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Xu J, Wang R, Zhang X, Zhuang W, Zhang Y, Lin J, Zhan P, Chen S, Lu H, Wang A, Liao C. Identification and expression profiling of GAPDH family genes involved in response to Sclerotinia sclerotiorum infection and phytohormones in Brassica napus. FRONTIERS IN PLANT SCIENCE 2024; 15:1360024. [PMID: 38745922 PMCID: PMC11091349 DOI: 10.3389/fpls.2024.1360024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/12/2024] [Indexed: 05/16/2024]
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a crucial enzyme in glycolysis, an essential metabolic pathway for carbohydrate metabolism across all living organisms. Recent research indicates that phosphorylating GAPDH exhibits various moonlighting functions, contributing to plant growth and development, autophagy, drought tolerance, salt tolerance, and bacterial/viral diseases resistance. However, in rapeseed (Brassica napus), the role of GAPDHs in plant immune responses to fungal pathogens remains unexplored. In this study, 28 genes encoding GAPDH proteins were revealed in B. napus and classified into three distinct subclasses based on their protein structural and phylogenetic relationships. Whole-genome duplication plays a major role in the evolution of BnaGAPDHs. Synteny analyses revealed orthologous relationships, identifying 23, 26, and 26 BnaGAPDH genes with counterparts in Arabidopsis, Brassica rapa, and Brassica oleracea, respectively. The promoter regions of 12 BnaGAPDHs uncovered a spectrum of responsive elements to biotic and abiotic stresses, indicating their crucial role in plant stress resistance. Transcriptome analysis characterized the expression profiles of different BnaGAPDH genes during Sclerotinia sclerotiorum infection and hormonal treatment. Notably, BnaGAPDH17, BnaGAPDH20, BnaGAPDH21, and BnaGAPDH22 exhibited sensitivity to S. sclerotiorum infection, oxalic acid, hormone signals. Intriguingly, under standard physiological conditions, BnaGAPDH17, BnaGAPDH20, and BnaGAPDH22 are primarily localized in the cytoplasm and plasma membrane, with BnaGAPDH21 also detectable in the nucleus. Furthermore, the nuclear translocation of BnaGAPDH20 was observed under H2O2 treatment and S. sclerotiorum infection. These findings might provide a theoretical foundation for elucidating the functions of phosphorylating GAPDH.
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Affiliation(s)
- Jing Xu
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rongbo Wang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xiong Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Zhuang
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Yang Zhang
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Jianxin Lin
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Penglin Zhan
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Shanhu Chen
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Heding Lu
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
| | - Airong Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Changjian Liao
- Institute of Crop Research, Fujian Academy of Agricultural Sciences (Fujian Germplasm Resources Center)/Fujian Province Characteristic Dry Crop Variety Breeding Engineering Technology Research Center, Fuzhou, China
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Shi M, Hou J, Liang W, Li Q, Shao S, Ci S, Shu C, Zhao X, Zhao S, Huang M, Wu C, Hu Z, He L, Guo Z, Pan F. GAPDH facilitates homologous recombination repair by stabilizing RAD51 in an HDAC1-dependent manner. EMBO Rep 2023; 24:e56437. [PMID: 37306047 PMCID: PMC10398663 DOI: 10.15252/embr.202256437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/13/2023] Open
Abstract
Homologous recombination (HR), a form of error-free DNA double-strand break (DSB) repair, is important for the maintenance of genomic integrity. Here, we identify a moonlighting protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as a regulator of HR repair, which is mediated through HDAC1-dependent regulation of RAD51 stability. Mechanistically, in response to DSBs, Src signaling is activated and mediates GAPDH nuclear translocation. Then, GAPDH directly binds with HDAC1, releasing it from its suppressor. Subsequently, activated HDAC1 deacetylates RAD51 and prevents it from undergoing proteasomal degradation. GAPDH knockdown decreases RAD51 protein levels and inhibits HR, which is re-established by overexpression of HDAC1 but not SIRT1. Notably, K40 is an important acetylation site of RAD51, which facilitates stability maintenance. Collectively, our findings provide new insights into the importance of GAPDH in HR repair, in addition to its glycolytic activity, and they show that GAPDH stabilizes RAD51 by interacting with HDAC1 and promoting HDAC1 deacetylation of RAD51.
