1
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Djurabekova A, Lasham J, Zdorevskyi O, Zickermann V, Sharma V. Long-range electron proton coupling in respiratory complex I - insights from molecular simulations of the quinone chamber and antiporter-like subunits. Biochem J 2024; 481:499-514. [PMID: 38572757 DOI: 10.1042/bcj20240009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
Respiratory complex I is a redox-driven proton pump. Several high-resolution structures of complex I have been determined providing important information about the putative proton transfer paths and conformational transitions that may occur during catalysis. However, how redox energy is coupled to the pumping of protons remains unclear. In this article, we review biochemical, structural and molecular simulation data on complex I and discuss several coupling models, including the key unresolved mechanistic questions. Focusing both on the quinone-reductase domain as well as the proton-pumping membrane-bound domain of complex I, we discuss a molecular mechanism of proton pumping that satisfies most experimental and theoretical constraints. We suggest that protonation reactions play an important role not only in catalysis, but also in the physiologically-relevant active/deactive transition of complex I.
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Affiliation(s)
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, Helsinki, Finland
| | | | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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2
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Agip ANA, Chung I, Sanchez-Martinez A, Whitworth AJ, Hirst J. Cryo-EM structures of mitochondrial respiratory complex I from Drosophila melanogaster. eLife 2023; 12:e84424. [PMID: 36622099 PMCID: PMC9977279 DOI: 10.7554/elife.84424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. Drosophila melanogaster is a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I from Drosophila and determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of the Drosophila enzyme is the mammalian-type 'ready-to-go' active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type 'deactive' pronounced resting state is not observed: in two minor states, the ubiquinone-binding site is unchanged, but a deactive-type π-bulge is present in ND6-TMH3. Our detailed structural knowledge of Drosophila complex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology.
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Affiliation(s)
- Ahmed-Noor A Agip
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Injae Chung
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Alvaro Sanchez-Martinez
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Alexander J Whitworth
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Judy Hirst
- The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical CampusCambridgeUnited Kingdom
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3
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Maldonado M, Fan Z, Abe KM, Letts JA. Plant-specific features of respiratory supercomplex I + III 2 from Vigna radiata. NATURE PLANTS 2023; 9:157-168. [PMID: 36581760 PMCID: PMC9873571 DOI: 10.1038/s41477-022-01306-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/08/2022] [Indexed: 05/07/2023]
Abstract
The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I-V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III2 from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III2 relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III2's mitochondrial processing peptidase domain and no participation of complex I's bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme's two arms, limiting large-scale conformational changes. Moreover, complex I's catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata, the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III2. Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.
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Affiliation(s)
- M Maldonado
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
- Department of Plant Biology, University of California, Davis, CA, USA.
| | - Z Fan
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - K M Abe
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - J A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
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4
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Wang S, Kang Y, Wang R, Deng J, Yu Y, Yu J, Wang J. Emerging Roles of NDUFS8 Located in Mitochondrial Complex I in Different Diseases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248754. [PMID: 36557887 PMCID: PMC9783039 DOI: 10.3390/molecules27248754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
NADH:ubiquinone oxidoreductase core subunit S8 (NDUFS8) is an essential core subunit and component of the iron-sulfur (FeS) fragment of mitochondrial complex I directly involved in the electron transfer process and energy metabolism. Pathogenic variants of the NDUFS8 are relevant to infantile-onset and severe diseases, including Leigh syndrome, cancer, and diabetes mellitus. With over 1000 nuclear genes potentially causing a mitochondrial disorder, the current diagnostic approach requires targeted molecular analysis, guided by a combination of clinical and biochemical features. Currently, there are only several studies on pathogenic variants of the NDUFS8 in Leigh syndrome, and a lack of literature on its precise mechanism in cancer and diabetes mellitus exists. Therefore, NDUFS8-related diseases should be extensively explored and precisely diagnosed at the molecular level with the application of next-generation sequencing technologies. A more distinct comprehension will be needed to shed light on NDUFS8 and its related diseases for further research. In this review, a comprehensive summary of the current knowledge about NDUFS8 structural function, its pathogenic mutations in Leigh syndrome, as well as its underlying roles in cancer and diabetes mellitus is provided, offering potential pathogenesis, progress, and therapeutic target of different diseases. We also put forward some problems and solutions for the following investigations.
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Affiliation(s)
- Sifan Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
- Xiangya School of Medicine, Central South University, Changsha 410013, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuanbo Kang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
- Xiangya School of Medicine, Central South University, Changsha 410013, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Ruifeng Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
| | - Junqi Deng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
| | - Yupei Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
| | - Jun Yu
- Department of Neurology, Third Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (J.Y.); (J.W.); Tel./Fax: +86-731-84805411 (J.W.)
| | - Junpu Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, China; (S.W.); (Y.K.); (R.W.); (J.D.); (Y.Y.)
- Department of Pathology, School of Basic Medicine, Central South University, Changsha 410008, China
- Xiangya School of Medicine, Central South University, Changsha 410013, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (J.Y.); (J.W.); Tel./Fax: +86-731-84805411 (J.W.)
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5
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Chung I, Grba DN, Wright JJ, Hirst J. Making the leap from structure to mechanism: are the open states of mammalian complex I identified by cryoEM resting states or catalytic intermediates? Curr Opin Struct Biol 2022; 77:102447. [PMID: 36087446 PMCID: PMC7614202 DOI: 10.1016/j.sbi.2022.102447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/07/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
Respiratory complex I (NADH:ubiquinone oxidoreductase) is a multi-subunit, energy-transducing mitochondrial enzyme that is essential for oxidative phosphorylation and regulating NAD+/NADH pools. Despite recent advances in structural knowledge and a long history of biochemical analyses, the mechanism of redox-coupled proton translocation by complex I remains unknown. Due to its ability to separate molecules in a mixed population into distinct classes, single-particle electron cryomicroscopy has enabled identification and characterisation of different complex I conformations. However, deciding on their catalytic and/or regulatory properties to underpin mechanistic hypotheses, especially without detailed biochemical characterisation of the structural samples, has proven challenging. In this review we explore different mechanistic interpretations of the closed and open states identified in cryoEM analyses of mammalian complex I.
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Affiliation(s)
- Injae Chung
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Daniel N Grba
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - John J Wright
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.
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6
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Laube E, Meier-Credo J, Langer JD, Kühlbrandt W. Conformational changes in mitochondrial complex I of the thermophilic eukaryote Chaetomium thermophilum. SCIENCE ADVANCES 2022; 8:eadc9952. [PMID: 36427319 PMCID: PMC9699679 DOI: 10.1126/sciadv.adc9952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/07/2022] [Indexed: 05/23/2023]
Abstract
Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the thermophilic fungus Chaetomium thermophilum, determined by cryoEM up to 2.4-Å resolution. We show that the complex undergoes a transition between two conformations, which we refer to as state 1 and state 2. The conformational switch is manifest in a twisting movement of the peripheral arm relative to the membrane arm, but most notably in substantial rearrangements of the Q-binding cavity and the E-channel, resulting in a continuous aqueous passage from the E-channel to subunit ND5 at the far end of the membrane arm. The conformational changes in the complex interior resemble those reported for mammalian complex I, suggesting a highly conserved, universal mechanism of coupling electron transport to proton pumping.
