review discusses the proteolytic and non-proteolytic functions of the proteasome in regulating gene expression and gene silencing-related heterochromatin formation. This article is part of a special issue on the regulation of gene expression and genome integrity by the ubiquitin-proteasome system.
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Affiliation(s)
- Hyesu Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Sungwook Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.
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13
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Bodrug T, Welsh KA, Bolhuis DL, Paulаkonis E, Martinez-Chacin RC, Liu B, Pinkin N, Bonacci T, Cui L, Xu P, Roscow O, Amann SJ, Grishkovskaya I, Emanuele MJ, Harrison JS, Steimel JP, Hahn KM, Zhang W, Zhong ED, Haselbach D, Brown NG. Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C). Nat Struct Mol Biol 2023; 30:1663-1674. [PMID: 37735619 PMCID: PMC10643132 DOI: 10.1038/s41594-023-01105-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/21/2023] [Indexed: 09/23/2023]
Abstract
Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight has thus far required artificially trapped structures to stabilize specific steps along the enzymatic process. So far, how any ubiquitin ligase builds a proteasomal degradation signal, which is canonically regarded as four or more ubiquitins, remains unclear. Here we present time-resolved cryogenic electron microscopy studies of the 1.2 MDa E3 ubiquitin ligase, known as the anaphase-promoting complex/cyclosome (APC/C), and its E2 co-enzymes (UBE2C/UBCH10 and UBE2S) during substrate polyubiquitination. Using cryoDRGN (Deep Reconstructing Generative Networks), a neural network-based approach, we reconstruct the conformational changes undergone by the human APC/C during polyubiquitination, directly visualize an active E3-E2 pair modifying its substrate, and identify unexpected interactions between multiple ubiquitins with parts of the APC/C machinery, including its coactivator CDH1. Together, we demonstrate how modification of substrates with nascent ubiquitin chains helps to potentiate processive substrate polyubiquitination, allowing us to model how a ubiquitin ligase builds a proteasomal degradation signal.
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Affiliation(s)
- Tatyana Bodrug
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Kaeli A Welsh
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Ethan Paulаkonis
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Raquel C Martinez-Chacin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Bei Liu
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- College of Future Technology, National Biomedical Imaging Center, Peking University, Beijing, China
| | - Nicholas Pinkin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Thomas Bonacci
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Liying Cui
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Pengning Xu
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Olivia Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
| | - Sascha Josef Amann
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Joshua P Steimel
- School of Engineering, California Polytechnic State University Humboldt, Arcata, CA, USA
| | - Klaus M Hahn
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario, Canada
| | - Ellen D Zhong
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - David Haselbach
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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14
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Tian R, Tian J, Zuo X, Ren S, Zhang H, Liu H, Wang Z, Cui Y, Niu R, Zhang F. RACK1 facilitates breast cancer progression by competitively inhibiting the binding of β-catenin to PSMD2 and enhancing the stability of β-catenin. Cell Death Dis 2023; 14:685. [PMID: 37848434 PMCID: PMC10582012 DOI: 10.1038/s41419-023-06191-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023]
Abstract
The receptor for activated C kinase 1 (RACK1) is a key scaffolding protein with multifunctional and multifaceted properties. By mediating protein-protein interactions, RACK1 integrates multiple intracellular signals involved in the regulation of various physiological and pathological processes. Dysregulation of RACK1 has been implicated in the initiation and progression of many tumors. However, the exact function of RACK1 in cancer cellular processes, especially in proliferation, remains controversial. Here, we show that RACK1 is required for breast cancer cell proliferation in vitro and tumor growth in vivo. This effect of RACK1 is associated with its ability to enhance β-catenin stability and activate the canonical WNT signaling pathway in breast cancer cells. We identified PSMD2, a key component of the proteasome, as a novel binding partner for RACK1 and β-catenin. Interestingly, although there is no interaction between RACK1 and β-catenin, RACK1 binds PSMD2 competitively with β-catenin. Moreover, RACK1 prevents ubiquitinated β-catenin from binding to PSMD2, thereby protecting β-catenin from proteasomal degradation. Collectively, our findings uncover a novel mechanism by which RACK1 increases β-catenin stability and promotes breast cancer proliferation.
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Affiliation(s)
- Ruinan Tian
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Jianfei Tian
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Xiaoyan Zuo
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Sixin Ren
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - He Zhang
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Hui Liu
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Zhiyong Wang
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Yanfen Cui
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Ruifang Niu
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China.
| | - Fei Zhang
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China.
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15
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Fiore APZP, Vogel C. Fractionation of Native Protein Complexes from Mammalian Cells to Determine the Differential Proteasome Activity and Abundance. Bio Protoc 2023; 13:e4822. [PMID: 37753477 PMCID: PMC10518779 DOI: 10.21769/bioprotoc.4822] [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: 05/02/2023] [Revised: 07/02/2023] [Accepted: 07/13/2023] [Indexed: 09/28/2023] Open
Abstract
Eukaryotic cells have different types of proteasomes that differ in size. The smallest proteolytically active particle is the 20S proteasome, which degrades damaged and oxidized proteins; the most common larger particle is the 26S proteasome, which degrades ubiquitylated proteins. The 26S proteasome is formed by a 20S particle capped with one or two regulatory particles, named 19S. While proteasome particles function in the cytoplasm, endoplasmic reticulum, and nucleus, our understanding of their abundance and activity in different cellular compartments is still limited. We provide a three-step protocol that first involves detergent-based fractionation of the cytoplasmic and nuclear compartments, maintaining the integrity and activity of proteasome complexes. Second, the protocol employs native gel separation of large multiprotein complexes in the fractions and a fluorescence-based in-gel quantitation of the activity and different proteasome particles. Finally, the protocol involves protein in-gel denaturation and transfer to a PVDF membrane. Western blotting then detects and quantifies the different proteasome particles. Therefore, the protocol allows for sensitive measurements of activity and abundance of individual proteasome particles from different cellular compartments. It has been optimized for motor neurons induced from mouse embryonic stem cells but can be applied to a variety of mammalian cell lines. Key features • Protocol for fractionation of active nuclear and cytoplasmic proteasome complexes. • Native electrophoresis and fluorescence-based in-gel activity assay, which allows the visualization and quantification of active complexes within the acrylamide gel matrix. • In-gel protein denaturation followed by transfer of complexes to PVDF membrane, which allows the analysis of complexes' abundance using antibodies.
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Affiliation(s)
| | - Christine Vogel
- Center of Genomic and System Biology, Department of Biology, New York University, New York, NY, USA
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16
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Zhang J, Fang S, Rong F, Jia M, Wang Y, Cui H, Hao P. PSMD4 drives progression of hepatocellular carcinoma via Akt/COX2 pathway and p53 inhibition. Hum Cell 2023; 36:1755-1772. [PMID: 37336868 DOI: 10.1007/s13577-023-00935-1] [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: 04/07/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
The ubiquitin-dependent proteolytic pathway is crucial for cellular regulation, including control of the cell cycle, differentiation, and apoptosis. Proteasome 26S Subunit Ubiquitin Receptor, Non-ATPase 4, (PSMD4) is a member of the ubiquitin proteasome family that is upregulated in multiple solid tumors, including hepatocellular carcinoma (HCC), and the existence of PSMD4 is associated with unfavorable prognosis. In this study, transcriptome sequencing of HCC tissues and non-tumor hepatic tissues from the public database Cancer Genome Atlas (TGCA) revealed a high expression of PSMD4. Additionally, PSMD4 loss in HCC cells suppressed the tumor development in mouse xenograft model. PSMD4, which is maintained by inflammatory factors secreted from tumor matrix cells, positively mediates cell growth and is associated with Akt/GSK-3β/ cyclooxygenase2 (COX2) pathway activation, inhibition of p53 promoter activity, and increased p53 degradation. However, the domain without the C-terminus (VWA+UIM1/2) sustained the activation of p53 transcription. Thus, our findings suggest that PSMD4 is involved in HCC tumor growth through COX2 expression and p53 downregulation. Therapeutic strategies targeting PSMD4 and its downstream effectors could be used for the treatment of PSMD4-abundant HCC patients.
