101
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Cromm PM, Crews CM. The Proteasome in Modern Drug Discovery: Second Life of a Highly Valuable Drug Target. ACS CENTRAL SCIENCE 2017; 3:830-838. [PMID: 28852696 PMCID: PMC5571462 DOI: 10.1021/acscentsci.7b00252] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 06/07/2023]
Abstract
As the central figure of the cellular protein degradation machinery, the proteasome is critical for cell survival. Having been extensively targeted for inhibition, the constitutive proteasome has proven its role as a highly valuable drug target. However, recent advances in the protein homeostasis field suggest that additional chapters can be added to this successful story. For example, selective immunoproteasome inhibition promises high clinical efficacy for autoimmune disorders and inflammation, and proteasome inhibitors might serve as novel therapeutics for malaria or other microorganisms. Furthermore, utilizing the destructive force of the proteasome for selective degradation of essential drivers of human disorders has opened up a new and exciting area of drug discovery. Thus, the field of proteasome drug discovery still holds exciting questions to be answered and does not simply end with inhibiting the constitutive proteasome.
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Affiliation(s)
- Philipp M. Cromm
- Department
of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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102
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Bixel K, Saini U, Kumar Bid H, Fowler J, Riley M, Wanner R, Deepa Priya Dorayappan K, Rajendran S, Konishi I, Matsumura N, Cohn DE, Selvendiran K. Targeting STAT3 by HO3867 induces apoptosis in ovarian clear cell carcinoma. Int J Cancer 2017. [PMID: 28646535 DOI: 10.1002/ijc.30847] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Advanced ovarian clear cell carcinoma (OCCC) carries a very poor prognosis in large part secondary to the extremely high rate of resistance to standard platinum and taxane chemotherapy. Signal transducer and activator of transcription 3(STAT3) expression and activation has been shown to regulate tumor progression in various human cancers, though has not been well studied in OCCC. Preliminary work in our lab has demonstrated constitutive activation of STAT3 (pSTAT3Tyr705 or pSTAT3727) in OCCC cell lines as well as human OCCC tumor tissue samples. Significantly, pSTAT3 is expressed in the absence of other forms of activated STAT (pSTAT1, 2, 6). Therefore, this work was planned to investigate the role of STAT3 and examine the efficacy of a novel anti-cancer compound -HO-3867, which is an inhibitor of STAT3, using known OCCC cell lines. Results demonstrate that treatment with HO-3867 decreased expression of pSTAT3 Tyr705 as well pSTAT3 Ser727, while total STAT3 remained constant. STAT3 overexpression increased the migration capability in OVTOKO cells in vitro and led to an increased tumor size when injected in vivo. The inhibitory effect of HO-3867 on cell proliferation and cell survival was accompanied by increased apoptosis, within 24 h post treatment. Treatment with HO-3867 resulted in a decrease in Bcl-2 and increase of cleavage of caspase 3, caspase 7, and PARP, confirming induction of apoptosis after treatment with HO-3867. In addition, HO-3867 significantly inhibited formation of human umbilical vein endothelial cells capillary-like structures and invasion at both 5 and 10 µM concentrations. STAT3 expression plays an important role in the spread of OCCC in vitro as well as in vivo. Thus, we can exploit the STAT3 pathway for targeted drug therapy. Inhibition of pSTAT3 using HO-3867in OCCC cell lines appears to be a promising therapy. This is of utmost importance given the poor response of OCCC to standard chemotherapy regimens.
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Affiliation(s)
- Kristin Bixel
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Uksha Saini
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Hemant Kumar Bid
- Cancer Therapeutics, Life Sciences Institute University of Michigan campus, Ann Arbor, MI
| | - John Fowler
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Maria Riley
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Ross Wanner
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Kalpana Deepa Priya Dorayappan
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Sneha Rajendran
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Ikuo Konishi
- Division of GYN/ONC, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Noriomi Matsumura
- Division of GYN/ONC, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - David E Cohn
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Karuppaiyah Selvendiran
- Division of Gynecologic Oncology, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH
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103
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Jiang Y, Kalodimos CG. NMR Studies of Large Proteins. J Mol Biol 2017; 429:2667-2676. [PMID: 28728982 DOI: 10.1016/j.jmb.2017.07.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 01/08/2023]
Abstract
Recent breakthroughs in isotope-labeling and pulse sequence techniques have enabled the NMR characterization of large protein systems with molecular masses of hundreds of kilodaltons. NMR studies of a great variety of large proteins have provided unique insights into the binding, dynamic, and allosteric mechanisms. Here we present a brief summary of these developments by highlighting few cases that exemplify the uniqueness of NMR in providing atomic resolution information into key dynamic processes and structures of protein complexes with high degree of flexibility.
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Affiliation(s)
- Yajun Jiang
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Charalampos G Kalodimos
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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104
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Galluzzi L, Baehrecke EH, Ballabio A, Boya P, Bravo-San Pedro JM, Cecconi F, Choi AM, Chu CT, Codogno P, Colombo MI, Cuervo AM, Debnath J, Deretic V, Dikic I, Eskelinen EL, Fimia GM, Fulda S, Gewirtz DA, Green DR, Hansen M, Harper JW, Jäättelä M, Johansen T, Juhasz G, Kimmelman AC, Kraft C, Ktistakis NT, Kumar S, Levine B, Lopez-Otin C, Madeo F, Martens S, Martinez J, Melendez A, Mizushima N, Münz C, Murphy LO, Penninger JM, Piacentini M, Reggiori F, Rubinsztein DC, Ryan KM, Santambrogio L, Scorrano L, Simon AK, Simon HU, Simonsen A, Tavernarakis N, Tooze SA, Yoshimori T, Yuan J, Yue Z, Zhong Q, Kroemer G. Molecular definitions of autophagy and related processes. EMBO J 2017; 36:1811-1836. [PMID: 28596378 PMCID: PMC5494474 DOI: 10.15252/embj.201796697] [Citation(s) in RCA: 1104] [Impact Index Per Article: 157.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 12/15/2022] Open
Abstract
Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the field attempts here to define several autophagy-related terms based on specific biochemical features. The ultimate objective of this collaborative exchange is to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagy research.
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Affiliation(s)
- Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Université Paris Descartes/Paris V, Paris, France
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Medical Genetics, Department of Pediatrics, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - José Manuel Bravo-San Pedro
- Université Paris Descartes/Paris V, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- INSERM, U1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
| | - Francesco Cecconi
- Department of Biology, University of Tor Vergata, Rome, Italy
- Unit of Cell Stress and Survival, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Pediatric Hematology and Oncology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Augustine M Choi
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Charleen T Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Patrice Codogno
- Université Paris Descartes/Paris V, Paris, France
- Institut Necker-Enfants Malades (INEM), Paris, France
- INSERM, U1151, Paris, France
- CNRS, UMR8253, Paris, France
| | - Maria Isabel Colombo
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología (IHEM)-CONICET, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jayanta Debnath
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Vojo Deretic
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt Main, Germany
- Department of Immunology and Medical Genetics, University of Split School of Medicine, Split, Croatia
| | | | - Gian Maria Fimia
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Simone Fulda
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David A Gewirtz
- Department of Pharmacology and Toxicology and Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Marja Jäättelä
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Gabor Juhasz
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest, Hungary
- Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Alec C Kimmelman
- Department of Radiation Oncology, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, USA
| | - Claudine Kraft
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | | | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, Australia
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute (HHMI), Dallas, TX, USA
| | - Carlos Lopez-Otin
- Department de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación en Red de Cáncer, Oviedo, Spain
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Sascha Martens
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Jennifer Martinez
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Alicia Melendez
- Department of Biology, Queens College, Queens, NY, USA
- Graduate Center, City University of New York, New York, NY, USA
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zurich, Switzerland
| | - Leon O Murphy
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Campus Vienna BioCentre, Vienna, Austria
| | - Mauro Piacentini
- Department of Biology, University of Tor Vergata, Rome, Italy
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Kevin M Ryan
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Luca Scorrano
- Department of Biology, University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine, Padova, Italy
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences Osaka University, Osaka, Japan
| | - Junying Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Ludwig Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Zhenyu Yue
- Department of Neurology, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qing Zhong
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guido Kroemer
- Université Paris Descartes/Paris V, Paris, France
- Université Pierre et Marie Curie/Paris VI, Paris, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- INSERM, U1138, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
- Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
- Pôle de Biologie, Hopitâl Européen George Pompidou, AP-HP, Paris, France
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105
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Abstract
The segregation of homologous chromosomes in meiosis depends on their ability to locate one another in the nucleus and establish a physical association through crossing over. A tightly regulated number of crossovers (COs) emerges following repair of induced DNA double-strand breaks by homologous recombination (HR), but the process of how HR intermediates transition into COs is still poorly understood. Two recent studies by Ahuja et al. and Rao et al. have revealed a role for chromosomally localized proteasomes in choreographing both homologous chromosome pairing and the evolution of HR intermediates into segregation-competent COs. Using chemical inhibition of the proteasome and mutant analysis, the collective data reveal conserved functions for both the proteasome and a family of E3 ligases that can direct or compete with its activity in ensuring CO formation. Here, we review these findings and the impact of the discovery that protein modification dynamics and proteasomal activity cooperate to regulate key meiotic processes.
