1
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Borek A, Wójcik-Augustyn A, Kuleta P, Ekiert R, Osyczka A. Identification of hydrogen bonding network for proton transfer at the quinol oxidation site of Rhodobacter capsulatus cytochrome bc 1. J Biol Chem 2023; 299:105249. [PMID: 37714464 PMCID: PMC10583091 DOI: 10.1016/j.jbc.2023.105249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023] Open
Abstract
Cytochrome bc1 catalyzes electron transfer from quinol (QH2) to cytochrome c in reactions coupled to proton translocation across the energy-conserving membrane. Energetic efficiency of the catalytic cycle is secured by a two-electron and two-proton bifurcation reaction leading to oxidation of QH2 and reduction of the Rieske cluster and heme bL. The proton paths associated with this reaction remain elusive. Here, we used site-directed mutagenesis and quantum mechanical calculations to analyze the contribution of protonable side chains located at the heme bL side of the QH2 oxidation site in Rhodobacter capsulatus cytochrome bc1. We observe that the proton path is effectively switched off when H276 and E295 are simultaneously mutated to the nonprotonable residues in the H276F/E295V double mutant. The two single mutants, H276F or E295V, are less efficient but still transfer protons at functionally relevant rates. Natural selection exposed two single mutations, N279S and M154T, that restored the functional proton transfers in H276F/E295V. Quantum mechanical calculations indicated that H276F/E295V traps the side chain of Y147 in a position distant from QH2, whereas either N279S or M154T induce local changes releasing Y147 from that position. This shortens the distance between the protonable groups of Y147 and D278 and/or increases mobility of the Y147 side chain, which makes Y147 efficient in transferring protons from QH2 toward D278 in H276F/E295V. Overall, our study identified an extended hydrogen bonding network, build up by E295, H276, D278, and Y147, involved in efficient proton removal from QH2 at the heme bL side of QH2 oxidation site.
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Affiliation(s)
- Arkadiusz Borek
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Wójcik-Augustyn
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Patryk Kuleta
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Robert Ekiert
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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2
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Brzezinski P, Moe A, Ädelroth P. Structure and Mechanism of Respiratory III-IV Supercomplexes in Bioenergetic Membranes. Chem Rev 2021; 121:9644-9673. [PMID: 34184881 PMCID: PMC8361435 DOI: 10.1021/acs.chemrev.1c00140] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/12/2022]
Abstract
In the final steps of energy conservation in aerobic organisms, free energy from electron transfer through the respiratory chain is transduced into a proton electrochemical gradient across a membrane. In mitochondria and many bacteria, reduction of the dioxygen electron acceptor is catalyzed by cytochrome c oxidase (complex IV), which receives electrons from cytochrome bc1 (complex III), via membrane-bound or water-soluble cytochrome c. These complexes function independently, but in many organisms they associate to form supercomplexes. Here, we review the structural features and the functional significance of the nonobligate III2IV1/2 Saccharomyces cerevisiae mitochondrial supercomplex as well as the obligate III2IV2 supercomplex from actinobacteria. The analysis is centered around the Q-cycle of complex III, proton uptake by CytcO, as well as mechanistic and structural solutions to the electronic link between complexes III and IV.
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Affiliation(s)
- Peter Brzezinski
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Agnes Moe
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics,
The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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3
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Iommarini L, Ghelli A, Leone G, Tropeano CV, Kurelac I, Amato LB, Gasparre G, Porcelli AM. Mild phenotypes and proper supercomplex assembly in human cells carrying the homoplasmic m.15557G > A mutation in cytochrome b gene. Hum Mutat 2017; 39:92-102. [PMID: 28967163 DOI: 10.1002/humu.23350] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/14/2022]
Abstract
Respiratory complex III (CIII) is the first enzymatic bottleneck of the mitochondrial respiratory chain both in its native dimeric form and in supercomplexes. The mammalian CIII comprises 11 subunits among which cytochrome b is central in the catalytic core, where oxidation of ubiquinol occurs at the Qo site. The Qo- or PEWY-motif of cytochrome b is the most conserved through species. Importantly, the highly conserved glutamate at position 271 (Glu271) has never been studied in higher eukaryotes so far and its role in the Q-cycle remains debated. Here, we showed that the homoplasmic m.15557G > A/MT-CYB, which causes the p.Glu271Lys amino acid substitution predicted to dramatically affect CIII, induces a mild mitochondrial dysfunction in human transmitochondrial cybrids. Indeed, we found that the severity of such mutation is mitigated by the proper assembly of CIII into supercomplexes, which may favor an optimal substrate channeling and buffer superoxide production in vitro.
