201
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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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202
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Yu C, Yang Y, Wang X, Guan S, Fang L, Liu F, Walters KJ, Kaiser P, Huang L. Characterization of Dynamic UbR-Proteasome Subcomplexes by In vivo Cross-linking (X) Assisted Bimolecular Tandem Affinity Purification (XBAP) and Label-free Quantitation. Mol Cell Proteomics 2016; 15:2279-92. [PMID: 27114451 DOI: 10.1074/mcp.m116.058271] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 12/14/2022] Open
Abstract
Proteasomes are protein degradation machines that exist in cells as heterogeneous and dynamic populations. A group of proteins function as ubiquitin receptors (UbRs) that can recognize and deliver ubiquitinated substrates to proteasome complexes for degradation. Defining composition of proteasome complexes engaged with UbRs is critical to understand proteasome function. However, because of the dynamic nature of UbR interactions with the proteasome, it remains technically challenging to capture and isolate UbR-proteasome subcomplexes using conventional purification strategies. As a result, distinguishing the molecular differences among these subcomplexes remains elusive. We have developed a novel affinity purification strategy, in vivo cross-linking (X) assisted bimolecular tandem affinity purification strategy (XBAP), to effectively isolate dynamic UbR-proteasome subcomplexes and define their subunit compositions using label-free quantitative mass spectrometry. In this work, we have analyzed seven distinctive UbR-proteasome complexes and found that all of them contain the same type of the 26S holocomplex. However, selected UbRs interact with a group of proteasome interacting proteins that may link each UbR to specific cellular pathways. The compositional similarities and differences among the seven UbR-proteasome subcomplexes have provided new insights on functional entities of proteasomal degradation machineries. The strategy described here represents a general and useful proteomic tool for isolating and studying dynamic and heterogeneous protein subcomplexes in cells that have not been fully characterized.
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Affiliation(s)
- Clinton Yu
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Yingying Yang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Xiaorong Wang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Shenheng Guan
- §Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Lei Fang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Fen Liu
- ¶Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Kylie J Walters
- ¶Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Peter Kaiser
- ‖Department of Biological Chemistry, University of California, Irvine, California 92697
| | - Lan Huang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697;
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203
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Wilmington SR, Matouschek A. An Inducible System for Rapid Degradation of Specific Cellular Proteins Using Proteasome Adaptors. PLoS One 2016; 11:e0152679. [PMID: 27043013 PMCID: PMC4820223 DOI: 10.1371/journal.pone.0152679] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/17/2016] [Indexed: 11/25/2022] Open
Abstract
A common way to study protein function is to deplete the protein of interest from cells and observe the response. Traditional methods involve disrupting gene expression but these techniques are only effective against newly synthesized proteins and leave previously existing and stable proteins untouched. Here, we introduce a technique that induces the rapid degradation of specific proteins in mammalian cells by shuttling the proteins to the proteasome for degradation in a ubiquitin-independent manner. We present two implementations of the system in human culture cells that can be used individually to control protein concentration. Our study presents a simple, robust, and flexible technology platform for manipulating intracellular protein levels.
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Affiliation(s)
- Shameika R. Wilmington
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Andreas Matouschek
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States of America
- * E-mail:
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204
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Caputi FF, Carboni L, Mazza D, Candeletti S, Romualdi P. Cocaine and ethanol target 26S proteasome activity and gene expression in neuroblastoma cells. Drug Alcohol Depend 2016; 161:265-75. [PMID: 26922280 DOI: 10.1016/j.drugalcdep.2016.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Ethanol and cocaine are widely abused drugs triggering long-lasting changes in neuronal circuits and synaptic transmission through the regulation of enzyme activity and gene expression. Compelling evidence indicates that the ubiquitin-proteasome system plays a role in the molecular changes induced by addictive substances, impacting on several mechanisms implicated in abuse. The goal of these studies was to evaluate the effects of cocaine or ethanol on proteasome activity in neuroblastoma cells. Moreover, the gene expression of specific subunits was assessed. METHODS Chymotrypsin-like activity was measured after 2 h, 24 h, and 48 h exposure to 5 μM cocaine or 40 mM ethanol. Proteasome subunit transcripts were evaluated by qPCR at the same time-points. RESULTS Treatments modified proteasome function in opposite directions, since cocaine increased and ethanol reduced chymotrypsin-like activity. Interestingly, we observed gene expression alterations induced by these drugs. In the core particle, the β1 and α5 subunits were mainly up-regulated by cocaine, whereas α6 transcripts were mostly decreased. β2 and β5 did not change. Similarly, ethanol exposure generally increased β1 and α5 mRNAs. Moreover, the β2 subunit was significantly up-regulated by ethanol only. The β5 and α6 subunits were not altered. In the regulatory particle, Rpt3 was increased by cocaine exposure, whereas it was reduced by ethanol. No significant Rpn9 alterations were observed. CONCLUSIONS These findings support the notion that addictive substances regulate proteasome function, contributing to the dysregulations related to drug abuse since the availability of adequate subunit amounts is necessary for proper complex assembly and function.
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Affiliation(s)
- Francesca Felicia Caputi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy.
| | - Lucia Carboni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Daria Mazza
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Sanzio Candeletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Patrizia Romualdi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Irnerio 48, 40126 Bologna, Italy
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205
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Ronau JA, Beckmann JF, Hochstrasser M. Substrate specificity of the ubiquitin and Ubl proteases. Cell Res 2016; 26:441-56. [PMID: 27012468 PMCID: PMC4822132 DOI: 10.1038/cr.2016.38] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Conjugation and deconjugation of ubiquitin and ubiquitin-like proteins (Ubls) to cellular proteins are highly regulated processes integral to cellular homeostasis. Most often, the C-termini of these small polypeptides are attached to lysine side chains of target proteins by an amide (isopeptide) linkage. Deubiquitinating enzymes (DUBs) and Ubl-specific proteases (ULPs) comprise a diverse group of proteases that recognize and remove ubiquitin and Ubls from their substrates. How DUBs and ULPs distinguish among different modifiers, or different polymeric forms of these modifiers, remains poorly understood. The specificity of ubiquitin/Ubl-deconjugating enzymes for particular substrates depends on multiple factors, ranging from the topography of specific substrate features, as in different polyubiquitin chain types, to structural elements unique to each enzyme. Here we summarize recent structural and biochemical studies that provide insights into mechanisms of substrate specificity among various DUBs and ULPs. We also discuss the unexpected specificities of non-eukaryotic proteases in these families.
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Affiliation(s)
- Judith A Ronau
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - John F Beckmann
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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206
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Padmanabhan A, Vuong SAT, Hochstrasser M. Assembly of an Evolutionarily Conserved Alternative Proteasome Isoform in Human Cells. Cell Rep 2016; 14:2962-74. [PMID: 26997268 DOI: 10.1016/j.celrep.2016.02.068] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/25/2016] [Accepted: 02/16/2016] [Indexed: 11/17/2022] Open
Abstract
Targeted intracellular protein degradation in eukaryotes is largely mediated by the proteasome. Here, we report the formation of an alternative proteasome isoform in human cells, previously found only in budding yeast, that bears an altered subunit arrangement in the outer ring of the proteasome core particle. These proteasomes result from incorporation of an additional α4 (PSMA7) subunit in the position normally occupied by α3 (PSMA4). Assembly of "α4-α4" proteasomes depends on the relative cellular levels of α4 and α3 and on the proteasome assembly chaperone PAC3. The oncogenic tyrosine kinases ABL and ARG and the tumor suppressor BRCA1 regulate cellular α4 levels and formation of α4-α4 proteasomes. Cells primed to assemble α4-α4 proteasomes exhibit enhanced resistance to toxic metal ions. Taken together, our results establish the existence of an alternative mammalian proteasome isoform and suggest a potential role in enabling cells to adapt to environmental stresses.
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Affiliation(s)
- Achuth Padmanabhan
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Simone Anh-Thu Vuong
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.
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207
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Kragelund BB, Schenstrøm SM, Rebula CA, Panse VG, Hartmann-Petersen R. DSS1/Sem1, a Multifunctional and Intrinsically Disordered Protein. Trends Biochem Sci 2016; 41:446-459. [PMID: 26944332 DOI: 10.1016/j.tibs.2016.02.004] [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] [Received: 11/12/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 01/24/2023]
Abstract
DSS1/Sem1 is a versatile intrinsically disordered protein. Besides being a bona fide subunit of the 26S proteasome, DSS1 associates with other protein complexes, including BRCA2-RPA, involved in homologous recombination; the Csn12-Thp3 complex, involved in RNA splicing; the integrator, involved in transcription; and the TREX-2 complex, involved in nuclear export of mRNA and transcription elongation. As a subunit of the proteasome, DSS1 functions both in complex assembly and possibly as a ubiquitin receptor. Here, we summarise structural and functional aspects of DSS1/Sem1 with particular emphasis on its multifunctional and disordered properties. We suggest that DSS1/Sem1 can act as a polyanionic adhesive to prevent nonproductive interactions during construction of protein assemblies, uniquely employing different structures when associating with the diverse multisubunit complexes.