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Affiliation(s)
- Aleksandar Vujin
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Monique Zetka
- Department of Biology, McGill University, Montreal, Quebec, Canada
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106
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Blockade of deubiquitylating enzyme Rpn11 triggers apoptosis in multiple myeloma cells and overcomes bortezomib resistance. Oncogene 2017; 36:5631-5638. [PMID: 28581522 DOI: 10.1038/onc.2017.172] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/03/2017] [Accepted: 05/01/2017] [Indexed: 12/11/2022]
Abstract
Proteasome inhibition is an effective therapy for multiple myeloma (MM) patients; however, the emergence of drug resistance is common. Novel therapeutic strategies to overcome proteasome inhibitor resistance are needed. In this study, we examined whether targeting deubiquitylating (DUB) enzymes upstream of 20S proteasome overcomes proteasome inhibitor resistance. Gene expression analysis, immunohistochemical studies of MM patient bone marrow, reverse transcription-PCR and protein analysis show that Rpn11/POH1, a DUB enzyme upstream of 20S proteasome, is more highly expressed in patient MM cells than in normal plasma cells. Importantly, Rpn11 expression directly correlates with poor patient survival. Loss-of-function studies show that Rpn11-siRNA knockdown decreases MM cell viability. Pharmacological inhibition of Rpn11 with O-phenanthroline (OPA) blocks cellular proteasome function, induces apoptosis in MM cells and overcomes resistance to proteasome inhibitor bortezomib. Mechanistically, Rpn11 inhibition in MM cells activates caspase cascade and endoplasmic stress response signaling. Human MM xenograft model studies demonstrate that OPA treatment reduces progression of tumor growth and prolongs survival in mice. Finally, blockade of Rpn11 increases the cytotoxic activity of anti-MM agents lenalidomide, pomalidomide or dexamethasone. Overall, our preclinical data provide the rationale for targeting DUB enzyme Rpn11 upstream of 20S proteasome to enhance cytotoxicity and overcome proteasome inhibitor resistance in MM.
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107
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Saeki Y. Ubiquitin recognition by the proteasome. J Biochem 2017; 161:113-124. [PMID: 28069863 DOI: 10.1093/jb/mvw091] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/21/2016] [Indexed: 12/14/2022] Open
Abstract
The 26S proteasome is a 2.5-MDa complex responsible for the selective, ATP-dependent degradation of ubiquitylated proteins in eukaryotic cells. Substrates in hundreds cellular pathways are timely ubiquitylated and converged to the proteasome by direct recognition or by multiple shuttle factors. Engagement of substrate protein triggers conformational changes of the proteasome, which drive substrate unfolding, deubiquitylation and translocation of substrates to proteolytic sites. Recent studies have challenged the previous paradigm that Lys48-linked tetraubiquitin is a minimal degradation signal: in addition, monoubiquitylation or multiple short ubiquitylations can serve as the targeting signal for proteasomal degradation. In this review, I highlight recent advances in our understanding of the proteasome structure, the ubiquitin topology in proteasome targeting, and the cellular factors that regulate proteasomal degradation.
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Affiliation(s)
- Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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108
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Lundh M, Bugliani M, Dahlby T, Chou DHC, Wagner B, Ghiasi SM, De Tata V, Chen Z, Lund MN, Davies MJ, Marchetti P, Mandrup-Poulsen T. The immunoproteasome is induced by cytokines and regulates apoptosis in human islets. J Endocrinol 2017; 233:369-379. [PMID: 28438776 PMCID: PMC5501413 DOI: 10.1530/joe-17-0110] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/24/2017] [Indexed: 12/11/2022]
Abstract
In addition to degrading misfolded and damaged proteins, the proteasome regulates the fate of cells in response to stress. The role of the proteasome in pro-inflammatory cytokine-induced human beta-cell apoptosis is unknown. Using INS-1, INS-1E and human islets exposed to combinations of IFNγ, IL-1β and TNFα with or without addition of small molecules, we assessed the role of the immunoproteasome in pancreatic beta-cell demise. Here, we show that cytokines induce the expression and activity of the immuno-proteasome in INS-1E cells and human islets. Cytokine-induced expression of immuno-proteasome subunits, but not activity, depended upon histone deacetylase 3 activation. Inhibition of JAK1/STAT1 signaling did not affect proteasomal activity. Inhibition of the immuno-proteasome subunit PSMB8 aggravated cytokine-induced human beta-cell apoptosis while reducing intracellular levels of oxidized proteins in INS-1 cells. While cytokines increased total cellular NFκB subunit P50 and P52 levels and reduced the cytosolic NFκB subunit P65 and IκB levels, these effects were unaffected by PSMB8 inhibition. We conclude that beta cells upregulate immuno-proteasome expression and activity in response to IFNγ, likely as a protective response to confine inflammatory signaling.
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Affiliation(s)
- Morten Lundh
- Department of Biomedical SciencesUniversity of Copenhagen, Copenhagen, Denmark
- Chemical Biology and Therapeutics ProgramBroad Institute of Harvard and MIT, Boston, Massachusetts, USA
| | - Marco Bugliani
- Department of Clinical and Experimental MedicineUniversity of Pisa, Pisa, Italy
| | - Tina Dahlby
- Department of Biomedical SciencesUniversity of Copenhagen, Copenhagen, Denmark
| | - Danny Hung-Chieh Chou
- Chemical Biology and Therapeutics ProgramBroad Institute of Harvard and MIT, Boston, Massachusetts, USA
| | - Bridget Wagner
- Chemical Biology and Therapeutics ProgramBroad Institute of Harvard and MIT, Boston, Massachusetts, USA
| | | | - Vincenzo De Tata
- Department of Biomedical SciencesUniversity of Copenhagen, Copenhagen, Denmark
| | - Zhifei Chen
- Department of Biomedical SciencesUniversity of Copenhagen, Copenhagen, Denmark
| | - Marianne Nissan Lund
- Department of Biomedical SciencesUniversity of Copenhagen, Copenhagen, Denmark
- Department of Food ScienceUniversity of Copenhagen, Copenhagen, Denmark
| | - Michael J Davies
- Department of Biomedical SciencesUniversity of Copenhagen, Copenhagen, Denmark
| | - Piero Marchetti
- Department of Clinical and Experimental MedicineUniversity of Pisa, Pisa, Italy
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109
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Defenouillère Q, Fromont-Racine M. The ribosome-bound quality control complex: from aberrant peptide clearance to proteostasis maintenance. Curr Genet 2017; 63:997-1005. [PMID: 28528489 DOI: 10.1007/s00294-017-0708-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 01/01/2023]
Abstract
Proteostasis in eukaryotes is maintained by compartment-specific quality control pathways, which enable the refolding or the degradation of defective polypeptides to prevent the toxicity that may arise from their aggregation. Among these processes, translational protein quality control is performed by the Ribosome-bound Quality Control complex (RQC), which recognizes nascent peptides translated from aberrant mRNAs, polyubiquitylates these aberrant peptides, extracts them from the stalled 60S subunit and finally escorts them to the proteasome for degradation. In this review, we focus on the mechanism of action of the RQC complex from stalled 60S binding to aberrant peptide delivery to the proteasome and describe the cellular consequences of a deficiency in the RQC pathway, such as aberrant protein aggregation. In addition, this review covers the recent discoveries concerning the role of cytosolic chaperones, as well as Tom1, to prevent the accumulation of aberrant protein aggregates in case of a deficiency in the RQC pathway.
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Affiliation(s)
- Quentin Defenouillère
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, 75724, Paris Cedex 15, France. .,Membrane Trafficking, Ubiquitin and Signaling, Institut Jacques Monod, UMR7592 CNRS/Université Paris-Diderot, 15 Rue Hélène Brion, Bât. Buffon, 75205, Paris Cedex 13, France.
| | - Micheline Fromont-Racine
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, 75724, Paris Cedex 15, France
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110
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Abstract
In most patients with chronic heart failure (HF), levels of circulating cytokines are elevated and the elevated cytokine levels correlate with the severity of HF and prognosis. Various stresses induce subcellular component abnormalities, such as mitochondrial damage. Damaged mitochondria induce accumulation of reactive oxygen species and apoptogenic proteins, and subcellular inflammation. The vicious cycle of subcellular component abnormalities, inflammatory cell infiltration and neurohumoral activation induces cardiomyocyte injury and death, and cardiac fibrosis, resulting in cardiac dysfunction and HF. Quality control mechanisms at both the protein and organelle levels, such as elimination of apoptogenic proteins and damaged mitochondria, maintain cellular homeostasis. An imbalance between protein synthesis and degradation is likely to result in cellular dysfunction and disease. Three major protein degradation systems have been identified, namely the cysteine protease system, autophagy, and the ubiquitin proteasome system. Autophagy was initially believed to be a non-selective process. However, recent studies have described the process of selective mitochondrial autophagy, known as mitophagy. Elimination of damaged mitochondria by autophagy is important for maintenance of cellular homeostasis. DNA and RNA degradation systems also play a critical role in regulating inflammation and maintaining cellular homeostasis mediated by damaged DNA clearance and post-transcriptional regulation, respectively. This review discusses some recent advances in understanding the role of sterile inflammation and degradation systems in HF.
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Affiliation(s)
- Kazuhiko Nishida
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence
| | - Kinya Otsu
- Cardiovascular Division, King's College London British Heart Foundation Centre of Excellence
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111
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Chojnacki M, Mansour W, Hameed DS, Singh RK, El Oualid F, Rosenzweig R, Nakasone MA, Yu Z, Glaser F, Kay LE, Fushman D, Ovaa H, Glickman MH. Polyubiquitin-Photoactivatable Crosslinking Reagents for Mapping Ubiquitin Interactome Identify Rpn1 as a Proteasome Ubiquitin-Associating Subunit. Cell Chem Biol 2017; 24:443-457.e6. [PMID: 28330605 DOI: 10.1016/j.chembiol.2017.02.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 12/29/2016] [Accepted: 02/23/2017] [Indexed: 01/05/2023]
Abstract
Ubiquitin (Ub) signaling is a diverse group of processes controlled by covalent attachment of small protein Ub and polyUb chains to a range of cellular protein targets. The best documented Ub signaling pathway is the one that delivers polyUb proteins to the 26S proteasome for degradation. However, studies of molecular interactions involved in this process have been hampered by the transient and hydrophobic nature of these interactions and the lack of tools to study them. Here, we develop Ub-phototrap (UbPT), a synthetic Ub variant containing a photoactivatable crosslinking side chain. Enzymatic polymerization into chains of defined lengths and linkage types provided a set of reagents that led to identification of Rpn1 as a third proteasome ubiquitin-associating subunit that coordinates docking of substrate shuttles, unloading of substrates, and anchoring of polyUb conjugates. Our work demonstrates the value of UbPT, and we expect that its future uses will help define and investigate the ubiquitin interactome.