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Affiliation(s)
- Munan Shi
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Jiajia Hou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Weichu Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Qianwen Li
- Department of Radiotherapy, Taikang Xianlin Drum Tower HospitalNanjing UniversityNanjingChina
| | - Shan Shao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Shusheng Ci
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
- School of Basic Medical SciencesNanjing Medical UniversityNanjingChina
| | - Chuanjun Shu
- Department of Bioinformatics, School of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjingChina
| | - Xingqi Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Shanmeizi Zhao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Miaoling Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Congye Wu
- Department of Oncology, Nanjing First HospitalNanjing Medical UniversityNanjingChina
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
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3
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Wegener M, Dietz KJ. The mutual interaction of glycolytic enzymes and RNA in post-transcriptional regulation. RNA (NEW YORK, N.Y.) 2022; 28:1446-1468. [PMID: 35973722 PMCID: PMC9745834 DOI: 10.1261/rna.079210.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
About three decades ago, researchers suggested that metabolic enzymes participate in cellular processes that are unrelated to their catalytic activity, and the term "moonlighting functions" was proposed. Recently developed advanced technologies in the field of RNA interactome capture now unveil the unexpected RNA binding activity of many metabolic enzymes, as exemplified here for the enzymes of glycolysis. Although for most of these proteins a precise binding mechanism, binding conditions, and physiological relevance of the binding events still await in-depth clarification, several well explored examples demonstrate that metabolic enzymes hold crucial functions in post-transcriptional regulation of protein synthesis. This widely conserved RNA-binding function of glycolytic enzymes plays major roles in controlling cell activities. The best explored examples are glyceraldehyde 3-phosphate dehydrogenase, enolase, phosphoglycerate kinase, and pyruvate kinase. This review summarizes current knowledge about the RNA-binding activity of the ten core enzymes of glycolysis in plant, yeast, and animal cells, its regulation and physiological relevance. Apparently, a tight bidirectional regulation connects core metabolism and RNA biology, forcing us to rethink long established functional singularities.
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Affiliation(s)
- Melanie Wegener
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany
| | - Karl-Josef Dietz
- Biochemistry and Physiology of Plants, Bielefeld University, 33615 Bielefeld, Germany
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Bi D, Shi M, Zheng D, Hu Q, Wang H, Peng L, Lou D, Zhang A, Hu Y. Mechanism underlying the targeted regulation of the SOD1 3'UTR by the AUF1/Dicer1/miR-155/SOD1 pathway in sodium arsenite-induced liver injury. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 243:113990. [PMID: 35998476 DOI: 10.1016/j.ecoenv.2022.113990] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/13/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Arsenic (As) is a natural hepatotoxicity inducer that is ubiquitous in water, soil, coal, and food. Studies have found that arsenite exposure elicits increased mRNA transcription and decreased protein expression of SOD1 in vivo and in vitro; however, the specific mechanisms remain unclear. Here, we established a model of arsenic-induced chronic liver injury by providing rats with drinking water containing different concentrations of sodium arsenite (NaAsO2) and found that NaAsO2 exposure decreased the mRNA and protein levels of AUF1 and the protein level of SOD1 and elevated the mRNA and protein levels of Dicer1 and miR-155 and the mRNA level of SOD1. Overexpression of AUF1 under NaAsO2 stress in vitro induced Dicer1 mRNA and protein expression and decreased miR-155 levels, which could be reversed by AUF1 siRNA. In addition, miR-155 overexpression downregulated SOD1 mRNA and protein levels, although this change was inhibited after transfection with an miR-155 inhibitor. Taken together, our findings showed that NaAsO2 could upregulate Dicer1 mRNA and protein, thereby increasing miR-155 expression by downregulating AUF1 mRNA and protein expression. A dual-luciferase reporter assay indicated that miR-155 decreased the mRNA and protein levels of SOD1 by targeting the SOD1 3'UTR, resulting in liver injury. This study provides an important research basis for further understanding the factors underlying arsenic-induced liver injury to improve the prevention and control strategies for arsenism.
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Affiliation(s)
- Dingnian Bi
- Key Laboratory of Enviromental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China
| | - Mingyang Shi
- Key Laboratory of Enviromental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China
| | - Dan Zheng
- Guiyang Maternity and Child Health Hospital, Guizhou, PR China
| | - Qian Hu
- Key Laboratory of Enviromental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China
| | - Hongling Wang
- Key Laboratory of Enviromental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China
| | - Liuyu Peng
- Key Laboratory of Enviromental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China
| | - Didong Lou
- Department of Forensic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, Guizhou, PR China; Key Laboratory of Traditional Chinese Medicine Toxicology in Forensic Medicine, Guizhou Education Department, Guiyang 550025, Guizhou, PR China
| | - Aihua Zhang
- Key Laboratory of Enviromental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China
| | - Yong Hu
- Key Laboratory of Enviromental Pollution Monitoring and Disease Control, Ministry of Education, School of Public Health, Guizhou Medical University, Guiyang 550025, Guizhou, PR China.
