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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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52
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Kerek EM, Yoon KH, Luo SY, Chen J, Valencia R, Julien O, Waskiewicz AJ, Hubbard BP. A conserved acetylation switch enables pharmacological control of tubby-like protein stability. J Biol Chem 2020; 296:100073. [PMID: 33187986 PMCID: PMC7948452 DOI: 10.1074/jbc.ra120.015839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/30/2020] [Accepted: 11/13/2020] [Indexed: 12/29/2022] Open
Abstract
Tubby-like proteins (TULPs) are characterized by a conserved C-terminal domain that binds phosphoinositides. Collectively, mammalian TULP1-4 proteins play essential roles in intracellular transport, cell differentiation, signaling, and motility. Yet, little is known about how the function of these proteins is regulated in cells. Here, we present the protein–protein interaction network of TULP3, a protein that is responsible for the trafficking of G-protein-coupled receptors to cilia and whose aberrant expression is associated with severe developmental disorders and polycystic kidney disease. We identify several protein interaction nodes linked to TULP3 that include enzymes involved in acetylation and ubiquitination. We show that acetylation of two key lysine residues on TULP3 by p300 increases TULP3 protein abundance and that deacetylation of these sites by HDAC1 decreases protein levels. Furthermore, we show that one of these sites is ubiquitinated in the absence of acetylation and that acetylation inversely correlates with ubiquitination of TULP3. This mechanism is evidently conserved across species and is active in zebrafish during development. Finally, we identify this same regulatory module in TULP1, TULP2, and TULP4 and demonstrate that the stability of these proteins is similarly modulated by an acetylation switch. This study unveils a signaling pathway that links nuclear enzymes to ciliary membrane receptors via TULP3, describes a dynamic mechanism for the regulation of all tubby-like proteins, and explores how to exploit it pharmacologically using drugs.
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Affiliation(s)
- Evan M Kerek
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin H Yoon
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Shu Y Luo
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jerry Chen
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Robert Valencia
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew J Waskiewicz
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Basil P Hubbard
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada.
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Teixeira CSS, Cerqueira NMFSA, Gomes P, Sousa SF. A Molecular Perspective on Sirtuin Activity. Int J Mol Sci 2020; 21:ijms21228609. [PMID: 33203121 PMCID: PMC7696986 DOI: 10.3390/ijms21228609] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
The protein acetylation of either the α-amino groups of amino-terminal residues or of internal lysine or cysteine residues is one of the major posttranslational protein modifications that occur in the cell with repercussions at the protein as well as at the metabolome level. The lysine acetylation status is determined by the opposing activities of lysine acetyltransferases (KATs) and lysine deacetylases (KDACs), which add and remove acetyl groups from proteins, respectively. A special group of KDACs, named sirtuins, that require NAD+ as a substrate have received particular attention in recent years. They play critical roles in metabolism, and their abnormal activity has been implicated in several diseases. Conversely, the modulation of their activity has been associated with protection from age-related cardiovascular and metabolic diseases and with increased longevity. The benefits of either activating or inhibiting these enzymes have turned sirtuins into attractive therapeutic targets, and considerable effort has been directed toward developing specific sirtuin modulators. This review summarizes the protein acylation/deacylation processes with a special focus on the current developments in the sirtuin research field.
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Affiliation(s)
- Carla S. S. Teixeira
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
| | - Pedro Gomes
- Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
- Center for Health Technology and Services Research (CINTESIS), University of Porto, R. Dr. Plácido da Costa, 4200-450 Porto, Portugal
- Institute of Pharmacology and Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Azinhaga Santa Comba, Celas, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Azinhaga Santa Comba, Celas, 3000-548 Coimbra, Portugal
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
- Correspondence: ; Tel.: +351-22-551-3600
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54
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Geng A, Tang H, Huang J, Qian Z, Qin N, Yao Y, Xu Z, Chen H, Lan L, Xie H, Zhang J, Jiang Y, Mao Z. The deacetylase SIRT6 promotes the repair of UV-induced DNA damage by targeting DDB2. Nucleic Acids Res 2020; 48:9181-9194. [PMID: 32789493 PMCID: PMC7498349 DOI: 10.1093/nar/gkaa661] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 12/22/2022] Open
Abstract
The NAD+-dependent deacetylase and mono-ADP-ribosyl transferase SIRT6 stabilizes the genome by promoting DNA double strand break repair, thereby acting as a tumor suppressor. However, whether SIRT6 regulates nucleotide excision repair (NER) remains unknown. Here, we showed that SIRT6 was recruited to sites of UV-induced DNA damage and stimulated the repair of UV-induced DNA damage. Mechanistic studies further indicated that SIRT6 interacted with DDB2, the major sensor initiating global genome NER (GG-NER), and that the interaction was enhanced upon UV irradiation. SIRT6 deacetylated DDB2 at two lysine residues, K35 and K77, upon UV stress and then promoted DDB2 ubiquitination and segregation from chromatin, thereby facilitating downstream signaling. In addition, we characterized several SIRT6 mutations derived from melanoma patients. These SIRT6 mutants ablated the stimulatory effect of SIRT6 on NER and destabilized the genome due to (i) partial loss of enzymatic activity (P27S or H50Y), (ii) a nonsense mutation (R150*) or (iii) high turnover rates (G134W). Overall, we demonstrate that SIRT6 promotes NER by deacetylating DDB2, thereby preventing the onset of melanomagenesis.
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Affiliation(s)
- Anke Geng
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Huanyin Tang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jin Huang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control of Ministry of Education, Guizhou Medical University, Guiyang 550025, China
| | - Zhen Qian
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Nan Qin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yunxia Yao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.,College of Pharmacy, Yanbian University, Yanji 133002, Jilin Province, China
| | - Zhu Xu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hao Chen
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Li Lan
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Hongjuan Xie
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine, 200025 Shanghai, China
| | - Ying Jiang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiyong Mao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.,Tsingtao Advanced Research Institute, Tongji University, 67 Yinchuan West Road, Qingdao 266071, China
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O'Connor M, Shentu YP, Wang G, Hu WT, Xu ZD, Wang XC, Liu R, Man HY. Acetylation of AMPA Receptors Regulates Receptor Trafficking and Rescues Memory Deficits in Alzheimer's Disease. iScience 2020; 23:101465. [PMID: 32861999 PMCID: PMC7476873 DOI: 10.1016/j.isci.2020.101465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 07/21/2020] [Accepted: 08/13/2020] [Indexed: 12/26/2022] Open
Abstract
In Alzheimer's disease (AD), decreases in the amount and synaptic localization of AMPA receptors (AMPARs) result in weakened synaptic activity and dysfunction in synaptic plasticity, leading to impairments in cognitive functions. We have previously found that AMPARs are subject to lysine acetylation, resulting in higher AMPAR stability and protein accumulation. Here we report that AMPAR acetylation was significantly reduced in AD and neurons with Aβ incubation. We identified p300 as the acetyltransferase responsible for AMPAR acetylation and found that enhancing GluA1 acetylation ameliorated Aβ-induced reductions in total and cell-surface AMPARs. Importantly, expression of acetylation mimetic GluA1 (GluA1-4KQ) in APP/PS1 mice rescued impairments in synaptic plasticity and memory. These findings indicate that Aβ-induced reduction in AMPAR acetylation and stability contributes to synaptopathy and memory deficiency in AD, suggesting that AMPAR acetylation may be an effective molecular target for AD therapeutics.
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Affiliation(s)
- Margaret O'Connor
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Yang-Ping Shentu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guan Wang
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Wen-Ting Hu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhen-Dong Xu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiao-Chuan Wang
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rong Liu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Heng-Ye Man
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, 72 East Concord St., L-603, Boston, MA 02118, USA
- Center for Systems Neuroscience, Boston University, 610 Commonwealth Avenue, Boston, MA, USA
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56
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Wu Y, Wang X, Xu F, Zhang L, Wang T, Fu X, Jin T, Zhang W, Ye L. The regulation of acetylation and stability of HMGA2 via the HBXIP-activated Akt-PCAF pathway in promotion of esophageal squamous cell carcinoma growth. Nucleic Acids Res 2020; 48:4858-4876. [PMID: 32313942 PMCID: PMC7229824 DOI: 10.1093/nar/gkaa232] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/02/2020] [Accepted: 04/12/2020] [Indexed: 12/16/2022] Open
Abstract
High-mobility group AT-hook 2 (HMGA2) is an architectural transcription factor that plays essential roles in embryonic development and cancer progression. However, the mechanism of HMGA2 regulation remains largely uncharacterized. Here, we demonstrate that HMGA2 can be modulated by hepatitis B X-interacting protein (HBXIP), an oncogenic transcriptional coactivator, in esophageal squamous cell carcinoma (ESCC). HMGA2 expression was positively associated with HBXIP expression in clinical ESCC tissues, and their high levels were associated with advanced tumor stage and reduced overall and disease-free survival. We found that oncogenic HBXIP could posttranslationally upregulate HMGA2 protein level in ESCC cells. HBXIP induced HMGA2 acetylation at the lysine 26 (K26), resulting in HMGA2 protein accumulation. In this process, HBXIP increased the acetyltransferase p300/CBP-associated factor (PCAF) phosphorylation and activation via the Akt pathway, then PCAF directly interacted with HMGA2, leading to HMGA2 acetylation in the cells. HMGA2 K26 acetylation enhanced its DNA binding capacity and blocked its ubiquitination and then inhibited proteasome-dependent degradation. Functionally, HBXIP-stabilized HMGA2 could promote ESCC cell growth in vitro and in vivo. Strikingly, aspirin suppressed ESCC growth by inhibiting HBXIP and HMGA2. Collectively, our findings disclose a new mechanism for the posttranslational regulation of HMGA2 mediated by HBXIP in ESCC.
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Affiliation(s)
- Yue Wu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Xue Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Feifei Xu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Lu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Tianjiao Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Xueli Fu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Tianzhi Jin
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Weiying Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Lihong Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, P.R. China
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Zmuda F, Chamberlain LH. Regulatory effects of post-translational modifications on zDHHC S-acyltransferases. J Biol Chem 2020; 295:14640-14652. [PMID: 32817054 PMCID: PMC7586229 DOI: 10.1074/jbc.rev120.014717] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
The human zDHHC S-acyltransferase family comprises 23 enzymes that mediate the S-acylation of a multitude of cellular proteins, including channels, receptors, transporters, signaling molecules, scaffolds, and chaperones. This reversible post-transitional modification (PTM) involves the attachment of a fatty acyl chain, usually derived from palmitoyl-CoA, to specific cysteine residues on target proteins, which affects their stability, localization, and function. These outcomes are essential to control many processes, including synaptic transmission and plasticity, cell growth and differentiation, and infectivity of viruses and other pathogens. Given the physiological importance of S-acylation, it is unsurprising that perturbations in this process, including mutations in ZDHHC genes, have been linked to different neurological pathologies and cancers, and there is growing interest in zDHHC enzymes as novel drug targets. Although zDHHC enzymes control a diverse array of cellular processes and are associated with major disorders, our understanding of these enzymes is surprisingly incomplete, particularly with regard to the regulatory mechanisms controlling these enzymes. However, there is growing evidence highlighting the role of different PTMs in this process. In this review, we discuss how PTMs, including phosphorylation, S-acylation, and ubiquitination, affect the stability, localization, and function of zDHHC enzymes and speculate on possible effects of PTMs that have emerged from larger screening studies. Developing a better understanding of the regulatory effects of PTMs on zDHHC enzymes will provide new insight into the intracellular dynamics of S-acylation and may also highlight novel approaches to modulate S-acylation for clinical gain.
