1
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Trogisch FA, Koser F, Michel S, Liem DA, Florea BI, Hecker M, Drews O. Genetic ablation of Lmp2 increases the susceptibility for impaired cardiac function. Front Mol Biosci 2024; 11:1148948. [PMID: 38516190 PMCID: PMC10955435 DOI: 10.3389/fmolb.2024.1148948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 01/26/2024] [Indexed: 03/23/2024] Open
Abstract
Proteasome degradation is an integral part of cellular growth and function. Proteasomal intervention may mitigate adverse myocardial remodeling, but is associated with the onset of heart failure. Previously, we have demonstrated that increasing abundance of cardiac Lmp2 and its incorporation into proteasome complexes is an endogenous mechanism for proteasome regulation during hypertrophic remodeling of the heart induced by chronic ß-adrenoreceptor stimulation. Here, we investigated whether Lmp2 is required for myocardial remodeling not driven by inflammation and show that Lmp2 is a tipping element for growth and function in the heart but not for proteasome insufficiency. While it has no apparent impact under unchallenged conditions, myocardial remodeling without Lmp2 exacerbates hypertrophy and restricts cardiac function. Under chronic ß-adrenoreceptor stimulation, as seen in the development of cardiovascular disease and the manifestation of heart failure, genetic ablation of Lmp2 in mice caused augmented concentric hypertrophy of the left ventricle. While the heart rate was similarly elevated as in wildtype, myocardial contractility was not maintained without Lmp2, and apparently uncoupled of the ß-adrenergic response. Normalized to the exacerbated myocardial mass, contractility was reduced by 41% of the pretreatment level, but would appear preserved at absolute level. The lack of Lmp2 interfered with elevated 26S proteasome activities during early cardiac remodeling reported previously, but did not cause bulk proteasome insufficiency, suggesting the Lmp2 containing proteasome subpopulation is required for a selected group of proteins to be degraded. In the myocardial interstitium, augmented collagen deposition suggested matrix stiffening in the absence of Lmp2. Indeed, echocardiography of left ventricular peak relaxation velocity (circumferential strain rate) was reduced in this treatment group. Overall, targeting Lmp2 in a condition mimicking chronic ß-adrenoreceptor stimulation exhibited the onset of heart failure. Anticancer therapy inhibiting proteasome activity, including Lmp2, is associated with adverse cardiac events, in particular heart failure. Sparing Lmp2 may be an avenue to reduce adverse cardiac events when chronic sympathetic nervous system activation cannot be excluded.
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Affiliation(s)
- Felix A. Trogisch
- European Center for Angioscience, Department of Cardiovascular Physiology, Mannheim Medical Faculty, Heidelberg University, Mannheim, Germany
- Department of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Franziska Koser
- Department of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - Synje Michel
- Department of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
| | - David A. Liem
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Bogdan I. Florea
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Markus Hecker
- Department of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Oliver Drews
- Department of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
- Biomedical Mass Spectrometry, Center for Medical Research, Johannes Kepler University, Linz, Austria
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2
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Efentakis P, Andreadou I, Iliodromitis KE, Triposkiadis F, Ferdinandy P, Schulz R, Iliodromitis EK. Myocardial Protection and Current Cancer Therapy: Two Opposite Targets with Inevitable Cost. Int J Mol Sci 2022; 23:ijms232214121. [PMID: 36430599 PMCID: PMC9696420 DOI: 10.3390/ijms232214121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022] Open
Abstract
Myocardial protection against ischemia/reperfusion injury (IRI) is mediated by various ligands, activating different cellular signaling cascades. These include classical cytosolic mediators such as cyclic-GMP (c-GMP), various kinases such as Phosphatydilinositol-3- (PI3K), Protein Kinase B (Akt), Mitogen-Activated-Protein- (MAPK) and AMP-activated (AMPK) kinases, transcription factors such as signal transducer and activator of transcription 3 (STAT3) and bioactive molecules such as vascular endothelial growth factor (VEGF). Most of the aforementioned signaling molecules constitute targets of anticancer therapy; as they are also involved in carcinogenesis, most of the current anti-neoplastic drugs lead to concomitant weakening or even complete abrogation of myocardial cell tolerance to ischemic or oxidative stress. Furthermore, many anti-neoplastic drugs may directly induce cardiotoxicity via their pharmacological effects, or indirectly via their cardiovascular side effects. The combination of direct drug cardiotoxicity, indirect cardiovascular side effects and neutralization of the cardioprotective defense mechanisms of the heart by prolonged cancer treatment may induce long-term ventricular dysfunction, or even clinically manifested heart failure. We present a narrative review of three therapeutic interventions, namely VEGF, proteasome and Immune Checkpoint inhibitors, having opposing effects on the same intracellular signal cascades thereby affecting the heart. Moreover, we herein comment on the current guidelines for managing cardiotoxicity in the clinical setting and on the role of cardiovascular confounders in cardiotoxicity.
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Affiliation(s)
- Panagiotis Efentakis
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Ioanna Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
- Correspondence: ; Tel.: +30-210-727-4827; Fax: +30-210-727-4747
| | | | | | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Rainer Schulz
- Institute of Physiology, Justus Liebig University Giessen, 35390 Giessen, Germany
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3
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Esfahanian N, Nelson M, Autenried R, Pattison JS, Callegari E, Rezvani K. Comprehensive Analysis of Proteasomal Complexes in Mouse Brain Regions Detects ENO2 as a Potential Partner of the Proteasome in the Striatum. Cell Mol Neurobiol 2022; 42:2305-2319. [PMID: 34037901 PMCID: PMC8617079 DOI: 10.1007/s10571-021-01106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/19/2021] [Indexed: 11/28/2022]
Abstract
Defects in the activity of the proteasome or its regulators are linked to several pathologies, including neurodegenerative diseases. We hypothesize that proteasome heterogeneity and its selective partners vary across brain regions and have a significant impact on proteasomal catalytic activities. Using neuronal cell cultures and brain tissues obtained from mice, we compared proteasomal activities from two distinct brain regions affected in neurodegenerative diseases, the striatum and the hippocampus. The results indicated that proteasome activities and their responses to proteasome inhibitors are determined by their subcellular localizations and their brain regions. Using an iodixanol gradient fractionation method, proteasome complexes were isolated, followed by proteomic analysis for proteasomal interaction partners. Proteomic results revealed brain region-specific non-proteasomal partners, including gamma-enolase (ENO2). ENO2 showed more association to proteasome complexes purified from the striatum than to those from the hippocampus. These results highlight a potential key role for non-proteasomal partners of proteasomes regarding the diverse activities of the proteasome complex recorded in several brain regions.
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Affiliation(s)
- Niki Esfahanian
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Morgan Nelson
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Rebecca Autenried
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - J Scott Pattison
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Eduardo Callegari
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Khosrow Rezvani
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA.
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4
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Bo Kim K. Proteasomal adaptations to FDA-approved proteasome inhibitors: a potential mechanism for drug resistance? CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2021; 4:634-645. [PMID: 34308274 PMCID: PMC8297691 DOI: 10.20517/cdr.2021.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
With proteasome inhibitors (PIs) becoming clinically available since 2003, outcomes for patients with multiple myeloma (MM) have dramatically changed, improving quality of life and survival. Despite the impressive treatment success, however, almost all MM patients who initially respond to these PIs eventually develop resistance. Furthermore, a portion of MM patients is inherently unresponsive to the PIs. Extensive mechanistic investigations identified several non-proteasomal signaling pathways suspected to be linked to the PI resistance, for which several excellent reviews are currently available. On the other hand, it is still unclear how cancer cells under high PI environments adapt to spare proteasome activity essential for survival and proliferation regardless of cancer evolution stages. This review outlines current progress towards understanding the proteasomal adaptations of cells in response to PI treatment to maintain necessary proteasome activity. A better understanding of cellular proteasomal changes in response to the PIs could provide a rationale to develop new therapeutics that could be used to overcome resistance to existing PI drugs.
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Affiliation(s)
- Kyung Bo Kim
- Department of Pharmaceutics, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
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5
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Omega-3 PUFAs Suppress IL-1β-Induced Hyperactivity of Immunoproteasomes in Astrocytes. Int J Mol Sci 2021; 22:ijms22115410. [PMID: 34063751 PMCID: PMC8196670 DOI: 10.3390/ijms22115410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The role of immunoproteasome (iP) in astroglia, the cellular component of innate immunity, has not been clarified. The results so far indicate that neuroinflammation, a prominent hallmark of Alzheimer’s disease, strongly activates the iP subunits expression. Since omega-3 PUFAs possess anti-inflammatory and pro-resolving activity in the brain, we investigated the effect of DHA and EPA on the gene expression of constitutive (β1 and β5) and inducible (iβ1/LMP2 and iβ5/LMP7) proteasome subunits and proteasomal activity in IL-1β-stimulated astrocytes. We found that both PUFAs downregulated the expression of IL-1β-induced the iP subunits, but not the constitutive proteasome subunits. The chymotrypsin-like activity was inhibited in a dose-dependent manner by DHA, and much strongly in the lower concentration by EPA. Furthermore, we established that C/EBPα and C/EBPβ transcription factors, being the cis-regulatory element of the transcription complex, frequently activated by inflammatory mediators, participate in a reduction in the iP subunits’ expression. Moreover, the expression of connexin 43 the major gap junction protein in astrocytes, negatively regulated by IL-1β was markedly increased in PUFA-treated cells. These findings indicate that omega-3 PUFAs attenuate inflammation-induced hyperactivity of iPs in astrocytes and have a beneficial effect on preservation of interastrocytic communication by gap junctions.
