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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] [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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Shen J, Qiao L. Proteomic and metabolic analysis of Moorella thermoacetica-g-C 3N 4 nanocomposite system for artificial photosynthesis. Talanta 2024; 278:126479. [PMID: 38941811 DOI: 10.1016/j.talanta.2024.126479] [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: 03/06/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
Artificial photosynthesis by microbe-semiconductor biohybrid systems has been demonstrated as a valuable strategy in providing sustainable energy and in carbon fixation. However, most of the developed biohybrid systems for light harvesting employ heavy metal materials, especially cadmium sulfide (CdS), which normally cause environmental pollution and restrict the widespread of the systems. Herein, we constructed an environmentally friendly biohybirid system based on a typical acetogenic bacteria, Moorella thermoacetica, coupling with a carbon-based semiconductor, graphitic carbon nitride (g-C3N4), to realize light-driven carbon fixation. The proposed biohybrid system displayed outstanding acetate productivity with a quantum yield of 2.66 ± 0.43 %. Non-targeted proteomic analysis indicated that the physiological activity of the bacteria was improved, coupling with the non-toxic material. We further proposed the mechanisms of energy generation, electron transfer and CO2 fixation of the irradiated biohybrid system by proteomic and metabolomic characterization. With the photoelectron generated in g-C3N4 under illumination, CO2 is finally converted to acetate via the Wood-Ljungdahl pathway (WLP). Other associated pathways were also proved to be activated, providing extra energy or substrates for acetate production. The study reveals that the future focus of the development of biohybrid systems for light harvesting can be on the metal-free biocompatible material, which can activate the expression of the key enzymes involved in the electron transfer and carbon metabolism under light irradiation.
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Affiliation(s)
- Jiayuan Shen
- Department of Chemistry, and Minhang Hospital, Fudan University, Shanghai, 200000, China
| | - Liang Qiao
- Department of Chemistry, and Minhang Hospital, Fudan University, Shanghai, 200000, China.
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3
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Yi S, Guo X, Lou W, Mao S, Luan G, Lu X. Structure, Regulation, and Significance of Cyanobacterial and Chloroplast Adenosine Triphosphate Synthase in the Adaptability of Oxygenic Photosynthetic Organisms. Microorganisms 2024; 12:940. [PMID: 38792770 PMCID: PMC11124002 DOI: 10.3390/microorganisms12050940] [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: 04/11/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
In cyanobacteria and chloroplasts (in algae and plants), ATP synthase plays a pivotal role as a photosynthetic membrane complex responsible for producing ATP from adenosine diphosphate and inorganic phosphate, utilizing a proton motive force gradient induced by photosynthesis. These two ATP synthases exhibit similarities in gene organization, amino acid sequences of subunits, structure, and functional mechanisms, suggesting that cyanobacterial ATP synthase is probably the evolutionary precursor to chloroplast ATP synthase. In this review, we explore the precise synthesis and assembly of ATP synthase subunits to address the uneven stoichiometry within the complex during transcription, translation, and assembly processes. We also compare the regulatory strategies governing ATP synthase activity to meet varying energy demands in cyanobacteria and chloroplasts amid fluctuating natural environments. Furthermore, we delve into the role of ATP synthase in stress tolerance and photosynthetic carbon fixation efficiency in oxygenic photosynthetic organisms (OPsOs), along with the current researches on modifying ATP synthase to enhance carbon fixation efficiency under stress conditions. This review aims to offer theoretical insights and serve as a reference for understanding the functional mechanisms of ATP synthase, sparking innovative ideas for enhancing photosynthetic carbon fixation efficiency by utilizing ATP synthase as an effective module in OPsOs.
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Affiliation(s)
- Siyan Yi
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China;
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha 410004, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
| | - Xin Guo
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
- College of Live Science, Henan University, Kaifeng 450001, China
| | - Wenjing Lou
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Shaoming Mao
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China;
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry & Technology, Changsha 410004, China
| | - Guodong Luan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; (X.G.); (G.L.); (X.L.)
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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Grandi M, Fabbian S, Solaini G, Baracca A, Bellanda M, Giorgio V. Peptides Targeting the IF1-ATP Synthase Complex Modulate the Permeability Transition Pore in Cancer HeLa Cells. Int J Mol Sci 2024; 25:4655. [PMID: 38731874 PMCID: PMC11083241 DOI: 10.3390/ijms25094655] [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: 02/14/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
The mitochondrial protein IF1 is upregulated in many tumors and acts as a pro-oncogenic protein through its interaction with the ATP synthase and the inhibition of apoptosis. We have recently characterized the molecular nature of the IF1-Oligomycin Sensitivity Conferring Protein (OSCP) subunit interaction; however, it remains to be determined whether this interaction could be targeted for novel anti-cancer therapeutic intervention. We generated mitochondria-targeting peptides to displace IF1 from the OSCP interaction. The use of one selective peptide led to displacement of the inhibitor IF1 from ATP synthase, as shown by immunoprecipitation. NMR spectroscopy analysis, aimed at clarifying whether these peptides were able to directly bind to the OSCP protein, identified a second peptide which showed affinity for the N-terminal region of this subunit overlapping the IF1 binding region. In situ treatment with the membrane-permeable derivatives of these peptides in HeLa cells, that are silenced for the IF1 inhibitor protein, showed significant inhibition in mitochondrial permeability transition and no effects on mitochondrial respiration. These peptides mimic the effects of the IF1 inhibitor protein in cancer HeLa cells and confirm that the IF1-OSCP interaction inhibits apoptosis. A third peptide was identified which counteracts the anti-apoptotic role of IF1, showing that OSCP is a promising target for anti-cancer therapies.
