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Lu J, Qian S, Sun Z. Targeting histone deacetylase in cardiac diseases. Front Physiol 2024; 15:1405569. [PMID: 38983721 PMCID: PMC11232433 DOI: 10.3389/fphys.2024.1405569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/31/2024] [Indexed: 07/11/2024] Open
Abstract
Histone deacetylases (HDAC) catalyze the removal of acetylation modifications on histones and non-histone proteins, which regulates gene expression and other cellular processes. HDAC inhibitors (HDACi), approved anti-cancer agents, emerge as a potential new therapy for heart diseases. Cardioprotective effects of HDACi are observed in many preclinical animal models of heart diseases. Genetic mouse models have been developed to understand the role of each HDAC in cardiac functions. Some of the findings are controversial. Here, we provide an overview of how HDACi and HDAC impact cardiac functions under physiological or pathological conditions. We focus on in vivo studies of zinc-dependent classical HDACs, emphasizing disease conditions involving cardiac hypertrophy, myocardial infarction (MI), ischemic reperfusion (I/R) injury, and heart failure. In particular, we review how non-biased omics studies can help our understanding of the mechanisms underlying the cardiac effects of HDACi and HDAC.
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Affiliation(s)
- Jiao Lu
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, TX, United States
| | - Sichong Qian
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, TX, United States
| | - Zheng Sun
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
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2
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Binek A, Castans C, Jorge I, Bagwan N, Rodríguez JM, Fernández-Jiménez R, Galán-Arriola C, Oliver E, Gómez M, Clemente-Moragón A, Ibanez B, Camafeita E, Vázquez J. Oxidative Post-translational Protein Modifications upon Ischemia/Reperfusion Injury. Antioxidants (Basel) 2024; 13:106. [PMID: 38247530 PMCID: PMC10812827 DOI: 10.3390/antiox13010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/30/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
While reperfusion, or restoration of coronary blood flow in acute myocardial infarction, is a requisite for myocardial salvage, it can paradoxically induce a specific damage known as ischemia/reperfusion (I/R) injury. Our understanding of the precise pathophysiological molecular alterations leading to I/R remains limited. In this study, we conducted a comprehensive and unbiased time-course analysis of post-translational modifications (PTMs) in the post-reperfused myocardium of two different animal models (pig and mouse) and evaluated the effect of two different cardioprotective therapies (ischemic preconditioning and neutrophil depletion). In pigs, a first wave of irreversible oxidative damage was observed at the earliest reperfusion time (20 min), impacting proteins essential for cardiac contraction. A second wave, characterized by irreversible oxidation on different residues and reversible Cys oxidation, occurred at late stages (6-12 h), affecting mitochondrial, sarcomere, and inflammation-related proteins. Ischemic preconditioning mitigated the I/R damage caused by the late oxidative wave. In the mouse model, the two-phase pattern of oxidative damage was replicated, and neutrophil depletion mitigated the late wave of I/R-related damage by preventing both Cys reversible oxidation and irreversible oxidation. Altogether, these data identify protein PTMs occurring late after reperfusion as an actionable therapeutic target to reduce the impact of I/R injury.
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Grants
- PGC2018-097019-B-I00, PID2021-122348NB-I00, PID2022-140176OB-I00 Spanish Ministry of Science, Innovation and Universities
- Fondo de Investigación Sanitaria grant PRB3 PT17/0019/0003- ISCIII-SGEFI / ERDF, ProteoRed Instituto de Salud Carlos III
- IMMUNO-VAR, P2022/BMD-7333, and RENIM-CM, P2022/BMD-7403 Comunidad de Madrid
- HR17-00247, HR22-00533 and HR22-00253 "la Caixa" Banking Foundation
- ERC Consolidator Grant "MATRIX", 819775 European Commission
- grant PI22/01560 ISCIII-Fondo de Investigación Sanitaria and European Union
- FP7-PEOPLE-2013-ITN-Cardionext European Union's Seventh Framework Programme
- Formacion del Profesorado Universitario (FPU14/05292) Spanish Ministry of Education, Culture and Sports
- PID2021-133167OB-100, RYC2020-028884-I, CEX2020-001041-S MCIN/AEI/10.13039/501100011033
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Affiliation(s)
- Aleksandra Binek
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Celia Castans
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Inmaculada Jorge
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Navratan Bagwan
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - José Manuel Rodríguez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Rodrigo Fernández-Jiménez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- Department of Cardiology, Hospital Universitario Clínico San Carlos, Profesor Martín Lagos, s/n, 28040 Madrid, Spain
| | - Carlos Galán-Arriola
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Eduardo Oliver
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mónica Gómez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
| | - Agustín Clemente-Moragón
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Borja Ibanez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- IIS-Fundación Jiménez Díaz Hospital, Avenida Reyes Católicos, 2, 28040 Madrid, Spain
| | - Emilio Camafeita
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Melchor Fernández Almagro, 3, 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
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3
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Chu T, Shang J, Jian H, Song C, Yang R, Bao D, Tan Q, Tang L. Potential Role of Lysine Acetylation and Autophagy in Brown Film Formation and Postripening of Lentinula edodes Mycelium. Microbiol Spectr 2023; 11:e0282322. [PMID: 37347174 PMCID: PMC10434168 DOI: 10.1128/spectrum.02823-22] [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: 07/23/2022] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Lentinula edodes is one of the most widely cultivated edible mushrooms in the world. When cultivated in sawdust, the surface mycelium of L. edodes needs a long postripening stage wherein it forms a brown film (BF) by secreting and accumulating pigments. BF formation is critical for the high quality and yield of fruiting bodies. Protein lysine acetylation (KAC) is an important post-translational modification that regulates growth and development. Previous studies have shown that deacetylase levels are significantly increased during BF formation in the postripening stage of L. edodes. The aim of this study was to assess the role of protein acetylation during BF formation. To this end, we compared the acetylome of L. edodes mycelia before and after BF formation using anti-acetyl antibody-based label-free quantitative proteomics. We identified 5,613 acetylation sites in 1,991 proteins, and quantitative information was available for 4,848 of these sites in 1,815 proteins. Comparative acetylome analysis showed that the modification of 699 sites increased and that of 562 sites decreased during BF formation. Bioinformatics analysis of the differentially acetylated proteins showed significant enrichment in the tricarboxylic acid (TCA) cycle and proteasome pathways. Furthermore, functional assays showed that BF formation is associated with significant changes in the activities of proteasome, citrate synthase, and isocitrate dehydrogenase. Consistent with this hypothesis, the lysine deacetylase inhibitor trichostatin (TSA) delayed autophagy and BF formation in L. edodes. Taken together, KAC and autophagy play important roles in the mycelial BF formation and postripening stage of L. edodes. IMPORTANCE Mycelial BF formation and postripening of L. edodes affects the quality and quantity of its edible fruiting bodies. In this study, we explored the role of protein KAC in this biological process, with the aim of optimizing the cultivation and yield of L. edodes.
