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Martin FJO, Santiveri M, Hu H, Taylor NMI. Ion-driven rotary membrane motors: From structure to function. Curr Opin Struct Biol 2024; 88:102884. [PMID: 39053417 DOI: 10.1016/j.sbi.2024.102884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/16/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Ion-driven membrane motors, essential across all domains of life, convert a gradient of ions across a membrane into rotational energy, facilitating diverse biological processes including ATP synthesis, substrate transport, and bacterial locomotion. Herein, we highlight recent structural advances in the understanding of two classes of ion-driven membrane motors: rotary ATPases and 5:2 motors. The recent structure of the human F-type ATP synthase is emphasised along with the gained structural insight into clinically relevant mutations. Furthermore, we highlight the diverse roles of 5:2 motors and recent mechanistic understanding gained through the resolution of ions in the structure of a sodium-driven motor, combining insights into potential unifying mechanisms of ion selectivity and rotational torque generation in the context of their function as part of complex biological systems.
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Affiliation(s)
- Freddie J O Martin
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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2
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Zhao Y, Yang M, Liu Y, Wan Z, Chen M, He Q, Liao Y, Shuai P, Shi J, Guo S. Pathogenesis of cardiovascular diseases: effects of mitochondrial CF6 on endothelial cell function. Mol Cell Biochem 2024:10.1007/s11010-024-05065-2. [PMID: 38985252 DOI: 10.1007/s11010-024-05065-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024]
Abstract
Cardiovascular disease (CVD) stands as a predominant global cause of morbidity and mortality, necessitating effective and cost-efficient therapies for cardiovascular risk reduction. Mitochondrial coupling factor 6 (CF6), identified as a novel proatherogenic peptide, emerges as a significant risk factor in endothelial dysfunction development, correlating with CVD severity. CF6 expression can be heightened by CVD risk factors like mechanical force, hypoxia, or high glucose stimuli through the NF-κB pathway. Many studies have explored the CF6-CVD relationship, revealing elevated plasma CF6 levels in essential hypertension, atherosclerotic cardiovascular disease (ASCVD), stroke, and preeclampsia patients. CF6 acts as a vasoactive and proatherogenic peptide in CVD, inducing intracellular acidosis in vascular endothelial cells, inhibiting nitric oxide (NO) and prostacyclin generation, increasing blood pressure, and producing proatherogenic molecules, significantly contributing to CVD development. CF6 induces an imbalance in endothelium-dependent factors, including NO, prostacyclin, and asymmetric dimethylarginine (ADMA), promoting vasoconstriction, vascular remodeling, thrombosis, and insulin resistance, possibly via C-src Ca2+ and PRMT-1/DDAH-2-ADMA-NO pathways. This review offers a comprehensive exploration of CF6 in the context of CVD, providing mechanistic insights into its role in processes impacting CVD, with a focus on CF6 functions, intracellular signaling, and regulatory mechanisms in vascular endothelial cells.
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Affiliation(s)
- Yingying Zhao
- Department of Geriatric Medicine, School of Medicine and Life Science, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ming Yang
- The Lab of Aging Research, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Youren Liu
- Department of Health Management Center, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Zhengwei Wan
- Department of Health Management Center, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Mengchun Chen
- Department of Geriatric Medicine, School of Medicine and Life Science, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiumei He
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yang Liao
- Department of Geriatric Medicine, School of Medicine and Life Science, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ping Shuai
- Department of Health Management Center, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
| | - Shujin Guo
- Department of Health Management Center, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
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3
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Nesterov SV, Ilyinsky NS, Plokhikh KS, Manuylov VD, Chesnokov YM, Vasilov RG, Kuznetsova IM, Turoverov KK, Gordeliy VI, Fonin AV, Uversky VN. Order wrapped in chaos: On the roles of intrinsically disordered proteins and RNAs in the arrangement of the mitochondrial enzymatic machines. Int J Biol Macromol 2024; 267:131455. [PMID: 38588835 DOI: 10.1016/j.ijbiomac.2024.131455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
The analysis of cryo-electron tomography images of human and rat mitochondria revealed that the mitochondrial matrix is at least as crowded as the cytosol. To mitigate the crowding effects, metabolite transport in the mitochondria primarily occurs through the intermembrane space, which is significantly less crowded. The scientific literature largely ignores how enzyme systems and metabolite transport are organized in the crowded environment of the mitochondrial matrix. Under crowded conditions, multivalent interactions carried out by disordered protein regions (IDRs), may become extremely important. We analyzed the human mitochondrial proteome to determine the presence and physiological significance of IDRs. Despite mitochondrial proteins being generally more ordered than cytosolic or overall proteome proteins, disordered regions plays a significant role in certain mitochondrial compartments and processes. Even in highly ordered enzyme systems, there are proteins with long IDRs. Some IDRs act as binding elements between highly ordered subunits, while the roles of others are not yet established. Mitochondrial systems, like their bacterial ancestors, rely less on IDRs and more on RNA for LLPS compartmentalization. More evolutionarily advanced subsystems that enable mitochondria-cell interactions contain more IDRs. The study highlights the crucial and often overlooked role played by IDRs and non-coding RNAs in mitochondrial organization.
