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Tan L, Qi X, Kong W, Jin J, Lu D, Zhang X, Wang Y, Wang S, Dong W, Shi X, Chen W, Wang J, Li K, Xie Y, Gao L, Guan F, Gao K, Li C, Wang C, Hu Z, Zhang L, Guo X, Shen B, Ma Y. A conditional knockout rat resource of mitochondrial protein-coding genes via a DdCBE-induced premature stop codon. SCIENCE ADVANCES 2023; 9:eadf2695. [PMID: 37058569 PMCID: PMC10104465 DOI: 10.1126/sciadv.adf2695] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Hundreds of pathogenic variants of mitochondrial DNA (mtDNA) have been reported to cause mitochondrial diseases, which still lack effective treatments. It is a huge challenge to install these mutations one by one. We repurposed the DddA-derived cytosine base editor to incorporate a premature stop codon in the mtProtein-coding genes to ablate mitochondrial proteins encoded in the mtDNA (mtProteins) instead of installing pathogenic variants and generated a library of both cell and rat resources with mtProtein depletion. In vitro, we depleted 12 of 13 mtProtein-coding genes with high efficiency and specificity, resulting in decreased mtProtein levels and impaired oxidative phosphorylation. Moreover, we generated six conditional knockout rat strains to ablate mtProteins using Cre/loxP system. Mitochondrially encoded ATP synthase membrane subunit 8 and NADH:ubiquinone oxidoreductase core subunit 1 were specifically depleted in heart cells or neurons, resulting in heart failure or abnormal brain development. Our work provides cell and rat resources for studying the function of mtProtein-coding genes and therapeutic strategies.
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Affiliation(s)
- Lei Tan
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaolong Qi
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Weining Kong
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Jiachuan Jin
- Center for Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dan Lu
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Xu Zhang
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Yue Wang
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Siting Wang
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Dong
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Xudong Shi
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Wei Chen
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Jianying Wang
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Keru Li
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Yuan Xie
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lijuan Gao
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Feifei Guan
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Kai Gao
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Chaojun Li
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lianfeng Zhang
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
- Neuroscience center, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Gusu School, Nanjing Medical University, Nanjing, Jiangsu, China
- Zhejiang Laboratory, Hangzhou, Zhejiang, China
| | - Yuanwu Ma
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
- Neuroscience center, Chinese Academy of Medical Sciences, Beijing, China
- National Human Diseases Animal Model Resource Center, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
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Takeuchi A, Matsuoka S. Physiological and Pathophysiological Roles of Mitochondrial Na +-Ca 2+ Exchanger, NCLX, in Hearts. Biomolecules 2021; 11:biom11121876. [PMID: 34944520 PMCID: PMC8699148 DOI: 10.3390/biom11121876] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022] Open
Abstract
It has been over 10 years since SLC24A6/SLC8B1, coding the Na+/Ca2+/Li+ exchanger (NCLX), was identified as the gene responsible for mitochondrial Na+-Ca2+ exchange, a major Ca2+ efflux system in cardiac mitochondria. This molecular identification enabled us to determine structure–function relationships, as well as physiological/pathophysiological contributions, and our understandings have dramatically increased. In this review, we provide an overview of the recent achievements in relation to NCLX, focusing especially on its heart-specific characteristics, biophysical properties, and spatial distribution in cardiomyocytes, as well as in cardiac mitochondria. In addition, we discuss the roles of NCLX in cardiac functions under physiological and pathophysiological conditions—the generation of rhythmicity, the energy metabolism, the production of reactive oxygen species, and the opening of mitochondrial permeability transition pores.
