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Wang T, Zou Y, Huang N, Teng J, Chen J. CCDC84 Acetylation Oscillation Regulates Centrosome Duplication by Modulating HsSAS-6 Degradation. Cell Rep 2020; 29:2078-2091.e5. [PMID: 31722219 DOI: 10.1016/j.celrep.2019.10.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/16/2019] [Accepted: 10/07/2019] [Indexed: 01/14/2023] Open
Abstract
In animal cells, centriole number is strictly controlled in order to guarantee faithful cell division and genetic stability, but the mechanism by which the accuracy of centrosome duplication is maintained is not fully understood. Here, we show that CCDC84 constrains centriole number by modulating APC/CCdh1-mediated HsSAS-6 degradation. More importantly, CCDC84 acetylation oscillates throughout the cell cycle, and the acetylation state of CCDC84 at lysine 31 is regulated by the deacetylase SIRT1 and the acetyltransferase NAT10. Deacetylated CCDC84 is responsible for its centrosome targeting, and acetylated CCDC84 promotes HsSAS-6 ubiquitination by enhancing the binding affinity of HsSAS-6 for Cdh1. Our findings shed new light on the function of (de)acetylation in centriole number regulation as well as refine the established centrosome duplication model.
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Affiliation(s)
- Tianning Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yuhong Zou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Ning Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China.
| | - Jianguo Chen
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China.
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202
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Hipólito A, Nunes SC, Vicente JB, Serpa J. Cysteine Aminotransferase (CAT): A Pivotal Sponsor in Metabolic Remodeling and an Ally of 3-Mercaptopyruvate Sulfurtransferase (MST) in Cancer. Molecules 2020; 25:molecules25173984. [PMID: 32882966 PMCID: PMC7504796 DOI: 10.3390/molecules25173984] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 12/16/2022] Open
Abstract
Metabolic remodeling is a critical skill of malignant cells, allowing their survival and spread. The metabolic dynamics and adaptation capacity of cancer cells allow them to escape from damaging stimuli, including breakage or cross-links in DNA strands and increased reactive oxygen species (ROS) levels, promoting resistance to currently available therapies, such as alkylating or oxidative agents. Therefore, it is essential to understand how metabolic pathways and the corresponding enzymatic systems can impact on tumor behavior. Cysteine aminotransferase (CAT) per se, as well as a component of the CAT: 3-mercaptopyruvate sulfurtransferase (MST) axis, is pivotal for this metabolic rewiring, constituting a central mechanism in amino acid metabolism and fulfilling the metabolic needs of cancer cells, thereby supplying other different pathways. In this review, we explore the current state-of-art on CAT function and its role on cancer cell metabolic rewiring as MST partner, and its relevance in cancer cells' fitness.
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Affiliation(s)
- Ana Hipólito
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculty of Medical Sciences, University NOVA of Lisbon, Campus dos Mártires da Pátria, 130, 1169-056 Lisbon, Portugal; (A.H.); (S.C.N.)
- Institute of Oncology Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisbon, Portugal
| | - Sofia C. Nunes
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculty of Medical Sciences, University NOVA of Lisbon, Campus dos Mártires da Pátria, 130, 1169-056 Lisbon, Portugal; (A.H.); (S.C.N.)
- Institute of Oncology Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisbon, Portugal
| | - João B. Vicente
- Institute of Technology, Chemistry and Biology António Xavier (ITQB NOVA), Avenida da República (EAN), 2780-157 Oeiras, Portugal
- Correspondence: (J.B.V.); (J.S.)
| | - Jacinta Serpa
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School|Faculty of Medical Sciences, University NOVA of Lisbon, Campus dos Mártires da Pátria, 130, 1169-056 Lisbon, Portugal; (A.H.); (S.C.N.)
- Institute of Oncology Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisbon, Portugal
- Correspondence: (J.B.V.); (J.S.)
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203
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Nassir F. Role of acetylation in nonalcoholic fatty liver disease: a focus on SIRT1 and SIRT3. EXPLORATION OF MEDICINE 2020. [DOI: 10.37349/emed.2020.00017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become the most prevalent liver chronic disease worldwide. The pathogenesis of NAFLD is complex and involves many metabolic enzymes and multiple pathways. Posttranslational modifications of proteins (PMPs) added another layer of complexity to the pathogenesis of NAFLD. PMPs change protein properties and regulate many biological functions, including cellular localization, stability, intracellular signaling, and protein function. Lysine acetylation is a common reversible PMP that consists of the transfer of an acetyl group from acetyl-coenzyme A (CoA) to a lysine residue on targeted proteins. The deacetylation reaction is catalyzed by deacetylases called sirtuins. This review summarizes the role of acetylation in NAFLD with a focus on sirtuins 1 and 3.
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Affiliation(s)
- Fatiha Nassir
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO 65212, USA
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204
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Toro TB, Watt TJ. Critical review of non-histone human substrates of metal-dependent lysine deacetylases. FASEB J 2020; 34:13140-13155. [PMID: 32862458 DOI: 10.1096/fj.202001301rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Lysine acetylation is a posttranslational modification that occurs on thousands of human proteins, most of which are cytoplasmic. Acetylated proteins are involved in numerous cellular processes and human diseases. Therefore, how the acetylation/deacetylation cycle is regulated is an important question. Eleven metal-dependent lysine deacetylases (KDACs) have been identified in human cells. These enzymes, along with the sirtuins, are collectively responsible for reversing lysine acetylation. Despite several large-scale studies which have characterized the acetylome, relatively few of the specific acetylated residues have been matched to a proposed KDAC for deacetylation. To understand the function of lysine acetylation, and its association with diseases, specific KDAC-substrate pairs must be identified. Identifying specific substrates of a KDAC is complicated both by the complexity of assaying relevant activity and by the non-catalytic interactions of KDACs with cellular proteins. Here, we discuss in vitro and cell-based experimental strategies used to identify KDAC-substrate pairs and evaluate each for the purpose of directly identifying non-histone substrates of metal-dependent KDACs. We propose criteria for a combination of reproducible experimental approaches that are necessary to establish a direct enzymatic relationship. This critical analysis of the literature identifies 108 proposed non-histone substrate-KDAC pairs for which direct experimental evidence has been reported. Of these, five pairs can be considered well-established, while another thirteen pairs have both cell-based and in vitro evidence but lack independent replication and/or sufficient cell-based evidence. We present a path forward for evaluating the remaining substrate leads and reliably identifying novel KDAC substrates.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA
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205
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Luteolin Protects Against CIRI, Potentially via Regulation of the SIRT3/AMPK/mTOR Signaling Pathway. Neurochem Res 2020; 45:2499-2515. [PMID: 32809175 DOI: 10.1007/s11064-020-03108-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 06/28/2020] [Accepted: 08/01/2020] [Indexed: 12/21/2022]
Abstract
Mitochondrial abnormalities accelerate the progression of ischemic brain damage. Sirtuin 3 (SIRT3) is mainly found in mitochondria and affects almost all major aspects of mitochondrial function. Luteolin, a flavonoid with diverse biological properties, including antioxidant activity, inhibition of cell apoptosis and regulation of autophagy. It also modulates the activity of AMP activated kinase and/or sirtuin 1 (SIRT 1) by regulating the expression of sirtuins. We investigated the protective effects of luteolin on cerebral ischemia-reperfusion. It was found through experiments that luteolin reduced the infarcted area of MCAO rat model, and based on the experimental results, it was inferred that luteolin affected the AMPK, mTOR and SIRT3 pathways, thereby protecting brain cells. As expected, we found that luteolin can reduce the neurological function score, the degree of cerebral edema, the cerebral infarction volume, alleviate morphological changes in the cortex and hippocampus, increase neuron survival and decrease the number of apoptotic neurons. At the same time, luteolin significantly reduced the number of GFAP and Iba-1 positive glial cells in the hippocampus while enhanced the scavenging of oxygen free radicals and the activity of SOD in mitochondria. Addtionally, it can also enhance antioxidant capacity via the reversal of mitochondrial swelling and the mitochondrial transmembrane potential. Moreover, luteolin can increase SIRT3-targeted expression in mitochondria, decrease the phosphorylation of AMPK, and increase phosphor-mTOR (p-mTOR) levels, which may have occurred specifically through activation of the SIRT3/AMPK/mTOR pathway. We speculate that luteolin reduces the pathological progression of CIRI by increasing SIRT3 expression and enhancing mitochondrial function. Therefore, the results indicate that luteolin can increase the transduction of SIRT3, providing a potential mechanism for neuroprotective effects in patients with cerebral ischemia.
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206
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Sun R, Kang X, Zhao Y, Wang Z, Wang R, Fu R, Li Y, Hu Y, Wang Z, Shan W, Zhou J, Tian X, Yao J. Sirtuin 3-mediated deacetylation of acyl-CoA synthetase family member 3 by protocatechuic acid attenuates non-alcoholic fatty liver disease. Br J Pharmacol 2020; 177:4166-4180. [PMID: 32520409 DOI: 10.1111/bph.15159] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/30/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND PURPOSE Hepatic fatty acid metabolism disorder, a key pathogenic mechanism underlying non-alcoholic fatty liver disease (NAFLD), is associated with the hyperacetylation of mitochondrial enzymes. Acyl-CoA synthetase family member 3 (ACSF3), which is involved in the regulation of fatty acid metabolism, was predicted to contain lysine acetylation sites related to the mitochondrial deacetylase sirtuin 3 (SIRT3). The purpose of this study was to explore the underlying mechanism by which SIRT3 deacetylates ACSF3 in NAFLD and the protective effect of the natural phenolic compound protocatechuic acid (PCA) against fatty acid metabolism disorder via the SIRT3/ACSF3 pathway. EXPERIMENTAL APPROACH The role of protocatechuic acid and its molecular mechanism in NAFLD were detected in rats and SIRT3-knockout mice fed a high-fat diet (HFD) and in AML-12 cells treated with palmitic acid (PA). KEY RESULTS Pharmacological treatment with protocatechuic acid significantly attenuated high-fat diet-induced fatty acid metabolism disorder in NAFLD. Molecular docking assays showed that protocatechuic acid specifically bound SIRT3 as a substrate and increased SIRT3 protein expression. However, the protective role of protocatechuic acid was abolished by SIRT3 knockdown, which increased ACSF3 expression and exacerbated fatty acid metabolism disorder. Mechanistically, SIRT3 was shown to specifically regulate the acetylation and degradation of ACSF3, which govern the capacity of ACSF3 to mediate fatty acid metabolism disorder during NAFLD. CONCLUSION AND IMPLICATIONS SIRT3-mediated ACSF3 deacetylation is a novel molecular mechanism in NAFLD therapy and protocatechuic acid confers protection against high-fat diet- and palmitic acid-induced hepatic fatty acid metabolism disorder through the SIRT3/ACSF3 pathway.