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Affiliation(s)
- Filip Zmuda
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
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Gcn5p and Ubp8p Affect Protein Ubiquitylation and Cell Proliferation by Altering the Fermentative/Respiratory Flux Balance in Saccharomyces cerevisiae. mBio 2020; 11:mBio.01504-20. [PMID: 32788380 PMCID: PMC7439465 DOI: 10.1128/mbio.01504-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We propose a study showing a novel role of Gcn5p and Ubp8p in the process of ubiquitylation of the yeast proteome which includes main glycolytic enzymes. Interestingly, in the absence of Gcn5p and Ubp8p glucose consumption and redox balance were altered in yeast. We believe that these results and the role of Gcn5p and Ubp8p in sugar metabolism might open new perspectives of research leading to novel protocols for counteracting the enhanced glycolysis in tumors. Protein ubiquitylation regulates not only endocellular trafficking and proteasomal degradation but also the catalytic activity of enzymes. In Saccharomyces cerevisiae, we analyzed the composition of the ubiquitylated proteomes in strains lacking acetyltransferase Gcn5p, Ub-protease Ubp8p, or both to understand their involvement in the regulation of protein ubiquitylation. We analyzed His6Ub proteins with a proteomic approach coupling micro-liquid chromatography and tandem mass spectrometry (μLC-MS/MS) in gcn5Δ, ubp8Δ and ubp8Δ gcn5Δ strains. The Ub-proteome altered in the absence of Gcn5p, Ubp8p, or both was characterized, showing that 43% of the proteins was shared in all strains, suggesting their functional relationship. Remarkably, all major glycolytic enzymes showed increased ubiquitylation. Phosphofructokinase 1, the key enzyme of glycolytic flux, showed a higher and altered pattern of ubiquitylation in gcn5Δ and ubp8Δ strains. Severe defects of growth in poor sugar and altered glucose consumption confirmed a direct role of Gcn5p and Ubp8p in affecting the REDOX balance of the cell.
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Regulation of organic anion transporters: Role in physiology, pathophysiology, and drug elimination. Pharmacol Ther 2020; 217:107647. [PMID: 32758646 DOI: 10.1016/j.pharmthera.2020.107647] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/27/2020] [Indexed: 12/24/2022]
Abstract
The members of the organic anion transporter (OAT) family are mainly expressed in kidney, liver, placenta, intestine, and brain. These transporters play important roles in the disposition of clinical drugs, pesticides, signaling molecules, heavy metal conjugates, components of phytomedicines, and toxins, and therefore critical for maintaining systemic homeostasis. Alterations in the expression and function of OATs contribute to the intra- and inter-individual variability of the therapeutic efficacy and the toxicity of many drugs, and to many pathophysiological conditions. Consequently, the activity of these transporters must be highly regulated to carry out their normal functions. This review will present an update on the recent advance in understanding the cellular and molecular mechanisms underlying the regulation of renal OATs, emphasizing on the post-translational modification (PTM), the crosstalk among these PTMs, and the remote sensing and signaling network of OATs. Such knowledge will provide significant insights into the roles of these transporters in health and disease.
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60
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Ray P, Raghunathan K, Ahsan A, Allam US, Shukla S, Basrur V, Veatch S, Lawrence TS, Nyati MK, Ray D. Ubiquitin ligase SMURF2 enhances epidermal growth factor receptor stability and tyrosine-kinase inhibitor resistance. J Biol Chem 2020; 295:12661-12673. [PMID: 32669362 DOI: 10.1074/jbc.ra120.013519] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
The discovery of activating epidermal growth factor receptor (EGFR) mutations spurred the use of EGFR tyrosine kinase inhibitors (TKIs), such as erlotinib, as the first-line treatment of lung cancers. We previously reported that differential degradation of TKI-sensitive (e.g. L858R) and resistant (T790M) EGFR mutants upon erlotinib treatment correlates with drug sensitivity. We also reported that SMAD ubiquitination regulatory factor 2 (SMURF2) ligase activity is important in stabilizing EGFR. However, the molecular mechanisms involved remain unclear. Here, using in vitro and in vivo ubiquitination assays, MS, and superresolution microscopy, we show SMURF2-EGFR functional interaction is important for EGFR stability and response to TKI. We demonstrate that L858R/T790M EGFR is preferentially stabilized by SMURF2-UBCH5 (an E3-E2)-mediated polyubiquitination. We identified four lysine residues as the sites of ubiquitination and showed that replacement of one of them with acetylation-mimicking glutamine increases the sensitivity of mutant EGFR to erlotinib-induced degradation. We show that SMURF2 extends membrane retention of EGF-bound EGFR, whereas SMURF2 knockdown increases receptor sorting to lysosomes. In lung cancer cell lines, SMURF2 overexpression increased EGFR levels, improving TKI tolerance, whereas SMURF2 knockdown decreased EGFR steady-state levels and sensitized lung cancer cells. Overall, we propose that SMURF2-mediated polyubiquitination of L858R/T790M EGFR competes with acetylation-mediated receptor internalization that correlates with enhanced receptor stability; therefore, disruption of the E3-E2 complex may be an attractive target to overcome TKI resistance.
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Affiliation(s)
- Paramita Ray
- Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Krishnan Raghunathan
- Department of Biophysics, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Aarif Ahsan
- Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Uday Sankar Allam
- Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shirish Shukla
- Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Venkatesha Basrur
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sarah Veatch
- Department of Biophysics, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Theodore S Lawrence
- Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Mukesh K Nyati
- Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Dipankar Ray
- Department of Radiation Oncology, The University of Michigan Medical School, Ann Arbor, Michigan, USA
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Hamminger P, Rica R, Ellmeier W. Histone deacetylases as targets in autoimmune and autoinflammatory diseases. Adv Immunol 2020; 147:1-59. [PMID: 32981634 DOI: 10.1016/bs.ai.2020.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Reversible lysine acetylation of histones is a key epigenetic regulatory process controlling gene expression. Reversible histone acetylation is mediated by two opposing enzyme families: histone acetyltransferases (HATs) and histone deacetylases (HDACs). Moreover, many non-histone targets of HATs and HDACs are known, suggesting a crucial role for lysine acetylation as a posttranslational modification on the cellular proteome and protein function far beyond chromatin-mediated gene regulation. The HDAC family consists of 18 members and pan-HDAC inhibitors (HDACi) are clinically used for the treatment of certain types of cancer. HDACi or individual HDAC member-deficient (cell lineage-specific) mice have also been tested in a large number of preclinical mouse models for several autoimmune and autoinflammatory diseases and in most cases HDACi treatment results in an attenuation of clinical disease severity. A reduction of disease severity has also been observed in mice lacking certain HDAC members. This indicates a high therapeutic potential of isoform-selective HDACi for immune-mediated diseases. Isoform-selective HDACi and thus targeted inactivation of HDAC isoforms might also overcome the adverse effects of current clinically approved pan-HDACi. This review provides a brief overview about the fundamental function of HDACs as epigenetic regulators, highlights the roles of HDACs beyond chromatin-mediated control of gene expression and summarizes the studies showing the impact of HDAC inhibitors and genetic deficiencies of HDAC members for the outcome of autoimmune and autoinflammatory diseases with a focus on rheumatoid arthritis, inflammatory bowel disease and experimental autoimmune encephalomyelitis (EAE) as an animal model of multiple sclerosis.
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Affiliation(s)
- Patricia Hamminger
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ramona Rica
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Wilfried Ellmeier
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
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Bonjoch L, Franch-Expósito S, Garre P, Belhadj S, Muñoz J, Arnau-Collell C, Díaz-Gay M, Gratacós-Mulleras A, Raimondi G, Esteban-Jurado C, Soares de Lima Y, Herrera-Pariente C, Cuatrecasas M, Ocaña T, Castells A, Fillat C, Capellá G, Balaguer F, Caldés T, Valle L, Castellví-Bel S. Germline Mutations in FAF1 Are Associated With Hereditary Colorectal Cancer. Gastroenterology 2020; 159:227-240.e7. [PMID: 32179092 DOI: 10.1053/j.gastro.2020.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/19/2020] [Accepted: 03/08/2020] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS A significant proportion of colorectal cancer (CRC) cases have familial aggregation but little is known about the genetic factors that contribute to these cases. We performed an exhaustive functional characterization of genetic variants associated with familial CRC. METHODS We performed whole-exome sequencing analyses of 75 patients from 40 families with a history of CRC (including early-onset cases) of an unknown germline basis (discovery cohort). We also sequenced specific genes in DNA from an external replication cohort of 473 families, including 488 patients with colorectal tumors that had normal expression of mismatch repair proteins (validation cohort). We disrupted the Fas-associated factor 1 gene (FAF1) in DLD-1 CRC cells using CRISPR/Cas9 gene editing; some cells were transfected with plasmids that express FAF1 missense variants. Cells were analyzed by immunoblots, quantitative real-time polymerase chain reaction, and functional assays monitoring apoptosis, proliferation, and assays for Wnt signaling or nuclear factor (NF)-kappa-B activity. RESULTS We identified predicted pathogenic variant in the FAF1 gene (c.1111G>A; p.Asp371Asn) in the discovery cohort; it was present in 4 patients of the same family. We identified a second variant in FAF1 in the validation cohort (c.254G>C; p.Arg85Pro). Both variants encoded unstable FAF1 proteins. Expression of these variants in CRC cells caused them to become resistant to apoptosis, accumulate beta-catenin in the cytoplasm, and translocate NF-kappa-B to the nucleus. CONCLUSIONS In whole-exome sequencing analyses of patients from families with a history of CRC, we identified variants in FAF1 that associate with development of CRC. These variants encode unstable forms of FAF1 that increase resistance of CRC cells to apoptosis and increase activity of beta-catenin and NF-kappa-B.
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Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Pilar Garre
- Molecular Oncology Laboratory, Centro Investigación Biomédica en Red de Cáncer (CIBERONC). Hospital Clínico San Carlos. Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Sami Belhadj
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Marcos Díaz-Gay
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Anna Gratacós-Mulleras
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Giulia Raimondi
- Gene Therapy and Cancer, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat de Barcelona, Barcelona, Spain
| | - Clara Esteban-Jurado
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Herrera-Pariente
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Fillat
- Gene Therapy and Cancer, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universitat de Barcelona, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Centro Investigación Biomédica en Red de Cáncer (CIBERONC). Hospital Clínico San Carlos. Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.