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Affiliation(s)
- Michal Chojnacki
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel; Department of Medical Biochemistry, Medical University of Łódź, Łódź, Poland
| | - Wissam Mansour
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Dharjath S Hameed
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Rajesh K Singh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Farid El Oualid
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Rina Rosenzweig
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mark A Nakasone
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Zanlin Yu
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Fabian Glaser
- The Technion Bioinformatics Knowledge Unit (BKU) of the Lorry Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
| | - Huib Ovaa
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel.
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112
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Defenouillère Q, Namane A, Mouaikel J, Jacquier A, Fromont-Racine M. The ribosome-bound quality control complex remains associated to aberrant peptides during their proteasomal targeting and interacts with Tom1 to limit protein aggregation. Mol Biol Cell 2017; 28:1165-1176. [PMID: 28298488 PMCID: PMC5415013 DOI: 10.1091/mbc.e16-10-0746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 11/16/2022] Open
Abstract
The RQC complex involved in protein quality control mechanisms also exists as a ribosome-unbound complex during the escort of aberrant peptides to the proteasome. The E3 ubiquitin ligase Tom1 is a newly identified partner of this light version of the RQC complex and is required for aggregate prevention. Protein quality control mechanisms eliminate defective polypeptides to ensure proteostasis and to avoid the toxicity of protein aggregates. In eukaryotes, the ribosome-bound quality control (RQC) complex detects aberrant nascent peptides that remain stalled in 60S ribosomal particles due to a dysfunction in translation termination. The RQC complex polyubiquitylates aberrant polypeptides and recruits a Cdc48 hexamer to extract them from 60S particles in order to escort them to the proteasome for degradation. Whereas the steps from stalled 60S recognition to aberrant peptide polyubiquitylation by the RQC complex have been described, the mechanism leading to proteasomal degradation of these defective translation products remains unknown. We show here that the RQC complex also exists as a ribosome-unbound complex during the escort of aberrant peptides to the proteasome. In addition, we identify a new partner of this light version of the RQC complex, the E3 ubiquitin ligase Tom1. Tom1 interacts with aberrant nascent peptides and is essential to limit their accumulation and aggregation in the absence of Rqc1; however, its E3 ubiquitin ligase activity is not required. Taken together, these results reveal new roles for Tom1 in protein quality control, aggregate prevention, and, therefore, proteostasis maintenance.
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Affiliation(s)
- Quentin Defenouillère
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France.,Sorbonne Universités, UPMC Paris 6, Complexité Du Vivant, 75252 Paris Cedex 05, France
| | - Abdelkader Namane
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - John Mouaikel
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - Alain Jacquier
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - Micheline Fromont-Racine
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
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113
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114
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Moody LR, Barrett-Wilt GA, Sussman MR, Messing A. Glial fibrillary acidic protein exhibits altered turnover kinetics in a mouse model of Alexander disease. J Biol Chem 2017; 292:5814-5824. [PMID: 28223355 DOI: 10.1074/jbc.m116.772020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/15/2017] [Indexed: 12/27/2022] Open
Abstract
Mutations in the astrocyte-specific intermediate filament glial fibrillary acidic protein (GFAP) lead to the rare and fatal disorder, Alexander disease (AxD). A prominent feature of the disease is aberrant accumulation of GFAP. It has been proposed that this accumulation occurs because of an increase in gene transcription coupled with impaired proteasomal degradation, yet this hypothesis remains untested. We therefore sought to directly investigate GFAP turnover in a mouse model of AxD that is heterozygous for a disease-causing point mutation (GfapR236H/+) (and thus expresses both wild-type and mutant protein). Stable isotope labeling by amino acids in cell culture, using primary cortical astrocytes, indicated that the in vitro half-lives of total GFAP in astrocytes from wild-type and mutant mice were similar at ∼3-4 days. Surprisingly, results obtained with stable isotope labeling of mammals revealed that, in vivo, the half-life of GFAP in mutant mice (15.4 ± 0.5 days) was much shorter than that in wild-type mice (27.5 ± 1.6 days). These unexpected in vivo data are most consistent with a model in which synthesis and degradation are both increased. Our work reveals that an AxD-causing mutation alters GFAP turnover kinetics in vivo and provides an essential foundation for future studies aimed at preventing or reducing the accumulation of GFAP. In particular, these data suggest that elimination of GFAP might be possible and occurs more quickly than previously surmised.
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Affiliation(s)
| | | | | | - Albee Messing
- From the Waisman Center, .,Comparative Biosciences, University of Wisconsin-Madison, Madison, Wisconsin 53705
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115
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Bibo-Verdugo B, Jiang Z, Caffrey CR, O'Donoghue AJ. Targeting proteasomes in infectious organisms to combat disease. FEBS J 2017; 284:1503-1517. [PMID: 28122162 DOI: 10.1111/febs.14029] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/21/2016] [Accepted: 01/23/2017] [Indexed: 01/04/2023]
Abstract
Proteasomes are multisubunit, energy-dependent, proteolytic complexes that play an essential role in intracellular protein turnover. They are present in eukaryotes, archaea, and in some actinobacteria species. Inhibition of proteasome activity has emerged as a powerful strategy for anticancer therapy and three drugs have been approved for treatment of multiple myeloma. These compounds react covalently with a threonine residue located in the active site of a proteasome subunit to block protein degradation. Proteasomes in pathogenic organisms such as Mycobacterium tuberculosis and Plasmodium falciparum also have a nucleophilic threonine residue in the proteasome active site and are therefore sensitive to these anticancer drugs. This review summarizes efforts to validate the proteasome in pathogenic organisms as a therapeutic target. We describe several strategies that have been used to develop inhibitors with increased potency and selectivity for the pathogen proteasome relative to the human proteasome. In addition, we highlight a cell-based chemical screening approach that identified a potent, allosteric inhibitor of proteasomes found in Leishmania and Trypanosoma species. Finally, we discuss the development of proteasome inhibitors as anti-infective agents.
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Affiliation(s)
- Betsaida Bibo-Verdugo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, CA, USA
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Chemistry & Biochemistry Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Conor R Caffrey
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, CA, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, CA, USA
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116
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Küry S, Besnard T, Ebstein F, Khan TN, Gambin T, Douglas J, Bacino CA, Craigen WJ, Sanders SJ, Lehmann A, Latypova X, Khan K, Pacault M, Sacharow S, Glaser K, Bieth E, Perrin-Sabourin L, Jacquemont ML, Cho MT, Roeder E, Denommé-Pichon AS, Monaghan KG, Yuan B, Xia F, Simon S, Bonneau D, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Pasquier L, Barbouth D, Shaw CA, Patel A, Smith JL, Bi W, Schmitt S, Deb W, Nizon M, Mercier S, Vincent M, Rooryck C, Malan V, Briceño I, Gómez A, Nugent KM, Gibson JB, Cogné B, Lupski JR, Stessman HA, Eichler EE, Retterer K, Yang Y, Redon R, Katsanis N, Rosenfeld JA, Kloetzel PM, Golzio C, Bézieau S, Stankiewicz P, Isidor B. De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder. Am J Hum Genet 2017; 100:352-363. [PMID: 28132691 DOI: 10.1016/j.ajhg.2017.01.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/04/2017] [Indexed: 10/25/2022] Open
Abstract
Degradation of proteins by the ubiquitin-proteasome system (UPS) is an essential biological process in the development of eukaryotic organisms. Dysregulation of this mechanism leads to numerous human neurodegenerative or neurodevelopmental disorders. Through a multi-center collaboration, we identified six de novo genomic deletions and four de novo point mutations involving PSMD12, encoding the non-ATPase subunit PSMD12 (aka RPN5) of the 19S regulator of 26S proteasome complex, in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features. We observed reduced PSMD12 levels and an accumulation of ubiquitinated proteins without any impairment of proteasome catalytic activity. Our PSMD12 loss-of-function zebrafish CRISPR/Cas9 model exhibited microcephaly, decreased convolution of the renal tubules, and abnormal craniofacial morphology. Our data support the biological importance of PSMD12 as a scaffolding subunit in proteasome function during development and neurogenesis in particular; they enable the definition of a neurodevelopmental disorder due to PSMD12 variants, expanding the phenotypic spectrum of UPS-dependent disorders.
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117
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Vriend J, Marzban H. The ubiquitin-proteasome system and chromosome 17 in cerebellar granule cells and medulloblastoma subgroups. Cell Mol Life Sci 2017; 74:449-467. [PMID: 27592301 PMCID: PMC11107675 DOI: 10.1007/s00018-016-2354-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/17/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022]
Abstract
Chromosome 17 abnormalities are often observed in medulloblastomas (MBs), particularly those classified in the consensus Groups 3 and 4. Herein we review MB signature genes associated with chromosome 17 and the relationship of these signature genes to the ubiquitin-proteasome system. While clinical investigators have not focused on the ubiquitin-proteasome system in relation to MB, a substantial amount of data on the topic has been hidden in the form of supplemental datasets of gene expression. A supplemental dataset associated with the Thompson classification of MBs shows that a subgroup of MB with 17p deletions is characterized by reduced expression of genes for several core particle subunits of the beta ring of the proteasome (β1, β4, β5, β7). One of these genes (PSMB6, the gene for the β1 subunit) is located on chromosome 17, near the telomeric end of 17p. By comparison, in the WNT group of MBs only one core proteasome subunit, β6, associated with loss of a gene (PSMB1) on chromosome 6, was down-regulated in this dataset. The MB subgroups with the worst prognosis have a significant association with chromosome 17 abnormalities and irregularities of APC/C cyclosome genes. We conclude that the expression of proteasome subunit genes and genes for ubiquitin ligases can contribute to prognostic classification of MBs. The therapeutic value of targeting proteasome subunits and ubiquitin ligases in the various subgroups of MB remains to be determined separately for each classification of MB.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Rm134, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
| | - Hassan Marzban
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Rm134, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
- Children's Hospital Research Institute of Manitoba (CHRIM), Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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118
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High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx. Cell Res 2017; 27:373-385. [PMID: 28106073 DOI: 10.1038/cr.2017.12] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/05/2016] [Accepted: 12/23/2016] [Indexed: 12/12/2022] Open
Abstract
The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide. The remaining two subunits, Rpt2 and Rpt6, with empty or only partially occupied nucleotide pocket exhibit pronounced conformational changes in the AAA-ATPase ring, which may represent a collective result of allosteric cooperativity of all the AAA-ATPase subunits responding to ATP hydrolysis. This collective motion of Rpt2 and Rpt6 results in an elevation of their pore loops, which could play an important role in substrate processing of proteasome. Our data also imply that the nucleotide occupancy pattern could be related to the activation status of the complex. Moreover, the HbYX tail insertion may not be sufficient to maintain the gate opening of 20S core particle. Our results provide new insights into the mechanisms of nucleotide-driven allosteric cooperativity of the complex and of the substrate processing by the proteasome.