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Affiliation(s)
- Martina Grandi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy
| | - Simone Fabbian
- Department of Chemical Science, University of Padova, 35121 Padova, Italy
| | - Giancarlo Solaini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy
| | - Alessandra Baracca
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy
| | - Massimo Bellanda
- Department of Chemical Science, University of Padova, 35121 Padova, Italy
- Institute of Biomolecular Chemistry of National Research Council of Italy (CNR), 35131 Padova, Italy
| | - Valentina Giorgio
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy
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Wang T, Sun F, Li C, Nan P, Song Y, Wan X, Mo H, Wang J, Zhou Y, Guo Y, Helali AE, Xu D, Zhan Q, Ma F, Qian H. MTA1, a Novel ATP Synthase Complex Modulator, Enhances Colon Cancer Liver Metastasis by Driving Mitochondrial Metabolism Reprogramming. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300756. [PMID: 37442756 PMCID: PMC10477900 DOI: 10.1002/advs.202300756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/22/2023] [Indexed: 07/15/2023]
Abstract
Liver metastasis is the most fatal event of colon cancer patients. Warburg effect has been long challenged by the fact of upregulated oxidative phosphorylation (OXPHOS), while its mechanism remains unclear. Here, metastasis-associated antigen 1 (MTA1) is identified as a newly identified adenosine triphosphate (ATP) synthase modulator by interacting with ATP synthase F1 subunit alpha (ATP5A), facilitates colon cancer liver metastasis by driving mitochondrial bioenergetic metabolism reprogramming, enhancing OXPHOS; therefore, modulating ATP synthase activity and downstream mTOR pathways. High-throughput screening of an anticancer drug shows MTA1 knockout increases the sensitivity of colon cancer to mitochondrial bioenergetic metabolism-targeted drugs and mTOR inhibitors. Inhibiting ATP5A enhances the sensitivity of liver-metastasized colon cancer to sirolimus in an MTA1-dependent manner. The therapeutic effects are verified in xenograft models and clinical cases. This research identifies a new modulator of mitochondrial bioenergetic reprogramming in cancer metastasis and reveals a new mechanism on upregulating mitochondrial OXPHOS as the reversal of Warburg effect in cancer metastasis is orchestrated.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Laboratory of Molecular OncologyPeking University Cancer Hospital & InstituteBeijing100142China
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
| | - Fangzhou Sun
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
| | - Chunxiao Li
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
- Department of Medical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
| | - Peng Nan
- Laboratory Medicine CenterDepartment of Clinical LaboratoryZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)Hangzhou310014China
| | - Yan Song
- Department of PathologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
| | - Xuhao Wan
- School of Electrical Engineering and AutomationWuhan UniversityWuhan430000China
| | - Hongnan Mo
- Department of Medical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
| | - Jinsong Wang
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
| | - Yantong Zhou
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
| | - Yuzheng Guo
- School of Electrical Engineering and AutomationWuhan UniversityWuhan430000China
| | - Aya Ei Helali
- Department of Clinical OncologyLi Ka Shing Faculty of MedicineUniversity of Hong KongHong Kong999077China
| | - Dongkui Xu
- Department of VIPNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing)Laboratory of Molecular OncologyPeking University Cancer Hospital & InstituteBeijing100142China
- Peking University International Cancer InstitutePeking UniversityBeijing100191China
- Institute of Cancer ResearchShenzhen Bay Laboratory, Cancer Institute, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Peking University Shenzhen Hospital, Shenzhen Peking University‐the Hong Kong University of Science and Technology (PKU‐HKUST) Medical CenterShenzhen518107China
- Research Unit of Molecular Cancer ResearchChinese Academy of Medical SciencesBeijing100021China
| | - Fei Ma
- Department of Medical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
- Department of Medical OncologyNational Cancer Center/National Clinical Research Center for Cancer/Hebei Cancer HospitalChinese Academy of Medical SciencesLangfang065001China
| | - Haili Qian
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021China
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6
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Nakano A, Kishikawa JI, Mitsuoka K, Yokoyama K. Mechanism of ATP hydrolysis dependent rotation of bacterial ATP synthase. Nat Commun 2023; 14:4090. [PMID: 37429854 DOI: 10.1038/s41467-023-39742-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
F1 domain of ATP synthase is a rotary ATPase complex in which rotation of central γ-subunit proceeds in 120° steps against a surrounding α3β3 fueled by ATP hydrolysis. How the ATP hydrolysis reactions occurring in three catalytic αβ dimers are coupled to mechanical rotation is a key outstanding question. Here we describe catalytic intermediates of the F1 domain in FoF1 synthase from Bacillus PS3 sp. during ATP mediated rotation captured using cryo-EM. The structures reveal that three catalytic events and the first 80° rotation occur simultaneously in F1 domain when nucleotides are bound at all the three catalytic αβ dimers. The remaining 40° rotation of the complete 120° step is driven by completion of ATP hydrolysis at αDβD, and proceeds through three sub-steps (83°, 91°, 101°, and 120°) with three associated conformational intermediates. All sub-steps except for one between 91° and 101° associated with phosphate release, occur independently of the chemical cycle, suggesting that the 40° rotation is largely driven by release of intramolecular strain accumulated by the 80° rotation. Together with our previous results, these findings provide the molecular basis of ATP driven rotation of ATP synthases.
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Affiliation(s)
- Atsuki Nakano
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Jun-Ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-ku, Kyoto, 603-8555, Japan.
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7
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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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F1·Fo ATP Synthase/ATPase: Contemporary View on Unidirectional Catalysis. Int J Mol Sci 2023; 24:ijms24065417. [PMID: 36982498 PMCID: PMC10049701 DOI: 10.3390/ijms24065417] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
F1·Fo-ATP synthases/ATPases (F1·Fo) are molecular machines that couple either ATP synthesis from ADP and phosphate or ATP hydrolysis to the consumption or production of a transmembrane electrochemical gradient of protons. Currently, in view of the spread of drug-resistant disease-causing strains, there is an increasing interest in F1·Fo as new targets for antimicrobial drugs, in particular, anti-tuberculosis drugs, and inhibitors of these membrane proteins are being considered in this capacity. However, the specific drug search is hampered by the complex mechanism of regulation of F1·Fo in bacteria, in particular, in mycobacteria: the enzyme efficiently synthesizes ATP, but is not capable of ATP hydrolysis. In this review, we consider the current state of the problem of “unidirectional” F1·Fo catalysis found in a wide range of bacterial F1·Fo and enzymes from other organisms, the understanding of which will be useful for developing a strategy for the search for new drugs that selectively disrupt the energy production of bacterial cells.
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Nesci S. Bacterial and mammalian F1FO-ATPase: Structural similarities and divergences to exploit in the battle against Mycobacterium tuberculosis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023. [DOI: 10.1016/bs.ircmb.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Iwamoto-Kihara A. Regulatory Mechanisms and Environmental Adaptation of the F-ATPase Family. Biol Pharm Bull 2022; 45:1412-1418. [PMID: 36184497 DOI: 10.1248/bpb.b22-00419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The F-type ATPase family of enzymes, including ATP synthases, are found ubiquitously in biological membranes. ATP synthesis from ADP and inorganic phosphate is driven by an electrochemical H+ gradient or H+ motive force, in which intramolecular rotation of F-type ATPase is generated with H+ transport across the membranes. Because this rotation is essential for energy coupling between catalysis and H+-transport, regulation of the rotation is important to adapt to environmental changes and maintain ATP concentration. Recently, a series of cryo-electron microscopy images provided detailed insights into the structure of the H+ pathway and the multiple subunit arrangement. However, the regulatory mechanism of the rotation has not been clarified. This review describes the inhibition mechanism of ATP hydrolysis in bacterial enzymes. In addition, properties of the F-type ATPase of Streptococcus mutans, which acts as a H+-pump in an acidic environment, are described. These findings may help in the development of novel antimicrobial agents.