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Kulka LAM, Fangmann PV, Panfilova D, Olzscha H. Impact of HDAC Inhibitors on Protein Quality Control Systems: Consequences for Precision Medicine in Malignant Disease. Front Cell Dev Biol 2020; 8:425. [PMID: 32582706 PMCID: PMC7291789 DOI: 10.3389/fcell.2020.00425] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/07/2020] [Indexed: 12/21/2022] Open
Abstract
Lysine acetylation is one of the major posttranslational modifications (PTM) in human cells and thus needs to be tightly regulated by the writers of this process, the histone acetyl transferases (HAT), and the erasers, the histone deacetylases (HDAC). Acetylation plays a crucial role in cell signaling, cell cycle control and in epigenetic regulation of gene expression. Bromodomain (BRD)-containing proteins are readers of the acetylation mark, enabling them to transduce the modification signal. HDAC inhibitors (HDACi) have been proven to be efficient in hematologic malignancies with four of them being approved by the FDA. However, the mechanisms by which HDACi exert their cytotoxicity are only partly resolved. It is likely that HDACi alter the acetylation pattern of cytoplasmic proteins, contributing to their anti-cancer potential. Recently, it has been demonstrated that various protein quality control (PQC) systems are involved in recognizing the altered acetylation pattern upon HDACi treatment. In particular, molecular chaperones, the ubiquitin proteasome system (UPS) and autophagy are able to sense the structurally changed proteins, providing additional targets. Recent clinical studies of novel HDACi have proven that proteins of the UPS may serve as biomarkers for stratifying patient groups under HDACi regimes. In addition, members of the PQC systems have been shown to modify the epigenetic readout of HDACi treated cells and alter proteostasis in the nucleus, thus contributing to changing gene expression profiles. Bromodomain (BRD)-containing proteins seem to play a potent role in transducing the signaling process initiating apoptosis, and many clinical trials are under way to test BRD inhibitors. Finally, it has been demonstrated that HDACi treatment leads to protein misfolding and aggregation, which may explain the effect of panobinostat, the latest FDA approved HDACi, in combination with the proteasome inhibitor bortezomib in multiple myeloma. Therefore, proteins of these PQC systems provide valuable targets for precision medicine in cancer. In this review, we give an overview of the impact of HDACi treatment on PQC systems and their implications for malignant disease. We exemplify the development of novel HDACi and how affected proteins belonging to PQC can be used to determine molecular signatures and utilized in precision medicine.
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Affiliation(s)
- Linda Anna Michelle Kulka
- Medical Faculty, Institute of Physiological Chemistry, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Pia-Victoria Fangmann
- Medical Faculty, Institute of Physiological Chemistry, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Diana Panfilova
- Medical Faculty, Institute of Physiological Chemistry, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Heidi Olzscha
- Medical Faculty, Institute of Physiological Chemistry, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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Hu S, Cho EH, Lee JY. Histone Deacetylase 9: Its Role in the Pathogenesis of Diabetes and Other Chronic Diseases. Diabetes Metab J 2020; 44:234-244. [PMID: 32347025 PMCID: PMC7188980 DOI: 10.4093/dmj.2019.0243] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
As a member of the class IIa histone deacetylases (HDACs), HDAC9 catalyzes the deacetylation of histones and transcription factors, commonly leading to the suppression of gene transcription. The activity of HDAC9 is regulated transcriptionally and post-translationally. HDAC9 is known to play an essential role in regulating myocyte and adipocyte differentiation and cardiac muscle development. Also, recent studies have suggested that HDAC9 is involved in the pathogenesis of chronic diseases, including cardiovascular diseases, osteoporosis, autoimmune disease, cancer, obesity, insulin resistance, and liver fibrosis. HDAC9 modulates the expression of genes related to the pathogenesis of chronic diseases by altering chromatin structure in their promotor region or reducing the transcriptional activity of their respective transcription factors. This review summarizes the current knowledge of the regulation of HDAC9 expression and activity. Also, the roles of HDAC9 in the pathogenesis of chronic diseases are discussed, along with potential underlying mechanisms.
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Affiliation(s)
- Siqi Hu
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT, USA
| | - Eun Hee Cho
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Ji Young Lee
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT, USA.
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Synthesis and biological evaluation of thiophene-based hydroxamate derivatives as HDACis with antitumor activities. Future Med Chem 2020; 12:655-672. [PMID: 32202140 DOI: 10.4155/fmc-2019-0343] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aim: Histone deacetylases (HDACs) are one of the validated targets for cancer treatments. In our previous work, we designed a series of bis-substituted aromatic amide HDAC inhibitors (HDACis), among which compounds 7 and 8 showed promising anticancer effects. However, the low solubilities prevented their subsequent developments. We developed additional thiophene-based hydroxamate HDACis in order to improve their physicochemical properties. Materials & methods: In vitro biological evaluations of these analogs revealed potent antiproliferative and antimigrated activities. More importantly, compound 10h exhibited excellent in vivo antitumor activities in MDA-MB-231 xenograft model mice. Furthermore, 10h showed better anticancer activities and drug-like properties than 7. Results & conclusion: Our results proved that thiophene-based hydroxamate HDACis can serve as a promising framework for developing potential anticancer agents.
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66
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Barbosa DM, Fahlbusch P, Herzfeld de Wiza D, Jacob S, Kettel U, Al-Hasani H, Krüger M, Ouwens DM, Hartwig S, Lehr S, Kotzka J, Knebel B. Rhein, a novel Histone Deacetylase (HDAC) inhibitor with antifibrotic potency in human myocardial fibrosis. Sci Rep 2020; 10:4888. [PMID: 32184434 PMCID: PMC7078222 DOI: 10.1038/s41598-020-61886-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/04/2020] [Indexed: 12/18/2022] Open
Abstract
Although fibrosis depicts a reparative mechanism, maladaptation of the heart due to excessive production of extracellular matrix accelerates cardiac dysfunction. The anthraquinone Rhein was examined for its anti-fibrotic potency to mitigate cardiac fibroblast-to-myofibroblast transition (FMT). Primary human ventricular cardiac fibroblasts were subjected to hypoxia and characterized with proteomics, transcriptomics and cell functional techniques. Knowledge based analyses of the omics data revealed a modulation of fibrosis-associated pathways and cell cycle due to Rhein administration during hypoxia, whereas p53 and p21 were identified as upstream regulators involved in the manifestation of cardiac fibroblast phenotypes. Mechanistically, Rhein acts inhibitory on HDAC classes I/II as enzymatic inhibitor. Rhein-mediated cellular effects were linked to the histone deacetylase (HDAC)-dependent protein stabilization of p53 under normoxic but not hypoxic conditions. Functionally, Rhein inhibited collagen contraction, indicating anti-fibrotic property in cardiac remodeling. This was accompanied by increased abundance of SMAD7, but not SMAD2/3, and consistently SMAD-specific E3 ubiquitin ligase SMURF2. In conclusion, this study identifies Rhein as a novel potent direct HDAC inhibitor that may contribute to the treatment of cardiac fibrosis as anti-fibrotic agent. As readily available drug with approved safety, Rhein constitutes a promising potential therapeutic approach in the supplemental and protective intervention of cardiac fibrosis.
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Affiliation(s)
- David Monteiro Barbosa
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.,Medical Faculty, Institute of Cardiovascular Physiology, Heinrich-Heine-University, Duesseldorf, Germany
| | - Pia Fahlbusch
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Daniella Herzfeld de Wiza
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Sylvia Jacob
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Ulrike Kettel
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Hadi Al-Hasani
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.,Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich-Heine-University, Duesseldorf, Germany
| | - Martina Krüger
- Medical Faculty, Institute of Cardiovascular Physiology, Heinrich-Heine-University, Duesseldorf, Germany
| | - D Margriet Ouwens
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.,Department of Endocrinology, Ghent University Hospital, Ghent, Belgium
| | - Sonja Hartwig
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Stefan Lehr
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Jorg Kotzka
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Birgit Knebel
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, Aufm Hennekamp 65, 40225, Duesseldorf, Germany. .,German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany.
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Concise Review: The Regulatory Mechanism of Lysine Acetylation in Mesenchymal Stem Cell Differentiation. Stem Cells Int 2020; 2020:7618506. [PMID: 32399051 PMCID: PMC7204305 DOI: 10.1155/2020/7618506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Nowadays, the use of MSCs has attracted considerable attention in the global science and technology field, with the self-renewal and multidirectional differentiation potential for diabetes, obesity treatment, bone repair, nerve repair, myocardial repair, and so on. Epigenetics plays an important role in the regulation of mesenchymal stem cell differentiation, which has become a research hotspot in the medical field. This review focuses on the role of lysine acetylation modification on the determination of MSC differentiation direction. During this progress, the recruitment of lysine acetyltransferases (KATs) and lysine deacetylases (KDACs) is the crux of transcriptional mechanisms in the dynamic regulation of key genes controlling MSC multidirectional differentiation.
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Thapa P, Shanmugam N, Pokrzywa W. Ubiquitin Signaling Regulates RNA Biogenesis, Processing, and Metabolism. Bioessays 2019; 42:e1900171. [PMID: 31778250 DOI: 10.1002/bies.201900171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/29/2019] [Indexed: 12/17/2022]
Abstract
The fate of eukaryotic proteins, from their synthesis to destruction, is supervised by the ubiquitin-proteasome system (UPS). The UPS is the primary pathway responsible for selective proteolysis of intracellular proteins, which is guided by covalent attachment of ubiquitin to target proteins by E1 (activating), E2 (conjugating), and E3 (ligating) enzymes in a process known as ubiquitylation. The UPS can also regulate protein synthesis by influencing multiple steps of RNA (ribonucleic acid) metabolism. Here, recent publications concerning the interplay between the UPS and different types of RNA are reviewed. This interplay mainly involves specific RNA-binding E3 ligases that link RNA-dependent processes with protein ubiquitylation. The emerging understanding of their modes of RNA binding, their RNA targets, and their molecular and cellular functions are primarily focused on. It is discussed how the UPS adapted to interact with different types of RNA and how RNA molecules influence the ubiquitin signaling components.
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Affiliation(s)
- Pankaj Thapa
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
| | - Nilesh Shanmugam
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
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69
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Chen Z, Liu X, Li F, Li C, Marquez-Lago T, Leier A, Akutsu T, Webb GI, Xu D, Smith AI, Li L, Chou KC, Song J. Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Brief Bioinform 2019; 20:2267-2290. [PMID: 30285084 PMCID: PMC6954452 DOI: 10.1093/bib/bby089] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 12/22/2022] Open
Abstract
Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse functions and biological processes of proteins. However, because of the large volumes of sequencing data generated from genome-sequencing projects, systematic identification of different types of lysine PTM substrates and PTM sites in the entire proteome remains a major challenge. In recent years, a number of computational methods for lysine PTM identification have been developed. These methods show high diversity in their core algorithms, features extracted and feature selection techniques and evaluation strategies. There is therefore an urgent need to revisit these methods and summarize their methodologies, to improve and further develop computational techniques to identify and characterize lysine PTMs from the large amounts of sequence data. With this goal in mind, we first provide a comprehensive survey on a large collection of 49 state-of-the-art approaches for lysine PTM prediction. We cover a variety of important aspects that are crucial for the development of successful predictors, including operating algorithms, sequence and structural features, feature selection, model performance evaluation and software utility. We further provide our thoughts on potential strategies to improve the model performance. Second, in order to examine the feasibility of using deep learning for lysine PTM prediction, we propose a novel computational framework, termed MUscADEL (Multiple Scalable Accurate Deep Learner for lysine PTMs), using deep, bidirectional, long short-term memory recurrent neural networks for accurate and systematic mapping of eight major types of lysine PTMs in the human and mouse proteomes. Extensive benchmarking tests show that MUscADEL outperforms current methods for lysine PTM characterization, demonstrating the potential and power of deep learning techniques in protein PTM prediction. The web server of MUscADEL, together with all the data sets assembled in this study, is freely available at http://muscadel.erc.monash.edu/. We anticipate this comprehensive review and the application of deep learning will provide practical guide and useful insights into PTM prediction and inspire future bioinformatics studies in the related fields.