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Zagirova D, Autenried R, Nelson ME, Rezvani K. Proteasome Complexes and Their Heterogeneity in Colorectal, Breast and Pancreatic Cancers. J Cancer 2021; 12:2472-2487. [PMID: 33854609 PMCID: PMC8040722 DOI: 10.7150/jca.52414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/09/2021] [Indexed: 11/26/2022] Open
Abstract
Targeting the ubiquitin-proteasome system (UPS) - in particular, the proteasome complex - has emerged as an attractive novel cancer therapy. While several proteasome inhibitors have been successfully approved by the Food and Drug Administration for the treatment of hematological malignancies, the clinical efficacy of these inhibitors is unexpectedly lower in the treatment of solid tumors due to the functional and structural heterogeneity of proteasomes in solid tumors. There are ongoing trials to examine the effectiveness of compound and novel proteasome inhibitors that can target solid tumors either alone or in combination with conventional chemotherapeutic agents. The modest therapeutic efficacy of proteasome inhibitors such as bortezomib in solid malignancies demands further research to clarify the exact effects of these proteasome inhibitors on different proteasomes present in cancer cells. The structural, cellular localization and functional analysis of the proteasome complexes in solid tumors originated from different tissues provides new insights into the diversity of proteasomes' responses to inhibitors. In this study, we used an optimized iodixanol gradient ultracentrifugation to purify a native form of proteasome complexes with their intact associated protein partners enriched within distinct cellular compartments. It is therefore possible to isolate proteasome subcomplexes with far greater resolution than sucrose or glycerol fractionations. We have identified differences in the catalytic activities, subcellular distribution, and inhibitor sensitivity of cytoplasmic proteasomes isolated from human colon, breast, and pancreatic cancer cell lines. Our developed techniques and generated results will serve as a valuable guideline for investigators developing a new generation of proteasome inhibitors as an effective targeted therapy for solid tumors.
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Affiliation(s)
- Diana Zagirova
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD 57069, USA
| | - Rebecca Autenried
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD 57069, USA
| | - Morgan E Nelson
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD 57069, USA
| | - Khosrow Rezvani
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD 57069, USA
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7
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Račková L, Csekes E. Proteasome Biology: Chemistry and Bioengineering Insights. Polymers (Basel) 2020; 12:E2909. [PMID: 33291646 PMCID: PMC7761984 DOI: 10.3390/polym12122909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Proteasomal degradation provides the crucial machinery for maintaining cellular proteostasis. The biological origins of modulation or impairment of the function of proteasomal complexes may include changes in gene expression of their subunits, ubiquitin mutation, or indirect mechanisms arising from the overall impairment of proteostasis. However, changes in the physico-chemical characteristics of the cellular environment might also meaningfully contribute to altered performance. This review summarizes the effects of physicochemical factors in the cell, such as pH, temperature fluctuations, and reactions with the products of oxidative metabolism, on the function of the proteasome. Furthermore, evidence of the direct interaction of proteasomal complexes with protein aggregates is compared against the knowledge obtained from immobilization biotechnologies. In this regard, factors such as the structures of the natural polymeric scaffolds in the cells, their content of reactive groups or the sequestration of metal ions, and processes at the interface, are discussed here with regard to their influences on proteasomal function.
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Affiliation(s)
- Lucia Račková
- Centre of Experimental Medicine, Institute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences, Dúbravská cesta 9, 841 04 Bratislava, Slovakia;
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8
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Mishra S, Dunkerly-Eyring BL, Keceli G, Ranek MJ. Phosphorylation Modifications Regulating Cardiac Protein Quality Control Mechanisms. Front Physiol 2020; 11:593585. [PMID: 33281625 PMCID: PMC7689282 DOI: 10.3389/fphys.2020.593585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022] Open
Abstract
Many forms of cardiac disease, including heart failure, present with inadequate protein quality control (PQC). Pathological conditions often involve impaired removal of terminally misfolded proteins. This results in the formation of large protein aggregates, which further reduce cellular viability and cardiac function. Cardiomyocytes have an intricately collaborative PQC system to minimize cellular proteotoxicity. Increased expression of chaperones or enhanced clearance of misfolded proteins either by the proteasome or lysosome has been demonstrated to attenuate disease pathogenesis, whereas reduced PQC exacerbates pathogenesis. Recent studies have revealed that phosphorylation of key proteins has a potent regulatory role, both promoting and hindering the PQC machinery. This review highlights the recent advances in phosphorylations regulating PQC, the impact in cardiac pathology, and the therapeutic opportunities presented by harnessing these modifications.
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Affiliation(s)
- Sumita Mishra
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Brittany L Dunkerly-Eyring
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, United States
| | - Gizem Keceli
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mark J Ranek
- Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Tsimokha AS, Artamonova TO, Diakonov EE, Khodorkovskii MA, Tomilin AN. Post-Translational Modifications of Extracellular Proteasome. Molecules 2020; 25:molecules25153504. [PMID: 32752045 PMCID: PMC7435879 DOI: 10.3390/molecules25153504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 12/29/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is one of the major protein degradation pathways in eukaryotic cells. Abnormal functioning of this system has been observed in cancer and neurological diseases. The 20S proteasomes, essential components of the UPS, are present not only within the cells but also in the extracellular space, and their concentration in blood plasma has been found to be elevated and dependent upon the disease state, being of prognostic significance in patients suffering from cancer, liver diseases, and autoimmune diseases. However, functions of extracellular proteasomes and mechanisms of their release by cells remain largely unknown. The main mechanism of proteasome activity regulation is provided by modulation of their composition and post-translational modifications (PTMs). Moreover, diverse PTMs of proteins are known to participate in the loading of specific elements into extracellular vesicles. Since previous studies have revealed that the transport of extracellular proteasomes may occur via extracellular vesicles, we have set out to explore the PTMs of extracellular proteasomes in comparison to cellular counterparts. In this work, cellular and extracellular proteasomes were affinity purified and separated by SDS-PAGE for subsequent trypsinization and matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) analysis. In total, we could identify 64 and 55 PTM sites in extracellular and cellular proteasomes, respectively, including phosphorylation, ubiquitination, acetylation, and succinylation. We observed novel sites of acetylation at K238 and K192 of the proteasome subunits β2 and β3, respectively, that are specific for extracellular proteasomes. Moreover, cellular proteasomes show specific acetylation at K227 of α2 and ubiquitination at K201 of β3. Interestingly, succinylation of β6 at the residue K228 seems not to be present exclusively in extracellular proteasomes, whereas both extracellular and cellular proteasomes may also be acetylated at this site. The same situation takes place at K201 of the β3 subunit where ubiquitination is seemingly specific for cellular proteasomes. Moreover, crosstalk between acetylation, ubiquitination, and succinylation has been observed in the subunit α3 of both proteasome populations. These data will serve as a basis for further studies, aimed at dissection of the roles of extracellular proteasome-specific PTMs in terms of the function of these proteasomes and mechanism of their transport into extracellular space.
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Affiliation(s)
- Anna S. Tsimokha
- Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 Saint-Petersburg, Russia; (T.O.A.); (E.E.D.); (M.A.K.); (A.N.T.)
- Correspondence: ; Tel.: +7-812-297-1829; Fax: +7-812-297-0341
| | - Tatiana O. Artamonova
- Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 Saint-Petersburg, Russia; (T.O.A.); (E.E.D.); (M.A.K.); (A.N.T.)
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str., 195251 Saint-Petersburg, Russia
| | - Egor E. Diakonov
- Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 Saint-Petersburg, Russia; (T.O.A.); (E.E.D.); (M.A.K.); (A.N.T.)
| | - Mikhail A. Khodorkovskii
- Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 Saint-Petersburg, Russia; (T.O.A.); (E.E.D.); (M.A.K.); (A.N.T.)
- Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str., 195251 Saint-Petersburg, Russia
| | - Alexey N. Tomilin
- Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 Saint-Petersburg, Russia; (T.O.A.); (E.E.D.); (M.A.K.); (A.N.T.)
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10
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Karim MR, Fisher CR, Kapphahn RJ, Polanco JR, Ferrington DA. Investigating AKT activation and autophagy in immunoproteasome-deficient retinal cells. PLoS One 2020; 15:e0231212. [PMID: 32275682 PMCID: PMC7147741 DOI: 10.1371/journal.pone.0231212] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/18/2020] [Indexed: 12/04/2022] Open
Abstract
Two major proteolytic systems, the proteasome and the autophagy pathway, are key components of the proteostasis network. The immunoproteasome, a proteasome subtype, and autophagy are upregulated under stress conditions, forming a coordinated unit designed to minimize the effect of cell stress. We investigated how genetic ablation of the LMP2 immunoproteasome subunit affects autophagy in retinal pigment epithelium (RPE) from WT and LMP2 knockout mice. We monitored autophagy regulation by measuring LC3, phosphorylation of AKT (S473), and phosphorylation of S6, a downstream readout of AKT (mTOR) pathway activation. We also evaluated transcription factor EB (TFEB) nuclear translocation, a transcription factor that controls expression of autophagy and lysosome genes. WT and LMP2 KO cells were monitored after treatment with EBSS to stimulate autophagy, insulin to stimulate AKT, or an AKT inhibitor (trehalose or MK-2206). Under basal conditions, we observed hyper-phosphorylation of AKT and S6, as well as lower nuclear-TFEB content in LMP2 KO RPE compared with WT. AKT inhibitors MK-2206 and trehalose significantly inhibited AKT phosphorylation and stimulated nuclear translocation of TFEB. Starvation and AKT inhibition upregulated autophagy, albeit to a lesser extent in LMP2 KO RPE. These data support the idea that AKT hyper-activation is an underlying cause of defective autophagy regulation in LMP2 KO RPE, revealing a unique link between two proteolytic systems and a previously unknown function in autophagy regulation by the immunoproteasome.
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Affiliation(s)
- Md. Razaul Karim
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Cody R. Fisher
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States of America
- Graduate Program in Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Rebecca J. Kapphahn
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jorge R. Polanco
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Deborah A. Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, United States of America
- Graduate Program in Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
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11
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Schipper-Krom S, Sanz AS, van Bodegraven EJ, Speijer D, Florea BI, Ovaa H, Reits EA. Visualizing Proteasome Activity and Intracellular Localization Using Fluorescent Proteins and Activity-Based Probes. Front Mol Biosci 2019; 6:56. [PMID: 31482094 PMCID: PMC6710370 DOI: 10.3389/fmolb.2019.00056] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
The proteasome is a multi-catalytic molecular machine that plays a key role in the degradation of many cytoplasmic and nuclear proteins. The proteasome is essential and proteasome malfunction is associated with various disease pathologies. Proteasome activity depends on its catalytic subunits which are interchangeable and also on the interaction with the associated regulatory cap complexes. Here, we describe and compare various methods that allow the study of proteasome function in living cells. Methods include the use of fluorescently tagged proteasome subunits and the use of activity-based proteasome probes. These probes can be used in both biochemical assays and in microscopy-based experiments. Together with tagged proteasomes, they can be used to study proteasome localization, dynamics, and activity.