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Affiliation(s)
- Eike Laube
- Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
| | - Jakob Meier-Credo
- Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
- Max-Planck-Institute for Brain Research, Frankfurt 60438, Germany
| | - Julian D. Langer
- Max-Planck-Institute of Biophysics, Frankfurt 60438, Germany
- Max-Planck-Institute for Brain Research, Frankfurt 60438, Germany
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7
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Effect of metformin on intact mitochondria from liver and brain: Concept revisited. Eur J Pharmacol 2022; 931:175177. [DOI: 10.1016/j.ejphar.2022.175177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/07/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022]
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8
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Meyer EH, Letts JA, Maldonado M. Structural insights into the assembly and the function of the plant oxidative phosphorylation system. THE NEW PHYTOLOGIST 2022; 235:1315-1329. [PMID: 35588181 DOI: 10.1111/nph.18259] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/05/2022] [Indexed: 05/23/2023]
Abstract
One of the key functions of mitochondria is the production of ATP to support cellular metabolism and growth. The last step of mitochondrial ATP synthesis is performed by the oxidative phosphorylation (OXPHOS) system, an ensemble of protein complexes embedded in the inner mitochondrial membrane. In the last 25 yr, many structures of OXPHOS complexes and supercomplexes have been resolved in yeast, mammals, and bacteria. However, structures of plant OXPHOS enzymes only became available very recently. In this review, we highlight the plant-specific features revealed by the recent structures and discuss how they advance our understanding of the function and assembly of plant OXPHOS complexes. We also propose new hypotheses to be tested and discuss older findings to be re-evaluated. Further biochemical and structural work on the plant OXPHOS system will lead to a deeper understanding of plant respiration and its regulation, with significant agricultural, environmental, and societal implications.
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Affiliation(s)
- Etienne H Meyer
- Institute of Plant Physiology, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, 06120, Halle (Saale), Germany
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Maria Maldonado
- Department of Molecular and Cellular Biology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
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9
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Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. Curr Opin Struct Biol 2022; 74:102350. [PMID: 35316665 PMCID: PMC7613608 DOI: 10.1016/j.sbi.2022.102350] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/25/2022] [Accepted: 02/08/2022] [Indexed: 11/26/2022]
Abstract
Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I.
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10
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Burger N, James AM, Mulvey JF, Hoogewijs K, Ding S, Fearnley IM, Loureiro-López M, Norman AAI, Arndt S, Mottahedin A, Sauchanka O, Hartley RC, Krieg T, Murphy MP. ND3 Cys39 in complex I is exposed during mitochondrial respiration. Cell Chem Biol 2022; 29:636-649.e14. [PMID: 34739852 PMCID: PMC9076552 DOI: 10.1016/j.chembiol.2021.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/21/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Mammalian complex I can adopt catalytically active (A-) or deactive (D-) states. A defining feature of the reversible transition between these two defined states is thought to be exposure of the ND3 subunit Cys39 residue in the D-state and its occlusion in the A-state. As the catalytic A/D transition is important in health and disease, we set out to quantify it by measuring Cys39 exposure using isotopic labeling and mass spectrometry, in parallel with complex I NADH/CoQ oxidoreductase activity. To our surprise, we found significant Cys39 exposure during NADH/CoQ oxidoreductase activity. Furthermore, this activity was unaffected if Cys39 alkylation occurred during complex I-linked respiration. In contrast, alkylation of catalytically inactive complex I irreversibly blocked the reactivation of NADH/CoQ oxidoreductase activity by NADH. Thus, Cys39 of ND3 is exposed in complex I during mitochondrial respiration, with significant implications for our understanding of the A/D transition and the mechanism of complex I.
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Affiliation(s)
- Nils Burger
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Andrew M James
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - John F Mulvey
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Kurt Hoogewijs
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; Medical Research Council-Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Shujing Ding
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ian M Fearnley
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Marta Loureiro-López
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | | | - Sabine Arndt
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Amin Mottahedin
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Olga Sauchanka
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | | | - Thomas Krieg
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Michael P Murphy
- Medical Research Council-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
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11
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Wright JJ, Biner O, Chung I, Burger N, Bridges HR, Hirst J. Reverse Electron Transfer by Respiratory Complex I Catalyzed in a Modular Proteoliposome System. J Am Chem Soc 2022; 144:6791-6801. [PMID: 35380814 PMCID: PMC9026280 DOI: 10.1021/jacs.2c00274] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Indexed: 02/02/2023]
Abstract
Respiratory complex I is an essential metabolic enzyme that uses the energy from NADH oxidation and ubiquinone reduction to translocate protons across an energy transducing membrane and generate the proton motive force for ATP synthesis. Under specific conditions, complex I can also catalyze the reverse reaction, Δp-linked oxidation of ubiquinol to reduce NAD+ (or O2), known as reverse electron transfer (RET). Oxidative damage by reactive oxygen species generated during RET underpins ischemia reperfusion injury, but as RET relies on several converging metabolic pathways, little is known about its mechanism or regulation. Here, we demonstrate Δp-linked RET through complex I in a synthetic proteoliposome system for the first time, enabling complete kinetic characterization of RET catalysis. We further establish the capability of our system by showing how RET in the mammalian enzyme is regulated by the active-deactive transition and by evaluating RET by complex I from several species in which direct assessment has not been otherwise possible. We thus provide new insights into the reversibility of complex I catalysis, an important but little understood mechanistic and physiological feature.
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Affiliation(s)
- John J. Wright
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | | | - Injae Chung
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | | | - Hannah R. Bridges
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
| | - Judy Hirst
- Medical Research Council
Mitochondrial Biology Unit, University of
Cambridge, Cambridge CB2 0XY, U.K.
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12
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Zhou L, Maldonado M, Padavannil A, Guo F, Letts JA. Structures of Tetrahymena's respiratory chain reveal the diversity of eukaryotic core metabolism. Science 2022; 376:831-839. [PMID: 35357889 DOI: 10.1126/science.abn7747] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate Tetrahymena thermophila (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt-complex I (CI) and Tt-CIII2 (Tt-SC I+III2) and a structure of Tt-CIV2. Tt-SC I+III2 (~2.3 MDa) is a curved assembly with structural and functional symmetry breaking. Tt-CIV2 is a ~2.7 MDa dimer with over 52 subunits per protomer, including mitochondrial carriers and a TIM83-TIM133-like domain. Our structural and functional study of the T. thermophila respiratory chain reveals divergence in key components of eukaryotic respiration, expanding our understanding of core metabolism.
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Affiliation(s)
- Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - María Maldonado
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Fei Guo
- BIOEM Facility, University of California, Davis, CA 95616, USA
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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13
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Padavannil A, Ayala-Hernandez MG, Castellanos-Silva EA, Letts JA. The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I. Front Mol Biosci 2022; 8:798353. [PMID: 35047558 PMCID: PMC8762328 DOI: 10.3389/fmolb.2021.798353] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023] Open
Abstract
Complex I (CI) is the largest protein complex in the mitochondrial oxidative phosphorylation electron transport chain of the inner mitochondrial membrane and plays a key role in the transport of electrons from reduced substrates to molecular oxygen. CI is composed of 14 core subunits that are conserved across species and an increasing number of accessory subunits from bacteria to mammals. The fact that adding accessory subunits incurs costs of protein production and import suggests that these subunits play important physiological roles. Accordingly, knockout studies have demonstrated that accessory subunits are essential for CI assembly and function. Furthermore, clinical studies have shown that amino acid substitutions in accessory subunits lead to several debilitating and fatal CI deficiencies. Nevertheless, the specific roles of CI’s accessory subunits have remained mysterious. In this review, we explore the possible roles of each of mammalian CI’s 31 accessory subunits by integrating recent high-resolution CI structures with knockout, assembly, and clinical studies. Thus, we develop a framework of experimentally testable hypotheses for the function of the accessory subunits. We believe that this framework will provide inroads towards the complete understanding of mitochondrial CI physiology and help to develop strategies for the treatment of CI deficiencies.
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Affiliation(s)
- Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Maria G Ayala-Hernandez
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Eimy A Castellanos-Silva
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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14
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Parey K, Lasham J, Mills DJ, Djurabekova A, Haapanen O, Yoga EG, Xie H, Kühlbrandt W, Sharma V, Vonck J, Zickermann V. High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism. SCIENCE ADVANCES 2021; 7:eabj3221. [PMID: 34767441 PMCID: PMC8589321 DOI: 10.1126/sciadv.abj3221] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/24/2021] [Indexed: 05/23/2023]
Abstract
Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined, but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1-Å resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which ~100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4-Å resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamic simulations, we define details of the proton translocation pathways and offer insights into the redox-coupled proton pumping mechanism of complex I.