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Affiliation(s)
- Jiamin Zhang
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, Hebei, China
- International Cooperation Laboratory of Stem Cell Research, Shijiazhuang, Hebei, China
| | - Shu Fang
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, Hebei, China
- International Cooperation Laboratory of Stem Cell Research, Shijiazhuang, Hebei, China
| | - Fanghao Rong
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, Hebei, China
- International Cooperation Laboratory of Stem Cell Research, Shijiazhuang, Hebei, China
| | - Miaomiao Jia
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, Hebei, China
- International Cooperation Laboratory of Stem Cell Research, Shijiazhuang, Hebei, China
| | - Yunpeng Wang
- Department of General Medicine, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Huixian Cui
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, Hebei, China.
- International Cooperation Laboratory of Stem Cell Research, Shijiazhuang, Hebei, China.
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, Hebei, China.
| | - Peipei Hao
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang, Hebei, China.
- International Cooperation Laboratory of Stem Cell Research, Shijiazhuang, Hebei, China.
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, Hebei, China.
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17
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Chinchankar MN, Taylor WB, Ko SH, Apple EC, Rodriguez KA, Chen L, Fisher AL. A novel endoplasmic reticulum adaptation is critical for the long-lived Caenorhabditis elegans rpn-10 proteasomal mutant. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194957. [PMID: 37355092 PMCID: PMC10528105 DOI: 10.1016/j.bbagrm.2023.194957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/24/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
The loss of proteostasis due to reduced efficiency of protein degradation pathways plays a key role in multiple age-related diseases and is a hallmark of the aging process. Paradoxically, we have previously reported that the Caenorhabditis elegans rpn-10(ok1865) mutant, which lacks the RPN-10/RPN10/PSMD4 subunit of the 19S regulatory particle of the 26S proteasome, exhibits enhanced cytosolic proteostasis, elevated stress resistance and extended lifespan, despite possessing reduced proteasome function. However, the response of this mutant against threats to endoplasmic reticulum (ER) homeostasis and proteostasis was unknown. Here, we find that the rpn-10 mutant is highly ER stress resistant compared to the wildtype. Under unstressed conditions, the ER unfolded protein response (UPR) is activated in the rpn-10 mutant as signified by increased xbp-1 splicing. This primed response appears to alter ER homeostasis through the upregulated expression of genes involved in ER protein quality control (ERQC), including those in the ER-associated protein degradation (ERAD) pathway. Pertinently, we find that ERQC is critical for the rpn-10 mutant longevity. These changes also alter ER proteostasis, as studied using the C. elegans alpha-1 antitrypsin (AAT) deficiency model, which comprises an intestinal ER-localised transgenic reporter of an aggregation-prone form of AAT called ATZ. The rpn-10 mutant shows a significant reduction in the accumulation of the ATZ reporter, thus indicating that its ER proteostasis is augmented. Via a genetic screen for suppressors of decreased ATZ aggregation in the rpn-10 mutant, we then identified ecps-2/H04D03.3, a novel ortholog of the proteasome-associated adaptor and scaffold protein ECM29/ECPAS. We further show that ecps-2 is required for improved ER proteostasis as well as lifespan extension of the rpn-10 mutant. Thus, we propose that ECPS-2-proteasome functional interactions, alongside additional putative molecular processes, contribute to a novel ERQC adaptation which underlies the superior proteostasis and longevity of the rpn-10 mutant.
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Affiliation(s)
- Meghna N Chinchankar
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio (UTHSCSA), SA, TX, United States of America; Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - William B Taylor
- Division of Geriatrics, Gerontology, and Palliative Medicine, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Su-Hyuk Ko
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio (UTHSCSA), SA, TX, United States of America; Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - Ellen C Apple
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio (UTHSCSA), SA, TX, United States of America; Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - Karl A Rodriguez
- Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - Lizhen Chen
- Barshop Institute for Longevity and Aging Studies, UT Health San Antonio (UTHSCSA), SA, TX, United States of America; Department of Cell Systems and Anatomy, UTHSCSA, SA, TX, United States of America
| | - Alfred L Fisher
- Division of Geriatrics, Gerontology, and Palliative Medicine, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, United States of America.
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18
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Anthony AJ, Gautam AKS, Miller LM, Ma Y, Hardwick AG, Sharma A, Ghatak S, Matouschek A, Jarrold MF, Clemmer DE. CDMS Analysis of Intact 19S, 20S, 26S, and 30S Proteasomes: Evidence for Higher-Order 20S Assemblies at a Low pH†. Anal Chem 2023; 95:12209-12215. [PMID: 37552619 PMCID: PMC10916762 DOI: 10.1021/acs.analchem.3c00472] [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: 08/10/2023]
Abstract
Charge detection mass spectrometry (CDMS) was examined as a means of studying proteasomes. To this end, the following masses of the 20S, 19S, 26S, and 30S proteasomes from Saccharomyces cerevisiae (budding yeast) were measured: m(20S) = 738.8 ± 2.9 kDa, m(19S) = 926.2 ± 4.8 kDa, m(26S) = 1,637.0 ± 7.6 kDa, and m(30S) = 2,534.2 ± 10.8 kDa. Under some conditions, larger (20S)x (where x = 1 to ∼13) assemblies are observed; the 19S regulatory particle also oligomerizes, but to a lesser extent, forming (19S)x complexes (where x = 1 to 4, favoring the x = 3 trimer). The (20S)x oligomers are favored in vitro, as the pH of the solution is lowered (from 7.0 to 5.4, in a 20 mM ammonium acetate solution) and may be related to in vivo proteasome storage granules that are observed under carbon starvation. From measurements of m(20S)x (x = 1 to ∼13) species, it appears that each multimer retains all 28 proteins of the 20S complex subunit. Several types of structures that might explain the formation of (20S)x assemblies are considered. We stress that each structural type [hypothetical planar, raft-like geometries (where individual proteasomes associate through side-by-side interactions); elongated, rodlike geometries (where subunits are bound end-to-end); and geometries that are roughly spherical (arising from aggregation through nonspecific subunit interactions)] is highly speculative but still interesting to consider, and a short discussion is provided. The utility of CDMS for characterizing proteasomes and related oligomers is discussed.
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Affiliation(s)
- Adam J Anthony
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Amit K S Gautam
- Department of Molecular Biosciences, University of Texas, Austin Texas 78712, United States
| | - Lohra M Miller
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Yiran Ma
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Anya G Hardwick
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Anu Sharma
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Subhadip Ghatak
- Indiana Center for Regenerative Medicine & Engineering, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Andreas Matouschek
- Department of Molecular Biosciences, University of Texas, Austin Texas 78712, United States
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
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19
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Davis C, Spaller BL, Choi E, Kurrasch J, Chong H, Elsasser S, Finley D, Matouschek A. A strict requirement in proteasome substrates for spacing between ubiquitin tag and degradation initiation elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552540. [PMID: 37609285 PMCID: PMC10441315 DOI: 10.1101/2023.08.08.552540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Proteins are typically targeted to the proteasome for degradation through the attachment of ubiquitin chains and the proteasome initiates degradation at a disordered region within the target protein. Yet some proteins with ubiquitin chains and disordered regions escape degradation. Here we investigate how the position of the ubiquitin chain on the target protein relative to the disordered region modulates degradation and show that the distance between the two determines whether a protein is degraded efficiently. This distance depends on the type of the degradation tag and is likely a result of the separation on the proteasome between the receptor that binds the tag and the site that engages the disordered region.
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20
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Kim Y, Kim EK, Chey Y, Song MJ, Jang HH. Targeted Protein Degradation: Principles and Applications of the Proteasome. Cells 2023; 12:1846. [PMID: 37508510 PMCID: PMC10378610 DOI: 10.3390/cells12141846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The proteasome is a multi-catalytic protease complex that is involved in protein quality control via three proteolytic activities (i.e., caspase-, trypsin-, and chymotrypsin-like activities). Most cellular proteins are selectively degraded by the proteasome via ubiquitination. Moreover, the ubiquitin-proteasome system is a critical process for maintaining protein homeostasis. Here, we briefly summarize the structure of the proteasome, its regulatory mechanisms, proteins that regulate proteasome activity, and alterations to proteasome activity found in diverse diseases, chemoresistant cells, and cancer stem cells. Finally, we describe potential therapeutic modalities that use the ubiquitin-proteasome system.