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Affiliation(s)
- Ruimin Sun
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Xiaohui Kang
- Department of Pharmacy, Dalian Medical University, Dalian, China
| | - Yan Zhao
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Zhanyu Wang
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ruiwen Wang
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Rong Fu
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Yang Li
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yan Hu
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Zhecheng Wang
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Wen Shan
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Junjun Zhou
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Xiaofeng Tian
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jihong Yao
- Department of Pharmacology, Dalian Medical University, Dalian, China
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207
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Joo SY, Aung JM, Shin M, Moon EK, Kong HH, Goo YK, Chung DI, Hong Y. The role of the Acanthamoeba castellanii Sir2-like protein in the growth and encystation of Acanthamoeba. Parasit Vectors 2020; 13:368. [PMID: 32698828 PMCID: PMC7376869 DOI: 10.1186/s13071-020-04237-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/15/2020] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The encystation of Acanthamoeba leads to the development of resilient cysts from vegetative trophozoites. This process is essential for the survival of parasites under unfavorable conditions. Previous studies have reported that, during the encystation of A. castellanii, the expression levels of encystation-related factors are upregulated. However, the regulatory mechanisms for their expression during the encystation process remains unknown. Proteins in the sirtuin family, which consists of nicotinamide adenine dinucleotide-dependent deacetylases, are known to play an important role in various cellular functions. In the present study, we identified the Acanthamoeba silent-information regulator 2-like protein (AcSir2) and examined its role in the growth and encystation of Acanthamoeba. METHODS We obtained the full-length sequence for AcSir2 using reverse-transcription polymerase chain reaction. In Acanthamoeba transfectants that constitutively overexpress AcSir2 protein, SIRT deacetylase activity was measured, and the intracellular localization of AcSir2 and the effects on the growth and encystation of trophozoites were examined. In addition, the sirtuin inhibitor salermide was used to determine whether these effects were caused by AcSir2 overexpression RESULTS: AcSir2 was classified as a class-IV sirtuin. AcSir2 exhibited functional SIRT deacetylase activity, localized mainly in the nucleus, and its transcription was upregulated during encystation. In trophozoites, AcSir2 overexpression led to greater cell growth, and this growth was inhibited by treatment with salermide, a sirtuin inhibitor. When AcSir2 was overexpressed in the cysts, the encystation rate was significantly higher; this was also reversed with salermide treatment. In AcSir2-overexpressing encysting cells, the transcription of cellulose synthase was highly upregulated compared with that of control cells, and this upregulation was abolished with salermide treatment. Transmission electron microscope-based ultrastructural analysis of salermide-treated encysting cells showed that the structure of the exocyst wall and intercyst space was impaired and that the endocyst wall had not formed. CONCLUSIONS These results indicate that AcSir2 is a SIRT deacetylase that plays an essential role as a regulator of a variety of cellular processes and that the regulation of AcSir2 expression is important for the growth and encystation of A. castellanii.
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Affiliation(s)
- So-Young Joo
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ja Moon Aung
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Minsang Shin
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Eun-Kyung Moon
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Hyun-Hee Kong
- Department of Parasitology, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Youn-Kyoung Goo
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Dong-Il Chung
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yeonchul Hong
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
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208
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Zou B, Zhao D, He G, Nian Y, Da D, Yan J, Li C. Acetylation and Phosphorylation of Proteins Affect Energy Metabolism and Pork Quality. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7259-7268. [PMID: 32543862 DOI: 10.1021/acs.jafc.0c01822] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Preslaughter handling has been shown to significantly affect meat quality, but the mechanisms are not fully understood. In this study, we investigated protein phosphorylation and acetylation in pig muscles at early postmortem time and their associations with meat quality attributes. Thirty pigs were randomly assigned to traditional (TH, n = 15) or mild handling (MH, n = 15). Compared with TH, MH reduced the incidence of pale, soft, and exudative (PSE) or dark, firm, and dry (DFD) pork. MH induced 65 and 20 peptides that match with 39 and 12 proteins to be more highly phosphorylated and acetylated, respectively. Creatine kinase, β-enolase, α-1,4-glucan phosphorylase, tropomyosin, and myosin heavy chain isoforms 1, 4, and 7 were found to be simultaneously phosphorylated and acetylated, which may involve glycolysis, tight junctions, and muscle contraction. The phosphorylation and acetylation levels of differential proteins showed significant correlations with meat quality traits. These findings indicate that preslaughter MH can improve meat quality by regulating protein phosphorylation and acetylation involving energy metabolism in muscle.
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Affiliation(s)
- Bo Zou
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MARA; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China
| | - Di Zhao
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MARA; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China
| | - Guangjie He
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MARA; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yingqun Nian
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MARA; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China
| | - Dandan Da
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MARA; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jing Yan
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MARA; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China
| | - Chunbao Li
- Key Laboratory of Meat Processing and Quality Control, MOE; Key Laboratory of Meat Processing, MARA; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, 210095 Nanjing, China
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209
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Le-Tian Z, Cheng-Zhang H, Xuan Z, Zhang Q, Zhen-Gui Y, Qing-Qing W, Sheng-Xuan W, Zhong-Jin X, Ran-Ran L, Ting-Jun L, Zhong-Qu S, Zhong-Hua W, Ke-Rong S. Protein acetylation in mitochondria plays critical functions in the pathogenesis of fatty liver disease. BMC Genomics 2020; 21:435. [PMID: 32586350 PMCID: PMC7318365 DOI: 10.1186/s12864-020-06837-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fatty liver is a high incidence of perinatal disease in dairy cows caused by negative energy balance, which seriously threatens the postpartum health and milk production. It has been reported that lysine acetylation plays an important role in substance and energy metabolism. Predictably, most metabolic processes in the liver, as a vital metabolic organ, are subjected to acetylation. Comparative acetylome study were used to quantify the hepatic tissues from the severe fatty liver group and normal group. Combined with bioinformatics analysis, this study provides new insights for the role of acetylation modification in fatty liver disease of dairy cows. RESULTS We identified 1841 differential acetylation sites on 665 proteins. Among of them, 1072 sites on 393 proteins were quantified. Functional enrichment analysis shows that higher acetylated proteins are significantly enriched in energy metabolic pathways, while lower acetylated proteins are significantly enriched in pathways related to immune response, such as drug metabolism and cancer. Among significantly acetylated proteins, many mitochondrial proteins were identified to be interacting with multiple proteins and involving in lipid metabolism. Furthermore, this study identified potential important proteins, such as HADHA, ACAT1, and EHHADH, which may be important regulatory factors through modification of acetylation in the development of fatty liver disease in dairy cows and possible therapeutic targets for NAFLD in human beings. CONCLUSION This study provided a comprehensive acetylome profile of fatty liver of dairy cows, and revealed important biological pathways associated with protein acetylation occurred in mitochondria, which were involved in the regulation of the pathogenesis of fatty liver disease. Furthermore, potential important proteins, such as HADHA, ACAT1, EHHADH, were predicted to be essential regulators during the pathogenesis of fatty liver disease. The work would contribute to the understanding the pathogenesis of NAFLD, and inspire in the development of new therapeutic strategies for NAFLD.
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Affiliation(s)
- Zhang Le-Tian
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Hu Cheng-Zhang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Zhang Xuan
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Qin Zhang
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Yan Zhen-Gui
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Wei Qing-Qing
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Wang Sheng-Xuan
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Xu Zhong-Jin
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Li Ran-Ran
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Liu Ting-Jun
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Su Zhong-Qu
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Wang Zhong-Hua
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China
| | - Shi Ke-Rong
- Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, Shandong, 271018, P. R. China.
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Abstract
IMPACT STATEMENT NAD is a central metabolite connecting energy balance and organismal growth with genomic integrity and function. It is involved in the development of malignancy and has a regulatory role in the aging process. These processes are mediated by a diverse series of enzymes whose common focus is either NAD's biosynthesis or its utilization as a redox cofactor or enzyme substrate. These enzymes include dehydrogenases, cyclic ADP-ribose hydrolases, mono(ADP-ribosyl)transferases, poly(ADP-ribose) polymerases, and sirtuin deacetylases. This article describes the manifold pathways that comprise NAD metabolism and promotes an increased awareness of how perturbations in these systems may be important in disease prevention and/or progression.
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Affiliation(s)
- John Wr Kincaid
- Department of Nutrition, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,151230Case Comprehensive Cancer Center, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nathan A Berger
- 151230Case Comprehensive Cancer Center, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Biochemistry, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Department of Medicine, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Center for Science, Health and Society, 12304Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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211
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Yeo D, Kang C, Ji LL. Aging alters acetylation status in skeletal and cardiac muscles. GeroScience 2020; 42:963-976. [PMID: 32300965 PMCID: PMC7286993 DOI: 10.1007/s11357-020-00171-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
During aging, organs such as skeletal muscle and heart require sufficient NAD+ both as a coenzyme for oxidative-reductive electron transfer and as a substrate for multiple signaling pathways. Sirtuins (SIRTs), a family of NAD+-dependent deacetylase, play an important role in regulating mitochondrial homeostasis and antioxidant defense by deacetylating transcription factors and enzymes such as PGC-1α, p65, GCN5, and SOD2. However, age-related DNA damage and increased SASP activate PARP-1 and CD38, the enzymes competing with SIRTs for NAD+. Thus, it is important to know how aging alters intracellular NAD+ status and NAD+-depending enzyme expression in muscles. In this study, we report that the acetylation level of muscle protein pool, as well as major SIRTs target proteins (PGC-1α, GCN5, p65, and SOD2), was significantly increased in hindlimb and cardiac muscles of 24-month old mice compared with their 6-month old counterparts, despite the fact that most members of the SIRT family were upregulated with aging. Aging increased the protein content of PARP-1 and CD38, whereas decreased NAD+ levels in both skeletal and heart muscles. Aged muscles demonstrated clear signs of mitochondrial dysfunction, oxidative stress, and inflammation. Taken together, our data suggest that despite the upregulation of SIRTs, aged muscles suffered from NAD+ deficit partly due to the competition of elevated CD38 and PARP-1. The enhanced acetylation of several key proteins involved in broad cellular functions may contribute to the age-related muscle deterioration.
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Affiliation(s)
- Dongwook Yeo
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, 55905, USA
- Laboratory of Physiological Hygiene and Exercise Science, School of Kinesiology, University of Minnesota Twin Cities, 1900 University Avenue SE, Minneapolis, MN, 55455, USA
| | - Chounghun Kang
- Department of Physical Education, Inha University, Incheon, 22212, South Korea
| | - Li Li Ji
- Laboratory of Physiological Hygiene and Exercise Science, School of Kinesiology, University of Minnesota Twin Cities, 1900 University Avenue SE, Minneapolis, MN, 55455, USA.
