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Klusch N, Dreimann M, Senkler J, Rugen N, Kühlbrandt W, Braun HP. Cryo-EM structure of the respiratory I + III 2 supercomplex from Arabidopsis thaliana at 2 Å resolution. NATURE PLANTS 2023; 9:142-156. [PMID: 36585502 PMCID: PMC9873573 DOI: 10.1038/s41477-022-01308-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/08/2022] [Indexed: 05/15/2023]
Abstract
Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III2 with a co-purified ubiquinone in the QO site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
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Affiliation(s)
- Niklas Klusch
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany.
| | - Maximilian Dreimann
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany
| | - Jennifer Senkler
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Nils Rugen
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max-Planck-Institute of Biophysics, Frankfurt, Germany
| | - Hans-Peter Braun
- Institut für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany.
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2
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Wang X, Wang J, Liu J, Liu A, He X, Xiang Q, Li Y, Yin H, Luo J, Guan G. Insights into the phylogenetic relationships and drug targets of Babesia isolates infective to small ruminants from the mitochondrial genomes. Parasit Vectors 2020; 13:378. [PMID: 32727571 PMCID: PMC7391622 DOI: 10.1186/s13071-020-04250-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/20/2020] [Indexed: 01/22/2023] Open
Abstract
Background Babesiosis, a tick-borne disease caused by protozoans of the genus Babesia, is widespread in subtropical and tropical countries. Mitochondria are essential organelles that are responsible for energy transduction and metabolism, calcium homeostasis and cell signaling. Mitochondrial genomes could provide new insights to help elucidate and investigate the biological features, genetic evolution and classification of the protozoans. Nevertheless, there are limited data on the mitochondrial genomes of ovine Babesia spp. in China. Methods Herein, we sequenced, assembled and annotated the mitochondrial genomes of six ovine Babesia isolates; analyzed the genome size, gene content, genome structure and cytochrome b (cytb) amino acid sequences and performed comparative mitochondrial genomics and phylogenomic analyses among apicomplexan parasites. Results The mitochondrial genomes range from 5767 to 5946 bp in length with a linear form and contain three protein-encoding genes, cytochrome c oxidase subunit 1 (cox1), cytochrome c oxidase subunit 3 (cox3) and cytb, six large subunit rRNA genes (LSU) and two terminal inverted repeats (TIR) on both ends. The cytb gene sequence analysis indicated the binding site of anti-Babesia drugs that targeted the cytochrome bc1 complex. Babesia microti and Babesia rodhaini have a dual flip-flop inversion of 184–1082 bp, whereas other Babesia spp. and Theileria spp. have one pair of TIRs, 25–1563 bp. Phylogenetic analysis indicated that the six ovine Babesia isolates were divided into two clades, Babesia sp. and Babesia motasi. Babesia motasi isolates were further separated into two small clades (B. motasi Hebei/Ningxian and B. motasi Tianzhu/Lintan). Conclusions The data provided new insights into the taxonomic relationships and drug targets of apicomplexan parasites. ![]()
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Affiliation(s)
- Xiaoxing Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Xin He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Quanjia Xiang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, 730046, Gansu, People's Republic of China.