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Affiliation(s)
- Zhen Chen
- School of Basic Medical Science, Qingdao University, Dengzhou Road, Qingdao, Shandong, China
| | - Xuhan Liu
- Medicinal Chemistry, Leiden Academic Centre for Drug Research,Einsteinweg, Leiden, The Netherlands
| | - Fuyi Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- Institute of Molecular Systems Biology, ETH Zürich,Auguste-Piccard-Hof, Zürich, Switzerland
| | - Tatiana Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research,Kyoto University, Uji, Kyoto, Japan
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia
| | - Dakang Xu
- Faculty of Medical Laboratory Science, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Molecular and Translational Science, Faculty of Medicine, Hudson Institute of Medical Research, Monash University, Melbourne, VIC, Australia
| | - Alexander Ian Smith
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
| | - Lei Li
- School of Basic Medical Science, Qingdao University, Dengzhou Road, Qingdao, Shandong, China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA, USA
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, VIC, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC, Australia
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70
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Vengayil V, Rashida Z, Laxman S. The E3 ubiquitin ligase Pib1 regulates effective gluconeogenic shutdown upon glucose availability. J Biol Chem 2019; 294:17209-17223. [PMID: 31604822 PMCID: PMC6873170 DOI: 10.1074/jbc.ra119.009822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/27/2019] [Indexed: 12/31/2022] Open
Abstract
Cells use multiple mechanisms to regulate their metabolic states in response to changes in their nutrient environment. One example is the response of cells to glucose. In Saccharomyces cerevisiae growing in glucose-depleted medium, the re-availability of glucose leads to the down-regulation of gluconeogenesis and the activation of glycolysis, leading to "glucose repression." However, our knowledge of the mechanisms mediating the glucose-dependent down-regulation of the gluconeogenic transcription factors is limited. Using the major gluconeogenic transcription factor Rds2 as a candidate, we identify here a novel role for the E3 ubiquitin ligase Pib1 in regulating the stability and degradation of Rds2. Glucose addition to cells growing under glucose limitation results in a rapid ubiquitination of Rds2, followed by its proteasomal degradation. Through in vivo and in vitro experiments, we establish Pib1 as the ubiquitin E3 ligase that regulates Rds2 ubiquitination and stability. Notably, this Pib1-mediated Rds2 ubiquitination, followed by proteasomal degradation, is specific to the presence of glucose. This Pib1-mediated ubiquitination of Rds2 depends on the phosphorylation state of Rds2, suggesting a cross-talk between ubiquitination and phosphorylation to achieve a metabolic state change. Using stable isotope-based metabolic flux experiments, we find that the loss of Pib1 results in an imbalanced gluconeogenic state, regardless of glucose availability. Pib1 is required for complete glucose repression and enables cells to optimally grow in competitive environments when glucose again becomes available. Our results reveal the existence of a Pib1-mediated regulatory program that mediates glucose repression when glucose availability is restored.
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Affiliation(s)
- Vineeth Vengayil
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
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71
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Ling H, Peng L, Wang J, Rahhal R, Seto E. Histone Deacetylase SIRT1 Targets Plk2 to Regulate Centriole Duplication. Cell Rep 2019; 25:2851-2865.e3. [PMID: 30517871 DOI: 10.1016/j.celrep.2018.11.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/04/2018] [Accepted: 11/02/2018] [Indexed: 11/17/2022] Open
Abstract
The protein deacetylase SIRT1 (Sirtuin 1) regulates many cellular processes, including cell-cycle progression, DNA damage response, and metabolism. Although the centrosome is a key regulator of cell-cycle progression and genome stability, little is known concerning SIRT1 controlled centrosome-associated events. Here we report that the centrosome protein Plk2 is acetylated and undergoes deacetylation by SIRT1. Acetylation protects Plk2 from ubiquitination, and SIRT1-mediated deacetylation promotes ubiquitin-dependent degradation of Plk2. SIRT1 controls centriole duplication by temporally modulating centrosomal Plk2 levels. AURKA phosphorylates SIRT1 and promotes the SIRT1-Plk2 interaction in mitosis. In early-mid G1, phosphorylated SIRT1 deacetylates and promotes Plk2 degradation. In late G1, SIRT1 is hypophosphorylated and its affinity to Plk2 is decreased, resulting in a rapid accumulation of centrosomal Plk2, which contributes to the timely initiation of centriole duplication. Collectively, our findings uncover a critical role of SIRT1 in centriole duplication and provide a mechanistic insight into SIRT1-mediated centrosome-associated functions.
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Affiliation(s)
- Hongbo Ling
- George Washington University Cancer Center, Washington, DC 20052, USA; Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA
| | - Lirong Peng
- George Washington University Cancer Center, Washington, DC 20052, USA; Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA
| | - Jianbo Wang
- Department of Oncology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Raneen Rahhal
- George Washington University Cancer Center, Washington, DC 20052, USA; Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA
| | - Edward Seto
- George Washington University Cancer Center, Washington, DC 20052, USA; Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine & Health Sciences, Washington, DC 20052, USA.
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72
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Yeh C, Sun L, Lai C, Yeh T, Lin J, Tsay S, Chen C, Chen W, Chen C, Tsai R. Effect of ethanol extracts of Hericium�erinaceus mycelium on morphine‑induced microglial migration. Mol Med Rep 2019; 20:5279-5285. [DOI: 10.3892/mmr.2019.10745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 08/06/2019] [Indexed: 11/06/2022] Open
Affiliation(s)
- Chung‑Hsin Yeh
- College of Nursing and Health Sciences, Da‑Yeh University, Changhua 51591, Taiwan, R.O.C
| | - Li‑Wei Sun
- Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung 40201, Taiwan, R.O.C
| | - Chang‑Mei Lai
- Department of Emergency Medicine, Asia University Hospital, Taichung 41354, Taiwan, R.O.C
| | - Tzu‑Pei Yeh
- School of Nursing, China Medical University, Taichung 40402, Taiwan, R.O.C
| | - Jong‑Ni Lin
- College of Nursing and Health Sciences, Da‑Yeh University, Changhua 51591, Taiwan, R.O.C
| | - Shiow‑Luan Tsay
- College of Nursing and Health Sciences, Da‑Yeh University, Changhua 51591, Taiwan, R.O.C
| | - Chin‑Chu Chen
- Grape King Biotechnology Inc., Zhong‑Li 32097, Taiwan, R.O.C
| | - Wan‑Ping Chen
- Grape King Biotechnology Inc., Zhong‑Li 32097, Taiwan, R.O.C
| | - Chien‑Min Chen
- College of Nursing and Health Sciences, Da‑Yeh University, Changhua 51591, Taiwan, R.O.C
| | - Ru‑Yin Tsai
- College of Nursing and Health Sciences, Da‑Yeh University, Changhua 51591, Taiwan, R.O.C
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73
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Stacy AJ, Zhang J, Craig MP, Hira A, Dole N, Kadakia MP. TIP60 up-regulates ΔNp63α to promote cellular proliferation. J Biol Chem 2019; 294:17007-17016. [PMID: 31601649 DOI: 10.1074/jbc.ra119.010388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/03/2019] [Indexed: 01/08/2023] Open
Abstract
An estimated 5.4 million cases of nonmelanoma skin cancer are reported in the United States at an associated cost of $4.8 billion. ΔNp63α, a proto-oncogene in the p53 family of transcription factors, is overexpressed in squamous cell carcinoma (SCC) and associated with poor prognosis and survival. ΔNp63α elicits its tumorigenic effects in part by promoting cellular proliferation and cell survival. Despite its importance in SCC, the upstream regulation of ΔNp63α is poorly understood. In this study, we identify TIP60 as a novel upstream regulator of ΔNp63α. Using a combination of overexpression, silencing, stable expression, and pharmacological approaches in multiple cell lines, we showed that TIP60 up-regulates ΔNp63α expression. Utilizing cycloheximide treatment, we showed that TIP60 catalytic activity is required for stabilization of ΔNp63α protein levels. We further showed that TIP60 coexpression inhibits ΔNp63α ubiquitination and proteasomal degradation. Stabilization of ΔNp63α protein was further associated with TIP60-mediated acetylation. Finally, we demonstrated that TIP60-mediated regulation of ΔNp63α increases cellular proliferation by promoting G2/M progression through MTS assays and flow cytometry. Taken together, our findings provide evidence that TIP60 may contribute to SCC progression by increasing ΔNp63α protein levels, thereby promoting cellular proliferation.
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Affiliation(s)
- Andrew J Stacy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Jin Zhang
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Michael P Craig
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Akshay Hira
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Nikhil Dole
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
| | - Madhavi P Kadakia
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435
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Kim EJ, Park MK, Kang GJ, Byun HJ, Kim HJ, Yu L, Kim B, Chae HS, Chin YW, Shim JG, Lee H, Lee CH. YDJC Induces Epithelial-Mesenchymal Transition via Escaping from Interaction with CDC16 through Ubiquitination of PP2A. JOURNAL OF ONCOLOGY 2019; 2019:3542537. [PMID: 31485224 PMCID: PMC6702825 DOI: 10.1155/2019/3542537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 01/06/2023]
Abstract
Lung cancer is the number 1 cause of cancer-related casualties in the world. Appropriate diagnostic markers and novel targets for lung cancer are needed. Chitooligosaccharide deacetylase homolog (YDJC) catalyzes the deacetylation of acetylated carbohydrates; however, the role of YDJC in lung cancer progression has yet to be studied. A549 lung cancer orthotopic mouse model was used for mice experiments. We found that YDJC overexpression contributes to lung cancer progression in an orthotopic mouse model. Long-term treatment (48 h) induces YDJC expression in sphingosylphosphorylcholine (SPC)-induced epithelial-mesenchymal transition (EMT). Gene silencing of YDJC (siYDJC) reduced N-cadherin expression and increased E-cadherin expression in SPC-induced EMT. Overexpression of YDJC reverses them but overexpression of the deacetylase deficient mutant YDJCD13A could not. Interestingly, overexpression of CDC16, a YDJC binding partner, suppressed EMT. ERK2 is activated in siCDC16-induced EMT. YDJC overexpression reduces expression of protein phosphatase 2A (PP2A), whereas CDC16 overexpression induces PP2A expression. YDJC overexpression induced ubiquitination of PP2A but YDJCD13A could not. CDC16 overexpression increased the ubiquitination of YDJC. These results suggest that YDJC contributes to the progression of lung cancer via enhancing EMT by inducing the ubiquitination of PP2A. Therefore, YDJC might be a new target for antitumor therapy against lung cancer.