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119
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Kristariyanto YA, Abdul Rehman SA, Weidlich S, Knebel A, Kulathu Y. A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. EMBO Rep 2017; 18:392-402. [PMID: 28082312 DOI: 10.15252/embr.201643205] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 11/09/2022] Open
Abstract
The eight different types of ubiquitin (Ub) chains that can be formed play important roles in diverse cellular processes. Linkage-selective recognition of Ub chains by Ub-binding domain (UBD)-containing proteins is central to coupling different Ub signals to specific cellular responses. The motif interacting with ubiquitin (MIU) is a small UBD that has been characterized for its binding to monoUb. The recently discovered deubiquitinase MINDY-1/FAM63A contains a tandem MIU repeat (tMIU) that is highly selective at binding to K48-linked polyUb. We here identify that this linkage-selective binding is mediated by a single MIU motif (MIU2) in MINDY-1. The crystal structure of MIU2 in complex with K48-linked polyubiquitin chains reveals that MIU2 on its own binds to all three Ub moieties in an open conformation that can only be accommodated by K48-linked triUb. The weak Ub binder MIU1 increases overall affinity of the tMIU for polyUb chains without affecting its linkage selectivity. Our analyses reveal new concepts for linkage selectivity and polyUb recognition by UBDs.
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Affiliation(s)
- Yosua Adi Kristariyanto
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Syed Arif Abdul Rehman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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120
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Marshall RS, Gemperline DC, Vierstra RD. Purification of 26S Proteasomes and Their Subcomplexes from Plants. Methods Mol Biol 2017; 1511:301-334. [PMID: 27730621 DOI: 10.1007/978-1-4939-6533-5_24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The 26S proteasome is a highly dynamic, multisubunit, ATP-dependent protease that plays a central role in cellular housekeeping and many aspects of plant growth and development by degrading aberrant polypeptides and key cellular regulators that are first modified by ubiquitin. Although the 26S proteasome was originally enriched from plants over 30 years ago, only recently have significant advances been made in our ability to isolate and study the plant particle. Here, we describe two robust methods for purifying the 26S proteasome and its subcomplexes from Arabidopsis thaliana; one that involves conventional chromatography techniques to isolate the complex from wild-type plants, and another that employs the genetic replacement of individual subunits with epitope-tagged variants combined with affinity purification. In addition to these purification protocols, we describe methods commonly used to analyze the activity and composition of the complex.
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Affiliation(s)
- Richard S Marshall
- Department of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, USA.,Department of Biology, Washington University in St Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO, 63130, USA
| | - David C Gemperline
- Department of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, USA
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, 425-G Henry Mall, Madison, WI, USA. .,Department of Biology, Washington University in St Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO, 63130, USA.
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121
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Ray A, Sarkar S. The proteasome of the differently-diverged eukaryote Giardia lamblia and its role in remodeling of the microtubule-based cytoskeleton. Crit Rev Microbiol 2016; 43:481-492. [PMID: 28033730 DOI: 10.1080/1040841x.2016.1262814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Atrayee Ray
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Srimonti Sarkar
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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122
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Singh SK, Sahu I, Mali SM, Hemantha HP, Kleifeld O, Glickman MH, Brik A. Synthetic Uncleavable Ubiquitinated Proteins Dissect Proteasome Deubiquitination and Degradation, and Highlight Distinctive Fate of Tetraubiquitin. J Am Chem Soc 2016; 138:16004-16015. [PMID: 27960333 DOI: 10.1021/jacs.6b09611] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various hypotheses have been proposed regarding how chain length, linkage type, position on substrate, and susceptibility to deubiquitinases (DUBs) affect processing of different substrates by proteasome. Here we report a new strategy for the chemical synthesis of ubiquitinated proteins to generate a set of well-defined conjugates bearing an oxime bond between the chain and the substrate. We confirmed that this isopeptide replacement is resistant to DUBs and to shaving by proteasome. Analyzing products generated by proteasomes ranked how chain length governed degradation outcome. Our results support that (1) the cleavage of the proximal isopeptide bond is not a prerequisite for proteasomal degradation, (2) by overcoming trimming at the proteasome, tetraUb is a fundamentally different signal than shorter chains, and (3) the tetra-ubiquitin chain can be degraded with the substrate. Together these results highlight the usefulness of chemistry to dissect the contribution of proteasome-associated DUBs and the complexity of the degradation process.
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Affiliation(s)
- Sumeet K Singh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Indrajit Sahu
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Sachitanand M Mali
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Hosahalli P Hemantha
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Oded Kleifeld
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Michael H Glickman
- Department of Biology Technion-Israel Institute of Technology , 3200008 Haifa, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology , 3200008 Haifa, Israel
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123
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Bonet-Costa V, Pomatto LCD, Davies KJA. The Proteasome and Oxidative Stress in Alzheimer's Disease. Antioxid Redox Signal 2016; 25:886-901. [PMID: 27392670 PMCID: PMC5124752 DOI: 10.1089/ars.2016.6802] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Alzheimer's disease is a neurodegenerative disorder that is projected to exceed more than 100 million cases worldwide by 2050. Aging is considered the primary risk factor for some 90% of Alzheimer's cases but a significant 10% of patients suffer from aggressive, early-onset forms of the disease. There is currently no effective Alzheimer's treatment and this, coupled with a growing aging population, highlights the necessity to understand the mechanism(s) of disease initiation and propagation. A major hallmark of Alzheimer's disease pathology is the accumulation of amyloid-β (Aβ) aggregates (an early marker of Alzheimer's disease), and neurofibrillary tangles, comprising the hyper-phosphorylated microtubule-associated protein Tau. Recent Advances: Protein oxidation is frequently invoked as a potential factor in the progression of Alzheimer's disease; however, whether it is a cause or a consequence of the pathology is still being debated. The Proteasome complex is a major regulator of intracellular protein quality control and an essential proteolytic enzyme for the processing of both Aβ and Tau. Recent studies have indicated that both protein oxidation and excessive phosphorylation may limit Proteasomal processing of Aβ and Tau in Alzheimer's disease. CRITICAL ISSUES Thus, the Proteasome may be a key factor in understanding the development of Alzheimer's disease pathology; however, its significance is still very much under investigation. FUTURE DIRECTIONS Discovering how the proteasome is affected, regulated, or dysregulated in Alzheimer's disease could be a valuable tool in the efforts to understand and, ultimately, eradicate the disease. Antioxid. Redox Signal. 25, 886-901.
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Affiliation(s)
- Vicent Bonet-Costa
- Leonard Davis School of Gerontology, Ethel Percy Andrus Gerontology Center, The Division of Molecular and Computational Biology, Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, The University of Southern California , Los Angeles, California
| | - Laura Corrales-Diaz Pomatto
- Leonard Davis School of Gerontology, Ethel Percy Andrus Gerontology Center, The Division of Molecular and Computational Biology, Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, The University of Southern California , Los Angeles, California
| | - Kelvin J A Davies
- Leonard Davis School of Gerontology, Ethel Percy Andrus Gerontology Center, The Division of Molecular and Computational Biology, Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, The University of Southern California , Los Angeles, California
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124
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Devkota S, Jeong H, Kim Y, Ali M, Roh JI, Hwang D, Lee HW. Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. Autophagy 2016; 12:2038-2053. [PMID: 27541728 PMCID: PMC5103340 DOI: 10.1080/15548627.2016.1217371] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Historically, the ubiquitin-proteasome system (UPS) and autophagy pathways were believed to be independent; however, recent data indicate that these pathways engage in crosstalk. To date, the players mediating this crosstalk have been elusive. Here, we show experimentally that EI24 (EI24, autophagy associated transmembrane protein), a key component of basal macroautophagy/autophagy, degrades 14 physiologically important E3 ligases with a RING (really interesting new gene) domain, whereas 5 other ligases were not degraded. Based on the degradation results, we built a statistical model that predicts the RING E3 ligases targeted by EI24 using partial least squares discriminant analysis. Of 381 RING E3 ligases examined computationally, our model predicted 161 EI24 targets. Those targets are primarily involved in transcription, proteolysis, cellular bioenergetics, and apoptosis and regulated by TP53 and MTOR signaling. Collectively, our work demonstrates that EI24 is an essential player in UPS-autophagy crosstalk via degradation of RING E3 ligases. These results indicate a paradigm shift regarding the fate of E3 ligases.
