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Arkinson C, Dong KC, Gee CL, Martin A. Mechanisms and regulation of substrate degradation by the 26S proteasome. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00778-0. [PMID: 39362999 DOI: 10.1038/s41580-024-00778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2024] [Indexed: 10/05/2024]
Abstract
The 26S proteasome is involved in degrading and regulating the majority of proteins in eukaryotic cells, which requires a sophisticated balance of specificity and promiscuity. In this Review, we discuss the principles that underly substrate recognition and ATP-dependent degradation by the proteasome. We focus on recent insights into the mechanisms of conventional ubiquitin-dependent and ubiquitin-independent protein turnover, and discuss the plethora of modulators for proteasome function, including substrate-delivering cofactors, ubiquitin ligases and deubiquitinases that enable the targeting of a highly diverse substrate pool. Furthermore, we summarize recent progress in our understanding of substrate processing upstream of the 26S proteasome by the p97 protein unfoldase. The advances in our knowledge of proteasome structure, function and regulation also inform new strategies for specific inhibition or harnessing the degradation capabilities of the proteasome for the treatment of human diseases, for instance, by using proteolysis targeting chimera molecules or molecular glues.
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Affiliation(s)
- Connor Arkinson
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Ken C Dong
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Christine L Gee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Andreas Martin
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA.
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2
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Samuel VP, Moglad E, Afzal M, Kazmi I, Alzarea SI, Ali H, Almujri SS, Abida, Imran M, Gupta G, Chinni SV, Tiwari A. Exploring Ubiquitin-specific proteases as therapeutic targets in Glioblastoma. Pathol Res Pract 2024; 260:155443. [PMID: 38981348 DOI: 10.1016/j.prp.2024.155443] [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: 06/01/2024] [Revised: 06/24/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024]
Abstract
Glioblastoma (GB) remains a formidable challenge and requires new treatment strategies. The vital part of the Ubiquitin-proteasome system (UPS) in cellular regulation has positioned it as a potentially crucial target in GB treatment, given its dysregulation oncolines. The Ubiquitin-specific proteases (USPs) in the UPS system were considered due to the garden role in the cellular processes associated with oncolines and their vital function in the apoptotic process, cell cycle regulation, and autophagy. The article provides a comprehensive summary of the evidence base for targeting USPs as potential factors for neoplasm treatment. The review considers the participation of the UPS system in the development, resulting in the importance of p53, Rb, and NF-κB, and evaluates specific goals for therapeutic administration using midnight proteasomal inhibitors and small molecule antagonists of E1 and E2 enzymes. Despite the slowed rate of drug creation, recent therapeutic discoveries based on USP system dynamics hold promise for specialized therapies. The review concludes with an analysis of future wanderers and the feasible effects of targeting USPs on personalized GB therapies, which can improve patient hydration in this current and unattractive therapeutic landscape. The manuscript emphasizes the possibility of USP oncogene therapy as a promising alternative treatment line for GB. It stresses the direct creation of research on the medical effectiveness of the approach.
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Affiliation(s)
- Vijaya Paul Samuel
- Department of Anatomy, RAK College of Medicine, RAK Medical and Health Sciences University, Ras Al Khaimah, the United Arab Emirates
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Al-Jouf, Saudi Arabia
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Aseer 61421, Saudi Arabia
| | - Abida
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Gaurav Gupta
- Centre for Research Impact & Outcome-Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Suresh V Chinni
- Department of Biochemistry, Faculty of Medicine, Bioscience, and Nursing, MAHSA University, Jenjarom, Selangor 42610, Malaysia
| | - Abhishek Tiwari
- Department of Pharmacy, Pharmacy Academy, IFTM University, Lodhipur-Rajpur, Moradabad 244102, India.
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3
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Wen P, Sun Y, Jiang TX, Qiu XB. PA200-Mediated Proteasomal Protein Degradation and Regulation of Cellular Senescence. Int J Mol Sci 2024; 25:5637. [PMID: 38891826 PMCID: PMC11171664 DOI: 10.3390/ijms25115637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 06/21/2024] Open
Abstract
Cellular senescence is closely related to DNA damage, proteasome inactivity, histone loss, epigenetic alterations, and tumorigenesis. The mammalian proteasome activator PA200 (also referred to as PSME4) or its yeast ortholog Blm10 promotes the acetylation-dependent degradation of the core histones during transcription, DNA repair, and spermatogenesis. According to recent studies, PA200 plays an important role in senescence, probably because of its role in promoting the degradation of the core histones. Loss of PA200 or Blm10 is a major cause of the decrease in proteasome activity during senescence. In this paper, recent research progress on the association of PA200 with cellular senescence is summarized, and the potential of PA200 to serve as a therapeutic target in age-related diseases is discussed.
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Affiliation(s)
- Pei Wen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
| | - Yan Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
| | - Tian-Xia Jiang
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Xiao-Bo Qiu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
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4
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Akizuki Y, Kaypee S, Ohtake F, Ikeda F. The emerging roles of non-canonical ubiquitination in proteostasis and beyond. J Cell Biol 2024; 223:e202311171. [PMID: 38517379 PMCID: PMC10959754 DOI: 10.1083/jcb.202311171] [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: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Ubiquitin regulates various cellular functions by posttranslationally modifying substrates with diverse ubiquitin codes. Recent discoveries of new ubiquitin chain topologies, types of bonds, and non-protein substrates have substantially expanded the complexity of the ubiquitin code. Here, we describe the ubiquitin system covering the basic principles and recent discoveries related to mechanisms, technologies, and biological importance.
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Affiliation(s)
- Yoshino Akizuki
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Stephanie Kaypee
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Fumiyo Ikeda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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5
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Lu X, Chandravanshi M, Sabbasani VR, Gaikwad S, Hughitt VK, Gyabaah-Kessie N, Scroggins BT, Das S, Myint W, Clapp ME, Schwieters CD, Dyba MA, Bolhuis DL, Koscielniak JW, Andresson T, Emanuele MJ, Brown NG, Matsuo H, Chari R, Citrin DE, Mock BA, Swenson RE, Walters KJ. A structure-based designed small molecule depletes hRpn13 Pru and a select group of KEN box proteins. Nat Commun 2024; 15:2485. [PMID: 38509117 PMCID: PMC10954691 DOI: 10.1038/s41467-024-46644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Proteasome subunit hRpn13 is partially proteolyzed in certain cancer cell types to generate hRpn13Pru by degradation of its UCHL5/Uch37-binding DEUBAD domain and retention of an intact proteasome- and ubiquitin-binding Pru domain. By using structure-guided virtual screening, we identify an hRpn13 binder (XL44) and solve its structure ligated to hRpn13 Pru by integrated X-ray crystallography and NMR to reveal its targeting mechanism. Surprisingly, hRpn13Pru is depleted in myeloma cells following treatment with XL44. TMT-MS experiments reveal a select group of off-targets, including PCNA clamp-associated factor PCLAF and ribonucleoside-diphosphate reductase subunit M2 (RRM2), that are similarly depleted by XL44 treatment. XL44 induces hRpn13-dependent apoptosis and also restricts cell viability by a PCLAF-dependent mechanism. A KEN box, but not ubiquitination, is required for XL44-induced depletion of PCLAF. Here, we show that XL44 induces ubiquitin-dependent loss of hRpn13Pru and ubiquitin-independent loss of select KEN box containing proteins.
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Affiliation(s)
- Xiuxiu Lu
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Monika Chandravanshi
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Venkata R Sabbasani
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Snehal Gaikwad
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - V Keith Hughitt
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nana Gyabaah-Kessie
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bradley T Scroggins
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Wazo Myint
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michelle E Clapp
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marzena A Dyba
- Biophysics Resource, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Janusz W Koscielniak
- Basic Science Program, Leidos Biomedical Research Inc., NMR Facility for Biological Research, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hiroshi Matsuo
- Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Deborah E Citrin
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rolf E Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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Osei-Amponsa V, Chandravanshi M, Lu X, Magidson V, Das S, Andresson T, Dyba M, Sabbasani VR, Swenson RE, Fromont C, Shrestha B, Zhao Y, Clapp ME, Chari R, Walters KJ. hRpn13 shapes the proteome and transcriptome through epigenetic factors HDAC8, PADI4, and transcription factor NF-κB p50. Mol Cell 2024; 84:522-537.e8. [PMID: 38151017 PMCID: PMC10872465 DOI: 10.1016/j.molcel.2023.11.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023]
Abstract
The anti-cancer target hRpn13 is a proteasome substrate receptor. However, hRpn13-targeting molecules do not impair its interaction with proteasomes or ubiquitin, suggesting other critical cellular activities. We find that hRpn13 depletion causes correlated proteomic and transcriptomic changes, with pronounced effects in myeloma cells for cytoskeletal and immune response proteins and bone-marrow-specific arginine deiminase PADI4. Moreover, a PROTAC against hRpn13 co-depletes PADI4, histone deacetylase HDAC8, and DNA methyltransferase MGMT. PADI4 binds and citrullinates hRpn13 and proteasomes, and proteasomes from PADI4-inhibited myeloma cells exhibit reduced peptidase activity. When off proteasomes, hRpn13 can bind HDAC8, and this interaction inhibits HDAC8 activity. Further linking hRpn13 to transcription, its loss reduces nuclear factor κB (NF-κB) transcription factor p50, which proteasomes generate by cleaving its precursor protein. NF-κB inhibition depletes hRpn13 interactors PADI4 and HDAC8. Altogether, we find that hRpn13 acts dually in protein degradation and expression and that proteasome constituency and, in turn, regulation varies by cell type.
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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
| | - Monika Chandravanshi
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Xiuxiu Lu
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Valentin Magidson
- Optical Microscopy and Image Analysis Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD 21702, USA
| | - Marzena Dyba
- Biophysics Resource, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Venkata R Sabbasani
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rolf E Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Caroline Fromont
- Sequencing Facility, Cancer Research and Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Biraj Shrestha
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Yongmei Zhao
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michelle E Clapp
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, 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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7
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Song J, Liu Y, Yin Y, Wang H, Zhang X, Li Y, Zhao X, Zhang G, Meng X, Jin Y, Lu D, Yin Y. PTIR1 acts as an isoform of DDX58 and promotes tumor immune resistance through activation of UCHL5. Cell Rep 2023; 42:113388. [PMID: 37934668 DOI: 10.1016/j.celrep.2023.113388] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/22/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Cancer evades host immune surveillance by virtue of poor immunogenicity. Here, we report an immune suppressor, designated as PTIR1, that acts as a promotor of tumor immune resistance. PTIR1 is selectively induced in human cancers via alternative splicing of DDX58 (RIG-I), and its induction is closely related to poor outcome in patients with cancer. Through blocking the recruitment of leukocytes, PTIR1 facilitates cancer immune escape and tumor-intrinsic resistance to immunotherapeutic treatments. Unlike RIG-I, PTIR1 is capable of binding to the C terminus of UCHL5 and activates its ubiquitinating function, which in turn inhibits immunoproteasome activity and limits neoantigen processing and presentation, consequently blocking T cell recognition and attack against cancer. Moreover, we find that the adenosine deaminase ADAR1 induces A-to-I RNA editing on DDX58 transcript, thus triggering PTIR1 production. Collectively, our data uncover the immunosuppressive role of PTIR1 in tumorigenesis and propose that ADAR1-PTIR1-UCHL5 signaling is a potential cancer immunotherapeutic target.