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Wu R, Liu T, Wu S, Li H, Song R, Song B. Synthesis, Antibacterial Activity, and Action Mechanism of Novel Sulfonamides Containing Oxyacetal and Pyrimidine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9305-9318. [PMID: 35858046 DOI: 10.1021/acs.jafc.2c02099] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial leaf blight (BLB) and bacterial leaf streak (BLS) are two serious bacterial diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively. However, the control of these diseases by conventional pesticides remains challenging due to development of resistances. We aimed to address this pending problem and developed a series of novel pyrimidine sulfonamide derivatives. Structurally, title compounds bear a unique oxyacetal group, which has a proven immune-activating effect. Compound E35 designed based on the 3D-QSAR model was demonstrated as the optimal in vitro activity against Xoo and Xoc, with EC50 values of 26.7 and 30.8 mg/L, respectively, which were higher than the positive controls bismerthiazol (29.9 and 32.7 mg/L) and thiodiazole copper (30.5 and 36.4 mg/L). On the prevention level, the biological activity test showed compound E35 had superior protective activity (43.7%) on BLS to thiodiazole copper (32.1%). The defense enzymes and proteomics results suggested that compound E35 could be a versatile candidate as it improved plant's resistance to disease.
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Affiliation(s)
- Rong Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Ting Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Sikai Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Hongde Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Runjiang Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
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Marshansky V. Discovery and Study of Transmembrane Rotary Ion-Translocating Nano-Motors: F-ATPase/Synthase of Mitochondria/Bacteria and V-ATPase of Eukaryotic Cells. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:702-719. [PMID: 36171652 DOI: 10.1134/s000629792208003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
This review discusses the history of discovery and study of the operation of the two rotary ion-translocating ATPase nano-motors: (i) F-ATPase/synthase (holocomplex F1FO) of mitochondria/bacteria and (ii) eukaryotic V-ATPase (holocomplex V1VO). Vacuolar adenosine triphosphatase (V-ATPase) is a transmembrane multisubunit complex found in all eukaryotes from yeast to humans. It is structurally and functionally similar to the F-ATPase/synthase of mitochondria/bacteria and the A-ATPase/synthase of archaebacteria, which indicates a common evolutionary origin of the rotary ion-translocating nano-motors built into cell membranes and invented by Nature billions of years ago. Previously we have published several reviews on this topic with appropriate citations of our original research. This review is focused on the historical analysis of the discovery and study of transmembrane rotary ion-translocating ATPase nano-motors functioning in bacteria, eukaryotic cells and mitochondria of animals.
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DeVore K, Chiu PL. Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity. Biomolecules 2022; 12:biom12050628. [PMID: 35625556 PMCID: PMC9138638 DOI: 10.3390/biom12050628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has become an indispensable tool to probe high-resolution structural detail of biomolecules. It enables direct visualization of the biomolecules and opens a possibility for averaging molecular images to reconstruct a three-dimensional Coulomb potential density map. Newly developed algorithms for data analysis allow for the extraction of structural heterogeneity from a massive and low signal-to-noise-ratio (SNR) cryo-EM dataset, expanding our understanding of multiple conformational states, or further implications in dynamics, of the target biomolecule. This review provides an overview that briefly describes the workflow of single-particle cryo-EM, including imaging and data processing, and new methods developed for analyzing the data heterogeneity to understand the structural variability of biomolecules.
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14
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Volkán-Kacsó S, Marcus RA. F 1-ATPase Rotary Mechanism: Interpreting Results of Diverse Experimental Modes With an Elastic Coupling Theory. Front Microbiol 2022; 13:861855. [PMID: 35531282 PMCID: PMC9072658 DOI: 10.3389/fmicb.2022.861855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
In this chapter, we review single-molecule observations of rotary motors, focusing on the general theme that their mechanical motion proceeds in substeps with each substep described by an angle-dependent rate constant. In the molecular machine F1-ATPase, the stepping rotation is described for individual steps by forward and back reaction rate constants, some of which depend strongly on the rotation angle. The rotation of a central shaft is typically monitored by an optical probe. We review our recent work on the theory for the angle-dependent rate constants built to treat a variety of single-molecule and ensemble experiments on the F1-ATPase, and relating the free energy of activation of a step to the standard free energy of reaction for that step. This theory, an elastic molecular transfer theory, provides a framework for a multistate model and includes the probe used in single-molecule imaging and magnetic manipulation experiments. Several examples of its application are the following: (a) treatment of the angle-dependent rate constants in stalling experiments, (b) use of the model to enhance the time resolution of the single-molecule imaging apparatus and to detect short-lived states with a microsecond lifetime, states hidden by the fluctuations of the imaging probe, (c) treatment of out-of-equilibrium "controlled rotation" experiments, (d) use of the model to predict, without adjustable parameters, the angle-dependent rate constants of nucleotide binding and release, using data from other experiments, and (e) insights obtained from correlation of kinetic and cryo-EM structural data. It is also noted that in the case where the release of ADP would be a bottleneck process, the binding of ATP to another site acts to accelerate the release by 5-6 orders of magnitude. The relation of the present set of studies to previous and current theoretical work in the field is described. An overall goal is to gain mechanistic insight into the biological function in relation to structure.
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Affiliation(s)
- Sándor Volkán-Kacsó
- Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United States
- Segerstrom Science Center, Azusa Pacific University, Azusa, CA, United States
| | - Rudolph A. Marcus
- Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA, United States
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15
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Reisman BJ, Guo H, Ramsey HE, Wright MT, Reinfeld BI, Ferrell PB, Sulikowski GA, Rathmell WK, Savona MR, Plate L, Rubinstein JL, Bachmann BO. Apoptolidin family glycomacrolides target leukemia through inhibition of ATP synthase. Nat Chem Biol 2022; 18:360-367. [PMID: 34857958 PMCID: PMC8967781 DOI: 10.1038/s41589-021-00900-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/17/2021] [Indexed: 11/11/2022]
Abstract
Cancer cells have long been recognized to exhibit unique bioenergetic requirements. The apoptolidin family of glycomacrolides are distinguished by their selective cytotoxicity towards oncogene-transformed cells, yet their molecular mechanism remains uncertain. We used photoaffinity analogs of the apoptolidins to identify the F1 subcomplex of mitochondrial ATP synthase as the target of apoptolidin A. Cryogenic electron microscopy (cryo-EM) of apoptolidin and ammocidin-ATP synthase complexes revealed a novel shared mode of inhibition that was confirmed by deep mutational scanning of the binding interface to reveal resistance mutations which were confirmed using CRISPR-Cas9. Ammocidin A was found to suppress leukemia progression in vivo at doses that were tolerated with minimal toxicity. The combination of cellular, structural, mutagenesis, and in vivo evidence defines the mechanism of action of apoptolidin family glycomacrolides and establishes a path to address oxidative phosphorylation-dependent cancers.