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3
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Li Y, Lin J, Yao W, Gao G, Jing D, Wu Y. Discovery of a new fungicide by screening triazole sulfonylhydrazone derivatives and its downy mildew inhibition in cucumber. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yitao Li
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Jian Lin
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Wenqiang Yao
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Guoliang Gao
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Dewang Jing
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
| | - Yang Wu
- Dongguan HEC Pesticides R&D Co., Ltd. Dongguan 523871, Guangdong People's Republic of China
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4
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Li Y, Yao W, Lin J, Li F, Wu Y, Xu J. Design, Synthesis, and Biological Activity of Novel Triazole Sulfonamide Derivatives Containing a Benzylamine Moiety. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yitao Li
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Wenqiang Yao
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Jian Lin
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Falin Li
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Yang Wu
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
| | - Junxing Xu
- Dongguan HEC AgroSciences R&D Co., Ltd. Dongguan Guangdong 523867 People's Republic of China
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5
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Cikánková T, Fišar Z, Bakhouche Y, Ľupták M, Hroudová J. In vitro effects of antipsychotics on mitochondrial respiration. Naunyn Schmiedebergs Arch Pharmacol 2019; 392:1209-1223. [PMID: 31104106 DOI: 10.1007/s00210-019-01665-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022]
Abstract
Assessment of drug-induced mitochondrial dysfunctions is important in drug development as well as in the understanding of molecular mechanism of therapeutic or adverse effects of drugs. The aim of this study was to investigate the effects of three typical antipsychotics (APs) and seven atypical APs on mitochondrial bioenergetics. The effects of selected APs on citrate synthase, electron transport chain complexes (ETC), and mitochondrial complex I- or complex II-linked respiratory rate were measured using mitochondria isolated from pig brain. Complex I activity was decreased by chlorpromazine, haloperidol, zotepine, aripiprazole, quetiapine, risperidone, and clozapine. Complex II + III was significantly inhibited by zotepine, aripiprazole, quetiapine, and risperidone. Complex IV was inhibited by zotepine, chlorpromazine, and levomepromazine. Mitochondrial respiratory rate was significantly inhibited by all tested APs, except for olanzapine. Typical APs did not exhibit greater efficacy in altering mitochondrial function compared to atypical APs except for complex I inhibition by chlorpromazine and haloperidol. A comparison of the effects of APs on individual respiratory complexes and on the overall mitochondrial respiration has shown that mitochondrial functions may not fully reflect the disruption of complexes of ETC, which indicates AP-induced modulation of other mitochondrial proteins. Due to the complicated processes associated with mitochondrial activity, it is necessary to measure not only the effect of the drug on individual mitochondrial enzymes but also the respiration rate of the mitochondria or a similar complex process. The experimental approach used in the study can be applied to mitochondrial toxicity testing of newly developed drugs.
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Affiliation(s)
- Tereza Cikánková
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 11, 120 00, Prague 2, Czech Republic
| | - Zdeněk Fišar
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 11, 120 00, Prague 2, Czech Republic
| | - Yousra Bakhouche
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 11, 120 00, Prague 2, Czech Republic
| | - Matej Ľupták
- Institute of Pharmacology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague 2, Czech Republic
| | - Jana Hroudová
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 11, 120 00, Prague 2, Czech Republic. .,Institute of Pharmacology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague 2, Czech Republic.
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6
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Vuono DC, Read RW, Hemp J, Sullivan BW, Arnone JA, Neveux I, Blank RR, Loney E, Miceli D, Winkler MKH, Chakraborty R, Stahl DA, Grzymski JJ. Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium. Front Microbiol 2019; 10:3. [PMID: 30723459 PMCID: PMC6349771 DOI: 10.3389/fmicb.2019.00003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/07/2019] [Indexed: 11/30/2022] Open
Abstract
Respiratory ammonification and denitrification are two evolutionarily unrelated dissimilatory nitrogen (N) processes central to the global N cycle, the activity of which is thought to be controlled by carbon (C) to nitrate (NO3 -) ratio. Here we find that Intrasporangium calvum C5, a novel dual-pathway denitrifier/respiratory ammonifier, disproportionately utilizes ammonification rather than denitrification when grown under low C concentrations, even at low C:NO3 - ratios. This finding is in conflict with the paradigm that high C:NO3 - ratios promote ammonification and low C:NO3 - ratios promote denitrification. We find that the protein atomic composition for denitrification modules (NirK) are significantly cost minimized for C and N compared to ammonification modules (NrfA), indicating that limitation for C and N is a major evolutionary selective pressure imprinted in the architecture of these proteins. The evolutionary precedent for these findings suggests ecological importance for microbial activity as evidenced by higher growth rates when I. calvum grows predominantly using its ammonification pathway and by assimilating its end-product (ammonium) for growth under ammonium-free conditions. Genomic analysis of I. calvum further reveals a versatile ecophysiology to cope with nutrient stress and redox conditions. Metabolite and transcriptional profiles during growth indicate that enzyme modules, NrfAH and NirK, are not constitutively expressed but rather induced by nitrite production via NarG. Mechanistically, our results suggest that pathway selection is driven by intracellular redox potential (redox poise), which may be lowered when resource concentrations are low, thereby decreasing catalytic activity of upstream electron transport steps (i.e., the bc1 complex) needed for denitrification enzymes. Our work advances our understanding of the biogeochemical flexibility of N-cycling organisms, pathway evolution, and ecological food-webs.