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Affiliation(s)
- Jia Song
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yang Liu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yue Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Hui Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xin Zhang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yang Li
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xuyang Zhao
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Guangze Zhang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Xiangyan Meng
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Yan Jin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Dan Lu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China.
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, P.R. China; Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen 518036, P.R. China.
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8
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Pispa J, Mikkonen E, Arpalahti L, Jin C, Martínez-Fernández C, Cerón J, Holmberg CI. AKIR-1 regulates proteasome subcellular function in Caenorhabditis elegans. iScience 2023; 26:107886. [PMID: 37767001 PMCID: PMC10520889 DOI: 10.1016/j.isci.2023.107886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/07/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Polyubiquitinated proteins are primarily degraded by the ubiquitin-proteasome system (UPS). Proteasomes are present both in the cytoplasm and nucleus. Here, we investigated mechanisms coordinating proteasome subcellular localization and activity in a multicellular organism. We identified the nuclear protein-encoding gene akir-1 as a proteasome regulator in a genome-wide Caenorhabditis elegans RNAi screen. We demonstrate that depletion of akir-1 causes nuclear accumulation of endogenous polyubiquitinated proteins in intestinal cells, concomitant with slower in vivo proteasomal degradation in this subcellular compartment. Remarkably, akir-1 is essential for nuclear localization of proteasomes both in oocytes and intestinal cells but affects differentially the subcellular distribution of polyubiquitinated proteins. We further reveal that importin ima-3 genetically interacts with akir-1 and influences nuclear localization of a polyubiquitin-binding reporter. Our study shows that the conserved AKIR-1 is an important regulator of the subcellular function of proteasomes in a multicellular organism, suggesting a role for AKIR-1 in proteostasis maintenance.
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Affiliation(s)
- Johanna Pispa
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Elisa Mikkonen
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Leena Arpalahti
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Congyu Jin
- Department of Anatomy, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Carmen Martínez-Fernández
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Julián Cerón
- Modeling Human Diseases in C. elegans Group, Genes, Diseases, and Therapies Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Carina I. Holmberg
- Department of Biochemistry and Developmental Biology, Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
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Zhu M, Cao Z, Mo F, Shi S, Hu J, Xu Q, Quan K, Liang J, Li W, Hong X, Zhang B, Liu X, Dai M. ADRM1/RPN13 attenuates cartilage extracellular matrix degradation via enhancing UCH37-mediated ALK5 deubiquitination. Int J Biol Macromol 2023; 247:125670. [PMID: 37406898 DOI: 10.1016/j.ijbiomac.2023.125670] [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: 04/24/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Osteoarthritis (OA) is the most common age-related joint disorder with no effective therapy, and its specific pathological mechanism remains to be fully clarified. Adhesion-regulating molecule 1 (ADRM1) has been proven to be involved in OA progression as a favorable gene. However, the exact mechanism of ADRM1 involved in OA were unknown. Here, we showed that the ADRM1 expression decreased in human OA cartilage, destabilization of the medial meniscus (DMM)-induced mouse OA cartilage, and interleukin (IL)-1β-induced primary mouse articular chondrocytes. Global knockout (KO) ADRM1 in cartilage or ADRM1 inhibitor (RA190) could accelerate the disorders of extracellular matrix (ECM) homeostasis, thereby accelerated DMM-induced cartilage degeneration, whereas overexpression of ADRM1 protected mice from DMM-induced OA development by maintaining the homeostasis of articular cartilage. The molecular mechanism study revealed that ADRM1 could upregulate ubiquitin carboxy-terminal hydrolase 37 (UCH37) expression and bind to UCH37 to activate its deubiquitination activity. Subsequently, increased and activated UCH37 enhanced activin receptor-like kinase 5 (ALK5) deubiquitination to stabilize ALK5 expression, thereby maintaining ECM homeostasis and attenuating cartilage degeneration. These findings indicated that ADRM1 could attenuate cartilage degeneration via enhancing UCH37-mediated ALK5 deubiquitination. Overexpression of ADRM1 in OA cartilage may provide a promising OA therapeutic strategy.
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Affiliation(s)
- Meisong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China.
| | - Zhiyou Cao
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China.
| | - Fengbo Mo
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China.
| | - Shoujie Shi
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China
| | - Jiawei Hu
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China
| | - Qiang Xu
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China
| | - Kun Quan
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China
| | - Jianhui Liang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China
| | - Wei Li
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China
| | - Xin Hong
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China
| | - Bin Zhang
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China
| | - Xuqiang Liu
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China.
| | - Min Dai
- Department of Orthopedics, The First Affiliated Hospital of Nanchang University, Artificial Joints Engineering and Technology Research Center of Jiangxi Province, Nanchang, Jiangxi province 330006, China.
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10
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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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11
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Estavoyer B, Messmer C, Echbicheb M, Rudd CE, Milot E, Affar EB. Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases. J Biol Chem 2022; 298:102198. [PMID: 35764170 PMCID: PMC9356280 DOI: 10.1016/j.jbc.2022.102198] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
Deubiquitinases (DUBs) are required for the reverse reaction of ubiquitination and act as major regulators of ubiquitin signaling processes. Emerging evidence suggests that these enzymes are regulated at multiple levels in order to ensure proper and timely substrate targeting and to prevent the adverse consequences of promiscuous deubiquitination. The importance of DUB regulation is highlighted by disease-associated mutations that inhibit or activate DUBs, deregulating their ability to coordinate cellular processes. Here, we describe the diverse mechanisms governing protein stability, enzymatic activity, and function of DUBs. In particular, we outline how DUBs are regulated by their protein domains and interacting partners. Intramolecular interactions can promote protein stability of DUBs, influence their subcellular localization, and/or modulate their enzymatic activity. Remarkably, these intramolecular interactions can induce self-deubiquitination to counteract DUB ubiquitination by cognate E3 ubiquitin ligases. In addition to intramolecular interactions, DUBs can also oligomerize and interact with a wide variety of cellular proteins, thereby forming obligate or facultative complexes that regulate their enzymatic activity and function. The importance of signaling and post-translational modifications in the integrated control of DUB function will also be discussed. While several DUBs are described with respect to the multiple layers of their regulation, the tumor suppressor BAP1 will be outlined as a model enzyme whose localization, stability, enzymatic activity, and substrate recognition are highly orchestrated by interacting partners and post-translational modifications.
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Affiliation(s)
- Benjamin Estavoyer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Clémence Messmer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Mohamed Echbicheb
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Christopher E Rudd
- Laboratory for Cell Signaling in Immunotherapy, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Laboratory for Malignant Hematopoiesis and Epigenetic Regulation of Gene Expression, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - El Bachir Affar
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada.
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12
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Du J, Babik S, Li Y, Deol KK, Eyles SJ, Fejzo J, Tonelli M, Strieter E. A cryptic K48 ubiquitin chain binding site on UCH37 is required for its role in proteasomal degradation. eLife 2022; 11:e76100. [PMID: 35451368 PMCID: PMC9033301 DOI: 10.7554/elife.76100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
Degradation by the 26 S proteasome is an intricately regulated process fine tuned by the precise nature of ubiquitin modifications attached to a protein substrate. By debranching ubiquitin chains composed of K48 linkages, the proteasome-associated ubiquitin C-terminal hydrolase UCHL5/UCH37 serves as a positive regulator of protein degradation. How UCH37 achieves specificity for K48 chains is unclear. Here, we use a combination of hydrogen-deuterium mass spectrometry, chemical crosslinking, small-angle X-ray scattering, nuclear magnetic resonance (NMR), molecular docking, and targeted mutagenesis to uncover a cryptic K48 ubiquitin (Ub) chain-specific binding site on the opposite face of UCH37 relative to the canonical S1 (cS1) ubiquitin-binding site. Biochemical assays demonstrate the K48 chain-specific binding site is required for chain debranching and proteasome-mediated degradation of proteins modified with branched chains. Using quantitative proteomics, translation shutoff experiments, and linkage-specific affinity tools, we then identify specific proteins whose degradation depends on the debranching activity of UCH37. Our findings suggest that UCH37 and potentially other DUBs could use more than one S1 site to perform different biochemical functions.
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Affiliation(s)
- Jiale Du
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Sandor Babik
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Yanfeng Li
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Kirandeep K Deol
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts AmherstAmherstUnited States
| | - Jasna Fejzo
- Biomolecular NMR Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts AmherstAmherstUnited States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-MadisonMadisonUnited States
| | - Eric Strieter
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
- Molecular & Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
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13
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Ni B, Hou J. Promising therapeutic approaches for relapsed/refractory multiple myeloma. Hematology 2022; 27:343-352. [PMID: 35287555 DOI: 10.1080/16078454.2022.2045724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE Treatment strategies for relapsed/refractory MM are particularly complex. In particular, patients who are refractory to the three classes of therapies have limited therapeutic options and poor survival. Fortunately, promising treatments are emerging, but their incorporation into existing treatments still needs to be defined. We will describe the latest trends and emerging developments in the field of therapies for RRMM by analyzing the most recent clinical data and new technologies in drug development. METHODS Pubmed, Embase and Cochrane Library were searched to select eligible studies, the clinical data of new promising treatments were reviewed. The key results of the most recent clinical trial were summarized in Table. RESULTS A total of 13 studies were included in the final analysis involving anti-BCMA CAR T-cell therapy, Combined CAR T-cell therapy, antibody-drug conjugates, bispecific Ab therapy and CELMoDs. The key efficacy and side effects of treatments were summarized. CONCLUSIONS There is great promise for a set of next-generation of rescue therapies, including CAR T-cell therapy, bispecific antibodies, antibody-drug conjugates, and novel PROteolysis Targeting Chimeras. Emerging new treatments for MM provide more choices for relapsed/refractory multiple myeloma (RRMM). The optimal therapy for each patient should be based on disease-related factors, such as previous therapies, duration of response to prior drugs, clinical and biochemical features of relapse, and the relationship of patient comorbidities with known AE profiles of the different therapies.
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Affiliation(s)
- Beiwen Ni
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jian Hou
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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14
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Singh Gautam AK, Yu H, Yellman C, Elcock AH, Matouschek A. Design principles that protect the proteasome from self-destruction. Protein Sci 2022; 31:556-567. [PMID: 34878680 PMCID: PMC8862440 DOI: 10.1002/pro.4251] [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: 08/05/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 11/07/2022]
Abstract
The proteasome is a powerful intracellular protease that can degrade effectively any protein, self or foreign, for regulation, quality control, or immune response. Proteins are targeted for degradation by localizing them to the proteasome, typically by ubiquitin tags. At the same time, the proteasome is built from ~33 subunits, and their assembly into the complex and activity are tuned by post-translational modifications on long disordered regions on the subunits. Molecular modeling and biochemical experiments show that some of the disordered regions of proteasomal subunits can access the substrate recognition sites. All disordered regions tested, independent of location, are constructed from amino acid sequences that escape recognition. Replacing a disordered region with a sequence that is recognized by the proteasome leads to self-degradation and, in the case of an essential subunit, cell death.