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Affiliation(s)
- Yosup Kim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Eun-Kyung Kim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Yoona Chey
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Min-Jeong Song
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Ho Hee Jang
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
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21
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Waite KA, Vontz G, Lee SY, Roelofs J. Proteasome condensate formation is driven by multivalent interactions with shuttle factors and K48-linked ubiquitin chains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.546446. [PMID: 37425862 PMCID: PMC10326979 DOI: 10.1101/2023.06.25.546446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome condensates in yeast depends on long K48-linked ubiquitin chains together with the proteasome shuttle factors Rad23 and Dsk2. These shuttle factors colocalize to these condensates. Strains deleted for the third shuttle factor gene, DDI1 , show proteasome condensates in the absence of cellular stress, consistent with the accumulation of substrates with long K48-linked ubiquitin chains that accumulate in this mutant. We propose a model where the long K48-linked ubiquitin chains function as a scaffold for the ubiquitin binding domains of the shuttle factors and the proteasome, allowing for the multivalent interactions that further drive condensate formation. Indeed, we determined different intrinsic ubiquitin receptors of the proteasome (Rpn1, Rpn10, and Rpn13) are critical under different condensate inducing conditions. In all, our data support a model where the cellular accumulation of substrates with long ubiquitin chains, potentially due to reduced cellular energy, allows for proteasome condensate formation. This suggests that proteasome condensates are not simply for proteasome storage, but function to sequester soluble ubiquitinated substrates together with inactive proteasomes. Significance Stress conditions can cause the relocalization of proteasomes to condensates in yeast as well as mammalian cells. Our work shows that the formation of proteasome condensates in yeast depends on long K48-linked ubiquitin chains, the proteasome binding shuttle factors Rad23 and Dsk2 and proteasome intrinsic ubiquitin receptors. Here, different receptors are critical for different condensate inducers. These results indicate distinct condensates can form with specific functionality. Our identification of key factors involved in the process is crucial for understanding the function of proteasome relocalization to condensates. We propose that cellular accumulation of substrates with long ubiquitin chains results in the formation of condensates comprising those ubiquitinated substrates, proteasomes, and proteasome shuttle factors, where the ubiquitin chains serve as the scaffold for condensate formation.
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22
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Henderson LW, Sharon EM, Gautam AKS, Anthony AJ, Jarrold MF, Russell DH, Matouschek A, Clemmer DE. Stability of 20S Proteasome Configurations: Preopening the Axial Gate. J Phys Chem Lett 2023; 14:5014-5017. [PMID: 37224454 PMCID: PMC10916758 DOI: 10.1021/acs.jpclett.3c01040] [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: 05/26/2023]
Abstract
Mass spectrometry studies of the stability of the S. cerevisiae 20S proteasome from 11 to 55 °C reveal a series of related configurations and coupled transitions that appear to be associated with opening of the proteolytic core. We find no evidence for dissociation, and all transitions are reversible. A thermodynamic analysis indicates that configurations fall into three general types of structures: enthalpically stabilized, tightly closed (observed as the +54 to +58 charge states) configurations; high-entropy (+60 to +66) states that are proposed as precursors to pore opening; and larger (+70 to +79) partially and fully open pore structures. In the absence of the 19S regulatory unit, the mechanism for opening the 20S pore appears to involve a charge-priming process that loosens the closed-pore configuration. Only a small fraction (≤2%) of these 20S precursor configurations appear to open and thus expose the catalytic cavity.
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Affiliation(s)
- Lucas W Henderson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Edie M Sharon
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Amit K S Gautam
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712, United States
| | - Adam J Anthony
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Andreas Matouschek
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
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23
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Zhou M, Fang R, Colson L, Donovan KA, Hunkeler M, Song Y, Zhang C, Chen S, Lee DH, Bradshaw GA, Eisert R, Ye Y, Kalocsay M, Goldberg A, Fischer ES, Lu Y. HUWE1 Amplifies Ubiquitin Modifications to Broadly Stimulate Clearance of Proteins and Aggregates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542866. [PMID: 37398461 PMCID: PMC10312588 DOI: 10.1101/2023.05.30.542866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Selective breakdown of proteins and aggregates is crucial for maintaining normal cellular activities and is involved in the pathogenesis of diverse diseases. How the cell recognizes and tags these targets in different structural states for degradation by the proteasome and autophagy pathways has not been well understood. Here, we discovered that a HECT-family ubiquitin ligase HUWE1 is broadly required for the efficient degradation of soluble factors and for the clearance of protein aggregates/condensates. Underlying this capacity of HUWE1 is a novel Ubiquitin-Directed ubiquitin Ligase (UDL) activity which recognizes both soluble substrates and aggregates that carry a high density of ubiquitin chains and rapidly expand the ubiquitin modifications on these targets. Ubiquitin signal amplification by HUWE1 recruits the ubiquitin-dependent segregase p97/VCP to process these targets for subsequent degradation or clearance. HUWE1 controls the cytotoxicity of protein aggregates, mediates Targeted Protein Degradation and regulates cell-cycle transitions with its UDL activity.
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24
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Andrés-Benito P, Íñigo-Marco I, Brullas M, Carmona M, del Rio JA, Fernández-Irigoyen J, Santamaría E, Povedano M, Ferrer I. Proteostatic modulation in brain aging without associated Alzheimer's disease-and age-related neuropathological changes. Aging (Albany NY) 2023; 15:3295-3330. [PMID: 37179123 PMCID: PMC10449282 DOI: 10.18632/aging.204698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023]
Abstract
AIMS (Phospho)proteomics of old-aged subjects without cognitive or behavioral symptoms, and without AD-neuropathological changes and lacking any other neurodegenerative alteration will increase understanding about the physiological state of human brain aging without associate neurological deficits and neuropathological lesions. METHODS (Phospho)proteomics using conventional label-free- and SWATH-MS (Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) has been assessed in the frontal cortex (FC) of individuals without NFTs, senile plaques (SPs) and age-related co-morbidities classified by age (years) in four groups; group 1 (young, 30-44); group 2 (middle-aged: MA, 45-52); group 3 (early-elderly, 64-70); and group 4 (late-elderly, 75-85). RESULTS Protein levels and deregulated protein phosphorylation linked to similar biological terms/functions, but involving different individual proteins, are found in FC with age. The modified expression occurs in cytoskeleton proteins, membranes, synapses, vesicles, myelin, membrane transport and ion channels, DNA and RNA metabolism, ubiquitin-proteasome-system (UPS), kinases and phosphatases, fatty acid metabolism, and mitochondria. Dysregulated phosphoproteins are associated with the cytoskeleton, including microfilaments, actin-binding proteins, intermediate filaments of neurons and glial cells, and microtubules; membrane proteins, synapses, and dense core vesicles; kinases and phosphatases; proteins linked to DNA and RNA; members of the UPS; GTPase regulation; inflammation; and lipid metabolism. Noteworthy, protein levels of large clusters of hierarchically-related protein expression levels are stable until 70. However, protein levels of components of cell membranes, vesicles and synapses, RNA modulation, and cellular structures (including tau and tubulin filaments) are markedly altered from the age of 75. Similarly, marked modifications occur in the larger phosphoprotein clusters involving cytoskeleton and neuronal structures, membrane stabilization, and kinase regulation in the late elderly. CONCLUSIONS Present findings may increase understanding of human brain proteostasis modifications in the elderly in the subpopulation of individuals not having AD neuropathological change and any other neurodegenerative change in any telencephalon region.
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Affiliation(s)
- Pol Andrés-Benito
- Neurologic Diseases and Neurogenetics Group - Bellvitge Institute for Biomedical Research (IDIBE LL), L’Hospitalet de Llobregat, Barcelona 08907, Spain
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Ignacio Íñigo-Marco
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, Pamplona 31008, Spain
| | - Marta Brullas
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Neuropathology Group, Institute of Biomedical Research, IDIBELL, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Margarita Carmona
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Neuropathology Group, Institute of Biomedical Research, IDIBELL, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - José Antonio del Rio
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Molecular and Cellular Neurobiotechnology Group, Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute for Science and Technology, Science Park Barcelona (PCB), Barcelona 08028, Spain
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona 08007, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, Pamplona 31008, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Proteored-ISCIII, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), diSNA, Pamplona 31008, Spain
| | - Mónica Povedano
- Neurologic Diseases and Neurogenetics Group - Bellvitge Institute for Biomedical Research (IDIBE LL), L’Hospitalet de Llobregat, Barcelona 08907, Spain
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Isidro Ferrer
- CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Neuropathology Group, Institute of Biomedical Research, IDIBELL, L’Hospitalet de Llobregat, Barcelona 08907, Spain
- Department of Pathology and Experimental Therapeutics, University of Barcelona, L’Hospitalet de Llobregat, Barcelona 08907, Spain
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25
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Gibertini S, Ruggieri A, Cheli M, Maggi L. Protein Aggregates and Aggrephagy in Myopathies. Int J Mol Sci 2023; 24:ijms24098456. [PMID: 37176163 PMCID: PMC10179229 DOI: 10.3390/ijms24098456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
A number of muscular disorders are hallmarked by the aggregation of misfolded proteins within muscle fibers. A specialized form of macroautophagy, termed aggrephagy, is designated to remove and degrade protein aggregates. This review aims to summarize what has been studied so far about the direct involvement of aggrephagy and the activation of the key players, among others, p62, NBR1, Alfy, Tollip, Optineurin, TAX1BP1 and CCT2 in muscular diseases. In the first part of the review, we describe the aggrephagy pathway with the involved proteins; then, we illustrate the muscular disorder histologically characterized by protein aggregates, highlighting the role of aggrephagy pathway abnormalities in these muscular disorders.