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Affiliation(s)
- Luisa Iommarini
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | - Anna Ghelli
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | - Giulia Leone
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
| | | | - Ivana Kurelac
- Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, Bologna, Italy
| | - Laura Benedetta Amato
- Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, Bologna, Italy
| | - Giuseppe Gasparre
- Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), U.O. Genetica Medica, Pol. Universitario S. Orsola-Malpighi, Università di Bologna, Bologna, Italy
| | - Anna Maria Porcelli
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy.,Centro Interdipartimentale di Ricerca Industriale Scienze della Vita e Tecnologie per la Salute, Università di Bologna, Bologna, Italy
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4
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Francia F, Malferrari M, Lanciano P, Steimle S, Daldal F, Venturoli G. The cytochrome b Zn binding amino acid residue histidine 291 is essential for ubihydroquinone oxidation at the Q o site of bacterial cytochrome bc 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1796-1806. [PMID: 27550309 DOI: 10.1016/j.bbabio.2016.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/27/2016] [Accepted: 08/17/2016] [Indexed: 11/18/2022]
Abstract
The ubiquinol:cytochrome (cyt) c oxidoreductase (or cyt bc1) is an important membrane protein complex in photosynthetic and respiratory energy transduction. In bacteria such as Rhodobacter capsulatus it is constituted of three subunits: the iron-sulfur protein, cyt b and cyt c1, which form two catalytic domains, the Qo (hydroquinone (QH2) oxidation) and Qi (quinone (Q) reduction) sites. At the Qo site, the pathways of bifurcated electron transfers emanating from QH2 oxidation are known, but the associated proton release routes are not well defined. In energy transducing complexes, Zn2+ binding amino acid residues often correlate with proton uptake or release pathways. Earlier, using combined EXAFS and structural studies, we identified Zn coordinating residues of mitochondrial and bacterial cyt bc1. In this work, using the genetically tractable bacterial cyt bc1, we substituted each of the proposed Zn binding residues with non-protonatable side chains. Among these mutants, only the His291Leu substitution destroyed almost completely the Qo site catalysis without perturbing significantly the redox properties of the cofactors or the assembly of the complex. In this mutant, which is unable to support photosynthetic growth, the bifurcated electron transfer reactions that result from QH2 oxidation at the Qo site, as well as the associated proton(s) release, were dramatically impaired. Based on these findings, on the putative role of His291 in liganding Zn, and on its solvent exposed and highly conserved position, we propose that His291 of cyt b is critical for proton release associated to QH2 oxidation at the Qo site of cyt bc1.
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Affiliation(s)
- Francesco Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Marco Malferrari
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Pascal Lanciano
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stefan Steimle
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy; Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
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5
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Song Z, Laleve A, Vallières C, McGeehan JE, Lloyd RE, Meunier B. Human Mitochondrial Cytochrome b Variants Studied in Yeast: Not All Are Silent Polymorphisms. Hum Mutat 2016; 37:933-41. [PMID: 27291790 PMCID: PMC5094555 DOI: 10.1002/humu.23024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/24/2016] [Indexed: 11/12/2022]
Abstract
Variations in mitochondrial DNA (mtDNA) cytochrome b (mt‐cyb) are frequently found within the healthy population, but also occur within a spectrum of mitochondrial and common diseases. mt‐cyb encodes the core subunit (MT‐CYB) of complex III, a central component of the oxidative phosphorylation system that drives cellular energy production and homeostasis. Despite significant efforts, most mt‐cyb variations identified are not matched with corresponding biochemical data, so their functional and pathogenic consequences in humans remain elusive. While human mtDNA is recalcitrant to genetic manipulation, it is possible to introduce human‐associated point mutations into yeast mtDNA. Using this system, we reveal direct links between human mt‐cyb variations in key catalytic domains of MT‐CYB and significant changes to complex III activity or drug sensitivity. Strikingly, m.15257G>A (p.Asp171Asn) increased the sensitivity of yeast to the antimalarial drug atovaquone, and m.14798T>C (p.Phe18Leu) enhanced the sensitivity of yeast to the antidepressant drug clomipramine. We demonstrate that while a small number of mt‐cyb variations had no functional effect, others have the capacity to alter complex III properties, suggesting they could play a wider role in human health and disease than previously thought. This compendium of new mt‐cyb‐biochemical relationships in yeast provides a resource for future investigations in humans.