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Sullo F, Pasquetti E, Patanè F, Lo Bianco M, Marino SD, Polizzi A, Falsaperla R, Ruggieri M, Zanghì A, Praticò AD. SCN1A and Its Related Epileptic Phenotypes. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1727260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractEpilepsy is one of the most common neurological disorders, with a lifetime incidence of 1 in 26. Approximately two-thirds of epilepsy has a substantial genetic component in its etiology. As a result, simultaneous screening for mutations in multiple genes and performing whole exome sequencing (WES) are becoming very frequent in the clinical evaluation of children with epilepsy. In this setting, mutations in voltage-gated sodium channel (SCN) α-subunit genes are the most commonly identified cause of epilepsy, with sodium channel genes (i.e., SCN1A, SCN2A, SCN8A) being the most frequently identified causative genes. SCN1A mutations result in a wide spectrum of epilepsy phenotypes ranging from simple febrile seizures to Dravet syndrome, a severe epileptic encephalopathy. In case of mutation of SCN1A, it is also possible to observe behavioral alterations, such as impulsivity, inattentiveness, and distractibility, which can be framed in an attention deficit hyperactivity disorder (ADHD) like phenotype. Despite more than 1,200 SCN1A mutations being reported, it is not possible to assess a clear phenotype–genotype correlations. Treatment remains a challenge and seizure control is often partial and transitory.
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Affiliation(s)
- Federica Sullo
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Elisa Pasquetti
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Francesca Patanè
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Manuela Lo Bianco
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Simona D. Marino
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Agata Polizzi
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Martino Ruggieri
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Antonio Zanghì
- Department of Medical and Surgical Sciences and Advanced Technology “G.F. Ingrassia,” University of Catania, Catania, Italy
| | - Andrea D. Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
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6
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Sirover MA. The role of posttranslational modification in moonlighting glyceraldehyde-3-phosphate dehydrogenase structure and function. Amino Acids 2021; 53:507-515. [PMID: 33651246 DOI: 10.1007/s00726-021-02959-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/06/2021] [Indexed: 11/26/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a moonlighting protein exhibiting distinct activities apart from its classical role in glycolysis. Regulation of its moonlighting functions and its subcellular localization may be dependent on its posttranslational modification (PTM). The latter include its phosphorylation, which is required for its role in intermembrane trafficking, synaptic transmission and cancer survival; nitrosylation, which is required for its function in apoptosis, heme metabolism and the immune response; acetylation which is necessary for its modulation of apoptotic gene regulation; and N-acetylglucosamine modification which may induce changes in GAPDH oligomeric structure. These findings suggest a structure function relationship between GAPDH posttranslational modification and its diverse moonlighting activities.
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Affiliation(s)
- Michael A Sirover
- Department of Pharmacology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA.
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Gao MM, Huang HY, Chen SY, Tang HL, He N, Feng WC, Lu P, Hu F, Yan HJ, Long YS. The ALOXE3 gene variants from patients with Dravet syndrome decrease gene expression and enzyme activity. Brain Res Bull 2021; 170:81-89. [PMID: 33581311 DOI: 10.1016/j.brainresbull.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 11/15/2022]
Abstract
Aberrant expression or dysfunction of a number of genes in the brain contributes to epilepsy, a common neurological disorder characterized by recurrent seizures. Local overexpression of arachidonate lipoxygenase 3 (ALOXE3), a key enzyme for arachidonic acid (AA) metabolic pathway, alleviates seizure severities. However, the relationship between the ALOXE3 gene mutation and epilepsy has not been reported until now. Here we firstly characterized the promoter of human ALOXE3 gene and found that the ALOXE3 promoter could drive luciferase gene expression in the human HEK-293 and SH-SY5Y cells. We then screened the ALOXE3 promoter region and all coding exons from those patients with Dravet syndrome and identified 5 variants c.-163T > C, c.-50C > G, c.-37G > A, c. + 228G > A and c. + 290G > T in the promoter region and one missense variant c.1939A > G (p.I647 V) in the exon. Of these variants in the promoter region, only -50C > G was a novel variant located on the transcriptional factor NFII-I binding element. Luciferase reporter gene analyses indicated that the c.-50C > G could decrease gene expression by preventing the TFII-I's binding. In addition, the variant p.I647 V was conserved among all analyzed species and located within the ALOXE3 functional domain for catalyzing its substrate. In cultured cell lines, overexpression of ALOXE3 significantly decreased the cellular AA levels and overexpression of ALOXE3-I647 V could restore the AA levels, suggesting that the p.I647 V mutant led to a decrease in enzyme activity. Taken together, the present study proposes that the identified ALOXE3 variants potentially contribute to the AA-pathway-mediated epileptogenesis, which should provide a novel avenue for clinical diagnosis of epilepsy.