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Affiliation(s)
- Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Signe M Schenstrøm
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Caio A Rebula
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Vikram Govind Panse
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Rasmus Hartmann-Petersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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208
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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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209
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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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210
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Tomko RJ, Taylor DW, Chen ZA, Wang HW, Rappsilber J, Hochstrasser M. A Single α Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly. Cell 2016; 163:432-44. [PMID: 26451487 PMCID: PMC4601081 DOI: 10.1016/j.cell.2015.09.022] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/19/2015] [Accepted: 08/19/2015] [Indexed: 11/11/2022]
Abstract
Most short-lived eukaryotic proteins are degraded by the proteasome. A proteolytic core particle (CP) capped by regulatory particles (RPs) constitutes the 26S proteasome complex. RP biogenesis culminates with the joining of two large subcomplexes, the lid and base. In yeast and mammals, the lid appears to assemble completely before attaching to the base, but how this hierarchical assembly is enforced has remained unclear. Using biochemical reconstitutions, quantitative cross-linking/mass spectrometry, and electron microscopy, we resolve the mechanistic basis for the linkage between lid biogenesis and lid-base joining. Assimilation of the final lid subunit, Rpn12, triggers a large-scale conformational remodeling of the nascent lid that drives RP assembly, in part by relieving steric clash with the base. Surprisingly, this remodeling is triggered by a single Rpn12 α helix. Such assembly-coupled conformational switching is reminiscent of viral particle maturation and may represent a commonly used mechanism to enforce hierarchical assembly in multisubunit complexes. First in vitro reconstitution of RP assembly with completely recombinant components Electron microscopy and cross-linking reveal massive remodeling of a lid precursor Remodeling of the lid relieves steric clash with the RP base to promote RP assembly Lid remodeling can be triggered by a single C-terminal α helix in the Rpn12 subunit
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Affiliation(s)
- Robert J Tomko
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - David W Taylor
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Zhuo A Chen
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Mayfield Road, Edinburgh EH9 3BF, Scotland
| | - Hong-Wei Wang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, PRC
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Max Born Crescent, Mayfield Road, Edinburgh EH9 3BF, Scotland; Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
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211
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Xin BT, de Bruin G, Plomp JW, Florea BI, van der Marel GA, Overkleeft HS. Incorporation of the Constrained Peptidomimetic, 5-Methylpyridin-2-one into Peptide Vinyl Sulfones and Peptide Epoxy Ketones is Detrimental for Proteasome Inhibition. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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212
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Guharoy M, Bhowmick P, Sallam M, Tompa P. Tripartite degrons confer diversity and specificity on regulated protein degradation in the ubiquitin-proteasome system. Nat Commun 2016; 7:10239. [PMID: 26732515 PMCID: PMC4729826 DOI: 10.1038/ncomms10239] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/17/2015] [Indexed: 12/26/2022] Open
Abstract
Specific signals (degrons) regulate protein turnover mediated by the ubiquitin-proteasome system. Here we systematically analyse known degrons and propose a tripartite model comprising the following: (1) a primary degron (peptide motif) that specifies substrate recognition by cognate E3 ubiquitin ligases, (2) secondary site(s) comprising a single or multiple neighbouring ubiquitinated lysine(s) and (3) a structurally disordered segment that initiates substrate unfolding at the 26S proteasome. Primary degron sequences are conserved among orthologues and occur in structurally disordered regions that undergo E3-induced folding-on-binding. Posttranslational modifications can switch primary degrons into E3-binding-competent states, thereby integrating degradation with signalling pathways. Degradation-linked lysines tend to be located within disordered segments that also initiate substrate degradation by effective proteasomal engagement. Many characterized mutations and alternative isoforms with abrogated degron components are implicated in disease. These effects result from increased protein stability and interactome rewiring. The distributed nature of degrons ensures regulation, specificity and combinatorial control of degradation.
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Affiliation(s)
- Mainak Guharoy
- VIB Structural Biology Research Center (SBRC), Vrije Universiteit Brussel (VUB), Building E, Pleinlaan 2, 1050 Brussels, Belgium
| | - Pallab Bhowmick
- VIB Structural Biology Research Center (SBRC), Vrije Universiteit Brussel (VUB), Building E, Pleinlaan 2, 1050 Brussels, Belgium
| | - Mohamed Sallam
- VIB Structural Biology Research Center (SBRC), Vrije Universiteit Brussel (VUB), Building E, Pleinlaan 2, 1050 Brussels, Belgium
| | - Peter Tompa
- VIB Structural Biology Research Center (SBRC), Vrije Universiteit Brussel (VUB), Building E, Pleinlaan 2, 1050 Brussels, Belgium
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary
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213
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Chen M, Ji M, Wen B, Liu L, Li S, Chen X, Gao D, Li L. GOLDEN 2-LIKE Transcription Factors of Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1509. [PMID: 27757121 PMCID: PMC5048441 DOI: 10.3389/fpls.2016.01509] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/22/2016] [Indexed: 05/18/2023]
Abstract
Golden2-like (GLK) transcription factors are members of the GARP family of Myb transcription factors with an established relationship to chloroplast development in the plant kingdom. In the last century, Golden2 was proposed as a second golden producing factor and identified as controlling cellular differentiation in maize leaves. Then, GLKs were also found to play roles in disease defense and their function is conserved in regulating chloroplast development. Recently, research on GLKs has rapidly increased and shown that GLKs control chloroplast development in green and non-green tissues. Moreover, links between phytohormones and GLKs were verified. In this mini-review, we summarize the history, conservation, function, potential targets and degradation of GLKs.
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Affiliation(s)
- Min Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural UniversityTaian, China
- College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and EfficiencyTaian, China
| | - Meiling Ji
- State Key Laboratory of Crop Biology, Shandong Agricultural UniversityTaian, China
- College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and EfficiencyTaian, China
| | - Binbin Wen
- State Key Laboratory of Crop Biology, Shandong Agricultural UniversityTaian, China
- College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and EfficiencyTaian, China
| | - Li Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural UniversityTaian, China
- College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and EfficiencyTaian, China
| | - Shaoxuan Li
- State Key Laboratory of Crop Biology, Shandong Agricultural UniversityTaian, China
- College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and EfficiencyTaian, China
| | - Xiude Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural UniversityTaian, China
- College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and EfficiencyTaian, China
| | - Dongsheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural UniversityTaian, China
- College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and EfficiencyTaian, China
- *Correspondence: Dongsheng Gao, Ling Li,
| | - Ling Li
- State Key Laboratory of Crop Biology, Shandong Agricultural UniversityTaian, China
- College of Horticulture Science and Engineering, Shandong Agricultural UniversityTaian, China
- Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and EfficiencyTaian, China
- *Correspondence: Dongsheng Gao, Ling Li,
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214
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Papaevgeniou N, Chondrogianni N. UPS Activation in the Battle Against Aging and Aggregation-Related Diseases: An Extended Review. Methods Mol Biol 2016; 1449:1-70. [PMID: 27613027 DOI: 10.1007/978-1-4939-3756-1_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Aging is a biological process accompanied by gradual increase of damage in all cellular macromolecules, i.e., nucleic acids, lipids, and proteins. When the proteostasis network (chaperones and proteolytic systems) cannot reverse the damage load due to its excess as compared to cellular repair/regeneration capacity, failure of homeostasis is established. This failure is a major hallmark of aging and/or aggregation-related diseases. Dysfunction of the major cellular proteolytic machineries, namely the proteasome and the lysosome, has been reported during the progression of aging and aggregation-prone diseases. Therefore, activation of these pathways is considered as a possible preventive or therapeutic approach against the progression of these processes. This chapter focuses on UPS activation studies in cellular and organismal models and the effects of such activation on aging, longevity and disease prevention or reversal.
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Affiliation(s)
- Nikoletta Papaevgeniou
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece
| | - Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece.
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215
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Samanovic MI, Darwin KH. Game of 'Somes: Protein Destruction for Mycobacterium tuberculosis Pathogenesis. Trends Microbiol 2016; 24:26-34. [PMID: 26526503 PMCID: PMC4698092 DOI: 10.1016/j.tim.2015.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/25/2015] [Accepted: 10/05/2015] [Indexed: 01/12/2023]
Abstract
The proteasome system of Mycobacterium tuberculosis is required for causing disease. Proteasomes are multisubunit chambered proteases and, until recently, were only known to participate in adenosine triphosphate (ATP)-dependent proteolysis in bacteria. In this review, we discuss the latest advances in understanding how both ATP-dependent and ATP-independent proteasome-regulated pathways contribute to M. tuberculosis virulence.