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Affiliation(s)
- Sabine Schipper-Krom
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Alicia Sanz Sanz
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Emma J. van Bodegraven
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Bogdan I. Florea
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Eric A. Reits
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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12
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Lesne J, Bousquet MP, Marcoux J, Locard-Paulet M. Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS. Bioinform Biol Insights 2019; 13:1177932219868223. [PMID: 31452600 PMCID: PMC6698994 DOI: 10.1177/1177932219868223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 12/04/2022] Open
Abstract
The rise of intact protein analysis by mass spectrometry (MS) was accompanied by
an increasing need for flexible tools allowing data visualization and analysis.
These include inspection of the deconvoluted molecular weights of the
proteoforms eluted alongside liquid chromatography (LC) through their
representation in three-dimensional (3D) liquid chromatography coupled to mass
spectrometry (LC-MS) maps (plots of deconvoluted molecular weights, retention
times, and intensity of the MS signal). With this aim, we developed a free and
open-source web application named VisioProt-MS (https://masstools.ipbs.fr/mstools/visioprot-ms/). VisioProt-MS
is highly compatible with many algorithms and software developed by the
community to integrate and deconvolute top-down and intact protein MS data. Its
dynamic and user-friendly features greatly facilitate analysis through several
graphical representations dedicated to MS and tandem mass spectrometry (MS/MS)
analysis of proteoforms in complex samples. Here, we will illustrate the
importance of LC-MS map visualization to optimize top-down acquisition/search
parameters and analyze intact protein MS data. We will go through the main
features of VisioProt-MS using the human proteasomal 20S core particle as a
user-case.
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Affiliation(s)
- Jean Lesne
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Pierre Bousquet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie Locard-Paulet
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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13
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Ganesan M, Krutik VM, Makarov E, Mathews S, Kharbanda KK, Poluektova LY, Casey CA, Osna NA. Acetaldehyde suppresses the display of HBV-MHC class I complexes on HBV-expressing hepatocytes. Am J Physiol Gastrointest Liver Physiol 2019; 317:G127-G140. [PMID: 31141391 PMCID: PMC6734374 DOI: 10.1152/ajpgi.00064.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hepatitis B virus (HBV) infection and alcoholism are major public health problems worldwide, contributing to the development of end-stage liver disease. Alcohol intake affects HBV infection pathogenesis and treatment outcomes. HBV-specific cytotoxic T lymphocytes (CTLs) play an important role in HBV clearance. Many previous studies have focused on alcohol-induced impairments of the immune response. However, it is not clear whether alcohol alters the presentation of HBV peptide-major histocompatibility complex (MHC) class I complexes on infected hepatocytes resulting in escape of its recognition by CTLs. Hence, the focus of this study was to investigate the mechanisms by which ethanol metabolism affects the presentation of CTL epitope on HBV-infected hepatocytes. As demonstrated here, although continuous cell exposure to acetaldehyde-generating system (AGS) increased HBV load in HepG2.2.15 cells, it decreased the expression of HBV core peptide 18-27-human leukocyte antigen-A2complex (CTL epitope) on the cell surface. Moreover, we observed AGS-induced suppression of chymotrypsin- and trypsin-like proteasome activities necessary for peptide processing by proteasome as well as a decline in IFNγ-stimulated immunoproteasome (IPR) function and expression of PA28 activator and immunoproteasome subunits LMP7 and LMP2. Furthermore, IFNγ-induced activation of peptide-loading complex (PLC) components, such as transporter associated with antigen processing (TAP1) and tapasin, were suppressed by AGS. The attenuation of IPR and PLC activation was attributed to AGS-triggered impairment of IFNγ signaling in HepG2.2.15 cells. Collectively, all these downstream events reduced the display of HBV peptide-MHC class I complexes on the hepatocyte surface, which may suppress CTL activation and the recognition of CTL epitopes on HBV-expressing hepatocytes by immune cells, thereby leading to persistence of liver inflammation.NEW & NOTEWORTHY Our study shows that in HBV-expressing HepG2.2.15 cells, acetaldehyde alters HBV peptide processing by suppressing chymotrypsin- and trypsin-like proteasome activities and decreases IFNγ-stimulated immunoproteasome function and expression of PA28 activator and immunoproteasome subunits. It also suppresses IFNγ-induced activation of peptide-loading complex (PLC) components due to impairment of IFNγ signaling via the JAK-STAT1 pathway. These acetaldehyde-induced dysfunctions reduced the display of HBV peptide-MHC class I complexes on the hepatocyte surface, thereby leading to persistence of HBV infection.
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Affiliation(s)
- Murali Ganesan
- Research Service, Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, Nebraska
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Vjaceslav M Krutik
- Research Service, Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, Nebraska
| | - Edward Makarov
- Department of Pharmacology and Experimental Neuroscience, Omaha, Nebraska
| | - Saumi Mathews
- Department of Pharmacology and Experimental Neuroscience, Omaha, Nebraska
| | - Kusum K Kharbanda
- Research Service, Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, Nebraska
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Carol A Casey
- Research Service, Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, Nebraska
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Natalia A Osna
- Research Service, Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, Nebraska
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
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14
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Zanker D, Pang K, Oveissi S, Lu C, Faou P, Nowell C, Mbogo GW, Carotta S, Quillici C, Karupiah G, Hibbs ML, Nutt SL, Neeson P, Puthalakath H, Chen W. LMP2 immunoproteasome promotes lymphocyte survival by degrading apoptotic BH3-only proteins. Immunol Cell Biol 2018; 96:981-993. [PMID: 29738610 DOI: 10.1111/imcb.12163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/09/2018] [Accepted: 05/02/2018] [Indexed: 11/28/2022]
Abstract
The role of the immunoproteasome is perceived as confined to adaptive immune responses given its ability to produce peptides ideal for MHC Class-I binding. Here, we demonstrate that the immunoproteasome subunit, LMP2, has functions beyond its immunomodulatory role. Using LMP2-deficient mice, we demonstrate that LMP2 is crucial for lymphocyte development and survival in the periphery. Moreover, LMP2-deficient lymphocytes show impaired degradation of key BH3-only proteins, resulting in elevated levels of pro-apoptotic BIM and increased cell death. Interestingly, LMP2 is the sole immunoproteasome subunit required for BIM degradation. Together, our results suggest LMP2 has important housekeeping functions and represents a viable therapeutic target for cancer.
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Affiliation(s)
- Damien Zanker
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, Australia
| | - Kenneth Pang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Australia.,Department of Psychiatry, University of Melbourne, Parkville, Australia.,Murdoch Children's Research Institute, Parkville, Australia
| | - Sara Oveissi
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, Australia
| | - Chunni Lu
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, Australia
| | - Pierre Faou
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, Australia
| | - Cameron Nowell
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - George W Mbogo
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, Australia
| | - Sebastian Carotta
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Australia
| | - Cathy Quillici
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Guna Karupiah
- Australian National University School of Medicine & College of Health and Medicine & University of Tasmania, Hobart, Australia
| | - Margaret L Hibbs
- Department of Immunology and Pathology, Monash University, AMREP Melbourne, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Australia
| | - Paul Neeson
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Hamsa Puthalakath
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, Australia
| | - Weisan Chen
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, Australia
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15
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Hewing B, Ludwig A, Dan C, Pötzsch M, Hannemann C, Petry A, Lauer D, Görlach A, Kaschina E, Müller DN, Baumann G, Stangl V, Stangl K, Wilck N. Immunoproteasome subunit ß5i/LMP7-deficiency in atherosclerosis. Sci Rep 2017; 7:13342. [PMID: 29042581 PMCID: PMC5645401 DOI: 10.1038/s41598-017-13592-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 08/17/2017] [Indexed: 12/23/2022] Open
Abstract
Management of protein homeostasis by the ubiquitin-proteasome system is critical for atherosclerosis development. Recent studies showed controversial results on the role of immunoproteasome (IP) subunit β5i/LMP7 in maintenance of protein homeostasis under cytokine induced oxidative stress. The present study aimed to investigate the effect of β5i/LMP7-deficiency on the initiation and progression of atherosclerosis as a chronic inflammatory, immune cell driven disease. LDLR-/-LMP7-/- and LDLR-/- mice were fed a Western-type diet for either 6 or 24 weeks to induce early and advanced stage atherosclerosis, respectively. Lesion burden was similar between genotypes in both stages. Macrophage content and abundance of polyubiquitin conjugates in aortic root plaques were unaltered by β5i/LMP7-deficiency. In vitro experiments using bone marrow-derived macrophages (BMDM) showed that β5i/LMP7-deficiency did not influence macrophage polarization or accumulation of polyubiquitinated proteins and cell survival upon hydrogen peroxide and interferon-γ treatment. Analyses of proteasome core particle composition by Western blot revealed incorporation of standard proteasome subunits in β5i/LMP7-deficient BMDM and spleen. Chymotrypsin-, trypsin- and caspase-like activities assessed by using short fluorogenic peptides in BMDM whole cell lysates were similar in both genotypes. Taken together, deficiency of IP subunit β5i/LMP7 does not disturb protein homeostasis and does not aggravate atherogenesis in LDLR-/- mice.
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Affiliation(s)
- Bernd Hewing
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Antje Ludwig
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Cristian Dan
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Max Pötzsch
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Carmen Hannemann
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Andreas Petry
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich, Munich, Germany
| | - Dilyara Lauer
- Institute of Pharmacology, Center for Cardiovascular Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Agnes Görlach
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich, Technical University Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich, Munich, Germany
| | - Elena Kaschina
- Institute of Pharmacology, Center for Cardiovascular Research, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik N Müller
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a joint cooperation of Max Delbrück Center for Molecular Medicine and Charité Medical Faculty, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Gert Baumann
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
| | - Verena Stangl
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Karl Stangl
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Nicola Wilck
- Medizinische Klinik m.S. Kardiologie und Angiologie, Charité-Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany.
