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Balsa E, Marco R, Perales-Clemente E, Szklarczyk R, Calvo E, Landázuri MO, Enríquez JA. NDUFA4 is a subunit of complex IV of the mammalian electron transport chain. Cell Metab 2012; 16:378-86. [PMID: 22902835 DOI: 10.1016/j.cmet.2012.07.015] [Citation(s) in RCA: 283] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/18/2012] [Accepted: 07/26/2012] [Indexed: 12/19/2022]
Abstract
The oxidative phosphorylation system is one of the best-characterized metabolic pathways. In mammals, the protein components and X-ray structures are defined for all complexes except complex I. Here, we show that NDUFA4, formerly considered a constituent of NADH Dehydrogenase (CI), is instead a component of the cytochrome c oxidase (CIV). Deletion of NDUFA4 does not perturb CI. Rather, proteomic, genetic, evolutionary, and biochemical analyses reveal that NDUFA4 plays a role in CIV function and biogenesis. The change in the attribution of the NDUFA4 protein requires renaming of the gene and reconsideration of the structure of CIV. Furthermore, NDUFA4 should be considered a candidate gene for CIV rather than CI deficiencies in humans.
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Affiliation(s)
- Eduardo Balsa
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, 28029, Spain
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202
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Verkhovsky M, Bloch DA, Verkhovskaya M. Tightly-bound ubiquinone in the Escherichia coli respiratory Complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1550-6. [DOI: 10.1016/j.bbabio.2012.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/23/2012] [Accepted: 04/25/2012] [Indexed: 12/12/2022]
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Irwin MH, Parameshwaran K, Pinkert CA. Mouse models of mitochondrial complex I dysfunction. Int J Biochem Cell Biol 2012; 45:34-40. [PMID: 22903069 DOI: 10.1016/j.biocel.2012.08.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 07/21/2012] [Accepted: 08/04/2012] [Indexed: 12/21/2022]
Abstract
Diseases of the mitochondria generally affect cells with high-energy demand, and appear to most profoundly affect excitatory cells that have localized high energy requirements, such as neurons and cardiac and skeletal muscle cells. Complex I of the mammalian mitochondrial respiratory chain is a very large, 45 subunit enzyme, and functional deficiency of complex I is the most frequently observed cause of oxidative phosphorylation (OXPHOS) disorders. Impairment of complex I results in decreased cellular energy production and is responsible for a variety of human encephalopathies, myopathies and cardiomyopathies. Complex I deficiency may be caused by mutations in any of the seven mitochondrial or 38 nuclear genes that encode complex I subunits or by mutations in various other nuclear genes that affect complex I assembly or function. Mouse models that faithfully mimic human complex I disorders are needed to better understand the role of complex I in health and disease and for evaluation of potential therapies for mitochondrial diseases. In this review we discuss existing mouse models of mitochondrial complex I dysfunction, focusing on those with similarities to human mitochondrial disorders. We also discuss some of the noteworthy murine genetic models in which complex I genes are not disrupted, but complex I dysfunction is observed, along with some of the more popular chemical compounds that inhibit complex I function and are useful for modeling complex I deficiency in mice. This article is part of a Directed Issue entitled: Bioenergetic dysfunction, adaptation and therapy.
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Affiliation(s)
- Michael H Irwin
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL, USA.
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204
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Kensche PR, Duarte I, Huynen MA. A three-dimensional topology of complex I inferred from evolutionary correlations. BMC STRUCTURAL BIOLOGY 2012; 12:19. [PMID: 22857522 PMCID: PMC3436739 DOI: 10.1186/1472-6807-12-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 06/28/2012] [Indexed: 11/22/2022]
Abstract
Background The quaternary structure of eukaryotic NADH:ubiquinone oxidoreductase (complex I), the largest complex of the oxidative phosphorylation, is still mostly unresolved. Furthermore, it is unknown where transiently bound assembly factors interact with complex I. We therefore asked whether the evolution of complex I contains information about its 3D topology and the binding positions of its assembly factors. We approached these questions by correlating the evolutionary rates of eukaryotic complex I subunits using the mirror-tree method and mapping the results into a 3D representation by multidimensional scaling. Results More than 60% of the evolutionary correlation among the conserved seven subunits of the complex I matrix arm can be explained by the physical distance between the subunits. The three-dimensional evolutionary model of the eukaryotic conserved matrix arm has a striking similarity to the matrix arm quaternary structure in the bacterium Thermus thermophilus (rmsd=19 Å) and supports the previous finding that in eukaryotes the N-module is turned relative to the Q-module when compared to bacteria. By contrast, the evolutionary rates contained little information about the structure of the membrane arm. A large evolutionary model of 45 subunits and assembly factors allows to predict subunit positions and interactions (rmsd = 52.6 Å). The model supports an interaction of NDUFAF3, C8orf38 and C2orf56 during the assembly of the proximal matrix arm and the membrane arm. The model further suggests a tight relationship between the assembly factor NUBPL and NDUFA2, which both have been linked to iron-sulfur cluster assembly, as well as between NDUFA12 and its paralog, the assembly factor NDUFAF2. Conclusions The physical distance between subunits of complex I is a major correlate of the rate of protein evolution in the complex I matrix arm and is sufficient to infer parts of the complex’s structure with high accuracy. The resulting evolutionary model predicts the positions of a number of subunits and assembly factors.
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Affiliation(s)
- Philip R Kensche
- Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, Nijmegen, HB, 6500, The Netherlands.
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205
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Achilli A, Iommarini L, Olivieri A, Pala M, Hooshiar Kashani B, Reynier P, La Morgia C, Valentino ML, Liguori R, Pizza F, Barboni P, Sadun F, De Negri AM, Zeviani M, Dollfus H, Moulignier A, Ducos G, Orssaud C, Bonneau D, Procaccio V, Leo-Kottler B, Fauser S, Wissinger B, Amati-Bonneau P, Torroni A, Carelli V. Rare primary mitochondrial DNA mutations and probable synergistic variants in Leber's hereditary optic neuropathy. PLoS One 2012; 7:e42242. [PMID: 22879922 PMCID: PMC3411744 DOI: 10.1371/journal.pone.0042242] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 07/02/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Leber's hereditary optic neuropathy (LHON) is a maternally inherited blinding disorder, which in over 90% of cases is due to one of three primary mitochondrial DNA (mtDNA) point mutations (m.11778G>A, m.3460G>A and m.14484T>C, respectively in MT-ND4, MT-ND1 and MT-ND6 genes). However, the spectrum of mtDNA mutations causing the remaining 10% of cases is only partially and often poorly defined. METHODOLOGY/PRINCIPAL FINDINGS In order to improve such a list of pathological variants, we completely sequenced the mitochondrial genomes of suspected LHON patients from Italy, France and Germany, lacking the three primary common mutations. Phylogenetic and conservation analyses were performed. Sixteen mitochondrial genomes were found to harbor at least one of the following nine rare LHON pathogenic mutations in genes MT-ND1 (m.3700G>A/p.A132T, m.3733G>A-C/p.E143K-Q, m.4171C>A/p.L289M), MT-ND4L (m.10663T>C/p.V65A) and MT-ND6 (m.14459G>A/p.A72V, m.14495A>G/p.M64I, m.14482C>A/p.L60S, and m.14568C>T/p.G36S). Phylogenetic analyses revealed that these substitutions were due to independent events on different haplogroups, whereas interspecies comparisons showed that they affected conserved amino acid residues or domains in the ND subunit genes of complex I. CONCLUSIONS/SIGNIFICANCE Our findings indicate that these nine substitutions are all primary LHON mutations. Therefore, despite their relative low frequency, they should be routinely tested for in all LHON patients lacking the three common mutations. Moreover, our sequence analysis confirms the major role of haplogroups J1c and J2b (over 35% in our probands versus 6% in the general population of Western Europe) and other putative synergistic mtDNA variants in LHON expression.
