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Scruggs SB, Zong NC, Wang D, Stefani E, Ping P. Post-translational modification of cardiac proteasomes: functional delineation enabled by proteomics. Am J Physiol Heart Circ Physiol 2012; 303:H9-18. [PMID: 22523251 DOI: 10.1152/ajpheart.00189.2012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteasomes are ubiquitously expressed multicatalytic complexes that serve as key regulators of protein homeostasis. There are several lines of evidence indicating that proteasomes exist in heterogeneous subpopulations in cardiac muscle, differentiated, in part, by post-translational modifications (PTMs). PTMs regulate numerous facets of proteasome function, including catalytic activities, complex assembly, interactions with associating partners, subcellular localization, substrate preference, and complex turnover. Classical technologies used to identify PTMs on proteasomes have lacked the ability to determine site specificity, quantify stoichiometry, and perform large-scale, multi-PTM analysis. Recent advancements in proteomic technologies have largely overcome these limitations. We present here a discussion on the importance of PTMs in modulating proteasome function in cardiac physiology and pathophysiology, followed by the presentation of a state-of-the-art proteomic workflow for identifying and quantifying PTMs of cardiac proteasomes.
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Affiliation(s)
- Sarah B Scruggs
- Division of Cardiology, Department of Physiology, University of California, Los Angeles, USA
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52
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Prudnikov IM, Smirnov AN. Short peptide tools for monitoring caspase and proteasome activities in embryonal and adult rat brain lysates: an approach for the differential identification of proteases. J Biochem 2012; 151:299-316. [PMID: 22228904 DOI: 10.1093/jb/mvs001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The numerous caspase-like activities present in nervous tissue can be investigated with labelled peptides. However, the cross-reactivities of peptides with both proteasomes and caspases complicate the analysis of protease activity. The pharmacological features of substrates and inhibitors specific for either caspases or proteasome caspase-like proteases in rat brain lysates were similar or identical to the profiles of commercially purified proteasome preparations. Caspase inhibitors bind directly to active proteasome centres, thus competing with selective antagonists of proteasomes. Separation of lysates by molecular weight does not separate active caspases from proteasomes because these enzymes co-localize under native electrophoresis. The addition of ATP or its analogues is associated with the differential modulation of proteasomal activity, which also leads to ambiguity in the data. However, induced caspase activity could be successfully differentiated from proteasome activity in embryonal brain lysates with the non-selective caspase inhibitors Z-VAD-FMK and Q-VD-OPh and the proteasome inhibitor AdaAhx(3)L(3)VS that are not cross-reactive. This strategy is proposed for the simultaneous examination of caspases and proteasomes using proteolysis experiments. The present study reveals that all of the caspase-like activities in the tissue lysates of non-injured adult rat brains were related to proteasomal caspase-like activities.
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Affiliation(s)
- Igor M Prudnikov
- Laboratory of stem cell biology, A. Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Bogomoletz str., 4, 01024, Kiev, Ukraine.
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Kalogeris T, Baines CP, Krenz M, Korthuis RJ. Cell biology of ischemia/reperfusion injury. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 298:229-317. [PMID: 22878108 PMCID: PMC3904795 DOI: 10.1016/b978-0-12-394309-5.00006-7] [Citation(s) in RCA: 1366] [Impact Index Per Article: 113.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Disorders characterized by ischemia/reperfusion (I/R), such as myocardial infarction, stroke, and peripheral vascular disease, continue to be among the most frequent causes of debilitating disease and death. Tissue injury and/or death occur as a result of the initial ischemic insult, which is determined primarily by the magnitude and duration of the interruption in the blood supply, and then subsequent damage induced by reperfusion. During prolonged ischemia, ATP levels and intracellular pH decrease as a result of anaerobic metabolism and lactate accumulation. As a consequence, ATPase-dependent ion transport mechanisms become dysfunctional, contributing to increased intracellular and mitochondrial calcium levels (calcium overload), cell swelling and rupture, and cell death by necrotic, necroptotic, apoptotic, and autophagic mechanisms. Although oxygen levels are restored upon reperfusion, a surge in the generation of reactive oxygen species occurs and proinflammatory neutrophils infiltrate ischemic tissues to exacerbate ischemic injury. The pathologic events induced by I/R orchestrate the opening of the mitochondrial permeability transition pore, which appears to represent a common end-effector of the pathologic events initiated by I/R. The aim of this treatise is to provide a comprehensive review of the mechanisms underlying the development of I/R injury, from which it should be apparent that a combination of molecular and cellular approaches targeting multiple pathologic processes to limit the extent of I/R injury must be adopted to enhance resistance to cell death and increase regenerative capacity in order to effect long-lasting repair of ischemic tissues.
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Affiliation(s)
- Theodore Kalogeris
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, USA
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Powell SR, Herrmann J, Lerman A, Patterson C, Wang X. The ubiquitin-proteasome system and cardiovascular disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 109:295-346. [PMID: 22727426 DOI: 10.1016/b978-0-12-397863-9.00009-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the past decade, the role of the ubiquitin-proteasome system (UPS) has been the subject of numerous studies to elucidate its role in cardiovascular physiology and pathophysiology. There have been many advances in this field including the use of proteomics to achieve a better understanding of how the cardiac proteasome is regulated. Moreover, improved methods for the assessment of UPS function and the development of genetic models to study the role of the UPS have led to the realization that often the function of this system deviates from the norm in many cardiovascular pathologies. Hence, dysfunction has been described in atherosclerosis, familial cardiac proteinopathies, idiopathic dilated cardiomyopathies, and myocardial ischemia. This has led to numerous studies of the ubiquitin protein (E3) ligases and their roles in cardiac physiology and pathophysiology. This has also led to the controversial proposition of treating atherosclerosis, cardiac hypertrophy, and myocardial ischemia with proteasome inhibitors. Furthering our knowledge of this system may help in the development of new UPS-based therapeutic modalities for mitigation of cardiovascular disease.
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Affiliation(s)
- Saul R Powell
- Center for Heart and Lung Research, The Feinstein Institute for Medical Research, Manhasset, New York, USA
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55
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Vigneron N, Van den Eynde BJ. Proteasome subtypes and the processing of tumor antigens: increasing antigenic diversity. Curr Opin Immunol 2011; 24:84-91. [PMID: 22206698 DOI: 10.1016/j.coi.2011.12.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/07/2011] [Indexed: 11/25/2022]
Abstract
Protein degradation by the proteasome releases peptides that can be loaded on MHC class I molecules and presented to cytolytic T lymphocytes. Several mechanisms were recently found to increase the diversity of antigenic peptides displayed at the cell surface, thereby maximizing the efficacy of immune responses. The proteasome was shown to produce spliced antigenic peptides, which are made of two fragments initially not contiguous in the parental protein. Different proteasome subtypes also produce distinct sets of antigenic peptides: the standard proteasome and the immunoproteasome, containing different catalytic subunits, have different cleavage specificities and produce different sets of peptides. Moreover, recent work confirmed the existence of two additional proteasome subtypes that are intermediate between the standard and the immunoproteasome, and each produce a unique peptide repertoire.