- Experimental and Clinical Research Center, a joint cooperation of Max Delbrück Center for Molecular Medicine and Charité Medical Faculty, Berlin, Germany.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
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16
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Gilda JE, Gomes AV. Proteasome dysfunction in cardiomyopathies. J Physiol 2017; 595:4051-4071. [PMID: 28181243 DOI: 10.1113/jp273607] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) plays a critical role in removing unwanted intracellular proteins and is involved in protein quality control, signalling and cell death. Because the heart is subject to continuous metabolic and mechanical stress, the proteasome plays a particularly important role in the heart, and proteasome dysfunction has been suggested as a causative factor in cardiac dysfunction. Proteasome impairment has been detected in cardiomyopathies, heart failure, myocardial ischaemia, and hypertrophy. Proteasome inhibition is also sufficient to cause cardiac dysfunction in healthy pigs, and patients using a proteasome inhibitor for cancer therapy have a higher incidence of heart failure. In this Topical Review we discuss the experimental data which suggest UPS dysfunction is a common feature of cardiomyopathies, with an emphasis on hypertrophic cardiomyopathy caused by sarcomeric mutations. We also propose potential mechanisms by which cardiomyopathy-causing mutations may lead to proteasome impairment, such as altered calcium handling and increased oxidative stress due to mitochondrial dysfunction.
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Affiliation(s)
- Jennifer E Gilda
- Department of Neurobiology, Physiology, and Behaviour, University of California, Davis, CA, 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology, and Behaviour, University of California, Davis, CA, 95616, USA.,Department of Physiology and Membrane Biology, University of California, Davis, CA, 95616, USA
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17
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Abstract
Ischemic disorders, such as myocardial infarction, stroke, and peripheral vascular disease, are the most common causes of debilitating disease and death in westernized cultures. The extent of tissue injury relates directly to the extent of blood flow reduction and to the length of the ischemic period, which influence the levels to which cellular ATP and intracellular pH are reduced. By impairing ATPase-dependent ion transport, ischemia causes intracellular and mitochondrial calcium levels to increase (calcium overload). Cell volume regulatory mechanisms are also disrupted by the lack of ATP, which can induce lysis of organelle and plasma membranes. Reperfusion, although required to salvage oxygen-starved tissues, produces paradoxical tissue responses that fuel the production of reactive oxygen species (oxygen paradox), sequestration of proinflammatory immunocytes in ischemic tissues, endoplasmic reticulum stress, and development of postischemic capillary no-reflow, which amplify tissue injury. These pathologic events culminate in opening of mitochondrial permeability transition pores as a common end-effector of ischemia/reperfusion (I/R)-induced cell lysis and death. Emerging concepts include the influence of the intestinal microbiome, fetal programming, epigenetic changes, and microparticles in the pathogenesis of I/R. The overall goal of this review is to describe these and other mechanisms that contribute to I/R injury. Because so many different deleterious events participate in I/R, it is clear that therapeutic approaches will be effective only when multiple pathologic processes are targeted. In addition, the translational significance of I/R research will be enhanced by much wider use of animal models that incorporate the complicating effects of risk factors for cardiovascular disease. © 2017 American Physiological Society. Compr Physiol 7:113-170, 2017.
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Affiliation(s)
- Theodore Kalogeris
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Christopher P. Baines
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, Missouri, USA
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
- Department of Biomedical Sciences, University of Missouri College of Veterinary Medicine, Columbia, Missouri, USA
| | - Maike Krenz
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, Missouri, USA
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
| | - Ronald J. Korthuis
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, Missouri, USA
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA
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18
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Song H, Xiong H, Che J, Xi QS, Huang L, Xiong HH, Zhang P. Gel-based chemical cross-linking analysis of 20S proteasome subunit-subunit interactions in breast cancer. ACTA ACUST UNITED AC 2016; 36:564-570. [PMID: 27465334 DOI: 10.1007/s11596-016-1626-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 12/29/2022]
Abstract
The ubiquitin-proteasome system plays a pivotal role in breast tumorigenesis by controlling transcription factors, thus promoting cell cycle growth, and degradation of tumor suppressor proteins. However, breast cancer patients have failed to benefit from proteasome inhibitor treatment partially due to proteasome heterogeneity, which is poorly understood in malignant breast neoplasm. Chemical crosslinking is an increasingly important tool for mapping protein three-dimensional structures and proteinprotein interactions. In the present study, two cross-linkers, bis (sulfosuccinimidyl) suberate (BS(3)) and its water-insoluble analog disuccinimidyl suberate (DSS), were used to map the subunit-subunit interactions in 20S proteasome core particle (CP) from MDA-MB-231 cells. Different types of gel electrophoresis technologies were used. In combination with chemical cross-linking and mass spectrometry, we applied these gel electrophoresis technologies to the study of the noncovalent interactions among 20S proteasome subunits. Firstly, the CP subunit isoforms were profiled. Subsequently, using native/SDSPAGE, it was observed that 0.5 mmol/L BS(3) was a relatively optimal cross-linking concentration for CP subunit-subunit interaction study. 2-DE analysis of the cross-linked CP revealed that α1 might preinteract with α2, and α3 might pre-interact with α4. Moreover, there were different subtypes of α1α2 and α3α4 due to proteasome heterogeneity. There was no significant difference in cross-linking pattern for CP subunits between BS(3) and DSS. Taken together, the gel-based characterization in combination with chemical cross-linking could serve as a tool for the study of subunit interactions within a multi-subunit protein complex. The heterogeneity of 20S proteasome subunit observed in breast cancer cells may provide some key information for proteasome inhibition strategy.
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Affiliation(s)
- Hai Song
- Department of Scientific Research and Teaching, Tangshan People's Hospital, Tangshan, 063001, China
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Che
- National Biological Experimental Teaching Demonstration Center, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qing-Song Xi
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Liu Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hui-Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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19
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de Bruin G, Xin BT, Florea BI, Overkleeft HS. Proteasome Subunit Selective Activity-Based Probes Report on Proteasome Core Particle Composition in a Native Polyacrylamide Gel Electrophoresis Fluorescence-Resonance Energy Transfer Assay. J Am Chem Soc 2016; 138:9874-80. [PMID: 27428761 DOI: 10.1021/jacs.6b04207] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most mammalian tissues contain a single proteasome species: constitutive proteasomes. Tissues able to express, next to the constitutive proteasome catalytic activities (β1c, β2c, β5c), the three homologous activities, β1i, β2i and β5i, may contain numerous distinct proteasome particles: immunoproteasomes (composed of β1i, β2i and β5i) and mixed proteasomes containing a mix of these activities. This work describes the development of new subunit-selective activity-based probes and their use in an activity-based protein profiling assay that allows the detection of various proteasome particles. Tissue extracts are treated with subunit-specific probes bearing distinct fluorophores and subunit-specific inhibitors. The samples are resolved by native polyacrylamide gel electrophoresis, after which fluorescence-resonance energy transfer (FRET) reports on the nature of proteasomes present.
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Affiliation(s)
- Gerjan de Bruin
- Gorlaeus Laboratories, Leiden Institute of Chemistry , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bo-Tao Xin
- Gorlaeus Laboratories, Leiden Institute of Chemistry , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bogdan I Florea
- Gorlaeus Laboratories, Leiden Institute of Chemistry , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S Overkleeft
- Gorlaeus Laboratories, Leiden Institute of Chemistry , Einsteinweg 55, 2333 CC Leiden, The Netherlands
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20
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Bergallo M, Loiacono E, Gambarino S, Vergano L, Tavormina P. Standard and immunoproteasome expression in pediatric tonsillectomy patients. Minerva Pediatr 2016; 72:159-162. [PMID: 27167592 DOI: 10.23736/s0026-4946.16.04463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Pro-inflammatory cytokines including TNF-α and IFN-γ, play an important role during the recurrent tonsillitis illness and proteasome and immunoproteasome stimulation. METHODS mRNA expression analysis of proteasome and immunoproteasome subunits was performed by PBMC whole blood isolation from children tonsillectomy patients. Total RNA was extracted from PBMC and retro-transcribed in cDNA. A real-time PCR with TaqMan probe was then performed. RESULTS PBMC of children with tonsillectomy showed, a significantly increased expression of proteasome constitutive subunit β2 encoding (1.52±0.61 vs. 0.88±0.5, P<0.0001) compared to healthy controls (HC). The same results were observed for immunoproteasome inducible subunit LMP2 (2.55±1.95 vs. 0.73±0.49, P<0.001), LMP7 (1.94±1.18 vs. 0.79±0.41, P<0.001), MECL1 (1.97±1.20 vs. 0.79±0.41, P<0.001). No differences were observed for proteasome subunit β1. Conversely a significantly decreased expression of proteasome constitutive subunit β5 encoding mRNA (0.96±0.39 vs. 1.28±0.65, P=0.0291) was observed. CONCLUSIONS In children with recurrent tonsillitis was observed an increased expression of β2, the corresponding iPS, β1i and β5i compared to healthy controls. Contrariwise β5 subunit mRNA expression was significantly decreased.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy - .,Laboratory of Cytoimmunodiagnostics, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Turin, Italy -
| | - Elisa Loiacono
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy.,Laboratory of Cytoimmunodiagnostics, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Turin, Italy
| | - Stefano Gambarino
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy.,Laboratory of Cytoimmunodiagnostics, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Turin, Italy
| | - Luca Vergano
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy.,Laboratory of Cytoimmunodiagnostics, Regina Margherita Children's Hospital, Città della Salute e della Scienza, Turin, Italy
| | - Paolo Tavormina
- Unit of Otorhinolaryngology, Regina Margherita Children's Hospital, Turin, Italy
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21
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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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22
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Mammalian proteasome subtypes: Their diversity in structure and function. Arch Biochem Biophys 2015; 591:132-40. [PMID: 26724758 DOI: 10.1016/j.abb.2015.12.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 12/22/2015] [Indexed: 11/21/2022]
Abstract
The 20S proteasome is a multicatalytic proteinase catalysing the degradation of the majority of intracellular proteins. Thereby it is involved in almost all basic cellular processes, which is facilitated by its association with various regulator complexes so that it appears in different disguises like 26S proteasome, hybrid-proteasome and others. The 20S proteasome has a cylindrical structure built up by four stacked rings composed of α- and β-subunits. Since the three active site-containing β-subunits can all or in part be replaced by immuno-subunits, three main subpopulations exist, namely standard-, immuno- and intermediate-proteasomes. Due to posttranslational modifications or/and genetic variations all α- and β-subunits occur in multiple iso- or proteoforms. This leads to the fact that each of the three subpopulations is composed of a variety of 20S proteasome subtypes. This review summarizes the knowledge of proteasome subtypes in mammalian cells and tissues and their possible biological and medical relevancy.