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Affiliation(s)
- Kristian Parey
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Jonathan Lasham
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Deryck J. Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Amina Djurabekova
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Outi Haapanen
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
| | - Etienne Galemou Yoga
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
| | - Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Vivek Sharma
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland
- HiLIFE Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
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15
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Ansari F, Yoval-Sánchez B, Niatsetskaya Z, Sosunov S, Stepanova A, Garcia C, Owusu-Ansah E, Ten V, Wittig I, Galkin A. Quantification of NADH:ubiquinone oxidoreductase (complex I) content in biological samples. J Biol Chem 2021; 297:101204. [PMID: 34543622 PMCID: PMC8503622 DOI: 10.1016/j.jbc.2021.101204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 12/14/2022] Open
Abstract
Impairments in mitochondrial energy metabolism have been implicated in human genetic diseases associated with mitochondrial and nuclear DNA mutations, neurodegenerative and cardiovascular disorders, diabetes, and aging. Alteration in mitochondrial complex I structure and activity has been shown to play a key role in Parkinson's disease and ischemia/reperfusion tissue injury, but significant difficulty remains in assessing the content of this enzyme complex in a given sample. The present study introduces a new method utilizing native polyacrylamide gel electrophoresis in combination with flavin fluorescence scanning to measure the absolute content of complex I, as well as α-ketoglutarate dehydrogenase complex, in any preparation. We show that complex I content is 19 ± 1 pmol/mg of protein in the brain mitochondria, whereas varies up to 10-fold in different mouse tissues. Together with the measurements of NADH-dependent specific activity, our method also allows accurate determination of complex I catalytic turnover, which was calculated as 104 min-1 for NADH:ubiquinone reductase in mouse brain mitochondrial preparations. α-ketoglutarate dehydrogenase complex content was determined to be 65 ± 5 and 123 ± 9 pmol/mg protein for mouse brain and bovine heart mitochondria, respectively. Our approach can also be extended to cultured cells, and we demonstrated that about 90 × 103 complex I molecules are present in a single human embryonic kidney 293 cell. The ability to determine complex I content should provide a valuable tool to investigate the enzyme status in samples after in vivo treatment in mutant organisms, cells in culture, or human biopsies.
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Affiliation(s)
- Fariha Ansari
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Belem Yoval-Sánchez
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Zoya Niatsetskaya
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Sergey Sosunov
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Anna Stepanova
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Christian Garcia
- Department of Physiology & Cellular Biophysics, Columbia University, New York, New York, USA
| | - Edward Owusu-Ansah
- Department of Physiology & Cellular Biophysics, Columbia University, New York, New York, USA
| | - Vadim Ten
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany; German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt am Main, Germany
| | - Alexander Galkin
- Division of Neonatology, Department of Pediatrics, Columbia University Medical Center, New York, New York, USA; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA.
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16
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Accessory Subunits of the Matrix Arm of Mitochondrial Complex I with a Focus on Subunit NDUFS4 and Its Role in Complex I Function and Assembly. Life (Basel) 2021; 11:life11050455. [PMID: 34069703 PMCID: PMC8161149 DOI: 10.3390/life11050455] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/19/2022] Open
Abstract
NADH:ubiquinone-oxidoreductase (complex I) is the largest membrane protein complex of the respiratory chain. Complex I couples electron transfer to vectorial proton translocation across the inner mitochondrial membrane. The L shaped structure of complex I is divided into a membrane arm and a matrix arm. Fourteen central subunits are conserved throughout species, while some 30 accessory subunits are typically found in eukaryotes. Complex I dysfunction is associated with mutations in the nuclear and mitochondrial genome, resulting in a broad spectrum of neuromuscular and neurodegenerative diseases. Accessory subunit NDUFS4 in the matrix arm is a hot spot for mutations causing Leigh or Leigh-like syndrome. In this review, we focus on accessory subunits of the matrix arm and discuss recent reports on the function of accessory subunit NDUFS4 and its interplay with NDUFS6, NDUFA12, and assembly factor NDUFAF2 in complex I assembly.
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17
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Di Luca A, Kaila VRI. Molecular strain in the active/deactive-transition modulates domain coupling in respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148382. [PMID: 33513365 DOI: 10.1016/j.bbabio.2021.148382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/08/2021] [Accepted: 01/21/2021] [Indexed: 12/14/2022]
Abstract
Complex I functions as a primary redox-driven proton pump in aerobic respiratory chains, establishing a proton motive force that powers ATP synthesis and active transport. Recent cryo-electron microscopy (cryo-EM) experiments have resolved the mammalian complex I in the biomedically relevant active (A) and deactive (D) states (Zhu et al., 2016; Fiedorczuk et al., 2016; Agip et al., 2018 [1-3]) that could regulate enzyme turnover, but it still remains unclear how the conformational state and activity are linked. We show here how global motion along the A/D transition accumulates molecular strain at specific coupling regions important for both redox chemistry and proton pumping. Our data suggest that the A/D motion modulates force propagation pathways between the substrate-binding site and the proton pumping machinery that could alter electrostatic and conformational coupling across large distances. Our findings provide a molecular basis to understand how global protein dynamics can modulate the biological activity of large molecular complexes.
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Affiliation(s)
- Andrea Di Luca
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden.
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18
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Grivennikova VG, Gladyshev GV, Vinogradov AD. Deactivation of mitochondrial NADH:ubiquinone oxidoreductase (respiratory complex I): Extrinsically affecting factors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148207. [DOI: 10.1016/j.bbabio.2020.148207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/13/2020] [Accepted: 04/14/2020] [Indexed: 12/14/2022]
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19
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Parey K, Wirth C, Vonck J, Zickermann V. Respiratory complex I - structure, mechanism and evolution. Curr Opin Struct Biol 2020; 63:1-9. [PMID: 32058886 DOI: 10.1016/j.sbi.2020.01.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Respiratory complex I is an intricate multi-subunit membrane protein with a central function in aerobic energy metabolism. During the last years, structures of mitochondrial complex I and respiratory supercomplexes were determined by cryo-EM at increasing resolution. Structural and computational studies have shed light on the dynamics of proton translocation pathways, the interaction of complex I with lipids and the unusual access pathway of ubiquinone to the active site. Recent advances in understanding complex I function include characterization of specific conformational changes that are critical for proton pumping. Cryo-EM structures of the NADH dehydrogenase-like (NDH) complex of photosynthesis and a bacterial membrane bound hydrogenase (MBH) have provided a broader perspective on the complex I superfamily.
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Affiliation(s)
- Kristian Parey
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany; Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Christophe Wirth
- Institute of Biochemistry and Molecular Biology, ZBMZ, Medical Faculty, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany; Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany.
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20
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Parey K, Haapanen O, Sharma V, Köfeler H, Züllig T, Prinz S, Siegmund K, Wittig I, Mills DJ, Vonck J, Kühlbrandt W, Zickermann V. High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease. SCIENCE ADVANCES 2019; 5:eaax9484. [PMID: 31844670 PMCID: PMC6905873 DOI: 10.1126/sciadv.aax9484] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/22/2019] [Indexed: 05/23/2023]
Abstract
Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast Yarrowia lipolytica by electron cryo-microscopy at 3.2-Å resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane.
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Affiliation(s)
- Kristian Parey
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Outi Haapanen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Harald Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Simone Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Karin Siegmund
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, SFB815 Core Unit, Medical School, Goethe University, Frankfurt am Main, Germany
| | - Deryck J. Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
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21
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Galkin A. Brain Ischemia/Reperfusion Injury and Mitochondrial Complex I Damage. BIOCHEMISTRY (MOSCOW) 2019; 84:1411-1423. [DOI: 10.1134/s0006297919110154] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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22
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Kaila VRI. Long-range proton-coupled electron transfer in biological energy conversion: towards mechanistic understanding of respiratory complex I. J R Soc Interface 2019; 15:rsif.2017.0916. [PMID: 29643224 PMCID: PMC5938582 DOI: 10.1098/rsif.2017.0916] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/13/2018] [Indexed: 12/20/2022] Open
Abstract
Biological energy conversion is driven by efficient enzymes that capture, store and transfer protons and electrons across large distances. Recent advances in structural biology have provided atomic-scale blueprints of these types of remarkable molecular machinery, which together with biochemical, biophysical and computational experiments allow us to derive detailed energy transduction mechanisms for the first time. Here, I present one of the most intricate and least understood types of biological energy conversion machinery, the respiratory complex I, and how its redox-driven proton-pump catalyses charge transfer across approximately 300 Å distances. After discussing the functional elements of complex I, a putative mechanistic model for its action-at-a-distance effect is presented, and functional parallels are drawn to other redox- and light-driven ion pumps.