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Affiliation(s)
- Sara Gibertini
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Alessandra Ruggieri
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Marta Cheli
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
| | - Lorenzo Maggi
- Neuroimmunology and Neuromuscular Diseases Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta", 20133 Milan, Italy
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26
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Collins MA, Avery R, Albert FW. Substrate-specific effects of natural genetic variation on proteasome activity. PLoS Genet 2023; 19:e1010734. [PMID: 37126494 PMCID: PMC10174532 DOI: 10.1371/journal.pgen.1010734] [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] [Received: 06/14/2022] [Revised: 05/11/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Protein degradation is an essential biological process that regulates protein abundance and removes misfolded and damaged proteins from cells. In eukaryotes, most protein degradation occurs through the stepwise actions of two functionally distinct entities, the ubiquitin system and the proteasome. Ubiquitin system enzymes attach ubiquitin to cellular proteins, targeting them for degradation. The proteasome then selectively binds and degrades ubiquitinated substrate proteins. Genetic variation in ubiquitin system genes creates heritable differences in the degradation of their substrates. However, the challenges of measuring the degradative activity of the proteasome independently of the ubiquitin system in large samples have limited our understanding of genetic influences on the proteasome. Here, using the yeast Saccharomyces cerevisiae, we built and characterized reporters that provide high-throughput, ubiquitin system-independent measurements of proteasome activity. Using single-cell measurements of proteasome activity from millions of genetically diverse yeast cells, we mapped 15 loci across the genome that influence proteasomal protein degradation. Twelve of these 15 loci exerted specific effects on the degradation of two distinct proteasome substrates, revealing a high degree of substrate-specificity in the genetics of proteasome activity. Using CRISPR-Cas9-based allelic engineering, we resolved a locus to a causal variant in the promoter of RPT6, a gene that encodes a subunit of the proteasome's 19S regulatory particle. The variant increases RPT6 expression, which we show results in increased proteasome activity. Our results reveal the complex genetic architecture of proteasome activity and suggest that genetic influences on the proteasome may be an important source of variation in the many cellular and organismal traits shaped by protein degradation.
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Affiliation(s)
- Mahlon A. Collins
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Randi Avery
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Frank W. Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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27
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Morgan EL, Toni T, Viswanathan R, Robbins Y, Yang X, Cheng H, Gunti S, Huynh A, Sowers AL, Mitchell JB, Allen CT, Chen Z, Van Waes C. Inhibition of USP14 promotes TNFα-induced cell death in head and neck squamous cell carcinoma (HNSCC). Cell Death Differ 2023; 30:1382-1396. [PMID: 37055579 PMCID: PMC10154301 DOI: 10.1038/s41418-023-01144-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 04/15/2023] Open
Abstract
TNFα is a key mediator of immune, chemotherapy and radiotherapy-induced cytotoxicity, but several cancers, including head and neck squamous cell carcinomas (HNSCC), display resistance to TNFα due to activation of the canonical NFκB pro-survival pathway. However, direct targeting of this pathway is associated with significant toxicity; thus, it is vital to identify novel mechanism(s) contributing to NFκB activation and TNFα resistance in cancer cells. Here, we demonstrate that the expression of proteasome-associated deubiquitinase USP14 is significantly increased in HNSCC and correlates with worse progression free survival in Human Papillomavirus (HPV)- HNSCC. Inhibition or depletion of USP14 inhibited the proliferation and survival of HNSCC cells. Further, USP14 inhibition reduced both basal and TNFα-inducible NFκB activity, NFκB-dependent gene expression and the nuclear translocation of the NFκB subunit RELA. Mechanistically, USP14 bound to both RELA and IκBα and reduced IκBα K48-ubiquitination leading to the degradation of IκBα, a critical inhibitor of the canonical NFκB pathway. Furthermore, we demonstrated that b-AP15, an inhibitor of USP14 and UCHL5, sensitized HNSCC cells to TNFα-mediated cell death, as well as radiation-induced cell death in vitro. Finally, b-AP15 delayed tumor growth and enhanced survival, both as a monotherapy and in combination with radiation, in HNSCC tumor xenograft models in vivo, which could be significantly attenuated by TNFα depletion. These data offer new insights into the activation of NFκB signaling in HNSCC and demonstrate that small molecule inhibitors targeting the ubiquitin pathway warrant further investigation as a novel therapeutic avenue to sensitize these cancers to TNFα- and radiation-induced cytotoxicity.
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Affiliation(s)
- Ethan L Morgan
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA.
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.
| | - Tiffany Toni
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
- NIH Medical Research Scholars Program, Bethesda, MD, USA
| | - Ramya Viswanathan
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Yvette Robbins
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Xinping Yang
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Hui Cheng
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Sreenivasulu Gunti
- Sinonasal and Skull Base Tumor Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Angel Huynh
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Anastasia L Sowers
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James B Mitchell
- Radiation Biology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clint T Allen
- Translational Tumor Immunology Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Zhong Chen
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Carter Van Waes
- Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
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28
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Abstract
Our understanding of the ubiquitin code has greatly evolved from conventional E1, E2 and E3 enzymes that modify Lys residues on specific substrates with a single type of ubiquitin chain to more complex processes that regulate and mediate ubiquitylation. In this Review, we discuss recently discovered endogenous mechanisms and unprecedented pathways by which pathogens rewrite the ubiquitin code to promote infection. These processes include unconventional ubiquitin modifications involving ester linkages with proteins, lipids and sugars, or ubiquitylation through a phosphoribosyl bridge involving Arg42 of ubiquitin. We also introduce the enzymatic pathways that write and reverse these modifications, such as the papain-like proteases of severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Furthermore, structural studies have revealed that the ultimate functions of ubiquitin are mediated not simply by straightforward recognition by ubiquitin-binding domains. Instead, elaborate multivalent interactions between ubiquitylated targets or ubiquitin chains and their readers (for example, the proteasome, the MLL1 complex or DOT1L) can elicit conformational changes that regulate protein degradation or transcription. The newly discovered mechanisms provide opportunities for innovative therapeutic interventions for diseases such as cancer and infectious diseases.
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Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
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29
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Sokolova O, Maubach G, Naumann M. Helicobacter pylori regulates TIFA turnover in gastric epithelial cells. Eur J Cell Biol 2023; 102:151307. [PMID: 36965415 DOI: 10.1016/j.ejcb.2023.151307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/01/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
The human pathogen Helicobacter pylori induces a strong inflammatory response in gastric mucosa manifested by the recruitment of neutrophils and macrophages to the places of infection, and by changes in epithelial integrity and function. At the molecular level, this innate immune response is essentially dependent on the activation of NF-κB transcription factors regulating the expression of chemotactic factors, e.g., IL-8. Recently, it has been demonstrated that the NF-κB signaling pathway is triggered by the bacterial heptose metabolites, which activate the host ALPK1-TIFA axis. TIFA has been suggested to promote oligomerization and activity of the E3 ubiquitin ligase TRAF6, which further stimulates TAK1-IKK signaling. Here, we demonstrate that ALPK1-dependent TIFA activation in H. pylori-infected gastric epithelial cells is followed in time by a decline in TIFA levels, and that this process is impeded by inhibitors of the proteasomal and lysosomal degradation. According to our data, TRAF2, TRAF6, TAK1 or NEMO are not required for TIFA degradation. Additionally, H. pylori promotes the interaction of TIFA with free polyubiquitin as well as with optineurin, TAX1BP1 and LAMP1, which are known protein adaptors involved in intracellular trafficking to lysosomes.