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Affiliation(s)
| | - Houqing Yu
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTexasUSA
| | - Christopher Yellman
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTexasUSA
| | - Adrian H. Elcock
- Department of Biochemistry, Carver College of MedicineUniversity of IowaIowa CityIowaUSA
| | - Andreas Matouschek
- Department of Molecular BiosciencesThe University of Texas at AustinAustinTexasUSA
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15
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Lu X, Sabbasani VR, Osei-Amponsa V, Evans CN, King JC, Tarasov SG, Dyba M, Das S, Chan KC, Schwieters CD, Choudhari S, Fromont C, Zhao Y, Tran B, Chen X, Matsuo H, Andresson T, Chari R, Swenson RE, Tarasova NI, Walters KJ. Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma. Nat Commun 2021; 12:7318. [PMID: 34916494 PMCID: PMC8677766 DOI: 10.1038/s41467-021-27570-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Proteasome substrate receptor hRpn13 is a promising anti-cancer target. By integrated in silico and biophysical screening, we identified a chemical scaffold that binds hRpn13 with non-covalent interactions that mimic the proteasome and a weak electrophile for Michael addition. hRpn13 Pru domain binds proteasomes and ubiquitin whereas its DEUBAD domain binds deubiquitinating enzyme UCHL5. NMR revealed lead compound XL5 to interdigitate into a hydrophobic pocket created by lateral movement of a Pru β-hairpin with an exposed end for Proteolysis Targeting Chimeras (PROTACs). Implementing XL5-PROTACs as chemical probes identified a DEUBAD-lacking hRpn13 species (hRpn13Pru) present naturally with cell type-dependent abundance. XL5-PROTACs preferentially target hRpn13Pru, causing its ubiquitination. Gene-editing and rescue experiments established hRpn13 requirement for XL5-PROTAC-triggered apoptosis. These data establish hRpn13 as an anti-cancer target for multiple myeloma and introduce an hRpn13-targeting scaffold that can be optimized for preclinical trials against hRpn13Pru-producing cancer types.
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Affiliation(s)
- Xiuxiu Lu
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Venkata R Sabbasani
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - 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
| | - Christine N Evans
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Julianna C King
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Sergey G Tarasov
- Biophysics Resource, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Marzena Dyba
- Biophysics Resource, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, 21702, USA
| | - King C Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, 21702, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-5620, USA
| | - Sulbha Choudhari
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Caroline Fromont
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Yongmei Zhao
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Xiang Chen
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Hiroshi Matsuo
- Basic Science Program, Center for Structural Biology, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, 21702, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Rolf E Swenson
- Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nadya I Tarasova
- Laboratory of Cancer Immunometabolism, 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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16
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Song A, Hazlett Z, Abeykoon D, Dortch J, Dillon A, Curtiss J, Martinez SB, Hill CP, Yu C, Huang L, Fushman D, Cohen RE, Yao T. Branched ubiquitin chain binding and deubiquitination by UCH37 facilitate proteasome clearance of stress-induced inclusions. eLife 2021; 10:72798. [PMID: 34761751 PMCID: PMC8635973 DOI: 10.7554/elife.72798] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022] Open
Abstract
UCH37, also known as UCHL5, is a highly conserved deubiquitinating enzyme (DUB) that associates with the 26S proteasome. Recently, it was reported that UCH37 activity is stimulated by branched ubiquitin (Ub) chain architectures. To understand how UCH37 achieves its unique debranching specificity, we performed biochemical and Nuclear Magnetic Resonance (NMR) structural analyses and found that UCH37 is activated by contacts with the hydrophobic patches of both distal Ubs that emanate from a branched Ub. In addition, RPN13, which recruits UCH37 to the proteasome, further enhances branched-chain specificity by restricting linear Ub chains from having access to the UCH37 active site. In cultured human cells under conditions of proteolytic stress, we show that substrate clearance by the proteasome is promoted by both binding and deubiquitination of branched polyubiquitin by UCH37. Proteasomes containing UCH37(C88A), which is catalytically inactive, aberrantly retain polyubiquitinated species as well as the RAD23B substrate shuttle factor, suggesting a defect in recycling of the proteasome for the next round of substrate processing. These findings provide a foundation to understand how proteasome degradation of substrates modified by a unique Ub chain architecture is aided by a DUB.
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Affiliation(s)
- Aixin Song
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Zachary Hazlett
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Dulith Abeykoon
- Department of Chemistry and Biochemistry, University of Maryland, College Park, United States
| | - Jeremy Dortch
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Andrew Dillon
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Justin Curtiss
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Sarah Bollinger Martinez
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, United States
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, United States
| | - Robert E Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
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17
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Kinectin1 depletion promotes EGFR degradation via the ubiquitin-proteosome system in cutaneous squamous cell carcinoma. Cell Death Dis 2021; 12:995. [PMID: 34689164 PMCID: PMC8542041 DOI: 10.1038/s41419-021-04276-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022]
Abstract
Depletion of kinectin1 (KTN1) provides a potential strategy for inhibiting tumorigenesis of cutaneous squamous cell carcinoma (cSCC) via reduction of epidermal growth factor receptor (EGFR) protein levels. Yet, the underlying mechanisms of KTN1 remain obscure. In this study, we demonstrate that KTN1 knockdown induces EGFR degradation in cSCC cells by promoting the ubiquitin-proteasome system, and that this effect is tumor cell-specific. KTN1 knockdown increases the expression of CCDC40, PSMA1, and ADRM1 to mediate tumor suppressor functions in vivo and in vitro. Mechanistically, c-Myc directly binds to the promoter region of CCDC40 to trigger the CCDC40-ADRM1-UCH37 axis and promote EGFR deubiquitination. Furthermore, KTN1 depletion accelerates EGFR degradation by strengthening the competitive interaction between PSMA1 and ADRM1 to inhibit KTN1/ADRM1 interaction at residues Met1-Ala252. These results are supported by studies in mouse xenografts and human patient samples. Collectively, our findings provide novel mechanistic insight into KTN1 regulation of EGFR degradation in cSCC.
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18
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Chirality and asymmetry increase the potency of candidate ADRM1/RPN13 inhibitors. PLoS One 2021; 16:e0256937. [PMID: 34506530 PMCID: PMC8432795 DOI: 10.1371/journal.pone.0256937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022] Open
Abstract
Bortezomib and the other licensed 20S proteasome inhibitors show robust activity against liquid tumors like multiple myeloma, but have disappointed against solid tumors including ovarian cancer. Consequently, interest is mounting in alternative non-peptide based drugs targeting the proteasome’s 19S regulatory particle subunit, including its ubiquitin receptor RPN13. RA183 and RA375 are more potent analogs of the prototypic inhibitor of RPN13 (iRPN13) called RA190, and they show promise for the treatment of ovarian cancer. Here we demonstrate that rendering these candidate RPN13 inhibitors chiral and asymmetric through the addition of a single methyl to the core piperidone moiety increases their potency against cancer cell lines, with the S-isomer being more active than the R-isomer. The enhanced cancer cell cytotoxicities of these compounds are associated with improved binding to RPN13 in cell lysates, ATP depletion by inhibition of glycolysis and mitochondrial electron chain transport, mitochondrial depolarization and perinuclear clustering, oxidative stress and glutathione depletion, and rapid accumulation of high molecular weight polyubiquitinated proteins with a consequent unresolved ubiquitin proteasome system (UPS) stress response. Cytotoxicity was associated with an early biomarker of apoptosis, increased surface annexin V binding. As for cisplatin, BRCA2 and ATM deficiency conferred increased sensitivity to these iRPN13s. Ubiquitination plays an important role in coordinating DNA damage repair and the iRPN13s may compromise this process by depletion of monomeric ubiquitin following its sequestration in high molecular weight polyubiquitinated protein aggregates. Indeed, a synergistic cytotoxic response was evident upon treatment of several ovarian cancer cell lines with either cisplatin or doxorubicin and our new candidate iRPN13s, suggesting that such a combination approach warrants further exploration for the treatment of ovarian cancer.
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19
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Chen X, Htet ZM, López-Alfonzo E, Martin A, Walters KJ. Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies. FEBS J 2021; 288:5231-5251. [PMID: 33211406 PMCID: PMC8131406 DOI: 10.1111/febs.15638] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022]
Abstract
The 26S proteasome is responsible for regulated proteolysis in eukaryotic cells. Its substrates are diverse in structure, function, sequence length, and amino acid composition, and are targeted to the proteasome by post-translational modification with ubiquitin. Ubiquitination occurs through a complex enzymatic cascade and can also signal for other cellular events, unrelated to proteasome-catalyzed degradation. Like other post-translational protein modifications, ubiquitination is reversible, with ubiquitin chain hydrolysis catalyzed by the action of deubiquitinating enzymes (DUBs), ~ 90 of which exist in humans and allow for temporal events and dynamic ubiquitin-chain remodeling. DUBs have been known for decades to be an integral part of the proteasome, as deubiquitination is coupled to substrate unfolding and translocation into the internal degradation chamber. Moreover, the proteasome also binds several ubiquitinating enzymes and shuttle factors that recruit ubiquitinated substrates. The role of this intricate machinery and how ubiquitinated substrates interact with proteasomes remains an area of active investigation. Here, we review what has been learned about the mechanisms used by the proteasome to bind ubiquitinated substrates, substrate shuttle factors, ubiquitination machinery, and DUBs. We also discuss many open questions that require further study or the development of innovative approaches to be answered. Finally, we address the promise of expanded therapeutic targeting that could benefit from such new discoveries.
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Affiliation(s)
- Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
| | - Erika López-Alfonzo
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California at Berkeley, CA, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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20
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Padmanabhan PK, Ferreira GR, Zghidi-Abouzid O, Oliveira C, Dumas C, Mariz FC, Papadopoulou B. Genetic depletion of the RNA helicase DDX3 leads to impaired elongation of translating ribosomes triggering co-translational quality control of newly synthesized polypeptides. Nucleic Acids Res 2021; 49:9459-9478. [PMID: 34358325 PMCID: PMC8450092 DOI: 10.1093/nar/gkab667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022] Open
Abstract
DDX3 is a multifaceted RNA helicase of the DEAD-box family that plays central roles in all aspects of RNA metabolism including translation initiation. Here, we provide evidence that the Leishmania DDX3 ortholog functions in post-initiation steps of translation. We show that genetic depletion of DDX3 slows down ribosome movement resulting in elongation-stalled ribosomes, impaired translation elongation and decreased de novo protein synthesis. We also demonstrate that the essential ribosome recycling factor Rli1/ABCE1 and termination factors eRF3 and GTPBP1 are less recruited to ribosomes upon DDX3 loss, suggesting that arrested ribosomes may be inefficiently dissociated and recycled. Furthermore, we show that prolonged ribosome stalling triggers co-translational ubiquitination of nascent polypeptide chains and a higher recruitment of E3 ubiquitin ligases and proteasome components to ribosomes of DDX3 knockout cells, which further supports that ribosomes are not elongating optimally. Impaired elongation of translating ribosomes also results in the accumulation of cytoplasmic protein aggregates, which implies that defects in translation overwhelm the normal quality controls. The partial recovery of translation by overexpressing Hsp70 supports this possibility. Collectively, these results suggest an important novel contribution of DDX3 to optimal elongation of translating ribosomes by preventing prolonged translation stalls and stimulating recycling of arrested ribosomes.