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Affiliation(s)
- Ville R I Kaila
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, Garching, Germany
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23
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Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps. Nat Commun 2018; 9:4500. [PMID: 30374105 PMCID: PMC6206036 DOI: 10.1038/s41467-018-06955-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023] Open
Abstract
Complex I (proton-pumping NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain and a significant source of reactive oxygen species (ROS). We hypothesized that during energy conversion by complex I, electron transfer onto ubiquinone triggers the concerted rearrangement of three protein loops of subunits ND1, ND3, and 49-kDa thereby generating the power-stoke driving proton pumping. Here we show that fixing loop TMH1-2ND3 to the nearby subunit PSST via a disulfide bridge introduced by site-directed mutagenesis reversibly disengages proton pumping without impairing ubiquinone reduction, inhibitor binding or the Active/Deactive transition. The X-ray structure of mutant complex I indicates that the disulfide bridge immobilizes but does not displace the tip of loop TMH1-2ND3. We conclude that movement of loop TMH1-2ND3 located at the ubiquinone-binding pocket is required to drive proton pumping corroborating one of the central predictions of our model for the mechanism of energy conversion by complex I proposed earlier. Proton pumping of mitochondrial complex I depends on the reduction of ubiquinone but the molecular mechanism of energy conversion is unclear. Here, the authors provide structural and biochemical evidence showing that movement of loop TMH1-2 in complex I subunit ND3 is required to drive proton pumping.
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24
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Parey K, Brandt U, Xie H, Mills DJ, Siegmund K, Vonck J, Kühlbrandt W, Zickermann V. Cryo-EM structure of respiratory complex I at work. eLife 2018; 7:39213. [PMID: 30277212 PMCID: PMC6168287 DOI: 10.7554/elife.39213] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast Yarrowia lipolytica both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.
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Affiliation(s)
- Kristian Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, The Netherlands.,Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Hao Xie
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Karin Siegmund
- Medical School, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany
| | - Volker Zickermann
- Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany.,Medical School, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
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25
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Fiedorczuk K, Sazanov LA. Mammalian Mitochondrial Complex I Structure and Disease-Causing Mutations. Trends Cell Biol 2018; 28:835-867. [PMID: 30055843 DOI: 10.1016/j.tcb.2018.06.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 06/14/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022]
Abstract
Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.
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Affiliation(s)
- Karol Fiedorczuk
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria; Present address: The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria.
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26
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Di Luca A, Mühlbauer ME, Saura P, Kaila VRI. How inter-subunit contacts in the membrane domain of complex I affect proton transfer energetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:734-741. [PMID: 29883589 DOI: 10.1016/j.bbabio.2018.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/08/2018] [Accepted: 06/02/2018] [Indexed: 10/14/2022]
Abstract
The respiratory complex I is a redox-driven proton pump that employs the free energy released from quinone reduction to pump protons across its complete ca. 200 Å wide membrane domain. Despite recently resolved structures and molecular simulations, the exact mechanism for the proton transport process remains unclear. Here we combine large-scale molecular simulations with quantum chemical density functional theory (DFT) models to study how contacts between neighboring antiporter-like subunits in the membrane domain of complex I affect the proton transfer energetics. Our combined results suggest that opening of conserved Lys/Glu ion pairs within each antiporter-like subunit modulates the barrier for the lateral proton transfer reactions. Our work provides a mechanistic suggestion for key coupling effects in the long-range force propagation process of complex I.
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Affiliation(s)
- Andrea Di Luca
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching, D-85747, Germany
| | - Max E Mühlbauer
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching, D-85747, Germany
| | - Patricia Saura
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching, D-85747, Germany
| | - Ville R I Kaila
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, Garching, D-85747, Germany.
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27
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Global collective motions in the mammalian and bacterial respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:326-332. [DOI: 10.1016/j.bbabio.2018.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 01/12/2023]
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28
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Blaza JN, Vinothkumar KR, Hirst J. Structure of the Deactive State of Mammalian Respiratory Complex I. Structure 2018; 26:312-319.e3. [PMID: 29395787 PMCID: PMC5807054 DOI: 10.1016/j.str.2017.12.014] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/03/2017] [Accepted: 12/27/2017] [Indexed: 12/20/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, active complex I gradually enters a pronounced resting or deactive state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly active preparation of Bos taurus complex I into the biochemically defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4.1 Å resolution. We show that the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles. Preparation of mammalian complex I in the deactive state that forms during ischemia The structure of the deactive state determined using electron cryomicroscopy Improved particle densities and orientations obtained using PEGylated gold grids Localized unfolding around the quinone-binding site in the deactive state
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Affiliation(s)
- James N Blaza
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Kutti R Vinothkumar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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29
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Abstract
Mitochondria are the power stations of the eukaryotic cell, using the energy released by the oxidation of glucose and other sugars to produce ATP. Electrons are transferred from NADH, produced in the citric acid cycle in the mitochondrial matrix, to oxygen by a series of large protein complexes in the inner mitochondrial membrane, which create a transmembrane electrochemical gradient by pumping protons across the membrane. The flow of protons back into the matrix via a proton channel in the ATP synthase leads to conformational changes in the nucleotide binding pockets and the formation of ATP. The three proton pumping complexes of the electron transfer chain are NADH-ubiquinone oxidoreductase or complex I, ubiquinone-cytochrome c oxidoreductase or complex III, and cytochrome c oxidase or complex IV. Succinate dehydrogenase or complex II does not pump protons, but contributes reduced ubiquinone. The structures of complex II, III and IV were determined by x-ray crystallography several decades ago, but complex I and ATP synthase have only recently started to reveal their secrets by advances in x-ray crystallography and cryo-electron microscopy. The complexes I, III and IV occur to a certain extent as supercomplexes in the membrane, the so-called respirasomes. Several hypotheses exist about their function. Recent cryo-electron microscopy structures show the architecture of the respirasome with near-atomic detail. ATP synthase occurs as dimers in the inner mitochondrial membrane, which by their curvature are responsible for the folding of the membrane into cristae and thus for the huge increase in available surface that makes mitochondria the efficient energy plants of the eukaryotic cell.
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Affiliation(s)
- Joana S Sousa
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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Belevich N, von Ballmoos C, Verkhovskaya M. Activation of Proton Translocation by Respiratory Complex I. Biochemistry 2017; 56:5691-5697. [PMID: 28960069 DOI: 10.1021/acs.biochem.7b00727] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Activation of proton pumping by reconstituted and native membrane-bound Complex I was studied using optical electric potential- and pH-sensitive probes. We find that reconstituted Complex I has a delay in proton translocation, which is significantly longer than the delay in quinone reductase activity, indicating an initially decoupled state of Complex I. Studies of the amount of NADH required for the activation of pumping indicate the prerequisite of multiple turnovers. Proton pumping by Complex I was also activated by NADPH, excluding significant reduction of Complex I and a preexisting Δψ as activation factors. Co-reconstitution of Complex I and ATPase did not indicate an increased membrane permeability for protons in the uncoupled Complex I state. The delay in Complex I proton pumping activation was also observed in subbacterial vesicles. While it is negligible at room temperature, it strongly increases at a lower temperature. We conclude that Complex I undergoes a conversion from a decoupled state to a coupled state upon activation. The possible origins and importance of the observed phenomenon are discussed.