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212
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Perumal N, Straßburger L, Herzog DP, Müller MB, Pfeiffer N, Grus FH, Manicam C. Bioenergetic shift and actin cytoskeleton remodelling as acute vascular adaptive mechanisms to angiotensin II in murine retina and ophthalmic artery. Redox Biol 2020; 34:101597. [PMID: 32513477 PMCID: PMC7327981 DOI: 10.1016/j.redox.2020.101597] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
Ocular vascular dysfunction is a major contributing factor to the pathogenesis of glaucoma. In recent years, there has been a renewed interest in the role of angiotensin II (Ang II) in mediating the disease progression. Despite its (patho)physiological importance, the molecular mechanisms underlying Ang II-mediated oxidative stress remain largely unexplored in the ocular vasculature. Here, we provide the first direct evidence of the alterations of proteome and signalling pathways underlying Ang II-elicited oxidative insult independent of arterial pressure changes in the ophthalmic artery (OA) and retina (R) employing an in vitro experimental model. Both R and OA were isolated from male C57Bl/6J mice (n = 15/group; n = 5/biological replicate) and incubated overnight in medium containing either vehicle or Ang II (0.1 μM) at physiological conditions. Label-free quantitative mass spectrometry (MS)-based proteomics analysis identified a differential expression of 107 and 34 proteins in the R and OA, respectively. Statistical and bioinformatics analyses revealed that protein clusters involved in actin cytoskeleton and integrin-linked kinase signalling were significantly activated in the OA. Conversely, a large majority of differentially expressed retinal proteins were involved in dysregulation of numerous energy-producing and metabolic signalling pathways, hinting to a possible shift in retinal cell bioenergetics. Particularly, Ang II-mediated downregulation of septin-7 (Sept7; p < 0.01) and superoxide dismutase [Cu-Zn] (Sod1; p < 0.05), and upregulation of troponin T, fast skeletal muscle (Tnnt3; p < 0.05) and tropomyosin alpha-3 chain (Tpm3; p < 0.01) in the OA, and significant decreased expressions of two crystallin proteins (Cryab; p < 0.05 and Crybb2; p < 0.0001) in the R were verified at the mRNA level, corroborating our proteomics findings. In summary, these results demonstrated that exogenous application of Ang II over an acute time period caused impairment of retinal bioenergetics and cellular demise, and actin cytoskeleton-mediated vascular remodelling in the OA. Acute Ang II stimulation elicits oxidative stress in ocular vasculature without pressor effect. . Dysregulation of energy-producing and metabolic pathways are implicated in the retina. . Actin cytoskeleton remodelling are vascular adaptation processes in the ophthalmic artery. .
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Affiliation(s)
- Natarajan Perumal
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Lars Straßburger
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - David P Herzog
- Department of Psychiatry and Psychotherapy & Focus Program Translational Neurosciences (FTN), University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Marianne B Müller
- Department of Psychiatry and Psychotherapy & Focus Program Translational Neurosciences (FTN), University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Franz H Grus
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Caroline Manicam
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany.
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213
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Li P, Zhang H, Zhao GP, Zhao W. Deacetylation enhances ParB-DNA interactions affecting chromosome segregation in Streptomyces coelicolor. Nucleic Acids Res 2020; 48:4902-4914. [PMID: 32313947 PMCID: PMC7229854 DOI: 10.1093/nar/gkaa245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/10/2020] [Accepted: 04/03/2020] [Indexed: 12/29/2022] Open
Abstract
Reversible lysine acetylation plays regulatory roles in diverse biological processes, including cell metabolism, gene transcription, cell apoptosis and ageing. Here, we show that lysine acetylation is involved in the regulation of chromosome segregation, a pivotal step during cell division in Streptomyces coelicolor. Specifically, deacetylation increases the DNA-binding affinity of the chromosome segregation protein ParB to the centromere-like sequence parS. Both biochemical and genetic experiments suggest that the deacetylation process is mainly modulated by a sirtuin-like deacetylase ScCobB1. The Lys-183 residue in the helix-turn-helix region of ParB is the major deacetylation site responsible for the regulation of ParB-parS binding. In-frame deletion of SccobB1 represses formation of ParB segregation complexes and leads to generation of abnormal spores. Taken together, these observations provide direct evidence that deacetylation participates in the regulation of chromosome segregation by targeting ParB in S. coelicolor.
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Affiliation(s)
- Peng Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Hong Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guo-Ping Zhao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,State Key Lab of Genetic Engineering & Institutes of Biomedical Sciences, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.,Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.,Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wei Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,College of Life Sciences, Shanghai Normal University, Shanghai 200232, China
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214
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Yan Z, Shen Z, Gao ZF, Chao Q, Qian CR, Zheng H, Wang BC. A comprehensive analysis of the lysine acetylome reveals diverse functions of acetylated proteins during de-etiolation in Zea mays. JOURNAL OF PLANT PHYSIOLOGY 2020; 248:153158. [PMID: 32240968 DOI: 10.1016/j.jplph.2020.153158] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/02/2020] [Accepted: 02/02/2020] [Indexed: 06/11/2023]
Abstract
Lysine acetylation is one of the most important post-translational modifications and is involved in multiple cellular processes in plants. There is evidence that acetylation may play an important role in light-induced de-etiolation, a key developmental switch from skotomorphogenesis to photomorphogenesis. During this transition, establishment of photosynthesis is of great significance. However, studies on acetylome dynamics during de-etiolation are limited. Here, we performed the first global lysine acetylome analysis for Zea mays seedlings undergoing de-etiolation, using nano liquid chromatography coupled to tandem mass spectrometry, and identified 814 lysine-acetylated sites on 462 proteins. Bioinformatics analysis of this acetylome showed that most of the lysine-acetylated proteins are predicted to be located in the cytoplasm, nucleus, chloroplast, and mitochondria. In addition, we detected ten lysine acetylation motifs and found that the accumulation of 482 lysine-acetylated peptides corresponding to 289 proteins changed significantly during de-etiolation. These proteins include transcription factors, histones, and proteins involved in chlorophyll synthesis, photosynthesis light reaction, carbon assimilation, glycolysis, the TCA cycle, amino acid metabolism, lipid metabolism, and nucleotide metabolism. Our study provides an in-depth dataset that extends our knowledge of in vivo acetylome dynamics during de-etiolation in monocots. This dataset promotes our understanding of the functional consequences of lysine acetylation in diverse cellular metabolic regulatory processes, and will be a useful toolkit for further investigations of the lysine acetylome and de-etiolation in plants.
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Affiliation(s)
- Zhen Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhuo Shen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China.
| | - Zhi-Fang Gao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100039, China.
| | - Chun-Rong Qian
- Institute of Crop Cultivation and Farming, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, New Jersey 08855, USA.
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100039, China.
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215
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Singh PK, Gao W, Liao P, Li Y, Xu FC, Ma XN, Long L, Song CP. Comparative acetylome analysis of wild-type and fuzzless-lintless mutant ovules of upland cotton (Gossypium hirsutum Cv. Xu142) unveils differential protein acetylation may regulate fiber development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 150:56-70. [PMID: 32114400 DOI: 10.1016/j.plaphy.2020.02.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
Protein acetylation (KAC) is a significant post-translational modification, which plays an essential role in the regulation of growth and development. Unfortunately, related studies are inadequately available in angiosperms, and to date, there is no report providing insight on the role of protein acetylation in cotton fiber development. Therefore, we first compared the lysine-acetylation proteome (acetylome) of upland cotton ovules in the early fiber development stages by using wild-type as well as its fuzzless-lintless mutant to identify the role of KAC in the fiber development. A total of 1696 proteins with 2754 acetylation sites identified with the different levels of acetylation belonging to separate subcellular compartments suggesting a large number of proteins differentially acetylated in two cotton cultivars. About 80% of the sites were predicted to localize in the cytoplasm, chloroplast, and mitochondria. Seventeen significantly enriched acetylation motifs were identified. Serine and threonine and cysteine located downstream and upstream to KAC sites. KEGG pathway enrichment analysis indicated oxidative phosphorylation, fatty acid, ribosome and protein, and folate biosynthesis pathways enriched significantly. To our knowledge, this is the first report of comparative acetylome analysis to compare the wild-type as well as its fuzzless-lintless mutant acetylome data to identify the differentially acetylated proteins, which may play a significant role in cotton fiber development.
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Affiliation(s)
- Prashant Kumar Singh
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization - The Volcani Center, Rishon LeZion, 7505101, Israel; State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China; Department of Biotechnology, Pachhunga University College, Mizoram University, Aizawl, 796001, India.
| | - Wei Gao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Peng Liao
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Yang Li
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Fu-Chun Xu
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Xiao-Nan Ma
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Lu Long
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China
| | - Chun-Peng Song
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Department of Biology, Henan University, Kaifeng, China.
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216
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Subramanian K, Hutt DM, Scott SM, Gupta V, Mao S, Balch WE. Correction of Niemann-Pick type C1 trafficking and activity with the histone deacetylase inhibitor valproic acid. J Biol Chem 2020; 295:8017-8035. [PMID: 32354745 DOI: 10.1074/jbc.ra119.010524] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
Niemann-Pick type C (NPC) disease is primarily caused by mutations in the NPC1 gene and is characterized by the accumulation of unesterified cholesterol and lipids in the late endosomal (LE) and lysosomal (Ly) compartments. The most prevalent disease-linked mutation is the I1061T variant of NPC1, which exhibits defective folding and trafficking from the endoplasmic reticulum to the LE/Ly compartments. We now show that the FDA-approved histone deacetylase inhibitor (HDACi) valproic acid (VPA) corrects the folding and trafficking defect associated with I1061T-NPC1 leading to restoration of cholesterol homeostasis, an effect that is largely driven by a reduction in HDAC7 expression. The VPA-mediated trafficking correction is in part associated with an increase in the acetylation of lysine residues in the cysteine-rich domain of NPC1. The HDACi-mediated correction is synergistically improved by combining it with the FDA-approved anti-malarial, chloroquine, a known lysosomotropic compound, which improved the stability of the LE/Ly-localized fraction of the I1061T variant. We posit that combining the activity of VPA, to modulate epigenetically the cellular acetylome, with chloroquine, to alter the lysosomal environment to favor stability of the trafficked I1061T variant protein can have a significant therapeutic benefit in patients carrying at least one copy of the I1061T variant of NPC1, the most common disease-associated mutation leading to NPC disease. Given its ability to cross the blood-brain barrier, we posit VPA provides a potential mechanism to improve the response to 2-hydroxypropyl-β-cyclodextrin, by restoring a functional NPC1 to the cholesterol managing compartment as an adjunct therapy.