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Affiliation(s)
- Semen V Nesterov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia; Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia; Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia.
| | - Nikolay S Ilyinsky
- Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia.
| | | | - Vladimir D Manuylov
- Moscow Institute of Physics and Techonology, Dolgoprudny, Moscow Region 141701, Russia
| | - Yuriy M Chesnokov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Raif G Vasilov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - Irina M Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | | | - Valentin I Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027 Grenoble, France
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
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4
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Del Dotto V, Musiani F, Baracca A, Solaini G. Variants in Human ATP Synthase Mitochondrial Genes: Biochemical Dysfunctions, Associated Diseases, and Therapies. Int J Mol Sci 2024; 25:2239. [PMID: 38396915 PMCID: PMC10889682 DOI: 10.3390/ijms25042239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial ATP synthase (Complex V) catalyzes the last step of oxidative phosphorylation and provides most of the energy (ATP) required by human cells. The mitochondrial genes MT-ATP6 and MT-ATP8 encode two subunits of the multi-subunit Complex V. Since the discovery of the first MT-ATP6 variant in the year 1990 as the cause of Neuropathy, Ataxia, and Retinitis Pigmentosa (NARP) syndrome, a large and continuously increasing number of inborn variants in the MT-ATP6 and MT-ATP8 genes have been identified as pathogenic. Variants in these genes correlate with various clinical phenotypes, which include several neurodegenerative and multisystemic disorders. In the present review, we report the pathogenic variants in mitochondrial ATP synthase genes and highlight the molecular mechanisms underlying ATP synthase deficiency that promote biochemical dysfunctions. We discuss the possible structural changes induced by the most common variants found in patients by considering the recent cryo-electron microscopy structure of human ATP synthase. Finally, we provide the state-of-the-art of all therapeutic proposals reported in the literature, including drug interventions targeting mitochondrial dysfunctions, allotopic gene expression- and nuclease-based strategies, and discuss their potential translation into clinical trials.
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Affiliation(s)
- Valentina Del Dotto
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40127 Bologna, Italy;
| | - Alessandra Baracca
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
| | - Giancarlo Solaini
- Laboratory of Biochemistry and Mitochondrial Pathophysiology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy; (V.D.D.); (G.S.)
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5
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Jiko C, Morimoto Y, Tsukihara T, Gerle C. Large-scale column-free purification of bovine F-ATP synthase. J Biol Chem 2024; 300:105603. [PMID: 38159856 PMCID: PMC10851226 DOI: 10.1016/j.jbc.2023.105603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024] Open
Abstract
Mammalian F-ATP synthase is central to mitochondrial bioenergetics and is present in the inner mitochondrial membrane in a dynamic oligomeric state of higher oligomers, tetramers, dimers, and monomers. In vitro investigations of mammalian F-ATP synthase are often limited by the ability to purify the oligomeric forms present in vivo at a quantity, stability, and purity that meets the demand of the planned experiment. We developed a purification approach for the isolation of bovine F-ATP synthase from heart muscle mitochondria that uses a combination of buffer conditions favoring inhibitor factor 1 binding and sucrose density gradient ultracentrifugation to yield stable complexes at high purity in the milligram range. By tuning the glyco-diosgenin to lauryl maltose neopentyl glycol ratio in a final gradient, fractions that are either enriched in tetrameric or monomeric F-ATP synthase can be obtained. It is expected that this large-scale column-free purification strategy broadens the spectrum of in vitro investigation on mammalian F-ATP synthase.
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Affiliation(s)
- Chimari Jiko
- Division of Radiation Life Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan.
| | - Yukio Morimoto
- Division of Radiation Life Science, Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Tomitake Tsukihara
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto, Kamigori, Hyogo, Japan; Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Christoph Gerle
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan; Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Hyogo, Japan.