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Affiliation(s)
- Prasad Kottayil Padmanabhan
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Gabriel Reis Ferreira
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Ouafa Zghidi-Abouzid
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Camila Oliveira
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Carole Dumas
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Filipe Colaço Mariz
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center-University Laval, Quebec, QC G1V 4G2, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC G1V 4G2, Canada
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21
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Deol KK, Strieter ER. The ubiquitin proteoform problem. Curr Opin Chem Biol 2021; 63:95-104. [PMID: 33813043 PMCID: PMC8384647 DOI: 10.1016/j.cbpa.2021.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/23/2022]
Abstract
The diversity of ubiquitin modifications is immense. A protein can be monoubiquitylated, multi-monoubiquitylated, and polyubiquitylated with chains varying in size and shape. Ubiquitin itself can be adorned with other ubiquitin-like proteins and smaller functional groups. Considering different combinations of post-translational modifications can give rise to distinct biological outcomes, characterizing ubiquitylated proteoforms of a given protein is paramount. In this Opinion, we review recent advances in detecting and quantifying various ubiquitin proteoforms using mass spectrometry.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
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22
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Small-Molecule Inhibitors Targeting Proteasome-Associated Deubiquitinases. Int J Mol Sci 2021; 22:ijms22126213. [PMID: 34207520 PMCID: PMC8226605 DOI: 10.3390/ijms22126213] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 02/06/2023] Open
Abstract
The 26S proteasome is the principal protease for regulated intracellular proteolysis. This multi-subunit complex is also pivotal for clearance of harmful proteins that are produced throughout the lifetime of eukaryotes. Recent structural and kinetic studies have revealed a multitude of conformational states of the proteasome in substrate-free and substrate-engaged forms. These conformational transitions demonstrate that proteasome is a highly dynamic machinery during substrate processing that can be also controlled by a number of proteasome-associated factors. Essentially, three distinct family of deubiquitinases–USP14, RPN11, and UCH37–are associated with the 19S regulatory particle of human proteasome. USP14 and UCH37 are capable of editing ubiquitin conjugates during the process of their dynamic engagement into the proteasome prior to the catalytic commitment. In contrast, RPN11-mediated deubiquitination is directly coupled to substrate degradation by sensing the proteasome’s conformational switch into the commitment steps. Therefore, proteasome-bound deubiquitinases are likely to tailor the degradation events in accordance with substrate processing steps and for dynamic proteolysis outcomes. Recent chemical screening efforts have yielded highly selective small-molecule inhibitors for targeting proteasomal deubiquitinases, such as USP14 and RPN11. USP14 inhibitors, IU1 and its progeny, were found to promote the degradation of a subset of substrates probably by overriding USP14-imposed checkpoint on the proteasome. On the other hand, capzimin, a RPN11 inhibitor, stabilized the proteasome substrates and showed the anti-proliferative effects on cancer cells. It is highly conceivable that these specific inhibitors will aid to dissect the role of each deubiquitinase on the proteasome. Moreover, customized targeting of proteasome-associated deubiquitinases may also provide versatile therapeutic strategies for induced or repressed protein degradation depending on proteolytic demand and cellular context.
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23
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Aliabadi F, Sohrabi B, Mostafavi E, Pazoki-Toroudi H, Webster TJ. Ubiquitin-proteasome system and the role of its inhibitors in cancer therapy. Open Biol 2021; 11:200390. [PMID: 33906413 PMCID: PMC8080017 DOI: 10.1098/rsob.200390] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite all the other cells that have the potential to prevent cancer development and metastasis through tumour suppressor proteins, cancer cells can upregulate the ubiquitin–proteasome system (UPS) by which they can degrade tumour suppressor proteins and avoid apoptosis. This system plays an extensive role in cell regulation organized in two steps. Each step has an important role in controlling cancer. This demonstrates the importance of understanding UPS inhibitors and improving these inhibitors to foster a new hope in cancer therapy. UPS inhibitors, as less invasive chemotherapy drugs, are increasingly used to alleviate symptoms of various cancers in malignant states. Despite their success in reducing the development of cancer with the lowest side effects, thus far, an appropriate inhibitor that can effectively inactivate this system with the least drug resistance has not yet been fully investigated. A fundamental understanding of the system is necessary to fully elucidate its role in causing/controlling cancer. In this review, we first comprehensively investigate this system, and then each step containing ubiquitination and protein degradation as well as their inhibitors are discussed. Ultimately, its advantages and disadvantages and some perspectives for improving the efficiency of these inhibitors are discussed.
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Affiliation(s)
- Fatemeh Aliabadi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Beheshteh Sohrabi
- Department of Chemistry, Surface Chemistry Research Laboratory, Iran University of Science and Technology, PO Box 16846-13114, Tehran, Iran
| | - Ebrahim Mostafavi
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA.,Stanford Cardiovascular Institute, Stanford, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Thomas J Webster
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
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24
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Chen X, Dou QP, Liu J, Tang D. Targeting Ubiquitin-Proteasome System With Copper Complexes for Cancer Therapy. Front Mol Biosci 2021; 8:649151. [PMID: 33928122 PMCID: PMC8076789 DOI: 10.3389/fmolb.2021.649151] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
Characterizing mechanisms of protein homeostasis, a process of balancing between protein synthesis and protein degradation, is important for understanding the potential causes of human diseases. The ubiquitin–proteasome system (UPS) is a well-studied mechanism of protein catabolism, which is responsible for eliminating misfolded, damaged, or aging proteins, thereby maintaining quality and quantity of cellular proteins. The UPS is composed of multiple components, including a series of enzymes (E1, E2, E3, and deubiquitinase [DUB]) and 26S proteasome (19S regulatory particles + 20S core particle). An impaired UPS pathway is involved in multiple diseases, including cancer. Several proteasome inhibitors, such as bortezomib, carfilzomib, and ixazomib, are approved to treat patients with certain cancers. However, their applications are limited by side effects, drug resistance, and drug–drug interactions observed in their clinical processes. To overcome these shortcomings, alternative UPS inhibitors have been searched for in many fields. Copper complexes (e.g., CuET, CuHQ, CuCQ, CuPDTC, CuPT, and CuHK) are found to be able to inhibit a core component of the UPS machinery, such as 20S proteasome, 19S DUBs, and NPLOC4/NPL4 complex, and are proposed to be one class of metal-based anticancer drugs. In this review, we will summarize functions and applications of copper complexes in a concise perspective, with a focus on connections between the UPS and cancer.
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Affiliation(s)
- Xin Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Q Ping Dou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China.,Department of Oncology, School of Medicine, Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States.,Departments of Pharmacology & Pathology, School of Medicine, Wayne State University, Detroit, MI, United States
| | - Jinbao Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, United States
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25
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Ubiquitome analysis reveals the involvement of lysine ubiquitination in the spermatogenesis process of adult buffalo (Bubalus bubalis) testis. Biosci Rep 2021; 40:225077. [PMID: 32469046 PMCID: PMC7298129 DOI: 10.1042/bsr20193537] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/18/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022] Open
Abstract
Protein ubiquitination, a major and conserved post-translational modification, is known to play a critical regulatory role in many biological processes in eukaryotes. Although several ubiquitinated proteins have been found in buffalo (Bubalus bubalis) testis in our previous studies, large-scale profiling of buffalo testis ubiquitome has not been reported to date. In the present study, we first identified a global profiling of lysine ubiquitination of adult buffalo testis using a highly sensitive LC-MS/MS coupled with immune-affinity enrichment of ubiquitinated peptides. In total, 422 lysine ubiquitination sites were identified in 262 proteins in adult buffalo testis tissue. Bioinformatics analysis showed that the ubiquitinated proteins are involved in a variety of biological processes and diverse subcellular localizations. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and protein interaction network analysis indicated that proteasome, glycolysis/gluconeogenesis and gap junction pathways are modulated by protein ubiquitination in testis. Besides, 44 ubiquitinated proteins may involve in spermatogenesis according to the SpermatogenesisOnline database, of which, the ubiquitination of HSPA2 and UCHL1 were confirmed by Immunoprecipitation (IP)/Western blot analysis. Taken together, these data provide a global view of ubiquitome in buffalo testis for the first time, and serve as an important resource for exploring the physiological role especially spermatogenesis of lysine ubiquitination in testis in mammals.
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26
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Proteasome in action: substrate degradation by the 26S proteasome. Biochem Soc Trans 2021; 49:629-644. [PMID: 33729481 PMCID: PMC8106498 DOI: 10.1042/bst20200382] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/16/2022]
Abstract
Ubiquitination is the major criteria for the recognition of a substrate-protein by the 26S proteasome. Additionally, a disordered segment on the substrate — either intrinsic or induced — is critical for proteasome engagement. The proteasome is geared to interact with both of these substrate features and prepare it for degradation. To facilitate substrate accessibility, resting proteasomes are characterised by a peripheral distribution of ubiquitin receptors on the 19S regulatory particle (RP) and a wide-open lateral surface on the ATPase ring. In this substrate accepting state, the internal channel through the ATPase ring is discontinuous, thereby obstructing translocation of potential substrates. The binding of the conjugated ubiquitin to the ubiquitin receptors leads to contraction of the 19S RP. Next, the ATPases engage the substrate at a disordered segment, energetically unravel the polypeptide and translocate it towards the 20S catalytic core (CP). In this substrate engaged state, Rpn11 is repositioned at the pore of the ATPase channel to remove remaining ubiquitin modifications and accelerate translocation. C-termini of five of the six ATPases insert into corresponding lysine-pockets on the 20S α-ring to complete 20S CP gate opening. In the resulting substrate processing state, the ATPase channel is fully contiguous with the translocation channel into the 20S CP, where the substrate is proteolyzed. Complete degradation of a typical ubiquitin-conjugate takes place over a few tens of seconds while hydrolysing tens of ATP molecules in the process (50 kDa/∼50 s/∼80ATP). This article reviews recent insight into biochemical and structural features that underlie substrate recognition and processing by the 26S proteasome.