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Affiliation(s)
- Nikolai Belevich
- Institute of Biotechnology, University of Helsinki , P.O. Box 65, Viikinkaari 1, FIN-00014 Helsinki, Finland
| | - Christoph von Ballmoos
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Marina Verkhovskaya
- Institute of Biotechnology, University of Helsinki , P.O. Box 65, Viikinkaari 1, FIN-00014 Helsinki, Finland
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31
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Abstract
Complex I functions as the initial electron acceptor in aerobic respiratory chains of most organisms. This gigantic redox-driven enzyme employs the energy from quinone reduction to pump protons across its complete approximately 200-Å membrane domain, thermodynamically driving synthesis of ATP. Despite recently resolved structures from several species, the molecular mechanism by which complex I catalyzes this long-range proton-coupled electron transfer process, however, still remains unclear. We perform here large-scale classical and quantum molecular simulations to study the function of the proton pump in complex I from Thermus thermophilus The simulations suggest that proton channels are established at symmetry-related locations in four subunits of the membrane domain. The channels open up by formation of quasi one-dimensional water chains that are sensitive to the protonation states of buried residues at structurally conserved broken helix elements. Our combined data provide mechanistic insight into long-range coupling effects and predictions for site-directed mutagenesis experiments.
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32
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Activation of respiratory Complex I from Escherichia coli studied by fluorescent probes. Heliyon 2017; 3:e00224. [PMID: 28070565 PMCID: PMC5219619 DOI: 10.1016/j.heliyon.2016.e00224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/25/2016] [Accepted: 12/20/2016] [Indexed: 02/01/2023] Open
Abstract
Respiratory Complex I from E. coli may exist in two interconverting forms: resting (R) and active (A). The R/A transition of purified, solubilized Complex I occurring upon turnover was studied employing two different fluorescent probes, Annine 6+, and NDB-acetogenin. NADH-induced fluorescent changes of both dyes bound to solubilized Complex I from E. coli were characterized as a function of the protein:dye ratio, temperature, ubiquinone redox state and the enzyme activity. Analysis of this data combined with time-resolved optical measurements of Complex I activity and spectral changes indicated two ubiquinone-binding sites; a possibility of reduction of the tightly-bound quinone in the resting state and reduction of the loosely-bound quinone in the active state is discussed. The results also indicate that upon the activation Complex I undergoes conformational changes which can be mapped to the junction of the hydrophilic and membrane domains in the region of the assumed acetogenin-binding site.
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33
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Onukwufor JO, Stevens D, Kamunde C. Combined effects of cadmium, temperature and hypoxia-reoxygenation on mitochondrial function in rainbow trout (Oncorhynchus mykiss). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 182:129-141. [PMID: 27893995 DOI: 10.1016/j.aquatox.2016.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 10/16/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
Although aquatic organisms face multiple environmental stressors that may interact to alter adverse outcomes, our knowledge of stressor-stressor interaction on cellular function is limited. We investigated the combined effects of cadmium (Cd), hypoxia-reoxygenation (H-R) and temperature on mitochondrial function. Liver mitochondria from juvenile rainbow trout were exposed to Cd (0-20μM) and H-R (0 and 5min) at 5, 13 and 25°C followed by measurements of mitochondrial Cd load, volume, complex І active (A)↔deactive (D) transition, membrane potential, ROS release and ultrastructural changes. At high temperature Cd exacerbated H-R-imposed reduction of maximal complex I (CI) respiration whereas at low temperature 5 and 10μM stimulated maximal CI respiration post H-R. The basal respiration showed a biphasic response at high temperatures with low Cd concentrations reducing the stimulatory effect of H-R and high concentrations enhancing this effect. At low temperature Cd monotonically enhanced H-R-induced stimulation of basal respiration. Cd and H-R reduced both the P/O ratio and the RCR at all 3 temperatures. Temperature rise alone increased mitochondrial Cd load and toxicity, but combined H-R and temperature exposure reduced mitochondrial Cd load but surprisingly exacerbated the mitochondrial dysfunction. Mitochondrial dysfunction induced by H-R was associated with swelling of the organelle and blocking of conversion of CІ D to A form. However, low amounts of Cd protected against H-R induced swelling and prevented the inhibition of H-R-induced CI D to A transition. Both H-R and Cd dissipated mitochondrial membrane potential Δψm and damaged mitochondrial structure. We observed increased reactive oxygen species (H2O2) release that together with the protection afforded by EGTA, vitamin E and N-acetylcysteine against the Δψm dissipation suggested direct involvement of Cd and oxidative stress. Overall, our findings indicate that mitochondrial sensitivity to Cd toxicity was enhanced by the effects of H-R and temperature, and changes in mitochondrial Cd load did not always explain this effect.
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Affiliation(s)
- John O Onukwufor
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Don Stevens
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada
| | - Collins Kamunde
- Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada.
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34
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Letts JA, Degliesposti G, Fiedorczuk K, Skehel M, Sazanov LA. Purification of Ovine Respiratory Complex I Results in a Highly Active and Stable Preparation. J Biol Chem 2016; 291:24657-24675. [PMID: 27672209 DOI: 10.1074/jbc.m116.735142] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/15/2016] [Indexed: 01/06/2023] Open
Abstract
NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies.
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Affiliation(s)
- James A Letts
- From the Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Gianluca Degliesposti
- the Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Karol Fiedorczuk
- From the Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria,; the Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
| | - Mark Skehel
- the Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Leonid A Sazanov
- From the Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria,.
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35
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Siebels I, Dröse S. Charge translocation by mitochondrial NADH:ubiquinone oxidoreductase (complex I) from Yarrowia lipolytica measured on solid-supported membranes. Biochem Biophys Res Commun 2016; 479:277-282. [PMID: 27639643 DOI: 10.1016/j.bbrc.2016.09.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 11/17/2022]
Abstract
The charge translocation by purified reconstituted mitochondrial complex I from the obligate aerobic yeast Yarrowia lipolytica was investigated after adsorption of proteoliposomes to solid-supported membranes. In presence of n-decylubiquinone (DBQ), pulses of NADH provided by rapid solution exchange induced charge transfer reflecting steady-state pumping activity of the reconstituted enzyme. The signal amplitude increased with time, indicating 'deactive→active' transition of the Yarrowia complex I. Furthermore, an increase of the membrane-conductivity after addition of 5-(N-ethyl-N-isopropyl)amiloride (EIPA) was detected which questiones the use of EIPA as an inhibitor of the Na+/H+-antiporter-like subunits of complex I. This investigation shows that electrical measurements on solid-supported membranes are a suitable method to analyze transport events and 'active/deactive' transition of mitochondrial complex I.
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Affiliation(s)
- Ilka Siebels
- Molecular Bioenergetics Group, Medical School, Johann Wolfgang Goethe-University, 60590, Frankfurt am Main, Germany; Goethe University Frankfurt, Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Protein Reaction Control Group, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Stefan Dröse
- Molecular Bioenergetics Group, Medical School, Johann Wolfgang Goethe-University, 60590, Frankfurt am Main, Germany; Department of Anesthesiology, Intensive-Care Medicine and Pain Therapy, University Hospital Frankfurt, 60590, Frankfurt am Main, Germany.
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36
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Belevich N, Verkhovskaya M. Resting state of respiratory Complex I from Escherichia coli. FEBS Lett 2016; 590:1570-5. [PMID: 27148945 DOI: 10.1002/1873-3468.12199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 12/31/2022]
Abstract
Respiratory Complex I from Escherichia coli may exist in two states, resting (R) and active (A). The conversion from the R- to A-forms occurs spontaneously upon turnover. The fast resting-to-active (R/A) transition of membrane-bound and purified Complex I was studied with the stopped-flow technique by following NADH oxidation either by absorption decay at 340 nm or using the fluorescent pH indicator, trisodium 8-hydroxypyrene-1,3,6-trisulfonate (pyranine). The R/A transition of Complex I from E. coli occurs upon its turnover in a time interval of ~ 1.5 s. Comparisons between the bacterial Complex I R/A transition and the active/deactive transition of mitochondrial Complex I are discussed.