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Affiliation(s)
- Benjamin J. Reisman
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Medical Scientist Training Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Hui Guo
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Haley E. Ramsey
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Madison T. Wright
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Bradley I. Reinfeld
- Medical Scientist Training Program, Vanderbilt University, Nashville, Tennessee, USA.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Cancer Biology Program, Vanderbilt University, Nashville, Tennessee, USA
| | - P. Brent Ferrell
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Cancer Biology Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Gary A. Sulikowski
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - W. Kimryn Rathmell
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Cancer Biology Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Michael R. Savona
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Cancer Biology Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Brian O. Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.,Correspondence to:
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16
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Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases. Nat Commun 2022; 13:1213. [PMID: 35260556 PMCID: PMC8904598 DOI: 10.1038/s41467-022-28832-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FoF1 ATP synthase. When powered by ATP hydrolysis, the V1 domain rotates the central rotor against the A3B3 hexamer, composed of three catalytic AB dimers adopting different conformations (ABopen, ABsemi, and ABclosed). Here, we report the atomic models of 18 catalytic intermediates of the V1 domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not rotate immediately after binding of ATP to the V1. Instead, three events proceed simultaneously with the 120˚ rotation of the shaft: hydrolysis of ATP in ABsemi, zipper movement in ABopen by the binding ATP, and unzipper movement in ABclosed with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in ABsemi, rather than the power stroke model proposed previously for F1-ATPase. The rotary ATPases use a rotary catalytic mechanism to drive transmembrane proton movement powered by ATP hydrolysis. Here, the authors report a collection of V/A-ATPase V1 domain structures, providing insights into rotary mechanism of the enzyme and potentially other rotary motor proteins driven by ATP hydrolysis.
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17
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Rieu M, Krutyholowa R, Taylor NMI, Berry RM. A new class of biological ion-driven rotary molecular motors with 5:2 symmetry. Front Microbiol 2022; 13:948383. [PMID: 35992645 PMCID: PMC9389320 DOI: 10.3389/fmicb.2022.948383] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
Several new structures of three types of protein complexes, obtained by cryo-electron microscopy (cryo-EM) and published between 2019 and 2021, identify a new family of natural molecular wheels, the "5:2 rotary motors." These span the cytoplasmic membranes of bacteria, and their rotation is driven by ion flow into the cell. They consist of a pentameric wheel encircling a dimeric axle within the cytoplasmic membrane of both Gram-positive and gram-negative bacteria. The axles extend into the periplasm, and the wheels extend into the cytoplasm. Rotation of these wheels has never been observed directly; it is inferred from the symmetry of the complexes and from the roles they play within the larger systems that they are known to power. In particular, the new structure of the stator complex of the Bacterial Flagellar Motor, MotA5B2, is consistent with a "wheels within wheels" model of the motor. Other 5:2 rotary motors are believed to share the core rotary function and mechanism, driven by ion-motive force at the cytoplasmic membrane. Their structures diverge in their periplasmic and cytoplasmic parts, reflecting the variety of roles that they perform. This review focuses on the structures of 5:2 rotary motors and their proposed mechanisms and functions. We also discuss molecular rotation in general and its relation to the rotational symmetry of molecular complexes.
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Affiliation(s)
- Martin Rieu
- Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building University of Oxford, Oxford, United Kingdom
| | - Roscislaw Krutyholowa
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nicholas M. I. Taylor
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Nicholas M. I. Taylor,
| | - Richard M. Berry
- Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building University of Oxford, Oxford, United Kingdom
- *Correspondence: Richard M. Berry,
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18
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IF1 inactivation attenuates experimental colitis through downregulation of neutrophil infiltration in colon mucosa. Int Immunopharmacol 2021; 99:107980. [PMID: 34298397 DOI: 10.1016/j.intimp.2021.107980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 01/11/2023]
Abstract
IF1 is a mitochondrial protein involved in the regulation of ATP synthase activity. The role of IF1 remains to be established in inflammatory bowel diseases (IBD). In this study, we report that IF1 gene inactivation generated protection against IBD in the dextran sodium sulfate (DSS) model. IF1 gene knockout (IF1-KO) mice developed less severe colitis than the wild type (WT) mice as judged by parameters including disease activity index (DAI), body weight loss, inflammatory cytokines, leukocyte infiltration and bacterial invasion in the colon tissue. The intestinal barrier integrity was protected in the colon tissue of IF1-KO mice through a reduction in apoptosis and inflammasomal activity. The protection was abolished in the KO mice after substitution of the immune cells with the wild type cells following bone marrow transplantation. Depletion of neutrophils with anti-Gr-1 antibody abolished the protection from colitis in IF1-KO mice. Neutrophil number was decreased in the peripheral blood of IF1-KO mice, which was associated with a reduction in LC3A/B proteins in the KO neutrophils in Rapamycin-induced autophagy response. Inhibition of autophagy with the lysosome inhibitor Chloroquine (CQ) decreased the absolute number of neutrophils in WT mice and protected the mice from colitis. Taken together, these findings suggest that IF1 may contribute to the pathogenesis of IBD through acceleration of neutrophil autophagy. The activity is attenuated in the IF1-KO mice through reduction of autophagy in neutrophils leading to resistance to IBD.
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19
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Almendro-Vedia V, Natale P, Valdivieso González D, Lillo MP, Aragones JL, López-Montero I. How rotating ATP synthases can modulate membrane structure. Arch Biochem Biophys 2021; 708:108939. [PMID: 34052190 DOI: 10.1016/j.abb.2021.108939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
F1Fo-ATP synthase (ATP synthase) is a central membrane protein that synthetizes most of the ATP in the cell through a rotational movement driven by a proton gradient across the hosting membrane. In mitochondria, ATP synthases can form dimers through specific interactions between some subunits of the protein. The dimeric form of ATP synthase provides the protein with a spontaneous curvature that sustain their arrangement at the rim of the high-curvature edges of mitochondrial membrane (cristae). Also, a direct interaction with cardiolipin, a lipid present in the inner mitochondrial membrane, induces the dimerization of ATP synthase molecules along cristae. The deletion of those biochemical interactions abolishes the protein dimerization producing an altered mitochondrial function and morphology. Mechanically, membrane bending is one of the key deformation modes by which mitochondrial membranes can be shaped. In particular, bending rigidity and spontaneous curvature are important physical factors for membrane remodelling. Here, we discuss a complementary mechanism whereby the rotatory movement of the ATP synthase might modify the mechanical properties of lipid bilayers and contribute to the formation and regulation of the membrane invaginations.
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Affiliation(s)
- Víctor Almendro-Vedia
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - Paolo Natale
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - David Valdivieso González
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain
| | - M Pilar Lillo
- Departamento Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Juan L Aragones
- Departamento de Física Teórica de la Materia Condensada, Instituto Nicolás Cabrera and Condensed Matter Physics Centre (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Iván López-Montero
- Departamento Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040, Madrid, Spain; Instituto de Investigación Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, 28041, Madrid, Spain.