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27
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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28
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Basar MA, Beck DB, Werner A. Deubiquitylases in developmental ubiquitin signaling and congenital diseases. Cell Death Differ 2021; 28:538-556. [PMID: 33335288 PMCID: PMC7862630 DOI: 10.1038/s41418-020-00697-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Metazoan development from a one-cell zygote to a fully formed organism requires complex cellular differentiation and communication pathways. To coordinate these processes, embryos frequently encode signaling information with the small protein modifier ubiquitin, which is typically attached to lysine residues within substrates. During ubiquitin signaling, a three-step enzymatic cascade modifies specific substrates with topologically unique ubiquitin modifications, which mediate changes in the substrate's stability, activity, localization, or interacting proteins. Ubiquitin signaling is critically regulated by deubiquitylases (DUBs), a class of ~100 human enzymes that oppose the conjugation of ubiquitin. DUBs control many essential cellular functions and various aspects of human physiology and development. Recent genetic studies have identified mutations in several DUBs that cause developmental disorders. Here we review principles controlling DUB activity and substrate recruitment that allow these enzymes to regulate ubiquitin signaling during development. We summarize key mechanisms of how DUBs control embryonic and postnatal differentiation processes, highlight developmental disorders that are caused by mutations in particular DUB members, and describe our current understanding of how these mutations disrupt development. Finally, we discuss how emerging tools from human disease genetics will enable the identification and study of novel congenital disease-causing DUBs.
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Affiliation(s)
- Mohammed A Basar
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Beck
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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29
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Rong C, Zhou R, Wan S, Su D, Wang SL, Hess J. Ubiquitin Carboxyl-Terminal Hydrolases and Human Malignancies: The Novel Prognostic and Therapeutic Implications for Head and Neck Cancer. Front Oncol 2021; 10:592501. [PMID: 33585209 PMCID: PMC7878561 DOI: 10.3389/fonc.2020.592501] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin C-terminal hydrolases (UCHs), a subfamily of deubiquitinating enzymes (DUBs), have been found in a variety of tumor entities and play distinct roles in the pathogenesis and development of various cancers including head and neck cancer (HNC). HNC is a heterogeneous disease arising from the mucosal epithelia of the upper aerodigestive tract, including different anatomic sites, distinct histopathologic types, as well as human papillomavirus (HPV)-positive and negative subgroups. Despite advances in multi-disciplinary treatment for HNC, the long-term survival rate of patients with HNC remains low. Emerging evidence has revealed the members of UCHs are associated with the pathogenesis and clinical prognosis of HNC, which highlights the prognostic and therapeutic implications of UCHs for patients with HNC. In this review, we summarize the physiological and pathological functions of the UCHs family, which provides enlightenment of potential mechanisms of UCHs family in HNC pathogenesis and highlights the potential consideration of UCHs as attractive drug targets.
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Affiliation(s)
- Chao Rong
- Department of Pathology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Ran Zhou
- Department of Pharmacy, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Shan Wan
- Department of Pathology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | - Dan Su
- Department of Pharmacy, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Shou-Li Wang
- Department of Pathology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | - Jochen Hess
- Section Experimental and Translational Head and Neck Oncology, Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
- Research Group Molecular Mechanisms of Head and Neck Tumors, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
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30
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Zhang ZH, Jiang TX, Chen LB, Zhou W, Liu Y, Gao F, Qiu XB. Proteasome subunit α4s is essential for formation of spermatoproteasomes and histone degradation during meiotic DNA repair in spermatocytes. J Biol Chem 2021; 296:100130. [PMID: 33262216 PMCID: PMC7949063 DOI: 10.1074/jbc.ra120.016485] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/18/2020] [Accepted: 12/01/2020] [Indexed: 11/24/2022] Open
Abstract
Meiosis, which produces haploid progeny, is critical to ensuring both faithful genome transmission and genetic diversity. Proteasomes play critical roles at various stages of spermatogenesis, including meiosis, but the underlying mechanisms remain unclear. The atypical proteasomes, which contain the activator PA200, catalyze the acetylation-dependent degradation of the core histones in elongated spermatids and DNA repair in somatic cells. We show here that the testis-specific proteasome subunit α4s/PSMA8 is essential for male fertility by promoting proper formation of spermatoproteasomes, which harbor both PA200 and constitutive catalytic subunits. Immunostaining of a spermatocyte marker, SYCP3, indicated that meiosis was halted at the stage of spermatocytes in the α4s-deficient testes. α4s stimulated the in vitro degradation of the acetylated core histones, instead of nonacetylated histones, by the PA200-proteasome. Deletion of α4s blocked degradation of the core histones at DNA damage loci in spermatocytes, leading to meiotic arrest at metaphase I. Thus, α4s is required for histone degradation at meiotic DNA damage loci, proper progression of meiosis, and fertility in males by promoting proper formation of spermatoproteasomes. These results are important for understanding male infertility and might provide potential targets for male contraception or treatment of male infertility.
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Affiliation(s)
- Zi-Hui Zhang
- Key Laboratory of Cell Proliferation & Regulation Biology, Ministry of Education and College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tian-Xia Jiang
- Key Laboratory of Cell Proliferation & Regulation Biology, Ministry of Education and College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Lian-Bin Chen
- Key Laboratory of Cell Proliferation & Regulation Biology, Ministry of Education and College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wenhui Zhou
- Medical Center for Human Reproduction, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yixun Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fei Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Bo Qiu
- Key Laboratory of Cell Proliferation & Regulation Biology, Ministry of Education and College of Life Sciences, Beijing Normal University, Beijing, China.
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31
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Deol KK, Crowe SO, Du J, Bisbee HA, Guenette RG, Strieter ER. Proteasome-Bound UCH37/UCHL5 Debranches Ubiquitin Chains to Promote Degradation. Mol Cell 2020; 80:796-809.e9. [PMID: 33156996 PMCID: PMC7718437 DOI: 10.1016/j.molcel.2020.10.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 09/13/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023]
Abstract
The linkage, length, and architecture of ubiquitin (Ub) chains are all important variables in providing tight control over many biological paradigms. There are clear roles for branched architectures in regulating proteasome-mediated degradation, but the proteins that selectively recognize and process these atypical chains are unknown. Here, using synthetic and enzyme-derived ubiquitin chains along with intact mass spectrometry, we report that UCH37/UCHL5, a proteasome-associated deubiquitinase, cleaves K48 branched chains. The activity and selectivity toward branched chains is markedly enhanced by the proteasomal Ub receptor RPN13/ADRM1. Using reconstituted proteasome complexes, we find that chain debranching promotes degradation of substrates modified with branched chains under multi-turnover conditions. These results are further supported by proteome-wide pulse-chase experiments, which show that the loss of UCH37 activity impairs global protein turnover. Our work therefore defines UCH37 as a debranching deubiquitinase important for promoting proteasomal degradation.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sean O Crowe
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiale Du
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Heather A Bisbee
- Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Robert G Guenette
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA; Molecular & Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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32
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Scholz N, Kurian KM, Siebzehnrubl FA, Licchesi JDF. Targeting the Ubiquitin System in Glioblastoma. Front Oncol 2020; 10:574011. [PMID: 33324551 PMCID: PMC7724090 DOI: 10.3389/fonc.2020.574011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma is the most common primary brain tumor in adults with poor overall outcome and 5-year survival of less than 5%. Treatment has not changed much in the last decade or so, with surgical resection and radio/chemotherapy being the main options. Glioblastoma is highly heterogeneous and frequently becomes treatment-resistant due to the ability of glioblastoma cells to adopt stem cell states facilitating tumor recurrence. Therefore, there is an urgent need for novel therapeutic strategies. The ubiquitin system, in particular E3 ubiquitin ligases and deubiquitinating enzymes, have emerged as a promising source of novel drug targets. In addition to conventional small molecule drug discovery approaches aimed at modulating enzyme activity, several new and exciting strategies are also being explored. Among these, PROteolysis TArgeting Chimeras (PROTACs) aim to harness the endogenous protein turnover machinery to direct therapeutically relevant targets, including previously considered "undruggable" ones, for proteasomal degradation. PROTAC and other strategies targeting the ubiquitin proteasome system offer new therapeutic avenues which will expand the drug development toolboxes for glioblastoma. This review will provide a comprehensive overview of E3 ubiquitin ligases and deubiquitinating enzymes in the context of glioblastoma and their involvement in core signaling pathways including EGFR, TGF-β, p53 and stemness-related pathways. Finally, we offer new insights into how these ubiquitin-dependent mechanisms could be exploited therapeutically for glioblastoma.
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Affiliation(s)
- Nico Scholz
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Kathreena M. Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, United Kingdom
| | - Florian A. Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
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33
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Chen X, Dorris Z, Shi D, Huang RK, Khant H, Fox T, de Val N, Williams D, Zhang P, Walters KJ. Cryo-EM Reveals Unanchored M1-Ubiquitin Chain Binding at hRpn11 of the 26S Proteasome. Structure 2020; 28:1206-1217.e4. [PMID: 32783951 PMCID: PMC7642156 DOI: 10.1016/j.str.2020.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/06/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022]
Abstract
The 26S proteasome is specialized for regulated protein degradation and formed by a dynamic regulatory particle (RP) that caps a hollow cylindrical core particle (CP) where substrates are proteolyzed. Its diverse substrates unify as proteasome targets by ubiquitination. We used cryogenic electron microscopy (cryo-EM) to study how human 26S proteasome interacts with M1-linked hexaubiquitin (M1-Ub6) unanchored to a substrate and E3 ubiquitin ligase E6AP/UBE3A. Proteasome structures are available with model substrates extending through the RP ATPase ring and substrate-conjugated K63-linked ubiquitin chains present at inhibited deubiquitinating enzyme hRpn11 and the nearby ATPase hRpt4/hRpt5 coiled coil. In this study, we find M1-Ub6 at the hRpn11 site despite the absence of conjugated substrate, indicating that ubiquitin binding at this location does not require substrate interaction with the RP. Moreover, unanchored M1-Ub6 binds to this hRpn11 site of the proteasome with the CP gating residues in both the closed and opened conformational states.
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Affiliation(s)
- Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zachary Dorris
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Frederick High School, Frederick, MD 21702, USA
| | - Dan Shi
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Rick K Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Htet Khant
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Dewight Williams
- John M. Cowley Center for High Resolution Electron Microscopy, Arizona State University, Tempe, AZ 85287, USA
| | - Ping Zhang
- Kinase Complexes Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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Tundo GR, Sbardella D, Santoro AM, Coletta A, Oddone F, Grasso G, Milardi D, Lacal PM, Marini S, Purrello R, Graziani G, Coletta M. The proteasome as a druggable target with multiple therapeutic potentialities: Cutting and non-cutting edges. Pharmacol Ther 2020; 213:107579. [PMID: 32442437 PMCID: PMC7236745 DOI: 10.1016/j.pharmthera.2020.107579] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 01/10/2023]
Abstract
Ubiquitin Proteasome System (UPS) is an adaptable and finely tuned system that sustains proteostasis network under a large variety of physiopathological conditions. Its dysregulation is often associated with the onset and progression of human diseases; hence, UPS modulation has emerged as a promising new avenue for the development of treatments of several relevant pathologies, such as cancer and neurodegeneration. The clinical interest in proteasome inhibition has considerably increased after the FDA approval in 2003 of bortezomib for relapsed/refractory multiple myeloma, which is now used in the front-line setting. Thereafter, two other proteasome inhibitors (carfilzomib and ixazomib), designed to overcome resistance to bortezomib, have been approved for treatment-experienced patients, and a variety of novel inhibitors are currently under preclinical and clinical investigation not only for haematological malignancies but also for solid tumours. However, since UPS collapse leads to toxic misfolded proteins accumulation, proteasome is attracting even more interest as a target for the care of neurodegenerative diseases, which are sustained by UPS impairment. Thus, conceptually, proteasome activation represents an innovative and largely unexplored target for drug development. According to a multidisciplinary approach, spanning from chemistry, biochemistry, molecular biology to pharmacology, this review will summarize the most recent available literature regarding different aspects of proteasome biology, focusing on structure, function and regulation of proteasome in physiological and pathological processes, mostly cancer and neurodegenerative diseases, connecting biochemical features and clinical studies of proteasome targeting drugs.