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Affiliation(s)
- Eun Ji Kim
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
| | - Mi Kyung Park
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Gyeoung-Jin Kang
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
| | - Hyun Jung Byun
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
| | - Hyun Ji Kim
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
| | - Lu Yu
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
| | - Boram Kim
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
| | - Hee-Sung Chae
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
| | - Young-Won Chin
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
| | - Jae Gal Shim
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Republic of Korea
| | - Chang Hoon Lee
- Pharmaceutical Biochemistry, College of Pharmacy, Dongguk University, Seoul, Goyang, 04620, Republic of Korea
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75
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Bone Remodeling: Histone Modifications as Fate Determinants of Bone Cell Differentiation. Int J Mol Sci 2019; 20:ijms20133147. [PMID: 31252653 PMCID: PMC6651527 DOI: 10.3390/ijms20133147] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023] Open
Abstract
The bone tissue is a dynamic complex that constitutes of several interdependent systems and is continuously remodeled through the concerted actions of bone cells. Osteoblasts are mononucleated cells, derived from mesenchymal stem cells, responsible for bone formation. Osteoclasts are large multinucleated cells that differentiate from hematopoietic progenitors of the myeloid lineage and are responsible for bone resorption. The lineage-specific differentiation of bone cells requires an epigenetic regulation of gene expressions involving chromatin dynamics. The key step for understanding gene regulatory networks during bone cell development lies in characterizing the chromatin modifying enzymes responsible for reorganizing and potentiating particular chromatin structure. This review covers the histone-modifying enzymes involved in bone development, discusses the impact of enzymes on gene expression, and provides future directions and clinical significance in this area.
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76
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Huang M, Huang J, Zheng Y, Sun Q. Histone acetyltransferase inhibitors: An overview in synthesis, structure-activity relationship and molecular mechanism. Eur J Med Chem 2019; 178:259-286. [PMID: 31195169 DOI: 10.1016/j.ejmech.2019.05.078] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 02/05/2023]
Abstract
Acetylation, a key component in post-translational modification regulated by HATs and HDACs, is relevant to many crucial cellular contexts in organisms. Based on crucial pharmacophore patterns and the structure of targeted proteins, HAT inhibitors are designed and modified for higher affinity and better bioactivity. However, there are still some challenges, such as cell permeability, selectivity, toxicity and synthetic availability, which limit the improvement of HAT inhibitors. So far, only few HAT inhibitors have been approved for commercialization, indicating the urgent need for more successful and effective structure-based drug design and synthetic strategies. Here, we summarized three classes of HAT inhibitors based on their sources and structural scaffolds, emphasizing on their synthetic methods and structure-activity relationships and molecular mechanisms, hoping to facilitate the development and further application of HAT inhibitors.
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Affiliation(s)
- Mengyuan Huang
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Jiangkun Huang
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yongcheng Zheng
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Qiu Sun
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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77
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Collesi C, Felician G, Secco I, Gutierrez MI, Martelletti E, Ali H, Zentilin L, Myers MP, Giacca M. Reversible Notch1 acetylation tunes proliferative signalling in cardiomyocytes. Cardiovasc Res 2019; 114:103-122. [PMID: 29186476 DOI: 10.1093/cvr/cvx228] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 11/23/2017] [Indexed: 01/07/2023] Open
Abstract
Aims The Notch signalling pathway regulates the balance between proliferation and differentiation in several tissues, including the heart. Our previous work has demonstrated that the proliferative potential of neonatal cardiomyocytes relies on Notch1 activity. A deep investigation on the biochemical regulation of the Notch signalling in cardiomyocytes is the focus of the current research. Methods and results We show that the Notch1 intracellular domain is acetylated in proliferating neonatal rat cardiomyocytes and that acetylation tightly controls the amplitude and duration of Notch signalling. We found that acetylation extends the half-life of the protein, and enhanced its transcriptional activity, therefore counteracting apoptosis and sustaining cardiomyocyte proliferation. Sirt1 acted as a negative modulator of Notch1 signalling; its overexpression in cardiomyocytes reverted Notch acetylation and dampened its stability. A constitutively acetylated fusion protein between Notch1 and the acetyltransferase domain of p300 promoted cardiomyocyte proliferation, which was remarkably sustained over time. Viral vector-mediated expression of this protein enhanced heart regeneration after apical resection in neonatal mice. Conclusion These results identify the reversible acetylation of Notch1 as a novel mechanism to modulate its signalling in the heart and tune the proliferative potential of cardiomyocytes.
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Affiliation(s)
- Chiara Collesi
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume 447, 34100 Trieste, Italy.,Center for Translational Cardiology, Azienda Sanitaria Universitaria Integrata, Via Valdoni 7, 34100 Trieste, Italy; and
| | - Giulia Felician
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Ilaria Secco
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Maria Ines Gutierrez
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Elisa Martelletti
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Hashim Ali
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Lorena Zentilin
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Michael P Myers
- Protein Networks Laboratories, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume 447, 34100 Trieste, Italy.,Center for Translational Cardiology, Azienda Sanitaria Universitaria Integrata, Via Valdoni 7, 34100 Trieste, Italy; and
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78
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Iaconelli J, Xuan L, Karmacharya R. HDAC6 Modulates Signaling Pathways Relevant to Synaptic Biology and Neuronal Differentiation in Human Stem-Cell-Derived Neurons. Int J Mol Sci 2019; 20:ijms20071605. [PMID: 30935091 PMCID: PMC6480207 DOI: 10.3390/ijms20071605] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/12/2019] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Recent studies show that histone deacetylase 6 (HDAC6) has important roles in the human brain, especially in the context of a number of nervous system disorders. Animal models of neurodevelopmental, neurodegenerative, and neuropsychiatric disorders show that HDAC6 modulates important biological processes relevant to disease biology. Pan-selective histone deacetylase (HDAC) inhibitors had been studied in animal behavioral assays and shown to induce synaptogenesis in rodent neuronal cultures. While most studies of HDACs in the nervous system have focused on class I HDACs located in the nucleus (e.g., HDACs 1,2,3), recent findings in rodent models suggest that the cytoplasmic class IIb HDAC, HDAC6, plays an important role in regulating mood-related behaviors. Human studies suggest a significant role for synaptic dysfunction in the prefrontal cortex (PFC) and hippocampus in depression. Studies of HDAC inhibitors (HDACi) in human neuronal cells show that HDAC6 inhibitors (HDAC6i) increase the acetylation of specific lysine residues in proteins involved in synaptogenesis. This has led to the hypothesis that HDAC6i may modulate synaptic biology not through effects on the acetylation of histones, but by regulating acetylation of non-histone proteins.
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Affiliation(s)
- Jonathan Iaconelli
- Center for Genomic Medicine, Harvard Medical School and Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Lucius Xuan
- Center for Genomic Medicine, Harvard Medical School and Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Rakesh Karmacharya
- Center for Genomic Medicine, Harvard Medical School and Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.
- Chemical Biology Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
- Schizophrenia and Bipolar Disorder Program, McLean Hospital, Belmont, MA 02478, USA.
- Program in Neuroscience, Harvard University, Cambridge, MA 02138, USA.
- Chemical Biology PhD Program, Harvard University, Cambridge, MA 02138, USA.
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79
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Ononye OE, Njeri CW, Balakrishnan L. Analysis of DNA Processing Enzyme FEN1 and Its Regulation by Protein Lysine Acetylation. Methods Mol Biol 2019; 1983:207-224. [PMID: 31087300 DOI: 10.1007/978-1-4939-9434-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular proteins are modified by lysine acetylation wherein an acetyltransferase transfers an acetyl group from acetyl co enzyme A onto the e-amino group of lysine residues. This modification is extremely dynamic and can be reversed by a deacetylase that removes the acetyl group. Addition of acetyl group to the lysine residue neutralizes its positive charge, thereby functioning as a molecular switch in regulating the enzymatic functions of the protein, its stability, and it cellular localization. Since this modification is extremely dynamic within the cell, biochemical studies characterizing changes in protein function are imperative to understand how this modification alters protein function in a specific cellular pathway. This unit describes in detail expression and purification of a recombinant nuclease and acetyltransferase, in vitro acetylation of the recombinant protein and biochemical assays to study the changes in enzymatic activity of the in vitro acetylated nuclease.
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Affiliation(s)
- Onyekachi E Ononye
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Catherine W Njeri
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Lata Balakrishnan
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA.
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80
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Ledesma L, Sandoval E, Cruz-Martínez U, Escalante AM, Mejía S, Moreno-Álvarez P, Ávila E, García E, Coello G, Torres-Quiroz F. YAAM: Yeast Amino Acid Modifications Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4797096. [PMID: 29688347 PMCID: PMC7206644 DOI: 10.1093/database/bax099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 12/06/2017] [Indexed: 01/29/2023]
Abstract
Proteins are dynamic molecules that regulate a myriad of cellular functions; these functions may be regulated by protein post-translational modifications (PTMs) that mediate the activity, localization and interaction partners of proteins. Thus, understanding the meaning of a single PTM or the combination of several of them is essential to unravel the mechanisms of protein regulation. Yeast Amino Acid Modification (YAAM) (http://yaam.ifc.unam.mx) is a comprehensive database that contains information from 121 921 residues of proteins, which are post-translationally modified in the yeast model Saccharomyces cerevisiae. All the PTMs contained in YAAM have been confirmed experimentally. YAAM database maps PTM residues in a 3D canvas for 680 proteins with a known 3D structure. The structure can be visualized and manipulated using the most common web browsers without the need for any additional plugin. The aim of our database is to retrieve and organize data about the location of modified amino acids providing information in a concise but comprehensive and user-friendly way, enabling users to find relevant information on PTMs. Given that PTMs influence almost all aspects of the biology of both healthy and diseased cells, identifying and understanding PTMs is critical in the study of molecular and cell biology. YAAM allows users to perform multiple searches, up to three modifications at the same residue, giving the possibility to explore possible regulatory mechanism for some proteins. Using YAAM search engine, we found three different PTMs of lysine residues involved in protein translation. This suggests an important regulatory mechanism for protein translation that needs to be further studied. Database URL: http://yaam.ifc.unam.mx/
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Affiliation(s)
- Leonardo Ledesma
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Eduardo Sandoval
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Uriel Cruz-Martínez
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Ana María Escalante
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Selene Mejía
- Coordinación de Difusión y Divulgación, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Paola Moreno-Álvarez
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Emiliano Ávila
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Erik García
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Gerardo Coello
- Unidad de Cómputo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
| | - Francisco Torres-Quiroz
- División de Ciencia Básica, Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Ciudad de México 04510, México
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81
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BK channel deacetylation by SIRT1 in dentate gyrus regulates anxiety and response to stress. Commun Biol 2018; 1:82. [PMID: 30271963 PMCID: PMC6123630 DOI: 10.1038/s42003-018-0088-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/30/2018] [Indexed: 11/09/2022] Open
Abstract
Previous genomic studies in humans indicate that SIRT1, a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase, is involved in anxiety and depression, but the mechanisms are unclear. We previously showed that SIRT1 is highly activated in the nuclear fraction of the dentate gyrus of the chronically stressed animals and inhibits memory formation and increases anhedonic behavior during chronic stress, but specific functional targets of cytoplasmic SIRT1 are unknown. Here, we demonstrate that SIRT1 activity rapidly modulates intrinsic and synaptic properties of the dentate gyrus granule cells and anxiety behaviors through deacetylation of BK channel α subunits in control animals. Chronic stress decreases BKα channel membrane expression, and SIRT1 activity has no rapid effects on synaptic transmission or intrinsic properties in the chronically stressed animal. These results suggest SIRT1 activity rapidly modulates the physiological function of the dentate gyrus, and this modulation participates in the maladaptive stress response. Diankun Yu et al. show that deacetylase SIRT1 rapidly modulates synaptic properties of the dentate gyrus granule cells and anxiety behaviors through deacetylation of BK channel α subunits. This study provides mechanistic insight into how SIRT1 regulates fight-or-flight stress response.