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Affiliation(s)
- Olga Sokolova
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany.
| | - Gunter Maubach
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
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30
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Buneeva OA, Kopylov AT, Medvedev AE. Proteasome Interactome and Its Role in the Mechanisms of Brain Plasticity. BIOCHEMISTRY (MOSCOW) 2023; 88:319-336. [PMID: 37076280 DOI: 10.1134/s0006297923030033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
Abstract
Proteasomes are highly conserved multienzyme complexes responsible for proteolytic degradation of the short-lived, regulatory, misfolded, and damaged proteins. They play an important role in the processes of brain plasticity, and decrease in their function is accompanied by the development of neurodegenerative pathology. Studies performed in different laboratories both on cultured mammalian and human cells and on preparations of the rat and rabbit brain cortex revealed a large number of proteasome-associated proteins. Since the identified proteins belong to certain metabolic pathways, multiple enrichment of the proteasome fraction with these proteins indicates their important role in proteasome functioning. Extrapolation of the experimental data, obtained on various biological objects, to the human brain suggests that the proteasome-associated proteins account for at least 28% of the human brain proteome. The proteasome interactome of the brain contains a large number of proteins involved in the assembly of these supramolecular complexes, regulation of their functioning, and intracellular localization, which could be changed under different conditions (for example, during oxidative stress) or in different phases of the cell cycle. In the context of molecular functions of the Gene Ontology (GO) Pathways, the proteins of the proteasome interactome mediate cross-talk between components of more than 30 metabolic pathways annotated in terms of GO. The main result of these interactions is binding of adenine and guanine nucleotides, crucial for realization of the nucleotide-dependent functions of the 26S and 20S proteasomes. Since the development of neurodegenerative pathology is often associated with regioselective decrease in the functional activity of proteasomes, a positive therapeutic effect would be obviously provided by the factors increasing proteasomal activity. In any case, pharmacological regulation of the brain proteasomes seems to be realized through the changes in composition and/or activity of the proteins associated with proteasomes (deubiquitinase, PKA, CaMKIIα, etc.).
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Affiliation(s)
- Olga A Buneeva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
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31
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Nguyen NH, Brodsky JL. The cellular pathways that maintain the quality control and transport of diverse potassium channels. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194908. [PMID: 36638864 PMCID: PMC9908860 DOI: 10.1016/j.bbagrm.2023.194908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Potassium channels are multi-subunit transmembrane proteins that permit the selective passage of potassium and play fundamental roles in physiological processes, such as action potentials in the nervous system and organismal salt and water homeostasis, which is mediated by the kidney. Like all ion channels, newly translated potassium channels enter the endoplasmic reticulum (ER) and undergo the error-prone process of acquiring post-translational modifications, folding into their native conformations, assembling with other subunits, and trafficking through the secretory pathway to reach their final destinations, most commonly the plasma membrane. Disruptions in these processes can result in detrimental consequences, including various human diseases. Thus, multiple quality control checkpoints evolved to guide potassium channels through the secretory pathway and clear potentially toxic, aggregation-prone misfolded species. We will summarize current knowledge on the mechanisms underlying potassium channel quality control in the secretory pathway, highlight diseases associated with channel misfolding, and suggest potential therapeutic routes.
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Affiliation(s)
- Nga H Nguyen
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, A320 Langley Hall, Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA.
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32
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Ambrosio FA, Costa G, Gallo Cantafio ME, Torcasio R, Trapasso F, Alcaro S, Viglietto G, Amodio N. Natural Agents as Novel Potential Source of Proteasome Inhibitors with Anti-Tumor Activity: Focus on Multiple Myeloma. Molecules 2023; 28:molecules28031438. [PMID: 36771100 PMCID: PMC9919276 DOI: 10.3390/molecules28031438] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Multiple myeloma (MM) is an aggressive and incurable disease for most patients, characterized by periods of treatment, remission and relapse. The introduction of new classes of drugs, such as proteasome inhibitors (PIs), has improved survival outcomes in these patient populations. The proteasome is the core of the ubiquitin-proteasome system (UPS), a complex and conserved pathway involved in the control of multiple cellular processes, including cell cycle control, transcription, DNA damage repair, protein quality control and antigen presentation. To date, PIs represent the gold standard for the treatment of MM. Bortezomib was the first PI approved by the FDA, followed by next generation of PIs, namely carfilzomib and ixazomib. Natural agents play an important role in anti-tumor drug discovery, and many of them have recently been reported to inhibit the proteasome, thus representing a new potential source of anti-MM drugs. Based on the pivotal biological role of the proteasome and on PIs' significance in the management of MM, in this review we aim to briefly summarize recent evidence on natural compounds capable of inhibiting the proteasome, thus triggering anti-MM activity.
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Affiliation(s)
- Francesca Alessandra Ambrosio
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: (G.C.); (N.A.)
| | - Maria Eugenia Gallo Cantafio
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Roberta Torcasio
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Department of Biology, Ecology and Earth Sciences (Di.B.E.S.T.), University of Calabria, 87036 Rende, Italy
| | - Francesco Trapasso
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Associazione CRISEA—Centro di Ricerca e Servizi Avanzati per l’Innovazione Rurale, Loc. Condoleo, 88055 Belcastro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Campus “S. Venuta”, University “Magna Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: (G.C.); (N.A.)
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The Ubiquitin-26S Proteasome Pathway and Its Role in the Ripening of Fleshy Fruits. Int J Mol Sci 2023; 24:ijms24032750. [PMID: 36769071 PMCID: PMC9917055 DOI: 10.3390/ijms24032750] [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: 11/26/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
The 26S proteasome is an ATP-dependent proteolytic complex in eukaryotes, which is mainly responsible for the degradation of damaged and misfolded proteins and some regulatory proteins in cells, and it is essential to maintain the balance of protein levels in the cell. The ubiquitin-26S proteasome pathway, which targets a wide range of protein substrates in plants, is an important post-translational regulatory mechanism involved in various stages of plant growth and development and in the maturation process of fleshy fruits. Fleshy fruit ripening is a complex biological process, which is the sum of a series of physiological and biochemical reactions, including the biosynthesis and signal transduction of ripening related hormones, pigment metabolism, fruit texture changes and the formation of nutritional quality. This paper reviews the structure of the 26S proteasome and the mechanism of the ubiquitin-26S proteasome pathway, and it summarizes the function of this pathway in the ripening process of fleshy fruits.
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Yu P, Hua Z. To Kill or to Be Killed: How Does the Battle between the UPS and Autophagy Maintain the Intracellular Homeostasis in Eukaryotes? Int J Mol Sci 2023; 24:ijms24032221. [PMID: 36768543 PMCID: PMC9917186 DOI: 10.3390/ijms24032221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
The ubiquitin-26S proteasome system and autophagy are two major protein degradation machineries encoded in all eukaryotic organisms. While the UPS is responsible for the turnover of short-lived and/or soluble misfolded proteins under normal growth conditions, the autophagy-lysosomal/vacuolar protein degradation machinery is activated under stress conditions to remove long-lived proteins in the forms of aggregates, either soluble or insoluble, in the cytoplasm and damaged organelles. Recent discoveries suggested an integrative function of these two seemly independent systems for maintaining the proteome homeostasis. One such integration is represented by their reciprocal degradation, in which the small 76-amino acid peptide, ubiquitin, plays an important role as the central signaling hub. In this review, we summarized the current knowledge about the activity control of proteasome and autophagosome at their structural organization, biophysical states, and turnover levels from yeast and mammals to plants. Through comprehensive literature studies, we presented puzzling questions that are awaiting to be solved and proposed exciting new research directions that may shed light on the molecular mechanisms underlying the biological function of protein degradation.
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Affiliation(s)
- Peifeng Yu
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
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Koçberber Z, Willemsen N, Bartelt A. The role of proteasome activators PA28αβ and PA200 in brown adipocyte differentiation and function. Front Endocrinol (Lausanne) 2023; 14:1176733. [PMID: 37201100 PMCID: PMC10187037 DOI: 10.3389/fendo.2023.1176733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/14/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction Brown adipocytes produce heat through non shivering thermogenesis (NST). To adapt to temperature cues, they possess a remarkably dynamic metabolism and undergo substantial cellular remodeling. The proteasome plays a central role in proteostasis and adaptive proteasome activity is required for sustained NST. Proteasome activators (PAs) are a class of proteasome regulators but the role of PAs in brown adipocytes is unknown. Here, we studied the roles of PA28α (encoded by Psme1) and PA200 (encoded by Psme4) in brown adipocyte differentiation and function. Methods We measured gene expression in mouse brown adipose tissue. In cultured brown adipocytes, we silenced Psme1 and/or Psme4 expression through siRNA transfection. We then assessed impact on the ubiquitin proteasome system, brown adipocyte differentiation and function. Results We found that Psme1 and Psme4 are expressed in brown adipocytes in vivo and in vitro. Through silencing of Psme1 and/or Psme4 expression in cultured brown adipocytes, we found that loss of PAs did not impair proteasome assembly or activity, and that PAs were not required for proteostasis in this model. Loss of Psme1 and/or Psme4 did not impair brown adipocyte development or activation, suggesting that PAs are neither required for brown adipogenesis nor NST. Discussion In summary, we found no role for Psme1 and Psme4 in brown adipocyte proteostasis, differentiation, or function. These findings contribute to our basic understanding of proteasome biology and the roles of proteasome activators in brown adipocytes.