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Affiliation(s)
- David C. Vuono
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Robert W. Read
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - James Hemp
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Benjamin W. Sullivan
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, Reno, NV, United States
| | - John A. Arnone
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Iva Neveux
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Robert R. Blank
- Agricultural Research Service, United States Department of Agriculture, Reno, NV, United States
| | - Evan Loney
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - David Miceli
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Mari-Karoliina H. Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Joseph J. Grzymski
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
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7
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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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8
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Identification of a New Isoindole-2-yl Scaffold as a Qo and Qi Dual Inhibitor of Cytochrome bc 1 Complex: Virtual Screening, Synthesis, and Biochemical Assay. Interdiscip Sci 2017; 10:781-791. [PMID: 28921079 DOI: 10.1007/s12539-017-0241-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 05/13/2017] [Accepted: 05/22/2017] [Indexed: 10/18/2022]
Abstract
Respiratory chain ubiquinol-cytochrome (cyt) c oxidoreductase (cyt bc 1 or complex III) has been demonstrated as a promising target for numerous antibiotics and fungicide applications. In this study, a virtual screening of NCI diversity database was carried out in order to find novel Qo/Qi cyt bc 1 complex inhibitors. Structure-based virtual screening and molecular docking methodology were employed to further screen compounds with inhibition activity against cyt bc 1 complex after extensive reliability validation protocol with cross-docking method and identification of the best score functions. Subsequently, the application of rational filtering procedure over the target database resulted in the elucidation of a novel class of cyt bc 1 complex potent inhibitors with comparable binding energies and biological activities to those of the standard inhibitor, antimycin.
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9
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Crofts AR, Rose SW, Burton RL, Desai AV, Kenis PJA, Dikanov SA. The Q-Cycle Mechanism of the bc1 Complex: A Biologist’s Perspective on Atomistic Studies. J Phys Chem B 2017; 121:3701-3717. [DOI: 10.1021/acs.jpcb.6b10524] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Antony R. Crofts
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 419 Roger Adams Lab, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, 179 Loomis, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Stuart W. Rose
- Center
for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, 179 Loomis, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Rodney L. Burton
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, 419 Roger Adams Lab, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Amit V. Desai
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Paul J. A. Kenis
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sergei A. Dikanov
- Department
of Veterinary Clinical Medicine, University of Illinois at Urbana−Champaign, 1008 West Hazelwood Drive, Urbana, Illinois 61801, United States
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10
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Zhang R, Wu QY, Tao J, Pan JH, Yang GF. An ionic liquid promoted approach to bitriazolyl compounds as succinate–ubiquinone oxidoreductase inhibitors. NEW J CHEM 2017. [DOI: 10.1039/c6nj02454h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bitriazolyl compounds, a novel skeleton that is totally different from existing commercialized SQR-inhibiting fungicides, could provide a new lead for further development of SQR inhibitors.