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Affiliation(s)
- Zehua Song
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - Anaïs Laleve
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - Cindy Vallières
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
| | - John E McGeehan
- Molecular Biophysics Laboratories, Institute of Biomedical and Biomolecular Science, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Rhiannon E Lloyd
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Science, School of Pharmacy and Biomedicine, University of Portsmouth, Portsmouth, UK
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, Cedex, 91198, France
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6
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Electron Transfer Reactions at the Qo Site of the Cytochrome bc 1 Complex: The Good, the Bad, and the Ugly. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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7
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Hagras MA, Hayashi T, Stuchebrukhov AA. Quantum Calculations of Electron Tunneling in Respiratory Complex III. J Phys Chem B 2015; 119:14637-51. [DOI: 10.1021/acs.jpcb.5b09424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Muhammad A. Hagras
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Tomoyuki Hayashi
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Alexei A. Stuchebrukhov
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
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8
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Song Z, Clain J, Iorga BI, Vallières C, Lalève A, Fisher N, Meunier B. Interplay between the hinge region of iron sulphur protein and the Qo site in the bc1 complex - Analysis of Plasmodium-like mutations in the yeast enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1487-94. [PMID: 26301481 DOI: 10.1016/j.bbabio.2015.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/21/2015] [Accepted: 08/19/2015] [Indexed: 10/23/2022]
Abstract
The respiratory chain bc1 complex is central to mitochondrial bioenergetics and the target of antiprotozoals. We characterized a modified yeast bc1 complex that more closely resemble Plasmodium falciparum enzyme. The mutant version was generated by replacing ten cytochrome b Qo site residues by P. falciparum equivalents. The Plasmodium-like changes caused a major dysfunction of the catalytic mechanism of the bc1 complex resulting in superoxide overproduction and respiratory growth defect. The defect was corrected by substitution of the conserved residue Y279 by a phenylalanine, or by mutations in or in the vicinity of the hinge domain of the iron-sulphur protein. It thus appears that side-reactions can be prevented by the substitution Y279F or the modification of the iron-sulphur protein hinge region. Interestingly, P. falciparum - and all the apicomplexan - contains an unusual hinge region. We replaced the yeast hinge region by the Plasmodium version and combined it with the Plasmodium-like version of the Qo site. This combination restored the respiratory growth competence. It could be suggested that, in the apicomplexan, the hinge region and the cytochrome b Qo site have co-evolved to maintain catalytic efficiency of the bc1 complex Qo site.
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Affiliation(s)
- Zehua Song
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Jérôme Clain
- UMR 216, Faculté de Pharmacie de Paris, Université Paris Descartes, and Institut de Recherche pour le Développement, 75006 Paris, France
| | - Bogdan I Iorga
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Labex LERMIT, 91198 Gif-sur-Yvette, France
| | - Cindy Vallières
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Anaïs Lalève
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif-sur-Yvette, France
| | - Nicholas Fisher
- Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA..
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif-sur-Yvette, France.