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Affiliation(s)
- Zeynep Koçberber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Nienke Willemsen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Alexander Bartelt
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Ludwig-Maximilians-University Hospital, Munich, Germany
- Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Molecular Metabolism and Sabri Ülker Center for Metabolic Research, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- *Correspondence: Alexander Bartelt,
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Niemeyer M, Parra JOF, Calderón Villalobos LIA. An In vitro Assay to Recapitulate Hormone-Triggered and SCF-Mediated Protein Ubiquitylation. Methods Mol Biol 2023; 2581:43-56. [PMID: 36413309 DOI: 10.1007/978-1-0716-2784-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Signaling proteins trigger a sequence of molecular switches in the cell, which permit development, growth, and rapid adaptation to changing environmental conditions. SCF-type E3 ubiquitin ligases recognize signaling proteins prompting changes in their fate, one of these being ubiquitylation followed by degradation by the proteasome. SCFs together with their ubiquitylation targets (substrates) often serve as phytohormone receptors, responding and/or assembling in response to fluctuating intracellular hormone concentrations. Tracing and understanding phytohormone perception and SCF-mediated ubiquitylation of proteins could provide powerful clues on the molecular mechanisms utilized for plant adaptation. Here, we describe an adaptable in vitro system that uses recombinant proteins and enables the study of hormone-triggered SCF-substrate interaction and the dynamics of protein ubiquitylation. This system can serve to predict the requirements for protein recognition and to understand how phytohormone levels have the power to control protein fate.
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Affiliation(s)
- Michael Niemeyer
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany
| | - Jhonny Oscar Figueroa Parra
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany
| | - Luz Irina A Calderón Villalobos
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.
- KWS Gateway Research Center, LLC, BRDG Park at the Danforth Plant Science Center, St. Louis, MO, USA.
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Abstract
Cellular homeostasis requires the swift and specific removal of damaged material. Selective autophagy represents a major pathway for the degradation of such cargo material. This is achieved by the sequestration of the cargo within double-membrane vesicles termed autophagosomes, which form de novo around the cargo and subsequently deliver their content to lysosomes for degradation. The importance of selective autophagy is exemplified by the various neurodegenerative diseases associated with defects in this pathway, including Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal dementia. It has become evident that cargo receptors are acting as Swiss army knives in selective autophagy by recognizing the cargo, orchestrating the recruitment of the machinery for autophagosome biogenesis, and closely aligning the membrane with the cargo. Furthermore, cargo receptors sequester ubiquitinated proteins into larger condensates upstream of autophagy induction. Here, we review recent insights into the mechanisms of action of cargo receptors in selective autophagy by focusing on the roles of sequestosome-like cargo receptors in the degradation of misfolded, ubiquitinated proteins and damaged mitochondria. We also highlight at which steps defects in their function result in the accumulation of harmful material and how this knowledge may guide the design of future therapies.
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Affiliation(s)
- Elias Adriaenssens
- Max Perutz Labs, Vienna BioCenter, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Luca Ferrari
- Max Perutz Labs, Vienna BioCenter, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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38
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Sparks A, Kelly CJ, Saville MK. Ubiquitin receptors play redundant roles in the proteasomal degradation of the p53 repressor MDM2. FEBS Lett 2022; 596:2746-2767. [PMID: 35735670 PMCID: PMC9796813 DOI: 10.1002/1873-3468.14436] [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: 05/11/2022] [Revised: 06/01/2022] [Accepted: 06/05/2022] [Indexed: 01/07/2023]
Abstract
Much remains to be determined about the participation of ubiquitin receptors in proteasomal degradation and their potential as therapeutic targets. Suppression of the ubiquitin receptor S5A/PSMD4/hRpn10 alone stabilises p53/TP53 but not the key p53 repressor MDM2. Here, we observed S5A and the ubiquitin receptors ADRM1/PSMD16/hRpn13 and RAD23A and B functionally overlap in MDM2 degradation. We provide further evidence that degradation of only a subset of ubiquitinated proteins is sensitive to S5A knockdown because ubiquitin receptor redundancy is commonplace. p53 can be upregulated by S5A modulation while degradation of substrates with redundant receptors is maintained. Our observations and analysis of Cancer Dependency Map (DepMap) screens show S5A depletion/loss substantially reduces cancer cell line viability. This and selective S5A dependency of proteasomal substrates make S5A a target of interest for cancer therapy.
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Affiliation(s)
| | - Christopher J. Kelly
- School of MedicineUniversity of DundeeUK,Institute of Infection, Immunity and InflammationUniversity of GlasgowUK
| | - Mark K. Saville
- School of MedicineUniversity of DundeeUK,Silver River EditingDundeeUK
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Osei-Amponsa V, Walters KJ. Proteasome substrate receptors and their therapeutic potential. Trends Biochem Sci 2022; 47:950-964. [PMID: 35817651 PMCID: PMC9588529 DOI: 10.1016/j.tibs.2022.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 11/22/2022]
Abstract
The ubiquitin-proteasome system (UPS) is critical for protein quality control and regulating protein lifespans. Following ubiquitination, UPS substrates bind multidomain receptors that, in addition to ubiquitin-binding sites, contain functional domains that bind to deubiquitinating enzymes (DUBs) or the E3 ligase E6AP/UBE3A. We provide an overview of the proteasome, focusing on its receptors and DUBs. We highlight the key role of dynamics and importance of the substrate receptors having domains for both binding and processing ubiquitin chains. The UPS is rich with therapeutic opportunities, with proteasome inhibitors used clinically and ongoing development of small molecule proteolysis targeting chimeras (PROTACs) for the degradation of disease-associated proteins. We discuss the therapeutic potential of proteasome receptors, including hRpn13, for which PROTACs have been developed.
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Affiliation(s)
- Vasty Osei-Amponsa
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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Lou Y, Ye M, Xu C, Tao F. Insight into the physiological and pathological roles of USP44, a potential tumor target (Review). Oncol Lett 2022; 24:455. [PMID: 36380875 PMCID: PMC9650596 DOI: 10.3892/ol.2022.13575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 10/06/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitin-specific peptidase 44 (USP44) is a member of the ubiquitin-specific proteases (USPs) family and its functions in various biological processes have been gradually elucidated in recent years. USP44 targets multiple downstream factors and regulates multiple mechanisms through its deubiquitination activity. Ubiquitination is, in essence, a process in which a single ubiquitin molecule or a multiubiquitin chain binds to a substrate protein to form an isopeptide bond. Deubiquitination is the catalyzing of the isopeptide bonds between ubiquitin and substrate proteins through deubiquitylating enzymes. These two processes serve an important role in the regulation of the expression, conformation, localization and function of substrate proteins by regulating their binding to ubiquitin. Based on existing research, this paper summarized the current state of knowledge about USP44. The physiological roles of USP44 in various cellular events and its pathophysiological roles in different cancer types are evaluated and the therapeutic potential of USP44 for cancer treatment is evaluated.