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Affiliation(s)
- Nathalie Vigneron
- Ludwig Institute for Cancer Research, Brussels Branch and de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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56
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Wang X, Li J, Zheng H, Su H, Powell SR. Proteasome functional insufficiency in cardiac pathogenesis. Am J Physiol Heart Circ Physiol 2011; 301:H2207-19. [PMID: 21949118 DOI: 10.1152/ajpheart.00714.2011] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ubiquitin-proteasome system (UPS) is responsible for the degradation of most cellular proteins. Alterations in cardiac UPS, including changes in the degradation of regulatory proteins and proteasome functional insufficiency, are observed in many forms of heart disease and have been shown to play an important role in cardiac pathogenesis. In the past several years, remarkable progress in understanding the mechanisms that regulate UPS-mediated protein degradation has been achieved. A transgenic mouse model of benign enhancement of cardiac proteasome proteolytic function has been created. This has led to the first demonstration of the necessity of proteasome functional insufficiency in the genesis of important pathological processes. Cardiomyocyte-restricted enhancement of proteasome proteolytic function by overexpression of proteasome activator 28α protects against cardiac proteinopathy and myocardial ischemia-reperfusion injury. Additionally, exciting advances have recently been achieved in the search for a pharmacological agent to activate the proteasome. These breakthroughs are expected to serve as an impetus to further investigation into the involvement of UPS dysfunction in molecular pathogenesis and to the development of new therapeutic strategies for combating heart disease. An interplay between the UPS and macroautophagy is increasingly suggested in noncardiac systems but is not well understood in the cardiac system. Further investigations into the interplay are expected to provide a more comprehensive picture of cardiac protein quality control and degradation.
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Affiliation(s)
- Xuejun Wang
- Division of Basic Biomedical Sciences, Protein Quality Control and Degradation Research Center, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota 57069, USA.
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Scruggs SB, Ping P, Zong C. Heterogeneous cardiac proteasomes: mandated by diverse substrates? Physiology (Bethesda) 2011; 26:106-14. [PMID: 21487029 DOI: 10.1152/physiol.00039.2010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Proteasome biology has taken central stage in cardiac physiology and pathophysiology. The molecular heterogeneity of proteasome subpopulations supports the specificity of proteasome function to degrade diverse substrate repertoires. Unveiling the dynamics of proteasome function should inspire new therapeutic strategies for combating cardiac disease.
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Affiliation(s)
- Sarah B Scruggs
- Departments of Physiology and Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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58
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Wang X, Zhao Z, Luo Y, Chen G, Li Z. Gel-based proteomics analysis of the heterogeneity of 20S proteasomes from four human pancreatic cancer cell lines. Proteomics Clin Appl 2011; 5:484-92. [PMID: 21751412 DOI: 10.1002/prca.201000149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 05/11/2011] [Accepted: 05/30/2011] [Indexed: 11/06/2022]
Abstract
PURPOSE The 20S proteasome is a multicatalytic protein complex, which plays a major role in intracellular protein degradation. In mammalian cells, it consists of 28 subunits arranged in four stacked rings (α1-7β1-7β1-7α1-7). The aim of this study is to characterize and compare subunit composition and heterogeneity (or subtypes) of the 20S proteasome from four human pancreatic cancer cell lines. EXPERIMENTAL DESIGN To study subunit compositions and heterogeneity of 20S proteasome from human pancreatic cancer cell lines, in the present study, 20S proteasome from four different pancreatic cancer cell lines (SW1990, a human exocrine adenocarcinoma, derived from spleen metastasis; PANC-1, a human ductal carcinoma in situ; BxPC-3, a human ductal carcinoma in situ; and CFPAC-1, a human ductal adenocarcinoma, derived from liver metastasis) were subjected to a gel-based proteomics analysis, respectively. RESULTS It was found that the differences in the subunit compositions and subtypes of the 20S proteasomes among four pancreatic cancer cell lines exist. Gel-based proteomics analysis showed that more than 60 subunits spots were separated and identified by MS. Our study revealed the presence of various isoforms for each of the subunits and different subtypes of the 20S proteasome. The significant differences among four cell lines are the relative abundances of immunoproteasome subunits, β1i and β2i, indicating that different subtypes of immunoproteasome among four cell lines exist. CONCLUSIONS AND CLINICAL RELEVANCE The 20S proteasome from four human pancreatic cancer cell lines was characterized. The different expression levels of immunoproteasome subunits, β1i and β2i, indicate that the 20S proteasome may have different subtypes among four cell lines, which may be related to cancer cell property and be useful for the establishment of personalized therapy using proteasome inhibitors in future.
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Affiliation(s)
- Xinli Wang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, P. R. China
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59
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Wang X, Chen G, Zhao Z, Wang X, Li Z. Proteomics-based Characterization of Protein Complexes from Human Pancreatic Cancer Cell Line. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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60
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Neelam S, Kakhniashvili DG, Wilkens S, Levene SD, Goodman SR. Functional 20S proteasomes in mature human red blood cells. Exp Biol Med (Maywood) 2011; 236:580-91. [DOI: 10.1258/ebm.2011.010394] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sudha Neelam
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210
| | - David G Kakhniashvili
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210
| | - Stephen D Levene
- Departments of Molecular and Cell Biology and Physics, University of Texas at Dallas, Richardson, TX 75083, USA
| | - Steven R Goodman
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210
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61
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Götze S, Saborowski R. Proteasomal activities in the claw muscle tissue of European lobster, Homarus gammarus, during larval development. J Comp Physiol B 2011; 181:861-71. [DOI: 10.1007/s00360-011-0574-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 03/25/2011] [Accepted: 03/27/2011] [Indexed: 12/31/2022]
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62
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63
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Qu KZ, Zhang K, Ma W, Li H, Wang X, Zhang X, Giles F, Lai M, Afdhal NH, Albitar M. Ubiquitin-proteasome profiling for enhanced detection of hepatocellular carcinoma in patients with chronic liver disease. J Gastroenterol Hepatol 2011; 26:751-8. [PMID: 21418304 DOI: 10.1111/j.1440-1746.2010.06491.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIM A reliable test for the detection of hepatocellular carcinoma (HCC) could improve disease management. Recent reports suggested a link between abnormalities in the ubiquitin-proteasome system (UPS) and HCC. We investigated the potential of using UPS markers, along with HCC markers, to differentiate HCC from chronic liver disease (CLD). METHODS Sera from 135 HCC and 262 CLD patients were retrospectively analyzed for levels of UPS markers (proteasome, ubiquitin, and proteasome enzymatic activities) and the conventional HCC markers alpha fetoprotein (AFP), AFP-L3, and des-gamma-carboxyprothrombin (DCP). Multivariate logistic regression analysis was used to develop a model for differentiating HCC from CLD. The model was developed using a subset of 98 HCC patients and 104 CLD patients with advanced fibrosis or cirrhosis (Metavir F3-4) and then validated using an independent set (37 HCC and 44 CLD (F3-4)). RESULTS A UPS signature model incorporating six markers (trypsin-like, caspase-like, chymotrypsin-like, and normalized chymotrypsin-like activities of proteasomes; AFP; and DCP) accurately differentiated HCC from CLD (area under the curve = 0.938 [95% confidence interval, 0.884-0.991]). When analysis was restricted to patients with tumors ≤ 3 cm, the UPS model exhibited higher sensitivity (83.1% vs 51.8%) and specificity (90.2% vs 83.7%) than the three conventional markers, with good positive predictive values (34.2% vs 15.1%). These results were confirmed in the independent validation set. CONCLUSION The UPS signature in combination with AFP and DCP provides sensitive and specific differentiation of HCC in patients with CLD. The importance of the UPS in HCC suggests that therapeutic approaches targeting the UPS should be explored.