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Affiliation(s)
- Mei-Mei Gao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China
| | - Hao-Ying Huang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China
| | - Si-Yu Chen
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China
| | - Hui-Ling Tang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China
| | - Na He
- Department of Neurology, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Wen-Cai Feng
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China
| | - Ping Lu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China
| | - Fei Hu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China
| | - Hua-Juan Yan
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China
| | - Yue-Sheng Long
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, 250 Changang East Road, Guangzhou, 510260, China.
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8
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Sirover MA. Moonlighting glyceraldehyde-3-phosphate dehydrogenase: posttranslational modification, protein and nucleic acid interactions in normal cells and in human pathology. Crit Rev Biochem Mol Biol 2020; 55:354-371. [PMID: 32646244 DOI: 10.1080/10409238.2020.1787325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Moonlighting glyceraldehyde-3-phosphate dehydrogenase (GAPDH) exhibits multiple functions separate and distinct from its historic role in energy production. Further, it exhibits dynamic changes in its subcellular localization which is an a priori requirement for its multiple activities. Separately, moonlighting GAPDH may function in the pathology of human disease, involved in tumorigenesis, diabetes, and age-related neurodegenerative disorders. It is suggested that moonlighting GAPDH function may be related to specific modifications of its protein structure as well as the formation of GAPDH protein: protein or GAPDH protein: nucleic acid complexes.
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Affiliation(s)
- Michael A Sirover
- Department of Pharmacology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
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9
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Kluckova D, Kolnikova M, Lacinova L, Jurkovicova-Tarabova B, Foltan T, Demko V, Kadasi L, Ficek A, Soltysova A. A Study among the Genotype, Functional Alternations, and Phenotype of 9 SCN1A Mutations in Epilepsy Patients. Sci Rep 2020; 10:10288. [PMID: 32581296 PMCID: PMC7314844 DOI: 10.1038/s41598-020-67215-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
Mutations in the voltage-gated sodium channel Nav1.1 (SCN1A) are linked to various epileptic phenotypes with different severities, however, the consequences of newly identified SCN1A variants on patient phenotype is uncertain so far. The functional impact of nine SCN1A variants, including five novel variants identified in this study, was studied using whole-cell patch-clamp recordings measurement of mutant Nav1.1 channels expressed in HEK293T mammalian cells. E78X, W384X, E1587K, and R1596C channels failed to produce measurable sodium currents, indicating complete loss of channel function. E788K and M909K variants resulted in partial loss of function by exhibiting reduced current density, depolarizing shifts of the activation and hyperpolarizing shifts of the inactivation curves, and slower recovery from inactivation. Hyperpolarizing shifts of the activation and inactivation curves were observed in D249E channels along with slower recovery from inactivation. Slower recovery from inactivation was observed in E78D and T1934I with reduced current density in T1934I channels. Various functional effects were observed with the lack of sodium current being mainly associated with severe phenotypes and milder symptoms with less damaging channel alteration. In vitro functional analysis is thus fundamental for elucidation of the molecular mechanisms of epilepsy, to guide patients' treatment, and finally indicate misdiagnosis of SCN1A related epilepsies.
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Affiliation(s)
- Daniela Kluckova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia
| | - Miriam Kolnikova
- Department of Pediatric Neurology, Comenius University Medical School and National Institute of Children's Diseases, Limbova 1, Bratislava, 833 40, Slovakia
| | - Lubica Lacinova
- Center of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dubravská cesta 9, Bratislava, 840 05, Slovakia
| | - Bohumila Jurkovicova-Tarabova
- Center of Biosciences, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Dubravská cesta 9, Bratislava, 840 05, Slovakia
| | - Tomas Foltan
- Department of Pediatric Neurology, Comenius University Medical School and National Institute of Children's Diseases, Limbova 1, Bratislava, 833 40, Slovakia
| | - Viktor Demko
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia.,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia
| | - Andrea Soltysova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, Bratislava, 842 15, Slovakia. .,Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia.