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Affiliation(s)
- Sushil Devkota
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
| | - Hyobin Jeong
- b Department of New Biology and Center for Plant Aging Research , Institute for Basic Science, DGIST , Daegu , Republic of Korea
| | - Yunmi Kim
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
| | - Muhammad Ali
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
| | - Jae-Il Roh
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
| | - Daehee Hwang
- b Department of New Biology and Center for Plant Aging Research , Institute for Basic Science, DGIST , Daegu , Republic of Korea
| | - Han-Woong Lee
- a Department of Biochemistry, College of Life Science and Biotechnology and Yonsei Laboratory Animal Research Center , Yonsei University , Seoul , Republic of Korea
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Marshall RS, McLoughlin F, Vierstra RD. Autophagic Turnover of Inactive 26S Proteasomes in Yeast Is Directed by the Ubiquitin Receptor Cue5 and the Hsp42 Chaperone. Cell Rep 2016; 16:1717-1732. [PMID: 27477278 DOI: 10.1016/j.celrep.2016.07.015] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/23/2016] [Accepted: 07/03/2016] [Indexed: 10/21/2022] Open
Abstract
The autophagic clearance of 26S proteasomes (proteaphagy) is an important homeostatic mechanism within the ubiquitin system that modulates proteolytic capacity and eliminates damaged particles. Here, we define two proteaphagy routes in yeast that respond to either nitrogen starvation or particle inactivation. Whereas the core autophagic machineries required for Atg8 lipidation and vesiculation are essential for both routes, the upstream Atg1 kinase participates only in starvation-induced proteaphagy. Following inactivation, 26S proteasomes become extensively modified with ubiquitin. Although prior studies with Arabidopsis implicated RPN10 in tethering ubiquitylated proteasomes to ATG8 lining the autophagic membranes, yeast proteaphagy employs the evolutionarily distinct receptor Cue5, which simultaneously binds ubiquitin and Atg8. Proteaphagy of inactivated proteasomes also requires the oligomeric Hsp42 chaperone, suggesting that ubiquitylated proteasomes are directed by Hsp42 to insoluble protein deposit (IPOD)-type structures before encapsulation. Together, Cue5 and Hsp42 provide a quality control checkpoint in yeast directed at recycling dysfunctional 26S proteasomes.
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Affiliation(s)
- Richard S Marshall
- Department of Genetics, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA; Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA; Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA.
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FBW7 mutations mediate resistance of colorectal cancer to targeted therapies by blocking Mcl-1 degradation. Oncogene 2016; 36:787-796. [PMID: 27399335 PMCID: PMC5226932 DOI: 10.1038/onc.2016.247] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/03/2016] [Accepted: 05/23/2016] [Indexed: 12/22/2022]
Abstract
Colorectal cancer (CRC), the second leading cause of cancer-related deaths in the US, has been treated with targeted therapies. However, the mechanisms of differential responses and resistance of CRCs to targeted therapies are not well understood. In this study, we found that genetic alterations of FBW7, an E3 ubiquitin ligase and a tumor suppressor frequently mutated in CRCs, contribute to resistance to targeted therapies. CRC cells containing FBW7-inactivating mutations are insensitive to clinically used multi-kinase inhibitors of RAS/RAF/MEK/ERK signaling, including regorafenib and sorafenib. In contrast, sensitivity to these agents is not affected by oncogenic mutations in KRAS, BRAF, PIK3CA or p53. These cells are defective in apoptosis owing to blocked degradation of Mcl-1, a pro-survival Bcl-2 family protein. Deleting FBW7 in FBW7-wild-type CRC cells abolishes Mcl-1 degradation and recapitulates the in vitro and in vivo drug-resistance phenotypes of FBW7-mutant cells. CRC cells selected for regorafenib resistance have progressive enrichment of pre-existing FBW7 hotspot mutations, and are cross-resistant to other targeted drugs that induce Mcl-1 degradation. Furthermore, a selective Mcl-1 inhibitor restores regorafenib sensitivity in CRC cells with intrinsic or acquired resistance. Together, our results demonstrate FBW7 mutational status as a key genetic determinant of CRC response to targeted therapies, and Mcl-1 as an attractive therapeutic target.
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127
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Sun P, Feng LX, Zhang DM, Liu M, Liu W, Mi T, Wu WY, Jiang BH, Yang M, Hu LH, Guo DA, Liu X. Bufalin derivative BF211 inhibits proteasome activity in human lung cancer cells in vitro by inhibiting β1 subunit expression and disrupting proteasome assembly. Acta Pharmacol Sin 2016; 37:908-18. [PMID: 27238210 DOI: 10.1038/aps.2016.30] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/28/2016] [Indexed: 12/20/2022] Open
Abstract
AIM Bufalin is one of the active components in the traditional Chinese medicine ChanSu that is used to treat arrhythmia, inflammation and cancer. BF211 is a bufalin derivative with stronger cytotoxic activity in cancer cells. The aim of this study was to identify the putative target proteins of BF211 and the signaling pathways in cancer cells. METHODS A549 human lung cancer cells were treated with BF211. A SILAC-based proteomic analysis was used to detect the protein expression profiles of BF211-treated A549 cells. Cellular proteasome activities were examined using fluorogenic peptide substrates, and the binding affinities of BF211 to recombinant proteasome subunit proteins were evaluated using the Biacore assay. The expression levels of proteasome subunits were determined using RT-PCR and Western blotting, and the levels of the integral 26S proteasome were evaluated using native PAGE analysis. RESULTS The proteomic analysis revealed that 1282 proteins were differentially expressed in BF211-treated A549 cells, and the putative target proteins of BF211 were associated with various cellular functions, including transcription, translation, mRNA splicing, ribosomal protein synthesis and proteasome function. In A549 cells, BF211 (5, 10, and 20 nmol/L) dose-dependently inhibited the enzymatic activities of proteasome. But BF211 displayed a moderate affinity in binding to proteasome β1 subunit and no binding affinity to the β2 and β5 subunits. Moreover, BF211 (0.1, 1, and 10 nmol/L) did not inhibit the proteasome activities in the cell lysates. BF211 (5, 10, and 20 nmol/L) significantly decreased the expression level of proteasome β1 subunit and the levels of integral 26S proteasome in A549 cells. Similarly, knockdown of the β1 subunit with siRNA in A549 cells significantly decreased integral 26S proteasome and proteasome activity. CONCLUSION BF211 inhibits proteasome activity in A549 cells by decreasing β1 subunit expression and disrupting proteasome assembly.
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128
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Vora SM, Phillips BT. The benefits of local depletion: The centrosome as a scaffold for ubiquitin-proteasome-mediated degradation. Cell Cycle 2016; 15:2124-2134. [PMID: 27294844 DOI: 10.1080/15384101.2016.1196306] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The centrosome is the major microtubule-organizing center in animal cells but is dispensable for proper microtubule spindle formation in many biological contexts and is thus thought to fulfill additional functions. Recent observations suggest that the centrosome acts as a scaffold for proteasomal degradation in the cell to regulate a variety of biological processes including cell fate acquisition, cell cycle control, stress response, and cell morphogenesis. Here, we review the body of studies indicating a role for the centrosome in promoting proteasomal degradation of ubiquitin-proteasome substrates and explore the functional relevance of this system in different biological contexts. We discuss a potential role for the centrosome in coordinating local degradation of proteasomal substrates, allowing cells to achieve stringent spatiotemporal control over various signaling processes.
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Affiliation(s)
- Setu M Vora
- a Department of Biological Sciences, University of Iowa , Iowa City , IA , USA
| | - Bryan T Phillips
- a Department of Biological Sciences, University of Iowa , Iowa City , IA , USA
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129
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Bhattacharyya S, Renn JP, Yu H, Marko JF, Matouschek A. An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates. Anal Biochem 2016; 509:50-59. [PMID: 27296635 DOI: 10.1016/j.ab.2016.05.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/13/2016] [Accepted: 05/31/2016] [Indexed: 12/12/2022]
Abstract
The 26S proteasome is the molecular machine at the center of the ubiquitin proteasome system and is responsible for adjusting the concentrations of many cellular proteins. It is a drug target in several human diseases, and assays for the characterization of modulators of its activity are valuable. The 26S proteasome consists of two components: a core particle, which contains the proteolytic sites, and regulatory caps, which contain substrate receptors and substrate processing enzymes, including six ATPases. Current high-throughput assays of proteasome activity use synthetic fluorogenic peptide substrates that report directly on the proteolytic activity of the proteasome, but not on the activities of the proteasome caps that are responsible for protein recognition and unfolding. Here, we describe a simple and robust assay for the activity of the entire 26S proteasome using fluorescence anisotropy to follow the degradation of fluorescently labeled protein substrates. We describe two implementations of the assay in a high-throughput format and show that it meets the expected requirement of ATP hydrolysis and the presence of a canonical degradation signal or degron in the target protein.
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Affiliation(s)
| | - Jonathan P Renn
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Houqing Yu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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130
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Di Renzo MA, Laverrière M, Schenkman S, Wehrendt DP, Tellez-Iñón MT, Potenza M. Characterization of TcCYC6 from Trypanosoma cruzi, a gene with homology to mitotic cyclins. Parasitol Int 2016; 65:196-204. [DOI: 10.1016/j.parint.2015.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 11/30/2022]
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131
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Gladman NP, Marshall RS, Lee KH, Vierstra RD. The Proteasome Stress Regulon Is Controlled by a Pair of NAC Transcription Factors in Arabidopsis. THE PLANT CELL 2016; 28:1279-96. [PMID: 27194708 PMCID: PMC4944403 DOI: 10.1105/tpc.15.01022] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/19/2016] [Accepted: 05/11/2016] [Indexed: 05/21/2023]
Abstract
Proteotoxic stress, which is generated by the accumulation of unfolded or aberrant proteins due to environmental or cellular perturbations, can be mitigated by several mechanisms, including activation of the unfolded protein response and coordinated increases in protein chaperones and activities that direct proteolysis, such as the 26S proteasome. Using RNA-seq analyses combined with chemical inhibitors or mutants that induce proteotoxic stress by impairing 26S proteasome capacity, we defined the transcriptional network that responds to this stress in Arabidopsis thaliana This network includes genes encoding core and assembly factors needed to build the complete 26S particle, alternative proteasome capping factors, enzymes involved in protein ubiquitylation/deubiquitylation and cellular detoxification, protein chaperones, autophagy components, and various transcriptional regulators. Many loci in this proteasome-stress regulon contain a consensus cis-element upstream of the transcription start site, which was previously identified as a binding site for the NAM/ATAF1/CUC2 78 (NAC78) transcription factor. Double mutants disrupting NAC78 and its closest relative NAC53 are compromised in the activation of this regulon and notably are strongly hypersensitive to the proteasome inhibitors MG132 and bortezomib. Given that NAC53 and NAC78 homo- and heterodimerize, we propose that they work as a pair in activating the expression of numerous factors that help plants survive proteotoxic stress and thus play a central regulatory role in maintaining protein homeostasis.