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9
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Abstract
Quinol oxidation in the catalytic quinol oxidation site (Qo site) of cytochrome (cyt) bc1 complexes is the key step of the Q cycle mechanism, which laid the ground for Mitchell’s chemiosmotic theory of energy conversion. Bifurcated electron transfer upon quinol oxidation enables proton uptake and release on opposite membrane sides, thus generating a proton gradient that fuels ATP synthesis in cellular respiration and photosynthesis. The Qo site architecture formed by cyt b and Rieske iron–sulfur protein (ISP) impedes harmful bypass reactions. Catalytic importance is assigned to four residues of cyt b formerly described as PEWY motif in the context of mitochondrial complexes, which we now denominate Qo motif as comprehensive evolutionary sequence analysis of cyt b shows substantial natural variance of the motif with phylogenetically specific patterns. In particular, the Qo motif is identified as PEWY in mitochondria, α- and ε-Proteobacteria, Aquificae, Chlorobi, Cyanobacteria, and chloroplasts. PDWY is present in Gram-positive bacteria, Deinococcus–Thermus and haloarchaea, and PVWY in β- and γ-Proteobacteria. PPWF only exists in Archaea. Distinct patterns for acidophilic organisms indicate environment-specific adaptations. Importantly, the presence of PDWY and PEWY is correlated with the redox potential of Rieske ISP and quinone species. We propose that during evolution from low to high potential electron-transfer systems in the emerging oxygenic atmosphere, cyt bc1 complexes with PEWY as Qo motif prevailed to efficiently use high potential ubiquinone as substrate, whereas cyt b with PDWY operate best with low potential Rieske ISP and menaquinone, with the latter being the likely composition of the ancestral cyt bc1 complex.
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Affiliation(s)
- Wei-Chun Kao
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
- Faculty of Biology, University of Freiburg, Germany
| | - Carola Hunte
- Institute for Biochemistry and Molecular Biology, ZBMZ, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany
- *Corresponding author: E-mail:
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10
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Nesti C, Meschini MC, Meunier B, Sacchini M, Doccini S, Romano A, Petrillo S, Pezzini I, Seddiki N, Rubegni A, Piemonte F, Donati MA, Brasseur G, Santorelli FM. Additive effect of nuclear and mitochondrial mutations in a patient with mitochondrial encephalomyopathy. Hum Mol Genet 2015; 24:3248-56. [PMID: 25736212 DOI: 10.1093/hmg/ddv078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/26/2015] [Indexed: 12/12/2022] Open
Abstract
We describe the case of a woman in whom combination of a mitochondrial (MT-CYB) and a nuclear (SDHB) mutation was associated with clinical and metabolic features suggestive of a mitochondrial disorder. The mutations impaired overall energy metabolism in the patient's muscle and fibroblasts and increased cellular susceptibility to oxidative stress. To clarify the contribution of each mutation to the phenotype, mutant yeast strains were generated. A significant defect in strains carrying the Sdh2 mutation, either alone or in combination with the cytb variant, was observed. Our data suggest that the SDHB mutation was causative of the mitochondrial disorder in our patient with a possible cumulative contribution of the MT-CYB variant. To our knowledge, this is the first association of bi-genomic variants in the mtDNA and in a nuclear gene encoding a subunit of complex II.
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Affiliation(s)
| | | | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Michele Sacchini
- Metabolic and Neuromuscular Unit, AOU Meyer Hospital, Florence, Italy
| | | | - Alessandro Romano
- Neuropathology Unit, Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Petrillo
- Unit for Neuromuscular and Neurodegenerative Diseases, "Bambino Gesù" Children's Hospital, Rome, Italy and
| | | | - Nadir Seddiki
- Laboratoire de Chimie Bactérienne, CNRS, 31 ch. J. Aiguier, 13402 Marseilles, France
| | - Anna Rubegni
- Molecular Medicine, IRCCS Stella Maris, Pisa, Italy
| | - Fiorella Piemonte
- Unit for Neuromuscular and Neurodegenerative Diseases, "Bambino Gesù" Children's Hospital, Rome, Italy and
| | - M Alice Donati
- Metabolic and Neuromuscular Unit, AOU Meyer Hospital, Florence, Italy
| | - Gael Brasseur
- Laboratoire de Chimie Bactérienne, CNRS, 31 ch. J. Aiguier, 13402 Marseilles, France
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11
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Lloyd RE, Keatley K, Littlewood DTJ, Meunier B, Holt WV, An Q, Higgins SC, Polyzoidis S, Stephenson KF, Ashkan K, Fillmore HL, Pilkington GJ, McGeehan JE. Identification and functional prediction of mitochondrial complex III and IV mutations associated with glioblastoma. Neuro Oncol 2015; 17:942-52. [PMID: 25731774 PMCID: PMC4474231 DOI: 10.1093/neuonc/nov020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/23/2015] [Indexed: 12/30/2022] Open