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Affiliation(s)
- Ting Chu
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- School of Food Sciences and Technology, Shanghai Ocean University, Shanghai, China
| | - Junjun Shang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chunyan Song
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ruiheng Yang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dapeng Bao
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qi Tan
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lihua Tang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Buneeva OA, Kopylov AT, Medvedev AE. Proteasome Interactome and Its Role in the Mechanisms of Brain Plasticity. BIOCHEMISTRY (MOSCOW) 2023; 88:319-336. [PMID: 37076280 DOI: 10.1134/s0006297923030033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
Abstract
Proteasomes are highly conserved multienzyme complexes responsible for proteolytic degradation of the short-lived, regulatory, misfolded, and damaged proteins. They play an important role in the processes of brain plasticity, and decrease in their function is accompanied by the development of neurodegenerative pathology. Studies performed in different laboratories both on cultured mammalian and human cells and on preparations of the rat and rabbit brain cortex revealed a large number of proteasome-associated proteins. Since the identified proteins belong to certain metabolic pathways, multiple enrichment of the proteasome fraction with these proteins indicates their important role in proteasome functioning. Extrapolation of the experimental data, obtained on various biological objects, to the human brain suggests that the proteasome-associated proteins account for at least 28% of the human brain proteome. The proteasome interactome of the brain contains a large number of proteins involved in the assembly of these supramolecular complexes, regulation of their functioning, and intracellular localization, which could be changed under different conditions (for example, during oxidative stress) or in different phases of the cell cycle. In the context of molecular functions of the Gene Ontology (GO) Pathways, the proteins of the proteasome interactome mediate cross-talk between components of more than 30 metabolic pathways annotated in terms of GO. The main result of these interactions is binding of adenine and guanine nucleotides, crucial for realization of the nucleotide-dependent functions of the 26S and 20S proteasomes. Since the development of neurodegenerative pathology is often associated with regioselective decrease in the functional activity of proteasomes, a positive therapeutic effect would be obviously provided by the factors increasing proteasomal activity. In any case, pharmacological regulation of the brain proteasomes seems to be realized through the changes in composition and/or activity of the proteins associated with proteasomes (deubiquitinase, PKA, CaMKIIα, etc.).
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Affiliation(s)
- Olga A Buneeva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
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5
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Morales-Tarré O, Alonso-Bastida R, Arcos-Encarnación B, Pérez-Martínez L, Encarnación-Guevara S. Protein lysine acetylation and its role in different human pathologies: a proteomic approach. Expert Rev Proteomics 2021; 18:949-975. [PMID: 34791964 DOI: 10.1080/14789450.2021.2007766] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Lysine acetylation is a reversible post-translational modification (PTM) regulated through the action of specific types of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (HDACs), in addition to bromodomains, which are a group of conserved domains which identify acetylated lysine residues, several of the players in the process of protein acetylation, including enzymes and bromodomain-containing proteins, have been related to the progression of several diseases. The combination of high-resolution mass spectrometry-based proteomics, and immunoprecipitation to enrich acetylated peptides has contributed in recent years to expand the knowledge about this PTM described initially in histones and nuclear proteins, and is currently reported in more than 5000 human proteins, that are regulated by this PTM. AREAS COVERED This review presents an overview of the main participant elements, the scenario in the development of protein lysine acetylation, and its role in different human pathologies. EXPERT OPINION Acetylation targets are practically all cellular processes in eukaryotes and prokaryotes organisms. Consequently, this modification has been linked to many pathologies like cancer, viral infection, obesity, diabetes, cardiovascular, and nervous system-associated diseases, to mention a few relevant examples. Accordingly, some intermediate mediators in the acetylation process have been projected as therapeutic targets.
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Affiliation(s)
- Orlando Morales-Tarré
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ramiro Alonso-Bastida
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Bolivar Arcos-Encarnación
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular Y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Leonor Pérez-Martínez
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular Y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sergio Encarnación-Guevara
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Caielli S, Cardenas J, de Jesus AA, Baisch J, Walters L, Blanck JP, Balasubramanian P, Stagnar C, Ohouo M, Hong S, Nassi L, Stewart K, Fuller J, Gu J, Banchereau JF, Wright T, Goldbach-Mansky R, Pascual V. Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE. Cell 2021; 184:4464-4479.e19. [PMID: 34384544 PMCID: PMC8380737 DOI: 10.1016/j.cell.2021.07.021] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/05/2021] [Accepted: 07/19/2021] [Indexed: 02/08/2023]
Abstract
Emerging evidence supports that mitochondrial dysfunction contributes to systemic lupus erythematosus (SLE) pathogenesis. Here we show that programmed mitochondrial removal, a hallmark of mammalian erythropoiesis, is defective in SLE. Specifically, we demonstrate that during human erythroid cell maturation, a hypoxia-inducible factor (HIF)-mediated metabolic switch is responsible for the activation of the ubiquitin-proteasome system (UPS), which precedes and is necessary for the autophagic removal of mitochondria. A defect in this pathway leads to accumulation of red blood cells (RBCs) carrying mitochondria (Mito+ RBCs) in SLE patients and in correlation with disease activity. Antibody-mediated internalization of Mito+ RBCs induces type I interferon (IFN) production through activation of cGAS in macrophages. Accordingly, SLE patients carrying both Mito+ RBCs and opsonizing antibodies display the highest levels of blood IFN-stimulated gene (ISG) signatures, a distinctive feature of SLE.
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Affiliation(s)
- Simone Caielli
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA; Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
| | | | - Adriana Almeida de Jesus
- Translational Autoinflammatory Diseases Section, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jeanine Baisch
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA; Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Preetha Balasubramanian
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA; Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Cristy Stagnar
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA; Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Marina Ohouo
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA; Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Seunghee Hong
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA; Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | - Lorien Nassi
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Katie Stewart
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Julie Fuller
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jinghua Gu
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA; Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA
| | | | - Tracey Wright
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Virginia Pascual
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA; Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
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7
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Expanding the role of proteasome homeostasis in Parkinson's disease: beyond protein breakdown. Cell Death Dis 2021; 12:154. [PMID: 33542205 PMCID: PMC7862491 DOI: 10.1038/s41419-021-03441-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Proteasome is the principal hydrolytic machinery responsible for the great majority of protein degradation. The past three decades have testified prominent advances about proteasome involved in almost every aspect of biological processes. Nonetheless, inappropriate increase or decrease in proteasome function is regarded as a causative factor in several diseases. Proteasome abundance and proper assembly need to be precisely controlled. Indeed, various neurodegenerative diseases including Parkinson's disease (PD) share a common pathological feature, intracellular protein accumulation such as α-synuclein. Proteasome activation may effectively remove aggregates and prevent the neurodegeneration in PD, which provides a potential application for disease-modifying treatment. In this review, we build on the valuable discoveries related to different types of proteolysis by distinct forms of proteasome, and how its regulatory and catalytic particles promote protein elimination. Additionally, we summarize the emerging ideas on the proteasome homeostasis regulation by targeting transcriptional, translational, and post-translational levels. Given the imbalanced proteostasis in PD, the strategies for intensifying proteasomal degradation are advocated as a promising approach for PD clinical intervention.
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Rookyard AW, Paulech J, Thyssen S, Liddy KA, Puckeridge M, Li DK, White MY, Cordwell SJ. A Global Profile of Reversible and Irreversible Cysteine Redox Post-Translational Modifications During Myocardial Ischemia/Reperfusion Injury and Antioxidant Intervention. Antioxid Redox Signal 2021; 34:11-31. [PMID: 32729339 DOI: 10.1089/ars.2019.7765] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aims: Cysteine (Cys) is a major target for redox post-translational modifications (PTMs) that occur in response to changes in the cellular redox environment. We describe multiplexed, peptide-based enrichment and quantitative mass spectrometry (MS) applied to globally profile reversible redox Cys PTM in rat hearts during ischemia/reperfusion (I/R) in the presence or absence of an aminothiol antioxidant, N-2-mercaptopropionylglycine (MPG). Parallel fractionation also allowed identification of irreversibly oxidized Cys peptides (Cys-SO2H/SO3H). Results: We identified 4505 reversibly oxidized Cys peptides of which 1372 were significantly regulated by ischemia and/or I/R. An additional 219 peptides (247 sites) contained Cys-SO2H/Cys-SO3H modifications, and these were predominantly identified from hearts subjected to I/R (n = 168 peptides). Parallel reaction monitoring MS (PRM-MS) enabled relative quantitation of 34 irreversibly oxidized Cys peptides. MPG attenuated a large cluster of I/R-associated reversibly oxidized Cys peptides and irreversible Cys oxidation to less than nonischemic controls (n = 24 and 34 peptides, respectively). PRM-MS showed that Cys sites oxidized during ischemia and/or I/R and "protected" by MPG were largely mitochondrial, and were associated with antioxidant functions (peroxiredoxins 5 and 6) and metabolic processes, including glycolysis. Metabolomics revealed I/R induced changes in glycolytic intermediates that were reversed in the presence of MPG, which were consistent with irreversible PTM of triose phosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), altered GAPDH enzyme activity, and reduced I/R glycolytic payoff as evidenced by adenosine triphosphate and NADH levels. Innovation: Novel enrichment and PRM-MS approaches developed here enabled large-scale relative quantitation of Cys redox sites modified by reversible and irreversible PTM during I/R and antioxidant remediation. Conclusions: Cys sites identified here are targets of reactive oxygen species that can contribute to protein dysfunction and the pathogenesis of I/R.