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Affiliation(s)
- Rui Zhang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
| | - Qiong-You Wu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
| | - Jun Tao
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
| | - Jin-Huan Pan
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry Central China Normal University
- Wuhan 430079
- P. R. China
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11
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Kao WC, Kleinschroth T, Nitschke W, Baymann F, Neehaul Y, Hellwig P, Richers S, Vonck J, Bott M, Hunte C. The obligate respiratory supercomplex from Actinobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1705-14. [PMID: 27472998 DOI: 10.1016/j.bbabio.2016.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/27/2016] [Accepted: 07/23/2016] [Indexed: 10/21/2022]
Abstract
Actinobacteria are closely linked to human life as industrial producers of bioactive molecules and as human pathogens. Respiratory cytochrome bcc complex and cytochrome aa3 oxidase are key components of their aerobic energy metabolism. They form a supercomplex in the actinobacterial species Corynebacterium glutamicum. With comprehensive bioinformatics and phylogenetic analysis we show that genes for cyt bcc-aa3 supercomplex are characteristic for Actinobacteria (Actinobacteria and Acidimicrobiia, except the anaerobic orders Actinomycetales and Bifidobacteriales). An obligatory supercomplex is likely, due to the lack of genes encoding alternative electron transfer partners such as mono-heme cyt c. Instead, subunit QcrC of bcc complex, here classified as short di-heme cyt c, will provide the exclusive electron transfer link between the complexes as in C. glutamicum. Purified to high homogeneity, the C. glutamicum bcc-aa3 supercomplex contained all subunits and cofactors as analyzed by SDS-PAGE, BN-PAGE, absorption and EPR spectroscopy. Highly uniform supercomplex particles in electron microscopy analysis support a distinct structural composition. The supercomplex possesses a dimeric stoichiometry with a ratio of a-type, b-type and c-type hemes close to 1:1:1. Redox titrations revealed a low potential bcc complex (Em(ISP)=+160mV, Em(bL)=-291mV, Em(bH)=-163mV, Em(cc)=+100mV) fined-tuned for oxidation of menaquinol and a mixed potential aa3 oxidase (Em(CuA)=+150mV, Em(a/a3)=+143/+317mV) mediating between low and high redox potential to accomplish dioxygen reduction. The generated molecular model supports a stable assembled supercomplex with defined architecture which permits energetically efficient coupling of menaquinol oxidation and dioxygen reduction in one supramolecular entity.
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Affiliation(s)
- Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, BIOSS Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Thomas Kleinschroth
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, BIOSS Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Wolfgang Nitschke
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/Aix Marseille Univ, FR3479, 13009 Marseille, France
| | - Frauke Baymann
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/Aix Marseille Univ, FR3479, 13009 Marseille, France
| | - Yashvin Neehaul
- Laboratoire de bioélectrochimie et spectroscopie, UMR 7140, Chimie de la matière complexe, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de bioélectrochimie et spectroscopie, UMR 7140, Chimie de la matière complexe, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Sebastian Richers
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, BIOSS Centre for Biological Signalling Studies, 79104 Freiburg, Germany.
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12
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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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13
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Cheng H, Shen YQ, Pan XY, Hou YP, Wu QY, Yang GF. Discovery of 1,2,4-triazole-1,3-disulfonamides as dual inhibitors of mitochondrial complex II and complex III. NEW J CHEM 2015. [DOI: 10.1039/c5nj00215j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1,2,4-Triazole-1,3-disulfonamide derivatives as dual function inhibitors of mitochondrial complex II (SQR) and complex III (cyt bc1) were discovered.
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Affiliation(s)
- Hua Cheng
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Yan-Qing Shen
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Xia-Yan Pan
- Department of Pesticide Science
- College of Plant Protection
- Nanjing Agricultural University
- Nanjing 210095
- P. R. China
| | - Yi-Ping Hou
- Department of Pesticide Science
- College of Plant Protection
- Nanjing Agricultural University
- Nanjing 210095
- P. R. China
| | - Qiong-You Wu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
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14
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Chauvet AAP, Al Haddad A, Kao WC, van Mourik F, Hunte C, Chergui M. Photo-induced dynamics of the heme centers in cytochrome bc1. Phys Chem Chem Phys 2015; 17:2143-51. [DOI: 10.1039/c4cp04805a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ultrafast response of cytochromebc1is investigated for the first time,viatransient absorption spectroscopy.