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20
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A Theoretical Model of Mitochondrial ATP Synthase Deficiencies. The Role of Mitochondrial Carriers. Processes (Basel) 2021. [DOI: 10.3390/pr9081424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The m.8993T>G mutation of the mitochondrial MT-ATP6 gene is associated with NARP syndrome (neuropathy, ataxia and retinitis pigmentosa). The equivalent point mutation introduced in yeast Saccharomyces cerevisiae mitochondrial DNA considerably reduced the activity of ATP synthase and of cytochrome-c-oxidase, preventing yeast growth on oxidative substrates. The overexpression of the mitochondrial oxodicarboxylate carrier (Odc1p) was able to rescue the growth on the oxidative substrate by increasing the substrate-level phosphorylation of ADP coupled to the conversion of α-ketoglutarate (AKG) into succinate with an increase in Complex IV activity. Previous studies showed that equivalent point mutations in ATP synthase behave similarly and can be rescued by Odc1p overexpression and/or the uncoupling of OXPHOS from ATP synthesis. In order to better understand the mechanism of the ATP synthase mutation bypass, we developed a core model of mitochondrial metabolism based on AKG as a respiratory substrate. We describe the different possible metabolite outputs and the ATP/O ratio values as a function of ATP synthase inhibition.
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21
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Vestergaard M, Roshanak S, Ingmer H. Targeting the ATP Synthase in Staphylococcus aureus Small Colony Variants, Streptococcus pyogenes and Pathogenic Fungi. Antibiotics (Basel) 2021; 10:antibiotics10040376. [PMID: 33918382 PMCID: PMC8067178 DOI: 10.3390/antibiotics10040376] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
The ATP synthase has been validated as a druggable target with the approval of the ATP synthase inhibitor, bedaquiline, for treatment of drug-resistant Mycobacterium tuberculosis, a bacterial species in which the ATP synthase is essential for viability. Gene inactivation studies have also shown that the ATP synthase is essential among Streptococci, and some studies even suggest that inhibition of the ATP synthase is a strategy for the elimination of Staphylococcus aureus small colony variants with deficiencies in the electron transport chain, as well as pathogenic fungi, such as Candida albicans. Here we investigated five structurally diverse ATP synthase inhibitors, namely N,N′-dicyclohexylcarbodiimide (DCCD), oligomycin A, tomatidine, resveratrol and piceatannol, for their growth inhibitory activity against the bacterial strains Streptococcus pyogenes, S. aureus and two isogenic small colony variants, as well as the pathogenic fungal species, C. albicans and Aspergillus niger. DCCD showed broad-spectrum inhibitory activity against all the strains (minimum inhibitory concentration (MIC) 2–16 µg/mL), except for S. aureus, where the ATP synthase is dispensable for growth. Contrarily, oligomycin A selectively inhibited the fungal strains (MIC 1–8 µg/mL), while tomatidine showed very potent, but selective, activity against small colony variants of S. aureus with compromised electron transport chain activity (MIC 0.0625 µg/mL). Small colony variants of S. aureus were also more sensitive to resveratrol and piceatannol than the wild-type strain, and piceatannol inhibited S. pyogenes at 16–32 µg/mL. We previously showed that transposon inactivation of the ATP synthase sensitizes S. aureus towards polymyxin B and colistin, and here we demonstrate that treatment with structurally diverse ATP synthase inhibitors sensitized S. aureus towards polymyxin B. Collectively, our data show that ATP synthase inhibitors can have selective inhibitory activity against pathogenic microorganisms in which the ATP synthase is essential. The data also show that the inhibition of the ATP synthase in Streptococcus pyogenes may be a new strategy for development of a narrow-spectrum antibiotic class. In other major bacterial pathogens, such as S. aureus and potentially Escherichia coli, where the ATP synthase is dispensable, the ATP synthase inhibitors may be applied in combination with antimicrobial peptides to provide new therapeutic options.
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Affiliation(s)
- Martin Vestergaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark; (M.V.); (S.R.)
| | - Sahar Roshanak
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark; (M.V.); (S.R.)
- Department of Food Science and Technology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark; (M.V.); (S.R.)
- Correspondence:
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22
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Hennell James R, Deme JC, Kjӕr A, Alcock F, Silale A, Lauber F, Johnson S, Berks BC, Lea SM. Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility. Nat Microbiol 2021; 6:221-233. [PMID: 33432152 PMCID: PMC7116788 DOI: 10.1038/s41564-020-00823-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022]
Abstract
Three classes of ion-driven protein motors have been identified to date: ATP synthase, the bacterial flagellar motor and a proton-driven motor that powers gliding motility and the type 9 protein secretion system in Bacteroidetes bacteria. Here, we present cryo-electron microscopy structures of the gliding motility/type 9 protein secretion system motors GldLM from Flavobacterium johnsoniae and PorLM from Porphyromonas gingivalis. The motor is an asymmetric inner membrane protein complex in which the single transmembrane helices of two periplasm-spanning GldM/PorM proteins are positioned inside a ring of five GldL/PorL proteins. Mutagenesis and single-molecule tracking identify protonatable amino acid residues in the transmembrane domain of the complex that are important for motor function. Our data provide evidence for a mechanism in which proton flow results in rotation of the periplasm-spanning GldM/PorM dimer inside the intra-membrane GldL/PorL ring to drive processes at the bacterial outer membrane.
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Affiliation(s)
- Rory Hennell James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK
| | - Andreas Kjӕr
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
- CBCB, Newcastle University, Newcastle upon Tyne, UK
| | - Augustinas Silale
- Department of Biochemistry, University of Oxford, Oxford, UK
- CBCB, Newcastle University, Newcastle upon Tyne, UK
| | - Frédéric Lauber
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK.
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23
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Cui H, Yang H, Abdel-Samie MA, Siva S, Lin L. Controlled-release casein/cinnamon essential oil nanospheres for the inactivation of Campylobacter jejuni in duck. Int J Food Microbiol 2021; 341:109074. [PMID: 33508583 DOI: 10.1016/j.ijfoodmicro.2021.109074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/10/2020] [Accepted: 01/09/2021] [Indexed: 12/18/2022]
Abstract
Campylobacter jejuni (C. jejuni) is one of the most common foodborne pathogens that cause human sickness mostly through the poultry food chain. Cinnamon essential oil (CEO) has excellent antibacterial ability against C. jejuni growth. This study investigated the antibacterial mechanism of CEO against C. jejuni primarily through metabolism, energy metabolism of essential enzymes (AKPase, β-galactosidase, and ATPase), and respiration metabolism. Results showed that the hexose monophosphate pathway (HMP) was inhibited, and that the enzyme activity of G6DPH substantially decreased upon treatment with CEO. Analysis of the effect of CEO on the expression of toxic genes was performed by the real-time PCR (RT-PCR). The expression levels of the toxic genes cadF, ciaB, fliA, and racR under CEO treatment were determined. Casein/CEO nanospheres were further prepared for the effective inhibition of C. jejuni and characterized by particle-size distribution, zeta-potential distribution, fluorescence, TEM, and GC-MS methods. Finally, the efficiency of CEO and casein/CEO nanospheres in terms of antibacterial activity against C. jejuni was verified. The casein/CEO nanospheres displayed high antibacterial activity on duck samples. The population of the test group decreased from 4.30 logCFU/g to 0.86 logCFU/g and 4.30 logCFU/g to 2.46 logCFU/g at 4 °C and at 25 °C for C. jejuni, respectively. Sensory evaluation and texture analysis were also conducted on various duck samples.