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82
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Bao W, Yuan CA, Zhang Y, Han K, Nandi AK, Honig B, Huang DS. Mutli-Features Prediction of Protein Translational Modification Sites. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1453-1460. [PMID: 28961121 DOI: 10.1109/tcbb.2017.2752703] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Post translational modification plays a significiant role in the biological processing. The potential post translational modification is composed of the center sites and the adjacent amino acid residues which are fundamental protein sequence residues. It can be helpful to perform their biological functions and contribute to understanding the molecular mechanisms that are the foundations of protein design and drug design. The existing algorithms of predicting modified sites often have some shortcomings, such as lower stability and accuracy. In this paper, a combination of physical, chemical, statistical, and biological properties of a protein have been ulitized as the features, and a novel framework is proposed to predict a protein's post translational modification sites. The multi-layer neural network and support vector machine are invoked to predict the potential modified sites with the selected features that include the compositions of amino acid residues, the E-H description of protein segments, and several properties from the AAIndex database. Being aware of the possible redundant information, the feature selection is proposed in the propocessing step in this research. The experimental results show that the proposed method has the ability to improve the accuracy in this classification issue.
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83
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Peroxisomes and cancer: The role of a metabolic specialist in a disease of aberrant metabolism. Biochim Biophys Acta Rev Cancer 2018; 1870:103-121. [PMID: 30012421 DOI: 10.1016/j.bbcan.2018.07.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/30/2018] [Accepted: 07/10/2018] [Indexed: 01/02/2023]
Abstract
Cancer is irrevocably linked to aberrant metabolic processes. While once considered a vestigial organelle, we now know that peroxisomes play a central role in the metabolism of reactive oxygen species, bile acids, ether phospholipids (e.g. plasmalogens), very-long chain, and branched-chain fatty acids. Immune system evasion is a hallmark of cancer, and peroxisomes have an emerging role in the regulation of cellular immune responses. Investigations of individual peroxisome proteins and metabolites support their pro-tumorigenic functions. However, a significant knowledge gap remains regarding how individual functions of proteins and metabolites of the peroxisome orchestrate its potential role as a pro-tumorigenic organelle. This review highlights new advances in our understanding of biogenesis, enzymatic functions, and autophagic degradation of peroxisomes (pexophagy), and provides evidence linking these activities to tumorigenesis. Finally, we propose avenues that may be exploited to target peroxisome-related processes as a mode of combatting cancer.
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84
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Narasumani M, Harrison PM. Discerning evolutionary trends in post-translational modification and the effect of intrinsic disorder: Analysis of methylation, acetylation and ubiquitination sites in human proteins. PLoS Comput Biol 2018; 14:e1006349. [PMID: 30096183 PMCID: PMC6105011 DOI: 10.1371/journal.pcbi.1006349] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/22/2018] [Accepted: 07/07/2018] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered regions (IDRs) of proteins play significant biological functional roles despite lacking a well-defined 3D structure. For example, IDRs provide efficient housing for large numbers of post-translational modification (PTM) sites in eukaryotic proteins. Here, we study the distribution of more than 15,000 experimentally determined human methylation, acetylation and ubiquitination sites (collectively termed 'MAU' sites) in ordered and disordered regions, and analyse their conservation across 380 eukaryotic species. Conservation signals for the maintenance and novel emergence of MAU sites are examined at 11 evolutionary levels from the whole eukaryotic domain down to the ape superfamily, in both ordered and disordered regions. We discover that MAU PTM is a major driver of conservation for arginines and lysines in both ordered and disordered regions, across the 11 levels, most significantly across the mammalian clade. Conservation of human methylatable arginines is very strongly favoured for ordered regions rather than for disordered, whereas methylatable lysines are conserved in either set of regions, and conservation of acetylatable and ubiquitinatable lysines is favoured in disordered over ordered. Notably, we find evidence for the emergence of new lysine MAU sites in disordered regions of proteins in deuterostomes and mammals, and in ordered regions after the dawn of eutherians. For histones specifically, MAU sites demonstrate an idiosyncratic significant conservation pattern that is evident since the last common ancestor of mammals. Similarly, folding-on-binding (FB) regions are highly enriched for MAU sites relative to either ordered or disordered regions, with ubiquitination sites in FBs being highly conserved at all evolutionary levels back as far as mammals. This investigation clearly demonstrates the complex patterns of PTM evolution across the human proteome and that it is necessary to consider conservation of sequence features at multiple evolutionary levels in order not to get an incomplete or misleading picture.
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85
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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86
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Park D, Goh CJ, Kim H, Lee JS, Hahn Y. Loss of conserved ubiquitylation sites in conserved proteins during human evolution. Int J Mol Med 2018; 42:2203-2212. [PMID: 30015863 DOI: 10.3892/ijmm.2018.3772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/06/2018] [Indexed: 11/06/2022] Open
Abstract
Ubiquitylation of lysine residues in proteins serves a pivotal role in the efficient removal of misfolded or unused proteins and in the control of various regulatory pathways by monitoring protein activity that may lead to protein degradation. The loss of ubiquitylated lysines may affect the ubiquitin‑mediated regulatory network and result in the emergence of novel phenotypes. The present study analyzed mouse ubiquitylation data and orthologous proteins from 62 mammals to identify 193 conserved ubiquitylation sites from 169 proteins that were lost in the Euarchonta lineage leading to humans. A total of 8 proteins, including betaine homocysteine S‑methyltransferase, clin and CBS domain divalent metal cation transport mediator 3, ribosome‑binding protein 1 and solute carrier family 37 member 4, lost 1 conserved lysine residue, which was ubiquitylated in the mouse ortholog, following the human‑chimpanzee divergence. A total of 17 of the lost ubiquitylated lysines are also known to be modified by acetylation and/or succinylation in mice. In 8 cases, a novel lysine evolved at positions flanking the lost conserved lysine residues, potentially as a method of compensation. We hypothesize that the loss of ubiquitylation sites during evolution may lead to the development of advantageous phenotypes, which are then fixed by selection. The ancestral ubiquitylation sites identified in the present study may be a useful resource for investigating the association between loss of ubiquitylation sites and the emergence of novel phenotypes during evolution towards modern humans.
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Affiliation(s)
- Dongbin Park
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Chul Jun Goh
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Hyein Kim
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Ji Seok Lee
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung‑Ang University, Seoul 06974, Republic of Korea
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87
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88
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Kovacs L, Kovacs-Kasa A, Verin AD, Fulton D, Lucas R, Su Y. Histone deacetylases in vascular permeability and remodeling associated with acute lung injury. ACTA ACUST UNITED AC 2018; 2. [PMID: 32099966 DOI: 10.20517/2574-1209.2018.06] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Acute lung injury (ALI) is a severe progressive disorder that arises from a wide range of causes such as toxins or inflammation, resulting in significant morbidity and mortality. There are no effective therapeutic options apart from mechanical ventilation strategies. While the mechanisms that govern the clinically relevant process of increased EC permeability and remodeling associated with ALI are under intense investigation, our knowledge of the processes that determine barrier enhancement or preservation are far from completion. Recently, epigenetic mechanisms have emerged as a major regulator of enduring changes in cell behavior and the therapeutic potential of inhibiting histone deacetylases (HDACs) for the treatment of cardiovascular and inflammatory diseases has gained remarkable attention. Although HDACs have been shown to play an important role in regulating EC barrier function, the involved HDAC subtypes and mechanisms remain undefined. Further investigation of the HDAC signaling may provide therapeutic approaches for the prevention and treatment of ALI.
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Affiliation(s)
- Laszlo Kovacs
- Department of Pharmacology & Toxicology, Augusta University, Augusta, GA 30912
| | | | - Alexander D Verin
- Vascular Biology Center, Augusta University, Augusta, GA 30912.,Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912
| | - David Fulton
- Department of Pharmacology & Toxicology, Augusta University, Augusta, GA 30912.,Vascular Biology Center, Augusta University, Augusta, GA 30912
| | - Rudolf Lucas
- Department of Pharmacology & Toxicology, Augusta University, Augusta, GA 30912.,Vascular Biology Center, Augusta University, Augusta, GA 30912.,Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912
| | - Yunchao Su
- Department of Pharmacology & Toxicology, Augusta University, Augusta, GA 30912.,Vascular Biology Center, Augusta University, Augusta, GA 30912.,Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912.,Research Service, Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia 30912
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89
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Min JS, Kim JC, Kim JA, Kang I, Ahn JK. SIRT2 reduces actin polymerization and cell migration through deacetylation and degradation of HSP90. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1230-1238. [PMID: 29908203 DOI: 10.1016/j.bbamcr.2018.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/26/2018] [Accepted: 06/12/2018] [Indexed: 01/07/2023]
Abstract
SIRT2, a member of the class III histone deacetylase family, has been identified as a tumor suppressor, which is associated with various cellular processes including metabolism and proliferation. However, the effects of SIRT2 on cancer cell migration caused by cytoskeletal rearrangement remain uncertain. Here we show that SIRT2 inhibits cell motility by suppressing actin polymerization. SIRT2 regulates actin dynamics through HSP90 destabilization and subsequent repression of LIM kinase (LIMK) 1/cofilin pathway. SIRT2 directly interacts with HSP90 and regulates its acetylation and ubiquitination. In addition, the deacetylase activity of SIRT2 is required for the regulation of actin polymerization and the ubiquitin-mediated proteasomal degradation of HSP90 induced by SIRT2.
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Affiliation(s)
- Jung Sun Min
- Department of Microbiology & Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jin Chul Kim
- Department of Microbiology & Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Ji Ae Kim
- Department of Microbiology & Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Inho Kang
- Department of Microbiology & Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeong Keun Ahn
- Department of Microbiology & Molecular Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea.
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90
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Wang G, Li S, Gilbert J, Gritton HJ, Wang Z, Li Z, Han X, Selkoe DJ, Man HY. Crucial Roles for SIRT2 and AMPA Receptor Acetylation in Synaptic Plasticity and Memory. Cell Rep 2018; 20:1335-1347. [PMID: 28793258 DOI: 10.1016/j.celrep.2017.07.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 04/14/2017] [Accepted: 07/13/2017] [Indexed: 01/06/2023] Open
Abstract
AMPA receptors (AMPARs) mediate fast excitatory synaptic transmission and are crucial for synaptic plasticity, learning, and memory. However, the molecular control of AMPAR stability and its neurophysiological significance remain unclear. Here, we report that AMPARs are subject to lysine acetylation at their C termini. Acetylation reduces AMPAR internalization and degradation, leading to increased cell-surface localization and prolonged receptor half-life. Through competition for the same lysine residues, acetylation intensity is inversely related to the levels of AMPAR ubiquitination. We find that sirtuin 2 (SIRT2) acts as an AMPAR deacetylase regulating AMPAR trafficking and proteostasis. SIRT2 knockout mice (Sirt2-/-) show marked upregulation in AMPAR acetylation and protein accumulation. Both Sirt2-/- mice and mice expressing acetylation mimetic GluA1 show aberrant synaptic plasticity, accompanied by impaired learning and memory. These findings establish SIRT2-regulated lysine acetylation as a form of AMPAR post-translational modification that regulates its turnover, as well as synaptic plasticity and cognitive function.