Abstract
Background Glioblastoma (GBM) is the most common primary brain tumor in adults, with a dismal prognosis. Treatment is hampered by GBM's unique biology, including differential cell response to therapy. Although several mitochondrial abnormalities have been identified, how mitochondrial DNA (mtDNA) mutations contribute to GBM biology and therapeutic response remains poorly described. We sought to determine the spectrum of functional complex III and IV mtDNA mutations in GBM. Methods The complete mitochondrial genomes of 10 GBM cell lines were obtained using next-generation sequencing and combined with another set obtained from 32 GBM tissues. Three-dimensional structural mapping and analysis of all the nonsynonymous mutations identified in complex III and IV proteins was then performed to investigate functional importance. Results Over 200 mutations were identified in the mtDNAs, including a significant proportion with very low mutational loads. Twenty-five were nonsynonymous mutations in complex III and IV, 9 of which were predicted to be functional and affect mitochondrial respiratory chain activity. Most of the functional candidates were GBM specific and not found in the general population, and 2 were present in the germ-line. Patient-specific maps reveal that 43% of tumors carry at least one functional candidate. Conclusions We reveal that the spectrum of GBM-associated mtDNA mutations is wider than previously thought, as well as novel structural-functional links between specific mtDNA mutations, abnormal mitochondria, and the biology of GBM. These results could provide tangible new prognostic indicators as well as targets with which to guide the development of patient-specific mitochondrially mediated chemotherapeutic approaches.
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Affiliation(s)
- Rhiannon E Lloyd
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Kathleen Keatley
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - D Timothy J Littlewood
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Brigitte Meunier
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - William V Holt
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Qian An
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Samantha C Higgins
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Stavros Polyzoidis
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Katie F Stephenson
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Keyoumars Ashkan
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Helen L Fillmore
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Geoffrey J Pilkington
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - John E McGeehan
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
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12
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Infante-Rodriguez C, Domon L, Breuilles P, Uguen D. Asymmetric Synthesis of Stigmatellin and Crocacin C. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Carolina Infante-Rodriguez
- Laboratoire de Synthèse Organique (associé au CNRS; UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, Université de Strasbourg
| | - Lisianne Domon
- Laboratoire de Synthèse Organique (associé au CNRS; UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, Université de Strasbourg
| | - Pascal Breuilles
- Laboratoire de Synthèse Organique (associé au CNRS; UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, Université de Strasbourg
| | - Daniel Uguen
- Laboratoire de Synthèse Organique (associé au CNRS; UMR 7509), Ecole Européenne de Chimie, Polymères et Matériaux, Université de Strasbourg
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13
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Sarewicz M, Osyczka A. Electronic connection between the quinone and cytochrome C redox pools and its role in regulation of mitochondrial electron transport and redox signaling. Physiol Rev 2015; 95:219-43. [PMID: 25540143 PMCID: PMC4281590 DOI: 10.1152/physrev.00006.2014] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria.
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Affiliation(s)
- Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
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14
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Crofts AR, Hong S, Wilson C, Burton R, Victoria D, Harrison C, Schulten K. The mechanism of ubihydroquinone oxidation at the Qo-site of the cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1362-77. [PMID: 23396004 PMCID: PMC3995752 DOI: 10.1016/j.bbabio.2013.01.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 12/12/2012] [Accepted: 01/18/2013] [Indexed: 01/04/2023]
Abstract