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Affiliation(s)
- Yuming Lou
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 321000, P.R. China,Department of Stomach and Intestine Surgery, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, P.R. China
| | - Minfeng Ye
- Department of Stomach and Intestine Surgery, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, P.R. China
| | - Chaoyang Xu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 321000, P.R. China,Department of Stomach and Intestine Surgery, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, P.R. China,Correspondence to: Dr Chaoyang Xu, Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, 365 Renmin East Road, Jinhua, Zhejiang 321000, P.R. China, E-mail:
| | - Feng Tao
- Department of Stomach and Intestine Surgery, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang 312000, P.R. China,Professor Feng Tao, Department of Stomach and Intestine Surgery, Shaoxing Hospital, Zhejiang University School of Medicine, 568 Zhongxing North Road, Shaoxing, Zhejiang 312000, P.R. China, E-mail:
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Biran A, Myers N, Steinberger S, Adler J, Riutin M, Broennimann K, Reuven N, Shaul Y. The C-Terminus of the PSMA3 Proteasome Subunit Preferentially Traps Intrinsically Disordered Proteins for Degradation. Cells 2022; 11:cells11203231. [PMID: 36291102 PMCID: PMC9600399 DOI: 10.3390/cells11203231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 12/29/2022] Open
Abstract
The degradation of intrinsically disordered proteins (IDPs) by a non-26S proteasome process does not require proteasomal targeting by polyubiquitin. However, whether and how IDPs are recognized by the non-26S proteasome, including the 20S complex, remains unknown. Analyses of protein interactome datasets revealed that the 20S proteasome subunit, PSMA3, preferentially interacts with many IDPs. In vivo and cell-free experiments revealed that the C-terminus of PSMA3, a 69-amino-acids-long fragment, is an IDP trapper. A recombinant trapper is sufficient to interact with many IDPs, and blocks IDP degradation in vitro by the 20S proteasome, possibly by competing with the native trapper. In addition, over a third of the PSMA3 trapper-binding proteins have previously been identified as 20S proteasome substrates and, based on published datasets, many of the trapper-binding proteins are associated with the intracellular proteasomes. The PSMA3-trapped IDPs that are proteasome substrates have the unique features previously recognized as characteristic 20S proteasome substrates in vitro. We propose a model whereby the PSMA3 C-terminal region traps a subset of IDPs to facilitate their proteasomal degradation.
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42
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Lin BC, Higgins NR, Phung TH, Monteiro MJ. UBQLN proteins in health and disease with a focus on UBQLN2 in ALS/FTD. FEBS J 2022; 289:6132-6153. [PMID: 34273246 PMCID: PMC8761781 DOI: 10.1111/febs.16129] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023]
Abstract
Ubiquilin (UBQLN) proteins are a dynamic and versatile family of proteins found in all eukaryotes that function in the regulation of proteostasis. Besides their canonical function as shuttle factors in delivering misfolded proteins to the proteasome and autophagy systems for degradation, there is emerging evidence that UBQLN proteins play broader roles in proteostasis. New information suggests the proteins function as chaperones in protein folding, protecting proteins prior to membrane insertion, and as guardians for mitochondrial protein import. In this review, we describe the evidence for these different roles, highlighting how different domains of the proteins impart these functions. We also describe how changes in the structure and phase separation properties of UBQLNs may regulate their activity and function. Finally, we discuss the pathogenic mechanisms by which mutations in UBQLN2 cause amyotrophic lateral sclerosis and frontotemporal dementia. We describe the animal model systems made for different UBQLN2 mutations and how lessons learnt from these systems provide fundamental insight into the molecular mechanisms by which UBQLN2 mutations drive disease pathogenesis through disturbances in proteostasis.
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Affiliation(s)
- Brian C. Lin
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicole R. Higgins
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Trong H. Phung
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mervyn J. Monteiro
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence. Commun Biol 2022; 5:1043. [PMID: 36180574 PMCID: PMC9525688 DOI: 10.1038/s42003-022-03998-2] [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: 05/13/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.
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44
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Yu P, Hua Z. The ubiquitin-26S proteasome system and autophagy relay proteome homeostasis regulation during silique development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1324-1339. [PMID: 35780489 PMCID: PMC9545597 DOI: 10.1111/tpj.15891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 06/20/2022] [Accepted: 06/28/2022] [Indexed: 05/26/2023]
Abstract
Functional studies of the ubiquitin-26S proteasome system (UPS) have demonstrated that virtually all aspects of the plant's life involve UPS-mediated turnover of abnormal or short-lived proteins. However, the role of the UPS during development, including in seeds and fruits, remains to be determined in detail, although mutants of several of its core elements are known to be embryonically lethal. Unfortunately, early termination of embryogenesis limits the possibility to characterize the activities of the UPS in reproductive organs. Given both the economic and the societal impact of reproductive production, such studies are indispensable. Here, we systematically compared expression of multiple 26S proteasome subunits along with the dynamics of proteasome activity and total protein ubiquitylation in seedlings, developing siliques, and embryos of Arabidopsis thaliana. Since autophagy plays the second largest role in maintaining proteome stability, we parallelly studied three rate-limiting enzymes that are involved in autophagy flux. Our experiments unexpectedly discovered that, in contrast to the activities in seedlings, both protein and transcript levels of six selected 26S proteasome subunits gradually decline in immature siliques or embryos toward maturation while the autophagy flux rises despite the nutrient-rich condition. We also discovered a reciprocal turnover pathway between the proteasome and autophagy. While the autophagy flux is suppressed in seedlings by UPS-mediated degradation of its three key enzymes, transcriptional reprogramming dampens this process in siliques, which in turn stimulates a bulk autophagic degradation of proteasomes. Collectively, our study of the developmental changes of the UPS and autophagy activities suggests that they relay the proteome homeostasis regulation in early silique and/or seed development, highlighting their interactions during development.
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Affiliation(s)
- Peifeng Yu
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701USA
- Interdisciplinary Program in Molecular and Cellular BiologyOhio UniversityAthensOhio45701USA
| | - Zhihua Hua
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701USA
- Interdisciplinary Program in Molecular and Cellular BiologyOhio UniversityAthensOhio45701USA
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Protein Quality Control in Glioblastoma: A Review of the Current Literature with New Perspectives on Therapeutic Targets. Int J Mol Sci 2022; 23:ijms23179734. [PMID: 36077131 PMCID: PMC9456419 DOI: 10.3390/ijms23179734] [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: 07/06/2022] [Revised: 08/12/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Protein quality control allows eukaryotes to maintain proteostasis under the stress of constantly changing conditions. In this review, we discuss the current literature on PQC, highlighting flaws that must exist for malignancy to occur. At the nidus of PQC, the expression of BAG1-6 reflects the cell environment; each isoform directs proteins toward different, parallel branches of the quality control cascade. The sum of these branches creates a net shift toward either homeostasis or apoptosis. With an established role in ALP, Bag3 is necessary for cell survival in stress conditions including those of the cancerous niche (i.e., hypoxia, hypermutation). Evidence suggests that excessive Bag3–HSP70 activity not only sustains, but also propagates cancers. Its role is anti-apoptotic—which allows malignant cells to persist—and intercellular—with the production of infectious ‘oncosomes’ enabling cancer expansion and recurrence. While Bag3 has been identified as a key prognostic indicator in several cancer types, its investigation is limited regarding glioblastoma. The cochaperone HSP70 has been strongly linked with GBM, while ALP inhibitors have been shown to improve GBM susceptibility to chemotherapeutics. Given the highly resilient, frequently recurrent nature of GBM, the targeting of Bag3 is a necessary consideration for the successful and definitive treatment of GBM.
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Anderson RT, Bradley TA, Smith DM. Hyperactivation of the proteasome in Caenorhabditis elegans protects against proteotoxic stress and extends lifespan. J Biol Chem 2022; 298:102415. [PMID: 36007615 PMCID: PMC9486566 DOI: 10.1016/j.jbc.2022.102415] [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: 06/01/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Virtually all age-related neurodegenerative diseases (NDs) can be characterized by the accumulation of proteins inside and outside the cell that are thought to significantly contribute to disease pathogenesis. One of the cell’s primary systems for the degradation of misfolded/damaged proteins is the ubiquitin proteasome system (UPS), and its impairment is implicated in essentially all NDs. Thus, upregulating this system to combat NDs has garnered a great deal of interest in recent years. Various animal models have focused on stimulating 26S activity and increasing 20S proteasome levels, but thus far, none have targeted intrinsic activation of the 20S proteasome itself. Therefore, we constructed an animal model that endogenously expresses a hyperactive, open gate proteasome in Caenorhabditis elegans. The gate-destabilizing mutation that we introduced into the nematode germline yielded a viable nematode population with enhanced proteasomal activity, including peptide, unstructured protein, and ubiquitin-dependent degradation activities. We determined these nematodes showed a significantly increased lifespan and substantial resistance to oxidative and proteotoxic stress but a significant decrease in fecundity. Our results show that introducing a constitutively active proteasome into a multicellular organism is feasible and suggests targeting the proteasome gating mechanism as a valid approach for future age-related disease research efforts in mammals.
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Affiliation(s)
- Raymond T Anderson
- Department of Biochemistry, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV 26506
| | - Thomas A Bradley
- Department of Biochemistry, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV 26506
| | - David M Smith
- Department of Biochemistry, West Virginia University School of Medicine, 64 Medical Center Dr., Morgantown, WV 26506.