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Affiliation(s)
- Alessandro Achilli
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Luisa Iommarini
- IRCCS Istituto delle Scienze Neurologiche di Bologna and Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Maria Pala
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | | | - Pascal Reynier
- UMR INSERM, U1083-CNRS6214, Angers, France
- University of Angers, School of Medicine, Angers, France
- University Hospital of Angers, Department of Biochemistry and Genetics, Angers, France
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna and Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Maria Lucia Valentino
- IRCCS Istituto delle Scienze Neurologiche di Bologna and Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Rocco Liguori
- IRCCS Istituto delle Scienze Neurologiche di Bologna and Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Fabio Pizza
- IRCCS Istituto delle Scienze Neurologiche di Bologna and Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
| | - Piero Barboni
- IRCCS Istituto delle Scienze Neurologiche di Bologna and Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
- Studio Oculistico D’Azeglio, Bologna, Italy
| | | | | | - Massimo Zeviani
- Unit of Molecular Neurogenetics, Pierfranco and Luisa Mariani Center for the Study of Children’s Mitochondrial Disorders, Foundation “C. Besta” Neurological Institute-IRCCS, Milan, Italy
| | - Helene Dollfus
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Antoine Moulignier
- Service de Neurologie, Fondation Ophtalmologique Adolphe de Rothschild, Paris, France
| | - Ghislaine Ducos
- Department of Ophthalmology, Saint Jean Languedoc Clinic, Toulouse, France
| | - Christophe Orssaud
- Centre de Référence des Maladies Rares en Ophtalmologie, Consultationd ‘Ophtalmologie, HEGP, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Dominique Bonneau
- UMR INSERM, U1083-CNRS6214, Angers, France
- University of Angers, School of Medicine, Angers, France
- University Hospital of Angers, Department of Biochemistry and Genetics, Angers, France
| | - Vincent Procaccio
- UMR INSERM, U1083-CNRS6214, Angers, France
- University of Angers, School of Medicine, Angers, France
- University Hospital of Angers, Department of Biochemistry and Genetics, Angers, France
| | - Beate Leo-Kottler
- Centre for Ophthalmology, University Clinics Tuebingen, Tubingen, Germany
| | - Sascha Fauser
- Department of Vitreo-Retinal Surgery, Center of Ophthalmology, University of Cologne, Cologne, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tuebingen, Tuebingen, Germany
| | - Patrizia Amati-Bonneau
- UMR INSERM, U1083-CNRS6214, Angers, France
- University Hospital of Angers, Department of Biochemistry and Genetics, Angers, France
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna and Dipartimento di Scienze Neurologiche, Università di Bologna, Bologna, Italy
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206
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Althoff T, Davies KM, Schulze S, Joos F, Kühlbrandt W. GRecon: a method for the lipid reconstitution of membrane proteins. Angew Chem Int Ed Engl 2012; 51:8343-7. [PMID: 22821803 PMCID: PMC3494379 DOI: 10.1002/anie.201202094] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Thorsten Althoff
- Max-Planck-Institut für Biophysik, Strukturbiologie, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
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207
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Althoff T, Davies KM, Schulze S, Joos F, Kühlbrandt W. GRecon: A Method for the Lipid Reconstitution of Membrane Proteins. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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208
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Control of electron transport routes through redox-regulated redistribution of respiratory complexes. Proc Natl Acad Sci U S A 2012; 109:11431-6. [PMID: 22733774 DOI: 10.1073/pnas.1120960109] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In cyanobacteria, respiratory electron transport takes place in close proximity to photosynthetic electron transport, because the complexes required for both processes are located within the thylakoid membranes. The balance of electron transport routes is crucial for cell physiology, yet the factors that control the predominance of particular pathways are poorly understood. Here we use a combination of tagging with green fluorescent protein and confocal fluorescence microscopy in live cells of the cyanobacterium Synechococcus elongatus PCC 7942 to investigate the distribution on submicron scales of two key respiratory electron donors, type-I NAD(P)H dehydrogenase (NDH-1) and succinate dehydrogenase (SDH). When cells are grown under low light, both complexes are concentrated in discrete patches in the thylakoid membranes, about 100-300 nm in diameter and containing tens to hundreds of complexes. Exposure to moderate light leads to redistribution of both NDH-1 and SDH such that they become evenly distributed within the thylakoid membranes. The effects of electron transport inhibitors indicate that redistribution of respiratory complexes is triggered by changes in the redox state of an electron carrier close to plastoquinone. Redistribution does not depend on de novo protein synthesis, and it is accompanied by a major increase in the probability that respiratory electrons are transferred to photosystem I rather than to a terminal oxidase. These results indicate that the distribution of complexes on the scale of 100-300 nm controls the partitioning of reducing power and that redistribution of electron transport complexes on these scales is a physiological mechanism to regulate the pathways of electron flow.
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209
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Larosa V, Coosemans N, Motte P, Bonnefoy N, Remacle C. Reconstruction of a human mitochondrial complex I mutation in the unicellular green alga Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:759-768. [PMID: 22268373 DOI: 10.1111/j.1365-313x.2012.04912.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Defects in complex I (NADH:ubiquinone oxidoreductase (EC 1.6.5.3)) are the most frequent cause of human respiratory disorders. The pathogenicity of a given human mitochondrial mutation can be difficult to demonstrate because the mitochondrial genome harbors large numbers of polymorphic base changes that have no pathogenic significance. In addition, mitochondrial mutations are usually found in the heteroplasmic state, which may hide the biochemical effect of the mutation. We propose that the unicellular green alga Chlamydomonas could be used to study such mutations because (i) respiratory complex-deficient mutants are viable and mitochondrial mutations are found in the homoplasmic state, (ii) transformation of the mitochondrial genome is feasible, and (iii) Chlamydomonas complex I is similar to that of humans. To illustrate this proposal, we introduced a Leu157Pro substitution into the Chlamydomonas ND4 subunit of complex I in two recipient strains by biolistic transformation, demonstrating that site-directed mutagenesis of the Chlamydomonas mitochondrial genome is possible. This substitution did not lead to any respiratory enzyme defects when present in the heteroplasmic state in a patient with chronic progressive external ophthalmoplegia. When present in the homoplasmic state in the alga, the mutation does not prevent assembly of whole complex I (950 kDa) and the NADH dehydrogenase activity of the peripheral arm of the complex is mildly affected. However, the NADH:duroquinone oxidoreductase activity is strongly reduced, suggesting that the substitution could affect binding of ubiquinone to the membrane domain. The in vitro defects correlate with a decrease in dark respiration and growth rate in vivo.
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Affiliation(s)
- Véronique Larosa
- Genetics of Microorganisms, Department of Life Sciences, Institute of Botany, University of Liege, B-4000 Liege, Belgium
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210
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Zurita Rendón O, Shoubridge EA. Early complex I assembly defects result in rapid turnover of the ND1 subunit. Hum Mol Genet 2012; 21:3815-24. [PMID: 22653752 DOI: 10.1093/hmg/dds209] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Complex I (CI, NADH ubiquinone oxidoreductase), the largest complex of the respiratory chain, is composed of 45 structural subunits, 7 of which are encoded in mtDNA. At least 10 factors necessary for holoenzyme assembly have been identified; however, the specific roles of most of them are not well understood. We investigated the role of NDUFAF3, NDUFAF4, C8orf38 and C20orf7, four early assembly factors, in the translation of the mtDNA-encoded CI structural subunits. Transient, or stable, siRNA-mediated knock-down of any of these factors abrogated the assembly of CI, and resulted in a specific decrease in the labeling of the ND1 subunit in a pulse translation experiment, whereas knock-down of NDUFAF2, a late assembly factor, did not affect ND1 translation. Pulse-chase experiments in cells knocked down for NDUFAF3 showed that the half-life of ND1 in the chase was reduced 4-fold, fully accounting for the decrease in pulse labeling. Transient, short-term knock-down of the m-AAA protease AGF3L2 in cells that had been depleted of any of the early CI assembly factors completely rescued the ND1 labeling phenotype, confirming that it is not a synthesis defect, but rather results from rapid proteolysis of newly synthesized ND1. NDUFAF3 co-immunoprecipitated with NDUFAF4, and three matrix arm structural subunits (NDUFS2, NDUFA9, NDUFS3) that are found in a 400 kDa assembly intermediate containing ND1. These data suggest that the four early CI assembly factors have non-redundant functions in the assembly of a module that docks and stabilizes newly synthesized ND1, nucleating assembly of the holoenzyme.