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Affiliation(s)
- Marie I Samanovic
- New York University School of Medicine, Department of Microbiology, 550 First Avenue, MSB 236 New York, NY 10016, USA
| | - K Heran Darwin
- New York University School of Medicine, Department of Microbiology, 550 First Avenue, MSB 236 New York, NY 10016, USA.
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216
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Dasgupta S, Fishman MA, Mahallati H, Castro LM, Tashima AK, Ferro ES, Fricker LD. Reduced Levels of Proteasome Products in a Mouse Striatal Cell Model of Huntington's Disease. PLoS One 2015; 10:e0145333. [PMID: 26691307 PMCID: PMC4686214 DOI: 10.1371/journal.pone.0145333] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022] Open
Abstract
Huntington's disease is the result of a long polyglutamine tract in the gene encoding huntingtin protein, which in turn causes a large number of cellular changes and ultimately results in neurodegeneration of striatal neurons. Although many theories have been proposed, the precise mechanism by which the polyglutamine expansion causes cellular changes is not certain. Some evidence supports the hypothesis that the long polyglutamine tract inhibits the proteasome, a multiprotein complex involved in protein degradation. However, other studies report normal proteasome function in cells expressing long polyglutamine tracts. The controversy may be due to the methods used to examine proteasome activity in each of the previous studies. In the present study, we measured proteasome function by examining levels of endogenous peptides that are products of proteasome cleavage. Peptide levels were compared among mouse striatal cell lines expressing either 7 glutamines (STHdhQ7/Q7) or 111 glutamines in the huntingtin protein, either heterozygous (STHdhQ7/Q111) or homozygous (STHdhQ111/Q111). Both of the cell lines expressing huntingtin with 111 glutamines showed a large reduction in nearly all of the peptides detected in the cells, relative to levels of these peptides in cells homozygous for 7 glutamines. Treatment of STHdhQ7/Q7 cells with proteasome inhibitors epoxomicin or bortezomib also caused a large reduction in most of these peptides, suggesting that they are products of proteasome-mediated cleavage of cellular proteins. Taken together, these results support the hypothesis that proteasome function is impaired by the expression of huntingtin protein containing long polyglutamine tracts.
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Affiliation(s)
- Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Michael A. Fishman
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Hana Mahallati
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
| | - Leandro M. Castro
- São Paulo State University (UNESP), Experimental Campus on the São Paulo Coast, São Vicente, 11330–900, SP, Brazil
| | - Alexandre K. Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of Sao Paulo, Sao Paulo, SP, 04023–901, SP, Brazil
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Science Institute, University of São Paulo, São Paulo, 05508–000, SP, Brazil
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, 10461, United States of America
- * E-mail:
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217
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Waite KA, De-La Mota-Peynado A, Vontz G, Roelofs J. Starvation Induces Proteasome Autophagy with Different Pathways for Core and Regulatory Particles. J Biol Chem 2015; 291:3239-53. [PMID: 26670610 PMCID: PMC4751371 DOI: 10.1074/jbc.m115.699124] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 12/21/2022] Open
Abstract
The proteasome is responsible for the degradation of many cellular proteins. If and how this abundant and normally stable complex is degraded by cells is largely unknown. Here we show that in yeast, upon nitrogen starvation, proteasomes are targeted for vacuolar degradation through autophagy. Using GFP-tagged proteasome subunits, we observed that autophagy of a core particle (CP) subunit depends on the deubiquitinating enzyme Ubp3, although a regulatory particle (RP) subunit does not. Furthermore, upon blocking of autophagy, RP remained largely nuclear, although CP largely localized to the cytosol as well as granular structures within the cytosol. In all, our data reveal a regulated process for the removal of proteasomes upon nitrogen starvation. This process involves CP and RP dissociation, nuclear export, and independent vacuolar targeting of CP and RP. Thus, in addition to the well characterized transcriptional up-regulation of genes encoding proteasome subunits, cells are also capable of down-regulating cellular levels of proteasomes through proteaphagy.
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Affiliation(s)
- Kenrick A Waite
- From the Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | | | - Gabrielle Vontz
- From the Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Jeroen Roelofs
- From the Division of Biology, Kansas State University, Manhattan, Kansas 66506
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218
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Ishii K, Noda M, Yagi H, Thammaporn R, Seetaha S, Satoh T, Kato K, Uchiyama S. Disassembly of the self-assembled, double-ring structure of proteasome α7 homo-tetradecamer by α6. Sci Rep 2015; 5:18167. [PMID: 26657688 PMCID: PMC4677347 DOI: 10.1038/srep18167] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/13/2015] [Indexed: 11/15/2022] Open
Abstract
The 20S core particle of the eukaryotic proteasome is composed of two α- and two β-rings, each of which is a hetero-heptamer composed of seven homologous but distinct subunits. Although formation of the eukaryotic proteasome is a highly ordered process assisted by assembly chaperones, α7, an α-ring component, has the unique property of self-assembling into a homo-tetradecamer. We used biophysical methods to characterize the oligomeric states of this proteasome subunit and its interaction with α6, which makes direct contacts with α7 in the proteasome α-ring. We determined a crystal structure of the α7 tetradecamer, which has a double-ring structure. Sedimentation velocity analytical ultracentrifugation and mass spectrometric analysis under non-denaturing conditions revealed that α7 exclusively exists as homo-tetradecamer in solution and that its double-ring structure is disassembled upon the addition of α6, resulting in a 1:7 hetero-octameric α6–α7 complex. Our findings suggest that proteasome formation involves the disassembly of non-native oligomers, which are assembly intermediates.
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Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Ratsupa Thammaporn
- Faculty of Science, Kasetsart University, Bangkean, Bangkok 10900, Thailand.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Supaporn Seetaha
- Faculty of Science, Kasetsart University, Bangkean, Bangkok 10900, Thailand.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan.,JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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219
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Wang L, Delahunty C, Fritz-Wolf K, Rahlfs S, Helena Prieto J, Yates JR, Becker K. Characterization of the 26S proteasome network in Plasmodium falciparum. Sci Rep 2015; 5:17818. [PMID: 26639022 PMCID: PMC4671066 DOI: 10.1038/srep17818] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/06/2015] [Indexed: 11/09/2022] Open
Abstract
In eukaryotic cells, the ubiquitin-proteasome system as a key regulator of protein quality control is an excellent drug target. We therefore aimed to analyze the 26S proteasome complex in the malaria parasite Plasmodium falciparum, which still threatens almost half of the world’s population. First, we established an affinity purification protocol allowing for the isolation of functional 26S proteasome complexes from the parasite. Subunit composition of the proteasome and component stoichiometry were studied and physiologic interacting partners were identified via in situ protein crosslinking. Furthermore, intrinsic ubiquitin receptors of the plasmodial proteasome were determined and their roles in proteasomal substrate recognition were analyzed. Notably, PfUSP14 was characterized as a proteasome-associated deubiquitinase resulting in the concept that targeting proteasomal deubiquitinating activity in P. falciparum may represent a promising antimalarial strategy. The data provide insights into a profound network orchestrated by the plasmodial proteasome and identified novel drug target candidates in the ubiquitin-proteasome system.
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Affiliation(s)
- Lihui Wang
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Claire Delahunty
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California
| | | | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
| | - Judith Helena Prieto
- Department of Chemistry, Western Connecticut State University, Danbury, Connecticut
| | - John R Yates
- Max-Planck Institute for Medical Research, Heidelberg, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen, Germany
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220
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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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221
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Inobe T, Genmei R. Inhibition of the 26S proteasome by peptide mimics of the coiled-coil region of its ATPase subunits. Biochem Biophys Res Commun 2015; 468:143-50. [DOI: 10.1016/j.bbrc.2015.10.144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/27/2015] [Indexed: 11/28/2022]
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222
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Joyce S. Immunoproteasomes edit tumors, which then escapes immune recognition. Eur J Immunol 2015; 45:3241-5. [PMID: 26527367 PMCID: PMC4695966 DOI: 10.1002/eji.201546100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 10/27/2015] [Accepted: 10/30/2015] [Indexed: 01/23/2023]
Abstract
In 1985, John Monaco--the discoverer of LMP-2 and -7, the inducible components of the immunoproteasome--asked his advanced immunology class as to why the MHC region contained not only structural genes, but several others as well, whose functions were then unknown. As we drew a blank, he quipped: perchance because many of the MHC genes are induced by IFN-γ! The ensuing three decades have witnessed the unveiling of the profound fundamental and clinical implications of that classroom tête-à-tête. Amongst its multitudinous effects, IFN-γ induces genes enhancing antigen processing and presentation to T cells; such as those encoding cellular proteases and activators of proteases. In this issue, Keller et al. [Eur. J. Immunol. 2015. 45: 3257-3268] demonstrate that the limited success of MART-1/Melan-A-targeted immunotherapy in melanoma patients could be due to inefficient MART-1(26-35) presentation, owing to the proteolytic activities of IFN-γ-inducible β2i/MECL-1, proteasome activator 28 (PA28), and endoplasmic reticulum-associated aminopeptidase-associated with antigen processing (ERAP). Specifically, whilst β2i and PA28 impede MART-1(26-35) liberation from its precursor protein, ERAP-1 degrades this epitope. Hence, critical to effective cancer immunotherapy is deep knowledge of T-cell-targeted tumor antigens and how cellular proteases generate protective epitope(s) from them, or destroy them.