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23
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Zhang H, Wang X. Priming the proteasome by protein kinase G: a novel cardioprotective mechanism of sildenafil. Future Cardiol 2015; 11:177-89. [PMID: 25760877 DOI: 10.2217/fca.15.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The proteasome mediates the degradation of most cellular proteins including misfolded proteins, pivotal to intracellular protein hemostasis. Proteasome functional insufficiency is implicated in a large subset of human failing hearts. Experimental studies have established proteasome functional insufficiency as a major pathogenic factor, rationalizing proteasome enhancement as a potentially new therapeutic strategy for congestive heart failure. Protein kinase G activation known to be cardioprotective was recently found to facilitate proteasomal degradation of misfolded proteins in cardiomyocytes; sildenafil was shown to activate myocardial protein kinase G, improve cardiac protein quality control and slow down the progression of cardiac proteinopathy in mice. This identifies the first clinically used drug that is capable of benign proteasome enhancement and unveils a potentially novel cardioprotective mechanism for sildenafil.
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Affiliation(s)
- Hanming Zhang
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA
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Zanker D, Chen W. Standard and immunoproteasomes show similar peptide degradation specificities. Eur J Immunol 2015; 44:3500-3. [PMID: 25399798 DOI: 10.1002/eji.201445272] [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: 11/05/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 11/06/2022]
Abstract
Vertebrates have evolved to express major histocompatibility complexes (MHCs) that present peptides of the intra-cellular proteome for immunosurveillance against viruses and tumor. The MHC class I (MHC-I) processing and presentation pathway allows for scrutiny of all cellular proteins and peptides by CD8(+) cytotoxic T cells. The proteasome is part of the specialised machinery that degrades proteins down to peptides with the correct sequence for MHC-I binding. However, much conjecture lies as to how the various proteasome isoforms and their active subunits create antigenic peptides, and if the specialised immunoproteasome solely performs this job. In this issue of the European Journal of Immunology, Mishto et al. [Eur. J. Immunol. 2014. 44: 3508-3521] address this question through systematic biochemical peptide degradation studies and provide new insights into the functions of proteasome β-subunits.
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Affiliation(s)
- Damien Zanker
- School of Molecular Science, La Trobe University, Bundoora, Victoria, Australia
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Abstract
This chapter presents two methods for assessment of proteasome function. The first is a modification of the standard fluorogenic peptide cleavage assay which takes into account the effect of ATP on proteasome activity. This method is described in both its macro and high throughput micro-assay forms. The second is the Proteasome Constitutive Immuno-Subunit (active site) ELISA or ProCISE method. ProCISE is a modification of active site directed probe analysis and allows for convenient differentiation between active constitutive and immuno-subunits. While the utility of measuring proteasome activity and its relationship to cytokine action and inflammation are clear, the assessment and interpretation is not always straightforward. Therefore, we also discuss the pitfalls of the standard fluorogenic assay, particularly in the interpretation of results obtained, and the advantages of the newer, ProCISE assay.
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Affiliation(s)
- Christopher J Kirk
- Onyx Pharmaceuticals, 249 Grand Avenue South, San Francisco, CA, 94080, USA
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Paniagua Soriano G, De Bruin G, Overkleeft HS, Florea BI. Toward understanding induction of oxidative stress and apoptosis by proteasome inhibitors. Antioxid Redox Signal 2014; 21:2419-43. [PMID: 24437477 DOI: 10.1089/ars.2013.5794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SIGNIFICANCE Proteasome inhibitors (PIs) are used in the clinic for the treatment of hematopoietic malignancies. PI inhibitors induce endoplasmatic reticulum (ER) stress and oxidative stress, disruption of signaling pathways, mitochondrial dysfunction, and, eventually, cell death by apoptosis. PIs designated as clinical candidates include natural product derivatives and compounds developed by rational design and feature a wide diversity of structural elements. The vast amount of literature on this topic underscores PIs significance in driving basic research alongside therapeutic benefit. RECENT ADVANCES Research in recent years has brought an in-depth insight into the molecular mechanisms of PI-induced apoptosis. However, there are some paradoxes and controversies in the literature. In this review, the advances and uncertainties, in particular on the time course events that make cells commit to apoptosis, are discussed. In addition, some mechanisms of evolved PI resistance are presented, and speculations on the difference in sensitivity between cell or tumor types are brought forward. The review concludes by giving an outlook of recent methods that may be employed to describe the system biology of how PIs impact cell survival decisions. CRITICAL ISSUES The biology of ER stress, reactive oxygen species (ROS) production, and apoptosis as induced by PIs is not well understood. Absorbed by the strong focus on PIs, one might overlook the importance of proteasome activity activators or modulators and the study of enzymatic pathways that lie up- or downstream from the proteasome function. FUTURE DIRECTIONS An increased understanding of the systems biology at mRNA and protein levels and the kinetics behind the interaction between PIs and cells is imperative. The design and synthesis of subunit specific inhibitors for each of the seven known proteasome activities and for the enzymes associated to proteasomes will aid in unraveling biology of the ubiquitin-proteasome system in relation to ER stress, ROS production, and apoptosis and will generate leads for therapeutic intervention.
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Affiliation(s)
- Guillem Paniagua Soriano
- Gorlaeus Laboratories, Leiden Institute of Chemistry and Netherlands Proteomics Centre , Leiden, The Netherlands
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Drews O, Taegtmeyer H. Targeting the ubiquitin-proteasome system in heart disease: the basis for new therapeutic strategies. Antioxid Redox Signal 2014; 21:2322-43. [PMID: 25133688 PMCID: PMC4241867 DOI: 10.1089/ars.2013.5823] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
SIGNIFICANCE Novel therapeutic strategies to treat heart failure are greatly needed. The ubiquitin-proteasome system (UPS) affects the structure and function of cardiac cells through targeted degradation of signaling and structural proteins. This review discusses both beneficial and detrimental consequences of modulating the UPS in the heart. RECENT ADVANCES Proteasome inhibitors were first used to test the role of the UPS in cardiac disease phenotypes, indicating therapeutic potential. In early cardiac remodeling and pathological hypertrophy with increased proteasome activities, proteasome inhibition prevented or restricted disease progression and contractile dysfunction. Conversely, enhancing proteasome activities by genetic manipulation, pharmacological intervention, or ischemic preconditioning also improved the outcome of cardiomyopathies and infarcted hearts with impaired cardiac and UPS function, which is, at least in part, caused by oxidative damage. CRITICAL ISSUES An understanding of the UPS status and the underlying mechanisms for its potential deregulation in cardiac disease is critical for targeted interventions. Several studies indicate that type and stage of cardiac disease influence the dynamics of UPS regulation in a nonlinear and multifactorial manner. Proteasome inhibitors targeting all proteasome complexes are associated with cardiotoxicity in humans. Furthermore, the type and dosage of proteasome inhibitor impact the pathogenesis in nonuniform ways. FUTURE DIRECTIONS Systematic analysis and targeting of individual UPS components with established and innovative tools will unravel and discriminate regulatory mechanisms that contribute to and protect against the progression of cardiac disease. Integrating this knowledge in drug design may reduce adverse effects on the heart as observed in patients treated with proteasome inhibitors against noncardiac diseases, especially cancer.
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Affiliation(s)
- Oliver Drews
- 1 Division of Cardiovascular Physiology, Institute of Physiology and Pathophysiology , Heidelberg University, Heidelberg, Germany
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Abstract
SIGNIFICANCE Impairment of the ubiquitin-proteasome system (UPS) has been implicated in the pathogenesis of a wide variety of neurodegenerative disorders, including Alzheimer's, Parkinson's, and Huntington's diseases. The most significant risk factor for the development of these disorders is aging, which is associated with a progressive decline in UPS activity and the accumulation of oxidatively modified proteins. To date, no therapies have been developed that can specifically up-regulate this system. RECENT ADVANCES In the neurodegenerative brain, dysfunction of the UPS has been associated with the deposition of ubiquitinated protein aggregates and widespread disruption of the proteostasis network. Recent research has identified further evidence of impairment in substrate ubiquitination and proteasomal degradation, which could contribute to the loss of cellular proteostasis in neurodegenerative disease. Novel strategies for activation of the UPS by genetic manipulation and treatment with synthetic compounds have also recently been identified. CRITICAL ISSUES Here, we discuss the specific roles of the UPS in the healthy central nervous system and establish how dysfunctional components can contribute to neurotoxicity in the context of disease. FUTURE DIRECTIONS Knowledge of the UPS components that are specifically or preferentially involved in neurodegenerative disease will be critical in the development of targeted therapies which aim at limiting the accumulation of misfolded proteins without gross disturbance of this major proteolytic pathway.