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37
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Wirth C, Brandt U, Hunte C, Zickermann V. Structure and function of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:902-14. [PMID: 26921811 DOI: 10.1016/j.bbabio.2016.02.013] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 12/13/2022]
Abstract
Proton-pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and most complicated enzyme of the respiratory chain. Fourteen central subunits represent the minimal form of complex I and can be assigned to functional modules for NADH oxidation, ubiquinone reduction, and proton pumping. In addition, the mitochondrial enzyme comprises some 30 accessory subunits surrounding the central subunits that are not directly associated with energy conservation. Complex I is known to release deleterious oxygen radicals (ROS) and its dysfunction has been linked to a number of hereditary and degenerative diseases. We here review recent progress in structure determination, and in understanding the role of accessory subunits and functional analysis of mitochondrial complex I. For the central subunits, structures provide insight into the arrangement of functional modules including the substrate binding sites, redox-centers and putative proton channels and pump sites. Only for two of the accessory subunits, detailed structures are available. Nevertheless, many of them could be localized in the overall structure of complex I, but most of these assignments have to be considered tentative. Strikingly, redox reactions and proton pumping machinery are spatially completely separated and the site of reduction for the hydrophobic substrate ubiquinone is found deeply buried in the hydrophilic domain of the complex. The X-ray structure of complex I from Yarrowia lipolytica provides clues supporting the previously proposed two-state stabilization change mechanism, in which ubiquinone redox chemistry induces conformational states and thereby drives proton pumping. The same structural rearrangements may explain the active/deactive transition of complex I implying an integrated mechanistic model for energy conversion and regulation. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Christophe Wirth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Ulrich Brandt
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, Nijmegen, The Netherlands; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
| | - Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, Frankfurt am Main, Germany; Cluster of Excellence Frankfurt "Macromolecular Complexes, Goethe-University, Germany.
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38
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Dröse S, Stepanova A, Galkin A. Ischemic A/D transition of mitochondrial complex I and its role in ROS generation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:946-57. [PMID: 26777588 PMCID: PMC4893024 DOI: 10.1016/j.bbabio.2015.12.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/11/2015] [Accepted: 12/25/2015] [Indexed: 12/12/2022]
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase) is a key enzyme in cellular energy metabolism and provides approximately 40% of the proton-motive force that is utilized during mitochondrial ATP production. The dysregulation of complex I function – either genetically, pharmacologically, or metabolically induced – has severe pathophysiological consequences that often involve an imbalance in the production of reactive oxygen species (ROS). Slow transition of the active (A) enzyme to the deactive, dormant (D) form takes place during ischemia in metabolically active organs such as the heart and brain. The reactivation of complex I occurs upon reoxygenation of ischemic tissue, a process that is usually accompanied by an increase in cellular ROS production. Complex I in the D-form serves as a protective mechanism preventing the oxidative burst upon reperfusion. Conversely, however, the D-form is more vulnerable to oxidative/nitrosative damage. Understanding the so-called active/deactive (A/D) transition may contribute to the development of new therapeutic interventions for conditions like stroke, cardiac infarction, and other ischemia-associated pathologies. In this review, we summarize current knowledge on the mechanism of A/D transition of mitochondrial complex I considering recently available structural data and site-specific labeling experiments. In addition, this review discusses in detail the impact of the A/D transition on ROS production by complex I and the S-nitrosation of a critical cysteine residue of subunit ND3 as a strategy to prevent oxidative damage and tissue damage during ischemia–reperfusion injury. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. The current knowledge on active/deactive (A/D) transition of complex I is reviewed. The mechanism and driving force of the A/D conformational change are discussed. The A/D transition can affect ROS production and ischemia/reperfusion injury.
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Affiliation(s)
- Stefan Dröse
- Clinic of Anesthesiology, Intensive-Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main 60590, Germany.
| | - Anna Stepanova
- Medical Biology Centre, School of Biological Sciences, Queens University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Alexander Galkin
- Medical Biology Centre, School of Biological Sciences, Queens University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, 407 East 61st Street, New York, NY 10065, USA.
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39
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Castro PJ, Silva AF, Marreiros BC, Batista AP, Pereira MM. Respiratory complex I: A dual relation with H(+) and Na(+)? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:928-37. [PMID: 26711319 DOI: 10.1016/j.bbabio.2015.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 12/10/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
Abstract
Respiratory complex I couples NADH:quinone oxidoreduction to ion translocation across the membrane, contributing to the buildup of the transmembrane difference of electrochemical potential. H(+) is well recognized to be the coupling ion of this system but some studies suggested that this role could be also performed by Na(+). We have previously observed NADH-driven Na(+) transport opposite to H(+) translocation by menaquinone-reducing complexes I, which indicated a Na(+)/H(+) antiporter activity in these systems. Such activity was also observed for the ubiquinone-reducing mitochondrial complex I in its deactive form. The relation of Na(+) with complex I may not be surprising since the enzyme has three subunits structurally homologous to bona fide Na(+)/H(+) antiporters and translocation of H(+) and Na(+) ions has been described for members of most types of ion pumps and transporters. Moreover, no clearly distinguishable motifs for the binding of H(+) or Na(+) have been recognized yet. We noticed that in menaquinone-reducing complexes I, less energy is available for ion translocation, compared to ubiquinone-reducing complexes I. Therefore, we hypothesized that menaquinone-reducing complexes I perform Na(+)/H(+) antiporter activity in order to achieve the stoichiometry of 4H(+)/2e(-). In agreement, the organisms that use ubiquinone, a high potential quinone, would have kept such Na(+)/H(+) antiporter activity, only operative under determined conditions. This would imply a physiological role(s) of complex I besides a simple "coupling" of a redox reaction and ion transport, which could account for the sophistication of this enzyme. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Paulo J Castro
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Andreia F Silva
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica, António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal.
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40
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Stepanova A, Valls A, Galkin A. Effect of monovalent cations on the kinetics of hypoxic conformational change of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1085-92. [PMID: 26009015 PMCID: PMC4607728 DOI: 10.1016/j.bbabio.2015.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 12/13/2022]
Abstract
Mitochondrial complex I is a large, membrane-bound enzyme central to energy metabolism, and its dysfunction is implicated in cardiovascular and neurodegenerative diseases. An interesting feature of mammalian complex I is the so-called A/D transition, when the idle enzyme spontaneously converts from the active (A) to the de-active, dormant (D) form. The A/D transition plays an important role in tissue response to ischemia and rate of the conversion can be a crucial factor determining outcome of ischemia/reperfusion. Here, we describe the effects of alkali cations on the rate of the D-to-A transition to define whether A/D conversion may be regulated by sodium. At neutral pH (7–7.5) sodium resulted in a clear increase of rates of activation (D-to-A conversion) while other cations had minor effects. The stimulating effect of sodium in this pH range was not caused by an increase in ionic strength. EIPA, an inhibitor of Na+/H+ antiporters, decreased the rate of D-to-A conversion and sodium partially eliminated this effect of EIPA. At higher pH (> 8.0), acceleration of the D-to-A conversion by sodium was abolished, and all tested cations decreased the rate of activation, probably due to the effect of ionic strength. The implications of this finding for the mechanism of complex I energy transduction and possible physiological importance of sodium stimulation of the D-to-A conversion at pathophysiological conditions in vivo are discussed. The active/dormant (A/D) transition of complex I is affected by monovalent cations. Na+ increases the rate of the D/A conversion at neutral pH. Lithium and caesium decrease D/A transition at all tested pH Matrix ion balance may influence the rate of the activation of the enzyme in situ.
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Affiliation(s)
- Anna Stepanova
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK; N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova Str., Moscow 119334, Russia
| | - Alba Valls
- University of Barcelona, Faculty of Biology, Diagonal, 643, 08028 Barcelona, Spain
| | - Alexander Galkin
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK.
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41
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Zickermann V, Wirth C, Nasiri H, Siegmund K, Schwalbe H, Hunte C, Brandt U. Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I. Science 2015; 347:44-9. [PMID: 25554780 DOI: 10.1126/science.1259859] [Citation(s) in RCA: 309] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proton-pumping complex I of the mitochondrial respiratory chain is among the largest and most complicated membrane protein complexes. The enzyme contributes substantially to oxidative energy conversion in eukaryotic cells. Its malfunctions are implicated in many hereditary and degenerative disorders. We report the x-ray structure of mitochondrial complex I at a resolution of 3.6 to 3.9 angstroms, describing in detail the central subunits that execute the bioenergetic function. A continuous axis of basic and acidic residues running centrally through the membrane arm connects the ubiquinone reduction site in the hydrophilic arm to four putative proton-pumping units. The binding position for a substrate analogous inhibitor and blockage of the predicted ubiquinone binding site provide a model for the "deactive" form of the enzyme. The proposed transition into the active form is based on a concerted structural rearrangement at the ubiquinone reduction site, providing support for a two-state stabilization-change mechanism of proton pumping.