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Affiliation(s)
- Haiying Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Hongying Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Mohamed A Abdel-Samie
- Department of Food and Dairy Sciences and Technology, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Subramanian Siva
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Lin Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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24
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He Y, Ma J, Joseph V, Wei Y, Liu M, Zhang Z, Li G, He Q, Li H. Potassium regulates the growth and toxin biosynthesis of Microcystis aeruginosa. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115576. [PMID: 32898730 DOI: 10.1016/j.envpol.2020.115576] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/24/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
Potassium (K+) is the most abundant cation in phytoplankton cells, but its impact on Microcystis aeruginosa (M. aeruginosa) has not been fully documented. This study presents evidence of how K+ availability affects the growth, oxidative stress and microcystin (MC) production of M. aeruginosa. The iTRAQ-based proteomic analysis revealed that during K+ deficiency, serious oxidative damage occurred and the photosynthesis-associated and ABC transporter-related proteins in M. aeruginosa were substantially downregulated. In the absence of K+, a 69.26% reduction in cell density was shown, and both the photosynthesis and iron uptake were depressed, which triggered a declined production of ATP and expression of MC synthetases genes (mcyA, B and D), and MC exporters (mcyH). Through the impairment of both the MC biosynthesis and MC transportation out of cells, K+ depletion caused an 85.89% reduction of extracellular MC content at the end of the study. However, with increasing in the available K+ concentrations, photosynthesis efficiency, the expression of ABC-transporter proteins, and the transcription of mcy genes displayed slight differences compared with those in the control group. This work represents evidence that K+ availability can regulate the physiological metabolic activity of M. aeruginosa and K+ deficiency leads to depressed growth and MC production in M. aeruginosa.
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Affiliation(s)
- Yixin He
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Jianrong Ma
- CAS Key Laboratory of Reservoir Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Vanderwall Joseph
- Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Yanyan Wei
- Cultivation Base of Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Mengzi Liu
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Zhaoxue Zhang
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Guo Li
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Qiang He
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing, 400044, China
| | - Hong Li
- Key Laboratory of Eco-Environment of Three Gorges Region, Ministry of Education, Chongqing University, Chongqing, 400044, China.
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25
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Wang L, Wu D, Robinson CV, Wu H, Fu TM. Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. Mol Cell 2020; 80:501-511.e3. [PMID: 33065002 PMCID: PMC7655608 DOI: 10.1016/j.molcel.2020.09.029] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/22/2022]
Abstract
Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. Here, we report cryoelectron microscopy structures of human V-ATPase in three rotational states at up to 2.9-Å resolution. Aided by mass spectrometry, we build all known protein subunits with associated N-linked glycans and identify glycolipids and phospholipids in the Vo complex. We define ATP6AP1 as a structural hub for Vo complex assembly because it connects to multiple Vo subunits and phospholipids in the c-ring. The glycolipids and the glycosylated Vo subunits form a luminal glycan coat critical for V-ATPase folding, localization, and stability. This study identifies mechanisms of V-ATPase assembly and biogenesis that rely on the integrated roles of ATP6AP1, glycans, and lipids.
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Affiliation(s)
- Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Tian-Min Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA.
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26
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Yang JH, Williams D, Kandiah E, Fromme P, Chiu PL. Structural basis of redox modulation on chloroplast ATP synthase. Commun Biol 2020; 3:482. [PMID: 32879423 PMCID: PMC7468127 DOI: 10.1038/s42003-020-01221-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/06/2020] [Indexed: 12/26/2022] Open
Abstract
In higher plants, chloroplast ATP synthase has a unique redox switch on its γ subunit that modulates enzyme activity to limit ATP hydrolysis at night. To understand the molecular details of the redox modulation, we used single-particle cryo-EM to determine the structures of spinach chloroplast ATP synthase in both reduced and oxidized states. The disulfide linkage of the oxidized γ subunit introduces a torsional constraint to stabilize the two β hairpin structures. Once reduced, free cysteines alleviate this constraint, resulting in a concerted motion of the enzyme complex and a smooth transition between rotary states to facilitate the ATP synthesis. We added an uncompetitive inhibitor, tentoxin, in the reduced sample to limit the flexibility of the enzyme and obtained high-resolution details. Our cryo-EM structures provide mechanistic insight into the redox modulation of the energy regulation activity of chloroplast ATP synthase. Jay-How Yang et al. use single-particle cryo-EM to determine the structures of spinach chloroplast ATP synthase in reduced and oxidized states. They report a torsional constraint in the oxidized γ subunit that is alleviated by free cysteines in the reduced state. Their work provides mechanistic insights into the redox modulation of the ATP synthesis by the chloroplast ATP synthase.
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Affiliation(s)
- Jay-How Yang
- Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dewight Williams
- Eyring Materials Center, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Petra Fromme
- Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, Tempe, AZ, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
| | - Po-Lin Chiu
- Center for Applied Structural Discovery (CASD), Biodesign Institute, Arizona State University, Tempe, AZ, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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27
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Su X, Dautant A, Godard F, Bouhier M, Zoladek T, Kucharczyk R, di Rago JP, Tribouillard-Tanvier D. Molecular Basis of the Pathogenic Mechanism Induced by the m.9191T>C Mutation in Mitochondrial ATP6 Gene. Int J Mol Sci 2020; 21:ijms21145083. [PMID: 32708436 PMCID: PMC7404254 DOI: 10.3390/ijms21145083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022] Open
Abstract
Probing the pathogenicity and functional consequences of mitochondrial DNA (mtDNA) mutations from patient’s cells and tissues is difficult due to genetic heteroplasmy (co-existence of wild type and mutated mtDNA in cells), occurrence of numerous mtDNA polymorphisms, and absence of methods for genetically transforming human mitochondria. Owing to its good fermenting capacity that enables survival to loss-of-function mtDNA mutations, its amenability to mitochondrial genome manipulation, and lack of heteroplasmy, Saccharomyces cerevisiae is an excellent model for studying and resolving the molecular bases of human diseases linked to mtDNA in a controlled genetic background. Using this model, we previously showed that a pathogenic mutation in mitochondrial ATP6 gene (m.9191T>C), that converts a highly conserved leucine residue into proline in human ATP synthase subunit a (aL222P), severely compromises the assembly of yeast ATP synthase and reduces by 90% the rate of mitochondrial ATP synthesis. Herein, we report the isolation of intragenic suppressors of this mutation. In light of recently described high resolution structures of ATP synthase, the results indicate that the m.9191T>C mutation disrupts a four α-helix bundle in subunit a and that the leucine residue it targets indirectly optimizes proton conduction through the membrane domain of ATP synthase.
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Affiliation(s)
- Xin Su
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - Alain Dautant
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - François Godard
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - Marine Bouhier
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (T.Z.); (R.K.)