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Affiliation(s)
- Alexander W Rookyard
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Jana Paulech
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Stine Thyssen
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Kiersten A Liddy
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Max Puckeridge
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Desmond K Li
- Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Melanie Y White
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, Australia.,Discipline of Pathology, School of Medical Sciences, The University of Sydney, Sydney, Australia.,Sydney Mass Spectrometry, The University of Sydney, Sydney, Australia
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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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10
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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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11
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Yang M, Zhang Y, Ren J. Acetylation in cardiovascular diseases: Molecular mechanisms and clinical implications. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165836. [PMID: 32413386 DOI: 10.1016/j.bbadis.2020.165836] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Acetylation belongs to a class of post-translational modification (PTM) processes that epigenetically regulate gene expression and gene transcriptional activity. Reversible histone acetylation on lysine residues governs the interactions between DNA and histones to mediate chromatin remodeling and gene transcription. Non-histone protein acetylation complicates cellular function whereas acetylation of key mitochondrial enzymes regulates bioenergetic metabolism. Acetylation and deacetylation of functional proteins are essential to the delicated homeostatic regulation of embryonic development, postnatal maturation, cardiomyocyte differentiation, cardiac remodeling and onset of various cardiovascular diseases including obesity, diabetes mellitus, cardiometabolic diseases, ischemia-reperfusion injury, cardiac remodeling, hypertension, and arrhythmias. Histone acetyltransferase (HATs) and histone deacetylases (HDACs) are essential enzymes mainly responsible for the regulation of lysine acetylation levels, thus providing possible drugable targets for therapeutic interventions in the management of cardiovascular diseases.
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Affiliation(s)
- Mingjie Yang
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 210032, China
| | - Yingmei Zhang
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 210032, China.
| | - Jun Ren
- Department of Cardiology and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 210032, China.
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12
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Panner Selvam MK, Samanta L, Agarwal A. Functional Analysis of Differentially Expressed Acetylated Spermatozoal Proteins in Infertile Men with Unilateral and Bilateral Varicocele. Int J Mol Sci 2020; 21:ijms21093155. [PMID: 32365753 PMCID: PMC7246524 DOI: 10.3390/ijms21093155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/15/2020] [Accepted: 04/26/2020] [Indexed: 12/31/2022] Open
Abstract
Sperm proteins undergo post-translational modifications, such as phosphorylation, acetylation, and ubiquitination, which in turn play a key role in determining their fertilizing ability. In the current study, we examined the sperm proteome of men with unilateral and bilateral varicocele to identify the key proteins affected by acetylation to gain an insight into the difference in the severity of affected sperm function in the latter. An LTQ-Orbitrap Elite hybrid mass spectrometer system was used to profile the sperm proteome in pooled unilateral and bilateral varicocele patients. Bioinformatics database and tools, such as UniProtKB, Ingenuity Pathway Analysis Software (IPA) and Metacore, were used to identify the differentially expressed proteins (DEPs) involved in the acetylation process. A total of 135 DEPs in the spermatozoa of unilateral and bilateral varicocele patients were found to be affected by acetylation. The majority of these DEPs found were regulated by key transcription factors such as androgen receptor, p53, and NRF2. Furthermore, the DEPs predicted to be affected by the acetylation process were associated with fertilization, acrosome reaction, mitochondrial dysfunction and oxidative stress. Aberrant expression of proteins and their differential acetylation process may affect the normal physiological functions of spermatozoa. Protein–protein interactions identified dysregulation of the proteasome complex in the bilateral varicocele group. Damage to the proteasome complex may result in aggregation of the misfolded proteins, which in turn increase sperm DNA damage and apoptosis in patients with bilateral varicocele.
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Affiliation(s)
- Manesh Kumar Panner Selvam
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; (M.K.P.S.); (L.S.)
| | - Luna Samanta
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; (M.K.P.S.); (L.S.)
- Redox Biology Laboratory, Department of Zoology, Ravenshaw University, Cuttack 753003, India
| | - Ashok Agarwal
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; (M.K.P.S.); (L.S.)
- Correspondence: ; Tel.: +1-216-444-9485
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13
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Herr DJ, Singh T, Dhammu T, Menick DR. Regulation of metabolism by mitochondrial enzyme acetylation in cardiac ischemia-reperfusion injury. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165728. [PMID: 32068115 DOI: 10.1016/j.bbadis.2020.165728] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 01/21/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022]
Abstract
Ischemia reperfusion injury (I/R injury) contributes significantly to morbidity and mortality following myocardial infarction (MI). Although rapid reperfusion of the ischemic myocardium was established decades ago as a highly beneficial therapy for MI, significant cell death still occurs after the onset of reperfusion. Mitochondrial dysfunction is closely associated with I/R injury, resulting in the uncontrolled production of reactive oxygen species (ROS). Considerable efforts have gone into understanding the metabolic perturbations elicited by I/R injury. Recent work has identified the critical role of reversible protein acetylation in maintaining normal mitochondrial biologic function and energy metabolism both in the normal heart and during I/R injury. Several studies have shown that modification of class I HDAC and/or Sirtuin (Sirt) activity is cardioprotective in the setting of I/R injury. A better understanding of the role of these metabolic pathways in reperfusion injury and their regulation by reversible protein acetylation presents a promising way forward in improving the treatment of cardiac reperfusion injury. Here we briefly review some of what is known about how acetylation regulates mitochondrial metabolism and how it relates to I/R injury.
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Affiliation(s)
- Daniel J Herr
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC, United States of America
| | - Toolika Singh
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC, United States of America
| | - Tajinder Dhammu
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC, United States of America
| | - Donald R Menick
- Department of Medicine, Division of Cardiology, Medical University of South Carolina, Charleston, SC, United States of America; Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC, United States of America.
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Coux O, Zieba BA, Meiners S. The Proteasome System in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:55-100. [DOI: 10.1007/978-3-030-38266-7_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Xu FQ, Xue HW. The ubiquitin-proteasome system in plant responses to environments. PLANT, CELL & ENVIRONMENT 2019; 42:2931-2944. [PMID: 31364170 DOI: 10.1111/pce.13633] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 05/12/2023]
Abstract
The ubiquitin-proteasome system (UPS) is a rapid regulatory mechanism for selective protein degradation in plants and plays crucial roles in growth and development. There is increasing evidence that the UPS is also an integral part of plant adaptation to environmental stress, such as drought, salinity, cold, nutrient deprivation and pathogens. This review focuses on recent studies illustrating the important functions of the UPS components E2s, E3s and subunits of the proteasome and describes the regulation of proteasome activity during plant responses to environment stimuli. The future research hotspots and the potential for utilization of the UPS to improve plant tolerance to stress are discussed.