1. Recent results suggest that the major flux is carried by a monomeric function, not by an intermonomer electron flow. 2. The bifurcated reaction at the Qo-site involves sequential partial processes, - a rate limiting first electron transfer generating a semiquinone (SQ) intermediate, and a rapid second electron transfer in which the SQ is oxidized by the low potential chain. 3. The rate constant for the first step in a strongly endergonic, proton-first-then-electron mechanism, is given by a Marcus-Brønsted treatment in which a rapid electron transfer is convoluted with a weak occupancy of the proton configuration needed for electron transfer. 4. A rapid second electron transfer pulls the overall reaction over. Mutation of Glu-295 of cyt b shows it to be a key player. 5. In more crippled mutants, electron transfer is severely inhibited and the bell-shaped pH dependence of wildtype is replaced by a dependence on a single pK at ~8.5 favoring electron transfer. Loss of a pK ~6.5 is explained by a change in the rate limiting step from the first to the second electron transfer; the pK ~8.5 may reflect dissociation of QH. 6. A rate constant (<10(3)s(-1)) for oxidation of SQ in the distal domain by heme bL has been determined, which precludes mechanisms for normal flux in which SQ is constrained there. 7. Glu-295 catalyzes proton exit through H(+) transfer from QH, and rotational displacement to deliver the H(+) to exit channel(s). This opens a volume into which Q(-) can move closer to the heme to speed electron transfer. 8. A kinetic model accounts well for the observations, but leaves open the question of gating mechanisms. For the first step we suggest a molecular "escapement"; for the second a molecular ballet choreographed through coulombic interactions. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Antony R Crofts
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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15
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Key role of water in proton transfer at the Qo-site of the cytochrome bc1 complex predicted by atomistic molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:761-8. [PMID: 23428399 DOI: 10.1016/j.bbabio.2013.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/24/2013] [Accepted: 02/11/2013] [Indexed: 12/21/2022]
Abstract
Cytochrome (cyt) bc1 complex, which is an integral part of the respiratory chain and related energy-conserving systems, has two quinone-binding cavities (Qo- and Qi-sites), where the substrate participates in electron and proton transfer. Due to its complexity, many of the mechanistic details of the cyt bc1 function have remained unclear especially regarding the substrate binding at the Qo-site. In this work we address this issue by performing extensive atomistic molecular dynamics simulations with the cyt bc1 complex of Rhodobacter capsulatus embedded in a lipid bilayer. Based on the simulations we are able to show the atom-level binding modes of two substrate forms: quinol (QH2) and quinone (Q). The QH2 binding at the Qo-site involves a coordinated water arrangement that produces an exceptionally close and stable interaction between the cyt b and iron sulfur protein subunits. In this arrangement water molecules are positioned suitably in relation to the hydroxyls of the QH2 ring to act as the primary acceptors of protons detaching from the oxidized substrate. In contrast, water does not have a similar role in the Q binding at the Qo-site. Moreover, the coordinated water molecule is also a prime candidate to act as a structural element, gating for short-circuit suppression at the Qo-site.
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16
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Victoria D, Burton R, Crofts AR. Role of the -PEWY-glutamate in catalysis at the Q(o)-site of the Cyt bc(1) complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:365-86. [PMID: 23123515 DOI: 10.1016/j.bbabio.2012.10.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 01/09/2023]
Abstract
We re-examine the pH dependence of partial processes of ubihydroquinone (QH(2)) turnover in Glu-295 mutants in Rhodobacter sphaeroides to clarify the mechanistic role. In more crippled mutants, the bell-shaped pH profile of wildtype was replaced by dependence on a single pK at ~8.5 favoring electron transfer. Loss of the pK at 6.5 reflects a change in the rate-limiting step from the first to the second electron transfer. Over the range of pH 6-8, no major pH dependence of formation of the initial reaction complex was seen, and the rates of bypass reactions were similar to the wildtype. Occupancy of the Q(o)-site by semiquinone (SQ) was similar in the wildtype and the Glu→Trp mutant. Since heme b(L) is initially oxidized in the latter, the bifurcated reaction can still occur, allowing estimation of an empirical rate constant <10(3)s(-1) for reduction of heme b(L) by SQ from the domain distal from heme b(L), a value 1000-fold smaller than that expected from distance. If the pK ~8.5 in mutant strains is due to deprotonation of the neutral semiquinone, with Q(•-) as electron donor to heme b(L), then in wildtype this low value would preclude mechanisms for normal flux in which semiquinone is constrained to this domain. A kinetic model in which Glu-295 catalyzes H(+) transfer from QH•, and delivery of the H(+) to exit channel(s) by rotational displacement, and facilitates rapid electron transfer from SQ to heme b(L) by allowing Q(•-) to move closer to the heme, accounts well for the observations.