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Affiliation(s)
- Kevin Z Qu
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
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64
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Wang D, Zong C, Koag MC, Wang Y, Drews O, Fang C, Scruggs SB, Ping P. Proteome dynamics and proteome function of cardiac 19S proteasomes. Mol Cell Proteomics 2011; 10:M110.006122. [PMID: 21357515 DOI: 10.1074/mcp.m110.006122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Myocardial proteasomes are comprised of 20S core particles and 19S regulatory particles, which together carry out targeted degradation of cardiac proteins. The 19S complex is unique among the regulators of proteasomes in that it affects both the capacity and specificity of protein degradation. However, a comprehensive molecular characterization of cardiac 19S complexes is lacking. In this investigation, we tailored a multidimensional chromatography-based purification strategy to isolate structurally intact and functionally viable 19S complexes from murine hearts. Two distinct subpopulations of 19S complexes were isolated based upon (1) potency of activating 20S proteolytic activity, and (2) molecular composition using a combination of immuno-detection, two-dimensional-differential gel electrophoresis, and MS-based approaches. Heat shock protein 90 (Hsp90) was identified to be characteristic to 19S subpopulation I. The physical interaction of Hsp90 with 19S complexes was demonstrated via multiple approaches. Inhibition of Hsp90 activity using geldanamycin or BIIB021 potentiated the ability of subpopulation I to activate 20S proteasomes in the murine heart, thus demonstrating functional specificity of Hsp90 in subpopulation I. This investigation has advanced our understanding of the molecular heterogeneity of cardiac proteasomes by identifying molecularly and functionally distinct cardiac 19S complexes. The preferential association of Hsp90 with 19S subpopulation I unveils novel targets for designing proteasome-based therapeutic interventions for combating cardiac disease.
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Affiliation(s)
- Ding Wang
- Department of Physiology and Medicine, Division of Cardiology, University of California at Los Angeles, UCLA School of Medicine, Los Angeles, California 90095, USA
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65
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Li YF, Wang X. The role of the proteasome in heart disease. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1809:141-9. [PMID: 20840877 PMCID: PMC3021001 DOI: 10.1016/j.bbagrm.2010.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Revised: 09/01/2010] [Accepted: 09/02/2010] [Indexed: 01/23/2023]
Abstract
Intensive investigations into the pathophysiological significance of the proteasome in the heart did not start until the beginning of the past decade but exciting progress has been made and summarized here as two fronts. First, strong evidence continues to emerge to support a novel hypothesis that proteasome functional insufficiency represents a common pathological phenomenon in a large subset of heart disease, compromises protein quality control in heart muscle cells, and thereby acts as a major pathogenic factor promoting the progression of the subset of heart disease to congestive heart failure. This front is represented by the studies on the ubiquitin-proteasome system (UPS) in cardiac proteinopathy, which have taken advantage of a transgenic mouse model expressing a fluorescence reporter for UPS proteolytic function. Second, pharmacological inhibition of the proteasome has been explored experimentally as a potential therapeutic strategy to intervene on some forms of heart disease, such as pressure-overload cardiac hypertrophy, viral myocarditis, and myocardial ischemic injury. Not only between the two fronts but also within each one, a multitude of inconsistencies and controversies remain to be explained and clarified. At present, the controversy perhaps reflects the sophistication of cardiac proteasomes in terms of the composition, assembly, and regulation, as well as the intricacy and diversity of heart disease in terms of its etiology and pathogenesis. A definitive role of altered proteasome function in the development of various forms of heart disease remains to be established. This article is part of a Special Issue entitled The 26S Proteasome: When degradation is just not enough!
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Affiliation(s)
- Yi-Fan Li
- Division of Basic, Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA
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66
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Endoplasmic reticulum stress activates autophagy but not the proteasome in neuronal cells: implications for Alzheimer's disease. Cell Death Differ 2011; 18:1071-81. [PMID: 21252911 DOI: 10.1038/cdd.2010.176] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Protein folding stress in the endoplasmic reticulum (ER) may lead to activation of the unfolded protein response (UPR), aimed to restore cellular homeostasis via transcriptional and post-transcriptional mechanisms. ER stress is also reported to activate the ER overload response (EOR), which activates transcription via NF-κB. We previously demonstrated that UPR activation is an early event in pre-tangle neurons in Alzheimer's disease (AD) brain. Misfolded and unfolded proteins are degraded via the ubiquitin proteasome system (UPS) or autophagy. UPR activation is found in AD neurons displaying both early UPS pathology and autophagic pathology. Here we investigate whether activation of the UPR and/or EOR is employed to enhance the proteolytic capacity of neuronal cells. Expression of the immunoproteasome subunits β2i and β5i is increased in AD brain. However, expression of the proteasome subunits is not increased by the UPR or EOR. UPR activation does not relocalize the proteasome or increase overall proteasome activity. Therefore proteasomal degradation is not increased by ER stress. In contrast, UPR activation enhances autophagy and LC3 levels are increased in neurons displaying UPR activation in AD brain. Our data suggest that autophagy is the major degradational pathway following UPR activation in neuronal cells and indicate a connection between UPR activation and autophagic pathology in AD brain.
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67
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Li J, Powell SR, Wang X. Enhancement of proteasome function by PA28α overexpression protects against oxidative stress. FASEB J 2010; 25:883-93. [PMID: 21098724 DOI: 10.1096/fj.10-160895] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The principal function of the proteasome is targeted degradation of intracellular proteins. Proteasome dysfunction has been observed in experimental cardiomyopathies and implicated in human congestive heart failure. Measures to enhance proteasome proteolytic function are currently lacking but would be beneficial in testing the pathogenic role of proteasome dysfunction and could have significant therapeutic potential. The association of proteasome activator 28 (PA28) with the 20S proteasome may play a role in antigen processing. It is unclear, however, whether the PA28 plays any important role outside of antigen presentation, although up-regulation of PA28 has been observed in certain types of cardiomyopathy. Here, we show that PA28α overexpression (PA28αOE) stabilized PA28β, increased 11S proteasomes, and enhanced the degradation of a previously validated proteasome surrogate substrate (GFPu) in cultured neonatal rat cardiomyocytes. PA28αOE significantly attenuated H(2)O(2)-induced increases in the protein carbonyls and markedly suppressed apoptosis in cultured cardiomyocytes under basal conditions or when stressed by H(2)O(2). We conclude that PA28αOE is sufficient to up-regulate 11S proteasomes, enhance proteasome-mediated removal of misfolded and oxidized proteins, and protect against oxidative stress in cardiomyocytes, providing a highly sought means to increase proteasomal degradation of abnormal cellular proteins.