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Affiliation(s)
- Fa-Qing Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
- Shanghai College of Life Science, University of Chinese Academy of Sciences, 200032, Shanghai, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 200032, Shanghai, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, China
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16
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Kors S, Geijtenbeek K, Reits E, Schipper-Krom S. Regulation of Proteasome Activity by (Post-)transcriptional Mechanisms. Front Mol Biosci 2019; 6:48. [PMID: 31380390 PMCID: PMC6646590 DOI: 10.3389/fmolb.2019.00048] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/11/2019] [Indexed: 12/23/2022] Open
Abstract
Intracellular protein synthesis, folding, and degradation are tightly controlled processes to ensure proper protein homeostasis. The proteasome is responsible for the degradation of the majority of intracellular proteins, which are often targeted for degradation via polyubiquitination. However, the degradation rate of proteins is also affected by the capacity of proteasomes to recognize and degrade these substrate proteins. This capacity is regulated by a variety of proteasome modulations including (1) changes in complex composition, (2) post-translational modifications, and (3) altered transcription of proteasomal subunits and activators. Various diseases are linked to proteasome modulation and altered proteasome function. A better understanding of these modulations may offer new perspectives for therapeutic intervention. Here we present an overview of these three proteasome modulating mechanisms to give better insight into the diversity of proteasomes.
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Affiliation(s)
- Suzan Kors
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Karlijne Geijtenbeek
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eric Reits
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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17
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Wang H, Schippers JHM. The Role and Regulation of Autophagy and the Proteasome During Aging and Senescence in Plants. Genes (Basel) 2019; 10:genes10040267. [PMID: 30987024 PMCID: PMC6523301 DOI: 10.3390/genes10040267] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/06/2019] [Accepted: 03/27/2019] [Indexed: 12/18/2022] Open
Abstract
Aging and senescence in plants has a major impact on agriculture, such as in crop yield, the value of ornamental crops, and the shelf life of vegetables and fruits. Senescence represents the final developmental phase of the leaf and inevitably results in the death of the organ. Still, the process is completely under the control of the plant. Plants use their protein degradation systems to maintain proteostasis and transport or salvage nutrients from senescing organs to develop reproductive parts. Herein, we present an overview of current knowledge about the main protein degradation pathways in plants during senescence: The proteasome and autophagy. Although both pathways degrade proteins, autophagy appears to prevent aging, while the proteasome functions as a positive regulator of senescence.
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Affiliation(s)
- Haojie Wang
- Institute of Biology I, RWTH Aachen University, 52074 Aachen, Germany.
| | - Jos H M Schippers
- Institute of Biology I, RWTH Aachen University, 52074 Aachen, Germany.
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18
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Morozov AV, Karpov VL. Biological consequences of structural and functional proteasome diversity. Heliyon 2018; 4:e00894. [PMID: 30417153 PMCID: PMC6218844 DOI: 10.1016/j.heliyon.2018.e00894] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/25/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
Cell homeostasis and regulation of metabolic pathways are ensured by synthesis, proper folding and efficient degradation of a vast amount of proteins. Ubiquitin-proteasome system (UPS) degrades most intracellular proteins and thus, participates in regulation of cellular metabolism. Within the UPS, proteasomes are the elements that perform substrate cleavage. However, the proteasomes in the organism are diverse. Structurally different proteasomes are present not only in different types of cells, but also in a single cell. The reason for proteasome heterogeneity is not fully understood. This review briefly encompasses mammalian proteasome structure and function, and discusses biological relevance of proteasome diversity for a range of important cellular functions including internal and external signaling.
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Affiliation(s)
- Alexey V Morozov
- W.A. Engelhardt Institute of Molecular Biology, RAS, 119991, Moscow, Russia
| | - Vadim L Karpov
- W.A. Engelhardt Institute of Molecular Biology, RAS, 119991, Moscow, Russia
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19
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Khullar M, Cheema BS, Raut SK. Emerging Evidence of Epigenetic Modifications in Vascular Complication of Diabetes. Front Endocrinol (Lausanne) 2017; 8:237. [PMID: 29085333 PMCID: PMC5649155 DOI: 10.3389/fendo.2017.00237] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 08/29/2017] [Indexed: 01/04/2023] Open
Abstract
Genes, dietary, and lifestyle factors have been shown to be important in the pathophysiology of diabetes and associated microvascular complications. Epigenetic modifications, such as DNA methylation, histone acetylation, and post-transcriptional RNA regulation, are being increasingly recognized as important mediators of the complex interplay between genes and the environment. Recent studies suggest that diabetes-induced dysregulation of epigenetic mechanisms resulting in altered gene expression in target cells can lead to diabetes-associated complications, such as diabetic cardiomyopathy, diabetic nephropathy, retinopathy, and so on, which are the major contributors to diabetes-associated morbidity and mortality. Thus, knowledge of dysregulated epigenetic pathways involved in diabetes can provide much needed new drug targets for these diseases. In this review, we constructed our search strategy to highlight the role of DNA methylation, modifications of histones and role of non-coding RNAs (microRNAs and long non-coding RNAs) in vascular complications of diabetes, including cardiomyopathy, nephropathy, and retinopathy.
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Affiliation(s)
- Madhu Khullar
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Satish K. Raut
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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20
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Hochrainer K. Protein Modifications with Ubiquitin as Response to Cerebral Ischemia-Reperfusion Injury. Transl Stroke Res 2017; 9:157-173. [DOI: 10.1007/s12975-017-0567-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/11/2017] [Accepted: 08/17/2017] [Indexed: 12/12/2022]
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21
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Im E, Chung KC. Precise assembly and regulation of 26S proteasome and correlation between proteasome dysfunction and neurodegenerative diseases. BMB Rep 2017; 49:459-73. [PMID: 27312603 PMCID: PMC5227139 DOI: 10.5483/bmbrep.2016.49.9.094] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 11/20/2022] Open
Abstract
Neurodegenerative diseases (NDs) often involve the formation of abnormal and toxic protein aggregates, which are thought to be the primary factor in ND occurrence and progression. Aged neurons exhibit marked increases in aggregated protein levels, which can lead to increased cell death in specific brain regions. As no specific drugs/therapies for treating the symptoms or/and progression of NDs are available, obtaining a complete understanding of the mechanism underlying the formation of protein aggregates is needed for designing a novel and efficient removal strategy. Intracellular proteolysis generally involves either the lysosomal or ubiquitin-proteasome system. In this review, we focus on the structure and assembly of the proteasome, proteasome-mediated protein degradation, and the multiple dynamic regulatory mechanisms governing proteasome activity. We also discuss the plausibility of the correlation between changes in proteasome activity and the occurrence of NDs. [BMB Reports 2016; 49(9): 459-473]
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Affiliation(s)
- Eunju Im
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Kwang Chul Chung
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
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22
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Ganai SA, Ramadoss M, Mahadevan V. Histone Deacetylase (HDAC) Inhibitors - emerging roles in neuronal memory, learning, synaptic plasticity and neural regeneration. Curr Neuropharmacol 2016; 14:55-71. [PMID: 26487502 PMCID: PMC4787286 DOI: 10.2174/1570159x13666151021111609] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/23/2015] [Accepted: 10/08/2015] [Indexed: 11/22/2022] Open
Abstract
Epigenetic regulation of neuronal signalling through histone acetylation dictates transcription programs that govern neuronal memory, plasticity and learning paradigms. Histone Acetyl Transferases (HATs) and Histone Deacetylases (HDACs) are antagonistic enzymes that regulate gene expression through acetylation and deacetylation of histone proteins around which DNA is wrapped inside a eukaryotic cell nucleus. The epigenetic control of HDACs and the cellular imbalance between HATs and HDACs dictate disease states and have been implicated in muscular dystrophy, loss of memory, neurodegeneration and autistic disorders. Altering gene expression profiles through inhibition of HDACs is now emerging as a powerful technique in therapy. This review presents evolving applications of HDAC inhibitors as potential drugs in neurological research and therapy. Mechanisms that govern their
expression profiles in neuronal signalling, plasticity and learning will be covered. Promising and exciting possibilities of HDAC inhibitors in memory formation, fear conditioning, ischemic stroke and neural regeneration have been detailed.
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Affiliation(s)
| | | | - Vijayalakshmi Mahadevan
- School of Chemical & Biotechnology SASTRA University Tirumalaisamudram, Thanjavur - 613 401 India.