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Chen X, Lin Y, Zhang Z, Tang Y, Ye P, Dai W, Zhang W, Liu H, Peng G, Huang S, Qiu J, Guo W, Zhu X, Wu Z, Kuang Y, Xu P, Zhou M. CHCHD2 Thr61Ile mutation impairs F1F0-ATPase assembly in in vitro and in vivo models of Parkinson's disease. Neural Regen Res 2024; 19:196-204. [PMID: 37488867 PMCID: PMC10479855 DOI: 10.4103/1673-5374.378010] [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: 09/04/2022] [Revised: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 07/26/2023] Open
Abstract
Mitochondrial dysfunction is a significant pathological alteration that occurs in Parkinson's disease (PD), and the Thr61Ile (T61I) mutation in coiled-coil helix coiled-coil helix domain containing 2 (CHCHD2), a crucial mitochondrial protein, has been reported to cause Parkinson's disease. F1F0-ATPase participates in the synthesis of cellular adenosine triphosphate (ATP) and plays a central role in mitochondrial energy metabolism. However, the specific roles of wild-type (WT) CHCHD2 and T61I-mutant CHCHD2 in regulating F1F0-ATPase activity in Parkinson's disease, as well as whether CHCHD2 or CHCHD2 T61I affects mitochondrial function through regulating F1F0-ATPase activity, remain unclear. Therefore, in this study, we expressed WT CHCHD2 and T61I-mutant CHCHD2 in an MPP+-induced SH-SY5Y cell model of PD. We found that CHCHD2 protected mitochondria from developing MPP+-induced dysfunction. Under normal conditions, overexpression of WT CHCHD2 promoted F1F0-ATPase assembly, while T61I-mutant CHCHD2 appeared to have lost the ability to regulate F1F0-ATPase assembly. In addition, mass spectrometry and immunoprecipitation showed that there was an interaction between CHCHD2 and F1F0-ATPase. Three weeks after transfection with AAV-CHCHD2 T61I, we intraperitoneally injected 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine into mice to establish an animal model of chronic Parkinson's disease and found that exogenous expression of the mutant protein worsened the behavioral deficits and dopaminergic neurodegeneration seen in this model. These findings suggest that WT CHCHD2 can alleviate mitochondrial dysfunction in PD by maintaining F1F0-ATPase structure and function.
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Affiliation(s)
- Xiang Chen
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Yuwan Lin
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhiling Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Yuting Tang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Panghai Ye
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Wei Dai
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Wenlong Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Hanqun Liu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Guoyou Peng
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Shuxuan Huang
- Department of Neurology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Jiewen Qiu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Wenyuan Guo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xiaoqin Zhu
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhuohua Wu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Yaoyun Kuang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Miaomiao Zhou
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Delbrouck JA, Murza A, Diachenko I, Ben Jamaa A, Devi R, Larose A, Chamberland S, Malouin F, Boudreault PL. From garden to lab: C-3 chemical modifications of tomatidine unveil broad-spectrum ATP synthase inhibitors to combat bacterial resistance. Eur J Med Chem 2023; 262:115886. [PMID: 37924710 DOI: 10.1016/j.ejmech.2023.115886] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/15/2023] [Indexed: 11/06/2023]
Abstract
Antibiotic resistance is escalating alarmingly worldwide. Bacterial resistance mechanisms are surfacing and proliferating across the globe, jeopardizing our capacity to manage prevalent infectious illnesses. Without drastic measures, we risk entering a post-antibiotic era, where even trivial infections and injuries can cause death again. In this context, we have developed a new class of antibiotics based on tomatidine (TO), a natural product derived from tomato plants, with a novel mode of action by targeting bacterial ATP synthases. The first generation of compounds proved highly specific for small-colony variants (SCVs) of Staphylococcus aureus. However, optimization of this scaffold through extensive structure-activity relationship studies has enabled us to broaden its effectiveness to include both Gram-positive and Gram-negative bacteria. Notably, the results showed that specific C3-modification of TO could improve ATP synthase inhibition and also bypass the outer membrane barrier of Gram-negative bacteria to gain substantial growth inhibition including against multi-resistant strains.
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Affiliation(s)
- Julien A Delbrouck
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Alexandre Murza
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Iryna Diachenko
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Abdelkhalek Ben Jamaa
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Runjun Devi
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| | - Audrey Larose
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, J1K 2R1, QC, Canada
| | - Suzanne Chamberland
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, J1K 2R1, QC, Canada
| | - François Malouin
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, J1K 2R1, QC, Canada.
| | - Pierre-Luc Boudreault
- Département de Pharmacologie-Physiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada; Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada.