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Affiliation(s)
- Chris McKinnon
- Department of Neurodegenerative Disease, University College London Institute of Neurology , London, United Kingdom
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Kaake RM, Kao A, Yu C, Huang L. Characterizing the dynamics of proteasome complexes by proteomics approaches. Antioxid Redox Signal 2014; 21:2444-56. [PMID: 24423446 PMCID: PMC4241863 DOI: 10.1089/ars.2013.5815] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
SIGNIFICANCE The proteasome is the degradation machine of the ubiquitin-proteasome system, which is critical in controlling many essential biological processes. Aberrant regulation of proteasome-dependent protein degradation can lead to various human diseases, and general proteasome inhibitors have shown efficacy for cancer treatments. Though clinically effective, current proteasome inhibitors have detrimental side effects and, thus, better therapeutic strategies targeting proteasomes are needed. Therefore, a comprehensive characterization of proteasome complexes will provide the molecular details that are essential for developing new and improved drugs. RECENT ADVANCES New mass spectrometry (MS)-based proteomics approaches have been developed to study protein interaction networks and structural topologies of proteasome complexes. The results have helped define the dynamic proteomes of proteasome complexes, thus providing new insights into the mechanisms underlying proteasome function and regulation. CRITICAL ISSUES The proteasome exists as heterogeneous populations in tissues/cells, and its proteome is highly dynamic and complex. In addition, proteasome complexes are regulated by various mechanisms under different physiological conditions. Consequently, complete proteomic profiling of proteasome complexes remains a major challenge for the field. FUTURE DIRECTIONS We expect that proteomic methodologies enabling full characterization of proteasome complexes will continue to evolve. Further advances in MS instrumentation and protein separation techniques will be needed to facilitate the detailed proteomic analysis of low-abundance components and subpopulations of proteasome complexes. The results will help us understand proteasome biology as well as provide new therapeutic targets for disease diagnostics and treatment.
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Affiliation(s)
- Robyn M Kaake
- Department of Physiology and Biophysics, University of California , Irvine, Irvine, California
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Cornish Carmony K, Sharma LK, Lee DM, Park JE, Lee W, Kim KB. Elucidating the catalytic subunit composition of distinct proteasome subtypes: a crosslinking approach employing bifunctional activity-based probes. Chembiochem 2014; 16:284-92. [PMID: 25477005 DOI: 10.1002/cbic.201402491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Indexed: 12/25/2022]
Abstract
In addition to two well-recognized proteasome subtypes-constitutive proteasomes and immunoproteasomes-mounting evidence also suggests the existence of intermediate proteasome subtypes containing unconventional mixtures of catalytic subunits. Although they appear to play unique biological roles, the lack of practical methods for detecting distinct proteasome subtypes has limited functional investigations. Here, we report the development of activity-based probes that crosslink two catalytic subunits within intact proteasome complexes. Identification of the crosslinked subunit pairs provides direct evidence of the catalytic subunit composition of proteasomes. Using these probes, we found that U266 multiple myeloma cells contain intermediate proteasomes comprising both β1i and β2, but not β1 and β2i, consistent with previous findings with other cell types. Our bifunctional probes can be utilized in functional investigations of distinct proteasome subtypes in various biological settings.
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Affiliation(s)
- Kimberly Cornish Carmony
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536-0596 (USA)
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31
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Ortega Z, Lucas JJ. Ubiquitin-proteasome system involvement in Huntington's disease. Front Mol Neurosci 2014; 7:77. [PMID: 25324717 PMCID: PMC4179678 DOI: 10.3389/fnmol.2014.00077] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/10/2014] [Indexed: 11/13/2022] Open
Abstract
Huntington’s disease (HD) is a genetic autosomal dominant neurodegenerative disease caused by the expansion of a CAG repeat in the huntingtin (htt) gene. This triplet expansion encodes a polyglutamine stretch (polyQ) in the N-terminus of the high molecular weight (348-kDa) and ubiquitously expressed protein htt. Normal individuals have between 6 and 35 CAG triplets, while expansions longer than 40 repeats lead to HD. The onset and severity of the disease depend on the length of the polyQ tract: the longer the polyglutamine stretch (polyQ) is, the earlier the disease begins and the more severe the symptoms are. One of the main histopathological hallmarks of HD is the presence of intraneuronal proteinaceous inclusion bodies, whose prominent and invariant feature is the presence of ubiquitin (Ub); therefore, they can be detected with anti-ubiquitin and anti-proteasome antibodies. This, together with the observation that mutations in components of the ubiquitin–proteasome system (UPS) give rise to some neurodegenerative diseases, suggests that UPS impairment may be causative of HD. Even though the link between disrupted Ub homeostasis and protein aggregation to HD is undisputed, the functional significance of these correlations and their mechanistic implications remains unresolved. Moreover, there is no consistent evidence documenting an accompanying decrease in levels of free Ub or disruption of Ub pool dynamics in neurodegenerative disease or models thus suggesting that the Ub-conjugate accumulation may be benign and just underlie lesion in 26S function. In this chapter we will elaborate on the different studies that have been performed using different experimental approaches, in order to shed light to this matter.
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Affiliation(s)
- Zaira Ortega
- Department of Molecular Biology, Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Centro Investigación Biomédica en Red Enfermedades Neurodegenerativa (CIBERNED), Madrid, Spain
| | - Jose J Lucas
- Department of Molecular Biology, Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Centro Investigación Biomédica en Red Enfermedades Neurodegenerativa (CIBERNED), Madrid, Spain
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Claud EC, McDonald JAK, He SM, Yu Y, Duong L, Sun J, Petrof EO. Differential expression of 26S proteasome subunits and functional activity during neonatal development. Biomolecules 2014; 4:812-26. [PMID: 25177858 PMCID: PMC4192673 DOI: 10.3390/biom4030812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/02/2014] [Accepted: 08/19/2014] [Indexed: 01/21/2023] Open
Abstract
Proteasomes regulate many essential cellular processes by degrading intracellular proteins. While aging is known to be associated with dysfunction of the proteasome, there are few reports detailing activity and function of proteasomes in the early stages of life. To elucidate the function and development of mammalian proteasomes, 26S proteasomes were affinity-purified from rat intestine, spleen and liver. The developmental expression of core, regulatory and immunoproteasome subunits was analyzed by immunoblotting and reverse-transcriptase PCR of mRNA subunits, and proteasome catalytic function was determined by fluorogenic enzymatic assays. The expression of core (β2, β5, α7 and β1) and regulatory (Rpt5) subunits was found to be present at low levels at birth and increased over time particularly at weaning. In contrast, while gradual developmental progression of proteasome structure was also seen with the immunoproteasome subunits (β1i, β5i, and β2i), these were not present at birth. Our studies demonstrate a developmental pattern to 26S proteasome activity and subunit expression, with low levels of core proteasome components and absence of immunoproteasomes at birth followed by increases at later developmental stages. This correlates with findings from other studies of a developmental hyporesponsiveness of the adaptive immune system to allow establishment of microbial colonization immediately after birth.
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Affiliation(s)
- Erika C Claud
- Departments of Pediatrics and Medicine, University of Chicago, Chicago, IL 60611, USA.
| | - Julie A K McDonald
- Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, ON K7L 2V7, Canada.
| | - Shu-Mei He
- Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, ON K7L 2V7, Canada.
| | - Yueyue Yu
- Departments of Pediatrics and Medicine, University of Chicago, Chicago, IL 60611, USA.
| | - Lily Duong
- Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, ON K7L 2V7, Canada.
| | - Jun Sun
- Department of Biochemistry, Rush University, Chicago, IL 60612, USA.
| | - Elaine O Petrof
- Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, ON K7L 2V7, Canada.
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Drews O. The left and right ventricle in the grip of protein degradation: Similarities and unique patterns in regulation. J Mol Cell Cardiol 2014; 72:52-5. [DOI: 10.1016/j.yjmcc.2014.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 02/24/2014] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
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Park JE, Wu Y, Carmony KC, Miller Z, Sharma LK, Lee DM, Kim DY, Lee W, Kim KB. A FRET-based approach for identification of proteasome catalytic subunit composition. MOLECULAR BIOSYSTEMS 2014; 10:196-200. [PMID: 24301521 PMCID: PMC3898201 DOI: 10.1039/c3mb70471h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mammalian cells have two main types of proteasomes, the constitutive proteasome and the immunoproteasome, each containing a distinct set of three catalytic subunits. Recently, additional proteasome subtypes containing a non-standard mixture of catalytic subunits have gained increasing attention, especially due to their presence in cancer settings. However, practical methods for identifying proteasome subtypes have been lacking. Here, we report the development of the first fluorescence resonance energy transfer (FRET)-based strategy that can be utilized to identify different proteasome subtypes present within cells. We have developed FRET donor- and acceptor-probes that are based on previously reported peptide epoxyketones and selectively target individual proteasome catalytic subunits. Using the purified proteasome and cancer cell lysates, we demonstrate the feasibility of a FRET-based approach for determining the catalytic subunit composition of individual 20S proteasome subtypes. Ultimately, this approach may be utilized to study the functions of individual proteasome subtypes in cells.
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Affiliation(s)
- Ji Eun Park
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA 40536-0596.
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35
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Proteomic remodeling of proteasome in right heart failure. J Mol Cell Cardiol 2014; 66:41-52. [DOI: 10.1016/j.yjmcc.2013.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 09/13/2013] [Accepted: 10/22/2013] [Indexed: 12/30/2022]
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36
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Lübkemeier I, Andrié R, Lickfett L, Bosen F, Stöckigt F, Dobrowolski R, Draffehn AM, Fregeac J, Schultze JL, Bukauskas FF, Schrickel JW, Willecke K. The Connexin40A96S mutation from a patient with atrial fibrillation causes decreased atrial conduction velocities and sustained episodes of induced atrial fibrillation in mice. J Mol Cell Cardiol 2013; 65:19-32. [PMID: 24060583 DOI: 10.1016/j.yjmcc.2013.09.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 09/11/2013] [Accepted: 09/13/2013] [Indexed: 12/22/2022]
Abstract
Atrial fibrillation (AF) is the most common type of cardiac arrhythmia and a major cause of stroke. In the mammalian heart the gap junction proteins connexin40 (Cx40) and connexin43 (Cx43) are strongly expressed in the atrial myocardium mediating effective propagation of electrical impulses. Different heterozygous mutations in the coding region for Cx40 were identified in patients with AF. We have generated transgenic Cx40A96S mice harboring one of these mutations, the loss-of-function Cx40A96S mutation, as a model for atrial fibrillation. Cx40A96S mice were characterized by immunochemical and electrophysiological analyses. Significantly reduced atrial conduction velocities and strongly prolonged episodes of atrial fibrillation were found after induction in Cx40A96S mice. Analyses of the gating properties of Cx40A96S channels in cultured HeLa cells also revealed significantly lower junctional conductance and enhanced sensitivity voltage gating of Cx40A96S in comparison to Cx40 wild-type gap junctions. This is caused by reduced open probabilities of Cx40A96S gap junction channels, while single channel conductance remained the same. Similar to the corresponding patient, heterozygous Cx40A96S mice revealed normal expression levels and localization of the Cx40 protein. We conclude that heterozygous Cx40A96S mice exhibit prolonged episodes of induced atrial fibrillation and severely reduced atrial conduction velocities similar to the corresponding human patient.