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Affiliation(s)
- Guan Wang
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Shaomin Li
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - James Gilbert
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Howard J Gritton
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Zemin Wang
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zhangyuan Li
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xue Han
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Dennis J Selkoe
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heng-Ye Man
- Department of Biology, Boston University, Boston, MA 02215, USA; Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA.
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91
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Abstract
The temporal activation of kinases and timely ubiquitin-mediated degradation is central to faithful mitosis. Here we present evidence that acetylation controlled by Coenzyme A synthase (COASY) and acetyltransferase CBP constitutes a novel mechanism that ensures faithful mitosis. We found that COASY knockdown triggers prolonged mitosis and multinucleation. Acetylome analysis reveals that COASY inactivation leads to hyper-acetylation of proteins associated with mitosis, including CBP and an Aurora A kinase activator, TPX2. During early mitosis, a transient CBP-mediated TPX2 acetylation is associated with TPX2 accumulation and Aurora A activation. The recruitment of COASY inhibits CBP-mediated TPX2 acetylation, promoting TPX2 degradation for mitotic exit. Consistently, we detected a stage-specific COASY-CBP-TPX2 association during mitosis. Remarkably, pharmacological and genetic inactivation of CBP effectively rescued the mitotic defects caused by COASY knockdown. Together, our findings uncover a novel mitotic regulation wherein COASY and CBP coordinate an acetylation network to enforce productive mitosis.
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92
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Wei J, Dong S, Yao K, Martinez MFYM, Fleisher PR, Zhao Y, Ma H, Zhao J. Histone acetyltransferase CBP promotes function of SCF FBXL19 ubiquitin E3 ligase by acetylation and stabilization of its F-box protein subunit. FASEB J 2018. [PMID: 29522376 DOI: 10.1096/fj.201701069r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Ubiquitin E3 ligases mediate ubiquitination and degradation of intracellular proteins. We have shown that a relatively new Skp, Cullin, F-box (SCF) protein E3 ligase, SCF FBXL19, has an anti-inflammatory effect and controls actin cytoskeleton dynamics via targeting cell membrane receptor and small GTPases for their ubiquitination and degradation, but the molecular regulation of its subunit FBXL19 stability remains unclear. Here we show that FBXL19 degradation is controlled by the balance between its ubiquitination and acetylation. FBXL19 is an unstable protein with a half-life of ∼3 h. FBXL19 can be polyubiquitinated, and the proteasome inhibitor MG-132 prolongs FBXL19 half-life, suggesting that FBXL19 degradation is mediated in the ubiquitin-proteasome system. FBXL19 can also be acetylated, and enhancing acetylation of FBXL19 by a deacetylase inhibitor reduces FBXL19 ubiquitination levels. Acetylation-mimic FBXL19 mutant exhibits a longer half-life than wild type. An acetyltransferase CBP catalyzes acetylation of FBXL19. Inhibition or down-regulation of CBP reduces FBXL19 stability, whereas it is increased in CBP-overexpressing cells. Taken together, the data indicate that CBP-mediated acetylation reduces ubiquitination and stabilizes FBXL19. Further, we demonstrate that FBXL19 targets small GTPase Cdc42 for its ubiquitination and degradation, whereas this effect is reversed by inhibition of CBP, suggesting that CBP increases the effect of SCF FBXL19 E3 ligase through acetylation and stabilization of FBXL19. Our study reveals a new molecular model for regulation of SCF E3 ligase function by acetylation and stabilization of its subunit F-box protein.-Wei, J., Dong, S., Yao, K., Martinez, M. F. Y. M., Fleisher, P. R., Zhao, Y., Ma, H., Zhao, J. Histone acetyltransferase CBP promotes function of SCF FBXL19 ubiquitin E3 ligase by acetylation and stabilization of its F-box protein subunit.
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Affiliation(s)
- Jianxin Wei
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Su Dong
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Anesthesia, First Hospital of Jilin University, Changchun, China
| | - Kangning Yao
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Paine R Fleisher
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yutong Zhao
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Haichun Ma
- Department of Anesthesia, First Hospital of Jilin University, Changchun, China
| | - Jing Zhao
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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93
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Turiján-Espinoza E, Salazar-González RA, Uresti-Rivera EE, Hernández-Hernández GE, Ortega-Juárez M, Milán R, Portales-Pérez D. A pilot study of the modulation of sirtuins on arylamine N-acetyltransferase 1 and 2 enzymatic activity. Acta Pharm Sin B 2018; 8:188-199. [PMID: 29719779 PMCID: PMC5926248 DOI: 10.1016/j.apsb.2017.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 11/25/2022] Open
Abstract
Arylamine N-acetyltransferase (NAT; E.C. 2.3.1.5) enzymes are responsible for the biotransformation of several arylamine and hydrazine drugs by acetylation. In this process, the acetyl group transferred to the acceptor substrate produces NAT deacetylation and, in consequence, it is susceptible of degradation. Sirtuins are protein deacetylases, dependent on nicotine adenine dinucleotide, which perform post-translational modifications on cytosolic proteins. To explore possible sirtuin participation in the enzymatic activity of arylamine NATs, the expression levels of NAT1, NAT2, SIRT1 and SIRT6 in peripheral blood mononuclear cells (PBMC) from healthy subjects were examined by flow cytometry and Western blot. The in situ activity of the sirtuins on NAT enzymatic activity was analyzed by HPLC, in the presence or absence of an agonist (resveratrol) and inhibitor (nicotinamide) of sirtuins. We detected a higher percentage of positive cells for NAT2 in comparison with NAT1, and higher numbers of SIRT1+ cells compared to SIRT6 in lymphocytes. In situ NAT2 activity in the presence of NAM inhibitors was higher than in the presence of its substrate, but not in the presence of resveratrol. In contrast, the activity of NAT1 was not affected by sirtuins. These results showed that NAT2 activity might be modified by sirtuins.
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Key Words
- APC, allophycocyanin
- Ac-INH, acetyl-Isoniazid
- Ac-PABA, acetyl-p-aminobenzoic acid
- Arylamine N-acetyltransferase
- CHO, Chinese hamster ovary cells
- DMEM, Dulbecco's modified Eagle's medium
- E2F1, E2F transctriptios factor 1
- ER81, ETS-related protein 81
- FITC, fluorescein IsoTioCyanate
- FOXO1, forkhead box protein O1
- HPLC, high performance liquid chromatography
- HeLa, adenocarcinoma epithelial cells
- INH, isoniazid
- NAD, nicotinamide adenine dinucleotide
- NAM, nicotinamide
- NAT
- NAT, arylamine N-acetyltranferase
- Nicotinamide
- PABA, p-aminobenzoic acid
- PAS, p-aminosalicilic acid
- PBMC, peripheral blood mononuclear cells
- PBS, phosphate-buffered saline
- PGAM1, phosphoglycerate mutase 1
- PGC-1α, peroxisome proliferator-activated receptor-gamma coactivator 1α
- Peripheral blood mononuclear cells
- RSV, resveratrol
- RUNX3, runt-related transcription factor 3
- Resveratrol
- SIRT, sirtuin
- SMZ, sulfamethazine
- SREBP1a, sterol regulatory element-binding protein 1a
- SREBP2, sterol regulatory element-binding protein 2
- Sirtuins
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Affiliation(s)
- Eneida Turiján-Espinoza
- Laboratory of Immunology and Cellular and Molecular Biology, Faculty of Chemical Science, UASLP, San Luis Potosi, Mexico
- Laboratory of Biopharmacy and Pharmacokinetics, Faculty of Chemical Science, UASLP, San Luis Potosi, Mexico
- Corresponding authors. Tel.: (52-44) 82624-40, ext. 6465 and 6594.
| | - Rául Alejandro Salazar-González
- Laboratory of Immunology and Cellular and Molecular Biology, Faculty of Chemical Science, UASLP, San Luis Potosi, Mexico
- Laboratory of Biopharmacy and Pharmacokinetics, Faculty of Chemical Science, UASLP, San Luis Potosi, Mexico
| | - Edith Elena Uresti-Rivera
- Laboratory of Immunology and Cellular and Molecular Biology, Faculty of Chemical Science, UASLP, San Luis Potosi, Mexico
| | | | - Montserrat Ortega-Juárez
- Laboratory of Immunology and Cellular and Molecular Biology, Faculty of Chemical Science, UASLP, San Luis Potosi, Mexico
| | - Rosa Milán
- Laboratory of Biopharmacy and Pharmacokinetics, Faculty of Chemical Science, UASLP, San Luis Potosi, Mexico
| | - Diana Portales-Pérez
- Laboratory of Immunology and Cellular and Molecular Biology, Faculty of Chemical Science, UASLP, San Luis Potosi, Mexico
- Corresponding authors. Tel.: (52-44) 82624-40, ext. 6465 and 6594.
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94
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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95
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Panfil AR, Al-Saleem J, Howard CM, Shkriabai N, Kvaratskhelia M, Green PL. Stability of the HTLV-1 Antisense-Derived Protein, HBZ, Is Regulated by the E3 Ubiquitin-Protein Ligase, UBR5. Front Microbiol 2018; 9:80. [PMID: 29441057 PMCID: PMC5797633 DOI: 10.3389/fmicb.2018.00080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/12/2018] [Indexed: 12/25/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) encodes a protein derived from the antisense strand of the proviral genome designated HBZ (HTLV-1 basic leucine zipper factor). HBZ is the only viral gene consistently expressed in infected patients and adult T-cell leukemia/lymphoma (ATL) tumor cell lines. It functions to antagonize many activities of the Tax viral transcriptional activator, suppresses apoptosis, and supports proliferation of ATL cells. Factors that regulate the stability of HBZ are thus important to the pathophysiology of ATL development. Using affinity-tagged protein and shotgun proteomics, we identified UBR5 as a novel HBZ-binding partner. UBR5 is an E3 ubiquitin-protein ligase that functions as a key regulator of the ubiquitin proteasome system in both cancer and developmental biology. Herein, we investigated the role of UBR5 in HTLV-1-mediated T-cell transformation and leukemia/lymphoma development. The UBR5/HBZ interaction was verified in vivo using over-expression constructs, as well as endogenously in T-cells. shRNA-mediated knockdown of UBR5 enhanced HBZ steady-state levels by stabilizing the HBZ protein. Interestingly, the related HTLV-2 antisense-derived protein, APH-2, also interacted with UBR5 in vivo. However, knockdown of UBR5 did not affect APH-2 protein stability. Co-immunoprecipitation assays identified ubiquitination of HBZ and knockdown of UBR5 resulted in a decrease in HBZ ubiquitination. MS/MS analysis identified seven ubiquitinated lysines in HBZ. Interestingly, UBR5 expression was upregulated in established T lymphocytic leukemia/lymphoma cell lines and the later stage of T-cell transformation in vitro. Finally, we demonstrated loss of UBR5 decreased cellular proliferation in transformed T-cell lines. Overall, our study provides evidence for UBR5 as a host cell E3 ubiquitin-protein ligase responsible for regulating HBZ protein stability. Additionally, our data suggests UBR5 plays an important role in maintaining the proliferative phenotype of transformed T-cell lines.