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Affiliation(s)
- Olga Zurita Rendón
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, QC, Canada H3A 2B4
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211
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Abstract
The mitochondrial respiratory chain is organized within an array of supercomplexes that function to minimize the generation of reactive oxygen species (ROS) during electron transfer reactions. Structural models of supercomplexes are now known. Another recent advance is the discovery of non-OXPHOS complex proteins that appear to adhere to and seal the individual respiratory complexes to form stable assemblages that prevent electron leakage. This review highlights recent advances in our understanding of the structures of supercomplexes and the factors that mediate their stability.
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212
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Batista AP, Marreiros BC, Pereira MM. The role of proton and sodium ions in energy transduction by respiratory complex I. IUBMB Life 2012; 64:492-8. [PMID: 22576956 DOI: 10.1002/iub.1050] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 04/17/2012] [Indexed: 11/08/2022]
Abstract
Respiratory complex I plays a central role in energy transduction. It catalyzes the oxidation of NADH and the reduction of quinone, coupled to cation translocation across the membrane, thereby establishing an electrochemical potential. For more than half a century, data on complex I has been gathered, including recently determined crystal structures, yet complex I is the least understood complex of the respiratory chain. The mechanisms of quinone reduction, charge translocation and their coupling are still unknown. The H(+) is accepted to be the coupling ion of the system; however, Na(+) has also been suggested to perform such a role. In this article, we address the relation of those two ions with complex I and refer ion pump and Na(+)/H(+) antiporter as possible transport mechanisms of the system. We put forward a hypothesis to explain some apparently contradictory data on the nature of the coupling ion, and we revisit the role of H(+) and Na(+) cycles in the overall bioenergetics of the cell.
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Affiliation(s)
- Ana P Batista
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
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213
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Ransac S, Heiske M, Mazat JP. From in silico to in spectro kinetics of respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1958-69. [PMID: 22510388 DOI: 10.1016/j.bbabio.2012.03.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/28/2012] [Accepted: 03/29/2012] [Indexed: 12/12/2022]
Abstract
An enzyme's activity is the consequence of its structure. The stochastic approach we developed to study the functioning of the respiratory complexes is based upon their 3D structure and their physical and chemical properties. Consequently it should predict their kinetic properties. In this paper we compare the predictions of our stochastic model derived for the complex I with a number of experiments performed with a large range of complex I substrates and products. A good fit was found between the experiments and the prediction of our stochastic approach. We show that, due to the spatial separation of the two half redox reactions (NADH/NAD and Q/QH(2)), the kinetics cannot necessarily obey a simple mechanism (ordered or ping-pong for instance). A plateau in the kinetics is observed at high substrates concentrations, well evidenced in the double reciprocal plots, which is explained by the limiting rate of quinone reduction as compared with the oxidation of NADH at the other end of complex I. Moreover, we show that the set of the seven redox reactions in between the two half redox reactions (NADH/NAD and Q/QH(2)) acts as an electron buffer. An inhibition of complex I activity by quinone is observed at high concentration of this molecule, which cannot be explained by a simple stochastic model based on the known structure. We hypothesize that the distance between the catalytic site close to N2 (iron/sulfur redox center that transfers electrons to quinone) and the membrane forces the quinone/quinol to take several positions in between these sites. We represent these possible positions by an extra site necessarily occupied by the quinone/quinol molecules on their way to the redox site. With this hypothesis, we are able to fit the kinetic experiments over a large range of substrates and products concentrations. The slow rate constants derived for the transition between the two sites could be an indication of a conformational change of the enzyme during the quinone/quinol movement. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Stéphane Ransac
- Institute of Biochemistry and Genetics of the Cell, Bordeaux cedex, France
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214
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EPR detection of two protein-associated ubiquinone components (SQ(Nf) and SQ(Ns)) in the membrane in situ and in proteoliposomes of isolated bovine heart complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1803-9. [PMID: 22503829 DOI: 10.1016/j.bbabio.2012.03.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 03/26/2012] [Accepted: 03/29/2012] [Indexed: 02/01/2023]
Abstract
The success of Sazanov's group in determining the X-ray structure of the whole bacterial complex I is a great contribution to the progress of complex I research. In this mini-review of 35years' history of my laboratory and collaborators, we characterized the function of protein-associated semiquinone molecules in the proton-pumping mechanism in complex I (NADH-quinone oxidoreductase). We have constructed most of the frame work of our hypothesis, utilizing EPR techniques before the X-ray structures of complex I were reported by Sazanov's and Brandt's groups. One of the semiquinones (SQ(Nf)) is extremely sensitive to a proton motive force imposed on the energy-transducing membrane, while the other (SQ(Ns)) is insensitive. Their sensitivity to rotenone inhibition also differs. These differences were exploited using tightly coupled bovine heart submitochondrial particles with a high respiratory control ratio (>8). We determined the distance between SQ(Nf) and iron-sulfur cluster N2 on the basis of their direct spin-spin interaction. We are extending this line of work using reconstituted bovine heart complex I proteoliposomes which shows a respiratory control ratio >5. Two frontier research groups support our view point based on their mutagenesis studies. High frequency (33.9GHz; Q-band) EPR experiments appear to favor our two-semiquinone model. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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215
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Sinha PK, Nakamaru-Ogiso E, Torres-Bacete J, Sato M, Castro-Guerrero N, Ohnishi T, Matsuno-Yagi A, Yagi T. Electron transfer in subunit NuoI (TYKY) of Escherichia coli NADH:quinone oxidoreductase (NDH-1). J Biol Chem 2012; 287:17363-17373. [PMID: 22474289 DOI: 10.1074/jbc.m111.329649] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial proton-translocating NADH:quinone oxidoreductase (NDH-1) consists of a peripheral and a membrane domain. The peripheral domain catalyzes the electron transfer from NADH to quinone through a chain of seven iron-sulfur (Fe/S) clusters. Subunit NuoI in the peripheral domain contains two [4Fe-4S] clusters (N6a and N6b) and plays a role in bridging the electron transfer from cluster N5 to the terminal cluster N2. We constructed mutants for eight individual Cys-coordinating Fe/S clusters. With the exception of C63S, all mutants had damaged architecture of NDH-1, suggesting that Cys-coordinating Fe/S clusters help maintain the NDH-1 structure. Studies of three mutants (C63S-coordinating N6a, P110A located near N6a, and P71A in the vicinity of N6b) were carried out using EPR measurement. These three mutations did not affect the EPR signals from [2Fe-2S] clusters and retained electron transfer activities. Signals at g(z) = 2.09 disappeared in C63S and P110A but not in P71A. Considering our data together with the available information, g(z,x) = 2.09, 1.88 signals are assigned to cluster N6a. It is of interest that, in terms of g(z,x) values, cluster N6a is similar to cluster N4. In addition, we investigated the residues (Ile-94 and Ile-100) that are predicted to serve as electron wires between N6a and N6b and between N6b and N2, respectively. Replacement of Ile-100 and Ile-94 with Ala/Gly did not affect the electron transfer activity significantly. It is concluded that conserved Ile-100 and Ile-94 are not essential for the electron transfer.
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Affiliation(s)
- Prem Kumar Sinha
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Eiko Nakamaru-Ogiso
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jesus Torres-Bacete
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Motoaki Sato
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Norma Castro-Guerrero
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Tomoko Ohnishi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Akemi Matsuno-Yagi
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037
| | - Takao Yagi
- Department of Molecular and Experimental Medicine, MEM-256, The Scripps Research Institute, La Jolla, California 92037.