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Affiliation(s)
- Adrien A. P. Chauvet
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Laboratoire de Spectroscopie Ultrarapide
- ISIC
- 1015 Lausanne
- Switzerland
| | - André Al Haddad
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Laboratoire de Spectroscopie Ultrarapide
- ISIC
- 1015 Lausanne
- Switzerland
| | - Wei-Chun Kao
- Albert-Ludwigs-Universität Freiburg
- BIOSS Centre for Biological Signalling Studies
- Institute for Biochemistry and Biology
- 79104 Freiburg
- Germany
| | - Frank van Mourik
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Laboratoire de Spectroscopie Ultrarapide
- ISIC
- 1015 Lausanne
- Switzerland
| | - Carola Hunte
- Albert-Ludwigs-Universität Freiburg
- BIOSS Centre for Biological Signalling Studies
- Institute for Biochemistry and Biology
- 79104 Freiburg
- Germany
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Laboratoire de Spectroscopie Ultrarapide
- ISIC
- 1015 Lausanne
- Switzerland
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15
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Grivennikova VG, Vinogradov AD. Mitochondrial production of reactive oxygen species. BIOCHEMISTRY (MOSCOW) 2014; 78:1490-511. [PMID: 24490736 DOI: 10.1134/s0006297913130087] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Numerous biochemical studies are aimed at elucidating the sources and mechanisms of formation of reactive oxygen species (ROS) because they are involved in cellular, organ-, and tissue-specific physiology. Mitochondria along with other cellular organelles of eukaryotes contribute significantly to ROS formation and utilization. This review is a critical account of the mitochondrial ROS production and methods for their registration. The physiological and pathophysiological significance of the mitochondrially produced ROS are discussed.
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Affiliation(s)
- V G Grivennikova
- Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, 119991, Russia.
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16
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Hasan SS, Zakharov SD, Chauvet A, Stadnytskyi V, Savikhin S, Cramer WA. A map of dielectric heterogeneity in a membrane protein: the hetero-oligomeric cytochrome b6f complex. J Phys Chem B 2014; 118:6614-25. [PMID: 24867491 PMCID: PMC4067154 DOI: 10.1021/jp501165k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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The
cytochrome b6f complex,
a member of the cytochrome bc family that
mediates energy transduction in photosynthetic and respiratory membranes,
is a hetero-oligomeric complex that utilizes two pairs of b-hemes in a symmetric dimer to accomplish trans-membrane
electron transfer, quinone oxidation–reduction, and generation
of a proton electrochemical potential. Analysis of electron storage
in this pathway, utilizing simultaneous measurement of heme reduction,
and of circular dichroism (CD) spectra, to assay heme–heme
interactions, implies a heterogeneous distribution of the dielectric
constants that mediate electrostatic interactions between the four
hemes in the complex. Crystallographic information was used to determine
the identity of the interacting hemes. The Soret band CD signal is
dominated by excitonic interaction between the intramonomer b-hemes, bn and bp, on the electrochemically negative and positive sides
of the complex. Kinetic data imply that the most probable pathway
for transfer of the two electrons needed for quinone oxidation–reduction
utilizes this intramonomer heme pair, contradicting the expectation
based on heme redox potentials and thermodynamics, that the two higher
potential hemes bn on different monomers
would be preferentially reduced. Energetically preferred intramonomer
electron storage of electrons on the intramonomer b-hemes is found to require heterogeneity of interheme dielectric
constants. Relative to the medium separating the two higher potential
hemes bn, a relatively large dielectric
constant must exist between the intramonomer b-hemes,
allowing a smaller electrostatic repulsion between the reduced hemes.
Heterogeneity of dielectric constants is an additional structure–function
parameter of membrane protein complexes.