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23
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Hong Y, Cao X, Han Q, Yuan C, Zhang M, Han Y, Zhu C, Lin T, Lu K, Li H, Fu Z, Lin J. Proteome-wide analysis of lysine acetylation in adult Schistosoma japonicum worm. J Proteomics 2016; 148:202-12. [PMID: 27535354 DOI: 10.1016/j.jprot.2016.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/30/2016] [Accepted: 08/09/2016] [Indexed: 12/14/2022]
Abstract
UNLABELLED Lysine acetylation, a ubiquitous and conserved posttranslational modification, has recently been shown to participate in many diverse non-chromatin-associated biological processes in prokaryotes and eukaryotes. However, the full extent and functional significance of acetylation in Schistosoma japonicum is still unknown. To investigate the nature, extent, and biological functions of lysine acetylation in schistosomes, immunoaffinity-based acetyl-lysine peptide enrichment, integrated with mass spectrometry, was used to comprehensively characterize the lysine-acetylated proteins in this parasite. In total, 1109 acetylated proteins and 2393 acetylation sites in S. japonicum were identified, representing the largest acetylome yet reported in a parasite. In a bioinformatic analysis showed that these acetylated proteins were mainly enriched in the biological process categories of metabolism, gene expression, translation, and transport. The classification according to molecular function revealed that the largest class involved the catalytic activity of different enzymes, including oxidoreductase, transferase, and pyrophosphatase activities. Most of the acetylated proteins in the cellular component category occurred in the cytoplasm, membrane, cytoskeleton, and nucleus. These data demonstrate the generality of lysine acetylation and provide the first global survey of acetylation in schistosomes. Our findings are an exciting starting point for the further exploration of the functions of acetylation in the biology of this parasite. SIGNIFICANCE Schistosomiasis is one of the world's most prevalent and neglected tropical parasitic zoonotic diseases, and it causes almost 200,000 deaths annually. To control and eradicate schistosomiasis, effective vaccines are urgently required, and drug targets that are essential for schistosome survival must be identified in fundamental studies of schistosome biology. Posttranslational modifications are complex, fundamental, and important mechanisms that regulate the physiological functions of organisms. Lysine acetylation, a ubiquitous and conserved posttranslational modification, has recently been shown to participate in many diverse non-chromatin-associated biological processes in prokaryotes and eukaryotes. However, the full extent and functional significance of acetylation in Schistosoma japonicum is still unknown. To investigate the nature, extent, and biological functions of lysine acetylation in S. japonicum, we employ immunoaffinity-based acetyl-lysine peptide enrichment, integrated with mass spectrometry to comprehensively characterize the lysine-acetylated proteins in this parasite. The results of our data demonstrate the generality of lysine acetylation and provide the first global survey of acetylation in schistosomes. Our findings are an exciting starting point for the further exploration of the functions of acetylation in the biology of this parasite. Meanwhile, identifying the mechanisms and proteins targeted by acetylation may also provide a promising avenue for specific drug design and the development of sophisticated therapeutic strategies.
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Affiliation(s)
- Yang Hong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Xiaodan Cao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Qian Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Chunxiu Yuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Min Zhang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan Province 471023, PR China
| | - Yanhui Han
- College of Animal Science, Henan Institute of Science and Technology, Xinxiang, Henan Province 453003, PR China
| | - Chuangang Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Tao Lin
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD 57007, United States
| | - Ke Lu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Hao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China
| | - Zhiqiang Fu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China.
| | - Jiaojiao Lin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai 200241, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009, PR China.
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The life cycle of the 26S proteasome: from birth, through regulation and function, and onto its death. Cell Res 2016; 26:869-85. [PMID: 27444871 PMCID: PMC4973335 DOI: 10.1038/cr.2016.86] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The 26S proteasome is a large, ∼2.5 MDa, multi-catalytic ATP-dependent protease complex that serves as the degrading arm of the ubiquitin system, which is the major pathway for regulated degradation of cytosolic, nuclear and membrane proteins in all eukaryotic organisms.
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25
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Lin YH, Warren CM, Li J, McKinsey TA, Russell B. Myofibril growth during cardiac hypertrophy is regulated through dual phosphorylation and acetylation of the actin capping protein CapZ. Cell Signal 2016; 28:1015-24. [PMID: 27185186 DOI: 10.1016/j.cellsig.2016.05.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 01/08/2023]
Abstract
The mechanotransduction signaling pathways initiated in heart muscle by increased mechanical loading are known to lead to long-term transcriptional changes and hypertrophy, but the rapid events for adaptation at the sarcomeric level are not fully understood. The goal of this study was to test the hypothesis that actin filament assembly during cardiomyocyte growth is regulated by post-translational modifications (PTMs) of CapZβ1. In rapidly hypertrophying neonatal rat ventricular myocytes (NRVMs) stimulated by phenylephrine (PE), two-dimensional gel electrophoresis (2DGE) of CapZβ1 revealed a shift toward more negative charge. Consistent with this, mass spectrometry identified CapZβ1 phosphorylation on serine-204 and acetylation on lysine-199, two residues which are near the actin binding surface of CapZβ1. Ectopic expression of dominant negative PKCɛ (dnPKCɛ) in NRVMs blunted the PE-induced increase in CapZ dynamics, as evidenced by the kinetic constant (Kfrap) of fluorescence recovery after photobleaching (FRAP), and concomitantly reduced phosphorylation and acetylation of CapZβ1. Furthermore, inhibition of class I histone deacetylases (HDACs) increased lysine-199 acetylation on CapZβ1, which increased Kfrap of CapZ and stimulated actin dynamics. Finally, we show that PE treatment of NRVMs results in decreased binding of HDAC3 to myofibrils, suggesting a signal-dependent mechanism for the regulation of sarcomere-associated CapZβ1 acetylation. Taken together, this dual regulation through phosphorylation and acetylation of CapZβ1 provides a novel model for the regulation of myofibril growth during cardiac hypertrophy.
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Affiliation(s)
- Ying-Hsi Lin
- Department of Physiology and Biophysics, University of Illinois at Chicago, College of Medicine, Chicago, IL 60612-7342, United States; Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL 60612-7342, United States
| | - Chad M Warren
- Department of Physiology and Biophysics, University of Illinois at Chicago, College of Medicine, Chicago, IL 60612-7342, United States; Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL 60612-7342, United States
| | - Jieli Li
- Department of Physiology and Biophysics, University of Illinois at Chicago, College of Medicine, Chicago, IL 60612-7342, United States; Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL 60612-7342, United States
| | - Timothy A McKinsey
- Department of Medicine, Division of Cardiology and Center for Fibrosis Research and Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045-0508, United States
| | - Brenda Russell
- Department of Physiology and Biophysics, University of Illinois at Chicago, College of Medicine, Chicago, IL 60612-7342, United States; Department of Physiology & Biophysics, Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL 60612-7342, United States.
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26
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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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Hirano H, Kimura Y, Kimura A. Biological significance of co- and post-translational modifications of the yeast 26S proteasome. J Proteomics 2015; 134:37-46. [PMID: 26642761 DOI: 10.1016/j.jprot.2015.11.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/04/2015] [Accepted: 11/16/2015] [Indexed: 02/05/2023]
Abstract
UNLABELLED In yeast (Saccharomyces cerevisiae), co- and post-translational modifications of the 26S proteasome, a large protein complex, were comprehensively detected by proteomic techniques, and their functions were investigated. The presence, number, site, and state of co- and post-translational modifications of the 26S proteasome differ considerably among yeast, human, and mouse. The roles of phosphorylation, N(α)-acetylation, N(α)-myristoylation, N(α)-methylation, and N-terminal truncation in the yeast 26S proteasome were investigated. Although there is only one modification site for either N(α)-acetylation, N(α)-myristoylation, or N(α)-methylation, these modifications play an important role in the functions of the yeast proteasome. In contrast, there are many phosphorylation sites in the yeast 26S proteasome. However, the phosphorylation patterns might be a few, suggesting that tiny modifications exert considerable effects on the function of the proteasome. BIOLOGICAL SIGNIFICANCE Protein co- and post-translational modifications produce different protein species which often have different functions. The yeast 26S proteasome, a large protein complex, consisting of many subunits has a number of co- and post-translational modification sites. This review describes the effects of the modifications on the function of the protein complex. This article is part of a Special Issue entitled: Protein species. Guest Editors: Peter Jungblut, Hartmut Schlüter and Bernd Thiede.