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216
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Angerer H, Nasiri HR, Niedergesäß V, Kerscher S, Schwalbe H, Brandt U. Tracing the tail of ubiquinone in mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1776-84. [PMID: 22484275 DOI: 10.1016/j.bbabio.2012.03.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 12/01/2022]
Abstract
Mitochondrial complex I (proton pumping NADH:ubiquinone oxidoreductase) is the largest and most complicated component of the respiratory electron transfer chain. Despite its central role in biological energy conversion the structure and function of this membrane integral multiprotein complex is still poorly understood. Recent insights into the structure of complex I by X-ray crystallography have shown that iron-sulfur cluster N2, the immediate electron donor for ubiquinone, resides about 30Å above the membrane domain and mutagenesis studies suggested that the active site for the hydrophobic substrate is located next to this redox-center. To trace the path for the hydrophobic tail of ubiquinone when it enters the peripheral arm of complex I, we performed an extensive structure/function analysis of complex I from Yarrowia lipolytica monitoring the interaction of site-directed mutants with five ubiquinone derivatives carrying different tails. The catalytic activity of a subset of mutants was strictly dependent on the presence of intact isoprenoid moieties in the tail. Overall a consistent picture emerged suggesting that the tail of ubiquinone enters through a narrow path at the interface between the 49-kDa and PSST subunits. Most notably we identified a set of methionines that seems to form a hydrophobic gate to the active site reminiscent to the M-domains involved in the interaction with hydrophobic targeting sequences with the signal recognition particle of the endoplasmic reticulum. Interestingly, two of the amino acids critical for the interaction with the ubiquinone tail are different in bovine complex I and we could show that one of these exchanges is responsible for the lower sensitivity of Y. lipolytica complex I towards the inhibitor rotenone. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Heike Angerer
- Goethe-University, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
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217
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Batista AP, Marreiros BC, Louro RO, Pereira MM. Study of ion translocation by respiratory complex I. A new insight using (23)Na NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1810-6. [PMID: 22445719 DOI: 10.1016/j.bbabio.2012.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/07/2012] [Accepted: 03/08/2012] [Indexed: 10/28/2022]
Abstract
The research on complex I has gained recently a new enthusiasm, especially after the resolution of the crystallographic structures of bacterial and mitochondrial complexes. Most attention is now dedicated to the investigation of the energy coupling mechanism(s). The proton has been identified as the coupling ion, although in the case of some bacterial complexes I Na(+) has been proposed to have that role. We have addressed the relation of some complexes I with Na(+) and developed an innovative methodology using (23)Na NMR spectroscopy. This allowed the investigation of Na(+) transport taking the advantage of directly monitoring changes in Na(+) concentration. Methodological aspects concerning the use of (23)Na NMR spectroscopy to measure accurately sodium transport in bacterial membrane vesicles are discussed here. External-vesicle Na(+) concentrations were determined by two different methods: 1) by integration of the resonance frequency peak and 2) using calibration curves of resonance frequency shift dependence on Na(+) concentration. Although the calibration curves are a suitable way to determine Na(+) concentration changes under conditions of fast exchange, it was shown not to be applicable to the bacterial membrane vesicle systems. In this case, the integration of the resonance frequency peak is the most appropriate analysis for the quantification of external-vesicle Na(+) concentration. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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218
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Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. Proc Natl Acad Sci U S A 2012; 109:4431-6. [PMID: 22392981 DOI: 10.1073/pnas.1120949109] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Complex I (NADH-ubiquinone oxidoreductase) in the respiratory chain of mitochondria and several bacteria functions as a redox-driven proton pump that contributes to the generation of the protonmotive force across the inner mitochondrial or bacterial membrane and thus to the aerobic synthesis of ATP. The stoichiometry of proton translocation is thought to be 4 H(+) per NADH oxidized (2 e(-)). Here we show that a H(+)/2 e(-) ratio of 3 appears more likely on the basis of the recently determined H(+)/ATP ratio of the mitochondrial F(1)F(o)-ATP synthase of animal mitochondria and of a set of carefully determined ATP/2 e(-) ratios for different segments of the mitochondrial respiratory chain. This lower H(+)/2 e(-) ratio of 3 is independently supported by thermodynamic analyses of experiments with both mitochondria and submitochondrial particles. A reduced H(+)/2 e(-) stoichiometry of 3 has important mechanistic implications for this proton pump. In a rough mechanistic model, we suggest a concerted proton translocation mechanism in the three homologous and tightly packed antiporter-like subunits L, M, and N of the proton-translocating membrane domain of complex I.
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219
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Schertl P, Sunderhaus S, Klodmann J, Grozeff GEG, Bartoli CG, Braun HP. L-galactono-1,4-lactone dehydrogenase (GLDH) forms part of three subcomplexes of mitochondrial complex I in Arabidopsis thaliana. J Biol Chem 2012; 287:14412-9. [PMID: 22378782 DOI: 10.1074/jbc.m111.305144] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
L-galactono-1,4-lactone dehydrogenase (GLDH) catalyzes the terminal step of the Smirnoff-Wheeler pathway for vitamin C (l-ascorbate) biosynthesis in plants. A GLDH in gel activity assay was developed to biochemically investigate GLDH localization in plant mitochondria. It previously has been shown that GLDH forms part of an 850-kDa complex that represents a minor form of the respiratory NADH dehydrogenase complex (complex I). Because accumulation of complex I is disturbed in the absence of GLDH, a role of this enzyme in complex I assembly has been proposed. Here we report that GLDH is associated with two further protein complexes. Using native gel electrophoresis procedures in combination with the in gel GLDH activity assay and immunoblotting, two mitochondrial complexes of 470 and 420 kDa were identified. Both complexes are of very low abundance. Protein identifications by mass spectrometry revealed that they include subunits of complex I. Finally, the 850-kDa complex was further investigated and shown to include the complete "peripheral arm" of complex I. GLDH is attached to a membrane domain, which represents a major fragment of the "membrane arm" of complex I. Taken together, our data further support a role of GLDH during complex I formation, which is based on its binding to specific assembly intermediates.
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Affiliation(s)
- Peter Schertl
- Institut für Pflanzengenetik, Abteilung Pflanzenproteomik, Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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220
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Shiraishi Y, Murai M, Sakiyama N, Ifuku K, Miyoshi H. Fenpyroximate Binds to the Interface between PSST and 49 kDa Subunits in Mitochondrial NADH-Ubiquinone Oxidoreductase. Biochemistry 2012; 51:1953-63. [DOI: 10.1021/bi300047h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yusuke Shiraishi
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Masatoshi Murai
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Naoto Sakiyama
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Kentaro Ifuku
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
| | - Hideto Miyoshi
- Division
of Applied Life Sciences, Graduate School of Agriculture, and ‡Division of
Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502,
Japan
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221
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Steimle S, Willistein M, Hegger P, Janoschke M, Erhardt H, Friedrich T. Asp563 of the horizontal helix of subunit NuoL is involved in proton translocation by the respiratory complex I. FEBS Lett 2012; 586:699-704. [PMID: 22326235 DOI: 10.1016/j.febslet.2012.01.056] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/30/2022]
Abstract
The NADH:ubiquinone oxidoreductase couples the electron transfer from NADH to ubiquinone with the translocation of protons across the membrane. It contains a 110Å long helix running parallel to the membrane part of the complex. Deletion of the helix resulted in a reduced H(+)/e(-) stoichiometry indicating its direct involvement in proton translocation. Here, we show that the mutation of the conserved amino acid D563(L), which is part of the horizontal helix of the Escherichia coli complex I, leads to a reduced H(+)/e(-) stoichiometry. It is discussed that this residue is involved in transferring protons to the membranous proton translocation site.
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Affiliation(s)
- Stefan Steimle
- Albert-Ludwigs-Universität Freiburg, Institut für Organische Chemie und Biochemie, Freiburg i. Br., Germany
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222
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Abstract
Mitochondria are essential organelles with multiple functions, the most well known being the production of adenosine triphosphate (ATP) through oxidative phosphorylation (OXPHOS). The mitochondrial diseases are defined by impairment of OXPHOS. They are a diverse group of diseases that can present in virtually any tissue in either adults or children. Here we review the main molecular mechanisms of mitochondrial diseases, as presently known. A number of disease-causing genetic defects, either in the nuclear genome or in the mitochondria's own genome, mitochondrial DNA (mtDNA), have been identified. The most classical genetic defect causing mitochondrial disease is a mutation in a gene encoding a structural OXPHOS subunit. However, mitochondrial diseases can also arise through impaired mtDNA maintenance, defects in mitochondrial translation factors, and various more indirect mechanisms. The putative consequences of mitochondrial dysfunction on a cellular level are discussed.
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Affiliation(s)
- Emil Ylikallio
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Finland.