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Affiliation(s)
- S Saif Hasan
- Department of Biological Sciences and ‡Department of Physics, Purdue University , West Lafayette, Indiana 47907, United States
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17
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Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action. Nat Commun 2014; 5:4029. [DOI: 10.1038/ncomms5029] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 05/02/2014] [Indexed: 11/08/2022] Open
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18
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Li H, Zhu XL, Yang WC, Yang GF. Comparative Kinetics ofQiSite Inhibitors of Cytochromebc1Complex: Picomolar Antimycin and Micromolar Cyazofamid. Chem Biol Drug Des 2013; 83:71-80. [DOI: 10.1111/cbdd.12199] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/17/2013] [Accepted: 07/26/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Li
- Key Laboratory of Pesticide & Chemical Biology; College of Chemistry; Ministry of Education; Central China Normal University; Wuhan 430079 China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology; College of Chemistry; Ministry of Education; Central China Normal University; Wuhan 430079 China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology; College of Chemistry; Ministry of Education; Central China Normal University; Wuhan 430079 China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology; College of Chemistry; Ministry of Education; Central China Normal University; Wuhan 430079 China
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19
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Cooley JW. Protein conformational changes involved in the cytochrome bc1 complex catalytic cycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1340-5. [PMID: 23876289 DOI: 10.1016/j.bbabio.2013.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/23/2013] [Accepted: 07/15/2013] [Indexed: 11/28/2022]
Abstract
Early structures of the cytochrome bc1 complex revealed heterogeneity in the position of the soluble portion of the Rieske iron sulfur protein subunit, implicating a movement of this domain during function. Subsequent biochemical and biophysical works have firmly established that the motion of this subunit acts in the capacity of a conformationally assisted electron transfer step during the already complicated catalytic mechanism described within the modified version of Peter Mitchells Q cycle. How the movement of this subunit is initiated or how the frequency of its motion is controlled as a function of other steps during the catalysis remain topics of debate within the active research communities. This review addresses the historical aspects of the discovery and description of this movement, while attempting to provide a context for the involvement of conformational motion in the catalysis and efficiency of the enzyme. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Jason W Cooley
- Department of Chemistry, University of Missouri, Columbia, MO 65211-7600, USA.
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20
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Bleier L, Dröse S. Superoxide generation by complex III: from mechanistic rationales to functional consequences. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:1320-31. [PMID: 23269318 DOI: 10.1016/j.bbabio.2012.12.002] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/05/2012] [Accepted: 12/12/2012] [Indexed: 01/21/2023]
Abstract
Apart from complex I (NADH:ubiquinone oxidoreductase) the mitochondrial cytochrome bc1 complex (complex III; ubiquinol:cytochrome c oxidoreductase) has been identified as the main producer of superoxide and derived reactive oxygen species (ROS) within the mitochondrial respiratory chain. Mitochondrial ROS are generally linked to oxidative stress, aging and other pathophysiological settings like in neurodegenerative diseases. However, ROS produced at the ubiquinol oxidation center (center P, Qo site) of complex III seem to have additional physiological functions as signaling molecules during cellular processes like the adaptation to hypoxia. The molecular mechanism of superoxide production that is mechanistically linked to the electron bifurcation during ubiquinol oxidation is still a matter of debate. Some insight comes from extensive kinetic studies with mutated complexes from yeast and bacterial cytochrome bc1 complexes. This review is intended to bridge the gap between those mechanistic studies and investigations on complex III ROS in cellular signal transduction and highlights factors that impact superoxide generation. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Lea Bleier
- Molecular Bioenergetics Group, Medical School, Johann Wolfgang Goethe-Universität, Frankfurt am Main, Germany
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21
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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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22
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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: 349] [Impact Index Per Article: 29.1] [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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23