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Affiliation(s)
- Sebastian Joyce
- Veterans Administration Tennessee Valley Healthcare System and the Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
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223
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Li X, Li Y, Arendt CS, Hochstrasser M. Distinct Elements in the Proteasomal β5 Subunit Propeptide Required for Autocatalytic Processing and Proteasome Assembly. J Biol Chem 2015; 291:1991-2003. [PMID: 26627836 DOI: 10.1074/jbc.m115.677047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Indexed: 01/02/2023] Open
Abstract
Eukaryotic 20S proteasome assembly remains poorly understood. The subunits stack into four heteroheptameric rings; three inner-ring subunits (β1, β2, and β5) bear the protease catalytic residues and are synthesized with N-terminal propeptides. These propeptides are removed autocatalytically late in assembly. In Saccharomyces cerevisiae, β5 (Doa3/Pre2) has a 75-residue propeptide, β5pro, that is essential for proteasome assembly and can work in trans. We show that deletion of the poorly conserved N-terminal half of the β5 propeptide nonetheless causes substantial defects in proteasome maturation. Sequences closer to the cleavage site have critical but redundant roles in both assembly and self-cleavage. A conserved histidine two residues upstream of the autocleavage site strongly promotes processing. Surprisingly, although β5pro is functionally linked to the Ump1 assembly factor, trans-expressed β5pro associates only weakly with Ump1-containing precursors. Several genes were identified as dosage suppressors of trans-expressed β5pro mutants; the strongest encoded the β7 proteasome subunit. Previous data suggested that β7 and β5pro have overlapping roles in bringing together two half-proteasomes, but the timing of β7 addition relative to half-mer joining was unclear. Here we report conditions where dimerization lags behind β7 incorporation into the half-mer. Our results suggest that β7 insertion precedes half-mer dimerization, and the β7 tail and β5 propeptide have unequal roles in half-mer joining.
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Affiliation(s)
- Xia Li
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Yanjie Li
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Cassandra S Arendt
- the Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Mark Hochstrasser
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and.
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224
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Finley D, Chen X, Walters KJ. Gates, Channels, and Switches: Elements of the Proteasome Machine. Trends Biochem Sci 2015; 41:77-93. [PMID: 26643069 DOI: 10.1016/j.tibs.2015.10.009] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/27/2015] [Accepted: 10/30/2015] [Indexed: 12/14/2022]
Abstract
The proteasome has emerged as an intricate machine that has dynamic mechanisms to regulate the timing of its activity, its selection of substrates, and its processivity. The 19-subunit regulatory particle (RP) recognizes ubiquitinated proteins, removes ubiquitin, and injects the target protein into the proteolytic chamber of the core particle (CP) via a narrow channel. Translocation into the CP requires substrate unfolding, which is achieved through mechanical force applied by a hexameric ATPase ring of the RP. Recent cryoelectron microscopy (cryoEM) studies have defined distinct conformational states of the RP, providing illustrative snapshots of what appear to be progressive steps of substrate engagement. Here, we bring together this new information with molecular analyses to describe the principles of proteasome activity and regulation.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
| | - Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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225
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226
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Caputi FF, Carretta D, Lattanzio F, Palmisano M, Candeletti S, Romualdi P. Proteasome subunit and opioid receptor gene expression down-regulation induced by paraquat and maneb in human neuroblastoma SH-SY5Y cells. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 40:895-900. [PMID: 26498265 DOI: 10.1016/j.etap.2015.09.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/21/2015] [Accepted: 09/26/2015] [Indexed: 06/05/2023]
Abstract
Paraquat (PQ) and maneb (MB) are able to induce neurotoxic effects by promoting α-synuclein (α-syn) aggregates and altering tyrosine hydroxylase (TH), thus increasing the risk of Parkinson's disease (PD). These pesticides promote neurotoxic effects also by affecting proteasome function that normally regulate protein turnover. We investigated the effects of the two pesticides exposure on multiple targets involved in PD, using SH-SY5Y cells. First, we evaluated TH and α-syn protein levels following PQ and MB cell exposure and a significant increase of these protein levels was observed. Subsequently, since a relationship between ubiquitin/proteasome and opioid receptors has been proposed, the effects of pesticides on their gene expression have been investigated. A decrease of β1 and Rpt3 proteasome subunit mRNA levels, together with the μ and δ opioid receptor down-regulation, was detected. The reported alterations, here simultaneously observed, help to clarify the involvement of multiple biological markers implicated in PD, often separately evaluated.
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Affiliation(s)
- Francesca Felicia Caputi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Donatella Carretta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Francesca Lattanzio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Martina Palmisano
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Sanzio Candeletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Irnerio 48, 40126 Bologna, Italy
| | - Patrizia Romualdi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Irnerio 48, 40126 Bologna, Italy.
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227
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Lacher SE, Lee JS, Wang X, Campbell MR, Bell DA, Slattery M. Beyond antioxidant genes in the ancient Nrf2 regulatory network. Free Radic Biol Med 2015; 88:452-465. [PMID: 26163000 PMCID: PMC4837897 DOI: 10.1016/j.freeradbiomed.2015.06.044] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/10/2015] [Accepted: 06/30/2015] [Indexed: 01/01/2023]
Abstract
Nrf2, a basic leucine zipper transcription factor encoded by the gene NFE2L2, is a master regulator of the transcriptional response to oxidative stress. Nrf2 is structurally and functionally conserved from insects to humans, and it heterodimerizes with the small MAF transcription factors to bind a consensus DNA sequence (the antioxidant response element, or ARE) and regulate gene expression. We have used genome-wide chromatin immunoprecipitation and gene expression data to identify direct Nrf2 target genes in Drosophila and humans. These data have allowed us to construct the deeply conserved ancient Nrf2 regulatory network-target genes that are conserved from Drosophila to human. The ancient network consists of canonical antioxidant genes, as well as genes related to proteasomal pathways and metabolism and a number of less expected genes. We have also used enhancer reporter assays and electrophoretic mobility-shift assays to confirm Nrf2-mediated regulation of ARE activity at a number of these novel target genes. Interestingly, the ancient network also highlights a prominent negative feedback loop; this, combined with the finding that Nrf2-mediated regulatory output is tightly linked to the quality of the ARE it is targeting, suggests that precise regulation of nuclear Nrf2 concentration is necessary to achieve proper quantitative regulation of distinct gene sets. Together, these findings highlight the importance of balance in the Nrf2-ARE pathway and indicate that Nrf2-mediated regulation of xenobiotic metabolism, glucose metabolism, and proteostasis has been central to this pathway since its inception.
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Affiliation(s)
- Sarah E Lacher
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Joslynn S Lee
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Xuting Wang
- Environmental Genomics Section, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Michelle R Campbell
- Environmental Genomics Section, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Douglas A Bell
- Environmental Genomics Section, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA.
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228
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Schneider K, Bertolotti A. Surviving protein quality control catastrophes--from cells to organisms. J Cell Sci 2015; 128:3861-9. [PMID: 26483388 DOI: 10.1242/jcs.173047] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Organisms have evolved mechanisms to cope with and adapt to unexpected challenges and harsh conditions. Unfolded or misfolded proteins represent a threat for cells and organisms, and the deposition of misfolded proteins is a defining feature of many age-related human diseases, including the increasingly prevalent neurodegenerative diseases. These protein misfolding diseases are devastating and currently cannot be cured, but are hopefully not incurable. In fact, the aggregation-prone and potentially harmful proteins at the origins of protein misfolding diseases are expressed throughout life, whereas the diseases are late onset. This reveals that cells and organisms are normally resilient to disease-causing proteins and survive the threat of misfolded proteins up to a point. This Commentary will outline the limits of the cellular resilience to protein misfolding, and discuss the possibility of pushing these limits to help cells and organisms to survive the threat of misfolding proteins and to avoid protein quality control catastrophes.