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223
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Pagniez-Mammeri H, Loublier S, Legrand A, Bénit P, Rustin P, Slama A. Mitochondrial complex I deficiency of nuclear origin I. Structural genes. Mol Genet Metab 2012; 105:163-72. [PMID: 22142868 DOI: 10.1016/j.ymgme.2011.11.188] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 11/09/2011] [Accepted: 11/09/2011] [Indexed: 10/15/2022]
Abstract
Complex I (or NADH-ubiquinone oxidoreductase), is by far the largest respiratory chain complex with 38 subunits nuclearly encoded and 7 subunits encoded by the mitochondrial genome. Its deficiency is the most frequently encountered in mitochondrial disorders. Here, we summarize recent data obtained on architecture of complex I, and review the pathogenic mutations identified to date in nuclear structural complex I genes. The structural NDUFS1, NDUFS2, NDUFV1, and NDUFS4 genes are mutational hot spot genes for isolated complex I deficiency. The majority of the pathogenic mutations are private and the genotype-phenotype correlation is inconsistent in the rare recurrent mutations.
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Affiliation(s)
- Hélène Pagniez-Mammeri
- Laboratoire de Biochimie, APHP Hôpital de Bicêtre, 78 rue du Général Leclerc, 94275 Le Kremlin Bicêtre cedex, France
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224
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Dröse S, Brandt U. Molecular mechanisms of superoxide production by the mitochondrial respiratory chain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 748:145-69. [PMID: 22729857 DOI: 10.1007/978-1-4614-3573-0_6] [Citation(s) in RCA: 362] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mitochondrial respiratory chain is a major source of reactive oxygen species (ROS) in eukaryotic cells. Mitochondrial ROS production associated with a dysfunction of respiratory chain complexes has been implicated in a number of degenerative diseases and biological aging. Recent findings suggest that mitochondrial ROS can be integral components of cellular signal transduction as well. Within the respiratory chain, complexes I (NADH:ubiquinone oxidoreductase) and III (ubiquinol:cytochrome c oxidoreductase; cytochrome bc (1) complex) are generally considered as the main producers of superoxide anions that are released into the mitochondrial matrix and the intermembrane space, respectively. The primary function of both respiratory chain complexes is to employ energy supplied by redox reactions to drive the vectorial transfer of protons into the mitochondrial intermembrane space. This process involves a set of distinct electron carriers designed to minimize the unwanted leak of electrons from reduced cofactors onto molecular oxygen and hence ROS generation under normal circumstances. Nevertheless, it seems plausible that superoxide is derived from intermediates of the normal catalytic cycles of complexes I and III. Therefore, a detailed understanding of the molecular mechanisms driving these enzymes is required to understand mitochondrial ROS production during oxidative stress and redox signalling. This review summarizes recent findings on the chemistry and control of the reactions within respiratory complexes I and III that result in increased superoxide generation. Regulatory contributions of other components of the respiratory chain, especially complex II (succinate:ubiquinone oxidoreductase) and the redox state of the ubiquinone pool (Q-pool) will be briefly discussed.
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Affiliation(s)
- Stefan Dröse
- Center for Membrane Proteomics, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany.
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225
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Papa S, Martino PL, Capitanio G, Gaballo A, De Rasmo D, Signorile A, Petruzzella V. The oxidative phosphorylation system in mammalian mitochondria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 942:3-37. [PMID: 22399416 DOI: 10.1007/978-94-007-2869-1_1] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The chapter provides a review of the state of art of the oxidative phosphorylation system in mammalian mitochondria. The sections of the paper deal with: (i) the respiratory chain as a whole: redox centers of the chain and protonic coupling in oxidative phosphorylation (ii) atomic structure and functional mechanism of protonmotive complexes I, III, IV and V of the oxidative phosphorylation system (iii) biogenesis of oxidative phosphorylation complexes: mitochondrial import of nuclear encoded subunits, assembly of oxidative phosphorylation complexes, transcriptional factors controlling biogenesis of the complexes. This advanced knowledge of the structure, functional mechanism and biogenesis of the oxidative phosphorylation system provides a background to understand the pathological impact of genetic and acquired dysfunctions of mitochondrial oxidative phosphorylation.
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Affiliation(s)
- Sergio Papa
- Department of Basic Medical Sciences, University of Bari, Bari, Italy.
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226
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Meyer EH. Proteomic investigations of complex I composition: how to define a subunit? FRONTIERS IN PLANT SCIENCE 2012; 3:106. [PMID: 22654890 PMCID: PMC3359495 DOI: 10.3389/fpls.2012.00106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 05/07/2012] [Indexed: 05/20/2023]
Abstract
Complex I is present in almost all aerobic species. Being the largest complex of the respiratory chain, it has a central role in energizing biological membranes and is essential for many organisms. Bacterial complex I is composed of 14 subunits that are sufficient to achieve the respiratory functions. Eukaryotic enzymes contain orthologs of the 14 bacterial subunits and around 30 additional subunits. This complexity suggests either that complex I requires more stabilizing subunits in mitochondria or that it fulfills additional functions. In many organisms recent work on complex I concentrated on the determination of its exact composition. This review summarizes the work done to elucidate complex I composition in the model plant Arabidopsis and proposes a model for the organization of its 44 confirmed subunits. The comparison of the different studies investigating the composition of complex I across species identifies sample preparation for the proteomic analysis as critical to differentiate between true subunits, assembly factors, or proteins associated with complex I. Coupling comparative proteomics with biochemical or genetic studies is thus required to define a subunit and its function within the complex.
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Affiliation(s)
- Etienne H. Meyer
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de StrasbourgStrasbourg, France
- *Correspondence: Etienne H. Meyer, Institut de Biologie Moléculaire des Plantes, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France. e-mail:
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227
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Assembly Factors of Human Mitochondrial Respiratory Chain Complexes: Physiology and Pathophysiology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 748:65-106. [DOI: 10.1007/978-1-4614-3573-0_4] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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228
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Kadenbach B. Introduction to mitochondrial oxidative phosphorylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 748:1-11. [PMID: 22729852 DOI: 10.1007/978-1-4614-3573-0_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The basic mechanism of ATP synthesis in the mitochondria by oxidative phosphorylation (OxPhos) was revealed in the second half of the twentieth century. The OxPhos complexes I-V have been analyzed concerning their subunit composition, genes, and X-ray structures. This book presents new developments regarding the morphology, biogenesis, gene evolution, heat, and reactive oxygen species (ROS) generation in mitochondria, as well as the structure and supercomplex formation of OxPhos complexes. In addition, multiple mitochondrial diseases based on mutations of nuclear-encoded genes have been identified. Little is known, however, of the regulation of OxPhos according to the variable cellular demands of ATP. In particular, the functions of the supernumerary (nuclear-encoded) subunits of mitochondrial OxPhos complexes, which are mostly absent in bacteria, remain largely unknown, although the corresponding and conserved core subunits exhibit the same catalytic activity. Identification of regulatory pathways modulating OxPhos activity, by subunit isoform expression, by allosteric interaction with ATP/ADP, by reversible phosphorylation of protein subunits, or by supercomplex formation, will help to understand the role of mitochondria in the many degenerative diseases, mostly based on ROS formation in mitochondria and/or insufficient energy production.
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229
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Enigmatic presence of mitochondrial complex I in Trypanosoma brucei bloodstream forms. EUKARYOTIC CELL 2011; 11:183-93. [PMID: 22158713 DOI: 10.1128/ec.05282-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The presence of mitochondrial respiratory complex I in the pathogenic bloodstream stages of Trypanosoma brucei has been vigorously debated: increased expression of mitochondrially encoded functional complex I mRNAs is countered by low levels of enzymatic activity that show marginal inhibition by the specific inhibitor rotenone. We now show that epitope-tagged versions of multiple complex I subunits assemble into α and β subcomplexes in the bloodstream stage and that these subcomplexes require the mitochondrial genome for their assembly. Despite the presence of these large (740- and 855-kDa) multisubunit complexes, the electron transport activity of complex I is not essential under experimental conditions since null mutants of two core genes (NUBM and NUKM) showed no growth defect in vitro or in mouse infection. Furthermore, the null mutants showed no decrease in NADH:ubiquinone oxidoreductase activity, suggesting that the observed activity is not contributed by complex I. This work conclusively shows that despite the synthesis and assembly of subunit proteins, the enzymatic function of the largest respiratory complex is neither significant nor important in the bloodstream stage. This situation appears to be in striking contrast to that for the other respiratory complexes in this parasite, where physical presence in a life-cycle stage always indicates functional significance.