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Affiliation(s)
- Jie Li
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, 414 East Clark St., Lee Medical Bldg., Vermillion, SD 57069, USA
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68
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Su H, Li J, Menon S, Liu J, Kumarapeli AR, Wei N, Wang X. Perturbation of cullin deneddylation via conditional Csn8 ablation impairs the ubiquitin-proteasome system and causes cardiomyocyte necrosis and dilated cardiomyopathy in mice. Circ Res 2010; 108:40-50. [PMID: 21051661 DOI: 10.1161/circresaha.110.230607] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RATIONALE Ubiquitin-proteasome system (UPS) dysfunction has been implicated in cardiac pathogenesis. Understanding how cardiac UPS function is regulated will facilitate delineating the pathophysiological significance of UPS dysfunction and developing new therapeutic strategies. The COP9 (constitutive photomorphogenesis mutant 9) signalosome (CSN) may regulate the UPS, but this has not been tested in a critical vertebrate organ. Moreover, the role of CSN in a postmitotic organ and the impact of cardiomyocyte-restricted UPS dysfunction on the heart have not been reported. OBJECTIVE We sought to determine the role of CSN-mediated deneddylation in UPS function and postnatal cardiac development and function. METHODS AND RESULTS Cardiomyocyte-restricted Csn8 gene knockout (CR-Csn8KO) in mice was achieved using a Cre-LoxP system. CR-Csn8KO impaired CSN holocomplex formation and cullin deneddylation and resulted in decreases in F-box proteins. Probing with a surrogate misfolded protein revealed severe impairment of UPS function in CR-Csn8KO hearts. Consequently, CR-Csn8KO mice developed cardiac hypertrophy, which rapidly progressed to heart failure and premature death. Massive cardiomyocyte necrosis rather than apoptosis appears to be the primary cause of the heart failure. This is because (1) massive necrotic cell death and increased infiltration of leukocytes were observed before increased apoptosis; (2) increased apoptosis was not detectable until overt heart failure was observed; and (3) cardiac overexpression of Bcl2 failed to ameliorate CR-Csn8KO mouse premature death. CONCLUSIONS Csn8/CSN plays an essential role in cullin deneddylation, UPS-mediated degradation of a subset of proteins, and the survival of cardiomyocytes and, therefore, is indispensable in postnatal development and function of the heart. Cardiomyocyte-restricted UPS malfunction can cause heart failure.
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Affiliation(s)
- Huabo Su
- Cardiovascular Research Institute, Sanford School of Medicine of the University of South Dakota, Vermillion, 57069, USA
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69
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Ubiquitin-proteasome system profiling in acute leukemias and its clinical relevance. Leuk Res 2010; 35:526-33. [PMID: 20951430 DOI: 10.1016/j.leukres.2010.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 09/06/2010] [Accepted: 09/10/2010] [Indexed: 11/24/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays a major role in the homeostasis of cellular protein. We demonstrate that each of the major hematologic diseases (AML, ALL, and MDS) has a specific and different plasma profile of UPS protein and enzymatic activities. While high levels of proteasome and ubiquitin proteins and enzymatic activities are detected in the plasma samples from patients, normalizing enzymatic activities, show that each proteasome has lower enzymatic activities in these diseases as compared with normal controls. Proteasome protein levels in AML are strong predictor of survival independently of cytogenetics, performance status and age. The Ch-L activity when normalized to the level of proteasome protein show significant negative correlation with survival in ALL.
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70
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Two abundant proteasome subtypes that uniquely process some antigens presented by HLA class I molecules. Proc Natl Acad Sci U S A 2010; 107:18599-604. [PMID: 20937868 DOI: 10.1073/pnas.1009778107] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Most antigenic peptides presented by MHC class I molecules result from the degradation of intracellular proteins by the proteasome. In lymphoid tissues and cells exposed to IFNγ, the standard proteasome is replaced by the immunoproteasome, in which all of the standard catalytic subunits β1, β2, and β5 are replaced by their inducible counterparts β1i, β2i, and β5i, which have different cleavage specificities. The immunoproteasome thereby shapes the repertoire of antigenic peptides. The existence of additional forms of proteasomes bearing a mixed assortment of standard and inducible catalytic subunits has been suggested. Using a new set of unique subunit-specific antibodies, we have now isolated, quantified, and characterized human proteasomes that are intermediate between the standard proteasome and the immunoproteasome. They contain only one (β5i) or two (β1i and β5i) of the three inducible catalytic subunits of the immunoproteasome. These intermediate proteasomes represent between one-third and one-half of the proteasome content of human liver, colon, small intestine, and kidney. They are also present in human tumor cells and dendritic cells. We identified two tumor antigens of clinical interest that are processed exclusively either by intermediate proteasomes β5i (MAGE-A3(271-279)) or by intermediate proteasomes β1i-β5i (MAGE-A10(254-262)). The existence of these intermediate proteasomes broadens the repertoire of antigens presented to CD8 T cells and implies that the antigens presented by a given cell depend on their proteasome content.
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Abstract
Advances in systems biology have allowed for global analyses of mRNA and protein expression, but large-scale studies of protein dynamics and turnover have not been conducted in vivo. Protein turnover is an important metabolic and regulatory mechanism in establishing proteome homeostasis, impacting many physiological and pathological processes. Here, we have used organism-wide isotopic labeling to measure the turnover rates of approximately 2,500 proteins in multiple mouse tissues, spanning four orders of magnitude. Through comparison of the brain with the liver and blood, we show that within the respective tissues, proteins performing similar functions often have similar turnover rates. Proteins in the brain have significantly slower turnover (average lifetime of 9.0 d) compared with those of the liver (3.0 d) and blood (3.5 d). Within some organelles (such as mitochondria), proteins have a narrow range of lifetimes, suggesting a synchronized turnover mechanism. Protein subunits within complexes of variable composition have a wide range of lifetimes, whereas those within well-defined complexes turn over in a coordinated manner. Together, the data represent the most comprehensive in vivo analysis of mammalian proteome turnover to date. The developed methodology can be adapted to assess in vivo proteome homeostasis in any model organism that will tolerate a labeled diet and may be particularly useful in the analysis of neurodegenerative diseases in vivo.
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Drews O, Tsukamoto O, Liem D, Streicher J, Wang Y, Ping P. Differential regulation of proteasome function in isoproterenol-induced cardiac hypertrophy. Circ Res 2010; 107:1094-101. [PMID: 20814020 DOI: 10.1161/circresaha.110.222364] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RATIONALE Proteasomal degradation is altered in many disease phenotypes including cardiac hypertrophy, a prevalent condition leading to heart failure. Our recent investigations identified heterogeneous subpopulations of proteasome complexes in the heart and implicated multiple mechanisms for their regulation. OBJECTIVE The study aimed at identification of molecular mechanisms changing proteasome function in the hypertrophic heart. METHOD AND RESULTS Proteasome function, expression, and assembly were analyzed during the development of cardiac hypertrophy induced by β-adrenergic stimulation. The analysis revealed, for the first time, divergent regulation of proteasome function in cardiac hypertrophy. Proteasome complexes have 3 different proteolytic activities, which are ATP-dependent for 26S complexes (19S assembled with 20S) and ATP-independent for 20S core particles. The 26S activities were enhanced in hypertrophic hearts, partially because of increased expression and assembly of 19S subunits with 20S core complexes. In contrast, caspase- and trypsin-like 20S activities were significantly decreased. Activation of endogenous cAMP-dependent protein kinase (PKA) rescued the depressed 20S functions, supporting the notion that PKA signaling is a positive regulator of protein degradation in the heart. Chymotrypsin-like 20S activity was stably maintained during cardiac remodeling, indicating a switch in proteasome subpopulations, which was supported by altered expression and incorporation of inducible β subunits. CONCLUSIONS Three novel mechanisms for the regulation of proteasome activities were discovered in the development of cardiac hypertrophy: (1) increased incorporation of inducible subunits in 20S proteasomes; (2) enhanced 20S sensitivity to PKA activation; and (3) increased 26S assembly. PKA modulation of proteasome complexes may provide a novel therapeutic avenue for restoration of cardiac function in the diseased myocardium.