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Dreier JE, Prestel A, Martins JM, Brøndum SS, Nielsen O, Garbers AE, Suga H, Boomsma W, Rogers JM, Hartmann-Petersen R, Kragelund BB. A context-dependent and disordered ubiquitin-binding motif. Cell Mol Life Sci 2022; 79:484. [PMID: 35974206 PMCID: PMC9381478 DOI: 10.1007/s00018-022-04486-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023]
Abstract
Ubiquitin is a small, globular protein that is conjugated to other proteins as a posttranslational event. A palette of small, folded domains recognizes and binds ubiquitin to translate and effectuate this posttranslational signal. Recent computational studies have suggested that protein regions can recognize ubiquitin via a process of folding upon binding. Using peptide binding arrays, bioinformatics, and NMR spectroscopy, we have uncovered a disordered ubiquitin-binding motif that likely remains disordered when bound and thus expands the palette of ubiquitin-binding proteins. We term this motif Disordered Ubiquitin-Binding Motif (DisUBM) and find it to be present in many proteins with known or predicted functions in degradation and transcription. We decompose the determinants of the motif showing it to rely on features of aromatic and negatively charged residues, and less so on distinct sequence positions in line with its disordered nature. We show that the affinity of the motif is low and moldable by the surrounding disordered chain, allowing for an enhanced interaction surface with ubiquitin, whereby the affinity increases ~ tenfold. Further affinity optimization using peptide arrays pushed the affinity into the low micromolar range, but compromised context dependence. Finally, we find that DisUBMs can emerge from unbiased screening of randomized peptide libraries, featuring in de novo cyclic peptides selected to bind ubiquitin chains. We suggest that naturally occurring DisUBMs can recognize ubiquitin as a posttranslational signal to act as affinity enhancers in IDPs that bind to folded and ubiquitylated binding partners.
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Affiliation(s)
- Jesper E Dreier
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - João M Martins
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Sebastian S Brøndum
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Olaf Nielsen
- Functional Genomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anna E Garbers
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen Ø, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
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48
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Rethi-Nagy Z, Abraham E, Udvardy K, Klement E, Darula Z, Pal M, Katona RL, Tubak V, Pali T, Kota Z, Sinka R, Udvardy A, Lipinszki Z. STABILON, a Novel Sequence Motif That Enhances the Expression and Accumulation of Intracellular and Secreted Proteins. Int J Mol Sci 2022; 23:ijms23158168. [PMID: 35897744 PMCID: PMC9332151 DOI: 10.3390/ijms23158168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
The dynamic balance of transcriptional and translational regulation together with degron-controlled proteolysis shapes the ever-changing cellular proteome. While a large variety of degradation signals has been characterized, our knowledge of cis-acting protein motifs that can in vivo stabilize otherwise short-lived proteins is very limited. We have identified and characterized a conserved 13-mer protein segment derived from the p54/Rpn10 ubiquitin receptor subunit of the Drosophila 26S proteasome, which fulfills all the characteristics of a protein stabilization motif (STABILON). Attachment of STABILON to various intracellular as well as medically relevant secreted model proteins resulted in a significant increase in their cellular or extracellular concentration in mammalian cells. We demonstrate that STABILON acts as a universal and dual function motif that, on the one hand, increases the concentration of the corresponding mRNAs and, on the other hand, prevents the degradation of short-lived fusion proteins. Therefore, STABILON may lead to a breakthrough in biomedical recombinant protein production.
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Affiliation(s)
- Zsuzsanna Rethi-Nagy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Edit Abraham
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | - Katalin Udvardy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | - Eva Klement
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), H-6726 Szeged, Hungary; (E.K.); (Z.D.)
- Biological Research Centre, Laboratory of Proteomics Research, ELKH, H-6726 Szeged, Hungary
| | - Zsuzsanna Darula
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), H-6726 Szeged, Hungary; (E.K.); (Z.D.)
- Biological Research Centre, Laboratory of Proteomics Research, ELKH, H-6726 Szeged, Hungary
| | - Margit Pal
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | | | - Vilmos Tubak
- Creative Laboratory Ltd., H-6726 Szeged, Hungary;
| | - Tibor Pali
- Biological Research Centre, Institute of Biophysics, ELKH, H-6726 Szeged, Hungary; (T.P.); (Z.K.)
| | - Zoltan Kota
- Biological Research Centre, Institute of Biophysics, ELKH, H-6726 Szeged, Hungary; (T.P.); (Z.K.)
| | - Rita Sinka
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Correspondence: (R.S.); (A.U.); (Z.L.)
| | - Andor Udvardy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Correspondence: (R.S.); (A.U.); (Z.L.)
| | - Zoltan Lipinszki
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Correspondence: (R.S.); (A.U.); (Z.L.)
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49
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Zhang M, Berk JM, Mehrtash AB, Kanyo J, Hochstrasser M. A versatile new tool derived from a bacterial deubiquitylase to detect and purify ubiquitylated substrates and their interacting proteins. PLoS Biol 2022; 20:e3001501. [PMID: 35771886 PMCID: PMC9278747 DOI: 10.1371/journal.pbio.3001501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/13/2022] [Accepted: 05/30/2022] [Indexed: 01/07/2023] Open
Abstract
Protein ubiquitylation is an important posttranslational modification affecting a wide range of cellular processes. Due to the low abundance of ubiquitylated species in biological samples, considerable effort has been spent on methods to purify and detect ubiquitylated proteins. We have developed and characterized a novel tool for ubiquitin detection and purification based on OtUBD, a high-affinity ubiquitin-binding domain (UBD) derived from an Orientia tsutsugamushi deubiquitylase (DUB). We demonstrate that OtUBD can be used to purify both monoubiquitylated and polyubiquitylated substrates from yeast and human tissue culture samples and compare their performance with existing methods. Importantly, we found conditions for either selective purification of covalently ubiquitylated proteins or co-isolation of both ubiquitylated proteins and their interacting proteins. As proof of principle for these newly developed methods, we profiled the ubiquitylome and ubiquitin-associated proteome of the budding yeast Saccharomyces cerevisiae. Combining OtUBD affinity purification with quantitative proteomics, we identified potential substrates for the E3 ligases Bre1 and Pib1. OtUBD provides a versatile, efficient, and economical tool for ubiquitin research with specific advantages over certain other methods, such as in efficiently detecting monoubiquitylation or ubiquitin linkages to noncanonical sites. This study presents OtUBD, a new tool derived from a bacterial deubiquitylase, for the purification and analysis of a broad range of endogenous ubiquitylated proteins, including monoubiquitylation, polyubiquitylation, non-lysine ubiquitylation and potentially other macromolecules.
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Affiliation(s)
- Mengwen Zhang
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jason M. Berk
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Adrian B. Mehrtash
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jean Kanyo
- W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut, United States of America
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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50
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Behl T, Kumar S, Althafar ZM, Sehgal A, Singh S, Sharma N, Badavath VN, Yadav S, Bhatia S, Al-Harrasi A, Almoshari Y, Almikhlafi MA, Bungau S. Exploring the Role of Ubiquitin-Proteasome System in Parkinson's Disease. Mol Neurobiol 2022; 59:4257-4273. [PMID: 35505049 DOI: 10.1007/s12035-022-02851-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023]
Abstract
Over the last decade, researchers have discovered that a group of apparently unrelated neurodegenerative disorders, such as Parkinson's disease, have remarkable cellular and molecular biology similarities. Protein misfolding and aggregation are involved in all of the neurodegenerative conditions; as a result, inclusion bodies aggregation starts in the cells. Chaperone proteins and ubiquitin (26S proteasome's proteolysis signal), which aid in refolding misfolded proteins, are frequently found in these aggregates. The discovery of disease-causing gene alterations that code for multiple ubiquitin-proteasome pathway proteins in Parkinson's disease has strengthened the relationship between the ubiquitin-proteasome system and neurodegeneration. The specific molecular linkages between these systems and pathogenesis, on the other hand, are unknown and controversial. We outline the current level of knowledge in this article, focusing on important unanswered problems.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Sachin Kumar
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Ziyad M Althafar
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences in Alquwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | | | - Shivam Yadav
- Yashraj Institute of Pharmacy, Uttar Pradesh, India
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.,School of Health Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Yosif Almoshari
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohannad A Almikhlafi
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibha University, Madinah, Saudi Arabia
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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