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Affiliation(s)
- G R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
| | | | - A M Santoro
- CNR, Institute of Crystallography, Catania, Italy
| | - A Coletta
- Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - F Oddone
- IRCCS-Fondazione Bietti, Rome, Italy
| | - G Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - D Milardi
- CNR, Institute of Crystallography, Catania, Italy
| | - P M Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, Rome, Italy
| | - S Marini
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - R Purrello
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - G Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - M Coletta
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
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Impact of Losing hRpn13 Pru or UCHL5 on Proteasome Clearance of Ubiquitinated Proteins and RA190 Cytotoxicity. Mol Cell Biol 2020; 40:MCB.00122-20. [PMID: 32631902 DOI: 10.1128/mcb.00122-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/26/2020] [Indexed: 01/18/2023] Open
Abstract
hRpn13/ADRM1 links substrate recruitment with deubiquitination at the proteasome through its proteasome- and ubiquitin-binding Pru domain and DEUBAD domain, which binds and activates deubiquitinating enzyme (DUB) UCHL5/Uch37. Here, we edit the HCT116 colorectal cancer cell line to delete part of the hRpn13 Pru, producing cells that express truncated hRpn13 (trRpn13), which is competent for UCHL5 binding but defective for proteasome interaction. trRpn13 cells demonstrate reduced levels of proteasome-bound ubiquitinated proteins, indicating that the loss of hRpn13 function at proteasomes cannot be fully compensated for by the two other dedicated substrate receptors (hRpn1 and hRpn10). Previous studies indicated that the loss of full-length hRpn13 causes a corresponding reduction of UCHL5. We find UCHL5 levels unaltered in trRpn13 cells, but hRpn11 is elevated in ΔhRpn13 and trRpn13 cells, perhaps from cell stress. Despite the ∼90 DUBs in human cells, including two others in addition to UCHL5 at the proteasome, we found deletion of UCHL5 from HCT116 cells to cause increased levels of ubiquitinated proteins in whole-cell extract and at proteasomes, suggesting that UCHL5 activity cannot be fully assumed by other DUBs. We also report anticancer molecule RA190, which binds covalently to hRpn13 and UCHL5, to require hRpn13 Pru and not UCHL5 for cytotoxicity.
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Transcriptional upregulation of proteasome activator Blm10 antagonizes cellular aging. Biochem Biophys Res Commun 2020; 532:211-218. [PMID: 32861419 DOI: 10.1016/j.bbrc.2020.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022]
Abstract
Cellular aging is associated with the damage to DNA, decline in proteasome activity, loss of histones and alteration of epigenetic marks. The atypical proteasome with the activator PA200 in mammals or its ortholog Blm10 in yeast promotes the acetylation-dependent degradation of the core histones during DNA repair or spermiogenesis. We show here that loss of PA200 or Blm10 is the leading cause of the decline in proteasome activity during aging, the latter of which conversely induces the transcription of Blm10. The transcription factor Crt1 suppressed, but the proteasome subunit Rpn4 promoted, the transcription of Blm10. On the contrary to deletion of Rpn4, deletion of Crt1 elevated Blm10 transcription upon DNA damage, reduced core histone levels during aging, and prolonged replicative lifespan. These results suggest that cells can antagonize aging by up-regulating transcription of Blm10, providing important insights into the mechanisms of aging and the aging-related diseases.
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Lu M, Tian X, Zhang Y, Aimulajiang K, Wang W, Ehsan M, Li C, Yan R, Xu L, Song X, Li X. Unveiling the immunomodulatory properties of Haemonchus contortus adhesion regulating molecule 1 interacting with goat T cells. Parasit Vectors 2020; 13:424. [PMID: 32811556 PMCID: PMC7432459 DOI: 10.1186/s13071-020-04297-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
Background Gastrointestinal nematodes could release excretory-secretory (ES) proteins into the host environment to ensure their survival. These ES proteins act as immunomodulators to suppress or subvert the host immune response via the impairment of immune cell functions, especially in chronic infections. In our preliminary study, Haemonchus contortus adhesion-regulating molecule 1 (HcADRM1) was identified from H. contortus ES proteins (HcESPs) that interacted with host T cells via liquid chromatography-tandem mass spectrometry analysis. However, little is known about HcADRM1 as an ES protein which may play a pivotal role at the parasite-host interface. Methods Based on bioinformatics approaches, multiple amino acid sequence alignment was conducted and the evolutionary relationship of HcADRM1 with ADRM1 orthologues was extrapolated. Employing RT-qPCR and immunohistochemistry assays, temporal transcriptional and spatial expression profiles of HcADRM1 were investigated. Using immunostaining approaches integrated with immunological bioassays, the immunomodulatory potentials of HcADRM1 on goat T cells were assessed. Results We hereby demonstrated that HcADRM1 with immunodiagnostic utility was a mammalian ADRM1 orthologue abundantly expressed at all developmental stages of H. contortus. Given the implications of ADRM1 proteins in cell growth, survival and development, we further investigated the immunomodulatory property of HcADRM1 as an individual ES protein acting at the parasite-host interface. The rHcADRM1 stimuli notably suppressed T cell viability, promoted intrinsic and extrinsic T cell apoptosis, inhibited T cell proliferation and induced cell cycle arrest at G1 phase. Simultaneously, rHcADRM1 stimuli exerted critical controls on T cell cytokine secretion profiles, predominantly by restraining the secretions of interleukin (IL)-4, IL-10 and interferon-gamma. Conclusions Importantly, HcADRM1 protein may have prophylactic potential for anti-H. contortus vaccine development. Together, these findings may contribute to the clarification of molecular and immunomodulatory traits of ES proteins, as well as improvement of our understanding of parasite immune evasion mechanism in H. contortus-host biology.![]()
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Affiliation(s)
- Mingmin Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xiaowei Tian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yang Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Kalibixiati Aimulajiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Wenjuan Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Muhammad Ehsan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Charles Li
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USA Department of Agriculture, Beltsville, MD, 20705, USA
| | - Ruofeng Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Lixin Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xiaokai Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Xiangrui Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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Shin JY, Muniyappan S, Tran NN, Park H, Lee SB, Lee BH. Deubiquitination Reactions on the Proteasome for Proteasome Versatility. Int J Mol Sci 2020; 21:E5312. [PMID: 32726943 PMCID: PMC7432943 DOI: 10.3390/ijms21155312] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/17/2022] Open
Abstract
The 26S proteasome, a master player in proteolysis, is the most complex and meticulously contextured protease in eukaryotic cells. While capable of hosting thousands of discrete substrates due to the selective recognition of ubiquitin tags, this protease complex is also dynamically checked through diverse regulatory mechanisms. The proteasome's versatility ensures precise control over active proteolysis, yet prevents runaway or futile degradation of many essential cellular proteins. Among the multi-layered processes regulating the proteasome's proteolysis, deubiquitination reactions are prominent because they not only recycle ubiquitins, but also impose a critical checkpoint for substrate degradation on the proteasome. Of note, three distinct classes of deubiquitinating enzymes-USP14, RPN11, and UCH37-are associated with the 19S subunits of the human proteasome. Recent biochemical and structural studies suggest that these enzymes exert dynamic influence over proteasome output with limited redundancy, and at times act in opposition. Such distinct activities occur spatially on the proteasome, temporally through substrate processing, and differentially for ubiquitin topology. Therefore, deubiquitinating enzymes on the proteasome may fine-tune the degradation depending on various cellular contexts and for dynamic proteolysis outcomes. Given that the proteasome is among the most important drug targets, the biology of proteasome-associated deubiquitination should be further elucidated for its potential targeting in human diseases.
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Affiliation(s)
- Ji Yeong Shin
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (J.Y.S.); (S.M.); (N.-N.T.); (H.P.)
- Protein Dynamics-based Proteotoxicity Control Lab, Basic Research Lab, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
- Center for Cell Fate Reprogramming & Control, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Srinivasan Muniyappan
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (J.Y.S.); (S.M.); (N.-N.T.); (H.P.)
| | - Non-Nuoc Tran
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (J.Y.S.); (S.M.); (N.-N.T.); (H.P.)
- Protein Dynamics-based Proteotoxicity Control Lab, Basic Research Lab, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
- Center for Cell Fate Reprogramming & Control, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Hyeonjeong Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (J.Y.S.); (S.M.); (N.-N.T.); (H.P.)
- Protein Dynamics-based Proteotoxicity Control Lab, Basic Research Lab, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
| | - Sung Bae Lee
- Protein Dynamics-based Proteotoxicity Control Lab, Basic Research Lab, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
- Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Byung-Hoon Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea; (J.Y.S.); (S.M.); (N.-N.T.); (H.P.)
- Protein Dynamics-based Proteotoxicity Control Lab, Basic Research Lab, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea;
- Center for Cell Fate Reprogramming & Control, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
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Gadhave K, Kumar P, Kapuganti SK, Uversky VN, Giri R. Unstructured Biology of Proteins from Ubiquitin-Proteasome System: Roles in Cancer and Neurodegenerative Diseases. Biomolecules 2020; 10:E796. [PMID: 32455657 PMCID: PMC7278180 DOI: 10.3390/biom10050796] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/17/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
The 26S proteasome is a large (~2.5 MDa) protein complex consisting of at least 33 different subunits and many other components, which form the ubiquitin proteasomal system (UPS), an ATP-dependent protein degradation system in the cell. UPS serves as an essential component of the cellular protein surveillance machinery, and its dysfunction leads to cancer, neurodegenerative and immunological disorders. Importantly, the functions and regulations of proteins are governed by the combination of ordered regions, intrinsically disordered protein regions (IDPRs) and molecular recognition features (MoRFs). The structure-function relationships of UPS components have not been identified completely; therefore, in this study, we have carried out the functional intrinsic disorder and MoRF analysis for potential neurodegenerative disease and anti-cancer targets of this pathway. Our report represents the presence of significant intrinsic disorder and disorder-based binding regions in several UPS proteins, such as extraproteasomal polyubiquitin receptors (UBQLN1 and UBQLN2), proteasome-associated polyubiquitin receptors (ADRM1 and PSMD4), deubiquitinating enzymes (DUBs) (ATXN3 and USP14), and ubiquitinating enzymes (E2 (UBE2R2) and E3 (STUB1) enzyme). We believe this study will have implications for the conformation-specific roles of different regions of these proteins. This will lead to a better understanding of the molecular basis of UPS-associated diseases.