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Affiliation(s)
- Oliver Drews
- School of Medicine, University of California-Los Angeles, 675 Charles E Young Drive, Los Angeles, CA 90095-1760, USA
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73
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Wang X, Chen G, Liu H, Zhao Z, Li Z. Four-Dimensional Orthogonal Electrophoresis System for Screening Protein Complexes and Protein−Protein Interactions Combined with Mass Spectrometry. J Proteome Res 2010; 9:5325-34. [DOI: 10.1021/pr100581x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaodong Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Guoqiang Chen
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Hui Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Zhiyun Zhao
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Zhili Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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74
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Schmidt F, Dahlmann B, Hustoft HK, Koehler CJ, Strozynski M, Kloss A, Zimny-Arndt U, Jungblut PR, Thiede B. Quantitative proteome analysis of the 20S proteasome of apoptotic Jurkat T cells. Amino Acids 2010; 41:351-61. [PMID: 20364280 DOI: 10.1007/s00726-010-0575-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 03/17/2010] [Indexed: 01/27/2023]
Abstract
Regulated proteolysis plays important roles in cell biology and pathological conditions. A crosstalk exists between apoptosis and the ubiquitin-proteasome system, two pathways responsible for regulated proteolysis executed by different proteases. To investigate whether the apoptotic process also affects the 20S proteasome, we performed three independent SILAC-based quantitative proteome approaches: 1-DE/MALDI-MS, small 2-DE/MALDI-MS and large 2-DE/nano-LC-ESI-MS. Taking the results of all experiments together, no quantitative changes were observed for the α- and β-subunits of the 20S proteasome except for subunit α7. This protein was identified in two protein spots with a down-regulation of the more acidic protein species (α7a) and up-regulation of the more basic protein species (α7b) during apoptosis. The difference in these two α7 protein species could be attributed to oxidation of cysteine-41 to cysteine sulfonic acid and phosphorylation at serine-250 near the C terminus in α7a, whereas these modifications were missing in α7b. These results pointed to the biological significance of posttranslational modifications of proteasome subunit α7 after induction of apoptosis.
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Affiliation(s)
- Frank Schmidt
- The Biotechnology Centre of Oslo, University of Oslo, Gaustadalleen 21, Blindern, P.O. Box 1125, 0317, Oslo, Norway
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75
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Gu C, Kolodziejek I, Misas-Villamil J, Shindo T, Colby T, Verdoes M, Richau KH, Schmidt J, Overkleeft HS, van der Hoorn RAL. Proteasome activity profiling: a simple, robust and versatile method revealing subunit-selective inhibitors and cytoplasmic, defense-induced proteasome activities. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:160-70. [PMID: 20042019 DOI: 10.1111/j.1365-313x.2009.04122.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The proteasome plays essential roles in nearly all biological processes in plant defense and development, yet simple methods for displaying proteasome activities in extracts and living tissues are not available to plant science. Here, we introduce an easy and robust method to simultaneously display the activities of all three catalytic proteasome subunits in plant extracts or living plant tissues. The method is based on a membrane-permeable, small-molecule fluorescent probe that irreversibly reacts with the catalytic site of the proteasome catalytic subunits in an activity-dependent manner. Activities can be quantified from fluorescent protein gels and used to study proteasome activities in vitro and in vivo. We demonstrate that proteasome catalytic subunits can be selectively inhibited by aldehyde-based inhibitors, including the notorious caspase-3 inhibitor DEVD. Furthermore, we show that the proteasome activity, but not its abundance, is significantly increased in Arabidopsis upon treatment with benzothiadiazole (BTH). This upregulation of proteasome activity depends on NPR1, and occurs mostly in the cytoplasm. The simplicity, robustness and versatility of this method will make this method widely applicable in plant science.
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Affiliation(s)
- Christian Gu
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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76
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Hensley SE, Zanker D, Dolan BP, David A, Hickman HD, Embry AC, Skon CN, Grebe KM, Griffin TA, Chen W, Bennink JR, Yewdell JW. Unexpected role for the immunoproteasome subunit LMP2 in antiviral humoral and innate immune responses. THE JOURNAL OF IMMUNOLOGY 2010; 184:4115-22. [PMID: 20228196 DOI: 10.4049/jimmunol.0903003] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Proteasomes are multisubunit proteases that initiate degradation of many Ags presented by MHC class I molecules. Vertebrates express alternate forms of each of the three catalytic proteasome subunits: standard subunits, and immunosubunits, which are constitutively expressed by APCs and are induced in other cell types by exposure to cytokines. The assembly of mixed proteasomes containing standard subunits and immunosubunits is regulated in a tissue specific manner. In this study, we report that the presence of mixed proteasomes in immune cells in LMP2(-/-) mice compromises multiple components that contribute to the generation of antiviral Ab responses, including splenic B cell numbers, survival and function of adoptively transferred B cells, Th cell function, and dendritic cell secretion of IL-6, TNF-alpha, IL-1beta, and type I IFNs. These defects did not result from compromised overall protein degradation, rather they were associated with altered NF-kappaB activity. These findings demonstrate an important role for immunoproteasomes in immune cell function beyond their contribution to Ag processing.
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Affiliation(s)
- Scott E Hensley
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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77
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Pelletier S, Schuurman KG, Berkers CR, Ovaa H, Heck AJR, Raijmakers R. Quantifying cross-tissue diversity in proteasome complexes by mass spectrometry. MOLECULAR BIOSYSTEMS 2010; 6:1450-3. [DOI: 10.1039/c004989a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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78
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CHEN GQ, LIU H, ZHANG HJ, DENG YC, LI ZL. Proteomic Characterization of Human Erythrocyte 20S Proteasome and Analysis of Species-dependent 20S Proteasome Heterogeneity. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2009. [DOI: 10.1016/s1872-2040(08)60147-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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79
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80
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Tsukamoto O, Minamino T, Kitakaze M. Functional alterations of cardiac proteasomes under physiological and pathological conditions. Cardiovasc Res 2009; 85:339-46. [PMID: 19684034 DOI: 10.1093/cvr/cvp282] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The cardiac proteasome is a complex, heterogeneous, and dynamic organelle. Its function is regulated by its molecular organization, post-translational modifications, and associated partner proteins. Pressure overload, ischaemic heart disease, or genetic mutations in contractile proteins can cause heart failure, during which misfolded protein levels are elevated. At the same time, numerous interconnected signal transduction pathways are activated that may modulate any of the three proteasomal regulatory mechanisms mentioned above, resulting in functional changes in cardiac proteasomes. Many lines of evidence support the important role of the ubiquitin-proteasome system (UPS) in the development of heart diseases. Many researchers have focused on the UPS, applying new drug discovery methods not only in the field of cancer research but also in cardiovascular fields such as cardiac hypertrophy and ischaemic heart diseases. More understanding of UPS in the pathophysiology of heart diseases will lead to new routes for therapy.