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Affiliation(s)
- Kim Schneider
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Anne Bertolotti
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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229
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Filteau M, Vignaud H, Rochette S, Diss G, Chrétien AÈ, Berger CM, Landry CR. Multi-scale perturbations of protein interactomes reveal their mechanisms of regulation, robustness and insights into genotype-phenotype maps. Brief Funct Genomics 2015; 15:130-7. [PMID: 26476431 DOI: 10.1093/bfgp/elv043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cellular architectures and signaling machineries are organized through protein-protein interactions (PPIs). High-throughput methods to study PPIs in yeast have opened a new perspective on the organization of the cell by allowing the study of whole protein interactomes. Recent investigations have moved from the description of this organization to the analysis of its dynamics by experimenting how protein interaction networks (PINs) are rewired in response to perturbations. Here we review studies that have used the budding yeast as an experimental system to explore these altered networks. Given the large space of possible PPIs and the diversity of potential genetic and environmental perturbations, high-throughput methods are an essential requirement to survey PIN perturbations on a large scale. Network perturbations are typically conceptualized as the removal of entire proteins (nodes), the modification of single PPIs (edges) or changes in growth conditions. These studies have revealed mechanisms of PPI regulation, PIN architectural organization, robustness and sensitivity to perturbations. Despite these major advances, there are still inherent limits to current technologies that lead to a trade-off between the number of perturbations and the number of PPIs that can be considered simultaneously. Nevertheless, as we exemplify here, targeted approaches combined with the existing resources remain extremely powerful to explore the inner organization of cells and their responses to perturbations.
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230
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Vriend J, Ghavami S, Marzban H. The role of the ubiquitin proteasome system in cerebellar development and medulloblastoma. Mol Brain 2015; 8:64. [PMID: 26475605 PMCID: PMC4609148 DOI: 10.1186/s13041-015-0155-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/08/2015] [Indexed: 01/12/2023] Open
Abstract
Cerebellar granule cells precursors are derived from the upper rhombic lip and migrate tangentially independent of glia along the subpial stream pathway to form the external germinal zone. Postnatally, granule cells migrate from the external germinal zone radially through the Purkinje cell layer, guided by Bergmann glia fibers, to the internal granular cell layer. Medulloblastomas (MBs) are the most common malignant childhood brain tumor. Many of these tumors develop from precursor cells of the embryonic rhombic lips. Four main groups of MB are recognized. The WNT group of MBs arise primarily from the lower rhombic lip and embryonic brainstem. The SHH group of MBs originate from cerebellar granule cell precursors in the external germinal zone of the embryonic cerebellum. The cellular origins of type 3 and type 4 MBs are not clear. Several ubiquitin ligases are revealed to be significant factors in development of the cerebellum as well as in the initiation and maintenance of MBs. Proteasome dysfunction at a critical stage of development may be a major factor in determining whether progenitor cells which are destined to become granule cells differentiate normally or become MB cells. We propose the hypothesis that proteasomal activity is essential to regulate the critical transition between proliferating granule cells and differentiated granule cells and that proteasome dysfunction may lead to MB. Proteasome dysfunction could also account for various mutations in MBs resulting from deficiencies in DNA checkpoint and repair mechanisms prior to development of MBs. Data showing a role for the ubiquitin ligases β-TrCP, FBW7, Huwe1, and SKP2 in MBs suggest the possibility of a classification of MBs based on the expression (over expression or under expression) of specific ubiquitin ligases which function as oncogenes, tumor suppressors or cell cycle regulators.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Rm129, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, Canada
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rm129, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba (CHRIM), College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Hassan Marzban
- Department of Human Anatomy and Cell Science, Rm129, BMSB, 745 Bannatyne Avenue, Winnipeg, MB, Canada. .,Children's Hospital Research Institute of Manitoba (CHRIM), College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
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231
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Abstract
Although proteasomes are critical in cell regulation and cancer therapy, little is known about the factors regulating proteasome content or activity. In this issue, Zhang et al. (2015) report that miR-101 suppresses the expression of chaperone POMP and 20S assembly, and certain cancers raise proteasome content by losing miR-101.
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232
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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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233
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Pauloin A, Adenot P, Hue-Beauvais C, Chanat E. The perilipin-2 (adipophilin) coat of cytosolic lipid droplets is regulated by an Arf1-dependent mechanism in HC11 mouse mammary epithelial cells. Cell Biol Int 2015; 40:143-55. [PMID: 26399370 DOI: 10.1002/cbin.10547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/19/2015] [Indexed: 12/11/2022]
Abstract
The cytosolic lipid droplets (cLDs) store excess intracellular lipids, and perilipin-2 is believed to protect cLDs from degradation. Here, we investigated the role of the small G-protein Arf1 and the proteasome in the fates of perilipin-2 and cLDs. In oleate-loaded cells, upon brefeldin A (BFA) treatment, perilipin-2 remained associated with cLDs for at least 30 min before significant release, and proteasomal degradation-mediated decrease was observed. Interestingly, the cLD population did not mimic the decline in perilipin-2. We tested several chemical modulators of regulators of Arf1 activity on the association of perilipin-2 with cLDs. QS11 and Exo2 accelerated the reduction in perilipin-2, although less than BFA. In contrast, Exo1 unexpectedly slowed down its degradation. Correlatively, BFA, QS11, and Exo2 enhanced the dissociation of perilipin-2 from cLDs, whereas Exo1 inhibited it. There was a synergistic effect of BFA with Exo2 and QS11, and of Exo2 with QS11, whereas Exo1 antagonized the effect of BFA without affecting that of Exo2 or QS11. We concluded that the Arf1 complex regulates the association of perilipin-2 with cLDs. Additionally, MG132 and BFA modified the number of cLDs over a relatively short period.
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Affiliation(s)
- Alain Pauloin
- INRA, UR1196 Génomique et Physiologie de la Lactation, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Pierre Adenot
- INRA-CRJ MIMA2 Platform, Domaine de Vilvert, UMR1198 Biologie du Développement et Reproduction, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Catherine Hue-Beauvais
- INRA, UR1196 Génomique et Physiologie de la Lactation, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Eric Chanat
- INRA, UR1196 Génomique et Physiologie de la Lactation, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
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234
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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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235
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Semren N, Habel-Ungewitter NC, Fernandez IE, Königshoff M, Eickelberg O, Stöger T, Meiners S. Validation of the 2nd Generation Proteasome Inhibitor Oprozomib for Local Therapy of Pulmonary Fibrosis. PLoS One 2015; 10:e0136188. [PMID: 26340365 PMCID: PMC4560391 DOI: 10.1371/journal.pone.0136188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 07/31/2015] [Indexed: 12/29/2022] Open
Abstract
Proteasome inhibition has been shown to prevent development of fibrosis in several organs including the lung. However, effects of proteasome inhibitors on lung fibrosis are controversial and cytotoxic side effects of the overall inhibition of proteasomal protein degradation cannot be excluded. Therefore, we hypothesized that local lung-specific application of a novel, selective proteasome inhibitor, oprozomib (OZ), provides antifibrotic effects without systemic toxicity in a mouse model of lung fibrosis. Oprozomib was first tested on the human alveolar epithelial cancer cell line A549 and in primary mouse alveolar epithelial type II cells regarding its cytotoxic effects on alveolar epithelial cells and compared to the FDA approved proteasome inhibitor bortezomib (BZ). OZ was less toxic than BZ and provided high selectivity for the chymotrypsin-like active site of the proteasome. In primary mouse lung fibroblasts, OZ showed significant anti-fibrotic effects, i.e. reduction of collagen I and α smooth muscle actin expression, in the absence of cytotoxicity. When applied locally into the lungs of healthy mice via instillation, OZ was well tolerated and effectively reduced proteasome activity in the lungs. In bleomycin challenged mice, however, locally applied OZ resulted in accelerated weight loss and increased mortality of treated mice. Further, OZ failed to reduce fibrosis in these mice. While upon systemic application OZ was well tolerated in healthy mice, it rather augmented instead of attenuated fibrotic remodelling of the lung in bleomycin challenged mice. To conclude, low toxicity and antifibrotic effects of OZ in pulmonary fibroblasts could not be confirmed for pulmonary fibrosis of bleomycin-treated mice. In light of these data, the use of proteasome inhibitors as therapeutic agents for the treatment of fibrotic lung diseases should thus be considered with caution.