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Affiliation(s)
- Volker Zickermann
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, 60438 Frankfurt am Main, Germany. Cluster of Excellence Frankfurt "Macromolecular Complexes," Goethe-University, 60438 Frankfurt am Main, Germany.
| | - Christophe Wirth
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Hamid Nasiri
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, 60438 Frankfurt am Main, Germany
| | - Karin Siegmund
- Structural Bioenergetics Group, Institute of Biochemistry II, Medical School, Goethe-University, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Cluster of Excellence Frankfurt "Macromolecular Complexes," Goethe-University, 60438 Frankfurt am Main, Germany. Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, 60438 Frankfurt am Main, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Ulrich Brandt
- Cluster of Excellence Frankfurt "Macromolecular Complexes," Goethe-University, 60438 Frankfurt am Main, Germany. Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Center, 6525 GA Nijmegen, Netherlands.
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42
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Bak DW, Weerapana E. Cysteine-mediated redox signalling in the mitochondria. MOLECULAR BIOSYSTEMS 2015; 11:678-97. [DOI: 10.1039/c4mb00571f] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review represents a novel look at the many sources, cysteine targets, and signaling processes of ROS in the mitochondria.
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Affiliation(s)
- D. W. Bak
- Department of Chemistry
- Merkert Chemistry Center
- Boston College
- Massachusetts 02467
- USA
| | - E. Weerapana
- Department of Chemistry
- Merkert Chemistry Center
- Boston College
- Massachusetts 02467
- USA
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43
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Belyaeva EA, Emelyanova LV, Korotkov SM, Brailovskaya IV, Savina MV. On the mechanism(s) of membrane permeability transition in liver mitochondria of lamprey, Lampetra fluviatilis L.: insights from cadmium. BIOMED RESEARCH INTERNATIONAL 2014; 2014:691724. [PMID: 24995321 PMCID: PMC4065708 DOI: 10.1155/2014/691724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/29/2014] [Accepted: 05/01/2014] [Indexed: 02/05/2023]
Abstract
Previously we have shown that opening of the mitochondrial permeability transition pore in its low conductance state is the case in hepatocytes of the Baltic lamprey (Lampetra fluviatilis L.) during reversible metabolic depression taking place in the period of its prespawning migration when the exogenous feeding is switched off. The depression is observed in the last year of the lamprey life cycle and is conditioned by reversible mitochondrial dysfunction (mitochondrial uncoupling in winter and coupling in spring). To further elucidate the mechanism(s) of induction of the mitochondrial permeability transition pore in the lamprey liver, we used Cd(2+) and Ca(2+) plus Pi as the pore inducers. We found that Ca(2+) plus Pi induced the high-amplitude swelling of the isolated "winter" mitochondria both in isotonic sucrose and ammonium nitrate medium while both low and high Cd(2+) did not produce the mitochondrial swelling in these media. Low Cd(2+) enhanced the inhibition of basal respiration rate of the "winter" mitochondria energized by NAD-dependent substrates whereas the same concentrations of the heavy metal evoked its partial stimulation on FAD-dependent substrates. The above changes produced by Cd(2+) or Ca(2+) plus Pi in the "winter" mitochondria were only weakly (if so) sensitive to cyclosporine A (a potent pharmacological desensitizer of the nonselective pore) added alone and they were not sensitive to dithiothreitol (a dithiol reducing agent). Under monitoring of the transmembrane potential of the "spring" lamprey liver mitochondria, we revealed that Cd(2+) produced its decrease on both types of the respiratory substrates used that was strongly hampered by cyclosporine A, and the membrane potential was partially restored by dithiothreitol. The effects of different membrane permeability modulators on the lamprey liver mitochondria function and the seasonal changes in their action are discussed.
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Affiliation(s)
- Elena A. Belyaeva
- I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, Saint Petersburg 194223, Russia
| | - Larisa V. Emelyanova
- I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, Saint Petersburg 194223, Russia
| | - Sergey M. Korotkov
- I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, Saint Petersburg 194223, Russia
| | - Irina V. Brailovskaya
- I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, Saint Petersburg 194223, Russia
| | - Margarita V. Savina
- I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez pr. 44, Saint Petersburg 194223, Russia
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Molecular mechanism and physiological role of active-deactive transition of mitochondrial complex I. Biochem Soc Trans 2014; 41:1325-30. [PMID: 24059527 PMCID: PMC3990385 DOI: 10.1042/bst20130088] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The unique feature of mitochondrial complex I is the so-called A/D transition (active–deactive transition). The A-form catalyses rapid oxidation of NADH by ubiquinone (k ~104 min−1) and spontaneously converts into the D-form if the enzyme is idle at physiological temperatures. Such deactivation occurs in vitro in the absence of substrates or in vivo during ischaemia, when the ubiquinone pool is reduced. The D-form can undergo reactivation given both NADH and ubiquinone availability during slow (k ~1–10 min−1) catalytic turnover(s). We examined known conformational differences between the two forms and suggested a mechanism exerting A/D transition of the enzyme. In addition, we discuss the physiological role of maintaining the enzyme in the D-form during the ischaemic period. Accumulation of the D-form of the enzyme would prevent reverse electron transfer from ubiquinol to FMN which could lead to superoxide anion generation. Deactivation would also decrease the initial burst of respiration after oxygen reintroduction. Therefore the A/D transition could be an intrinsic protective mechanism for lessening oxidative damage during the early phase of reoxygenation. Exposure of Cys39 of mitochondrially encoded subunit ND3 makes the D-form susceptible for modification by reactive oxygen species and nitric oxide metabolites which arrests the reactivation of the D-form and inhibits the enzyme. The nature of thiol modification defines deactivation reversibility, the reactivation timescale, the status of mitochondrial bioenergetics and therefore the degree of recovery of the ischaemic tissues after reoxygenation.
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Babot M, Birch A, Labarbuta P, Galkin A. Characterisation of the active/de-active transition of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1083-92. [PMID: 24569053 PMCID: PMC4331042 DOI: 10.1016/j.bbabio.2014.02.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 12/12/2022]
Abstract
Oxidation of NADH in the mitochondrial matrix of aerobic cells is catalysed by mitochondrial complex I. The regulation of this mitochondrial enzyme is not completely understood. An interesting characteristic of complex I from some organisms is the ability to adopt two distinct states: the so-called catalytically active (A) and the de-active, dormant state (D). The A-form in situ can undergo de-activation when the activity of the respiratory chain is limited (i.e. in the absence of oxygen). The mechanisms and driving force behind the A/D transition of the enzyme are currently unknown, but several subunits are most likely involved in the conformational rearrangements: the accessory subunit 39 kDa (NDUFA9) and the mitochondrially encoded subunits, ND3 and ND1. These three subunits are located in the region of the quinone binding site. The A/D transition could represent an intrinsic mechanism which provides a fast response of the mitochondrial respiratory chain to oxygen deprivation. The physiological role of the accumulation of the D-form in anoxia is most probably to protect mitochondria from ROS generation due to the rapid burst of respiration following reoxygenation. The de-activation rate varies in different tissues and can be modulated by the temperature, the presence of free fatty acids and divalent cations, the NAD+/NADH ratio in the matrix, the presence of nitric oxide and oxygen availability. Cysteine-39 of the ND3 subunit, exposed in the D-form, is susceptible to covalent modification by nitrosothiols, ROS and RNS. The D-form in situ could react with natural effectors in mitochondria or with pharmacological agents. Therefore the modulation of the re-activation rate of complex I could be a way to ameliorate the ischaemia/reperfusion damage. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference. Guest Editors: Manuela Pereira and Miguel Teixeira. The potential mechanism of complex I A/D transition is discussed. An —SH group exposed in the D-form is susceptible to covalent modification. The role of A/D transition in tissue response to ischaemia is proposed.