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Affiliation(s)
- Nicholas P Gladman
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard S Marshall
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706 Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Kwang-Hee Lee
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706 Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
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132
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Nakayama H, Nishida K, Otsu K. Macromolecular Degradation Systems and Cardiovascular Aging. Circ Res 2016; 118:1577-92. [DOI: 10.1161/circresaha.115.307495] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/29/2016] [Indexed: 11/16/2022]
Abstract
Aging-related cardiovascular diseases are a rapidly increasing problem worldwide. Cardiac aging demonstrates progressive decline of diastolic dysfunction of ventricle and increase in ventricular and arterial stiffness accompanied by increased fibrosis stimulated by angiotensin II and proinflammatory cytokines. Reactive oxygen species and multiple signaling pathways on cellular senescence play major roles in the process. Aging is also associated with an alteration in steady state of macromolecular dynamics including a dysfunction of protein synthesis and degradation. Currently, impaired macromolecular degradation is considered to be closely related to enhanced inflammation and be involved in the process and mechanism of cardiac aging. Herein, we review the role and mechanisms of the degradation system of intracellular macromolecules in the process and pathophysiology of cardiovascular aging.
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Affiliation(s)
- Hiroyuki Nakayama
- From the Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan (H.N.); and Cardiovascular Division, King’s College London British Heart Foundation Centre of Research Excellence, London, United Kingdom (K.N., K.O.)
| | - Kazuhiko Nishida
- From the Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan (H.N.); and Cardiovascular Division, King’s College London British Heart Foundation Centre of Research Excellence, London, United Kingdom (K.N., K.O.)
| | - Kinya Otsu
- From the Laboratory of Clinical Science and Biomedicine, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan (H.N.); and Cardiovascular Division, King’s College London British Heart Foundation Centre of Research Excellence, London, United Kingdom (K.N., K.O.)
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133
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Wen X, Klionsky DJ. The proteasome subunit RPN10 functions as a specific receptor for degradation of the 26S proteasome by macroautophagy in Arabidopsis. Autophagy 2016; 12:905-6. [PMID: 27159576 DOI: 10.1080/15548627.2016.1171949] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) and macroautophagy/autophagy are 2 main degradative routes, which are important for cellular homeostasis. In a study conducted by Marshall et al., the authors demonstrated that the UPS and autophagy converge in Arabidopsis (see the punctum in issue #11-10). In particular, they found that the 26S proteasome is degraded by autophagy, either nonselectively (induced by nitrogen starvation) or selectively (induced by proteasome inhibition). The selective phenotype is mediated through the proteasome subunit RPN10, which can bind both ubiquitin and ATG8. This newly identified autophagic degradation of the proteasome is termed "proteaphagy," and the process reveals an interesting relationship between these degradative systems.
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Affiliation(s)
- Xin Wen
- a Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor , MI, USA
| | - Daniel J Klionsky
- a Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan , Ann Arbor , MI, USA
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134
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Zheng N, Zhou Q, Wang Z, Wei W. Recent advances in SCF ubiquitin ligase complex: Clinical implications. Biochim Biophys Acta Rev Cancer 2016; 1866:12-22. [PMID: 27156687 DOI: 10.1016/j.bbcan.2016.05.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/09/2022]
Abstract
F-box proteins, which are subunit recruiting modules of SCF (SKP1-Cullin 1-F-box protein) E3 ligase complexes, play critical roles in the development and progression of human malignancies through governing multiple cellular processes including cell proliferation, apoptosis, invasion and metastasis. Moreover, there are emerging studies that lead to the development of F-box proteins inhibitors with promising therapeutic potential. In this article, we describe how F-box proteins including but not restricted to well-established Fbw7, Skp2 and β-TRCP, are involved in tumorigenesis. However, in-depth investigation is required to further explore the mechanism and the physiological contribution of undetermined F-box proteins in carcinogenesis. Lastly, we suggest that targeting F-box proteins could possibly open new avenues for the treatment and prevention of human cancers.
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Affiliation(s)
- Nana Zheng
- The Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital, Soochow University, Suzhou 215123, China
| | - Quansheng Zhou
- The Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital, Soochow University, Suzhou 215123, China
| | - Zhiwei Wang
- The Cyrus Tang Hematology Center and Collaborative Innovation Center of Hematology, Jiangsu Institute of Hematology, the First Affiliated Hospital, Soochow University, Suzhou 215123, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, MA 02215, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, MA 02215, USA.
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135
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ahg12 is a dominant proteasome mutant that affects multiple regulatory systems for germination of Arabidopsis. Sci Rep 2016; 6:25351. [PMID: 27139926 PMCID: PMC4853794 DOI: 10.1038/srep25351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/14/2016] [Indexed: 11/15/2022] Open
Abstract
The ubiquitin-proteasome system is fundamentally involved in myriad biological phenomena of eukaryotes. In plants, this regulated protein degradation system has a pivotal role in the cellular response mechanisms for both internal and external stimuli, such as plant hormones and environmental stresses. Information about substrate selection by the ubiquitination machinery has accumulated, but there is very little information about selectivity for substrates at the proteasome. Here, we report characterization of a novel abscisic acid (ABA)-hypersensitive mutant named ABA hypersensitive germination12 (ahg12) in Arabidopsis. The ahg12 mutant showed a unique pleiotropic phenotype, including hypersensitivity to ABA and ethylene, and hyposensitivity to light. Map-based cloning identified the ahg12 mutation to cause an amino acid conversion in the L23 loop of RPT5a, which is predicted to form the pore structure of the 19S RP complex of the proteasome. Transient expression assays demonstrated that some plant-specific signaling components accumulated at higher levels in the ahg12 mutant. These results suggest that the ahg12 mutation led to changes in the substrate preference of the 26S proteasome. The discovery of the ahg12 mutation thus will contribute to elucidate the characteristics of the regulated protein degradation system.
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136
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Semren N, Welk V, Korfei M, Keller IE, Fernandez IE, Adler H, Günther A, Eickelberg O, Meiners S. Regulation of 26S Proteasome Activity in Pulmonary Fibrosis. Am J Respir Crit Care Med 2016. [PMID: 26207697 DOI: 10.1164/rccm.201412-2270oc] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The ubiquitin-proteasome system is critical for maintenance of protein homeostasis by degrading polyubiquitinated proteins in a spatially and temporally controlled manner. Cell and protein homeostasis are altered upon pathological tissue remodeling. Dysregulation of the proteasome has been reported for several chronic diseases of the heart, brain, and lung. We hypothesized that proteasome function is altered upon fibrotic lung remodeling, thereby contributing to the pathogenesis of idiopathic pulmonary fibrosis (IPF). OBJECTIVES To investigate proteasome function during myofibroblast differentiation. METHODS We treated lung fibroblasts with transforming growth factor (TGF)-β and examined proteasome composition and activity. For in vivo analysis, we used mouse models of lung fibrosis and fibrotic human lung tissue. MEASUREMENTS AND MAIN RESULTS We demonstrate that induction of myofibroblast differentiation by TGF-β involves activation of the 26S proteasome, which is critically dependent on the regulatory subunit Rpn6. Silencing of Rpn6 in primary human lung fibroblasts counteracted TGF-β-induced myofibroblast differentiation. Activation of the 26S proteasome and increased expression of Rpn6 were detected during bleomycin-induced lung remodeling and fibrosis. Importantly, Rpn6 is overexpressed in myofibroblasts and basal cells of the bronchiolar epithelium in lungs of patients with IPF, which is accompanied by enhanced protein polyubiquitination. CONCLUSIONS We identified Rpn6-dependent 26S proteasome activation as an essential feature of myofibroblast differentiation in vitro and in vivo, and our results suggest it has an important role in IPF pathogenesis.
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Affiliation(s)
- Nora Semren
- 1 Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians University (LMU), LMU, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Vanessa Welk
- 1 Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians University (LMU), LMU, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Martina Korfei
- 2 Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Justus-Liebig-University Giessen, Member of the DZL, Giessen, Germany
| | - Ilona E Keller
- 1 Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians University (LMU), LMU, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Isis E Fernandez
- 1 Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians University (LMU), LMU, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Heiko Adler
- 3 Research Unit Gene Vectors, Helmholtz Zentrum München, Munich, Germany
| | - Andreas Günther
- 2 Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Justus-Liebig-University Giessen, Member of the DZL, Giessen, Germany.,4 Agaplesion Lung Clinic Waldhof Elgershausen, Greifenstein, Germany; and.,5 European IPF Network and European IPF Registry, Giessen, Germany
| | - Oliver Eickelberg
- 1 Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians University (LMU), LMU, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Silke Meiners
- 1 Comprehensive Pneumology Center (CPC), University Hospital of the Ludwig-Maximilians University (LMU), LMU, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
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137
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Song Y, Ray A, Li S, Das DS, Tai YT, Carrasco RD, Chauhan D, Anderson KC. Targeting proteasome ubiquitin receptor Rpn13 in multiple myeloma. Leukemia 2016; 30:1877-86. [PMID: 27118409 DOI: 10.1038/leu.2016.97] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/01/2016] [Accepted: 04/07/2016] [Indexed: 12/13/2022]
Abstract
Proteasome inhibitor bortezomib is an effective therapy for relapsed and newly diagnosed multiple myeloma (MM); however, dose-limiting toxicities and the development of resistance can limit its long-term utility. Recent research has focused on targeting ubiquitin receptors upstream of 20S proteasome, with the aim of generating less toxic therapies. Here we show that 19S proteasome-associated ubiquitin receptor Rpn13 is more highly expressed in MM cells than in normal plasma cells. Rpn13-siRNA (small interfering RNA) decreases MM cell viability. A novel agent RA190 targets Rpn13 and inhibits proteasome function, without blocking the proteasome activity or the 19S deubiquitylating activity. CRISPR/Cas9 Rpn13-knockout demonstrates that RA190-induced activity is dependent on Rpn13. RA190 decreases viability in MM cell lines and patient MM cells, inhibits proliferation of MM cells even in the presence of bone marrow stroma and overcomes bortezomib resistance. Anti-MM activity of RA190 is associated with induction of caspase-dependent apoptosis and unfolded protein response-related apoptosis. MM xenograft model studies show that RA190 is well tolerated, inhibits tumor growth and prolongs survival. Combining RA190 with bortezomib, lenalidomide or pomalidomide induces synergistic anti-MM activity. Our preclinical data validates targeting Rpn13 to overcome bortezomib resistance, and provides the framework for clinical evaluation of Rpn13 inhibitors, alone or in combination, to improve patient outcome in MM.