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Affiliation(s)
- Nora Semren
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Nunja C. Habel-Ungewitter
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Isis E. Fernandez
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Melanie Königshoff
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Tobias Stöger
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
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236
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Tundo GR, Sbardella D, Ciaccio C, De Pascali S, Campanella V, Cozza P, Tarantino U, Coletta M, Fanizzi FP, Marini S. Effect of cisplatin on proteasome activity. J Inorg Biochem 2015; 153:253-258. [PMID: 26387966 DOI: 10.1016/j.jinorgbio.2015.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 02/01/2023]
Abstract
Cisplatin is a widely used chemotherapy drug which exerts cytotoxic activity by affecting both nuclear and cytosolic pathways. Herewith, we report, for the first time, that cisplatin inhibits proteasome activity in vitro. Cisplatin induces a dose dependent inhibition of the three enzymatic activities of proteasome (i.e., the chymotrypsin-like activity, the trypsin-like activity and the caspase-like activity). Moreover, cisplatin administration to neuroblastoma cells brings about a fast loss of proteasome particle activity, which is followed by a de novo synthesis of proteasome. Lastly, we report that the simultaneous administration of lactacystin and cisplatin enhances the cytotoxicity of cisplatin alone. The overall bulk of data opens to an intriguing scenario, concerning the biological effects of cisplatin in the control of cellular life, which goes beyond the well established genotoxic effect.
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Affiliation(s)
- G R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy; CIRCMSB, Via C. Ulpiani 27, I-70125 Bari, Italy
| | - D Sbardella
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy; CIRCMSB, Via C. Ulpiani 27, I-70125 Bari, Italy
| | - C Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy; CIRCMSB, Via C. Ulpiani 27, I-70125 Bari, Italy
| | - S De Pascali
- CIRCMSB, Via C. Ulpiani 27, I-70125 Bari, Italy; Department of Environmental Biological Sciences and Technologies (Di.S.Te.B.A.), University of Salento, Lecce, Italy
| | - V Campanella
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy
| | - P Cozza
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy
| | - U Tarantino
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy; Center for Space Biomedicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy
| | - M Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy; CIRCMSB, Via C. Ulpiani 27, I-70125 Bari, Italy; Center for Space Biomedicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy
| | - F P Fanizzi
- CIRCMSB, Via C. Ulpiani 27, I-70125 Bari, Italy; Department of Environmental Biological Sciences and Technologies (Di.S.Te.B.A.), University of Salento, Lecce, Italy
| | - S Marini
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy; CIRCMSB, Via C. Ulpiani 27, I-70125 Bari, Italy; Center for Space Biomedicine, University of Roma Tor Vergata, Via Montpellier 1, I-00133 Roma, Italy.
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237
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Tsvetkov P, Mendillo ML, Zhao J, Carette JE, Merrill PH, Cikes D, Varadarajan M, van Diemen FR, Penninger JM, Goldberg AL, Brummelkamp TR, Santagata S, Lindquist S. Compromising the 19S proteasome complex protects cells from reduced flux through the proteasome. eLife 2015; 4. [PMID: 26327695 PMCID: PMC4551903 DOI: 10.7554/elife.08467] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/29/2015] [Indexed: 12/11/2022] Open
Abstract
Proteasomes are central regulators of protein homeostasis in eukaryotes. Proteasome function is vulnerable to environmental insults, cellular protein imbalance and targeted pharmaceuticals. Yet, mechanisms that cells deploy to counteract inhibition of this central regulator are little understood. To find such mechanisms, we reduced flux through the proteasome to the point of toxicity with specific inhibitors and performed genome-wide screens for mutations that allowed cells to survive. Counter to expectation, reducing expression of individual subunits of the proteasome's 19S regulatory complex increased survival. Strong 19S reduction was cytotoxic but modest reduction protected cells from inhibitors. Protection was accompanied by an increased ratio of 20S to 26S proteasomes, preservation of protein degradation capacity and reduced proteotoxic stress. While compromise of 19S function can have a fitness cost under basal conditions, it provided a powerful survival advantage when proteasome function was impaired. This means of rebalancing proteostasis is conserved from yeast to humans.
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Affiliation(s)
- Peter Tsvetkov
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Marc L Mendillo
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Jinghui Zhao
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Parker H Merrill
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Ferdy R van Diemen
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Thijn R Brummelkamp
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sandro Santagata
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, United States
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238
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Alpha-ring Independent Assembly of the 20S Proteasome. Sci Rep 2015; 5:13130. [PMID: 26286114 PMCID: PMC4541365 DOI: 10.1038/srep13130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/20/2015] [Indexed: 12/17/2022] Open
Abstract
Archaeal proteasomes share many features with their eukaryotic counterparts and serve as important models for assembly. Proteasomes are also found in certain bacterial lineages yet their assembly mechanism is thought to be fundamentally different. Here we investigate α-ring formation using recombinant proteasomes from the archaeon Methanococcus maripaludis. Through an engineered disulfide cross-linking strategy, we demonstrate that double α-rings are structurally analogous to half-proteasomes and can form independently of single α-rings. More importantly, via targeted mutagenesis, we show that single α-rings are not required for the efficient assembly of 20S proteasomes. Our data support updating the currently held "α-ring first" view of assembly, initially proposed in studies of archaeal proteasomes, and present a way to reconcile the seemingly separate bacterial assembly mechanism with the rest of the proteasome realm. We suggest that a common assembly network underpins the absolutely conserved architecture of proteasomes across all domains of life.
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239
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Hickey CM, Hochstrasser M. STUbL-mediated degradation of the transcription factor MATα2 requires degradation elements that coincide with corepressor binding sites. Mol Biol Cell 2015; 26:3401-12. [PMID: 26246605 PMCID: PMC4591686 DOI: 10.1091/mbc.e15-06-0436] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/30/2015] [Indexed: 11/16/2022] Open
Abstract
The yeast cell type regulator MATα (α2) is degraded through two ubiquitylation pathways, one of which has been minimally characterized. We identify two regions in α2 important for this pathway and show that these regions overlap specific binding sites for α2 corepressors, suggesting that α2 degradation is coordinated with its functional status. The yeast transcription factor MATα2 (α2) is a short-lived protein known to be ubiquitylated by two distinct pathways, one involving the ubiquitin-conjugating enzymes (E2s) Ubc6 and Ubc7 and the ubiquitin ligase (E3) Doa10 and the other operating with the E2 Ubc4 and the heterodimeric E3 Slx5/Slx8. Although Slx5/Slx8 is a small ubiquitin-like modifier (SUMO)-targeted ubiquitin ligase (STUbL), it does not require SUMO to target α2 but instead directly recognizes α2. Little is known about the α2 determinants required for its Ubc4- and STUbL-mediated degradation or how these determinants substitute for SUMO in recognition by the STUbL pathway. We describe two distinct degradation elements within α2, both of which are necessary for α2 recognition specifically by the Ubc4 pathway. Slx5/Slx8 can directly ubiquitylate a C-terminal fragment of α2, and mutating one of the degradation elements impairs this ubiquitylation. Surprisingly, both degradation elements identified here overlap specific interaction sites for α2 corepressors: the Mcm1 interaction site in the central α2 linker and the Ssn6 (Cyc8) binding site in the α2 homeodomain. We propose that competitive binding to α2 by the ubiquitylation machinery and α2 cofactors is balanced so that α2 can function in transcription repression yet be short lived enough to allow cell-type switching.
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Affiliation(s)
- Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
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240
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Inobe T, Genmei R. N-Terminal Coiled-Coil Structure of ATPase Subunits of 26S Proteasome Is Crucial for Proteasome Function. PLoS One 2015. [PMID: 26208326 PMCID: PMC4514846 DOI: 10.1371/journal.pone.0134056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The proteasome is an essential proteolytic machine in eukaryotic cells, where it removes damaged proteins and regulates many cellular activities by degrading ubiquitinated proteins. Its heterohexameric AAA+ ATPase Rpt subunits play a central role in proteasome activity by the engagement of substrate unfolding and translocation for degradation; however, its detailed mechanism remains poorly understood. In contrast to AAA+ ATPase domains, their N-terminal regions of Rpt subunits substantially differ from each other. Here, to investigate the requirements and roles of the N-terminal regions of six Rpt subunits derived from Saccharomyces cerevisiae, we performed systematic mutational analysis using conditional knockdown yeast strains for each Rpt subunit and bacterial heterologous expression system of the base subcomplex. We showed that the formation of the coiled-coil structure was the most important for the N-terminal region of Rpt subunits. The primary role of coiled-coil structure would be the maintenance of the ring structure with the defined order. However, the coiled-coil region would be also be involved in substrate recognition and an interaction between lid and base subcomplexes.