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Affiliation(s)
- Osamu Tsukamoto
- Department of Cardiovascular Medicine, National Cardiovascular Center, Suita 565-8565, Japan
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81
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Kloss A, Meiners S, Ludwig A, Dahlmann B. Multiple cardiac proteasome subtypes differ in their susceptibility to proteasome inhibitors. Cardiovasc Res 2009; 85:367-75. [PMID: 19564153 DOI: 10.1093/cvr/cvp217] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AIMS The proteasome is the proteolytically active core of the ubiquitin-proteasome system, which regulates vital processes and which can cause various diseases when it malfunctions. Therefore, the proteasome has become an attractive target for pharmaceutical interventions. Inhibition of the cardiac proteasome by specific proteasome inhibitors has been shown to attenuate cardiac hypertrophy and ischaemia reperfusion injury of the heart. We have resolved the cardiac proteasome into its subtypes and have addressed the key question of how proteasome inhibitors affect single cardiac proteasomal subtypes. METHODS AND RESULTS The 20S proteasome from rat heart was dissected into three different subpopulations (groups I-III), each comprising 4-7 different subtypes. The major group (group II) comprises standard proteasome subtypes; the two minor subpopulations (groups I and III) contain intermediate proteasome subtypes. All subtypes exhibit chymotrypsin-, trypsin-, and caspase-like activity but to different degrees. We have tested the effect of two common proteasome inhibitors on the chymotrypsin-like activity of all subtypes: 20-30 nmol/L MG132 caused 50% inhibition of all subtypes from groups I and II, whereas 100 nmol/L was necessary to affect group III subtypes to the same extent. However, another inhibitor, bortezomib (VELCADE), already used clinically, inhibited 50% of the activity of group III proteasome subtypes even below 20 nmol/L, a concentration showing almost no effect on group I and II proteasome subtypes. The caspase-like activity of group II proteasome subtypes was not affected by MG132 and was inhibited by bortezomib only at concentrations above 100 nmol/L. CONCLUSION These data show that different inhibitors have differential inhibitory effects on the various cardiac proteasome subtypes. Different cardiac subtypes are inhibited by the same dose of proteasome inhibitor to a different extent.
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Affiliation(s)
- Alexander Kloss
- Institut für Biochemie/CCM, Charité-Universitätsmedizin Berlin, Monbijoustr 2, Berlin 10117, Germany
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82
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Hassan WM, Merin DA, Fonte V, Link CD. AIP-1 ameliorates beta-amyloid peptide toxicity in a Caenorhabditis elegans Alzheimer's disease model. Hum Mol Genet 2009; 18:2739-47. [PMID: 19414486 DOI: 10.1093/hmg/ddp209] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Multiple neurodegenerative diseases are causally linked to aggregation-prone proteins. Cellular mechanisms involving protein turnover may be key defense mechanisms against aggregating protein disorders. We have used a transgenic Caenorhabditis elegans Alzheimer's disease model to identify cellular responses to proteotoxicity resulting from expression of the human beta amyloid peptide (Abeta). We show up-regulation of aip-1 in Abeta-expressing animals. Mammalian homologues of AIP-1 have been shown to associate with, and regulate the function of, the 26S proteasome, leading us to hypothesize that induction of AIP-1 may be a protective cellular response directed toward modulating proteasomal function in response to toxic protein aggregation. Using our transgenic model, we show that overexpression of AIP-1 protected against, while RNAi knockdown of AIP-1 exacerbated, Abeta toxicity. AIP-1 overexpression also reduced accumulation of Abeta in this model, which is consistent with AIP-1 enhancing protein degradation. Transgenic expression of one of the two human aip-1 homologues (AIRAPL), but not the other (AIRAP), suppressed Abeta toxicity in C. elegans, which advocates the biological relevance of the data to human biology. Interestingly, AIRAPL and AIP-1 contain a predicted farnesylation site, which is absent from AIRAP. This farnesylation site was shown by others to be essential for an AIP-1 prolongevity function. Consistent with this, we show that an AIP-1 mutant lacking the predicted farnesylation site failed to protect against Abeta toxicity. Our results implicate AIP-1 in the regulation of protein turnover and protection against Abeta toxicity and point at AIRAPL as the functional mammalian homologue of AIP-1.
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Affiliation(s)
- Wail M Hassan
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO 80303, USA.
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83
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Akazawa H, Komuro I. “Change can happen” by PKA: Proteasomes in in vivo hearts. J Mol Cell Cardiol 2009; 46:445-7. [DOI: 10.1016/j.yjmcc.2008.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Revised: 12/15/2008] [Accepted: 12/20/2008] [Indexed: 01/07/2023]
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84
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Tosello V, Zamarchi R, Merlo A, Gorza M, Piovan E, Mandruzzato S, Bronte V, Wang X, Ferrone S, Amadori A, Zanovello P. Differential expression of constitutive and inducible proteasome subunits in human monocyte-derived DC differentiated in the presence of IFN-alpha or IL-4. Eur J Immunol 2009; 39:56-66. [PMID: 19065646 DOI: 10.1002/eji.200738098] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Several studies strongly suggest that DC differentiated in vitro in the presence of type I IFN acquire more potent immune stimulatory properties, compared with DC differentiated in vitro with IL-4. However, little is known about the molecular mechanisms underlying this phenomenon. To address this question, we compared the Ag-processing machinery (APM) profile in human DC grown in the presence of IFN-alpha ((IFN)DC) or IL-4 ((IL-4)DC). Using a panel of APM component-specific mAb in Western blot experiments, we found that (IFN)DC preferentially express inducible proteasome subunits (LMP2, LMP7, and MECL1) both at immature and mature stages. In contrast, immature (IL-4)DC co-express both constitutive (beta1, beta2, and beta5) and inducible subunits, as shown by Western blotting analysis. In addition, immature (IFN)DC express higher levels of TAP1, TAP2, calnexin, calreticulin, tapasin, and HLA class I molecules than (IL-4)DC. The different proteasome profiles of (IFN)DC and (IL-4)DC were associated with a greater ability of (IFN)DC to present an immunodominant epitope that requires LMP7 expression for its processing. In general, these data show the impact of cytokines on APM component expression and hence the Ag-processing ability of DC.