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Affiliation(s)
- Y Song
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - A Ray
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - S Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - D S Das
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Y T Tai
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - R D Carrasco
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - D Chauhan
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - K C Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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138
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The Vpu-interacting Protein SGTA Regulates Expression of a Non-glycosylated Tetherin Species. Sci Rep 2016; 6:24934. [PMID: 27103333 PMCID: PMC4840321 DOI: 10.1038/srep24934] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 04/07/2016] [Indexed: 01/02/2023] Open
Abstract
The HIV-1 accessory protein Vpu enhances virus release by counteracting the host restriction factor tetherin. To further understand the role of host cell proteins in Vpu function, we carried out yeast two-hybrid screening and identified a previously reported Vpu-interacting host factor, small glutamine-rich tetratricopeptide repeat-containing protein (SGTA). While RNAi-mediated depletion of SGTA did not significantly affect levels of tetherin or virus release efficiency, we observed that overexpression of SGTA inhibited HIV-1 release in a Vpu- and tetherin-independent manner. Overexpression of SGTA in the presence of Vpu, but not in its absence, resulted in a marked stabilization and cytosolic relocalization of a 23-kDa, non-glycosylated tetherin species. Coimmunoprecipitation studies indicated that non-glycosylated tetherin is stabilized through the formation of a ternary SGTA/Vpu/tetherin complex. This accumulation of non-glycosylated tetherin is due to inhibition of its degradation, independent of the ER-associated degradation (ERAD) pathway. Because the SGTA-stabilized tetherin species is partially localized to the cytosol, we propose that overexpression of SGTA in the presence of Vpu blocks the translocation of tetherin across the ER membrane, resulting in cytosolic accumulation of a non-glycosylated tetherin species. Although our results do not provide support for a physiological function of SGTA in HIV-1 replication, they demonstrate that SGTA overexpression regulates tetherin expression and stability, thus providing insights into the function of SGTA in ER translocation and protein degradation.
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139
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Huang X, Dixit VM. Drugging the undruggables: exploring the ubiquitin system for drug development. Cell Res 2016; 26:484-98. [PMID: 27002218 PMCID: PMC4822129 DOI: 10.1038/cr.2016.31] [Citation(s) in RCA: 324] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Dynamic modulation of protein levels is tightly controlled in response to physiological cues. In mammalian cells, much of the protein degradation is carried out by the ubiquitin-proteasome system (UPS). Similar to kinases, components of the ubiquitin system are often dysregulated, leading to a variety of diseases, including cancer and neurodegeneration, making them attractive drug targets. However, so far there are only a handful of drugs targeting the ubiquitin system that have been approved by the FDA. Here, we review possible therapeutic intervention nodes in the ubiquitin system, analyze the challenges, and highlight the most promising strategies to target the UPS.
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Affiliation(s)
- Xiaodong Huang
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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140
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Guo X, Wang X, Wang Z, Banerjee S, Yang J, Huang L, Dixon JE. Site-specific proteasome phosphorylation controls cell proliferation and tumorigenesis. Nat Cell Biol 2016; 18:202-12. [PMID: 26655835 PMCID: PMC4844191 DOI: 10.1038/ncb3289] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 11/12/2015] [Indexed: 02/07/2023]
Abstract
Despite the fundamental importance of proteasomal degradation in cells, little is known about whether and how the 26S proteasome itself is regulated in coordination with various physiological processes. Here we show that the proteasome is dynamically phosphorylated during the cell cycle at Thr 25 of the 19S subunit Rpt3. CRISPR/Cas9-mediated genome editing, RNA interference and biochemical studies demonstrate that blocking Rpt3-Thr25 phosphorylation markedly impairs proteasome activity and impedes cell proliferation. Through a kinome-wide screen, we have identified dual-specificity tyrosine-regulated kinase 2 (DYRK2) as the primary kinase that phosphorylates Rpt3-Thr25, leading to enhanced substrate translocation and degradation. Importantly, loss of the single phosphorylation of Rpt3-Thr25 or knockout of DYRK2 significantly inhibits tumour formation by proteasome-addicted human breast cancer cells in mice. These findings define an important mechanism for proteasome regulation and demonstrate the biological significance of proteasome phosphorylation in regulating cell proliferation and tumorigenesis.
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Affiliation(s)
- Xing Guo
- Department of Pharmacology, University of California-San Diego, La Jolla, CA 92093
| | - Xiaorong Wang
- Departments of Physiology and Biophysics and of Developmental and Cell Biology, University of California, Irvine, CA 92697
| | - Zhiping Wang
- Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093
| | - Sourav Banerjee
- Department of Pharmacology, University of California-San Diego, La Jolla, CA 92093
| | - Jing Yang
- Department of Pharmacology, University of California-San Diego, La Jolla, CA 92093
| | - Lan Huang
- Departments of Physiology and Biophysics and of Developmental and Cell Biology, University of California, Irvine, CA 92697
| | - Jack E. Dixon
- Department of Pharmacology, University of California-San Diego, La Jolla, CA 92093
- Departments of Cellular and Molecular Medicine and of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093
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141
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Tang X, Miao M, Niu X, Zhang D, Cao X, Jin X, Zhu Y, Fan Y, Wang H, Liu Y, Sui Y, Wang W, Wang A, Xiao F, Giovannoni J, Liu Y. Ubiquitin-conjugated degradation of golden 2-like transcription factor is mediated by CUL4-DDB1-based E3 ligase complex in tomato. THE NEW PHYTOLOGIST 2016; 209:1028-39. [PMID: 26352615 DOI: 10.1111/nph.13635] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/11/2015] [Indexed: 05/19/2023]
Abstract
CULLIN4-RING ubiquitin ligases (CRL4s) as well as their targets are fundamental regulators functioning in many key developmental and stress responses in eukaryotes. In tomato (Solanum lycopersicum), molecular cloning has revealed that the underlying genes of natural spontaneous mutations high pigment 1 (hp1), high pigment 2 (hp2) and uniform ripening (u) encode UV-DAMAGED DNA BINDING PROTEIN 1 (DDB1), DE-ETIOLATED 1 (DET1) and GOLDEN 2-LIKE (GLK2), respectively. However, the molecular basis of the opposite actions of tomato GLK2 vs CUL4-DDB1-DET1 complex on regulating plastid level and fruit quality remains unknown. Here, we provide molecular evidence showing that the tomato GLK2 protein is a substrate of the CUL4-DDB1-DET1 ubiquitin ligase complex for the proteasome degradation. SlGLK2 is degraded by the ubiquitin-proteasome system, which is mainly determined by two lysine residues (K11 and K253). SlGLK2 associates with the CUL4-DDB1-DET1 E3 complex in plant cells. Genetically impairing CUL4, DDB1 or DET1 results in a retardation of SlGLK2 degradation by the 26S proteasome. These findings are relevant to the potential of nutrient accumulation in tomato fruit by mediating the plastid level and contribute to a deeper understanding of an important regulatory loop, linking protein turnover to gene regulation.
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Affiliation(s)
- Xiaofeng Tang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Min Miao
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xiangli Niu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Danfeng Zhang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xulv Cao
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Xichen Jin
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yunye Zhu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Youhong Fan
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Hongtao Wang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Ying Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yuan Sui
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Wenjie Wang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
- Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Anquan Wang
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
- Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY, 14853, USA
| | - Fangming Xiao
- Department of Plant, Soil, and Entomological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Jim Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Tower Road, Ithaca, NY, 14853, USA
| | - Yongsheng Liu
- School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
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142
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Moriwaki K, Chan FKM. Regulation of RIPK3- and RHIM-dependent Necroptosis by the Proteasome. J Biol Chem 2016; 291:5948-5959. [PMID: 26786097 DOI: 10.1074/jbc.m115.700997] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 11/06/2022] Open
Abstract
Receptor-interacting protein kinase 3 (RIPK3) is a serine/threonine kinase with essential function in necroptosis. The activity of RIPK3 is controlled by phosphorylation. Once activated, RIPK3 phosphorylates and activates the downstream effector mixed lineage kinase domain-like (MLKL) to induce necroptosis. In certain situations, RIPK3 has also been shown to promote apoptosis or cytokine expression in a necroptosis and kinase-independent manner. The ubiquitin-proteasome system is the major pathway for selective degradation of cellular proteins and thus has a critical role in many cellular processes such as cell survival and cell death. Clinically, proteasome inhibition has shown promise as an anti-cancer agent. Here we show that the proteasome inhibitors MG132 and bortezomib activate the RIPK3-MLKL necroptotic pathway in mouse fibroblasts as well as human leukemia cells. Unlike necroptosis induced by classical TNF-like cytokines, necroptosis induced by proteasome inhibitors does not require caspase inhibition. However, an intact RIP homotypic interaction motif (RHIM) is essential. Surprisingly, when recruitment of MLKL to RIPK3 is restricted, proteasome inhibitors induced RIPK3-dependent apoptosis. Proteasome inhibition led to accumulation of K48-linked ubiquitinated RIPK3, which was partially reduced when Lys-264 was mutated. Taken together, these results reveal the ubiquitin-proteasome system as a novel regulatory mechanism for RIPK3-dependent necroptosis.
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Affiliation(s)
- Kenta Moriwaki
- From the Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Francis Ka-Ming Chan
- From the Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605.