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Affiliation(s)
- Hisashi Hirano
- Yokohama City University, Advanced Medical Research Center, Japan.
| | - Yayoi Kimura
- Yokohama City University, Advanced Medical Research Center, Japan
| | - Ayuko Kimura
- Yokohama City University, Advanced Medical Research Center, Japan
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Wende AR. Post-translational modifications of the cardiac proteome in diabetes and heart failure. Proteomics Clin Appl 2015; 10:25-38. [PMID: 26140508 PMCID: PMC4698356 DOI: 10.1002/prca.201500052] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/03/2015] [Accepted: 06/29/2015] [Indexed: 12/19/2022]
Abstract
Cardiovascular complications are the leading cause of death in diabetic patients. Decades of research has focused on altered gene expression, altered cellular signaling, and altered metabolism. This work has led to better understanding of disease progression and treatments aimed at reversing or stopping this deadly process. However, one of the pieces needed to complete the puzzle and bridge the gap between altered gene expression and changes in signaling/metabolism is the proteome and its host of modifications. Defining the mechanisms of regulation includes examining protein levels, localization, and activity of the functional component of cellular machinery. Excess or misutilization of nutrients in obesity and diabetes may lead to PTMs contributing to cardiovascular disease progression. PTMs link regulation of metabolic changes in the healthy and diseased heart with regulation of gene expression itself (e.g. epigenetics), protein enzymatic activity (e.g. mitochondrial oxidative capacity), and function (e.g. contractile machinery). Although a number of PTMs are involved in each of these pathways, we will highlight the role of the serine and threonine O‐linked addition of β‐N‐acetyl‐glucosamine or O‐GlcNAcylation. This nexus of nutrient supply, utilization, and storage allows for the modification and translation of mitochondrial function to many other aspects of the cell.
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Affiliation(s)
- Adam R Wende
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
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Singh R, Kuai D, Guziewicz KE, Meyer J, Wilson M, Lu J, Smith M, Clark E, Verhoeven A, Aguirre GD, Gamm DM. Pharmacological Modulation of Photoreceptor Outer Segment Degradation in a Human iPS Cell Model of Inherited Macular Degeneration. Mol Ther 2015; 23:1700-1711. [PMID: 26300224 DOI: 10.1038/mt.2015.141] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/23/2015] [Indexed: 12/16/2022] Open
Abstract
Degradation of photoreceptor outer segments (POS) by retinal pigment epithelium (RPE) is essential for vision, and studies have implicated altered POS processing in the pathogenesis of some retinal degenerative diseases. Consistent with this concept, a recently established hiPSC-RPE model of inherited macular degeneration, Best disease (BD), displayed reduced rates of POS breakdown. Herein we utilized this model to determine (i) if disturbances in protein degradation pathways are associated with delayed POS digestion and (ii) whether such defect(s) can be pharmacologically targeted. We found that BD hiPSC-RPE cultures possessed increased protein oxidation, decreased free-ubiquitin levels, and altered rates of exosome secretion, consistent with altered POS processing. Application of valproic acid (VPA) with or without rapamycin increased rates of POS degradation in our model, whereas application of bafilomycin-A1 decreased such rates. Importantly, the negative effect of bafilomycin-A1 could be fully reversed by VPA. The utility of hiPSC-RPE for VPA testing was further evident following examination of its efficacy and metabolism in a complementary canine disease model. Our findings suggest that disturbances in protein degradation pathways contribute to the POS processing defect observed in BD hiPSC-RPE, which can be manipulated pharmacologically. These results have therapeutic implications for BD and perhaps other maculopathies.
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Affiliation(s)
- Ruchira Singh
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; McPherson Eye Research Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - David Kuai
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Karina E Guziewicz
- Department of Clinical Studies-Philadelphia, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jackelyn Meyer
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Molly Wilson
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jianfeng Lu
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Molly Smith
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric Clark
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amelia Verhoeven
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gustavo D Aguirre
- Department of Clinical Studies-Philadelphia, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David M Gamm
- Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; McPherson Eye Research Institute, University of Wisconsin, Madison, Wisconsin, USA; Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, USA.
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30
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Meraviglia V, Azzimato V, Colussi C, Florio MC, Binda A, Panariti A, Qanud K, Suffredini S, Gennaccaro L, Miragoli M, Barbuti A, Lampe PD, Gaetano C, Pramstaller PP, Capogrossi MC, Recchia FA, Pompilio G, Rivolta I, Rossini A. Acetylation mediates Cx43 reduction caused by electrical stimulation. J Mol Cell Cardiol 2015; 87:54-64. [PMID: 26264759 DOI: 10.1016/j.yjmcc.2015.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 01/13/2023]
Abstract
Communication between cardiomyocytes depends upon gap junctions (GJ). Previous studies have demonstrated that electrical stimulation induces GJ remodeling and modifies histone acetylase (HAT) and deacetylase (HDAC) activities, although these two results have not been linked. The aim of this work was to establish whether electrical stimulation modulates GJ-mediated cardiac cell-cell communication by acetylation-dependent mechanisms. Field stimulation of HL-1 cardiomyocytes at 0.5 Hz for 24 h significantly reduced connexin43 (Cx43) expression and cell-cell communication. HDAC activity was down-regulated whereas HAT activity was not modified resulting in increased acetylation of Cx43. Consistent with a post-translational mechanism, we did not observe a reduction in Cx43 mRNA in electrically stimulated cells, while the proteasomal inhibitor MG132 maintained Cx43 expression. Further, the treatment of paced cells with the HAT inhibitor Anacardic Acid maintained both the levels of Cx43 and cell-cell communication. Finally, we observed increased acetylation of Cx43 in the left ventricles of dogs subjected to chronic tachypacing as a model of abnormal ventricular activation. In conclusion, our findings suggest that altered electrical activity can regulate cardiomyocyte communication by influencing the acetylation status of Cx43.
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Affiliation(s)
- Viviana Meraviglia
- Laboratory of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Milano, Italy; Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano Italy
| | - Valerio Azzimato
- Laboratory of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Milano, Italy; Department of Pharmacology, Chemotherapy and Medical Toxicology, Università degli Studi di Milano, Milano, Italy
| | - Claudia Colussi
- Istituto di Patologia Medica, Università Cattolica del SacroCuore, Roma, Italy
| | | | - Anna Binda
- Department of Health Science, University of Milano Bicocca, Monza, Italy
| | - Alice Panariti
- Department of Health Science, University of Milano Bicocca, Monza, Italy
| | - Khaled Qanud
- Department of Physiology, New York Medical College, Valhalla, NY, United States
| | - Silvia Suffredini
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano Italy
| | - Laura Gennaccaro
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano Italy; Department of Life Sciences, University of Parma, Parma, Italy
| | - Michele Miragoli
- CERT, Center of Excellence for Toxicological Research, INAIL, ex ISPESL, University of Parma, Parma, Italy; Humanitas Clinical and Research Center, Rozzano Milano, Italy
| | - Andrea Barbuti
- The PaceLab, Department of Biosciences, Università di Milano, Italy
| | - Paul D Lampe
- Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Carlo Gaetano
- Division of Cardiovascular Epigenetics, Department of Cardiology, Goethe University, Frankfurt am Main, Germany
| | - Peter P Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano Italy
| | - Maurizio C Capogrossi
- Laboratory of Vascular Pathology, Istituto Dermopatico dell'Immacolata IRCCS, Roma, Italy
| | - Fabio A Recchia
- Department of Physiology, Temple University School of Medicine, Philadelphia, PA, United States; Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Giulio Pompilio
- Laboratory of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino IRCCS, Milano, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milano, Italy
| | - Ilaria Rivolta
- Department of Health Science, University of Milano Bicocca, Monza, Italy
| | - Alessandra Rossini
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano Italy.