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Affiliation(s)
- Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India; (K.G.); (P.K.); (S.K.K.)
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India; (K.G.); (P.K.); (S.K.K.)
| | - Shivani K. Kapuganti
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India; (K.G.); (P.K.); (S.K.K.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA;
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Cientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290 Moscow, Russia
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh 175005, India; (K.G.); (P.K.); (S.K.K.)
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Lu X, Ebelle DL, Matsuo H, Walters KJ. An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure. Structure 2020; 28:495-506.e3. [PMID: 32160516 DOI: 10.1016/j.str.2020.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/06/2020] [Accepted: 02/26/2020] [Indexed: 12/24/2022]
Abstract
Rpn13/Adrm1 is recruited to the proteasome by PSMD1/Rpn2, where it serves as a substrate receptor that binds preferentially to K48-linked ubiquitin chains, an established signal for protein proteolysis. Here, we use NMR to solve the structure of hRpn13 Pru:hRpn2 (940-953):K48-diubiquitin. Surprisingly, hRpn2-bound hRpn13 selects a dynamic, extended conformation of K48-diubiquitin that is unique from previously determined structures. NMR experiments on free K48-diubiquitin demonstrate the presence of the reported "closed" conformation observed by crystallography, but also this more extended state, in which the hRpn13-binding surface is exposed. This extended K48-diubiquitin conformation is defined by interactions between L73 from G76-linked (distal) ubiquitin and a Y59-centered surface of K48-linked (proximal) ubiquitin. Furthermore, hRpn13 exchanges between the two ubiquitins within 100 ms, although prefers the proximal ubiquitin due to interactions with the K48 linker region. Altogether, these data lead to a revised model of how ubiquitinated substrates interact with the proteasome.
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Affiliation(s)
- Xiuxiu Lu
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Danielle L Ebelle
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hiroshi Matsuo
- Basic Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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41
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Buel GR, Chen X, Chari R, O'Neill MJ, Ebelle DL, Jenkins C, Sridharan V, Tarasov SG, Tarasova NI, Andresson T, Walters KJ. Structure of E3 ligase E6AP with a proteasome-binding site provided by substrate receptor hRpn10. Nat Commun 2020; 11:1291. [PMID: 32157086 PMCID: PMC7064531 DOI: 10.1038/s41467-020-15073-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/15/2020] [Indexed: 12/16/2022] Open
Abstract
Regulated proteolysis by proteasomes involves ~800 enzymes for substrate modification with ubiquitin, including ~600 E3 ligases. We report here that E6AP/UBE3A is distinguished from other E3 ligases by having a 12 nM binding site at the proteasome contributed by substrate receptor hRpn10/PSMD4/S5a. Intrinsically disordered by itself, and previously uncharacterized, the E6AP-binding domain in hRpn10 locks into a well-defined helical structure to form an intermolecular 4-helix bundle with the E6AP AZUL, which is unique to this E3. We thus name the hRpn10 AZUL-binding domain RAZUL. We further find in human cells that loss of RAZUL by CRISPR-based gene editing leads to loss of E6AP at proteasomes. Moreover, proteasome-associated ubiquitin is reduced following E6AP knockdown or displacement from proteasomes, suggesting that E6AP ubiquitinates substrates at or for the proteasome. Altogether, our findings indicate E6AP to be a privileged E3 for the proteasome, with a dedicated, high affinity binding site contributed by hRpn10.
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Affiliation(s)
- Gwen R Buel
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Maura J O'Neill
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Danielle L Ebelle
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Conor Jenkins
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Vinidhra Sridharan
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Sergey G Tarasov
- Biophysics Resource, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Nadya I Tarasova
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
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The proteasome 19S cap and its ubiquitin receptors provide a versatile recognition platform for substrates. Nat Commun 2020; 11:477. [PMID: 31980598 PMCID: PMC6981147 DOI: 10.1038/s41467-019-13906-8] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/20/2019] [Indexed: 01/28/2023] Open
Abstract
Proteins are targeted to the proteasome by the attachment of ubiquitin chains, which are markedly varied in structure. Three proteasome subunits–Rpn10, Rpn13, and Rpn1–can recognize ubiquitin chains. Here we report that proteins with single chains of K48-linked ubiquitin are targeted for degradation almost exclusively through binding to Rpn10. Rpn1 can act as a co-receptor with Rpn10 for K63 chains and for certain other chain types. Differences in targeting do not correlate with chain affinity to receptors. Surprisingly, in steady-state assays Rpn13 retarded degradation of various single-chain substrates. Substrates with multiple short ubiquitin chains can be presented for degradation by any of the known receptors, whereas those targeted to the proteasome through a ubiquitin-like domain are degraded most efficiently when bound by Rpn13 or Rpn1. Thus, the proteasome provides an unexpectedly versatile binding platform that can recognize substrates targeted for degradation by ubiquitin chains differing greatly in length and topology. Ubiquitylated proteins are degraded by the proteasome and the three proteasome subunits Rpn10, Rpn13 and Rpn1 recognize ubiquitin chains. Here the authors employ biochemical and kinetic assays and characterise the ubiquitin chain type specificities of these three ubiquitin receptors.
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Repurposing old drugs as new inhibitors of the ubiquitin-proteasome pathway for cancer treatment. Semin Cancer Biol 2019; 68:105-122. [PMID: 31883910 DOI: 10.1016/j.semcancer.2019.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/30/2019] [Accepted: 12/15/2019] [Indexed: 12/25/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays a central role in the degradation of cellular proteins. Targeting protein degradation has been validated as an effective strategy for cancer therapy since 2003. Several components of the UPS have been validated as potential anticancer targets, including 20S proteasomes, 19S proteasome-associated deubiquitinases (DUBs) and ubiquitin ligases (E3s). 20S proteasome inhibitors (such as bortezomib/BTZ and carfilzomib/CFZ) have been approved by the U.S. Food and Drug Administration (FDA) for the treatment of multiple myeloma (MM) and some other liquid tumors. Although survival of MM patients has been improved by the introduction of BTZ-based therapies, these clinical 20S proteasome inhibitors have several limitations, including emergence of resistance in MM patients, neuro-toxicities, and little efficacy in solid tumors. One of strategies to improve the current status of cancer treatment is to repurpose old drugs with UPS-inhibitory properties as new anticancer agents. Old drug reposition represents an attractive drug discovery approach compared to the traditional de novo drug discovery process which is time-consuming and costly. In this review, we summarize status of repurposed inhibitors of various UPS components, including 20S proteasomes, 19S-associated DUBs, and ubiquitin ligase E3s. The original and new mechanisms of action, molecular targets, and potential anticancer activities of these repurposed UPS inhibitors are reviewed, and their new uses including combinational therapies for cancer treatment are discussed.
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Wu W, Zhong J, Chen J, Niu P, Ding Y, Han S, Xu J, Dai L. Prognostic and Therapeutic Significance of Adhesion-regulating Molecule 1 in Estrogen Receptor-positive Breast Cancer. Clin Breast Cancer 2019; 20:131-144.e3. [PMID: 31669266 DOI: 10.1016/j.clbc.2019.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 07/11/2019] [Accepted: 07/27/2019] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Adhesion-regulating molecule 1 (ADRM1) is a polyubiquitin receptor on the 26S proteasome. ADRM1 is upregulated in many cancers. In this study, we evaluated the potential prognostic and predictive value of ADRM1 in breast cancer. MATERIALS AND METHODS Individual and pooled survival analyses were performed on 19 independent breast cancer microarray datasets. Gene signatures enriched by ADRM1 were also analyzed in pooled datasets. RESULTS Gene set enrichment analysis revealed that high expression of ADRM1 was significantly associated with aggressive breast cancer. Our findings revealed that ADRM1 mRNA levels were significantly associated with estrogen receptor (ER) status, progesterone receptor status, tumor size, lymph node status, histologic grade, and molecular subtypes. We also found that higher mRNA ADRM1 expression was significantly correlated with poor survival in patients with breast cancer. The prognostic power of ADRM1 mRNA was similar to the 70-gene wound response genes and 21 gene recurrence score; it was superior to TNM staging. The prognostic value of ADRM1 was better in ER-positive (ER+) breast cancer cases than in ER-negative breast cancer cases. In cases involving stage II breast cancer, radiotherapy significantly reduced the relative risk of OS in the ADRM1-low subgroup. CONCLUSION ADRM1 mRNA levels were significantly related to poor outcome in our breast cancer sample population. It could serve as a prognostic biomarker, especially in ER+ breast cancer and Luminal A breast cancer cases, as well as a predictive biomarker for ER+ breast cancer.
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Affiliation(s)
- Wanbo Wu
- Department of General Surgery, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
| | - Jing Zhong
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China.
| | - Jing Chen
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
| | - Pingping Niu
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
| | - Yunfeng Ding
- Department of General Surgery, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
| | - Shuwen Han
- Department of Medical Oncology, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
| | - Jiewei Xu
- Department of General Surgery, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
| | - Licheng Dai
- Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang Province, China
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45
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González-Velasco Ó, De Las Rivas J, Lacal J. Proteomic and Transcriptomic Profiling Identifies Early Developmentally Regulated Proteins in Dictyostelium Discoideum. Cells 2019; 8:cells8101187. [PMID: 31581556 PMCID: PMC6830349 DOI: 10.3390/cells8101187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023] Open
Abstract
Cyclic AMP acts as a secondary messenger involving different cellular functions in eukaryotes. Here, proteomic and transcriptomic profiling has been combined to identify novel early developmentally regulated proteins in eukaryote cells. These proteomic and transcriptomic experiments were performed in Dictyostelium discoideum given the unique advantages that this organism offers as a eukaryotic model for cell motility and as a nonmammalian model of human disease. By comparing whole-cell proteome analysis of developed (cAMP-pulsed) wild-type AX2 cells and an independent transcriptomic analysis of developed wild-type AX4 cells, our results show that up to 70% of the identified proteins overlap in the two independent studies. Among them, we have found 26 proteins previously related to cAMP signaling and identified 110 novel proteins involved in calcium signaling, adhesion, actin cytoskeleton, the ubiquitin-proteasome pathway, metabolism, and proteins that previously lacked any annotation. Our study validates previous findings, mostly for the canonical cAMP-pathway, and also generates further insight into the complexity of the transcriptomic changes during early development. This article also compares proteomic data between parental and cells lacking glkA, a GSK-3 kinase implicated in substrate adhesion and chemotaxis in Dictyostelium. This analysis reveals a set of proteins that show differences in expression in the two strains as well as overlapping protein level changes independent of GlkA.
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Affiliation(s)
- Óscar González-Velasco
- Bioinformatics and Functional Genomics Research Group. Cancer Research Center (CIC-IBMCC, CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Research Group. Cancer Research Center (CIC-IBMCC, CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
| | - Jesus Lacal
- Department of Microbiology and Genetics, Faculty of Biology, University of Salamanca, 37007 Salamanca, Spain.