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230
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Bridges HR, Bill E, Hirst J. Mössbauer spectroscopy on respiratory complex I: the iron-sulfur cluster ensemble in the NADH-reduced enzyme is partially oxidized. Biochemistry 2011; 51:149-58. [PMID: 22122402 PMCID: PMC3254188 DOI: 10.1021/bi201644x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
In mitochondria, complex I (NADH:quinone oxidoreductase)
couples
electron transfer to proton translocation across an energy-transducing
membrane. It contains a flavin mononucleotide to oxidize NADH, and
an unusually long series of iron–sulfur (FeS) clusters that
transfer the electrons to quinone. Understanding electron transfer
in complex I requires spectroscopic and structural data to be combined
to reveal the properties of individual clusters and of the ensemble.
EPR studies on complex I from Bos taurus have established
that five clusters (positions 1, 2, 3, 5, and 7 along the seven-cluster
chain extending from the flavin) are (at least partially) reduced
by NADH. The other three clusters, positions 4 and 6 plus a cluster
on the other side of the flavin, are not observed in EPR spectra from
the NADH-reduced enzyme: they may remain oxidized, have unusual or
coupled spin states, or their EPR signals may be too fast relaxing.
Here, we use Mössbauer spectroscopy on 57Fe-labeled
complex I from the mitochondria of Yarrowia lipolytica to show that the cluster ensemble is only partially reduced in the
NADH-reduced enzyme. The three EPR-silent clusters are oxidized, and
only the terminal 4Fe cluster (position 7) is fully reduced. Together
with the EPR analyses, our results reveal an alternating profile of
higher and lower potential clusters between the two active sites in
complex I; they are not consistent with the consensus picture of a
set of isopotential clusters. The implications for intramolecular
electron transfer along the extended chain of cofactors in complex
I are discussed.
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Affiliation(s)
- Hannah R Bridges
- Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge, CB2 0XY, UK
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231
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Mutations in the Gene Encoding C8orf38 Block Complex I Assembly by Inhibiting Production of the Mitochondria-Encoded Subunit ND1. J Mol Biol 2011; 414:413-26. [DOI: 10.1016/j.jmb.2011.10.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/07/2011] [Accepted: 10/07/2011] [Indexed: 12/11/2022]
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232
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Kalashnikov DS, Grivennikova VG, Vinogradov AD. Submitochondrial fragments of brain mitochondria: general characteristics and catalytic properties of NADH:ubiquinone oxidoreductase (complex I). BIOCHEMISTRY (MOSCOW) 2011; 76:209-16. [PMID: 21568854 DOI: 10.1134/s0006297911020076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A number of genetic or drug-induced pathophysiological disorders, particularly neurodegenerative diseases, have been reported to correlate with catalytic impairments of NADH:ubiquinone oxidoreductase (mitochondrial complex I). The vast majority of the data on catalytic properties of this energy-transducing enzyme have been accumulated from studies on bovine heart complex I preparations of different degrees of resolution, whereas almost nothing is known about the functional activities of the enzyme in neuronal tissues. Here a procedure for preparation of coupled inside-out submitochondrial particles from brain is described and their NADH oxidase activity is characterized. The basic characteristics of brain complex I, particularly the parameters of A/D-transition are found to be essentially the same as those previously reported for heart enzyme. The results show that coupled submitochondrial particles prepared from either heart or brain can equally be used as a model system for in vitro studies aimed to delineate neurodegenerative-associated defects of complex I.
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Affiliation(s)
- D S Kalashnikov
- Department of Biochemistry, Faculty of Biology, Lomonosov Moscow State University, Russia
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233
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Cramer WA, Zakharov SD, Saif Hasan S, Zhang H, Baniulis D, Zhalnina MV, Soriano GM, Sharma O, Rochet JC, Ryan C, Whitelegge J, Kurisu G, Yamashita E. Membrane proteins in four acts: function precedes structure determination. Methods 2011; 55:415-20. [PMID: 22079407 DOI: 10.1016/j.ymeth.2011.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/30/2011] [Accepted: 11/01/2011] [Indexed: 10/15/2022] Open
Abstract
Studies on four membrane protein systems, which combine information derived from crystal structures and biophysical studies have emphasized, as a precursor to crystallization, demonstration of functional activity. These assays have relied on sensitive spectrophotometric, electrophysiological, and microbiological assays of activity to select purification procedures that lead to functional complexes and with greater likelihood to successful crystallization: (I), Hetero-oligomeric proteins involved in electron transport/proton translocation. (1) Crystal structures of the eight subunit hetero-oligomeric trans-membrane dimeric cytochrome b(6)f complex were obtained from cyanobacteria using a protocol that allowed an analysis of the structure and function of internal lipids at specific intra-membrane, intra-protein sites. Proteolysis and monomerization that inactivated the complex and prevented crystallization was minimized through the use of filamentous cyanobacterial strains that seem to have a different set of membrane-active proteases. (2) An NADPH-quinone oxido-reductase isolated from cyanobacteria contains an expanded set of 17 monotopic and polytopic hetero-subunits. (II) β-Barrel outer membrane proteins (OMPs). High resolution structures of the vitamin B(12) binding protein, BtuB, solved in meso and in surfo, provide the best example of the differences in such structures that were anticipated in the first application of the lipid cubic phase to membrane proteins [1]. A structure of the complex of BtuB with the colicin E3 and E2 receptor binding domain established a "fishing pole" model for outer membrane receptor function in cellular import of nuclease colicins. (III) A modified faster purification procedure contributed to significantly improved resolution (1.83Å) of the universal porin, OmpF, the first membrane protein for which meaningful 3D crystals have been obtained [2]. A crystal structure of the N-terminal translocation domain of colicin E3 complexed to OmpF established the role of OmpF as an import channel for colicin nuclease cytotoxins. (IV) α-Synuclein, associated with the etiology of Parkinson's Disease, is an example of a protein, which is soluble and disordered in solution, but which can assume an ordered predominantly α-helical conformation upon binding to membranes. When subjected in its membrane-bound form to a trans-membrane electrical potential, α-synuclein can form voltage-gated ion channels. Summary of methods to assay functions/activities: (i) sensitive spectrophotometric assay to measure electron transfer activities; (ii) hydrophobic chromatography to deplete lipids, allowing reconstitution with specific lipids for studies on lipid-protein interactions; (iii) microbiological screen to assay high affinity binding of colicin receptor domains to Escherichia coli outer membrane receptors; (iv) electrophysiology/channel analysis (a) to select channel-occluding ligands for co-crystallization with ion channels of OmpF, and (b) to provide a unique description of voltage-gated ion channels of α-synuclein.
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Affiliation(s)
- W A Cramer
- Department of Biological Sciences, Purdue University, Hall of Structural Biology, 240 Hockmeyer Hall, West Lafayette, IN 47907-1354, USA.
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Couch V, Popovic D, Stuchebrukhov A. Redox-coupled protonation of respiratory complex I: the hydrophilic domain. Biophys J 2011; 101:431-8. [PMID: 21767496 DOI: 10.1016/j.bpj.2011.05.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 05/20/2011] [Accepted: 05/25/2011] [Indexed: 11/24/2022] Open
Abstract
Respiratory complex I, NADH:ubiquinone oxidoreductase, is a large and complex integral membrane enzyme found in respiring bacteria and mitochondria. It is responsible in part for generating the proton gradient necessary for ATP production. Complex I serves as both a proton pump and an entry point for electrons into the respiratory chain. Although complex I is one of the most important of the respiratory complexes, it is also one of the least understood, with detailed structural information only recently available. In this study, full-finite-difference Poisson-Boltzmann calculations of the protonation state of respiratory complex I in various redox states are presented. Since complex I couples the oxidation and reduction of the NADH/ubiquinone redox couple to proton translocation, the interaction of the protonation and redox states of the enzyme are of the utmost significance. Various aspects of complex I function are presented, including the redox-Bohr effect, intercofactor interactions, and the effects of both the protein dielectric and inclusion of the membrane.