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Chen Y, Du J, Zhao YT, Zhang L, Lv G, Zhuang S, Qin G, Zhao TC. Histone deacetylase (HDAC) inhibition improves myocardial function and prevents cardiac remodeling in diabetic mice. Cardiovasc Diabetol 2015; 14:99. [PMID: 26245924 PMCID: PMC4527099 DOI: 10.1186/s12933-015-0262-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 07/18/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent evidence indicates that inhibition of histone deacetylase (HDAC) protects the heart against myocardial injury and stimulates endogenous angiomyogenesis. However, it remains unknown whether HDAC inhibition produces the protective effect in the diabetic heart. We sought to determine whether HDAC inhibition preserves cardiac performance and suppresses cardiac remodeling in diabetic cardiomyopathy. METHODS Adult ICR mice received an intraperitoneal injection of either streptozotocin (STZ, 200 mg/kg) to establish the diabetic model or vehicle to serve as control. Once hyperglycemia was confirmed, diabetic mice received sodium butyrate (1%), a specific HDAC inhibitor, in drinking water on a daily basis to inhibit HDAC activity. Mice were randomly divided into following groups, which includes Control, Control + Sodium butyrate (NaBu), STZ and STZ + Sodium butyrate (NaBu), respectively. Myocardial function was serially assessed at 7, 14, 21 weeks following treatments. RESULTS Echocardiography demonstrated that cardiac function was depressed in diabetic mice, but HDAC inhibition resulted in a significant functional improvement in STZ-injected mice. Likewise, HDAC inhibition attenuates cardiac hypertrophy, as evidenced by a reduced heart/tibia ratio and areas of cardiomyocytes, which is associated with reduced interstitial fibrosis and decreases in active caspase-3 and apoptotic stainings, but also increased angiogenesis in diabetic myocardium. Notably, glucose transporters (GLUT) 1 and 4 were up-regulated following HDAC inhibition, which was accompanied with increases of GLUT1 acetylation and p38 phosphorylation. Furthermore, myocardial superoxide dismutase, an important antioxidant, was elevated following HDAC inhibition in the diabetic mice. CONCLUSION HDAC inhibition plays a critical role in improving cardiac function and suppressing myocardial remodeling in diabetic heart.
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Affiliation(s)
- Youfang Chen
- Department of Surgery, Boston University Medical School, Roger Williams Medical Center, Boston University, 50 Maude Street, Providence, RI, 02908, USA.
| | - Jianfeng Du
- Department of Surgery, Boston University Medical School, Roger Williams Medical Center, Boston University, 50 Maude Street, Providence, RI, 02908, USA.
| | - Yu Tina Zhao
- Department of Surgery, Boston University Medical School, Roger Williams Medical Center, Boston University, 50 Maude Street, Providence, RI, 02908, USA.
| | - Ling Zhang
- Department of Medicine, Rhode Island Hospital, Brown University, Providence, RI, USA.
| | - Guorong Lv
- Department of Ultrasound, Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.
| | - Shougang Zhuang
- Department of Medicine, Rhode Island Hospital, Brown University, Providence, RI, USA.
| | - Gangjian Qin
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, USA.
| | - Ting C Zhao
- Department of Surgery, Boston University Medical School, Roger Williams Medical Center, Boston University, 50 Maude Street, Providence, RI, 02908, USA.
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Ranek MJ, Zheng H, Huang W, Kumarapeli AR, Li J, Liu J, Wang X. Genetically induced moderate inhibition of 20S proteasomes in cardiomyocytes facilitates heart failure in mice during systolic overload. J Mol Cell Cardiol 2015; 85:273-81. [PMID: 26116868 PMCID: PMC4530032 DOI: 10.1016/j.yjmcc.2015.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
Abstract
The in vivo function status of the ubiquitin-proteasome system (UPS) in pressure overloaded hearts remains undefined. Cardiotoxicity was observed during proteasome inhibitor chemotherapy, especially in those with preexisting cardiovascular conditions; however, proteasome inhibition (PsmI) was also suggested by some experimental studies as a potential therapeutic strategy to curtail cardiac hypertrophy. Here we used genetic approaches to probe cardiac UPS performance and determine the impact of cardiomyocyte-restricted PsmI (CR-PsmI) on cardiac responses to systolic overload. Transgenic mice expressing an inverse reporter of the UPS (GFPdgn) were subject to transverse aortic constriction (TAC) to probe myocardial UPS performance during systolic overload. Mice with or without moderate CR-PsmI were subject to TAC and temporally characterized for cardiac responses to moderate and severe systolic overload. After moderate TAC (pressure gradient: ~40mmHg), cardiac UPS function was upregulated during the first two weeks but turned to functional insufficiency between 6 and 12weeks as evidenced by the dynamic changes in GFPdgn protein levels, proteasome peptidase activities, and total ubiquitin conjugates. Severe TAC (pressure gradients >60mmHg) led to UPS functional insufficiency within a week. Moderate TAC elicited comparable hypertrophic responses between mice with and without genetic CR-PsmI but caused cardiac malfunction in CR-PsmI mice significantly earlier than those without CR-PsmI. In mice subject to severe TAC, CR-PsmI inhibited cardiac hypertrophy but led to rapidly progressed heart failure and premature death, associated with a pronounced increase in cardiomyocyte death. It is concluded that cardiac UPS function is dynamically altered, with the initial brief upregulation of proteasome function being adaptive; and CR-PsmI facilitates cardiac malfunction during systolic overload.
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Affiliation(s)
- Mark J Ranek
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA.
| | - Hanqiao Zheng
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA.
| | - Wei Huang
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA.
| | - Asangi R Kumarapeli
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA.
| | - Jie Li
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA.
| | - Jinbao Liu
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA; State Key Lab of Respiratory Disease, Protein Modification and Degradation Lab, Department of Pathophysiology, Guangzhou Medical University, Guangdong 510182, China.
| | - Xuejun Wang
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA.
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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Meiners S, Keller IE, Semren N, Caniard A. Regulation of the proteasome: evaluating the lung proteasome as a new therapeutic target. Antioxid Redox Signal 2014; 21:2364-82. [PMID: 24437504 DOI: 10.1089/ars.2013.5798] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE Lung diseases are on the second rank worldwide with respect to morbidity and mortality. For most respiratory diseases, no effective therapies exist. Whereas the proteasome has been successfully evaluated as a novel target for therapeutic interventions in cancer, neurodegenerative, and cardiac disorders, there is a profound lack of knowledge on the regulation of proteasome activity in chronic and acute lung diseases. RECENT ADVANCES There are various means of how the amount of active proteasome complexes in the cell can be regulated such as transcriptional regulation of proteasomal subunit expression, association with different regulators, assembly and half-life of proteasomes and regulatory complexes, as well as post-translational modifications. It also becomes increasingly evident that proteasome activity is fine-tuned and depends on the state of the cell. We propose here that 20S proteasomes and their regulators can be regarded as dynamic building blocks, which assemble or disassemble in response to cellular needs. The composition of proteasome complexes in a cell may vary depending on tissue, cell type and compartment, stage of development, or pathological context. CRITICAL ISSUES AND FUTURE DIRECTIONS Dissecting the expression and regulation of the various catalytic forms of 20S proteasomes, such as constitutive, immuno-, and mixed proteasomes, together with their associated regulatory complexes will not only greatly enhance our understanding of proteasome function in lung pathogenesis but will also pave the way to develop new classes of drugs that inhibit or activate proteasome function in a defined setting for treatment of lung diseases.