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8
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Nesterov SV, Yaguzhinsky LS. Directed proton transfer from F o to F 1 extends the multifaceted proton functions in ATP synthase. Biophys Rev 2023; 15:859-873. [PMID: 37975013 PMCID: PMC10643803 DOI: 10.1007/s12551-023-01132-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The role of protons in ATP synthase is typically considered to be energy storage in the form of an electrochemical potential, as well as an operating element proving rotation. However, this review emphasizes that protons also act as activators of conformational changes in F1 and as direct participants in phosphorylation reaction. The protons transferred through Fo do not immediately leave to the bulk aqueous phase, but instead provide for the formation of a pH gradient between acidifying Fo and alkalizing F1. It facilitates a directed inter-subunit proton transfer to F1, where they are used in the ATP synthesis reaction. This ensures that the enzyme activity is not limited by a lack of protons in the alkaline mitochondrial matrix or chloroplast stroma. Up to one hundred protons bind to the carboxyl groups of the F1 subunit, altering the electrical interactions between the amino acids of the enzyme. This removes the inhibition of ATP synthase caused by the electrostatic attraction of charged amino acids of the stator and rotor and also makes the enzyme more prone to conformational changes. Protonation occurs during ATP synthesis initiation and during phosphorylation, while deprotonation blocks the rotation inhibiting both synthesis and hydrolysis. Thus, protons participate in the functioning of all main components of ATP synthase molecular machine making it effectively a proton-driven electric machine. The review highlights the key role of protons as a coupling factor in ATP synthase with multifaceted functions, including charge and energy transport, torque generation, facilitation of conformational changes, and participation in the ATP synthesis reaction.
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Affiliation(s)
- Semen V. Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Lev S. Yaguzhinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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9
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Osipov SD, Ryzhykau YL, Zinovev EV, Minaeva AV, Ivashchenko SD, Verteletskiy DP, Sudarev VV, Kuklina DD, Nikolaev MY, Semenov YS, Zagryadskaya YA, Okhrimenko IS, Gette MS, Dronova EA, Shishkin AY, Dencher NA, Kuklin AI, Ivanovich V, Uversky VN, Vlasov AV. I-Shaped Dimers of a Plant Chloroplast F OF 1-ATP Synthase in Response to Changes in Ionic Strength. Int J Mol Sci 2023; 24:10720. [PMID: 37445905 DOI: 10.3390/ijms241310720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/12/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
F-type ATP synthases play a key role in oxidative and photophosphorylation processes generating adenosine triphosphate (ATP) for most biochemical reactions in living organisms. In contrast to the mitochondrial FOF1-ATP synthases, those of chloroplasts are known to be mostly monomers with approx. 15% fraction of oligomers interacting presumably non-specifically in a thylakoid membrane. To shed light on the nature of this difference we studied interactions of the chloroplast ATP synthases using small-angle X-ray scattering (SAXS) method. Here, we report evidence of I-shaped dimerization of solubilized FOF1-ATP synthases from spinach chloroplasts at different ionic strengths. The structural data were obtained by SAXS and demonstrated dimerization in response to ionic strength. The best model describing SAXS data was two ATP-synthases connected through F1/F1' parts, presumably via their δ-subunits, forming "I" shape dimers. Such I-shaped dimers might possibly connect the neighboring lamellae in thylakoid stacks assuming that the FOF1 monomers comprising such dimers are embedded in parallel opposing stacked thylakoid membrane areas. If this type of dimerization exists in nature, it might be one of the pathways of inhibition of chloroplast FOF1-ATP synthase for preventing ATP hydrolysis in the dark, when ionic strength in plant chloroplasts is rising. Together with a redox switch inserted into a γ-subunit of chloroplast FOF1 and lateral oligomerization, an I-shaped dimerization might comprise a subtle regulatory process of ATP synthesis and stabilize the structure of thylakoid stacks in chloroplasts.