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Affiliation(s)
| | - Darren M Hutt
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Samantha M Scott
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Vijay Gupta
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Shu Mao
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA
| | - William E Balch
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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217
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Baeza J, Lawton AJ, Fan J, Smallegan MJ, Lienert I, Gandhi T, Bernhardt OM, Reiter L, Denu JM. Revealing Dynamic Protein Acetylation across Subcellular Compartments. J Proteome Res 2020; 19:2404-2418. [PMID: 32290654 DOI: 10.1021/acs.jproteome.0c00088] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein acetylation is a widespread post-translational modification implicated in many cellular processes. Recent advances in mass spectrometry have enabled the cataloging of thousands of sites throughout the cell; however, identifying regulatory acetylation marks have proven to be a daunting task. Knowledge of the kinetics and stoichiometry of site-specific acetylation is an important factor to uncover function. Here, an improved method of quantifying acetylation stoichiometry was developed and validated, providing a detailed landscape of dynamic acetylation stoichiometry within cellular compartments. The dynamic nature of site-specific acetylation in response to serum stimulation was revealed. In two distinct human cell lines, growth factor stimulation led to site-specific, temporal acetylation changes, revealing diverse kinetic profiles that clustered into several groups. Overlap of dynamic acetylation sites among two different human cell lines suggested similar regulatory control points across major cellular pathways that include splicing, translation, and protein homeostasis. Rapid increases in acetylation on protein translational machinery suggest a positive regulatory role under progrowth conditions. Finally, higher median stoichiometry was observed in cellular compartments where active acetyltransferases are well described. Data sets can be accessed through ProteomExchange via the MassIVE repository (ProteomExchange: PXD014453; MassIVE: MSV000084029).
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Affiliation(s)
- Josue Baeza
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, 53706 Madison, Wisconsin, United States.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
| | - Alexis J Lawton
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, 53706 Madison, Wisconsin, United States.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
| | - Jing Fan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States.,Morgridge Institute for Research, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
| | - Michael J Smallegan
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, 53706 Madison, Wisconsin, United States.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
| | - Ian Lienert
- Biognosys AG, Wagistrasse 25, CH-8952 Schlieren, Switzerland
| | - Tejas Gandhi
- Biognosys AG, Wagistrasse 25, CH-8952 Schlieren, Switzerland
| | | | - Lukas Reiter
- Biognosys AG, Wagistrasse 25, CH-8952 Schlieren, Switzerland
| | - John M Denu
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, 53706 Madison, Wisconsin, United States.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
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218
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Schiffer TA, Lundberg JO, Weitzberg E, Carlström M. Modulation of mitochondria and NADPH oxidase function by the nitrate-nitrite-NO pathway in metabolic disease with focus on type 2 diabetes. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165811. [PMID: 32339643 DOI: 10.1016/j.bbadis.2020.165811] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/15/2022]
Abstract
Mitochondria play fundamental role in maintaining cellular metabolic homeostasis, and metabolic disorders including type 2 diabetes (T2D) have been associated with mitochondrial dysfunction. Pathophysiological mechanisms are coupled to increased production of reactive oxygen species and oxidative stress, together with reduced bioactivity/signaling of nitric oxide (NO). Novel strategies restoring these abnormalities may have therapeutic potential in order to prevent or even treat T2D and associated cardiovascular and renal co-morbidities. A diet rich in green leafy vegetables, which contains high concentrations of inorganic nitrate, has been shown to reduce the risk of T2D. To this regard research has shown that in addition to the classical NO synthase (NOS) dependent pathway, nitrate from our diet can work as an alternative precursor for NO and other bioactive nitrogen oxide species via serial reductions of nitrate (i.e. nitrate-nitrite-NO pathway). This non-conventional pathway may act as an efficient back-up system during various pathological conditions when the endogenous NOS system is compromised (e.g. acidemia, hypoxia, ischemia, aging, oxidative stress). A number of experimental studies have demonstrated protective effects of nitrate supplementation in models of obesity, metabolic syndrome and T2D. Recently, attention has been directed towards the effects of nitrate/nitrite on mitochondrial functions including beiging/browning of white adipose tissue, PGC-1α and SIRT3 dependent AMPK activation, GLUT4 translocation and mitochondrial fusion-dependent improvements in glucose homeostasis, as well as dampening of NADPH oxidase activity. In this review, we examine recent research related to the effects of bioactive nitrogen oxide species on mitochondrial function with emphasis on T2D.
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Affiliation(s)
- Tomas A Schiffer
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
| | - Jon O Lundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Eddie Weitzberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Mattias Carlström
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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219
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Olp MD, Sprague DJ, Goetz CJ, Kathman SG, Wynia-Smith SL, Shishodia S, Summers SB, Xu Z, Statsyuk AV, Smith BC. Covalent-Fragment Screening of BRD4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites. ACS Chem Biol 2020; 15:1036-1049. [PMID: 32149490 DOI: 10.1021/acschembio.0c00058] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BRD4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to nonhomologous cysteine residues within the C-terminal BRD4 bromodomain (BRD4-BD2), we performed a midthroughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify BRD4. Subsequent mass spectrometry, NMR, and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to BRD4 among human bromodomains. This site is orthogonal to the BRD4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays nor an acetylated histone peptide in AlphaScreen assays. Finally, we tethered our top-performing covalent fragment to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace BRD4 from chromatin.
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Affiliation(s)
- Michael D. Olp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Daniel J. Sprague
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Christopher J. Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Stefan G. Kathman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Sarah L. Wynia-Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Shifali Shishodia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Steven B. Summers
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Ziyang Xu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander V. Statsyuk
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- College of Pharmacy, University of Houston, Houston, Texas 77004, United States
| | - Brian C. Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
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220
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Bæk M, Martín‐Gago P, Laursen JS, Madsen JLH, Chakladar S, Olsen CA. Photo Cross-Linking Probes Containing ϵ-N-Thioacyllysine and ϵ-N-Acyl-(δ-aza)lysine Residues. Chemistry 2020; 26:3862-3869. [PMID: 31922630 PMCID: PMC7154546 DOI: 10.1002/chem.201905338] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/07/2020] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications (PTMs) are important in the regulation of protein function, trafficking, localization, and marking for degradation. This work describes the development of peptide activity/affinity-based probes for the discovery of proteins that recognize novel acyl-based PTMs on lysine residues in the proteome. The probes contain surrogates of ϵ-N-acyllysine by introduction of either hydrazide or thioamide functionalities to circumvent hydrolysis of the modification during the experiments. In addition to the modified PTMs, the developed chemotypes were analyzed with respect to the effect of peptide sequence. The photo cross-linking conditions and subsequent functionalization of the covalent adducts were systematically optimized by applying fluorophore labeling and gel electrophoresis (in-gel fluorescence measurements). Finally, selected probes, containing the ϵ-N-glutaryllysine and ϵ-N-myristoyllysine analogues, were successfully applied for the enrichment of native, endogenous proteins from cell lysate, recapitulating the expected interactions of SIRT5 and SIRT2, respectively. Interestingly, the latter mentioned was able to pull down two different splice variants of SIRT2, which has not been achieved with a covalent probe before. Based on this elaborate proof-of-concept study, we expect that the technology will have broad future applications for pairing of novel PTMs with the proteins that target them in the cell.
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Affiliation(s)
- Michael Bæk
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Jonas S. Laursen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Julie L. H. Madsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Saswati Chakladar
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
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Schreiber KJ, Lewis JD. Protein Acetylation in Pathogen Virulence and Host Defense: In Vitro Detection of Protein Acetylation by Radiolabeled Acetyl Coenzyme A. Methods Mol Biol 2020; 1991:23-32. [PMID: 31041759 DOI: 10.1007/978-1-4939-9458-8_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein acetylation has emerged as a common modification that modulates multiple aspects of protein function, including localization, stability, and protein-protein interactions. It is increasingly evident that protein acetylation significantly impacts the outcome of host-microbe interactions. In order to characterize novel putative acetyltransferase enzymes and their substrates, we describe a simple protocol for the detection of acetyltransferase activity in vitro. Purified proteins are incubated with 14C-acetyl CoA and separated electrophoretically, and acetylated proteins are detected by phosphorimaging or autoradiography.
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Affiliation(s)
- Karl J Schreiber
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA. .,Plant Gene Expression Center, United States Department of Agriculture, Albany, CA, USA.
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Rodríguez-Fdez S, Fernández-Nevado L, Lorenzo-Martín LF, Bustelo XR. Lysine Acetylation Reshapes the Downstream Signaling Landscape of Vav1 in Lymphocytes. Cells 2020; 9:cells9030609. [PMID: 32143292 PMCID: PMC7140538 DOI: 10.3390/cells9030609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Vav1 works both as a catalytic Rho GTPase activator and an adaptor molecule. These functions, which are critical for T cell development and antigenic responses, are tyrosine phosphorylation-dependent. However, it is not known whether other posttranslational modifications can contribute to the regulation of the biological activity of this protein. Here, we show that Vav1 becomes acetylated on lysine residues in a stimulation- and SH2 domain-dependent manner. Using a collection of both acetylation- and deacetylation-mimicking mutants, we show that the acetylation of four lysine residues (Lys222, Lys252, Lys587, and Lys716) leads to the downmodulation of the adaptor function of Vav1 that triggers the stimulation of the nuclear factor of activated T cells (NFAT). These sites belong to two functional subclasses according to mechanistic criteria. We have also unveiled additional acetylation sites potentially involved in either the stimulation (Lys782) or the downmodulation (Lys335, Lys374) of specific Vav1-dependent downstream responses. Collectively, these results indicate that Nε-lysine acetylation can play variegated roles in the regulation of Vav1 signaling. Unlike the case of the tyrosine phosphorylation step, this new regulatory layer is not conserved in other Vav family paralogs.
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Affiliation(s)
- Sonia Rodríguez-Fdez
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain; (S.R.-F.); (L.F.-N.); (L.F.L.-M.)
- Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Lucía Fernández-Nevado
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain; (S.R.-F.); (L.F.-N.); (L.F.L.-M.)
- Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - L. Francisco Lorenzo-Martín
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain; (S.R.-F.); (L.F.-N.); (L.F.L.-M.)
- Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Xosé R. Bustelo
- Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain; (S.R.-F.); (L.F.-N.); (L.F.L.-M.)
- Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007 Salamanca, Spain
- Correspondence: ; Tel.: +34-663194634
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223
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Agudelo Garcia PA, Nagarajan P, Parthun MR. Hat1-Dependent Lysine Acetylation Targets Diverse Cellular Functions. J Proteome Res 2020; 19:1663-1673. [PMID: 32081014 DOI: 10.1021/acs.jproteome.9b00843] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lysine acetylation has emerged as one of the most important post-translational modifications, regulating different biological processes. However, its regulation by lysine acetyltransferases is still unclear in most cases. Hat1 is a lysine acetyltransferase originally identified based on its ability to acetylate histones. Using an unbiased proteomics approach, we have determined how loss of Hat1 affects the mammalian acetylome. Hat1+/+ and Hat1-/- mouse embryonic fibroblast cell lines were grown in both glucose- and galactose-containing media, as Hat1 is required for growth on galactose, and Hat1-/- cells exhibit defects in mitochondrial function. Following trypsin digestion of whole cell extracts, acetylated peptides were enriched by acetyllysine affinity purification, and acetylated peptides were identified and analyzed by label-free quantitation. Comparison of the acetylome from Hat1+/+ cells grown on galactose and glucose demonstrated that there are large carbon source-dependent changes in the mammalian acetylome where the acetylation of enzymes involved in glycolysis were the most affected. Comparisons of the acetylomes from Hat1+/+ and Hat1-/- cells identified 65 proteins whose acetylation decreased by at least 2.5-fold in cells lacking Hat1. In Hat1-/- cells, acetylation of the autoregulatory loop of CBP (CREB-binding protein) was the most highly affected, decreasing by up to 20-fold. In addition to the proteins involved in chromatin structure, Hat1-dependent acetylation was also found in a number of transcriptional regulators, including p53 and mitochondrial proteins. Hat1 mitochondrial localization suggests that it may be directly involved in the acetylation of mitochondrial proteins. Data are available via ProteomeXchange with identifier PXD017362.
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Affiliation(s)
- Paula A Agudelo Garcia
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Prabakaran Nagarajan
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
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224
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Lacroix M, Riscal R, Arena G, Linares LK, Le Cam L. Metabolic functions of the tumor suppressor p53: Implications in normal physiology, metabolic disorders, and cancer. Mol Metab 2020; 33:2-22. [PMID: 31685430 PMCID: PMC7056927 DOI: 10.1016/j.molmet.2019.10.002] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/24/2019] [Accepted: 10/05/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The TP53 gene is one of the most commonly inactivated tumor suppressors in human cancers. p53 functions during cancer progression have been linked to a variety of transcriptional and non-transcriptional activities that lead to the tight control of cell proliferation, senescence, DNA repair, and cell death. However, converging evidence indicates that p53 also plays a major role in metabolism in both normal and cancer cells. SCOPE OF REVIEW We provide an overview of the current knowledge on the metabolic activities of wild type (WT) p53 and highlight some of the mechanisms by which p53 contributes to whole body energy homeostasis. We will also pinpoint some evidences suggesting that deregulation of p53-associated metabolic activities leads to human pathologies beyond cancer, including obesity, diabetes, liver, and cardiovascular diseases. MAJOR CONCLUSIONS p53 is activated when cells are metabolically challenged but the origin, duration, and intensity of these stresses will dictate the outcome of the p53 response. p53 plays pivotal roles both upstream and downstream of several key metabolic regulators and is involved in multiple feedback-loops that ensure proper cellular homeostasis. The physiological roles of p53 in metabolism involve complex mechanisms of regulation implicating both cell autonomous effects as well as autocrine loops. However, the mechanisms by which p53 coordinates metabolism at the organismal level remain poorly understood. Perturbations of p53-regulated metabolic activities contribute to various metabolic disorders and are pivotal during cancer progression.
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Affiliation(s)
- Matthieu Lacroix
- Institut de Recherche en Cancérologie de Montpellier, INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France; Equipe labélisée Ligue Contre le Cancer, France
| | - Romain Riscal
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Giuseppe Arena
- Gustave Roussy Cancer Campus, INSERM U1030, Villejuif, France
| | - Laetitia Karine Linares
- Institut de Recherche en Cancérologie de Montpellier, INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France; Equipe labélisée Ligue Contre le Cancer, France
| | - Laurent Le Cam
- Institut de Recherche en Cancérologie de Montpellier, INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier, Montpellier, France; Equipe labélisée Ligue Contre le Cancer, France.
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225
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Li ST, Huang D, Shen S, Cai Y, Xing S, Wu G, Jiang Z, Hao Y, Yuan M, Wang N, Zhu L, Yan R, Yang D, Wang L, Liu Z, Hu X, Zhou R, Qu K, Li A, Duan X, Zhang H, Gao P. Myc-mediated SDHA acetylation triggers epigenetic regulation of gene expression and tumorigenesis. Nat Metab 2020; 2:256-269. [PMID: 32694775 DOI: 10.1038/s42255-020-0179-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 02/11/2020] [Indexed: 01/16/2023]
Abstract
The transcriptional role of cMyc (or Myc) in tumorigenesis is well appreciated; however, it remains to be fully established how extensively Myc is involved in the epigenetic regulation of gene expression. Here, we show that by deactivating succinate dehydrogenase complex subunit A (SDHA) via acetylation, Myc triggers a regulatory cascade in cancer cells that leads to H3K4me3 activation and gene expression. We find that Myc facilitates the acetylation-dependent deactivation of SDHA by activating the SKP2-mediated degradation of SIRT3 deacetylase. We further demonstrate that Myc inhibition of SDH-complex activity leads to cellular succinate accumulation, which triggers H3K4me3 activation and tumour-specific gene expression. We demonstrate that acetylated SDHA at Lys 335 contributes to tumour growth in vitro and in vivo, and we confirm increased tumorigenesis in clinical samples. This study illustrates a link between acetylation-dependent SDHA deactivation and Myc-driven epigenetic regulation of gene expression, which is critical for cancer progression.
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Affiliation(s)
- Shi-Ting Li
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - De Huang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Shengqi Shen
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Yongping Cai
- Department of Pathology, School of Medicine, Anhui Medical University, Hefei, China
| | - Songge Xing
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Gongwei Wu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Zetan Jiang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Yijie Hao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Mengqiu Yuan
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, China
| | - Nana Wang
- Department of Pathology, School of Medicine, Anhui Medical University, Hefei, China
| | - Lianbang Zhu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Ronghui Yan
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Dongdong Yang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Lin Wang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Zhaoji Liu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, China
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, China
| | - Xin Hu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Rongbin Zhou
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Kun Qu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Ailing Li
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
| | - Xiaotao Duan
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China.
| | - Huafeng Zhang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China.
| | - Ping Gao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China.
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, China.
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, China.
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China.
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Al-Attar R, Storey KB. Suspended in time: Molecular responses to hibernation also promote longevity. Exp Gerontol 2020; 134:110889. [PMID: 32114078 DOI: 10.1016/j.exger.2020.110889] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022]
Abstract
Aging in most animals is an inevitable process that causes or is a result of physiological, biochemical, and molecular changes in the body, and has a strong influence on an organism's lifespan. Although advancement in medicine has allowed humans to live longer, the prevalence of age-associated medical complications is continuously burdening older adults worldwide. Current animal models used in research to study aging have provided novel information that has helped investigators understand the aging process; however, these models are limiting. Aging is a complex process that is regulated at multiple biological levels, and while a single manipulation in these models can provide information on a process, it is not enough to understand the global regulation of aging. Some mammalian hibernators live up to 9.8-times higher than their expected average lifespan, and new research attributes this increase to their ability to hibernate. A common theme amongst these mammalian hibernators is their ability to greatly reduce their metabolic rate to a fraction of their normal rate and initiate cytoprotective responses that enable their survival. Metabolic rate depression is strictly regulated at different biological levels in order to enable the animal to not only survive, but to also do so by relying mainly on their limited internal fuels. As such, understanding both the global and specific regulatory mechanisms used to promote survival during hibernation could, in theory, allow investigators to have a better understanding of the aging process. This can also allow pharmaceutical industries to find therapeutics that could delay or reverse age-associated medical complications and promote healthy aging and longevity in humans.
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Affiliation(s)
- Rasha Al-Attar
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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227
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A Newly Synthesized Rhamnoside Derivative Alleviates Alzheimer's Amyloid- β-Induced Oxidative Stress, Mitochondrial Dysfunction, and Cell Senescence through Upregulating SIRT3. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:7698560. [PMID: 32104538 PMCID: PMC7040408 DOI: 10.1155/2020/7698560] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/23/2019] [Accepted: 01/10/2020] [Indexed: 12/11/2022]
Abstract
Oxidative stress-induced mitochondrial dysfunction and cell senescence are considered critical contributors to Alzheimer's disease (AD), and oxidant/antioxidant imbalance has been a therapeutic target in AD. SIRT3 is a mitochondrial protein regulating metabolic enzyme activity by deacetylation and its downregulation is associated with AD pathology. In the present study, we showed that a newly synthesized rhamnoside derivative PL171 inhibited the generation of reactive oxidant species (ROS) induced by amyloid-β42 oligomers (Aβ42O), major AD pathological proteins. Moreover, the reduction of mitochondrial membrane potential (MMP) and the impairment of mitochondrial oxygen consumption triggered by Aβ42O were also prevented by PL171. Further experiments demonstrated that PL171 reduced the acetylation of mitochondrial proteins, and particularly the acetylation of manganese superoxide dismutase (MnSOD) and oligomycin-sensitivity-conferring protein (OSCP), two mitochondrial SIRT3 substrates, was suppressed by PL171. Mechanism studies revealed that PL171 upregulated SIRT3 and its upstream peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) under basal and Aβ42O-treated conditions. The inhibition of SIRT3 activity could eliminate the protective effects of PL171. Further, long-term treatment with Aβ42O increased the number of senescent neuronal cell, which was also alleviated by PL171 in a SIRT3-dependent manner. Taken together, our results indicated that PL171 rescued Aβ42O-induced oxidative stress, mitochondrial dysfunction, and cell senescence via upregulating SIRT3 and might be a potential drug candidate against AD.
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228
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Sowah SA, Hirche F, Milanese A, Johnson TS, Grafetstätter M, Schübel R, Kirsten R, Ulrich CM, Kaaks R, Zeller G, Kühn T, Stangl GI. Changes in Plasma Short-Chain Fatty Acid Levels after Dietary Weight Loss Among Overweight and Obese Adults over 50 Weeks. Nutrients 2020; 12:nu12020452. [PMID: 32053988 PMCID: PMC7071291 DOI: 10.3390/nu12020452] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/14/2022] Open
Abstract
Gut microbial-derived short-chain fatty acids (SCFAs) may regulate energy homeostasis and exert anti-carcinogenic, immunomodulatory and anti-inflammatory effects. Smaller trials indicate that dietary weight loss may lead to decreased SCFA production, but findings have been inconclusive. SCFA concentrations were measured by HPLC-MS/MS in plasma samples of 150 overweight or obese adults in a trial initially designed to evaluate the metabolic effects of intermittent (ICR) versus continuous (CCR) calorie restriction (NCT02449148). For the present post hoc analyses, participants were classified by quartiles of weight loss, irrespective of the dietary intervention. Linear mixed models were used to analyze weight-loss-induced changes in SCFA concentrations after 12, 24 and 50 weeks. There were no differential changes in SCFA levels across the initial study arms (ICR versus CCR versus control) after 12 weeks, but acetate concentrations significantly decreased with overall weight loss (mean log-relative change of −0.7 ± 1.8 in the lowest quartile versus. −7.6 ± 2 in the highest, p = 0.026). Concentrations of propionate, butyrate and other SCFAs did not change throughout the study. Our results show that weight-loss, achieved through calorie restriction, may lead to smaller initial decreases in plasma acetate, while plasma SCFAs generally remain remarkably stable over time.