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Affiliation(s)
- Vernon Couch
- Department of Chemistry, University of California, Davis, California, USA
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235
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Belevich G, Knuuti J, Verkhovsky MI, Wikström M, Verkhovskaya M. Probing the mechanistic role of the long α-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis. Mol Microbiol 2011; 82:1086-95. [PMID: 22060017 PMCID: PMC3274701 DOI: 10.1111/j.1365-2958.2011.07883.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The C-terminus of the NuoL subunit of Complex I includes a long amphipathic α-helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston-like function. First, NuoL was truncated at its C- and N-termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the amphipathic α-helix: Asp and Lys residues and a Pro were substituted for acidic, basic or neutral residues. All these variants exhibited almost a wild-type phenotype. Third, several substitutions and insertions were made to reduce rigidity of the amphipathic α-helix, and/or to change its geometry. Most insertions/substitutions resulted in a normal growth phenotype, albeit often with reduced stability of Complex I. In contrast, insertion of six to seven amino acids at a site of the long α-helix between NuoL and M resulted in substantial loss of proton pumping efficiency. The implications of these results for the proton pumping mechanism of Complex I are discussed.
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Affiliation(s)
- Galina Belevich
- Helsinki Bioenergetics Group, Institute of Biotechnology, FIN-00014, University of Helsinki, Helsinki, Finland
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236
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Pätsi J, Maliniemi P, Pakanen S, Hinttala R, Uusimaa J, Majamaa K, Nyström T, Kervinen M, Hassinen IE. LHON/MELAS overlap mutation in ND1 subunit of mitochondrial complex I affects ubiquinone binding as revealed by modeling in Escherichia coli NDH-1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:312-8. [PMID: 22079202 DOI: 10.1016/j.bbabio.2011.10.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 10/27/2011] [Accepted: 10/28/2011] [Indexed: 10/15/2022]
Abstract
Defects in complex I due to mutations in mitochondrial DNA are associated with clinical features ranging from single organ manifestation like Leber hereditary optic neuropathy (LHON) to multiorgan disorders like mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome. Specific mutations cause overlap syndromes combining several phenotypes, but the mechanisms of their biochemical effects are largely unknown. The m.3376G>A transition leading to p.E24K substitution in ND1 with LHON/MELAS phenotype was modeled here in a homologous position (NuoH-E36K) in the Escherichia coli enzyme and it almost totally abolished complex I activity. The more conservative mutation NuoH-E36Q resulted in higher apparent K(m) for ubiquinone and diminished inhibitor sensitivity. A NuoH homolog of the m.3865A>G transition, which has been found concomitantly in the overlap syndrome patient with the m.3376G>A, had only a minor effect. Consequences of a primary LHON-mutation m.3460G>A affecting the same extramembrane loop as the m.3376G>A substitution were also studied in the E. coli model and were found to be mild. The results indicate that the overlap syndrome-associated m.3376G>A transition in MTND1 is the pathogenic mutation and m.3865A>G transition has minor, if any, effect on presentation of the disease. The kinetic effects of the NuoH-E36Q mutation suggest its proximity to the putative ubiquinone binding domain in 49kD/PSST subunits. In all, m.3376G>A perturbs ubiquinone binding, a phenomenon found in LHON, and decreases the activity of fully assembled complex I as in MELAS.
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Affiliation(s)
- Jukka Pätsi
- Department of Medical Biochemistry and Molecular Biology, University of Oulu, Finland
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237
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Mitochondrial NADH:ubiquinone oxidoreductase (complex I) in eukaryotes: A highly conserved subunit composition highlighted by mining of protein databases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1390-7. [DOI: 10.1016/j.bbabio.2011.06.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 06/18/2011] [Accepted: 06/22/2011] [Indexed: 11/22/2022]
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238
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Erhardt H, Steimle S, Muders V, Pohl T, Walter J, Friedrich T. Disruption of individual nuo-genes leads to the formation of partially assembled NADH:ubiquinone oxidoreductase (complex I) in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:863-71. [PMID: 22063474 DOI: 10.1016/j.bbabio.2011.10.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/14/2011] [Accepted: 10/21/2011] [Indexed: 10/15/2022]
Abstract
The proton-pumping NADH:ubiquinone oxidoreductase, respiratory complex I, couples the electron transfer from NADH to ubiquinone with the translocation of protons across the membrane. In Escherichia coli the complex is made up of 13 different subunits encoded by the so-called nuo-genes. Mutants, in which each of the nuo-genes was individually disrupted by the insertion of a resistance cartridge were unable to assemble a functional complex I. Each disruption resulted in the loss of complex I-mediated activity and the failure to extract a structurally intact complex. Thus, all nuo-genes are required either for the assembly or the stability of a functional E. coli complex I. The three subunits comprising the soluble NADH dehydrogenase fragment of the complex were detected in the cytoplasm of several nuo-mutants as one distinct band after BN-PAGE. It is discussed that the fully assembled NADH dehydrogenase fragment represents an assembly intermediate of the E. coli complex I. A partially assembled complex I bound to the membrane was detected in the nuoK and nuoL mutants, respectively. Overproduction of the ΔNuoL variant resulted in the accumulation of two populations of a partially assembled complex in the cytoplasmic membranes. Both populations are devoid of NuoL. One population is enzymatically active, while the other is not. The inactive population is missing cluster N2 and is tightly associated with the inducible lysine decarboxylase. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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Affiliation(s)
- Heiko Erhardt
- Albert-Ludwigs-Universität, Freiburg, Institut für Organische Chemie und Biochemie and Spemann Graduate School of Biology and Medicine, Albertstr. 21, 79104 Freiburg i. Br., Germany
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239
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Abstract
Mitochondrial dysfunction often leads to cell death and disease. We can now draw correlations between the dysfunction of one of the most important mitochondrial enzymes, NADH:ubiquinone reductase or complex I, and its structural organization thanks to the recent advances in the X-ray structure of its bacterial homologs. The new structural information on bacterial complex I provide essential clues to finally understand how complex I may work. However, the same information remains difficult to interpret for many scientists working on mitochondrial complex I from different angles, especially in the field of cell death. Here, we present a novel way of interpreting the bacterial structural information in accessible terms. On the basis of the analogy to semi-automatic shotguns, we propose a novel functional model that incorporates recent structural information with previous evidence derived from studies on mitochondrial diseases, as well as functional bioenergetics.
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240
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Virzintiene E, Trane M, Hägerhäll C. Revised transmembrane orientation of the NADH:quinone oxidoreductase subunit NuoA. FEBS Lett 2011; 585:3277-83. [PMID: 21925501 DOI: 10.1016/j.febslet.2011.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/04/2011] [Accepted: 09/05/2011] [Indexed: 01/14/2023]
Abstract
NuoA is a small membrane spanning subunit of respiratory chain NADH:quinone oxidoreductase (complex I). Unlike the other complex I core protein subunits, the NuoA protein has no known homologue in other enzyme systems. The transmembrane orientation of NuoA cannot be unambiguously predicted, due to the small size of the polypeptide and the varying distribution of charged amino acid residues in NuoA from different organisms. Novel analyses of NuoA from Escherichia coli complex I expressed as fusion proteins to cytochrome c and to alkaline phosphatase demonstrated that the c-terminal end of the polypeptide is localized in the bacterial cytoplasm, in contrast to what was previously reported for the homologous NQO7 subunit from Paracoccus denitrificans complex I.
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Affiliation(s)
- Egle Virzintiene
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden
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241
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Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD, Pyle AM. Structural insights into RNA recognition by RIG-I. Cell 2011; 147:409-22. [PMID: 22000018 PMCID: PMC3222294 DOI: 10.1016/j.cell.2011.09.023] [Citation(s) in RCA: 311] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 08/02/2011] [Accepted: 09/16/2011] [Indexed: 12/19/2022]
Abstract
Intracellular RIG-I-like receptors (RLRs, including RIG-I, MDA-5, and LGP2) recognize viral RNAs as pathogen-associated molecular patterns (PAMPs) and initiate an antiviral immune response. To understand the molecular basis of this process, we determined the crystal structure of RIG-I in complex with double-stranded RNA (dsRNA). The dsRNA is sheathed within a network of protein domains that include a conserved "helicase" domain (regions HEL1 and HEL2), a specialized insertion domain (HEL2i), and a C-terminal regulatory domain (CTD). A V-shaped pincer connects HEL2 and the CTD by gripping an α-helical shaft that extends from HEL1. In this way, the pincer coordinates functions of all the domains and couples RNA binding with ATP hydrolysis. RIG-I falls within the Dicer-RIG-I clade of the superfamily 2 helicases, and this structure reveals complex interplay between motor domains, accessory mechanical domains, and RNA that has implications for understanding the nanomechanical function of this protein family and other ATPases more broadly.