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Affiliation(s)
- Valeria Tosello
- Department of Oncology and Surgical Sciences, Oncology Section, University of Padova, Padova, Italy
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85
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Zong C, Young GW, Wang Y, Lu H, Deng N, Drews O, Ping P. Two-dimensional electrophoresis-based characterization of post-translational modifications of mammalian 20S proteasome complexes. Proteomics 2009; 8:5025-37. [PMID: 19003867 DOI: 10.1002/pmic.200800387] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PTMs serve as key regulatory mechanisms for 20S proteasome functions. Alterations in 20S PTMs have been previously observed with changes in modified protein degradation patterns and altered cellular phenotypes. Despite decades of investigation, our knowledge pertaining to the various PTMs of 20S complexes and their biological significance remain limited. In this investigation, we show that 2-DE offers an analytical tool with high resolution and reproducibility. Accordingly, it has been applied for the characterization of PTMs including glycosylation, phosphorylation, oxidation, and nitrosylation. The PTMs of murine cardiac 20S proteasomes and their associating proteins were examined. Our 2-DE analyses displayed over 25 spots for the 20S complexes (17 subunits), indicating multiply modified subunits of cardiac proteasomes. The identification of specific PTM sites subsequent to 2-DE was supported by MS. These PTMs included phosphorylation and oxidation. Most of the PTMs occurred in low stoichiometry and required enrichment to enhance the detection sensitivity. In conclusion, our studies support 2-DE as a central tool in the analyses of 20S proteasome PTMs. The approaches utilized in this investigation demonstrate their application in mapping the PTMs of the 20S proteasomes in cardiac tissue, which are applicable to other samples and biological conditions.
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Affiliation(s)
- Chenggong Zong
- Department of Physiology, University of California at Los Angeles, UCLA School of Medicine, Los Angeles, CA 90095, USA
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86
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Mearini G, Schlossarek S, Willis MS, Carrier L. The ubiquitin–proteasome system in cardiac dysfunction. Biochim Biophys Acta Mol Basis Dis 2008; 1782:749-63. [DOI: 10.1016/j.bbadis.2008.06.009] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 06/12/2008] [Accepted: 06/18/2008] [Indexed: 12/31/2022]
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87
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Nissum M, Foucher AL. Analysis of human plasma proteins: a focus on sample collection and separation using free-flow electrophoresis. Expert Rev Proteomics 2008; 5:571-87. [PMID: 18761468 DOI: 10.1586/14789450.5.4.571] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Due to ease of accessibility, plasma has become the sample of choice for proteomics studies directed towards biomarker discovery intended for use in diagnostics, prognostics and even in theranostics. The result of these extensive efforts is a long list of potential biomarkers, very few of which have led to clinical utility. Why have so many potential biomarkers failed validation? Herein, we address certain issues encountered, which complicate biomarker discovery efforts originating from plasma. The advantages of stabilizing the sample at collection by the addition of protease inhibitors are discussed. The principles of free-flow electrophoresis (FFE) separation are provided together with examples applying to various studies. Finally, particular attention is given to plasma or serum analysis using multidimensional separation strategies into which the FFE is incorporated. The advantages of using FFE separation in these workflows are discussed.
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Affiliation(s)
- Mikkel Nissum
- BD Diagnostics, Am Klopferspitz 19a, D-82152 Martinsried, Germany.
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88
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Gomes AV, Young GW, Wang Y, Zong C, Eghbali M, Drews O, Lu H, Stefani E, Ping P. Contrasting proteome biology and functional heterogeneity of the 20 S proteasome complexes in mammalian tissues. Mol Cell Proteomics 2008; 8:302-15. [PMID: 18931337 DOI: 10.1074/mcp.m800058-mcp200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 20 S proteasome complexes are major contributors to the intracellular protein degradation machinery in mammalian cells. Systematic administration of proteasome inhibitors to combat disease (e.g. cancer) has resulted in positive outcomes as well as adversary effects. The latter was attributed to, at least in part, a lack of understanding in the organ-specific responses to inhibitors and the potential diversity of proteomes of these complexes in different tissues. Accordingly, we conducted a proteomic study to characterize the 20 S proteasome complexes and their postulated organ-specific responses in the heart and liver. The cardiac and hepatic 20 S proteasomes were isolated from the same mouse strain with identical genetic background. We examined the molecular composition, complex assembly, post-translational modifications and associating partners of these proteasome complexes. Our results revealed an organ-specific molecular organization of the 20 S proteasomes with distinguished patterns of post-translational modifications as well as unique complex assembly characteristics. Furthermore, the proteome diversities are concomitant with a functional heterogeneity of the proteolytic patterns exhibited by these two organs. In particular, the heart and liver displayed distinct activity profiles to two proteasome inhibitors, epoxomicin and Z-Pro-Nle-Asp-H. Finally, the heart and liver demonstrated contrasting regulatory mechanisms from the associating partners of these proteasomes. The functional heterogeneity of the mammalian 20 S proteasome complexes underscores the concept of divergent proteomes among organs in the context of an identical genome.
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Affiliation(s)
- Aldrin V Gomes
- Department of Physiology and Medicine, Cardiac Proteomics and Signaling Laboratory at Cardiovascular Research Laboratory, University of California Los Angeles, School of Medicine, Los Angeles, CA 90095, USA
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Characterization of the proteasome interaction network using a QTAX-based tag-team strategy and protein interaction network analysis. Proc Natl Acad Sci U S A 2008; 105:13333-8. [PMID: 18757749 DOI: 10.1073/pnas.0801870105] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantitative analysis of tandem-affinity purified cross-linked (x) protein complexes (QTAX) is a powerful technique for the identification of protein interactions, including weak and/or transient components. Here, we apply a QTAX-based tag-team mass spectrometry strategy coupled with protein network analysis to acquire a comprehensive and detailed assessment of the protein interaction network of the yeast 26S proteasome. We have determined that the proteasome network is composed of at least 471 proteins, significantly more than the total number of proteins identified by previous reports using proteasome subunits as baits. Validation of the selected proteasome-interacting proteins by reverse copurification and immunoblotting experiments with and without cross-linking, further demonstrates the power of the QTAX strategy for capturing protein interactions of all natures. In addition, >80% of the identified interactions have been confirmed by existing data using protein network analysis. Moreover, evidence obtained through network analysis links the proteasome to protein complexes associated with diverse cellular functions. This work presents the most complete analysis of the proteasome interaction network to date, providing an inclusive set of physical interaction data consistent with physiological roles for the proteasome that have been suggested primarily through genetic analyses. Moreover, the methodology described here is a general proteomic tool for the comprehensive study of protein interaction networks.
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90
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Fischer DF, van Dijk R, van Tijn P, Hobo B, Verhage MC, van der Schors RC, Li KW, van Minnen J, Hol EM, van Leeuwen FW. Long-term proteasome dysfunction in the mouse brain by expression of aberrant ubiquitin. Neurobiol Aging 2008; 30:847-63. [PMID: 18760506 DOI: 10.1016/j.neurobiolaging.2008.06.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 05/28/2008] [Accepted: 06/18/2008] [Indexed: 02/06/2023]
Abstract
Many neurodegenerative diseases are characterized by deposits of ubiquitinated and aberrant proteins, suggesting a failure of the ubiquitin-proteasome system (UPS). The aberrant ubiquitin UBB(+1) is one of the ubiquitinated proteins accumulating in tauopathies such as Alzheimer's disease (AD) and polyglutamine diseases such as Huntington's disease. We have generated UBB(+1) transgenic mouse lines with post-natal neuronal expression of UBB(+1), resulting in increased levels of ubiquitinated proteins in the cortex. Moreover, by proteomic analysis, we identified expression changes in proteins involved in energy metabolism or organization of the cytoskeleton. These changes show a striking resemblance to the proteomic profiles of both AD brain and several AD mouse models. Moreover, UBB(+1) transgenic mice show a deficit in contextual memory in both water maze and fear conditioning paradigms. Although UBB(+1) partially inhibits the UPS in the cortex, these mice do not have an overt neurological phenotype. These mouse models do not replicate the full spectrum of AD-related changes, yet provide a tool to understand how the UPS is involved in AD pathological changes and in memory formation.