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Affiliation(s)
- Solomon A. Sowah
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; (T.S.J.); (M.G.); (R.S.); (R.K.); (T.K.)
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
| | - Frank Hirche
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.H.); (G.I.S.)
| | - Alessio Milanese
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, 69117 Heidelberg, Germany; (A.M.); (G.Z.)
| | - Theron S. Johnson
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; (T.S.J.); (M.G.); (R.S.); (R.K.); (T.K.)
| | - Mirja Grafetstätter
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; (T.S.J.); (M.G.); (R.S.); (R.K.); (T.K.)
- Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany
| | - Ruth Schübel
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; (T.S.J.); (M.G.); (R.S.); (R.K.); (T.K.)
| | - Romy Kirsten
- Biobank of the National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany;
| | - Cornelia M. Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA;
| | - Rudolf Kaaks
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; (T.S.J.); (M.G.); (R.S.); (R.K.); (T.K.)
| | - Georg Zeller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, 69117 Heidelberg, Germany; (A.M.); (G.Z.)
| | - Tilman Kühn
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; (T.S.J.); (M.G.); (R.S.); (R.K.); (T.K.)
| | - Gabriele I. Stangl
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.H.); (G.I.S.)
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229
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Oviedo-Rouco S, Perez-Bertoldi JM, Spedalieri C, Castro MA, Tomasina F, Tortora V, Radi R, Murgida DH. Electron transfer and conformational transitions of cytochrome c are modulated by the same dynamical features. Arch Biochem Biophys 2020; 680:108243. [DOI: 10.1016/j.abb.2019.108243] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/11/2019] [Accepted: 12/29/2019] [Indexed: 01/17/2023]
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230
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Minde DP, Ramakrishna M, Lilley KS. Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions. Commun Biol 2020; 3:38. [PMID: 31969649 PMCID: PMC6976632 DOI: 10.1038/s42003-020-0758-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
Intrinsically Disordered Regions (IDRs) are enriched in disease-linked proteins known to have multiple post-translational modifications, but there is limited in vivo information about how locally unfolded protein regions contribute to biological functions. We reasoned that IDRs should be more accessible to targeted in vivo biotinylation than ordered protein regions, if they retain their flexibility in human cells. Indeed, we observed increased biotinylation density in predicted IDRs in several cellular compartments >20,000 biotin sites from four proximity proteomics studies. We show that in a biotin ‘painting’ time course experiment, biotinylation events in Escherichia coli ribosomes progress from unfolded and exposed regions at 10 s, to structured and less accessible regions after five minutes. We conclude that biotin proximity tagging favours sites of local disorder in proteins and suggest the possibility of using biotin painting as a method to gain unique insights into in vivo condition-dependent subcellular plasticity of proteins. David-Paul Minde, Manasa Ramakrishna et al. look at intrinsically disordered regions of disease-linked proteins in vivo by biotinylation. They show that biotin “painting” could be used as a method to examine the condition-dependent plasticity of proteins in vivo.
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Affiliation(s)
- David-Paul Minde
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Manasa Ramakrishna
- Medical Research Council Toxicology Unit, University of Cambridge, Lancaster Road, Leicester, LE1 9HN, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
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Bechter O, Schöffski P. Make your best BET: The emerging role of BET inhibitor treatment in malignant tumors. Pharmacol Ther 2020; 208:107479. [PMID: 31931101 DOI: 10.1016/j.pharmthera.2020.107479] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Bromodomains are protein-protein interaction modules with a great diversity in terms of number of proteins and their function. The bromodomain and extraterminal protein (BET) represents a distinct subclass of bromodomain proteins mainly involved in transcriptional regulation via their interaction with acetylated chromatin. In cancer cells BET proteins are found to be altered in many ways such as overexpression, mutations and fusions of BET proteins or their interference with cancer relevant signaling pathways and transcriptional programs in order to sustain cancer growth and viability. Blocking BET protein function with small molecules is associated with therapeutic activity. Consequently, a variety of small molecules have been developed and a number of phase I clinical trials have explored their tolerability and efficacy in patients with solid tumors and hematological malignancies. We will review the rational for applying BET inhibitors in the clinic and we will discuss the toxicity profile as well as efficacy of this new class of protein inhibitors. We will also highlight the emerging problem of treatment resistance and the potential these drugs might have when combined with other anti-cancer therapies.
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Affiliation(s)
- Oliver Bechter
- Leuven Cancer Institute, Department of General Medical Oncology, University Hospitals Leuven, Belgium; Department of Oncology, KU, Leuven, Belgium.
| | - Patrick Schöffski
- Leuven Cancer Institute, Department of General Medical Oncology, University Hospitals Leuven, Belgium; Department of Oncology, KU, Leuven, Belgium.
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232
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Schilling B, Meyer JG, Wei L, Ott M, Verdin E. High-Resolution Mass Spectrometry to Identify and Quantify Acetylation Protein Targets. Methods Mol Biol 2020; 1983:3-16. [PMID: 31087289 DOI: 10.1007/978-1-4939-9434-2_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The dynamic nature of protein posttranslational modification (PTM) allows cells to rapidly respond to changes in their environment, such as nutrition, stress, or signaling. Lysine residues are targets for several types of modifications, including methylation, ubiquitination, and various acylation groups, especially acetylation. Currently, one of the best methods for identification and quantification of protein acetylation is immunoaffinity enrichment in combination with high-resolution mass spectrometry. As we are using a relatively novel and comprehensive mass spectrometric approach, data-independent acquisition (DIA), this protocol provides high-throughput, accurate, and reproducible label-free PTM quantification. Here we describe detailed protocols to process relatively small amounts of mouse liver tissue that integrate isolation of proteins, proteolytic digestion into peptides, immunoaffinity enrichment of acetylated peptides, identification of acetylation sites, and comprehensive quantification of relative abundance changes for thousands of identified lysine acetylation sites.
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Affiliation(s)
| | - Jesse G Meyer
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Lei Wei
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Melanie Ott
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA
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233
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Mereweather LJ, Montes Aparicio CN, Heather LC. Positioning Metabolism as a Central Player in the Diabetic Heart. J Lipid Atheroscler 2020; 9:92-109. [PMID: 32821724 PMCID: PMC7379068 DOI: 10.12997/jla.2020.9.1.92] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/28/2019] [Accepted: 12/29/2019] [Indexed: 12/13/2022] Open
Abstract
In type 2 diabetes (T2D), the leading cause of death is cardiovascular complications. One mechanism contributing to cardiac pathogenesis is alterations in metabolism, with the diabetic heart exhibiting increased fatty acid oxidation and reduced glucose utilisation. The processes classically thought to underlie this metabolic shift include the Randle cycle and changes to gene expression. More recently, alternative mechanisms have been proposed, most notably, changes in post-translational modification of mitochondrial proteins in the heart. This increased understanding of how metabolism is altered in the diabetic heart has highlighted new therapeutic targets, with an aim to improve cardiac function in T2D. This review focuses on metabolism in the healthy heart and how this is modified in T2D, providing evidence for the mechanisms underlying this shift. There will be emphasis on the current treatments for the heart in diabetes, alongside efforts for metabocentric pharmacological therapies.
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Affiliation(s)
- Laura J Mereweather
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | | | - Lisa C Heather
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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234
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Disruption of Acetyl-Lysine Turnover in Muscle Mitochondria Promotes Insulin Resistance and Redox Stress without Overt Respiratory Dysfunction. Cell Metab 2020; 31:131-147.e11. [PMID: 31813822 PMCID: PMC6952241 DOI: 10.1016/j.cmet.2019.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/30/2019] [Accepted: 11/07/2019] [Indexed: 12/23/2022]
Abstract
This study sought to examine the functional significance of mitochondrial protein acetylation using a double knockout (DKO) mouse model harboring muscle-specific deficits in acetyl-CoA buffering and lysine deacetylation, due to genetic ablation of carnitine acetyltransferase and Sirtuin 3, respectively. DKO mice are highly susceptible to extreme hyperacetylation of the mitochondrial proteome and develop a more severe form of diet-induced insulin resistance than either single KO mouse line. However, the functional phenotype of hyperacetylated DKO mitochondria is largely normal. Of the >120 measures of respiratory function assayed, the most consistently observed traits of a markedly heightened acetyl-lysine landscape are enhanced oxygen flux in the context of fatty acid fuel and elevated rates of electron leak. In sum, the findings challenge the notion that lysine acetylation causes broad-ranging damage to mitochondrial quality and performance and raise the possibility that acetyl-lysine turnover, rather than acetyl-lysine stoichiometry, modulates redox balance and carbon flux.
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235
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Abstract
Nε-lysine acetylation was discovered more than half a century ago as a post-translational modification of histones and has been extensively studied in the context of transcription regulation. In the past decade, proteomic analyses have revealed that non-histone proteins are frequently acetylated and constitute a major portion of the acetylome in mammalian cells. Indeed, non-histone protein acetylation is involved in key cellular processes relevant to physiology and disease, such as gene transcription, DNA damage repair, cell division, signal transduction, protein folding, autophagy and metabolism. Acetylation affects protein functions through diverse mechanisms, including by regulating protein stability, enzymatic activity, subcellular localization and crosstalk with other post-translational modifications and by controlling protein-protein and protein-DNA interactions. In this Review, we discuss recent progress in our understanding of the scope, functional diversity and mechanisms of non-histone protein acetylation.