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; (T.Z.); (R.K.)
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
| | - Déborah Tribouillard-Tanvier
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France; (X.S.); (A.D.); (F.G.); (M.B.); (J.-P.d.R.)
- Correspondence:
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28
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Kishikawa JI, Nakanishi A, Furuta A, Kato T, Namba K, Tamakoshi M, Mitsuoka K, Yokoyama K. Mechanical inhibition of isolated V o from V/A-ATPase for proton conductance. eLife 2020; 9:56862. [PMID: 32639230 PMCID: PMC7367684 DOI: 10.7554/elife.56862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V1 domain, with proton flow through the Vo membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V1 domain, the Vo domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the Vo domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and isolated Vo at near-atomic resolution, respectively. These structures clarify how the isolated Vo domain adopts the auto-inhibited form and how the holo complex prevents formation of the inhibited Vo form.
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Affiliation(s)
- Jun-Ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Institute for Protein Research, Osaka University, Suita, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Research Center for Ultra-High Voltage Electron Microscopy, Mihogaoka, Osaka, Japan
| | - Aya Furuta
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Suita, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, Suita, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Research Center for Ultra-High Voltage Electron Microscopy, Mihogaoka, Osaka, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
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29
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Waltz F, Corre N, Hashem Y, Giegé P. Specificities of the plant mitochondrial translation apparatus. Mitochondrion 2020; 53:30-37. [PMID: 32334144 DOI: 10.1016/j.mito.2020.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 12/16/2022]
Abstract
Mitochondria are endosymbiotic organelles responsible for energy production in most eukaryotic cells. They host a genome and a fully functional gene expression machinery. In plants this machinery involves hundreds of pentatricopeptide repeat (PPR) proteins. Translation, the final step of mitochondrial gene expression is performed by mitochondrial ribosomes (mitoribosomes). The nature of these molecular machines remained elusive for a very long time. Because of their bacterial origin, it was expected that mitoribosomes would closely resemble bacterial ribosomes. However, recent advances in cryo-electron microscopy have revealed the extraordinary diversity of mitoribosome structure and composition. The plant mitoribosome was characterized for Arabidopsis. In plants, in contrast to other species such as mammals and kinetoplastids where rRNA has been largely reduced, the mitoribosome could be described as a protein/RNA-augmented bacterial ribosome. It has an oversized small subunit formed by expanded ribosomal RNAs and additional protein components when compared to bacterial ribosomes. The same holds true for the large subunit. The small subunit is characterized by a new elongated domain on the head. Among its additional proteins, several PPR proteins are core mitoribosome proteins. They mainly act at the structural level to stabilize and maintain the plant-specific ribosomal RNA expansions but could also be involved in translation initiation. Recent advances in plant mitoribosome composition and structure, its specialization for membrane protein synthesis, translation initiation, the regulation and dynamics of mitochondrial translation are reviewed here and put in perspective with the diversity of mitochondrial translation processes in the green lineage and in the wider context of eukaryote evolution.
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Affiliation(s)
- Florent Waltz
- Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, F 33600 Pessac, France
| | - Nicolas Corre
- Institut de biologie de moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, F 67084 Strasbourg, France
| | - Yaser Hashem
- Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, F 33600 Pessac, France
| | - Philippe Giegé
- Institut de biologie de moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, F 67084 Strasbourg, France.
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30
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Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science 2020; 365:365/6455/eaaw9144. [PMID: 31439765 DOI: 10.1126/science.aaw9144] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022]
Abstract
V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the rotary-catalysis mechanism. They belong to the V-type ATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthases in overall architecture. We solved cryo-electron microscopy structures of the intact Thermus thermophilus V/A-ATPase, reconstituted into lipid nanodiscs, in three rotational states and two substates. These structures indicate substantial flexibility between V1 and Vo in a working enzyme, which results from mechanical competition between central shaft rotation and resistance from the peripheral stalks. We also describe details of adenosine diphosphate inhibition release, V1-Vo torque transmission, and proton translocation, which are relevant for the entire V-type ATPase family.
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Affiliation(s)
- Long Zhou
- Institute of Science and Technology Austria, Klosterneuberg 3400, Austria
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Klosterneuberg 3400, Austria.
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31
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Decoupling Filamentous Phage Uptake and Energy of the TolQRA Motor in Escherichia coli. J Bacteriol 2020; 202:JB.00428-19. [PMID: 31636109 DOI: 10.1128/jb.00428-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Filamentous phages are nonlytic viruses that specifically infect bacteria, establishing a persistent association with their host. The phage particle has no machinery for generating energy and parasitizes its host's existing structures in order to cross the bacterial envelope and deliver its genetic material. The import of filamentous phages across the bacterial periplasmic space requires some of the components of a macrocomplex of the envelope known as the Tol system. This complex uses the energy provided by the proton motive force (pmf) of the inner membrane to perform essential and highly energy-consuming functions of the cell, such as envelope integrity maintenance and cell division. It has been suggested that phages take advantage of pmf-driven conformational changes in the Tol system to transit across the periplasm. However, this hypothesis has not been formally tested. In order to decouple the role of the Tol system in cell physiology and during phage parasitism, we used mutations on conserved essential residues known for inactivating pmf-dependent functions of the Tol system. We identified impaired Tol complexes that remain fully efficient for filamentous phage uptake. We further demonstrate that the TolQ-TolR homologous motor ExbB-ExbD, normally operating with the TonB protein, is able to promote phage infection along with full-length TolA.IMPORTANCE Filamentous phages are widely distributed symbionts of Gram-negative bacteria, with some of them being linked to genome evolution and virulence of their host. However, the precise mechanism that permits their uptake across the cell envelope is poorly understood. The canonical phage model Fd requires the TolQRA protein complex in the host envelope, which is suspected to translocate protons across the inner membrane. In this study, we show that phage uptake proceeds in the presence of the assembled but nonfunctional TolQRA complex. Moreover, our results unravel an alternative route for phage import that relies on the ExbB-ExbD proteins. This work provides new insights into the fundamental mechanisms of phage infection and might be generalized to other filamentous phages responsible for pathogen emergence.
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32
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Raven JA, Beardall J, Quigg A. Light-Driven Oxygen Consumption in the Water-Water Cycles and Photorespiration, and Light Stimulated Mitochondrial Respiration. PHOTOSYNTHESIS IN ALGAE: BIOCHEMICAL AND PHYSIOLOGICAL MECHANISMS 2020. [DOI: 10.1007/978-3-030-33397-3_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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33
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Novitskaia O, Buslaev P, Gushchin I. Assembly of Spinach Chloroplast ATP Synthase Rotor Ring Protein-Lipid Complex. Front Mol Biosci 2019; 6:135. [PMID: 31850368 PMCID: PMC6896225 DOI: 10.3389/fmolb.2019.00135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/13/2019] [Indexed: 11/19/2022] Open
Abstract
Rotor ATPases are large multisubunit membrane protein complexes found in all kingdoms of life. The membrane parts of these ATPases include a ring-like assembly, so-called c-ring, consisting of several subunits c, plugged by a patch of phospholipids. In this report, we use a nature-inspired approach to model the assembly of the spinach (Spinacia oleracea) c14 ring protein-lipid complex, where partially assembled oligomers are pulled toward each other using a biasing potential. The resulting assemblies contain 23 to 26 encapsulated plug lipids, general position of which corresponds well to experimental maps. However, best fit to experimental data is achieved with 15 to 17 lipids inside the c-ring. In all of the simulations, the lipids from one leaflet (loop side of the c subunit) are ordered and static, whereas the lipids from the other leaflet are disordered and dynamic. Spontaneous permeation of water molecules toward Glu61 at the active site is also observed. The presented assembly approach is expected to be generalizable to other protein complexes with encapsulated lipid patches.