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Affiliation(s)
- Doreen Victoria
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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17
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Lee DW, El Khoury Y, Francia F, Zambelli B, Ciurli S, Venturoli G, Hellwig P, Daldal F. Zinc inhibition of bacterial cytochrome bc(1) reveals the role of cytochrome b E295 in proton release at the Q(o) site. Biochemistry 2011; 50:4263-72. [PMID: 21500804 DOI: 10.1021/bi200230e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cytochrome (cyt) bc(1) complex (cyt bc(1)) plays a major role in the electrogenic extrusion of protons across the membrane responsible for the proton motive force to produce ATP. Proton-coupled electron transfer underlying the catalysis of cyt bc(1) is generally accepted, but the molecular basis of coupling and associated proton efflux pathway(s) remains unclear. Herein we studied Zn(2+)-induced inhibition of Rhodobacter capsulatus cyt bc(1) using enzyme kinetics, isothermal titration calorimetry (ITC), and electrochemically induced Fourier transform infrared (FTIR) difference spectroscopy with the purpose of understanding the Zn(2+) binding mechanism and its inhibitory effect on cyt bc(1) function. Analogous studies were conducted with a mutant of cyt b, E295, a residue previously proposed to bind Zn(2+) on the basis of extended X-ray absorption fine-structure spectroscopy. ITC analysis indicated that mutation of E295 to valine, a noncoordinating residue, results in a decrease in Zn(2+) binding affinity. The kinetic study showed that wild-type cyt bc(1) and its E295V mutant have similar levels of apparent K(m) values for decylbenzohydroquinone as a substrate (4.9 ± 0.2 and 3.1 ± 0.4 μM, respectively), whereas their K(I) values for Zn(2+) are 8.3 and 38.5 μM, respectively. The calorimetry-based K(D) values for the high-affinity site of cyt bc(1) are on the same order of magnitude as the K(I) values derived from the kinetic analysis. Furthermore, the FTIR signal of protonated acidic residues was perturbed in the presence of Zn(2+), whereas the E295V mutant exhibited no significant change in electrochemically induced FTIR difference spectra measured in the presence and absence of Zn(2+). Our overall results indicate that the proton-active E295 residue near the Q(o) site of cyt bc(1) can bind directly to Zn(2+), resulting in a decrease in the electron transferring activity without changing drastically the redox potentials of the cofactors of the enzyme. We conclude that E295 is involved in proton efflux coupled to electron transfer at the Q(o) site of cyt bc(1).
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Affiliation(s)
- Dong-Woo Lee
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Busso C, Tahara EB, Ogusucu R, Augusto O, Ferreira-Junior JR, Tzagoloff A, Kowaltowski AJ, Barros MH. Saccharomyces cerevisiae coq10 null mutants are responsive to antimycin A. FEBS J 2010; 277:4530-8. [PMID: 20875086 DOI: 10.1111/j.1742-4658.2010.07862.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Deletion of COQ10 in Saccharomyces cerevisiae elicits a respiratory defect characterized by the absence of cytochrome c reduction, which is correctable by the addition of exogenous diffusible coenzyme Q(2). Unlike other coq mutants with hampered coenzyme Q(6) (Q(6) ) synthesis, coq10 mutants have near wild-type concentrations of Q(6). In the present study, we used Q-cycle inhibitors of the coenzyme QH(2)-cytochrome c reductase complex to assess the electron transfer properties of coq10 cells. Our results show that coq10 mutants respond to antimycin A, indicating an active Q-cycle in these mutants, even though they are unable to transport electrons through cytochrome c and are not responsive to myxothiazol. EPR spectroscopic analysis also suggests that wild-type and coq10 mitochondria accumulate similar amounts of Q(6) semiquinone, despite a lower steady-state level of coenzyme QH(2)-cytochrome c reductase complex in the coq10 cells. Confirming the reduced respiratory chain state in coq10 cells, we found that the expression of the Aspergillus fumigatus alternative oxidase in these cells leads to a decrease in antimycin-dependent H(2)O(2) release and improves their respiratory growth.