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236
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Zhang L, Wang W, Zhang S, Wang Y, Guo W, Liu Y, Wang Y, Zhang Y. Identification of lysine acetylome in cervical cancer by label-free quantitative proteomics. Cancer Cell Int 2020; 20:182. [PMID: 32489318 PMCID: PMC7247262 DOI: 10.1186/s12935-020-01266-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lysine acetylation is a post-translational modification that regulates a diversity of biological processes, including cancer development. METHODS Here, we performed the quantitative acetylproteomic analysis of three primary cervical cancer tissues and corresponding adjacent normal tissues by using the label-free proteomics approach. RESULTS We identified a total of 928 lysine acetylation sites from 1547 proteins, in which 495 lysine acetylation sites corresponding to 296 proteins were quantified. Further, 41 differentially expressed lysine acetylation sites corresponding to 30 proteins were obtained in cervical cancer tissues compared with adjacent normal tissues (Fold change > 2 and P < 0.05), of which 1 was downregulated, 40 were upregulated. Moreover, 75 lysine acetylation sites corresponding to 58 proteins were specifically detected in cancer tissues or normal adjacent tissues. Motif-X analysis showed that kxxxkxxxk, GkL, AxxEk, kLxE, and kkxxxk are the most enriched motifs with over four-fold increases when compared with the background matches. KEGG analysis showed that proteins identified from differently and specifically expressed peptides may influence key pathways, such as Notch signaling pathway, viral carcinogenesis, RNA transport, and Jak-STAT, which play an important role in tumor progression. Furthermore, the acetylated levels of CREBBP and S100A9 in cervical cancer tissues were confirmed by immunoprecipitation (IP) and Western blot analysis. CONCLUSIONS Taken together, our data provide novel insights into the role of protein lysine acetylation in cervical carcinogenesis.
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Affiliation(s)
- Lu Zhang
- Department of Gynecology, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081 Heilongjiang Province China
| | - Wanyue Wang
- School of Basic Medical Sciences, Qiqihar Medical University, Qiqihar, 161006 Heilongjiang China
| | - Shanqiang Zhang
- Medical Research Center, Yue Bei People’s Hospital Affiliated to Shantou University Medical College, Shaoguan, 512025 Guangdong China
| | - Yuxin Wang
- Department of Gynecology, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081 Heilongjiang Province China
| | - Weikang Guo
- Department of Gynecology, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081 Heilongjiang Province China
| | - Yunduo Liu
- Department of Gynecology, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081 Heilongjiang Province China
| | - Yaoxian Wang
- Department of Gynecology, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081 Heilongjiang Province China
| | - Yunyan Zhang
- Department of Gynecology, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081 Heilongjiang Province China
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237
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Gomes P, Viana SD, Nunes S, Rolo AP, Palmeira CM, Reis F. The yin and yang faces of the mitochondrial deacetylase sirtuin 3 in age-related disorders. Ageing Res Rev 2020; 57:100983. [PMID: 31740222 DOI: 10.1016/j.arr.2019.100983] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/08/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023]
Abstract
Aging, the most important risk factor for many of the chronic diseases affecting Western society, is associated with a decline in mitochondrial function and dynamics. Sirtuin 3 (SIRT3) is a mitochondrial deacetylase that has emerged as a key regulator of fundamental processes which are frequently dysregulated in aging and related disorders. This review highlights recent advances and controversies regarding the yin and yang functions of SIRT3 in metabolic, cardiovascular and neurodegenerative diseases, as well as the use of SIRT3 modulators as a therapeutic strategy against those disorders. Although most studies point to a protective role upon SIRT3 activation, there are conflicting findings that need a better elucidation. The discovery of novel SIRT3 modulators with higher selectivity together with the assessment of the relative importance of different SIRT3 enzymatic activities and the relevance of crosstalk between distinct sirtuin isoforms will be pivotal to validate SIRT3 as a useful drug target for the prevention and treatment of age-related diseases.
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Affiliation(s)
- Pedro Gomes
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal; Department of Biomedicine, Faculty of Medicine, University of Porto, Portugal; CINTESIS - Center for Health Technology and Services Research, University of Porto, Portugal
| | - Sofia D Viana
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal; Polytechnic Institute of Coimbra, ESTESC-Coimbra Health School, Pharmacy, Coimbra, Portugal
| | - Sara Nunes
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal
| | - Anabela P Rolo
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal; Department of Life Sciences, University of Coimbra, Portugal
| | - Carlos M Palmeira
- CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Portugal; Department of Life Sciences, University of Coimbra, Portugal
| | - Flávio Reis
- Institute of Pharmacology & Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Portugal; CIBB - Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal.
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238
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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: 85] [Impact Index Per Article: 14.2] [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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239
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van Pijkeren A, Bischoff R, Kwiatkowski M. Mass spectrometric analysis of PTM dynamics using stable isotope labeled metabolic precursors in cell culture. Analyst 2019; 144:6812-6833. [PMID: 31650141 DOI: 10.1039/c9an01258c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological organisms represent highly dynamic systems, which are continually exposed to environmental factors and always strive to restore steady-state homeostasis. Posttranslational modifications are key regulators with which biological systems respond to external stimuli. To understand how homeostasis is restored, it is important to study the kinetics of posttranslational modifications. In this review we discuss proteomic approaches using stable isotope labeled metabolic precursors to study dynamics of posttranslational modifications in cell culture.
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Affiliation(s)
- Alienke van Pijkeren
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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240
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Li Y, Xue H, Bian DR, Xu G, Piao C. Acetylome analysis of lysine acetylation in the plant pathogenic bacterium Brenneria nigrifluens. Microbiologyopen 2019; 9:e00952. [PMID: 31677250 PMCID: PMC6957402 DOI: 10.1002/mbo3.952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/28/2022] Open
Abstract
Protein lysine acetylation, a dynamic and reversible posttranslational modification, plays a crucial role in several cellular processes, including cell cycle regulation, metabolism, enzymatic activities, and protein interactions. Brenneria nigrifluens is a pathogen of walnut trees with shallow bark canker and can cause serious disease in walnut trees. Until now, a little has been known about the roles of lysine acetylation in plant pathogenic bacteria. In the present study, the lysine acetylome of B. nigrifluens was determined by high‐resolution LC‐MS/MS analysis. In total, we identified 1,866 lysine acetylation sites distributed in 737 acetylated proteins. Bioinformatics results indicated that acetylated proteins participate in many different biological functions in B. nigrifluens. Four conserved motifs, namely, LKac, Kac*F, I*Kac, and L*Kac, were identified in this bacterium. Protein interaction network analysis indicated that all kinds of interactions are modulated by protein lysine acetylation. Overall, 12 acetylated proteins were related to the virulence of B. nigrifluens.
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Affiliation(s)
- Yong Li
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Han Xue
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Dan-Ran Bian
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Guantang Xu
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Chungen Piao
- The Key Laboratory of National Forestry and Grassland Administration on Forest Protection, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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241
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Qin W, Wang T, Huang H, Gao Y. Profiling of lysine-acetylated proteins in human urine. SCIENCE CHINA. LIFE SCIENCES 2019; 62:1514-1520. [PMID: 30820853 DOI: 10.1007/s11427-017-9367-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/20/2018] [Indexed: 06/09/2023]
Abstract
A biomarker is a measurable indicator associated with changes in physiological state or disease. In contrast to the blood which is under homeostatic controls, urine reflects changes in the body earlier and more sensitively, and is therefore a better biomarker source. Lysine acetylation is an abundant and highly regulated post-translational modification. It plays a pivotal role in modulating diverse biological processes and is associated with various important diseases. Enrichment or visualization of proteins with specific post-translational modifications provides a method for sampling the urinary proteome and reducing sample complexity. In this study, we used anti-acetyllysine antibody-based immunoaffinity enrichment combined with high-resolution mass spectrometry to profile lysine-acetylated proteins in normal human urine. A total of 629 acetylation sites on 315 proteins were identified, including some very low-abundance proteins. This is the first proteome-wide characterization of lysine acetylation proteins in normal human urine. Our dataset provides a useful resource for the further discovery of lysine-acetylated proteins as biomarkers in urine.
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Affiliation(s)
- Weiwei Qin
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, 100875, China
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao, 266071, China
| | - Ting Wang
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, 100875, China
| | - He Huang
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, 100875, China.
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242
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Label-Free Quantitative Acetylome Analysis Reveals Toxoplasma gondii Genotype-Specific Acetylomic Signatures. Microorganisms 2019; 7:microorganisms7110510. [PMID: 31671511 PMCID: PMC6921067 DOI: 10.3390/microorganisms7110510] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 11/16/2022] Open
Abstract
Distinct genotypic and pathogenic differences exist between Toxoplasma gondii genotypes. For example, genotype I is highly virulent, whereas genotype II and genotype III are less virulent. Moreover, Chinese 1 genotype (ToxoDB#9) is also virulent. Here, we compare the acetylomes of genotype 1 (RH strain) and Chinese 1 genotype (ToxoDB#9, PYS strain) of T. gondii. Using mass spectrometry enriched for acetylated peptides, we found a relationship between the levels of protein acetylation and parasite genotype-specific virulence. Notably, lysine acetylation was the largest (458 acetylated proteins) in RH strain, followed by PYS strain (188 acetylated proteins), whereas only 115 acetylated proteins were detected in PRU strain. Our analysis revealed four, three, and four motifs in RH strain, PRU strain and PYS strain, respectively. Three conserved sequences around acetylation sites, namely, xxxxxKAcHxxxx, xxxxxKAcFxxxx, and xxxxGKAcSxxxx, were detected in the acetylome of the three strains. However, xxxxxKAcNxxxx (asparagine) was found in RH and PYS strains but was absent in PRU strain. Our analysis also identified 15, 3, and 26 differentially expressed acetylated proteins in RH strain vs. PRU strain, PRU strain vs. PYS strain and PYS strain vs. RH strain, respectively. KEGG pathway analysis showed that a large proportion of the acetylated proteins are involved in metabolic processes. Pathways for the biosynthesis of secondary metabolites, biosynthesis of antibiotics and microbial metabolism in diverse environments were featured in the top five enriched pathways in all three strains. However, acetylated proteins from the virulent strains (RH and PYS) were more enriched in the pyruvate metabolism pathway compared to acetylated proteins from PRU strain. Increased levels of histone-acetyl-transferase and glycyl-tRNA synthase were detected in RH strain compared to PRU strain and PYS strain. Both enzymes play roles in stress tolerance and proliferation, key features in the parasite virulence. These findings reveal novel insight into the acetylomic profiles of major T. gondii genotypes and provide a new important resource for further investigations of the roles of the acetylated parasite proteins in the modulation of the host cell response to the infection of T. gondii.