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10
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Liu SJ, Tang HL, He Q, Lu P, Fu T, Xu XL, Su T, Gao MM, Duan S, Luo Y, Long YS. FTO is a transcriptional repressor to auto-regulate its own gene and potentially associated with homeostasis of body weight. J Mol Cell Biol 2020; 11:118-132. [PMID: 29771336 DOI: 10.1093/jmcb/mjy028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/26/2018] [Accepted: 05/15/2018] [Indexed: 01/11/2023] Open
Abstract
Fat mass and obesity-associated (FTO) protein is a ferrous ion (Fe2+)/2-oxoglutarate (2-OG)-dependent demethylase preferentially catalyzing m6A sites in RNA. The FTO gene is highly expressed in the hypothalamus with fluctuation in response to various nutritional conditions, which is believed to be involved in the control of whole body metabolism. However, the underlying mechanism in response to different nutritional cues remains poorly understood. Here we show that ketogenic diet-derived ketone body β-hydroxybutyrate (BHB) transiently increases FTO expression in both mouse hypothalamus and cultured cells. Interestingly, the FTO protein represses Fto promoter activity, which can be offset by BHB. We then demonstrate that FTO binds to its own gene promoter, and Fe2+, but not 2-OG, impedes this binding and increases FTO expression. The BHB-induced occupancy of the promoter by FTO influences the assembly of the basal transcriptional machinery. Importantly, a loss-of-function FTO mutant (I367F), which induces a lean phenotype in FTOI367F mice, exhibits augmented binding and elevated potency to repress the promoter. Furthermore, FTO fails to bind to its own promoter that promotes FTO expression in the hypothalamus of high-fat diet-induced obese and 48-h fasting mice, suggesting a disruption of the stable expression of this gene. Taken together, this study uncovers a new function of FTO as a Fe2+-sensitive transcriptional repressor dictating its own gene switch to form an auto-regulatory loop that may link with the hypothalamic control of body weight.
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Affiliation(s)
- Shu-Jing Liu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui-Ling Tang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qian He
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Ping Lu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tao Fu
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Xu-Ling Xu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tao Su
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mei-Mei Gao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shumin Duan
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Luo
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Yue-Sheng Long
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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11
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de Lange IM, Mulder F, van 't Slot R, Sonsma ACM, van Kempen MJA, Nijman IJ, Ernst RF, Knoers NVAM, Brilstra EH, Koeleman BPC. Modifier genes in SCN1A-related epilepsy syndromes. Mol Genet Genomic Med 2020; 8:e1103. [PMID: 32032478 PMCID: PMC7196470 DOI: 10.1002/mgg3.1103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022] Open
Abstract
Background SCN1A is one of the most important epilepsy‐related genes, with pathogenic variants leading to a range of phenotypes with varying disease severity. Different modifying factors have been hypothesized to influence SCN1A‐related phenotypes. We investigate the presence of rare and more common variants in epilepsy‐related genes as potential modifiers of SCN1A‐related disease severity. Methods 87 patients with SCN1A‐related epilepsy were investigated. Whole‐exome sequencing was performed by the Beijing Genomics Institute (BGI). Functional variants in 422 genes associated with epilepsy and/or neuronal excitability were investigated. Differences in proportions of variants between the epilepsy genes and four control gene sets were calculated, and compared to the proportions of variants in the same genes in the ExAC database. Results Statistically significant excesses of variants in epilepsy genes were observed in the complete cohort and in the combined group of mildly and severely affected patients, particularly for variants with minor allele frequencies of <0.05. Patients with extreme phenotypes showed much greater excesses of epilepsy gene variants than patients with intermediate phenotypes. Conclusion Our results indicate that relatively common variants in epilepsy genes, which would not necessarily be classified as pathogenic, may play a large role in modulating SCN1A phenotypes. They may modify the phenotypes of both severely and mildly affected patients. Our results may be a first step toward meaningful testing of modifier gene variants in regular diagnostics for individual patients, to provide a better estimation of disease severity for newly diagnosed patients.