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Affiliation(s)
- Dahai Luo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
| | - Steve C. Ding
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Adriana Vela
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Andrew Kohlway
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Brett D. Lindenbach
- Section of Microbial Pathogenesis, Yale University, New Haven, Connecticut 06520
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
- Department of Chemistry, Yale University, New Haven, Connecticut 06520
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
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242
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A two-state stabilization-change mechanism for proton-pumping complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1364-9. [DOI: 10.1016/j.bbabio.2011.04.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Revised: 04/17/2011] [Accepted: 04/19/2011] [Indexed: 11/18/2022]
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243
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Garvin MR, Bielawski JP, Gharrett AJ. Positive Darwinian selection in the piston that powers proton pumps in complex I of the mitochondria of Pacific salmon. PLoS One 2011; 6:e24127. [PMID: 21969854 PMCID: PMC3182164 DOI: 10.1371/journal.pone.0024127] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 08/04/2011] [Indexed: 11/23/2022] Open
Abstract
The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm.
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Affiliation(s)
- Michael R Garvin
- Fisheries Division, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, United States of America.
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244
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Calvaruso MA, Willems P, van den Brand M, Valsecchi F, Kruse S, Palmiter R, Smeitink J, Nijtmans L. Mitochondrial complex III stabilizes complex I in the absence of NDUFS4 to provide partial activity. Hum Mol Genet 2011; 21:115-20. [DOI: 10.1093/hmg/ddr446] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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245
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The mitochondrial-encoded subunits of respiratory complex I (NADH:ubiquinone oxidoreductase): identifying residues important in mechanism and disease. Biochem Soc Trans 2011; 39:799-806. [PMID: 21599651 DOI: 10.1042/bst0390799] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is crucial to respiration in many aerobic organisms. The hydrophilic domain of complex I, containing nine or more redox cofactors, and comprising seven conserved core subunits, protrudes into the mitochondrial matrix or bacterial cytoplasm. The α-helical membrane-bound hydrophobic domain contains a further seven core subunits that are mitochondrial-encoded in eukaryotes and named the ND subunits (ND1-ND6 and ND4L). Complex I couples the oxidation of NADH in the hydrophilic domain to ubiquinone reduction and proton translocation in the hydrophobic domain. Although the mechanisms of NADH oxidation and intramolecular electron transfer are increasingly well understood, the mechanisms of ubiquinone reduction and proton translocation remain only poorly defined. Recently, an α-helical model of the hydrophobic domain of bacterial complex I [Efremov, Baradaran and Sazanov (2010) Nature 465, 441-447] revealed how the 63 transmembrane helices of the seven core subunits are arranged, and thus laid a foundation for the interpretation of functional data and the formulation of mechanistic proposals. In the present paper, we aim to correlate information from sequence analyses, site-directed mutagenesis studies and mutations that have been linked to human diseases, with information from the recent structural model. Thus we aim to identify and discuss residues in the ND subunits of mammalian complex I which are important in catalysis and for maintaining the enzyme's structural and functional integrity.
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246
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Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1. EMBO J 2011; 30:4652-64. [PMID: 21909073 PMCID: PMC3243592 DOI: 10.1038/emboj.2011.324] [Citation(s) in RCA: 255] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/11/2011] [Indexed: 11/18/2022] Open
Abstract
The respiratory chain complexes of the mitochondrial inner membrane are organized as three higher-order multi-enzyme complexes. This study puts forward the first cryo-EM map for one of these supercomplexes and provides insight into possible pathways for efficient electron transfer. The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-Å 3D map of the 1.7-MDa amphipol-solubilized supercomplex I1III2IV1 from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X-ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol-binding sites of complexes I and III, and of 10–11 nm between the cytochrome c binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred.
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247
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A scaffold of accessory subunits links the peripheral arm and the distal proton-pumping module of mitochondrial complex I. Biochem J 2011; 437:279-88. [PMID: 21545356 DOI: 10.1042/bj20110359] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a very large membrane protein complex with a central function in energy metabolism. Complex I from the aerobic yeast Yarrowia lipolytica comprises 14 central subunits that harbour the bioenergetic core functions and at least 28 accessory subunits. Despite progress in structure determination, the position of individual accessory subunits in the enzyme complex remains largely unknown. Proteomic analysis of subcomplex Iδ revealed that it lacked eleven subunits, including the central subunits ND1 and ND3 forming the interface between the peripheral and the membrane arm in bacterial complex I. This unexpected observation provided insight into the structural organization of the connection between the two major parts of mitochondrial complex I. Combining recent structural information, biochemical evidence on the assignment of individual subunits to the subdomains of complex I and sequence-based predictions for the targeting of subunits to different mitochondrial compartments, we derived a model for the arrangement of the subunits in the membrane arm of mitochondrial complex I.
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248
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Abstract
The prokaryotic and eukaryotic homologues of complex I (proton-pumping NADH:quinone oxidoreductase) perform the same function in energy transduction, but the eukaryotic enzymes are twice as big as their prokaryotic cousins, and comprise three times as many subunits. Fourteen core subunits are conserved in all complexes I, and are sufficient for catalysis - so why are the eukaryotic enzymes embellished by so many supernumerary or accessory subunits? In this issue of the Biochemical Journal, Angerer et al. have provided new evidence to suggest that the supernumerary subunits are important for enzyme stability. This commentary aims to put this suggestion into context.
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249
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Understanding mitochondrial complex I assembly in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1817:851-62. [PMID: 21924235 DOI: 10.1016/j.bbabio.2011.08.010] [Citation(s) in RCA: 306] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/17/2011] [Accepted: 08/27/2011] [Indexed: 12/12/2022]
Abstract
Complex I (NADH:ubiquinone oxidoreductase) is the largest multimeric enzyme complex of the mitochondrial respiratory chain, which is responsible for electron transport and the generation of a proton gradient across the mitochondrial inner membrane to drive ATP production. Eukaryotic complex I consists of 14 conserved subunits, which are homologous to the bacterial subunits, and more than 26 accessory subunits. In mammals, complex I consists of 45 subunits, which must be assembled correctly to form the properly functioning mature complex. Complex I dysfunction is the most common oxidative phosphorylation (OXPHOS) disorder in humans and defects in the complex I assembly process are often observed. This assembly process has been difficult to characterize because of its large size, the lack of a high resolution structure for complex I, and its dual control by nuclear and mitochondrial DNA. However, in recent years, some of the atomic structure of the complex has been resolved and new insights into complex I assembly have been generated. Furthermore, a number of proteins have been identified as assembly factors for complex I biogenesis and many patients carrying mutations in genes associated with complex I deficiency and mitochondrial diseases have been discovered. Here, we review the current knowledge of the eukaryotic complex I assembly process and new insights from the identification of novel assembly factors. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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250
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Genova ML, Lenaz G. New developments on the functions of coenzyme Q in mitochondria. Biofactors 2011; 37:330-54. [PMID: 21989973 DOI: 10.1002/biof.168] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 04/06/2011] [Indexed: 12/12/2022]
Abstract
The notion of a mobile pool of coenzyme Q (CoQ) in the lipid bilayer has changed with the discovery of respiratory supramolecular units, in particular the supercomplex comprising complexes I and III; in this model, the electron transfer is thought to be mediated by tunneling or microdiffusion, with a clear kinetic advantage on the transfer based on random collisions. The CoQ pool, however, has a fundamental function in establishing a dissociation equilibrium with bound quinone, besides being required for electron transfer from other dehydrogenases to complex III. The mechanism of CoQ reduction by complex I is analyzed regarding recent developments on the crystallographic structure of the enzyme, also in relation to the capacity of complex I to generate superoxide. Although the mechanism of the Q-cycle is well established for complex III, involvement of CoQ in proton translocation by complex I is still debated. Some additional roles of CoQ are also examined, such as the antioxidant effect of its reduced form and the capacity to bind the permeability transition pore and the mitochondrial uncoupling proteins. Finally, a working hypothesis is advanced on the establishment of a vicious circle of oxidative stress and supercomplex disorganization in pathological states, as in neurodegeneration and cancer.
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