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Affiliation(s)
- Tomonao Inobe
- Frontier Research Core for Life Sciences, University of Toyama, 3190 Gofuku, Toyma-shi, Toyama, 930-8555, Japan
| | - Reiko Genmei
- Frontier Research Core for Life Sciences, University of Toyama, 3190 Gofuku, Toyma-shi, Toyama, 930-8555, Japan
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241
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Abstract
SIGNIFICANCE The molecular mechanism of aging is still vigorously debated, although a general consensus exists that mitochondria are significantly involved in this process. However, the previously postulated role of mitochondrial-derived reactive oxygen species (ROS) as the damaging agents inducing functional loss in aging has fallen out of favor in the recent past. In this review, we critically examine the role of ROS in aging in the light of recent advances on the relationship between mitochondrial structure and function. RECENT ADVANCES The functional mitochondrial respiratory chain is now recognized as a reflection of the dynamic association of respiratory complexes in the form of supercomplexes (SCs). Besides providing kinetic advantage (channeling), SCs control ROS generation by the respiratory chain, thus providing a means to regulate ROS levels in the cell. Depending on their concentration, these ROS are either physiological signals essential for the life of the cell or toxic species that damage cell structure and functions. CRITICAL ISSUES We propose that under physiological conditions the dynamic nature of SCs reversibly controls the generation of ROS as signals involved in mitochondrial-nuclear communication. During aging, there is a progressive loss of control of ROS generation so that their production is irreversibly enhanced, inducing a vicious circle in which signaling is altered and structural damage takes place. FUTURE DIRECTIONS A better understanding on the forces affecting SC association would allow the manipulation of ROS generation, directing these species to their physiological signaling role.
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Affiliation(s)
- Maria Luisa Genova
- Dipartimento di Scienze Biomediche e Neuromotorie, Alma Mater Studiorum-Università di Bologna , Bologna, Italy
| | - Giorgio Lenaz
- Dipartimento di Scienze Biomediche e Neuromotorie, Alma Mater Studiorum-Università di Bologna , Bologna, Italy
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242
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Proteasome Activity Is Affected by Fluctuations in Insulin-Degrading Enzyme Distribution. PLoS One 2015; 10:e0132455. [PMID: 26186340 PMCID: PMC4506093 DOI: 10.1371/journal.pone.0132455] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 06/11/2015] [Indexed: 01/13/2023] Open
Abstract
Insulin-Degrading-Enzyme (IDE) is a Zn2+-dependent peptidase highly conserved throughout evolution and ubiquitously distributed in mammalian tissues wherein it displays a prevalent cytosolic localization. We have recently demonstrated a novel Heat Shock Protein-like behaviour of IDE and its association with the 26S proteasome. In the present study, we examine the mechanistic and molecular features of IDE-26S proteasome interaction in a cell experimental model, extending the investigation also to the effect of IDE on the enzymatic activities of the 26S proteasome. Further, kinetic investigations indicate that the 26S proteasome activity undergoes a functional modulation by IDE through an extra-catalytic mechanism. The IDE-26S proteasome interaction was analyzed during the Heat Shock Response and we report novel findings on IDE intracellular distribution that might be of critical relevance for cell metabolism.
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243
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Abstract
In eukaryotes, damaged or unneeded proteins are typically degraded by the ubiquitin-proteasome system. In this system, the protein substrate is often first covalently modified with a chain of ubiquitin polypeptides. This chain serves as a signal for delivery to the 26S proteasome, a 2.5-MDa, ATP-dependent multisubunit protease complex. The proteasome consists of a barrel-shaped 20S core particle (CP) that is capped on one or both of its ends by a 19S regulatory particle (RP). The RP is responsible for recognizing the substrate, unfolding it, and translocating it into the CP for destruction. Here we describe simple, one-step purifications scheme for isolating the 26S proteasome and its 19S RP and 20S CP subcomplexes from the yeast Saccharomyces cerevisiae, as well as assays for measuring ubiquitin-dependent and ubiquitin-independent proteolytic activity in vitro.
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Affiliation(s)
- Yanjie Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Robert J Tomko
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.,Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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244
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Soss SE, Rose KL, Hill S, Jouan S, Chazin WJ. Biochemical and Proteomic Analysis of Ubiquitination of Hsc70 and Hsp70 by the E3 Ligase CHIP. PLoS One 2015; 10:e0128240. [PMID: 26010904 PMCID: PMC4444009 DOI: 10.1371/journal.pone.0128240] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/23/2015] [Indexed: 01/24/2023] Open
Abstract
The E3 ubiquitin ligase CHIP is involved in protein triage, serving as a co-chaperone for refolding as well as catalyzing ubiquitination of substrates. CHIP functions with both the stress induced Hsp70 and constitutive Hsc70 chaperones, and also plays a role in maintaining their balance in the cell. When the chaperones carry no client proteins, CHIP catalyzes their polyubiquitination and subsequent proteasomal degradation. Although Hsp70 and Hsc70 are highly homologous in sequence and similar in structure, CHIP mediated ubiquitination promotes degradation of Hsp70 with a higher efficiency than for Hsc70. Here we report a detailed and systematic investigation to characterize if there are significant differences in the CHIP in vitro ubiquitination of human Hsp70 and Hsc70. Proteomic analysis by mass spectrometry revealed that only 12 of 39 detectable lysine residues were ubiquitinated by UbcH5a in Hsp70 and only 16 of 45 in Hsc70. The only conserved lysine identified as ubiquitinated in one but not the other heat shock protein was K159 in Hsc70. Ubiquitination assays with K-R ubiquitin mutants showed that multiple Ub chain types are formed and that the distribution is different for Hsp70 versus Hsc70. CHIP ubiquitination with the E2 enzyme Ube2W is predominantly directed to the N-terminal amine of the substrate; however, some internal lysine modifications were also detected. Together, our results provide a detailed view of the differences in CHIP ubiquitination of these two very similar proteins, and show a clear example where substantial differences in ubiquitination can be generated by a single E3 ligase in response to not only different E2 enzymes but subtle differences in the substrate.
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Affiliation(s)
- Sarah E. Soss
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kristie L. Rose
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Salisha Hill
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Sophie Jouan
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Walter J. Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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245
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Marshall RS, Li F, Gemperline DC, Book AJ, Vierstra RD. Autophagic Degradation of the 26S Proteasome Is Mediated by the Dual ATG8/Ubiquitin Receptor RPN10 in Arabidopsis. Mol Cell 2015; 58:1053-66. [PMID: 26004230 DOI: 10.1016/j.molcel.2015.04.023] [Citation(s) in RCA: 302] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/19/2015] [Accepted: 04/17/2015] [Indexed: 02/02/2023]
Abstract
Autophagic turnover of intracellular constituents is critical for cellular housekeeping, nutrient recycling, and various aspects of growth and development in eukaryotes. Here we show that autophagy impacts the other major degradative route involving the ubiquitin-proteasome system by eliminating 26S proteasomes, a process we termed proteaphagy. Using Arabidopsis proteasomes tagged with GFP, we observed their deposition into vacuoles via a route requiring components of the autophagy machinery. This transport can be initiated separately by nitrogen starvation and chemical or genetic inhibition of the proteasome, implying distinct induction mechanisms. Proteasome inhibition stimulates comprehensive ubiquitylation of the complex, with the ensuing proteaphagy requiring the proteasome subunit RPN10, which can simultaneously bind both ATG8 and ubiquitin. Collectively, we propose that Arabidopsis RPN10 acts as a selective autophagy receptor that targets inactive 26S proteasomes by concurrent interactions with ubiquitylated proteasome subunits/targets and lipidated ATG8 lining the enveloping autophagic membranes.
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Affiliation(s)
- Richard S Marshall
- Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
| | - Faqiang Li
- Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
| | - David C Gemperline
- Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
| | - Adam J Book
- Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA.
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246
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Beenukumar RR, Gödderz D, Palanimurugan R, Dohmen RJ. Polyamines directly promote antizyme-mediated degradation of ornithine decarboxylase by the proteasome. MICROBIAL CELL 2015; 2:197-207. [PMID: 28357293 PMCID: PMC5349141 DOI: 10.15698/mic2015.06.206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ornithine decarboxylase (ODC), a ubiquitin-independent substrate of the proteasome, is a homodimeric protein with a rate-limiting function in polyamine biosynthesis. Polyamines regulate ODC levels by a feedback mechanism mediated by ODC antizyme (OAZ). Higher cellular polyamine levels trigger the synthesis of OAZ and also inhibit its ubiquitin-dependent proteasomal degradation. OAZ binds ODC monomers and targets them to the proteasome. Here, we report that polyamines, aside from their role in the control of OAZ synthesis and stability, directly enhance OAZ-mediated ODC degradation by the proteasome. Using a stable mutant of OAZ, we show that polyamines promote ODC degradation in Saccharomyces cerevisiae cells even when OAZ levels are not changed. Furthermore, polyamines stimulated the in vitro degradation of ODC by the proteasome in a reconstituted system using purified components. In these assays, spermine shows a greater effect than spermidine. By contrast, polyamines do not have any stimulatory effect on the degradation of ubiquitin-dependent substrates.