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143
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Hernebring M. 26S and PA28-20S Proteasome Activity in Cytosolic Extracts from Embryonic Stem Cells. Methods Mol Biol 2016; 1341:359-367. [PMID: 25762294 DOI: 10.1007/7651_2015_216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The proteasome is a complex multisubunit protease that plays a major role in the degradation of proteins in eukaryotic cells. Proteasome function is one of the key players regulating the proteome and it is vital for many cellular processes. The method described here makes it possible to assay the proteolytic capacities of proteasome complexes separately in crude cytosolic extracts from ES cells. The method is based on hydrolysis of a fluorogenic peptide substrate in lysates prepared under conditions that favor the interactions of the 20S proteasomal catalytical core with either the 19S or the PA28αβ proteasome regulator.
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Affiliation(s)
- Malin Hernebring
- Discovery Sciences, AstraZeneca R&D, SE-431 83, Mölndal, Sweden.
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144
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Roberts JD, Thapaliya A, Martínez-Lumbreras S, Krysztofinska EM, Isaacson RL. Structural and Functional Insights into Small, Glutamine-Rich, Tetratricopeptide Repeat Protein Alpha. Front Mol Biosci 2015; 2:71. [PMID: 26734616 PMCID: PMC4683186 DOI: 10.3389/fmolb.2015.00071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/29/2015] [Indexed: 11/21/2022] Open
Abstract
The small glutamine-rich, tetratricopeptide repeat-containing protein alpha (SGTA) is an emerging player in the quality control of secretory and membrane proteins mislocalized to the cytosol, with established roles in tail-anchored (TA) membrane protein biogenesis. SGTA consists of three structural domains with individual functions, an N-terminal dimerization domain that assists protein sorting pathways, a central tetratricopeptide repeat (TPR) domain that mediates interactions with heat-shock proteins, proteasomal, and hormonal receptors, and viral proteins, and a C-terminal glutamine rich region that binds hydrophobic substrates. SGTA has been linked to viral lifecycles and hormone receptor signaling, with implications in the pathogenesis of various disease states. Thus far, a range of biophysical techniques have been employed to characterize SGTA structure in some detail, and to investigate its interactions with binding partners in different biological contexts. A complete description of SGTA structure, together with further investigation into its function as a co-chaperone involved quality control, could provide us with useful insights into its role in maintaining cellular proteostasis, and broaden our understanding of mechanisms underlying associated pathologies. This review describes how some structural features of SGTA have been elucidated, and what this has uncovered about its cellular functions. A brief background on the structure and function of SGTA is given, highlighting its importance to biomedicine and related fields. The current level of knowledge and what remains to be understood about the structure and function of SGTA is summarized, discussing the potential direction of future research.
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145
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Yu G, Rosenberg JN, Betenbaugh MJ, Oyler GA. Pac-Man for biotechnology: co-opting degrons for targeted protein degradation to control and alter cell function. Curr Opin Biotechnol 2015; 36:199-204. [DOI: 10.1016/j.copbio.2015.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
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146
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Nikesitch N, Ling SCW. Molecular mechanisms in multiple myeloma drug resistance. J Clin Pathol 2015; 69:97-101. [PMID: 26598624 PMCID: PMC4752637 DOI: 10.1136/jclinpath-2015-203414] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023]
Abstract
Multiple myeloma (MM) is predominantly an incurable malignancy despite high-dose chemotherapy, autologous stem cell transplant and novel agents. MM is a genetically heterogeneous disease and the complexity increases as the disease progresses to a more aggressive stage. MM arises from a plasma cell, which produces and secretes non-functioning immunoglobulins. Most MM cells are sensitive to proteasome inhibitors (PIs), which have become the main drug in the treatment of newly diagnosed and relapsed MM. However, not all MM is sensitive to PIs. This review summarises the literature regarding molecular biology of MM with a focus on the unfolded protein response and explores how this could affect drug sensitivity and progression of disease.
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Affiliation(s)
- Nicholas Nikesitch
- School of Medicine, University of Western Sydney, Campbelltown, New South Wales, Australia Haematology Research Group, Ingham Institute of Applied Medical Research, Liverpool, New South Wales, Australia
| | - Silvia C W Ling
- Haematology Research Group, Ingham Institute of Applied Medical Research, Liverpool, New South Wales, Australia Department of Haematology, Liverpool Hospital, Liverpool, New South Wales, Australia
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147
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Kim YC, Snoberger A, Schupp J, Smith DM. ATP binding to neighbouring subunits and intersubunit allosteric coupling underlie proteasomal ATPase function. Nat Commun 2015; 6:8520. [PMID: 26465836 PMCID: PMC4608255 DOI: 10.1038/ncomms9520] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 08/30/2015] [Indexed: 12/31/2022] Open
Abstract
The primary functions of the proteasome are driven by a highly allosteric ATPase complex. ATP binding to only two subunits in this hexameric complex triggers substrate binding, ATPase–20S association and 20S gate opening. However, it is unclear how ATP binding and hydrolysis spatially and temporally coordinates these allosteric effects to drive substrate translocation into the 20S. Here, we use FRET to show that the proteasomal ATPases from eukaryotes (RPTs) and archaea (PAN) bind ATP with high affinity at neighbouring subunits, which complements the well-established spiral-staircase topology of the 26S ATPases. We further show that two conserved arginine fingers in PAN located at the subunit interface work together as a single allosteric unit to mediate the allosteric effects of ATP binding, without altering the nucleotide-binding pattern. Rapid kinetics analysis also shows that ring resetting of a sequential hydrolysis mechanism can be explained by thermodynamic equilibrium binding of ATP. These data support a model whereby these two functionally distinct allosteric networks cooperate to translocate polypeptides into the 20S for degradation. The 26S proteasome contains a hexamer of ATPase subunits, which binds, unfolds and translocates substrates in an ATP-dependent manner. Kim et al. use FRET to show that ATP binding preferentially occurs at neighbouring subunits of the hexamer, and identify two allosteric systems that coordinate translocation.
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Affiliation(s)
- Young-Chan Kim
- Department of Biochemistry, West Virginia University, 1 Medical Center Drive, Morgantown, West Virginia 26506, USA
| | - Aaron Snoberger
- Department of Biochemistry, West Virginia University, 1 Medical Center Drive, Morgantown, West Virginia 26506, USA
| | - Jane Schupp
- Department of Biochemistry, West Virginia University, 1 Medical Center Drive, Morgantown, West Virginia 26506, USA
| | - David M Smith
- Department of Biochemistry, West Virginia University, 1 Medical Center Drive, Morgantown, West Virginia 26506, USA
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148
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Grigoreva TA, Tribulovich VG, Garabadzhiu AV, Melino G, Barlev NA. The 26S proteasome is a multifaceted target for anti-cancer therapies. Oncotarget 2015; 6:24733-49. [PMID: 26295307 PMCID: PMC4694792 DOI: 10.18632/oncotarget.4619] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 07/10/2015] [Indexed: 12/30/2022] Open
Abstract
Proteasomes play a critical role in the fate of proteins that are involved in major cellular processes, including signal transduction, gene expression, cell cycle, replication, differentiation, immune response, cellular response to stress, etc. In contrast to non-specific degradation by lysosomes, proteasomes are highly selective and destroy only the proteins that are covalently labelled with small proteins, called ubiquitins. Importantly, many diseases, including neurodegenerative diseases and cancers, are intimately connected to the activity of proteasomes making them an important pharmacological target. Currently, the vast majority of inhibitors are aimed at blunting the proteolytic activities of proteasomes. However, recent achievements in solving structures of proteasomes at very high resolution provided opportunities to design new classes of small molecules that target other physiologically-important enzymatic activities of proteasomes, including the de-ubiquitinating one. This review attempts to catalog the information available to date about novel classes of proteasome inhibitors that may have important pharmacological ramifications.
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Affiliation(s)
- Tatyana A Grigoreva
- St. Petersburg State Technological Institute (Technical University), St. Petersburng, Russia
| | | | | | - Gerry Melino
- St. Petersburg State Technological Institute (Technical University), St. Petersburng, Russia
- University of Rome Tor Vergata, Roma, Italy
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149
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SLUG is required for SOX9 stabilization and functions to promote cancer stem cells and metastasis in human lung carcinoma. Oncogene 2015; 35:2824-33. [PMID: 26387547 PMCID: PMC4801727 DOI: 10.1038/onc.2015.351] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 07/31/2015] [Accepted: 08/14/2015] [Indexed: 02/07/2023]
Abstract
Cancer stem cells (CSCs) are a promising target for cancer therapy, particularly for metastatic lung cancers, but how CSCs are regulated is largely unknown. We identify two proteins, SLUG (encoded by SNAI2 gene) and SOX9, that are associated with advanced stage lung cancers and are implicated in the regulation of CSCs. Inhibition of either SLUG or SOX9 sufficiently inhibits CSCs in human lung cancer cells and attenuates experimental lung metastasis in a xenograft mouse model. Correlation between SLUG and SOX9 levels was observed remarkably, we therefore sought to explore their mechanistic relationship and regulation. SLUG, beyond its known function as an epithelial-mesenchymal transition transcription factor, was found to regulate SOX9 by controlling its stability via a post-translational modification process. SLUG interacts directly with SOX9 and prevents it from ubiquitin-mediated proteasomal degradation. SLUG expression and binding are necessary for SOX9 promotion of lung CSCs and metastasis in a mouse model. Together, our findings provide a novel mechanistic insight into the regulation of CSCs via SLUG-SOX9 regulatory axis, which represents a potential novel target for CSC therapy that may overcome cancer chemoresistance and relapse.
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150
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Liu L, Jiang L, Ding XD, Liu JF, Zhang Q. The regulation of glucose on milk fat synthesis is mediated by the ubiquitin-proteasome system in bovine mammary epithelial cells. Biochem Biophys Res Commun 2015; 465:59-63. [DOI: 10.1016/j.bbrc.2015.07.129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/25/2015] [Indexed: 10/23/2022]
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