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Affiliation(s)
- Indra Lübkemeier
- Life and Medical Sciences (LIMES) Institute, Molecular Genetics, University of Bonn, Bonn, Germany
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Minagar A, Ma W, Zhang X, Wang X, Zhang K, Alexander JS, Gonzalez-Toledo E, Albitar M. Plasma ubiquitin–proteasome system profile in patients with multiple sclerosis: correlation with clinical features, neuroimaging, and treatment with interferon-beta-1b. Neurol Res 2013; 34:611-8. [DOI: 10.1179/1743132812y.0000000055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Alireza Minagar
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Wanlong Ma
- Department of Hematopathology and OncologyQuest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Xi Zhang
- Department of Hematopathology and OncologyQuest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Xiuqiang Wang
- Department of Hematopathology and OncologyQuest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Ke Zhang
- Department of Hematopathology and OncologyQuest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | | | - Eduardo Gonzalez-Toledo
- Department of Radiology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Maher Albitar
- Department of Hematopathology and OncologyQuest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
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38
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Ferrington DA, Gregerson DS. Immunoproteasomes: structure, function, and antigen presentation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 109:75-112. [PMID: 22727420 DOI: 10.1016/b978-0-12-397863-9.00003-1] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Immunoproteasomes contain replacements for the three catalytic subunits of standard proteasomes. In most cells, oxidative stress and proinflammatory cytokines are stimuli that lead to elevated production of immunoproteasomes. Immune system cells, especially antigen-presenting cells, express a higher basal level of immunoproteasomes. A well-described function of immunoproteasomes is to generate peptides with a hydrophobic C terminus that can be processed to fit in the groove of MHC class I molecules. This display of peptides on the cell surface allows surveillance by CD8 T cells of the adaptive immune system for pathogen-infected cells. Functions of immunoproteasomes, other than generating peptides for antigen presentation, are emerging from studies in immunoproteasome-deficient mice, and are complemented by recently described diseases linked to mutations or single-nucleotide polymorphisms in immunoproteasome subunits. Thus, this growing body of literature suggests a more pleiotropic role in cell function for the immunoproteasome.
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Affiliation(s)
- Deborah A Ferrington
- Department of Ophthalmology, University of Minnesota, Minneapolis, Minnesota, USA
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39
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Wang D, Fang C, Zong NC, Liem DA, Cadeiras M, Scruggs SB, Yu H, Kim AK, Yang P, Deng M, Lu H, Ping P. Regulation of acetylation restores proteolytic function of diseased myocardium in mouse and human. Mol Cell Proteomics 2013; 12:3793-802. [PMID: 24037710 DOI: 10.1074/mcp.m113.028332] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteasome complexes play essential roles in maintaining cellular protein homeostasis and serve fundamental roles in cardiac function under normal and pathological conditions. A functional detriment in proteasomal activities has been recognized as a major contributor to the progression of cardiovascular diseases. Therefore, approaches to restore proteolytic function within the setting of the diseased myocardium would be of great clinical significance. In this study, we discovered that the cardiac proteasomal activity could be regulated by acetylation. Histone deacetylase (HDAC) inhibitors (suberoylanilide hydroxamic acid and sodium valproate) enhanced the acetylation of 20S proteasome subunits in the myocardium and led to an elevation of proteolytic capacity. This regulatory paradigm was present in both healthy and acutely ischemia/reperfusion (I/R) injured murine hearts, and HDAC inhibition in vitro restored proteolytic capacities to baseline sham levels in injured hearts. This mechanism of regulation was also viable in failing human myocardium. With 20S proteasomal complexes purified from murine myocardium treated with HDAC inhibitors in vivo, we confirmed that acetylation of 20S subunits directly, at least in part, presents a molecular explanation for the improvement in function. Furthermore, using high-resolution LC-MS/MS, we unraveled the first cardiac 20S acetylome, which identified the acetylation of nine N-termini and seven internal lysine residues. Acetylation on four lysine residues and four N-termini on cardiac proteasomes were novel discoveries of this study. In addition, the acetylation of five lysine residues was inducible via HDAC inhibition, which correlated with the enhancement of 20S proteasomal activity. Taken as a whole, our investigation unveiled a novel mechanism of proteasomal function regulation in vivo and established a new strategy for the potential rescue of compromised proteolytic function in the failing heart using HDAC inhibitors.
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Affiliation(s)
- Ding Wang
- Department of Physiology, UCLA School of Medicine, Los Angeles, California 90095
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40
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Tan C, Chen W, Wu Y, Lin J, Lin R, Tan X, Chen S. Chronic aspirin via dose-dependent and selective inhibition of cardiac proteasome possibly contributed a potential risk to the ischemic heart. Exp Gerontol 2013; 48:812-23. [PMID: 23567078 DOI: 10.1016/j.exger.2013.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 03/13/2013] [Accepted: 03/31/2013] [Indexed: 01/04/2023]
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41
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Drews O. High-resolution separation of cardiovascular proteomes: two-dimensional electrophoresis and liquid chromatography. ACTA ACUST UNITED AC 2013; 5:592. [PMID: 23074339 DOI: 10.1161/circgenetics.110.958637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Oliver Drews
- Institute of Physiology and Pathophysiology, Division of Cardiovascular Physiology, University of Heidelberg, Heidelberg, Germany.
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42
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Abstract
Maintenance of protein quality control is a critical function of the ubiquitin proteasome system (UPS). Evidence is rapidly mounting to link proteasome dysfunction with a multitude of cardiac diseases, including ischemia, reperfusion, atherosclerosis, hypertrophy, heart failure, and cardiomyopathies. Recent studies have demonstrated a remarkable level of complexity in the regulation of the UPS in the heart and suggest that our understanding of how UPS dysfunction might contribute to the pathophysiology of such a wide range of cardiac afflictions is still very limited. Whereas experimental systems, including animal models, are invaluable for exploring mechanisms and establishing pathogenicity of UPS dysfunction in cardiac disease, studies using human heart tissue provide a vital adjunct for establishing clinical relevance of experimental findings and promoting new hypotheses. Accordingly, this review will focus on UPS dysfunction in human dilated and hypertrophic cardiomyopathies and highlight areas rich for further study in this expanding field.
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Affiliation(s)
- Sharlene M Day
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA.
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Li H, Zong NC, Liang X, Kim AK, Choi JH, Deng N, Zelaya I, Lam M, Duan H, Ping P. A novel spectral library workflow to enhance protein identifications. J Proteomics 2013; 81:173-84. [PMID: 23391412 DOI: 10.1016/j.jprot.2013.01.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 01/18/2013] [Accepted: 01/26/2013] [Indexed: 10/27/2022]
Abstract
The innovations in mass spectrometry-based investigations in proteome biology enable systematic characterization of molecular details in pathophysiological phenotypes. However, the process of delineating large-scale raw proteomic datasets into a biological context requires high-throughput data acquisition and processing. A spectral library search engine makes use of previously annotated experimental spectra as references for subsequent spectral analyses. This workflow delivers many advantages, including elevated analytical efficiency and specificity as well as reduced demands in computational capacity. In this study, we created a spectral matching engine to address challenges commonly associated with a library search workflow. Particularly, an improved sliding dot product algorithm, that is robust to systematic drifts of mass measurement in spectra, is introduced. Furthermore, a noise management protocol distinguishes spectra correlation attributed from noise and peptide fragments. It enables elevated separation between target spectral matches and false matches, thereby suppressing the possibility of propagating inaccurate peptide annotations from library spectra to query spectra. Moreover, preservation of original spectra also accommodates user contributions to further enhance the quality of the library. Collectively, this search engine supports reproducible data analyses using curated references, thereby broadening the accessibility of proteomics resources to biomedical investigators. This article is part of a Special Issue entitled: From protein structures to clinical applications.
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Affiliation(s)
- Haomin Li
- Department of Physiology, UCLA School of Medicine, Los Angeles, CA 90095, USA
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Effect of chronic renal failure medium on the ubiquitin‑proteasome pathway of arterial muscle cells. Mol Med Rep 2013; 7:1021-5. [PMID: 23314938 DOI: 10.3892/mmr.2013.1269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/18/2012] [Indexed: 11/05/2022] Open
Abstract
The ubiquitin‑proteasome pathway (UPP) is involved in the occurrence and development of atherosclerosis through inhibitor of κB (IκB) degradation which activates nuclear factor-κB (NF‑κB). However, the correlation between UPP and vascular complications of uramia remains unknown. The aim of the present study was to determine whether the UPP is activated in aortic smooth muscle cells (ASMCs) when cultured with uremic serum and to examine the role of the UPP on the dysfunction of ASMCs in uremia. ASMCs were cultured with pooled normal sera or chronic renal failure sera. The mRNA expression levels for ubiquitin (Ub) and Ub-activating enzyme (E1) were analyzed using reverse transcription PCR and levels of the ubiquitinated proteins E1 and IκBα were measured using western blot analysis. The enzymatic activities of three 20S proteasomes were examined using specific fluorogenic peptide substrates. Compared with normal serum, chronic renal serum increased E1 mRNA and protein expression of rabbit ASMCs (both P<0.01). In addition, the mRNA expression of Ub also increased and the expression of IκBα was observed to decrease significantly (both P<0.01). Ubiquitinated proteins in the normal and chronic renal failure groups were not found to be significantly different, but the activity of proteasomes increased significantly (P<0.01). Chronic renal failure medium induced the activation of the UPP in ASMCs.