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Affiliation(s)
- Amanda R Panfil
- Department of Veterinary Biosciences, Center for Retrovirus Research, The Ohio State University, Columbus, OH, United States
| | - Jacob Al-Saleem
- Department of Veterinary Biosciences, Center for Retrovirus Research, The Ohio State University, Columbus, OH, United States
| | - Cory M Howard
- Department of Veterinary Biosciences, Center for Retrovirus Research, The Ohio State University, Columbus, OH, United States
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Patrick L Green
- Department of Veterinary Biosciences, Center for Retrovirus Research, The Ohio State University, Columbus, OH, United States.,Comprehensive Cancer Center and Solove Research Institute, The Ohio State University, Columbus, OH, United States
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96
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Yang Y, Tong M, Bai X, Liu X, Cai X, Luo X, Zhang P, Cai W, Vallée I, Zhou Y, Liu M. Comprehensive Proteomic Analysis of Lysine Acetylation in the Foodborne Pathogen Trichinella spiralis. Front Microbiol 2018; 8:2674. [PMID: 29375535 PMCID: PMC5768625 DOI: 10.3389/fmicb.2017.02674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/21/2017] [Indexed: 01/08/2023] Open
Abstract
Lysine acetylation is a dynamic and highly conserved post-translational modification that plays a critical role in regulating diverse cellular processes. Trichinella spiralis is a foodborne parasite with a considerable socio-economic impact. However, to date, little is known regarding the role of lysine acetylation in this parasitic nematode. In this study, we utilized a proteomic approach involving anti-acetyl lysine-based enrichment and highly sensitive mass spectrometry to identify the global acetylated proteome and investigate lysine acetylation in T. spiralis. In total, 3872 lysine modification sites were identified in 1592 proteins that are involved in a wide variety of biological processes. Consistent with the results of previous studies, a large number of the acetylated proteins appear to be involved in metabolic and biosynthetic processes. Interestingly, according to the functional enrichment analysis, 29 acetylated proteins were associated with phagocytosis, suggesting an important role of lysine acetylation in this process. Among the identified proteins, 15 putative acetylation motifs were detected. The presence of serine downstream of the lysine acetylation site was commonly observed in the regions surrounding the sites. Moreover, protein interaction network analysis revealed that various interactions are regulated by protein acetylation. These data represent the first report of the acetylome of T. spiralis and provide an important resource for further explorations of the role of lysine acetylation in this foodborne pathogen.
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Affiliation(s)
- Yong Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun, China.,Wu Xi Medical School, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Mingwei Tong
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xue Bai
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaolei Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuepeng Cai
- China Institute of Veterinary Drug Control, Beijing, China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuenong Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Peihao Zhang
- Wu Xi Medical School, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Wei Cai
- Wu Xi Medical School, Jiangnan University, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Isabelle Vallée
- JRU BIPAR, ANSES, École Nationale Vétérinaire d'Alfort, INRA, Université Paris-Est, Animal Health Laboratory, Maisons-Alfort, France
| | - Yonghua Zhou
- Jiangsu Institute of Parasitic Disease, Wuxi, China
| | - Mingyuan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine, Jilin University, Changchun, China
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97
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McMillan LJ, Hwang S, Farah RE, Koh J, Chen S, Maupin-Furlow JA. Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses. Environ Microbiol 2017; 20:385-401. [PMID: 29194950 DOI: 10.1111/1462-2920.14014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023]
Abstract
Stable isotope labelling of amino acids in cell culture (SILAC) is a quantitative proteomic method that can illuminate new pathways used by cells to adapt to different lifestyles and niches. Archaea, while thriving in extreme environments and accounting for ∼20%-40% of the Earth's biomass, have not been analyzed with the full potential of SILAC. Here, we report SILAC for quantitative comparison of archaeal proteomes, using Haloferax volcanii as a model. A double auxotroph was generated that allowed for complete incorporation of 13 C/15 N-lysine and 13 C-arginine such that each peptide derived from trypsin digestion was labelled. This strain was found amenable to multiplex SILAC by case study of responses to oxidative stress by hypochlorite. A total of 2565 proteins was identified by LC-MS/MS analysis (q-value ≤ 0.01) that accounted for 64% of the theoretical proteome. Of these, 176 proteins were altered at least 1.5-fold (p-value < 0.05) in abundance during hypochlorite stress. Many of the differential proteins were of unknown function. Those of known function included transcription factor homologs related to oxidative stress by 3D-homology modelling and orthologous group comparisons. Thus, SILAC is found to be an ideal method for quantitative proteomics of archaea that holds promise to unravel gene function.
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Affiliation(s)
- Lana J McMillan
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Sungmin Hwang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Rawan E Farah
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Sixue Chen
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA.,Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA.,Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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98
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Gene expression regulation by heat-shock proteins: the cardinal roles of HSF1 and Hsp90. Biochem Soc Trans 2017; 46:51-65. [PMID: 29273620 DOI: 10.1042/bst20170335] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/21/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022]
Abstract
The ability to permit gene expression is managed by a set of relatively well known regulatory mechanisms. Nonetheless, this property can also be acquired during a life span as a consequence of environmental stimuli. Interestingly, some acquired information can be passed to the next generation of individuals without modifying gene information, but instead by the manner in which cells read and process such information. Molecular chaperones are classically related to the proper preservation of protein folding and anti-aggregation properties, but one of them, heat-shock protein 90 (Hsp90), is a refined sensor of protein function facilitating the biological activity of properly folded client proteins that already have a preserved tertiary structure. Interestingly, Hsp90 can also function as a critical switch able to regulate biological responses due to its association with key client proteins such as histone deacetylases or DNA methylases. Thus, a growing amount of evidence has connected the action of Hsp90 to post-translational modifications of soluble nuclear factors, DNA, and histones, which epigenetically affect gene expression upon the onset of an unfriendly environment. This response is commanded by the activation of the transcription factor heat-shock factor 1 (HSF1). Even though numerous stresses of diverse nature are known to trigger the stress response by activation of HSF1, it is still unknown whether there are different types of molecular sensors for each type of stimulus. In the present review, we will discuss various aspects of the regulatory action of HSF1 and Hsp90 on transcriptional regulation, and how this regulation may affect genetic assimilation mechanisms and the health of individuals.
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99
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Li Q, Zhao N, Liu M, Shen H, Huang L, Mo X, Xu B, Zhang X, Hu W. Comparative Analysis of Proteome-Wide Lysine Acetylation in Juvenile and Adult Schistosoma japonicum. Front Microbiol 2017; 8:2248. [PMID: 29250037 PMCID: PMC5715381 DOI: 10.3389/fmicb.2017.02248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/31/2017] [Indexed: 12/05/2022] Open
Abstract
Schistosomiasis is a devastating parasitic disease caused by tremotodes of the genus Schistosoma. Eggs produced by sexually mature schistosomes are the causative agents of for pathogenesis and transmission. Elucidating the molecular mechanism of schistosome development and sexual maturation would facilitate the prevention and control of schistosomiasis. Acetylation of lysine is a dynamic and reversible post-translational modification playing keys role in many biological processes including development in both eukaryotes and prokaryotes. To investigate the impacts of lysine acetylation on Schistosoma japonicum (S. japonicum) development and sexual maturation, we used immunoaffinity-based acetyllysine peptide enrichment combined with mass spectrometry (MS), to perform the first comparative analysis of proteome-wide lysine acetylation in both female and male, juvenile (18 days post infection, 18 dpi) and adult (28 dpi) schistosome samples. In total, we identified 874 unique acetylated sites in 494 acetylated proteins. The four samples shared 47 acetylated sites and 46 proteins. More acetylated sites and proteins shared by both females and males were identified in 28 dpi adults (189 and 143, respectively) than in 18 dpi schistosomula (76 and 59, respectively). More stage-unique acetylated sites and proteins were also identified in 28 dpi adults (494 and 210, respectively) than in 18 dpi schistosomula (73 and 44, respectively). Functional annotation showed that in different developmental stages and genders, a number of proteins involving in muscle movement, glycometabolism, lipid metabolism, energy metabolism, environmental stress resistance, antioxidation, etc., displayed distinct acetylation profiles, which was in accordance with the changes of their biological functions during schistosome development, suggesting that lysine acetylation modification exerted important regulatory roles in schistosome development. Taken together, our data provided the first comparative global survey of lysine acetylation in juvenile and adult S. japonicum, which would deepen our understanding of the molecular mechanism of schistosome development and sexual maturation, and provide clues for the development of new anti-schistosome strategies.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Nan Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Mu Liu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Haimo Shen
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China
| | - Lin Huang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaojin Mo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Wei Hu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Ministry of Science and Technology, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China
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100
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Lalonde J, Reis SA, Sivakumaran S, Holland CS, Wesseling H, Sauld JF, Alural B, Zhao WN, Steen JA, Haggarty SJ. Chemogenomic analysis reveals key role for lysine acetylation in regulating Arc stability. Nat Commun 2017; 8:1659. [PMID: 29162813 PMCID: PMC5698418 DOI: 10.1038/s41467-017-01750-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 10/11/2017] [Indexed: 01/11/2023] Open
Abstract
The role of Arc in synaptic plasticity and memory consolidation has been investigated for many years with recent evidence that defects in the expression or activity of this immediate-early gene may also contribute to the pathophysiology of brain disorders including schizophrenia and fragile X syndrome. These results bring forward the concept that reversing Arc abnormalities could provide an avenue to improve cognitive or neurological impairments in different disease contexts, but how to achieve this therapeutic objective has remained elusive. Here, we present results from a chemogenomic screen that probed a mechanistically diverse library of small molecules for modulators of BDNF-induced Arc expression in primary cortical neurons. This effort identified compounds with a range of influences on Arc, including promoting its acetylation-a previously uncharacterized post-translational modification of this protein. Together, our data provide insights into the control of Arc that could be targeted to harness neuroplasticity for clinical applications.
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Affiliation(s)
- Jasmin Lalonde
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA.
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1.
| | - Surya A Reis
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Sudhir Sivakumaran
- Department of Anatomy and Neurobiology, Boston University School of Medicine, 72 East Concord, Boston, MA, 02118, USA
| | - Carl S Holland
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Hendrik Wesseling
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - John F Sauld
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Begum Alural
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA
- Department of Neuroscience, Institute of Health Sciences, Dokuz Eylul University, Izmir, 35210, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University, Izmir, 35210, Turkey
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Judith A Steen
- Boston Children's Hospital, F.M. Kirby Center for Neurobiology, Harvard Medical School, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Massachusetts General Hospital, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA.
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