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Affiliation(s)
- Iris M de Lange
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Flip Mulder
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ruben van 't Slot
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anja C M Sonsma
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjan J A van Kempen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Isaac J Nijman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert F Ernst
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Eva H Brilstra
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P C Koeleman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
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12
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GAPDH as a model non-canonical AU-rich RNA binding protein. Semin Cell Dev Biol 2019; 86:162-173. [DOI: 10.1016/j.semcdb.2018.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
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13
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de Lange IM, Koudijs MJ, van 't Slot R, Gunning B, Sonsma ACM, van Gemert LJJM, Mulder F, Carbo EC, van Kempen MJA, Verbeek NE, Nijman IJ, Ernst RF, Savelberg SMC, Knoers NVAM, Brilstra EH, Koeleman BPC. Mosaicism of de novo pathogenic SCN1A
variants in epilepsy is a frequent phenomenon that correlates with variable phenotypes. Epilepsia 2018; 59:690-703. [DOI: 10.1111/epi.14021] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Iris M. de Lange
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Marco J. Koudijs
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Ruben van 't Slot
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | | | - Anja C. M. Sonsma
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | | | - Flip Mulder
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Ellen C. Carbo
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Marjan J. A. van Kempen
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Nienke E. Verbeek
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Isaac J. Nijman
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Robert F. Ernst
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Sanne M. C. Savelberg
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Nine V. A. M. Knoers
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Eva H. Brilstra
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
| | - Bobby P. C. Koeleman
- Department of Genetics; Center for Molecular Medicine; University Medical Center Utrecht; Utrecht the Netherlands
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14
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MDH2 is an RNA binding protein involved in downregulation of sodium channel Scn1a expression under seizure condition. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1492-1499. [PMID: 28433711 DOI: 10.1016/j.bbadis.2017.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/31/2017] [Accepted: 04/18/2017] [Indexed: 12/13/2022]
Abstract
Voltage-gated sodium channel α-subunit type I (NaV1.1, encoded by SCN1A gene) plays a critical role in the excitability of brain. Downregulation of SCN1A expression is associated with epilepsy, a common neurological disorder characterized by recurrent seizures. Here we reveal a novel role of malate dehydrogenase 2 (MDH2) in the posttranscriptional regulation of SCN1A expression under seizure condition. We identified that MDH2 was an RNA binding protein that could bind two of the four conserved regions in the 3' UTRs of SCN1A. We further showed that knockdown of MDH2 or inactivation of MDH2 activity in HEK-293 cells increased the reporter gene expression through the 3' UTR of SCN1A, and MDH2 overexpression decreased gene expression by affecting mRNA stability. In the hippocampus of seizure mice, the upregulation of MDH2 expression contributed to the decrease of the NaV1.1 levels at posttranscriptional level. In addition, we showed that the H2O2 levels increased in the hippocampus of the seizure mice, and H2O2 could promote the binding of MDH2 to the binding sites of Scn1a gene, whereas β-mercaptoethanol decreased the binding capability, indicating an important effect of the seizure-induced oxidation on the MDH2-mediated downregulation of Scn1a expression. Taken together, these data suggest that MDH2, functioning as an RNA-binding protein, is involved in the posttranscriptional downregulation of SCN1A expression under seizure condition.
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15
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Chakravorty S, Hegde M. Gene and Variant Annotation for Mendelian Disorders in the Era of Advanced Sequencing Technologies. Annu Rev Genomics Hum Genet 2017; 18:229-256. [PMID: 28415856 DOI: 10.1146/annurev-genom-083115-022545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations. We describe the emerging field of translational functional genomics, which integrates other functional "-omics" approaches that support next-generation sequencing genomic data in order to facilitate personalized diagnostics, disease management, biomarker discovery, and medicine. We also discuss the utility of this integrated approach for diagnostic clinics and medical databases and its role in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
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16
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Abstract
Aside from its well-established role in glycolysis, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been shown to possess many key functions in cells. These functions are regulated by protein oligomerization , biomolecular interactions, post-translational modifications , and variations in subcellular localization . Several GAPDH functions and regulatory mechanisms overlap with one another and converge around its role in intermediary metabolism. Several structural determinants of the protein dictate its function and regulation. GAPDH is ubiquitously expressed and is found in all domains of life. GAPDH has been implicated in many diseases, including those of pathogenic, cardiovascular, degenerative, diabetic, and tumorigenic origins. Understanding the mechanisms by which GAPDH can switch between its functions and how these functions are regulated can provide insights into ways the protein can be modulated for therapeutic outcomes.
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17
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Lin GW, Lu P, Zeng T, Tang HL, Chen YH, Liu SJ, Gao MM, Zhao QH, Yi YH, Long YS. GAPDH-mediated posttranscriptional regulations of sodium channel Scn1a and Scn3a genes under seizure and ketogenic diet conditions. Neuropharmacology 2016; 113:480-489. [PMID: 27816501 DOI: 10.1016/j.neuropharm.2016.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 01/12/2023]
Abstract
Abnormal expressions of sodium channel SCN1A and SCN3A genes alter neural excitability that are believed to contribute to the pathogenesis of epilepsy, a long-term risk of recurrent seizures. Ketogenic diet (KD), a high-fat and low-carbohydrate treatment for difficult-to-control (refractory) epilepsy in children, has been suggested to reverse gene expression patterns. Here, we reveal a novel role of GAPDH on the posttranscriptional regulation of mouse Scn1a and Scn3a expressions under seizure and KD conditions. We show that GAPDH binds to a conserved region in the 3' UTRs of human and mouse SCN1A and SCN3A genes, which decreases and increases genes' expressions by affecting mRNA stability through SCN1A 3' UTR and SCN3A 3' UTR, respectively. In seizure mice, the upregulation and phosphorylation of GAPDH enhance its binding to the 3' UTR, which lead to downregulation of Scn1a and upregulation of Scn3a. Furthermore, administration of KD generates β-hydroxybutyric acid which rescues the abnormal expressions of Scn1a and Scn3a by weakening the GAPDH's binding to the element. Taken together, these data suggest that GAPDH-mediated expression regulation of sodium channel genes may be associated with epilepsy and the anticonvulsant action of KD.