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Affiliation(s)
- Marion Babot
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Amanda Birch
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Paola Labarbuta
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Alexander Galkin
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK.
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Dröse S, Brandt U, Wittig I. Mitochondrial respiratory chain complexes as sources and targets of thiol-based redox-regulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1344-54. [PMID: 24561273 DOI: 10.1016/j.bbapap.2014.02.006] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/05/2014] [Accepted: 02/08/2014] [Indexed: 02/06/2023]
Abstract
The respiratory chain of the inner mitochondrial membrane is a unique assembly of protein complexes that transfers the electrons of reducing equivalents extracted from foodstuff to molecular oxygen to generate a proton-motive force as the primary energy source for cellular ATP-synthesis. Recent evidence indicates that redox reactions are also involved in regulating mitochondrial function via redox-modification of specific cysteine-thiol groups in subunits of respiratory chain complexes. Vice versa the generation of reactive oxygen species (ROS) by respiratory chain complexes may have an impact on the mitochondrial redox balance through reversible and irreversible thiol-modification of specific target proteins involved in redox signaling, but also pathophysiological processes. Recent evidence indicates that thiol-based redox regulation of the respiratory chain activity and especially S-nitrosylation of complex I could be a strategy to prevent elevated ROS production, oxidative damage and tissue necrosis during ischemia-reperfusion injury. This review focuses on the thiol-based redox processes involving the respiratory chain as a source as well as a target, including a general overview on mitochondria as highly compartmentalized redox organelles and on methods to investigate the redox state of mitochondrial proteins. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.
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Affiliation(s)
- Stefan Dröse
- Clinic of Anesthesiology, Intensive-Care Medicine and Pain Therapy, University Hospital Frankfurt, 60590 Frankfurt am Main, Germany
| | - Ulrich Brandt
- Radboud University Medical Centre, Nijmegen Centre for Mitochondrial Disorders, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands; Cluster of Excellence "Macromolecular Complexes", Goethe-University, Frankfurt am Main, Germany.
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany; Cluster of Excellence "Macromolecular Complexes", Goethe-University, Frankfurt am Main, Germany
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MCJ/DnaJC15, an endogenous mitochondrial repressor of the respiratory chain that controls metabolic alterations. Mol Cell Biol 2013; 33:2302-14. [PMID: 23530063 DOI: 10.1128/mcb.00189-13] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Mitochondria are the main engine that generates ATP through oxidative phosphorylation within the respiratory chain. Mitochondrial respiration is regulated according to the metabolic needs of cells and can be modulated in response to metabolic changes. Little is known about the mechanisms that regulate this process. Here, we identify MCJ/DnaJC15 as a distinct cochaperone that localizes at the mitochondrial inner membrane, where it interacts preferentially with complex I of the electron transfer chain. We show that MCJ impairs the formation of supercomplexes and functions as a negative regulator of the respiratory chain. The loss of MCJ leads to increased complex I activity, mitochondrial membrane potential, and ATP production. Although MCJ is dispensable for mitochondrial function under normal physiological conditions, MCJ deficiency affects the pathophysiology resulting from metabolic alterations. Thus, enhanced mitochondrial respiration in the absence of MCJ prevents the pathological accumulation of lipids in the liver in response to both fasting and a high-cholesterol diet. Impaired expression or loss of MCJ expression may therefore result in a "rapid" metabolism that mitigates the consequences of metabolic disorders.
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Ciano M, Fuszard M, Heide H, Botting CH, Galkin A. Conformation-specific crosslinking of mitochondrial complex I. FEBS Lett 2013; 587:867-72. [PMID: 23454639 DOI: 10.1016/j.febslet.2013.02.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/11/2013] [Accepted: 02/14/2013] [Indexed: 11/17/2022]
Abstract
Complex I is the only component of the eukaryotic respiratory chain of which no high-resolution structure is yet available. A notable feature of mitochondrial complex I is the so-called active/de-active conformational transition of the idle enzyme from the active (A) to the de-active, (D) form. Using an amine- and sulfhydryl-reactive crosslinker of 6.8Å length (SPDP) we found that in the D-form of complex I the ND3 subunit crosslinked to the 39 kDa (NDUFA9) subunit. These proteins could not be crosslinked in the A-form. Most likely, both subunits are closely located in the critical junction region connecting the peripheral hydrophilic domain to the membrane arm of the enzyme where the entrance path for substrate ubiquinone is and where energy transduction takes place.
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Affiliation(s)
- Margherita Ciano
- Queen's University Belfast, School of Biological Sciences, Medical Biology Centre, Belfast, UK
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Roberts PG, Hirst J. The deactive form of respiratory complex I from mammalian mitochondria is a Na+/H+ antiporter. J Biol Chem 2012; 287:34743-51. [PMID: 22854968 PMCID: PMC3464577 DOI: 10.1074/jbc.m112.384560] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/23/2012] [Indexed: 11/21/2022] Open
Abstract
In mitochondria, complex I (NADH:ubiquinone oxidoreductase) uses the redox potential energy from NADH oxidation by ubiquinone to transport protons across the inner membrane, contributing to the proton-motive force. However, in some prokaryotes, complex I may transport sodium ions instead, and three subunits in the membrane domain of complex I are closely related to subunits from the Mrp family of Na(+)/H(+) antiporters. Here, we define the relationship between complex I from Bos taurus heart mitochondria, a close model for the human enzyme, and sodium ion transport across the mitochondrial inner membrane. In accord with current consensus, we exclude the possibility of redox-coupled Na(+) transport by B. taurus complex I. Instead, we show that the "deactive" form of complex I, which is formed spontaneously when enzyme turnover is precluded by lack of substrates, is a Na(+)/H(+) antiporter. The antiporter activity is abolished upon reactivation by the addition of substrates and by the complex I inhibitor rotenone. It is specific for Na(+) over K(+), and it is not exhibited by complex I from the yeast Yarrowia lipolytica, which thus has a less extensive deactive transition. We propose that the functional connection between the redox and transporter modules of complex I is broken in the deactive state, allowing the transport module to assert its independent properties. The deactive state of complex I is formed during hypoxia, when respiratory chain turnover is slowed, and may contribute to determining the outcome of ischemia-reperfusion injury.
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Affiliation(s)
- Philippa G. Roberts
- From The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Judy Hirst
- From The Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom
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50
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Ischemia-induced inhibition of mitochondrial complex I in rat brain: effect of permeabilization method and electron acceptor. Neurochem Res 2012; 37:965-76. [PMID: 22219133 DOI: 10.1007/s11064-011-0689-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 12/18/2011] [Accepted: 12/23/2011] [Indexed: 12/23/2022]
Abstract
In this study we have examined the effect of global brain ischemia/reperfusion on biochemical properties of the mitochondrial respiratory complex I (CI) in rat hippocampus and cortex. Since the inner mitochondrial membrane forms the permeability barrier for NADH, the methodology of enzymatic activity determinations employs membrane permeabilization methods. This action affects the basic character of electrostatic and hydrophobic interactions inside the membrane and might influence functional properties of membrane embedded proteins. Therefore we have performed the comparative analysis of two permeabilization methods (sonication, detergent) and their impact on CI enzymatic activities under global brain ischemic-reperfusion conditions. We have observed that ischemia led to significant decrease of CI activities using both permeabilization methods in both brain areas. However, significant differencies in enzymatic activities were registered during reperfusion intervals according to used permeabilization method. We have also tested the effect of electron acceptors (decylubiquinone, potassium ferricyanide, nitrotetrazolium blue) on CI activities during I/R. Based on our results we assume that the critical site where ischemia affects CI activities is electron transfer to electron acceptor. Further, the observed mitochondrial dysfunction was analyzed by means of one and 2-dimensional BN PAGE/SDS PAGE with the focus on 3-nitrotyrosine immunodetection as a marker of oxidative damage to proteins. Add to this, initialization of p53 mitochondrial apoptosis through p53, Bax, Bcl-X(L) proteins and a possible involvement of GRIM-19, the CI structural subunit, in apoptotic processes were also studied.
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