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243
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Santo-Domingo J, Dayon L, Wiederkehr A. Protein Lysine Acetylation: Grease or Sand in the Gears of β-Cell Mitochondria? J Mol Biol 2019; 432:1446-1460. [PMID: 31628953 DOI: 10.1016/j.jmb.2019.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 02/06/2023]
Abstract
Mitochondria carry out many essential functions in metabolism. A central task is the oxidation of nutrients and the generation of ATP by oxidative phosphorylation. Mitochondrial metabolism needs to be tightly regulated for the cell to respond to changes in ATP demand and nutrient supply. Here, we review how protein lysine acetylation contributes to the regulation of mitochondrial metabolism in insulin target tissues and the insulin-secreting pancreatic β-cell. We summarize recent evidence showing that in pancreatic β-cells, lysine acetylation occurs on a large number of proteins involved in metabolism. Furthermore, we give a brief overview of the molecular mechanism that controls lysine acetylation dynamics. We propose that protein lysine acetylation is an important mechanism for the fine-tuning of mitochondrial activity in β-cells during normal physiology. In contrast, nutrient oversupply, oxidative stress, or inhibition of the mitochondrial deacetylase SIRT3 leads to protein lysine hyperacetylation, which impairs mitochondrial function. By perturbing mitochondrial activity in β-cells and insulin target tissues, protein lysine hyperacetylation may contribute to the development of type 2 diabetes.
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Affiliation(s)
- Jaime Santo-Domingo
- Mitochondrial Function, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Andreas Wiederkehr
- Mitochondrial Function, Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland.
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244
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The NSL complex maintains nuclear architecture stability via lamin A/C acetylation. Nat Cell Biol 2019; 21:1248-1260. [PMID: 31576060 DOI: 10.1038/s41556-019-0397-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/21/2019] [Indexed: 12/26/2022]
Abstract
While nuclear lamina abnormalities are hallmarks of human diseases, their interplay with epigenetic regulators and precise epigenetic landscape remain poorly understood. Here, we show that loss of the lysine acetyltransferase MOF or its associated NSL-complex members KANSL2 or KANSL3 leads to a stochastic accumulation of nuclear abnormalities with genomic instability patterns including chromothripsis. SILAC-based MOF and KANSL2 acetylomes identified lamin A/C as an acetylation target of MOF. HDAC inhibition or acetylation-mimicking lamin A derivatives rescue nuclear abnormalities observed in MOF-deficient cells. Mechanistically, loss of lamin A/C acetylation resulted in its increased solubility, defective phosphorylation dynamics and impaired nuclear mechanostability. We found that nuclear abnormalities include EZH2-dependent histone H3 Lys 27 trimethylation and loss of nascent transcription. We term this altered epigenetic landscape "heterochromatin enrichment in nuclear abnormalities" (HENA). Collectively, the NSL-complex-dependent lamin A/C acetylation provides a mechanism that maintains nuclear architecture and genome integrity.
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Softic S, Meyer JG, Wang GX, Gupta MK, Batista TM, Lauritzen HPMM, Fujisaka S, Serra D, Herrero L, Willoughby J, Fitzgerald K, Ilkayeva O, Newgard CB, Gibson BW, Schilling B, Cohen DE, Kahn CR. Dietary Sugars Alter Hepatic Fatty Acid Oxidation via Transcriptional and Post-translational Modifications of Mitochondrial Proteins. Cell Metab 2019; 30:735-753.e4. [PMID: 31577934 PMCID: PMC7816129 DOI: 10.1016/j.cmet.2019.09.003] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/06/2019] [Accepted: 09/05/2019] [Indexed: 01/25/2023]
Abstract
Dietary sugars, fructose and glucose, promote hepatic de novo lipogenesis and modify the effects of a high-fat diet (HFD) on the development of insulin resistance. Here, we show that fructose and glucose supplementation of an HFD exert divergent effects on hepatic mitochondrial function and fatty acid oxidation. This is mediated via three different nodes of regulation, including differential effects on malonyl-CoA levels, effects on mitochondrial size/protein abundance, and acetylation of mitochondrial proteins. HFD- and HFD plus fructose-fed mice have decreased CTP1a activity, the rate-limiting enzyme of fatty acid oxidation, whereas knockdown of fructose metabolism increases CPT1a and its acylcarnitine products. Furthermore, fructose-supplemented HFD leads to increased acetylation of ACADL and CPT1a, which is associated with decreased fat metabolism. In summary, dietary fructose, but not glucose, supplementation of HFD impairs mitochondrial size, function, and protein acetylation, resulting in decreased fatty acid oxidation and development of metabolic dysregulation.
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Affiliation(s)
- Samir Softic
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115, USA; Division of Gastroenterology, Hepatology, Nutrition, Department of Pediatrics, University of Kentucky College of Medicine and Kentucky Children's Hospital, Lexington, KY 40506, USA.
| | - Jesse G Meyer
- Chemistry & Mass Spectrometry, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Guo-Xiao Wang
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Manoj K Gupta
- Islet Cell and Regenerative Medicine, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Thiago M Batista
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Hans P M M Lauritzen
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shiho Fujisaka
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; First Department of Internal Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Dolors Serra
- School of Pharmacy, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Laura Herrero
- School of Pharmacy, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Spain; Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid 28029, Spain
| | | | | | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Departments of Pharmacology & Cancer Biology and Medicine, Duke University Medical Center, Durham, NC 27701, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Departments of Pharmacology & Cancer Biology and Medicine, Duke University Medical Center, Durham, NC 27701, USA
| | - Bradford W Gibson
- Chemistry & Mass Spectrometry, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Birgit Schilling
- Chemistry & Mass Spectrometry, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College New York, New York, NY 10021, USA
| | - C Ronald Kahn
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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Mitochondria Lysine Acetylation and Phenotypic Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:59-70. [PMID: 31452135 DOI: 10.1007/978-981-13-8367-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mitochondria have a central role in cellular metabolism and reversible post-translational modifications regulate activity of mitochondrial proteins. Thanks to advances in proteomics, lysine acetylation has arisen as an important post-translational modification in the mitochondrion. During acetylation an acetyl group is covalently attached to the epsilon amino group in the side chain of lysine residues using acetyl-CoA as the substrate donor. Therefore the positive charge is neutralized, and this can affect the function of proteins thereby regulating enzyme activity, protein interactions, and protein stability. The major deacetylase in mitochondria is SIRT3 whose activity regulates many mitochondrial enzymes. The method of choice for the analysis of acetylated proteins foresees the combination of mass spectrometry-based proteomics with affinity enrichment techniques. Beyond the identification of lysine-acetylated proteins, many studies are moving towards the characterization of acetylated patterns in different diseases. Indeed, modifications in lysine acetylation status can directly alter mitochondrial function and, therefore, be linked to human diseases such as metabolic diseases, cancer, myocardial injury and neurodegenerative diseases. Despite the progress in the characterization of different lysine acetylation sites, additional studies are needed to differentiate the specific changes with a significant biological relevance.
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Xu D, Wang X. Lysine Acetylation is an Important Post-Translational Modification that Modulates Heat Shock Response in the Sea Cucumber Apostichopus japonicus. Int J Mol Sci 2019; 20:ijms20184423. [PMID: 31505730 PMCID: PMC6770049 DOI: 10.3390/ijms20184423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 12/19/2022] Open
Abstract
Heat stress (HS) is an important factor for the survival of the marine organism Apostichopus japonicus. Lysine acetylation is a pivotal post-translational modification that modulates diverse physiological processes including heat shock response (HSR). In this study, 4028 lysine acetylation sites in 1439 proteins were identified in A. japonicus by acetylproteome sequencing. A total of 13 motifs were characterized around the acetylated lysine sites. Gene Ontology analysis showed that major acetylated protein groups were involved in “oxidation–reduction process”, “ribosome”, and “protein binding” terms. Compared to the control group, the acetylation quantitation of 25 and 41 lysine sites changed after 6 and 48 h HS. Notably, lysine acetyltransferase CREB-binding protein (CBP) was identified to have differential acetylation quantitation at multiple lysine sites under HS. Various chaperones, such as caseinolytic peptidase B protein homolog (CLBP), T-complex protein 1 (TCP1), and cyclophilin A (CYP1), showed differential acetylation quantitation after 48 h HS. Additionally, many translation-associated proteins, such as ribosomal proteins, translation initiation factor (IF), and elongation factors (EFs), had differential acetylation quantitation under HS. These proteins represented specific interaction networks. Collectively, our results offer novel insight into the complex HSR in A. japonicus and provide a resource for further mechanistic studies examining the regulation of protein function by lysine acetylation.
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Affiliation(s)
- Dongxue Xu
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - Xuan Wang
- Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China.
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A comprehensive atlas of lysine acetylome in onion thrips (Thrips tabaci Lind.) revealed by proteomics analysis. J Proteomics 2019; 207:103465. [DOI: 10.1016/j.jprot.2019.103465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/07/2019] [Accepted: 07/21/2019] [Indexed: 12/13/2022]
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Yang H, Zhao C, Tang MC, Wang Y, Wang SP, Allard P, Furtos A, Mitchell GA. Inborn errors of mitochondrial acyl-coenzyme a metabolism: acyl-CoA biology meets the clinic. Mol Genet Metab 2019; 128:30-44. [PMID: 31186158 DOI: 10.1016/j.ymgme.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/30/2019] [Accepted: 05/05/2019] [Indexed: 12/18/2022]
Abstract
The last decade saw major advances in understanding the metabolism of Coenzyme A (CoA) thioesters (acyl-CoAs) and related inborn errors (CoA metabolic diseases, CAMDs). For diagnosis, acylcarnitines and organic acids, both derived from acyl-CoAs, are excellent markers of most CAMDs. Clinically, each CAMD is unique but strikingly, three main patterns emerge: first, systemic decompensations with combinations of acidosis, ketosis, hypoglycemia, hyperammonemia and fatty liver; second, neurological episodes, particularly acute "stroke-like" episodes, often involving the basal ganglia but sometimes cerebral cortex, brainstem or optic nerves and third, especially in CAMDs of long chain fatty acyl-CoA metabolism, lipid myopathy, cardiomyopathy and arrhythmia. Some patients develop signs from more than one category. The pathophysiology of CAMDs is not precisely understood. Available data suggest that signs may result from CoA sequestration, toxicity and redistribution (CASTOR) in the mitochondrial matrix has been suggested to play a role. This predicts that most CAMDs cause deficiency of CoA, limiting mitochondrial energy production, and that toxic effects from the abnormal accumulation of acyl-CoAs and from extramitochondrial functions of acetyl-CoA may also contribute. Recent progress includes the following. (1) Direct measurements of tissue acyl-CoAs in mammalian models of CAMDs have been related to clinical features. (2) Inborn errors of CoA biosynthesis were shown to cause clinical changes similar to those of inborn errors of acyl-CoA degradation. (3) CoA levels in cells can be influenced pharmacologically. (4) Roles for acetyl-CoA are increasingly identified in all cell compartments. (5) Nonenzymatic acyl-CoA-mediated acylation of intracellular proteins occurs in mammalian tissues and is increased in CAMDs.
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Affiliation(s)
- Hao Yang
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Chen Zhao
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada; College of Animal Science and Technology, Northwest A&F University, China
| | | | - Youlin Wang
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Shu Pei Wang
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Pierre Allard
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | | | - Grant A Mitchell
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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