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Affiliation(s)
- Olga Novitskaia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Pavel Buslaev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Nanoscience Center, Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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34
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Du B, Liu G, Ke M, Zhang Z, Zheng M, Lu T, Sun L, Qian H. Proteomic analysis of the hepatotoxicity of Microcystis aeruginosa in adult zebrafish (Danio rerio) and its potential mechanisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113019. [PMID: 31419664 DOI: 10.1016/j.envpol.2019.113019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 08/03/2019] [Accepted: 08/03/2019] [Indexed: 06/10/2023]
Abstract
Microcystis aeruginosa is one of the main species of cyanobacteria that causes water blooms. M. aeruginosa can release into the water several types of microcystins (MCs), which are harmful to aquatic organisms and even humans. However, few studies have investigated the hepatotoxicity of M. aeruginosa itself in zebrafish in environments that simulate natural aquatic systems. The objective of this study was to evaluate the hepatotoxicity of M. aeruginosa in adult zebrafish (Danio rerio) after short-term (96 h) exposure and to elucidate the potential underlying mechanisms. Distinct histological changes in the liver, such as enlargement of the peripheral nuclei and sinusoids and the appearance of fibroblasts, were observed in zebrafish grown in M. aeruginosa culture. In addition, antioxidant enzyme activity was activated and protein phosphatase (PP) activity was significantly decreased with increasing microalgal density. A proteomic analysis revealed alterations in a number of protein pathways, including ribosome translation, immune response, energy metabolism and oxidative phosphorylation pathways. Western blot and real-time PCR analyses confirmed the results of the proteomic analysis. All results indicated that M. aeruginosa could disrupt hepatic functions in adult zebrafish, thus highlighting the necessity of ecotoxicity assessments for M. aeruginosa at environmentally relevant densities.
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Affiliation(s)
- Benben Du
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Guangfu Liu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Meng Zheng
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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35
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Kamariah N, Huber RG, Nartey W, Bhushan S, Bond PJ, Grüber G. Structure and subunit arrangement of Mycobacterial F1FO ATP synthase and novel features of the unique mycobacterial subunit δ. J Struct Biol 2019; 207:199-208. [DOI: 10.1016/j.jsb.2019.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
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36
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Gu J, Zhang L, Zong S, Guo R, Liu T, Yi J, Wang P, Zhuo W, Yang M. Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1. Science 2019; 364:1068-1075. [PMID: 31197009 DOI: 10.1126/science.aaw4852] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 05/23/2019] [Indexed: 12/26/2022]
Abstract
The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom resolution using a single-particle cryo-electron microscopy method. Two classical V-shaped ATP synthase dimers lie antiparallel to each other to form an H-shaped ATP synthase tetramer, as viewed from the matrix. ATP synthase inhibitory factor subunit 1 (IF1) is a well-known in vivo inhibitor of mammalian ATP synthase at low pH. Two IF1 dimers link two ATP synthase dimers, which is consistent with the ATP synthase tetramer adopting an inhibited state. Within the tetramer, we refined structures of intact ATP synthase in two different rotational conformations at 3.34- and 3.45-Å resolution.
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Affiliation(s)
- Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuai Zong
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingbo Yi
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peiyi Wang
- SUSTech Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei Zhuo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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37
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Mitochondrial F-ATP Synthase and Its Transition into an Energy-Dissipating Molecular Machine. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:8743257. [PMID: 31178976 PMCID: PMC6501240 DOI: 10.1155/2019/8743257] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/18/2019] [Indexed: 01/27/2023]
Abstract
The mitochondrial F-ATP synthase is the principal energy-conserving nanomotor of cells that harnesses the proton motive force generated by the respiratory chain to make ATP from ADP and phosphate in a process known as oxidative phosphorylation. In the energy-converting membranes, F-ATP synthase is a multisubunit complex organized into a membrane-extrinsic F1 sector and a membrane-intrinsic FO domain, linked by central and peripheral stalks. Due to its essential role in the cellular metabolism, malfunction of F-ATP synthase has been associated with a variety of pathological conditions, and the enzyme is now considered as a promising drug target for multiple disease conditions and for the regulation of energy metabolism. We discuss structural and functional features of mitochondrial F-ATP synthase as well as several conditions that partially or fully inhibit the coupling between the F1 catalytic activities and the FO proton translocation, thus decreasing the cellular metabolic efficiency and transforming the enzyme into an energy-dissipating structure through molecular mechanisms that still remain to be defined.
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38
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Scheckhuber CQ. Studying the mechanisms and targets of glycation and advanced glycation end-products in simple eukaryotic model systems. Int J Biol Macromol 2019; 127:85-94. [DOI: 10.1016/j.ijbiomac.2019.01.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 12/20/2022]
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Sielaff H, Yanagisawa S, Frasch WD, Junge W, Börsch M. Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases. Molecules 2019; 24:E504. [PMID: 30704145 PMCID: PMC6384691 DOI: 10.3390/molecules24030504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
| | - Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wolfgang Junge
- Department of Biology & Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
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Applications of In-Cell NMR in Structural Biology and Drug Discovery. Int J Mol Sci 2019; 20:ijms20010139. [PMID: 30609728 PMCID: PMC6337603 DOI: 10.3390/ijms20010139] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/24/2018] [Accepted: 12/29/2018] [Indexed: 01/23/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) is a method to provide the structural information of a target at an atomic level under physiological conditions and a full view of the conformational changes of a protein caused by ligand binding, post-translational modifications or protein⁻protein interactions in living cells. Previous in-cell NMR studies have focused on proteins that were overexpressed in bacterial cells and isotopically labeled proteins injected into oocytes of Xenopus laevis or delivered into human cells. Applications of in-cell NMR in probing protein modifications, conformational changes and ligand bindings have been carried out in mammalian cells by monitoring isotopically labeled proteins overexpressed in living cells. The available protocols and successful examples encourage wide applications of this technique in different fields such as drug discovery. Despite the challenges in this method, progress has been made in recent years. In this review, applications of in-cell NMR are summarized. The successful applications of this method in mammalian and bacterial cells make it feasible to play important roles in drug discovery, especially in the step of target engagement.
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