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Affiliation(s)
- Ayako Takeuchi
- Department of Integrative and Systems Physiology, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan;
- Life Science Innovation Center, University of Fukui, Fukui 910-1193, Japan
- Correspondence: ; Tel.: +81-776-61-8311
| | - Satoshi Matsuoka
- Department of Integrative and Systems Physiology, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan;
- Life Science Innovation Center, University of Fukui, Fukui 910-1193, Japan
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Tarraf B, Suraniti E, Colin C, Arbault S, Diolez P, Leguèbe M, Coudière Y. A simple model of cardiac mitochondrial respiration with experimental validation. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:5758-5789. [PMID: 34517511 DOI: 10.3934/mbe.2021291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cardiac mitochondria are intracellular organelles that play an important role in energy metabolism and cellular calcium regulation. In particular, they influence the excitation-contraction cycle of the heart cell. A large number of mathematical models have been proposed to better understand the mitochondrial dynamics, but they generally show a high level of complexity, and their parameters are very hard to fit to experimental data. We derived a model based on historical free energy-transduction principles, and results from the literature. We proposed simple expressions that allow to reduce the number of parameters to a minimum with respect to the mitochondrial behavior of interest for us. The resulting model has thirty-two parameters, which are reduced to twenty-three after a global sensitivity analysis of its expressions based on Sobol indices. We calibrated our model to experimental data that consists of measurements of mitochondrial respiration rates controlled by external ADP additions. A sensitivity analysis of the respiration rates showed that only seven parameters can be identified using these observations. We calibrated them using a genetic algorithm, with five experimental data sets. At last, we used the calibration results to verify the ability of the model to accurately predict the values of a sixth dataset. Results show that our model is able to reproduce both respiration rates of mitochondria and transitions between those states, with very low variability of the parameters between each experiment. The same methodology may apply to recover all the parameters of the model, if corresponding experimental data were available.
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Affiliation(s)
- Bachar Tarraf
- Inria Bordeaux-Sud-Ouest, team CARMEN, Talence, France
- IHU Liryc, Fondation Bordeaux Université, Pessac, France
- Institut de Mathématiques de Bordeaux, UMR CNRS 5251, Talence, France
| | | | - Camille Colin
- IHU Liryc, Fondation Bordeaux Université, Pessac, France
- ISM, CNRS UMR 5255, Bordeaux, France
| | | | - Philippe Diolez
- IHU Liryc, Fondation Bordeaux Université, Pessac, France
- Université de Bordeaux, Bordeaux, France
- INSERM, Centre de Recherche Cardio-Thoracique de Bordeaux, U-1045, Bordeaux, France
| | - Michael Leguèbe
- Inria Bordeaux-Sud-Ouest, team CARMEN, Talence, France
- IHU Liryc, Fondation Bordeaux Université, Pessac, France
- Institut de Mathématiques de Bordeaux, UMR CNRS 5251, Talence, France
| | - Yves Coudière
- Inria Bordeaux-Sud-Ouest, team CARMEN, Talence, France
- IHU Liryc, Fondation Bordeaux Université, Pessac, France
- Institut de Mathématiques de Bordeaux, UMR CNRS 5251, Talence, France
- Université de Bordeaux, Bordeaux, France
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Islam MM, Takeuchi A, Matsuoka S. Membrane current evoked by mitochondrial Na +-Ca 2+ exchange in mouse heart. J Physiol Sci 2020; 70:24. [PMID: 32354321 PMCID: PMC10717124 DOI: 10.1186/s12576-020-00752-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/24/2020] [Indexed: 01/19/2023]
Abstract
The electrogenicity of mitochondrial Na+-Ca2+ exchange (NCXm) had been controversial and no membrane current through it had been reported. We succeeded for the first time in recording NCXm-mediated currents using mitoplasts derived from mouse ventricle. Under conditions that K+, Cl-, and Ca2+ uniporter currents were inhibited, extra-mitochondrial Na+ induced inward currents with 1 μM Ca2+ in the pipette. The half-maximum concentration of Na+ was 35.6 mM. The inward current was diminished without Ca2+ in the pipette, and was augmented with 10 μM Ca2+. The Na+-induced inward currents were largely inhibited by CGP-37157, an NCXm blocker. However, the reverse mode of NCXm, which should be detected as an outward current, was hardly induced by extra-mitochondrial application of Ca2+ with Na+ in the pipette. It was concluded that NCXm is electrogenic. This property may be advantageous for facilitating Ca2+ extrusion from mitochondria, which has large negative membrane potential.
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Affiliation(s)
- Mohammed M Islam
- Department of Integrative and Systems Physiology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan
| | - Ayako Takeuchi
- Department of Integrative and Systems Physiology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan
- Life Science Innovation Center, University of Fukui, Fukui, 910-1193, Japan
| | - Satoshi Matsuoka
- Department of Integrative and Systems Physiology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan.
- Life Science Innovation Center, University of Fukui, Fukui, 910-1193, Japan.
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