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Zhou Z, Yao X, Pang S, Chen P, Jiang W, Shan Z, Zhang Q. The deubiquitinase UCHL5/UCH37 positively regulates Hedgehog signaling by deubiquitinating Smoothened. J Mol Cell Biol 2019; 10:243-257. [PMID: 28992318 DOI: 10.1093/jmcb/mjx036] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 08/21/2017] [Indexed: 01/20/2023] Open
Abstract
The Hedgehog (Hh) signaling pathway plays important roles in developmental processes including pattern formation and tissue homeostasis. The seven-pass transmembrane receptor Smoothened (Smo) is the pivotal transducer in the pathway; it, and thus the pathway overall, is regulated by ubiquitin-mediated degradation, which occurs in the absence of Hh. In the presence of Hh, the ubiquitination levels of Smo are decreased, but the molecular basis for this outcome is not well understood. Here, we identify the deubiquitinase UCHL5 as a positive regulator of the Hh pathway. We provide both genetic and biochemical evidence that UCHL5 interacts with and deubiquitinates Smo, increasing stability and promoting accumulation at the cell membrane. Strikingly, we find that Hh enhances the interaction between UCHL5 and Smo, thereby stabilizing Smo. We also find that proteasome subunit RPN13, an activator of UCHL5, could enhance the effect of UCHL5 on Smo protein level. More importantly, we find that the mammalian counterpart of UCHL5, UCH37, plays the same role in the regulation of Hh signaling by modulating hSmo ubiquitination and stability. Our findings thus identify UCHL5/UCH37 as a critical regulator of Hh signaling and potential therapeutic target for cancers.
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Affiliation(s)
- Zizhang Zhou
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Xia Yao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Shu Pang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Ping Chen
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Weirong Jiang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Zhaoliang Shan
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | - Qing Zhang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China.,Collaborative Innovation Center of Genetics and Development, Shanghai, China
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Chen H, Gao F, He M, Ding XF, Wong AM, Sze SC, Yu AC, Sun T, Chan AW, Wang X, Wong N. Long-Read RNA Sequencing Identifies Alternative Splice Variants in Hepatocellular Carcinoma and Tumor-Specific Isoforms. Hepatology 2019; 70:1011-1025. [PMID: 30637779 PMCID: PMC6766942 DOI: 10.1002/hep.30500] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/28/2018] [Indexed: 12/19/2022]
Abstract
Alternative splicing (AS) allows generation of cell type-specific mRNA transcripts and contributes to hallmarks of cancer. Genome-wide analysis for AS in human hepatocellular carcinoma (HCC), however, is limited. We sought to obtain a comprehensive AS landscape in HCC and define tumor-associated variants. Single-molecule real-time long-read RNA sequencing was performed on patient-derived HCC cells, and presence of splice junctions was defined by SpliceMap-LSC-IDP algorithm. We obtained an all-inclusive map of annotated AS variants and further discovered 362 alternative spliced variants that are not previously reported in any database (neither RefSeq nor GENCODE). They were mostly derived from intron retention and early termination codon with an in-frame open reading frame in 81.5%. We corroborated many of these predicted unannotated and annotated variants to be tumor specific in an independent cohort of primary HCC tumors and matching nontumoral liver. Using the combined Sanger sequencing and TaqMan junction assays, unique and common expressions of spliced variants including enzyme regulators (ARHGEF2, SERPINH1), chromatin modifiers (DEK, CDK9, RBBP7), RNA-binding proteins (SRSF3, RBM27, MATR3, YBX1), and receptors (ADRM1, CD44v8-10, vitamin D receptor, ROR1) were determined in HCC tumors. We further focused functional investigations on ARHGEF2 variants (v1 and v3) that arise from the common amplified site chr.1q22 of HCC. Their biological significance underscores two major cancer hallmarks, namely cancer stemness and epithelial-to-mesenchymal transition-mediated cell invasion and migration, although v3 is consistently more potent than v1. Conclusion: Alternative isoforms and tumor-specific isoforms that arise from aberrant splicing are common during the liver tumorigenesis. Our results highlight insights gained from the analysis of AS in HCC.
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Affiliation(s)
- Hui Chen
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong KongShatin Hong KongChina
| | - Feng Gao
- Department of Biomedical SciencesCity University of Hong KongKowloon TongHong KongChina
| | - Mian He
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong KongShatin Hong KongChina
| | - Xiao Fan Ding
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong KongShatin Hong KongChina
| | - Aikha M. Wong
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong KongShatin Hong KongChina
| | - Siu Ching Sze
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong KongShatin Hong KongChina
| | - Allen C. Yu
- School of Life SciencesThe Chinese University of Hong KongShatinHong KongChina
| | - Tingting Sun
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong KongShatin Hong KongChina
| | - Anthony W‐H. Chan
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong KongShatin Hong KongChina
| | - Xin Wang
- Department of Biomedical SciencesCity University of Hong KongKowloon TongHong KongChina
| | - Nathalie Wong
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong KongShatin Hong KongChina
- State Key Laboratory in Translational OncologyThe Chinese University of Hong KongShatin Hong KongChina
- State Key Laboratory of Digestive DiseaseSir YK Pao Centre for Cancer, The Chinese University of Hong KongShatin Hong KongChina
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Gottlieb CD, Thompson ACS, Ordureau A, Harper JW, Kopito RR. Acute unfolding of a single protein immediately stimulates recruitment of ubiquitin protein ligase E3C (UBE3C) to 26S proteasomes. J Biol Chem 2019; 294:16511-16524. [PMID: 31375563 DOI: 10.1074/jbc.ra119.009654] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/16/2019] [Indexed: 01/26/2023] Open
Abstract
The intracellular accumulation of aggregated misfolded proteins is a cytopathological hallmark of neurodegenerative diseases. However, the functional relationship between protein misfolding or aggregation and the cellular proteostasis network that monitors and maintains proteome health is poorly understood. Previous studies have associated translational suppression and transcriptional remodeling with the appearance of protein aggregates, but whether these responses are induced by aggregates or their misfolded monomeric or oligomeric precursors remains unclear. Because aggregation in cells is rapid, nonlinear, and asynchronous, it has not been possible to deconvolve these kinetically linked processes to determine the earliest cellular responses to misfolded proteins. Upon removal of the synthetic, biologically inert ligand shield-1 (S1), AgDD, an engineered variant FK506-binding protein (FKBP1A), rapidly (t ½ ∼5 min) unfolds and self-associates, forming detergent-insoluble, microscopic cytoplasmic aggregates. Using global diglycine-capture (K-GG) proteomics, we found here that this solubility transition is associated with immediate increases in ubiquitylation of AgDD itself, along with that of endogenous proteins that are components of the ribosome and the 26S proteasome. We also found that the earliest cellular responses to acute S1 removal include recruitment of ubiquitin protein ligase E3C (UBE3C) to the 26S proteasome and ubiquitylation of two key proteasomal ubiquitin receptors, 26S proteasome regulatory subunit RPN10 (RPN10) and Rpn13 homolog (RPN13 or ADRM1). We conclude that these proteasomal responses are due to AgDD protein misfolding and not to the presence of detergent-insoluble aggregates.
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Affiliation(s)
- Colin D Gottlieb
- Department of Biology, Stanford University, Stanford, California 94305
| | | | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts 02115
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, California 94305
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Muli CS, Tian W, Trader DJ. Small-Molecule Inhibitors of the Proteasome's Regulatory Particle. Chembiochem 2019; 20:1739-1753. [PMID: 30740849 PMCID: PMC6765334 DOI: 10.1002/cbic.201900017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Indexed: 12/11/2022]
Abstract
Cells need to synthesize and degrade proteins consistently. Maintaining a balanced level of protein in the cell requires a carefully controlled system and significant energy. Degradation of unwanted or damaged proteins into smaller peptide units can be accomplished by the proteasome. The proteasome is composed of two main subunits. The first is the core particle (20S CP), and within this core particle are three types of threonine proteases. The second is the regulatory complex (19S RP), which has a myriad of activities including recognizing proteins marked for degradation and shuttling the protein into the 20S CP to be degraded. Small-molecule inhibitors of the 20S CP have been developed and are exceptional treatments for multiple myeloma (MM). 20S CP inhibitors disrupt the protein balance, leading to cellular stress and eventually to cell death. Unfortunately, the 20S CP inhibitors currently available have dose-limiting off-target effects and resistance can be acquired rapidly. Herein, we discuss small molecules that have been discovered to interact with the 19S RP subunit or with a protein closely associated with 19S RP activity. These molecules still elicit their toxicity by preventing the proteasome from degrading proteins, but do so through different mechanisms of action.
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Affiliation(s)
- Christine S. Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Wenzhi Tian
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Darci J. Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
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50
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Parvathi MS, Nataraja KN, Nanja Reddy YA, Naika MBN, Channabyre Gowda MV. Transcriptome analysis of finger millet ( Eleusine coracana (L.) Gaertn.) reveals unique drought responsive genes. J Genet 2019; 98:46. [PMID: 31204698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Finger millet (Eleusine coracana (L.) Gaertn.), an important C4 species is known for its stress hardiness and nutritional significance. To identify novel drought responsive mechanisms, we generated transcriptome data from leaf tissue of finger millet, variety GPU-28, exposed to gravimetrically imposed drought stress so as to simulate field stress conditions. De novo assembly based approach yielded 80,777 and 90,830 transcripts from well-irrigated (control) and drought-stressed samples, respectively. A total of 1790 transcripts were differentially expressed between the control and drought-stress treatments. Functional annotation and pathway analysis indicated activation of diverse drought-stress signalling cascade genes such as serine threonine protein phosphatase 2A (PP2A), calcineurin B-like interacting protein kinase31 (CIPK31), farnesyl pyrophosphate synthase (FPS), signal recognition particle receptor α (SRPR α) etc. The basal regulatory genes such as TATA-binding protein (TBP)-associated factors (TAFs) werefound to be drought responsive, indicating that genes associated with housekeeping or basal regulatory processes are activated underdrought in finger millet. A significant portion of the expressed genes was uncharacterized, belonging to the category of proteins of unknown functions (PUFs). Among the differentially expressed PUFs, we attempted to assign putative function for a few, using anovel annotation tool, Proteins of Unknown Function Annotation Server. Analysis of PUFs led to the discovery of novel drought responsive genes such as pentatricopeptide repeat proteins and tetratricopeptide repeat proteins that serve as interaction modules in multiprotein interactions. The transcriptome data generated can be utilized for comparative analysis, and functional validation of the genes identified would be useful to understand the drought adaptive mechanisms operating under field conditions in finger millet, as has been already attempted for a few candidates such as CIPK31 and TAF6. Such an attempt is needed to enhance the productivity of finger millet under water-limited conditions, and/or to adopt the implicated mechanisms in other related crops.
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Affiliation(s)
- M S Parvathi
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India.
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