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Abstract
The ubiquitin proteasome system (UPS) has been the subject of intensive research over the past 20 years to define its role in normal physiology and in pathophysiology. Many of these studies have focused in on the cardiovascular system and have determined that the UPS becomes dysfunctional in several pathologies such as familial and idiopathic cardiomyopathies, atherosclerosis, and myocardial ischemia. This review presents a synopsis of the literature as it relates to the role of the UPS in myocardial ischemia. Studies have shown that the UPS is dysfunctional during myocardial ischemia, and recent studies have shed some light on possible mechanisms. Other studies have defined a role for the UPS in ischemic preconditioning which is best associated with myocardial ischemia and is thus presented here. Very recent studies have started to define roles for specific proteasome subunits and components of the ubiquitination machinery in various aspects of myocardial ischemia. Lastly, despite the evidence linking myocardial ischemia and proteasome dysfunction, there are continuing suggestions that proteasome inhibitors may be useful to mitigate ischemic injury. This review presents the rationale behind this and discusses both supportive and nonsupportive studies and presents possible future directions that may help in clarifying this controversy.
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Affiliation(s)
- Justine Calise
- Center for Heart and Lung Research, The Feinstein Institute for Medical Research, Manhasset, New York 11030, USA
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Engelke R, Becker AC, Dengjel J. The degradative inventory of the cell: proteomic insights. Antioxid Redox Signal 2012; 17:803-12. [PMID: 22074050 DOI: 10.1089/ars.2011.4393] [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: 01/22/2023]
Abstract
SIGNIFICANCE Protein degradation has been identified as being deregulated in numerous human diseases. Hence, proteins involved in proteasomal as well as lysosomal degradation are regarded as interesting potential drug targets and are thoroughly investigated in clinical studies. RECENT ADVANCES Technical advances in the field of quantitative mass spectrometry (MS)-based proteomics allow for detailed investigations of protein degradation dynamics and identifications of responsible protein-protein interaction networks enabling a systematic analysis of the degradative inventory of the cell and its underlying molecular mechanisms. CRITICAL ISSUES In the current review we outline recent technical advances and their limitations in MS-based proteomics and discuss their use for the analysis of protein dynamics involved in degradation processes. FUTURE DIRECTIONS In the next years the analysis of crosstalk between different posttranslational modifications (PTMs) will be a major focus of MS-based proteomics studies. Increasing evidence highlights the complexity of PTMs with positive and negative feedbacks being discovered. In this regard, the generation of absolute quantitative proteomic data will be essential for theoretical scientists to construct predictive network models that constitute a valuable tool for fast hypothesis testing and for explaining underlying molecular mechanisms.
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Affiliation(s)
- Rudolf Engelke
- Freiburg Institute for Advanced Studies, School of Life Science-LifeNet, University of Freiburg, Germany
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Thomas SN, Waters KM, Morgan WF, Yang AJ, Baulch JE. Quantitative proteomic analysis of mitochondrial proteins reveals prosurvival mechanisms in the perpetuation of radiation-induced genomic instability. Free Radic Biol Med 2012; 53:618-28. [PMID: 22569412 PMCID: PMC4708885 DOI: 10.1016/j.freeradbiomed.2012.03.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Revised: 03/05/2012] [Accepted: 03/27/2012] [Indexed: 11/26/2022]
Abstract
Radiation-induced genomic instability is a well-studied phenomenon that is measured as mitotically heritable genetic alterations observed in the progeny of an irradiated cell. The mechanisms that perpetuate this instability are unclear; however, a role for chronic oxidative stress has consistently been demonstrated. In the chromosomally unstable LS12 cell line, oxidative stress and genomic instability were correlated with mitochondrial dysfunction. To clarify this mitochondrial dysfunction and gain insight into the mechanisms underlying radiation-induced genomic instability we have evaluated the mitochondrial subproteome and performed quantitative mass spectrometry analysis of LS12 cells. Of 98 quantified mitochondrial proteins, 17 met criteria for fold changes and reproducibility; and 11 were statistically significant in comparison with the stable parental GM10115 cell line. Previous observations implicated defects in the electron transport chain (ETC) in the LS12 cell mitochondrial dysfunction. Proteomic analysis supports these observations, demonstrating significantly reduced levels of mitochondrial cytochrome c, the intermediary between complexes III and IV of the ETC. Results also suggest that LS12 cells compensate for ETC dysfunction and oxidative stress through increased levels of tricarboxylic acid cycle enzymes and upregulation of proteins that protect against oxidative stress and apoptosis. More than one cellular defect is likely to contribute to the genomic instability phenotype, and evaluation of gene and microRNA expression suggests that epigenetics play a role in the phenotype. These data suggest that LS12 cells have adapted mechanisms that allow survival under suboptimal conditions of oxidative stress and compromised mitochondrial function to perpetuate genomic instability.
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Affiliation(s)
- Stefani N. Thomas
- Radiation Oncology Research Laboratory, Department of Radiation Oncology, University of Maryland, Baltimore, Baltimore, MD 21201, USA
- The Greenebaum Cancer Center, University of Maryland, Baltimore, Baltimore, MD 21201, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - William F. Morgan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Austin J. Yang
- The Greenebaum Cancer Center, University of Maryland, Baltimore, Baltimore, MD 21201, USA
- Department of Anatomy and Neurobiology, University of Maryland, Baltimore, MD 21201, USA
| | - Janet E. Baulch
- Radiation Oncology Research Laboratory, Department of Radiation Oncology, University of Maryland, Baltimore, Baltimore, MD 21201, USA
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Bousquet-Dubouch MP, Fabre B, Monsarrat B, Burlet-Schiltz O. Proteomics to study the diversity and dynamics of proteasome complexes: from fundamentals to the clinic. Expert Rev Proteomics 2012; 8:459-81. [PMID: 21819302 DOI: 10.1586/epr.11.41] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This article covers the latest contributions of proteomics to the structural and functional characterization of proteasomes and their associated proteins, but also to the detection of proteasomes as clinical biomarkers in diseases. Proteasomes are highly heterogenous supramolecular complexes and constitute important cellular proteases controlling the pool of proteins involved in key cellular functions. The comprehension of the structure/function relationship of proteasomes is therefore of major interest in biology. Numerous biochemical methods have been employed to purify proteasomes, and have led to the identification of complexes of various compositions - depending on the experimental conditions and the type of strategy used. In association with protein separation and enrichment techniques, modern mass spectrometry instruments and mass spectrometry-based quantitative methods, they have led to unprecedented breakthroughs in the in-depth analysis of the diversity and dynamics of proteasome composition and localization under various stimuli or pathological contexts. Proteasome inhibitors are now used in clinics for the treatment of cancer, and recent studies propose that the proteasome should be considered as a predictive biomarker for various pathologies.
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Xu Q, Cui Z, Venkatraman G, Gomes AV. The use of biophysical proteomic techniques in advancing our understanding of diseases. Biophys Rev 2012; 4:125-135. [PMID: 28510094 PMCID: PMC5418381 DOI: 10.1007/s12551-012-0070-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 01/26/2012] [Indexed: 12/14/2022] Open
Abstract
The use of proteomic approaches in investigating diseases is continuing to expand and has started to provide answers to substantial gaps in our understanding of disease pathogenesis as well as in the development of effective strategies for the early diagnosis and treatment of diseases. Biophysical techniques form a crucial part of the advanced proteomic techniques currently used and include mass spectrometry and protein separation techniques, such as two-dimensional gel electrophoresis and liquid chromatography. The application of biophysical proteomic techniques in the study of disease includes delineation of altered protein expression, not only at the whole-cell or tissue levels, but also in subcellular structures, protein complexes, and biological fluids. These techniques are also being used for the discovery of novel disease biomarkers, exploration of the pathogenesis of diseases, development of new diagnostic methodologies, and identification of new targets for therapeutics. Proteomic techniques also have the potential for accelerating drug development through more effective strategies for evaluating a specific drug's therapeutic effects and toxicity. This article discusses the application of biophysical proteomic techniques in delineating cardiovascular disease and other diseases, as well as the limitations and future research directions required for these techniques to gain greater acceptance and have a larger impact.
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Affiliation(s)
- Qian Xu
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, 176 Briggs Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Ziyou Cui
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, 176 Briggs Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Gayathi Venkatraman
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, 176 Briggs Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, 176 Briggs Hall, One Shields Avenue, Davis, CA, 95616, USA.
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Rezvani K, Baalman K, Teng Y, Mee MP, Dawson SP, Wang H, De Biasi M, Mayer RJ. Proteasomal degradation of the metabotropic glutamate receptor 1α is mediated by Homer-3 via the proteasomal S8 ATPase: Signal transduction and synaptic transmission. J Neurochem 2012; 122:24-37. [PMID: 22486777 DOI: 10.1111/j.1471-4159.2012.07752.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The metabotropic glutamate receptors (mGluRs) fine-tune the efficacy of synaptic transmission. This unique feature makes mGluRs potential targets for the treatment of various CNS disorders. There is ample evidence to show that the ubiquitin proteasome system mediates changes in synaptic strength leading to multiple forms of synaptic plasticity. The present study describes a novel interaction between post-synaptic adaptors, long Homer-3 proteins, and one of the 26S proteasome regulatory subunits, the S8 ATPase, that influences the degradation of the metabotropic glutamate receptor 1α (mGluR1α). We have shown that the two human long Homer-3 proteins specifically interact with human proteasomal S8 ATPase. We identified that mGluR1α and long Homer-3s immunoprecipitate with the 26S proteasome both in vitro and in vivo. We further found that the mGluR1α receptor can be ubiquitinated and degraded by the 26S proteasome and that Homer-3A facilitates this process. Furthermore, the siRNA mediated silencing of Homer-3 led to increased levels of total and plasma membrane-associated mGluR1α receptors. These results suggest that long Homer-3 proteins control the degradation of mGluR1α receptors by shuttling ubiquitinated mGluR-1α receptors to the 26S proteasome via the S8 ATPase which may modulate synaptic transmission.
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Affiliation(s)
- Khosrow Rezvani
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, Vermillion, SD 57069, USA.
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