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Affiliation(s)
- Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital , Ludwig-Maximilians University, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
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35
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Zong N, Ping P, Lau E, Choi HJH, Ng DCM, Meyer D, Fang C, Li H, Wang D, Zelaya IM, Yates JR, Lam MPY. Lysine ubiquitination and acetylation of human cardiac 20S proteasomes. Proteomics Clin Appl 2014; 8:590-594. [PMID: 24957502 PMCID: PMC5094860 DOI: 10.1002/prca.201400029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/12/2014] [Accepted: 06/10/2014] [Indexed: 11/06/2022]
Abstract
PURPOSE Altered proteasome functions are associated with multiple cardiomyopathies. While the proteasome targets polyubiquitinated proteins for destruction, it itself is modifiable by ubiquitination. We aim to identify the exact ubiquitination sites on cardiac proteasomes and examine whether they are also subject to acetylations. EXPERIMENTAL DESIGN Assembled cardiac 20S proteasome complexes were purified from five human hearts with ischemic cardiomyopathy, then analyzed by high-resolution MS to identify ubiquitination and acetylation sites. We developed a library search strategy that may be used to complement database search in identifying PTM in different samples. RESULTS We identified 63 ubiquitinated lysines from intact human cardiac 20S proteasomes. In parallel, 65 acetylated residues were also discovered, 39 of which shared with ubiquitination sites. CONCLUSION AND CLINICAL RELEVANCE This is the most comprehensive characterization of cardiac proteasome ubiquitination to date. There are significant overlaps between the discovered ubiquitination and acetylation sites, permitting potential crosstalk in regulating proteasome functions. The information presented here will aid future therapeutic strategies aimed at regulating the functions of cardiac proteasomes.
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Affiliation(s)
- Nobel Zong
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Peipei Ping
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Edward Lau
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Howard JH Choi
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Dominic CM Ng
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Meyer
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Caiyun Fang
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Haomin Li
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ding Wang
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ivette M Zelaya
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Maggie PY Lam
- The NHLBI Proteomics Center at UCLA, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Departments of Physiology and Medicine/Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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36
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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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Cui Z, Scruggs SB, Gilda JE, Ping P, Gomes AV. Regulation of cardiac proteasomes by ubiquitination, SUMOylation, and beyond. J Mol Cell Cardiol 2014; 71:32-42. [PMID: 24140722 PMCID: PMC3990655 DOI: 10.1016/j.yjmcc.2013.10.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/21/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
The ubiquitin-proteasome system (UPS) is the major intracellular degradation system, and its proper function is critical to the health and function of cardiac cells. Alterations in cardiac proteasomes have been linked to several pathological phenotypes, including cardiomyopathies, ischemia-reperfusion injury, heart failure, and hypertrophy. Defects in proteasome-dependent cellular protein homeostasis can be causal for the initiation and progression of certain cardiovascular diseases. Emerging evidence suggests that the UPS can specifically target proteins that govern pathological signaling pathways for degradation, thus altering downstream effectors and disease outcomes. Alterations in UPS-substrate interactions in disease occur, in part, due to direct modifications of 19S, 11S or 20S proteasome subunits. Post-translational modifications (PTMs) are one facet of this proteasomal regulation, with over 400 known phosphorylation sites, over 500 ubiquitination sites and 83 internal lysine acetylation sites, as well as multiple sites for caspase cleavage, glycosylation (such as O-GlcNAc modification), methylation, nitrosylation, oxidation, and SUMOylation. Changes in cardiac proteasome PTMs, which occur in ischemia and cardiomyopathies, are associated with changes in proteasome activity and proteasome assembly; however several features of this regulation remain to be explored. In this review, we focus on how some of the less common PTMs affect proteasome function and alter cellular protein homeostasis. This article is part of a Special Issue entitled "Protein Quality Control, the Ubiquitin Proteasome System, and Autophagy".
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Affiliation(s)
- Ziyou Cui
- Department of Neurobiology, Physiology and Behavior, University of California, Davis CA 95616, USA
| | - Sarah B Scruggs
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
| | - Jennifer E Gilda
- Department of Neurobiology, Physiology and Behavior, University of California, Davis CA 95616, USA
| | - Peipei Ping
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology and Behavior, University of California, Davis CA 95616, USA; Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, USA.
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38
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X'avia Chan CY, Wang D, Cadeiras M, Deng MC, Ping P. S-nitrosylation of TRIM72 mends the broken heart: a molecular modifier-mediated cardioprotection. J Mol Cell Cardiol 2014; 72:292-5. [PMID: 24735828 DOI: 10.1016/j.yjmcc.2014.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 04/01/2014] [Accepted: 04/04/2014] [Indexed: 11/16/2022]
Affiliation(s)
- C Y X'avia Chan
- NHLBI Proteomics Center at UCLA, Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, CA 90095, USA; Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, CA 90095, USA.
| | - Ding Wang
- NHLBI Proteomics Center at UCLA, Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, CA 90095, USA; Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, CA 90095, USA.
| | - Martin Cadeiras
- Ronald Reagan UCLA Medical Center, UCLA Medical Center, Santa Monica, USA.
| | - Mario C Deng
- Ronald Reagan UCLA Medical Center, UCLA Medical Center, Santa Monica, USA.
| | - Peipei Ping
- NHLBI Proteomics Center at UCLA, Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, CA 90095, USA; Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, CA 90095, USA.
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Gregorich ZR, Chang YH, Ge Y. Proteomics in heart failure: top-down or bottom-up? Pflugers Arch 2014; 466:1199-209. [PMID: 24619480 DOI: 10.1007/s00424-014-1471-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 01/31/2014] [Accepted: 02/04/2014] [Indexed: 01/11/2023]
Abstract
The pathophysiology of heart failure (HF) is diverse, owing to multiple etiologies and aberrations in a number of cellular processes. Therefore, it is essential to understand how defects in the molecular pathways that mediate cellular responses to internal and external stressors function as a system to drive the HF phenotype. Mass spectrometry (MS)-based proteomics strategies have great potential for advancing our understanding of disease mechanisms at the systems level because proteins are the effector molecules for all cell functions and, thus, are directly responsible for determining cell phenotype. Two MS-based proteomics strategies exist: peptide-based bottom-up and protein-based top-down proteomics--each with its own unique strengths and weaknesses for interrogating the proteome. In this review, we will discuss the advantages and disadvantages of bottom-up and top-down MS for protein identification, quantification, and analysis of post-translational modifications, as well as highlight how both of these strategies have contributed to our understanding of the molecular and cellular mechanisms underlying HF. Additionally, the challenges associated with both proteomics approaches will be discussed and insights will be offered regarding the future of MS-based proteomics in HF research.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
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40
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Wang X, Robbins J. Proteasomal and lysosomal protein degradation and heart disease. J Mol Cell Cardiol 2013; 71:16-24. [PMID: 24239609 DOI: 10.1016/j.yjmcc.2013.11.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 01/08/2023]
Abstract
In the cell, the proteasome and lysosomes represent the most important proteolytic machineries, responsible for the protein degradation in the ubiquitin-proteasome system (UPS) and autophagy, respectively. Both the UPS and autophagy are essential to protein quality and quantity control. Alterations in cardiac proteasomal and lysosomal degradation are remarkably associated with most heart disease in humans and are implicated in the pathogenesis of congestive heart failure. Studies carried out in animal models and in cell culture have begun to establish both sufficiency and, in some cases, the necessity of proteasomal functional insufficiency or lysosomal insufficiency as a major pathogenic factor in the heart. This review article highlights some recent advances in the research into proteasome and lysosome protein degradation in relation to cardiac pathology and examines the emerging evidence for enhancing degradative capacities of the proteasome and/or lysosome as a new therapeutic strategy for heart disease. This article is part of a Special Issue entitled "Protein Quality Control, the Ubiquitin Proteasome System, and Autophagy".
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Affiliation(s)
- Xuejun Wang
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD 57069, USA.
| | - Jeffrey Robbins
- Division of Molecular Cardiovascular Biology, The Heart Institute, Department of Pediatrics, The Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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