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Affiliation(s)
- Guo-Wang Lin
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Ping Lu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Tao Zeng
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Hui-Ling Tang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Yong-Hong Chen
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Shu-Jing Liu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Mei-Mei Gao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Qi-Hua Zhao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Yong-Hong Yi
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China
| | - Yue-Sheng Long
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 501260, China.
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18
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The genetic variants in 3' untranslated region of voltage-gated sodium channel alpha 1 subunit gene affect the mRNA-microRNA interactions and associate with epilepsy. BMC Genet 2016; 17:111. [PMID: 27473590 PMCID: PMC4966731 DOI: 10.1186/s12863-016-0417-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 07/15/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND mRNA expression in a cell or subcellular organelle is precisely regulated for the purpose of gene function regulation. The 3' untranslated region (3'UTR) of mRNA is the binding target of microRNA and RNA binding proteins. Their interactions regulate mRNA level in specific subcellular regions and determine the intensity of gene repression. The mutations in the coding region of voltage-gated sodium channel alpha 1 subunit gene, SCN1A, were identified in epileptic patients and confirmed as causative factors of epilepsy. We investigated if there were genetic variants in 3'UTR of SCN1A, affecting the microRNA-mRNA 3'UTR interaction and SCN1A gene repression, potentially associated with epilepsy. RESULTS In this case-control study, we identified twelve variants, NM_001202435.1:n.6277A > G, n.6568_6571del, n.6761C > T, n.6874A > T, n.6907 T > C, n.6978A > G, n.7065_7066insG, n.7282 T > C, n.7338_7344del, n.7385 T > A, n.7996C > T, and n.8212C > T in 3'UTR of SCN1A gene. We found that the variant of n.6978A > G in all our samples was completely mutated (G/G). In male group, T allele in n.7282 T > C was associated with epilepsy, while C allele was significantly less frequent in epileptic patients than in normal males (OR 0.424). Consequently, the haplotype "CTTACATGACGA" / "CTCTA" was significantly less frequent in male epileptic patients (0.173) than in normal males (0.305). The frequency of haplotype block found in females, "TTTAACA", "TTCAACA", and "CTTAACA" was 0.499, 0.254 and 0.234 respectively. Within STarMir model analysis, the "CTCTA" haplotype showed significantly higher site accessibility to microRNA targeting and higher downstream sequence accessibility for nonconserved binding than that of other haplotypes. Overall, the male genotypes have the higher accessibility of the downstream 30nt block of nonconserved site than the female genotypes. CONCLUSIONS NM_001202435.1:n.7282 T > C is the genetic variant associated with epilepsy in males, and the related haplotype "CTTACATGACGA" / "CTCTA" in the region of chr2: 165991297-165989081, which has high site accessibility for microRNA binding, is the genetic protective factor against epilepsy in males. In female subset, the frequencies of haplotype block "TTTAACA", "TTCAACA", and "CTTAACA" were 0.499,0.254 and 0.234 respectively. Alleles and haplotypes distribution did not differ in female cases in comparison to female controls.
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19
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Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. BMC Med Genomics 2016; 9:19. [PMID: 27067391 PMCID: PMC4828881 DOI: 10.1186/s12920-016-0178-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 03/15/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT) and prioritizing patients with large intragenic deletions. METHODS We captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream of ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, and TP53 were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk, anonymized patients without identified mutations in BRCA1/2. Aside from protein coding and copy number changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented by in silico and laboratory analysis of UTR structure. RESULTS 15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. An intragenic 32.1 kb interval in BRCA2 that was likely hemizygous was detected in one patient. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels). CONCLUSIONS We have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.
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Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Natasha G Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ami M Perri
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ruipeng Lu
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3290, USA
| | - Matthew Halvorsen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada
- Cytognomix Inc., London, Canada
| | - Peter K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada.
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada.
- Cytognomix Inc., London, Canada.
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada.