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Affiliation(s)
- Cleverson Busso
- Departamento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Sao Paulo, Brazil
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19
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Covian R, Trumpower BL. The rate-limiting step in the cytochrome bc1 complex (Ubiquinol-Cytochrome c Oxidoreductase) is not changed by inhibition of cytochrome b-dependent deprotonation: implications for the mechanism of ubiquinol oxidation at center P of the bc1 complex. J Biol Chem 2009; 284:14359-67. [PMID: 19325183 DOI: 10.1074/jbc.m109.000596] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quinol oxidation at center P of the cytochrome bc(1) complex involves bifurcated electron transfer to the Rieske iron-sulfur protein and cytochrome b. It is unknown whether both electrons are transferred from the same domain close to the Rieske protein, or if an unstable semiquinone anion intermediate diffuses rapidly to the vicinity of the b(L) heme. We have determined the pre-steady state rate and activation energy (E(a)) for quinol oxidation in purified yeast bc(1) complexes harboring either a Y185F mutation in the Rieske protein, which decreases the redox potential of the FeS cluster, or a E272Q cytochrome b mutation, which eliminates the proton acceptor in cytochrome b. The rate of the bifurcated reaction in the E272Q mutant (<10% of the wild type) was even lower than that of the Y185F enzyme ( approximately 20% of the wild type). However, the E272Q enzyme showed the same E(a) (61 kJ mol(-1)) with respect to the wild type (62 kJ mol(-1)), in contrast with the Y185F mutation, which increased E(a) to 73 kJ mol(-1). The rate and E(a) of the slow reaction of quinol with oxygen that are observed after cytochrome b is reduced were unaffected by the E272Q substitution, whereas the Y185F mutation modified only its rate. The Y185F/E272Q double mutation resulted in a synergistic decrease in the rate of quinol oxidation (0.7% of the wild type). These results are inconsistent with a sequential "movable semiquinone" mechanism but are consistent with a model in which both electrons are transferred simultaneously from the same domain in center P.
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Affiliation(s)
- Raul Covian
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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20
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Kleinschroth T, Anderka O, Ritter M, Stocker A, Link TA, Ludwig B, Hellwig P. Characterization of mutations in crucial residues around the Qo binding site of the cytochrome bc1 complex from Paracoccus denitrificans. FEBS J 2008; 275:4773-85. [DOI: 10.1111/j.1742-4658.2008.06611.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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The Q-cycle reviewed: How well does a monomeric mechanism of the bc(1) complex account for the function of a dimeric complex? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1001-19. [PMID: 18501698 DOI: 10.1016/j.bbabio.2008.04.037] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 03/26/2008] [Accepted: 04/23/2008] [Indexed: 11/20/2022]
Abstract
Recent progress in understanding the Q-cycle mechanism of the bc(1) complex is reviewed. The data strongly support a mechanism in which the Q(o)-site operates through a reaction in which the first electron transfer from ubiquinol to the oxidized iron-sulfur protein is the rate-determining step for the overall process. The reaction involves a proton-coupled electron transfer down a hydrogen bond between the ubiquinol and a histidine ligand of the [2Fe-2S] cluster, in which the unfavorable protonic configuration contributes a substantial part of the activation barrier. The reaction is endergonic, and the products are an unstable ubisemiquinone at the Q(o)-site, and the reduced iron-sulfur protein, the extrinsic mobile domain of which is now free to dissociate and move away from the site to deliver an electron to cyt c(1) and liberate the H(+). When oxidation of the semiquinone is prevented, it participates in bypass reactions, including superoxide generation if O(2) is available. When the b-heme chain is available as an acceptor, the semiquinone is oxidized in a process in which the proton is passed to the glutamate of the conserved -PEWY- sequence, and the semiquinone anion passes its electron to heme b(L) to form the product ubiquinone. The rate is rapid compared to the limiting reaction, and would require movement of the semiquinone closer to heme b(L) to enhance the rate constant. The acceptor reactions at the Q(i)-site are still controversial, but likely involve a "two-electron gate" in which a stable semiquinone stores an electron. Possible mechanisms to explain the cyt b(150) phenomenon are discussed, and the information from pulsed-EPR studies about the structure of the intermediate state is reviewed. The mechanism discussed is applicable to a monomeric bc(1) complex. We discuss evidence in the literature that has been interpreted as shown that the dimeric structure participates in a more complicated mechanism involving electron transfer across the dimer interface. We show from myxothiazol titrations and mutational analysis of Tyr-199, which is at the interface between monomers, that no such inter-monomer electron transfer is detected at the level of the b(L) hemes. We show from analysis of strains with mutations at Asn-221 that there are coulombic interactions between the b-hemes in a monomer. The data can also be interpreted as showing similar coulombic interaction across the dimer interface, and we discuss mechanistic implications.
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