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Affiliation(s)
- R R Beenukumar
- Institute for Genetics, University of Cologne, Biocenter, Zülpicher Str. 47a, D-50674 Cologne, Germany
| | - Daniela Gödderz
- Institute for Genetics, University of Cologne, Biocenter, Zülpicher Str. 47a, D-50674 Cologne, Germany. ; Present address: Karolinska Institute, Department for Cell- and Molecular Biology, Von Eulers väg 3, 171 77 Stockholm
| | - R Palanimurugan
- Institute for Genetics, University of Cologne, Biocenter, Zülpicher Str. 47a, D-50674 Cologne, Germany. ; Present address: Center for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad 500007, India
| | - R J Dohmen
- Institute for Genetics, University of Cologne, Biocenter, Zülpicher Str. 47a, D-50674 Cologne, Germany
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247
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Dysfunction in protein clearance by the proteasome: impact on autoinflammatory diseases. Semin Immunopathol 2015; 37:323-33. [PMID: 25963519 DOI: 10.1007/s00281-015-0486-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
Abstract
During innate immune responses, proteostasis is greatly impacted by synthesis of pathogen proteins as well as by inflammatory tissue damage through radicals or other damaging molecules released by phagocytes. An adequate adaptation of cellular clearance pathways to the increased burden of damaged proteins is thus of fundamental importance for cells and tissues to prevent protein aggregation, inclusion body formation, and ultimately cell death. We here review the current understanding of the pivotal role of the ubiquitin proteasome system (UPS) in this proteostasis network. The proteolytic capacity of the UPS can be adjusted by differential gene expression, the incorporation and maturation kinetics of alternative active sites, and the attachment of different regulators. Dysregulation of this fine-tuning is likely to induce cell death but seen more often to promote inflammation as well. The link between proteostasis impairment and inflammation may play a crucial role in autoinflammation as well as in age-related diseases and currently uncharacterized diseases. Recent studies on proteasome-associated autoinflammatory syndromes (PRAAS) discovered that IFN signaling drives the inflammation caused by reduction of degradation capacity. Elucidation of these syndromes will reveal further insights in the understanding of inadequate immune responses. Knowledge related to the diversity of this degradation system will raise the awareness of potential pitfalls in the molecular diagnostics of autoinflammatory syndromes and may help to identify novel drug targets.
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248
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Abstract
All living organisms require protein degradation to terminate biological processes and remove damaged proteins. One such machine is the 20S proteasome, a specialized barrel-shaped and compartmentalized multicatalytic protease. The activity of the 20S proteasome generally requires the binding of regulators/proteasome activators (PAs), which control the entrance of substrates. These include the PA700 (19S complex), which assembles with the 20S and forms the 26S proteasome and allows the efficient degradation of proteins usually labeled by ubiquitin tags, PA200 and PA28, which are involved in proteolysis through ubiquitin-independent mechanisms and PI31, which was initially identified as a 20S inhibitor in vitro. Unlike 20S proteasome, shown to be present in all Eukaryotes and Archaea, the evolutionary history of PAs remained fragmentary. Here, we made a comprehensive survey and phylogenetic analyses of the four types of regulators in 17 clades covering most of the eukaryotic supergroups. We found remarkable conservation of each PA700 subunit in all eukaryotes, indicating that the current complex PA700 structure was already set up in the last eukaryotic common ancestor (LECA). Also present in LECA, PA200, PA28, and PI31 showed a more contrasted evolutionary picture, because many lineages have subsequently lost one or two of them. The paramount conservation of PA700 composition in all eukaryotes and the dynamic evolution of PA200, PA28, and PI31 are discussed in the light of current knowledge on their physiological roles.
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Affiliation(s)
- Philippe Fort
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France
| | - Andrey V Kajava
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France Institut de Biologie Computationnelle, Montpellier, France
| | - Fredéric Delsuc
- Université de Montpellier, France CNRS, IRD, Institut des Sciences de l'Evolution, UMR 5554, Montpellier, France
| | - Olivier Coux
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France
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249
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Üstün S, Börnke F. The Xanthomonas campestris type III effector XopJ proteolytically degrades proteasome subunit RPT6. PLANT PHYSIOLOGY 2015; 168:107-19. [PMID: 25739698 PMCID: PMC4424027 DOI: 10.1104/pp.15.00132] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/04/2015] [Indexed: 05/20/2023]
Abstract
Many animal and plant pathogenic bacteria inject type III effector (T3E) proteins into their eukaryotic host cells to suppress immunity. The Yersinia outer protein J (YopJ) family of T3Es is a widely distributed family of effector proteins found in both animal and plant pathogens, and its members are highly diversified in virulence functions. Some members have been shown to possess acetyltransferase activity; however, whether this is a general feature of YopJ family T3Es is currently unknown. The T3E Xanthomonas outer protein J (XopJ), a YopJ family effector from the plant pathogen Xanthomonas campestris pv vesicatoria, interacts with the proteasomal subunit Regulatory Particle AAA-ATPase6 (RPT6) in planta to suppress proteasome activity, resulting in the inhibition of salicylic acid-related immune responses. Here, we show that XopJ has protease activity to specifically degrade RPT6, leading to reduced proteasome activity in the cytoplasm as well as in the nucleus. Proteolytic degradation of RPT6 was dependent on the localization of XopJ to the plasma membrane as well as on its catalytic triad. Mutation of the Walker B motif of RPT6 prevented XopJ-mediated degradation of the protein but not XopJ interaction. This indicates that the interaction of RPT6 with XopJ is dependent on the ATP-binding activity of RPT6, but proteolytic cleavage additionally requires its ATPase activity. Inhibition of the proteasome impairs the proteasomal turnover of Nonexpressor of Pathogenesis-Related1 (NPR1), the master regulator of salicylic acid responses, leading to the accumulation of ubiquitinated NPR1, which likely interferes with the full induction of NPR1 target genes. Our results show that YopJ family T3Es are not only highly diversified in virulence function but also appear to possess different biochemical activities.
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Affiliation(s)
- Suayib Üstün
- Plant Metabolism Group, Leibniz Institute of Vegetable and Ornamental Crops, 14979 Grossbeeren, Germany (S.Ü., F.B.);Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, 91058 Erlangen, Germany (S.Ü., F.B.); andInstitut of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (F.B.)
| | - Frederik Börnke
- Plant Metabolism Group, Leibniz Institute of Vegetable and Ornamental Crops, 14979 Grossbeeren, Germany (S.Ü., F.B.);Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Division of Biochemistry, 91058 Erlangen, Germany (S.Ü., F.B.); andInstitut of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany (F.B.)
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250
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Jastrab JB, Wang T, Murphy JP, Bai L, Hu K, Merkx R, Huang J, Chatterjee C, Ovaa H, Gygi SP, Li H, Darwin KH. An adenosine triphosphate-independent proteasome activator contributes to the virulence of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2015; 112:E1763-72. [PMID: 25831519 PMCID: PMC4394314 DOI: 10.1073/pnas.1423319112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis encodes a proteasome that is highly similar to eukaryotic proteasomes and is required to cause lethal infections in animals. The only pathway known to target proteins for proteasomal degradation in bacteria is pupylation, which is functionally analogous to eukaryotic ubiquitylation. However, evidence suggests that the M. tuberculosis proteasome contributes to pupylation-independent pathways as well. To identify new proteasome cofactors that might contribute to such pathways, we isolated proteins that bound to proteasomes overproduced in M. tuberculosis and found a previously uncharacterized protein, Rv3780, which formed rings and capped M. tuberculosis proteasome core particles. Rv3780 enhanced peptide and protein degradation by proteasomes in an adenosine triphosphate (ATP)-independent manner. We identified putative Rv3780-dependent proteasome substrates and found that Rv3780 promoted robust degradation of the heat shock protein repressor, HspR. Importantly, an M. tuberculosis Rv3780 mutant had a general growth defect, was sensitive to heat stress, and was attenuated for growth in mice. Collectively, these data demonstrate that ATP-independent proteasome activators are not confined to eukaryotes and can contribute to the virulence of one the world's most devastating pathogens.
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Affiliation(s)
- Jordan B Jastrab
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Tong Wang
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973
| | - J Patrick Murphy
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Lin Bai
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973
| | - Kuan Hu
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - Remco Merkx
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and
| | - Jessica Huang
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | | | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Huilin Li
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, New York, NY 10016;
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