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Affiliation(s)
- David F Fischer
- Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands.
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91
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Young GW, Wang Y, Ping P. Understanding proteasome assembly and regulation: importance to cardiovascular medicine. Trends Cardiovasc Med 2008; 18:93-8. [PMID: 18436147 DOI: 10.1016/j.tcm.2008.01.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 01/18/2008] [Accepted: 01/24/2008] [Indexed: 01/30/2023]
Abstract
The cardiac proteasome is increasingly recognized as a complex, heterogeneous, and dynamic organelle contributing to the modulation of cardiac function in health and diseases. The emerging picture of the proteasome system reveals a highly regulated and organized molecular machine integrated into multiple biologic processes of the cell. Full appreciation of its cardiovascular relevance requires an understanding of its proteolytic function as well as its underlying regulatory mechanisms, of which assembly, stoichiometry, posttranslational modification, and the role of the associating partners are increasingly poignant.
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Affiliation(s)
- Glen W Young
- Department of Physiology, Medicine/Division of Cardiology, David Geffen School of Medicine at UCLA, University of California-Los Angeles, CA 90095, USA
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92
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Lu H, Zong C, Wang Y, Young GW, Deng N, Souda P, Li X, Whitelegge J, Drews O, Yang PY, Ping P. Revealing the dynamics of the 20 S proteasome phosphoproteome: a combined CID and electron transfer dissociation approach. Mol Cell Proteomics 2008; 7:2073-89. [PMID: 18579562 DOI: 10.1074/mcp.m800064-mcp200] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The 20 S proteasomes play a critical role in intracellular homeostasis and stress response. Their function is tuned by covalent modifications, such as phosphorylation. In this study, we performed a comprehensive characterization of the phosphoproteome for the 20 S proteasome complexes in both the murine heart and liver. A platform combining parallel approaches in differential sample fractionation (SDS-PAGE, IEF, and two-dimensional electrophoresis), enzymatic digestion (trypsin and chymotrypsin), phosphopeptide enrichment (TiO(2)), and peptide fragmentation (CID and electron transfer dissociation (ETD)) has proven to be essential for identifying low abundance phosphopeptides. As a result, a total of 52 phosphorylation identifications were made in mammalian tissues; 44 of them were novel. These identifications include single (serine, threonine, and tyrosine) and dual phosphorylation peptides. 34 phosphopeptides were identified by CID; 10 phosphopeptides, including a key modification on the catalytically essential beta5 subunit, were identified only by ETD; eight phosphopeptides were shared identifications by both CID and ETD. Besides the commonly shared phosphorylation sites, unique sites were detected in the murine heart and liver, documenting variances in phosphorylation between tissues within the proteasome populations. Furthermore the biological significance of these 20 S phosphoproteomes was evaluated. The role of cAMP-dependent protein kinase A (PKA) to modulate these phosphoproteomes was examined. Using a proteomics approach, many of the cardiac and hepatic 20 S subunits were found to be substrate targets of PKA. Incubation of the intact 20 S proteasome complexes with active PKA enhanced phosphorylation in both existing PKA phosphorylation sites as well as novel sites in these 20 S subunits. Furthermore treatment with active PKA significantly elevated all three peptidase activities (beta1 caspase-like, beta2 trypsin-like, and beta5 chymotrypsin-like), demonstrating a functional role of PKA in governing these 20 S phosphoproteomes.
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Affiliation(s)
- Haojie Lu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, 200032 Shanghai, China
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93
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MacLellan WR, Wang Y, Vondriska TM, Weiss JN, Ping P. Proteomic insights into cardiac cell death and survival. Proteomics Clin Appl 2008; 2:837-44. [PMID: 21136883 PMCID: PMC3808833 DOI: 10.1002/prca.200780121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Indexed: 11/06/2022]
Abstract
Cardiovascular disease is the leading cause of death and disability in the developed world. To design novel therapeutic strategies to treat and prevent this disease, better understanding of cardiac cell function is necessary. In addition to (and, indeed, in combination with) genetics, physiology and molecular biology, proteomics plays a critical role in our understanding of cardiovascular systems at multiple scales. The purpose of this review is to examine recent developments in the field of myocardial injury and protection, examining how proteomics has informed investigations into organelles, signaling complexes, and cardiac phenotype.
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Affiliation(s)
- W. Robb MacLellan
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
- Department of Physiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
| | - Yibin Wang
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
- Department of Physiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
- Department of Anesthesiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
| | - Thomas M. Vondriska
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
- Department of Physiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
- Department of Anesthesiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
| | - James N. Weiss
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
- Department of Physiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
| | - Peipei Ping
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
- Department of Physiology, Cardiovascular Research Laboratories, University of California, Los Angeles, CA, USA
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94
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Wang X, Su H, Ranek MJ. Protein quality control and degradation in cardiomyocytes. J Mol Cell Cardiol 2008; 45:11-27. [PMID: 18495153 DOI: 10.1016/j.yjmcc.2008.03.025] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 03/23/2008] [Accepted: 03/29/2008] [Indexed: 12/19/2022]
Abstract
The heart is constantly under stress and cardiomyocytes face enormous challenges to correctly fold nascent polypeptides and keep mature proteins from denaturing. To meet the challenge, cardiomyocytes have developed multi-layered protein quality control (PQC) mechanisms which are carried out primarily by chaperones and ubiquitin-proteasome system mediated proteolysis. Autophagy may also participate in PQC in cardiomyocytes, especially under pathological conditions. Cardiac PQC often becomes inadequate in heart disease, which may play an important role in the development of congestive heart failure.
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Affiliation(s)
- Xuejun Wang
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA.
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95
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Li F, Zhang L, Craddock J, Bruce-Keller AJ, Dasuri K, Nguyen A, Keller JN. Aging and dietary restriction effects on ubiquitination, sumoylation, and the proteasome in the heart. Mech Ageing Dev 2008; 129:515-21. [PMID: 18533226 DOI: 10.1016/j.mad.2008.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Revised: 04/15/2008] [Accepted: 04/22/2008] [Indexed: 10/22/2022]
Abstract
Dietary restriction (DR), in the absence of malnutrition, is the only intervention known to reliably increase average and maximal lifespan in a variety of organisms including mammals. Because the effects of DR on the heart are poorly understood, in the present study we examined the effects of DR on the ubiquitin-proteasome pathway (UPP) in the heart. In these studies we observed that DR significantly reduced age-related impairments in proteasome-mediated protein degradation, and reduced age-related increases in ubiquitinated, oxidized, and sumoylated protein in the heart. Interestingly, DR did not significantly increase the expression of 20S proteasome subunits or the proteasome maturation factor (POMP-1). These data demonstrate for the first time the effects of aging and DR on proteasome biogenesis and sumoylation in the heart. Cumulatively, our data indicate that DR has many beneficial effects towards the UPP in the heart, and suggests that a preservation of the UPP may be a potential mechanism by which DR mediates beneficial effects on the cardiovascular system.
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Affiliation(s)
- Feng Li
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
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