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20
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A Point Mutation in SCN1A 5' Genomic Region Decreases the Promoter Activity and Is Associated with Mild Epilepsy and Seizure Aggravation Induced by Antiepileptic Drug. Mol Neurobiol 2016; 54:2428-2434. [PMID: 26969601 DOI: 10.1007/s12035-016-9800-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/16/2016] [Indexed: 01/05/2023]
Abstract
The SCN1A gene with 1274 point mutations in the coding regions or genomic rearrangements is the most clinically relevant epilepsy gene. Recent studies have demonstrated that variations in the noncoding regions are potentially associated with epilepsies, but no distinct mutation has been reported. We sequenced the 5' upstream region of SCN1A in 166 patients with epilepsy and febrile seizures who were negative for point mutations in the coding regions or genomic rearrangements. A heterozygous mutation h1u-1962 T > G was identified in a patient with partial epilepsy and febrile seizures, which was aggravated by oxcarbazepine. This mutation was transmitted from the patient's asymptomatic mother and not found in the 110 normal controls. h1u-1962 T > G was located upstream the most frequently used noncoding exon and within the promoter sequences. Further experiments showed that this mutation decreased the promoter activity by 42.1 % compared with that of the paired haplotype (P < 0.001). In contrast to the null expression that results in haploinsufficiency and severe phenotype, this mutation caused relatively less impairment, explaining the mild epilepsy with incomplete penetrance. The antiepileptic drug-induced seizure aggravation in this patient suggests clinical attention for mutations or variations in noncoding regions that may affect SCN1A expression.
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21
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White MR, Garcin ED. The sweet side of RNA regulation: glyceraldehyde-3-phosphate dehydrogenase as a noncanonical RNA-binding protein. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 7:53-70. [PMID: 26564736 DOI: 10.1002/wrna.1315] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 01/26/2023]
Abstract
The glycolytic protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has a vast array of extraglycolytic cellular functions, including interactions with nucleic acids. GAPDH has been implicated in the translocation of transfer RNA (tRNA), the regulation of cellular messenger RNA (mRNA) stability and translation, as well as the regulation of replication and gene expression of many single-stranded RNA viruses. A growing body of evidence supports GAPDH-RNA interactions serving as part of a larger coordination between intermediary metabolism and RNA biogenesis. Despite the established role of GAPDH in nucleic acid regulation, it is still unclear how and where GAPDH binds to its RNA targets, highlighted by the absence of any conserved RNA-binding sequences. This review will summarize our current understanding of GAPDH-mediated regulation of RNA function. WIREs RNA 2016, 7:53-70. doi: 10.1002/wrna.1315 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Michael R White
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
| | - Elsa D Garcin
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, USA
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22
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Meng H, Xu HQ, Yu L, Lin GW, He N, Su T, Shi YW, Li B, Wang J, Liu XR, Tang B, Long YS, Yi YH, Liao WP. TheSCN1AMutation Database: Updating Information and Analysis of the Relationships among Genotype, Functional Alteration, and Phenotype. Hum Mutat 2015; 36:573-80. [PMID: 25754450 DOI: 10.1002/humu.22782] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/25/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Heng Meng
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
- Department of Neurology; The First Affiliated Hospital of Jinan University; Guangzhou China
| | - Hai-Qing Xu
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Lu Yu
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Guo-Wang Lin
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Na He
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Tao Su
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Yi-Wu Shi
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Bin Li
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Jie Wang
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Xiao-Rong Liu
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Bin Tang
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Yue-Sheng Long
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Yong-Hong Yi
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
| | - Wei-Ping Liao
- Institute of Neuroscience and The Second Affiliated Hospital of Guangzhou Medical University; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China; Guangzhou China
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Structural analysis of glyceraldehyde-3-phosphate dehydrogenase functional diversity. Int J Biochem Cell Biol 2014; 57:20-6. [PMID: 25286305 DOI: 10.1016/j.biocel.2014.09.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 09/26/2014] [Accepted: 09/27/2014] [Indexed: 11/23/2022]
Abstract
Multifunctional proteins provide a new mechanism to expand exponentially cell information and capability beyond that indicated by conventional gene analyses. As such, examination of their structure-function relationships provides a means to define the mechanisms through which cells accomplish critical yet disparate activities required for cell viability and survival. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) may be considered the quintessential multidimensional protein which exhibits a variety of functions unrelated to its classical role in energy production. This review discusses new insights into the structure-function mechanisms through which defined GAPDH amino acid domains are utilized for its diverse activities, the importance of its post-translational modification, and, intriguingly, the logic inherent in the presence or the absence of specific signaling domains.
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