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Affiliation(s)
- Stepan D Osipov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Yury L Ryzhykau
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
| | - Egor V Zinovev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Andronika V Minaeva
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Sergey D Ivashchenko
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Dmitry P Verteletskiy
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Vsevolod V Sudarev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Daria D Kuklina
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Mikhail Yu Nikolaev
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Yury S Semenov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Yuliya A Zagryadskaya
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Ivan S Okhrimenko
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Margarita S Gette
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Elizaveta A Dronova
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Aleksei Yu Shishkin
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Norbert A Dencher
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Alexander I Kuklin
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
| | - Valentin Ivanovich
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Alexey V Vlasov
- Research Center for Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia
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10
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Wei Q, Chen B, Wang J, Huang M, Gui Y, Sayyed A, Tan BC. PHB3 Is Required for the Assembly and Activity of Mitochondrial ATP Synthase in Arabidopsis. Int J Mol Sci 2023; 24:ijms24108787. [PMID: 37240131 DOI: 10.3390/ijms24108787] [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: 04/12/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondrial ATP synthase is a multiprotein complex, which consists of a matrix-localized F1 domain (F1-ATPase) and an inner membrane-embedded Fo domain (Fo-ATPase). The assembly process of mitochondrial ATP synthase is complex and requires the function of many assembly factors. Although extensive studies on mitochondrial ATP synthase assembly have been conducted on yeast, much less study has been performed on plants. Here, we revealed the function of Arabidopsis prohibitin 3 (PHB3) in mitochondrial ATP synthase assembly by characterizing the phb3 mutant. The blue native PAGE (BN-PAGE) and in-gel activity staining assays showed that the activities of ATP synthase and F1-ATPase were significantly decreased in the phb3 mutant. The absence of PHB3 resulted in the accumulation of the Fo-ATPase and F1-ATPase intermediates, whereas the abundance of the Fo-ATPase subunit a was decreased in the ATP synthase monomer. Furthermore, we showed that PHB3 could interact with the F1-ATPase subunits β and δ in the yeast two-hybrid system (Y2H) and luciferase complementation imaging (LCI) assay and with Fo-ATPase subunit c in the LCI assay. These results indicate that PHB3 acts as an assembly factor required for the assembly and activity of mitochondrial ATP synthase.
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Affiliation(s)
- Qingqing Wei
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Baoyin Chen
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Junjun Wang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Manna Huang
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yuanye Gui
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Aqib Sayyed
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
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11
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Mendoza-Hoffmann F, Zarco-Zavala M, Ortega R, Celis-Sandoval H, Torres-Larios A, García-Trejo JJ. Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IF 1 Subunits of the F 1F O-ATPase as Related to the Endosymbiotic Origin of Mitochondria. Microorganisms 2022; 10:microorganisms10071372. [PMID: 35889091 PMCID: PMC9317440 DOI: 10.3390/microorganisms10071372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/03/2022] [Accepted: 07/03/2022] [Indexed: 12/10/2022] Open
Abstract
The F1FO-ATP synthase nanomotor synthesizes >90% of the cellular ATP of almost all living beings by rotating in the “forward” direction, but it can also consume the same ATP pools by rotating in “reverse.” To prevent futile F1FO-ATPase activity, several different inhibitory proteins or domains in bacteria (ε and ζ subunits), mitochondria (IF1), and chloroplasts (ε and γ disulfide) emerged to block the F1FO-ATPase activity selectively. In this study, we analyze how these F1FO-ATPase inhibitory proteins have evolved. The phylogeny of the α-proteobacterial ε showed that it diverged in its C-terminal side, thus losing both the inhibitory function and the ATP-binding/sensor motif that controls this inhibition. The losses of inhibitory function and the ATP-binding site correlate with an evolutionary divergence of non-inhibitory α-proteobacterial ε and mitochondrial δ subunits from inhibitory bacterial and chloroplastidic ε subunits. Here, we confirm the lack of inhibitory function of wild-type and C-terminal truncated ε subunits of P. denitrificans. Taken together, the data show that ζ evolved to replace ε as the primary inhibitor of the F1FO-ATPase of free-living α-proteobacteria. However, the ζ inhibitory function was also partially lost in some symbiotic α-proteobacteria and totally lost in some strictly parasitic α-proteobacteria such as the Rickettsiales order. Finally, we found that ζ and IF1 likely evolved independently via convergent evolution before and after the endosymbiotic origin mitochondria, respectively. This led us to propose the ε and ζ subunits as tracer genes of the pre-endosymbiont that evolved into the actual mitochondria.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California (UABC)—Campus Tijuana, Tijuana C.P. 22390, Baja California, Mexico
- Correspondence: (F.M.-H.); (J.J.G.-T.)
| | - Mariel Zarco-Zavala
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Heliodoro Celis-Sandoval
- Instituto de Fisiología Celular (IFC), Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - Alfredo Torres-Larios
- Instituto de Fisiología Celular (IFC), Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de Mexico C.P. 04510, Coyoacan, Mexico
- Correspondence: (F.M.-H.); (J.J.G.-T.)
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