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X-ray structure of the dimeric cytochrome bc(1) complex from the soil bacterium Paracoccus denitrificans at 2.7-Å resolution. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1606-15. [PMID: 21996020 DOI: 10.1016/j.bbabio.2011.09.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/21/2011] [Accepted: 09/27/2011] [Indexed: 11/21/2022]
Abstract
The respiratory cytochrome bc(1) complex is a fundamental enzyme in biological energy conversion. It couples electron transfer from ubiquinol to cytochrome c with generation of proton motive force which fuels ATP synthesis. The complex from the α-proteobacterium Paracoccus denitrificans, a model for the medically relevant mitochondrial complexes, lacked structural characterization. We show by LILBID mass spectrometry that truncation of the organism-specific, acidic N-terminus of cytochrome c(1) changes the oligomerization state of the enzyme to a dimer. The fully functional complex was crystallized and the X-ray structure determined at 2.7-Å resolution. It has high structural homology to mitochondrial complexes and to the Rhodobacter sphaeroides complex especially for subunits cytochrome b and ISP. Species-specific binding of the inhibitor stigmatellin is noteworthy. Interestingly, cytochrome c(1) shows structural differences to the mitochondrial and even between the two Rhodobacteraceae complexes. The structural diversity in the cytochrome c(1) surface facing the ISP domain indicates low structural constraints on that surface for formation of a productive electron transfer complex. A similar position of the acidic N-terminal domains of cytochrome c(1) and yeast subunit QCR6p is suggested in support of a similar function. A model of the electron transfer complex with membrane-anchored cytochrome c(552), the natural substrate, shows that it can adopt the same orientation as the soluble substrate in the yeast complex. The full structural integrity of the P. denitrificans variant underpins previous mechanistic studies on intermonomer electron transfer and paves the way for using this model system to address open questions of structure/function relationships and inhibitor binding.
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Cramer WA, Hasan SS, Yamashita E. The Q cycle of cytochrome bc complexes: a structure perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:788-802. [PMID: 21352799 DOI: 10.1016/j.bbabio.2011.02.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/08/2011] [Accepted: 02/13/2011] [Indexed: 12/01/2022]
Abstract
Aspects of the crystal structures of the hetero-oligomeric cytochrome bc(1) and b(6)f ("bc") complexes relevant to their electron/proton transfer function and the associated redox reactions of the lipophilic quinones are discussed. Differences between the b(6)f and bc(1) complexes are emphasized. The cytochrome bc(1) and b(6)f dimeric complexes diverge in structure from a core of subunits that coordinate redox groups consisting of two bis-histidine coordinated hemes, a heme b(n) and b(p) on the electrochemically negative (n) and positive (p) sides of the complex, the high potential [2Fe-2S] cluster and c-type heme at the p-side aqueous interface and aqueous phase, respectively, and quinone/quinol binding sites on the n- and p-sides of the complex. The bc(1) and b(6)f complexes diverge in subunit composition and structure away from this core. b(6)f Also contains additional prosthetic groups including a c-type heme c(n) on the n-side, and a chlorophyll a and β-carotene. Common structure aspects; functions of the symmetric dimer. (I) Quinone exchange with the bilayer. An inter-monomer protein-free cavity of approximately 30Å along the membrane normal×25Å (central inter-monomer distance)×15Å (depth in the center), is common to both bc(1) and b(6)f complexes, providing a niche in which the lipophilic quinone/quinol (Q/QH(2)) can be exchanged with the membrane bilayer. (II) Electron transfer. The dimeric structure and the proximity of the two hemes b(p) on the electrochemically positive side of the complex in the two monomer units allow the possibility of two alternate routes of electron transfer across the complex from heme b(p) to b(n): intra-monomer and inter-monomer involving electron cross-over between the two hemes b(p). A structure-based summary of inter-heme distances in seven bc complexes, representing mitochondrial, chromatophore, cyanobacterial, and algal sources, indicates that, based on the distance parameter, the intra-monomer pathway would be favored kinetically. (III) Separation of quinone binding sites. A consequence of the dimer structure and the position of the Q/QH(2) binding sites is that the p-side QH(2) oxidation and n-side Q reduction sites are each well separated. Therefore, in the event of an overlap in residence time by QH(2) or Q molecules at the two oxidation or reduction sites, their spatial separation would result in minimal steric interference between extended Q or QH(2) isoprenoid chains. (IV) Trans-membrane QH(2)/Q transfer. (i) n/p-side QH(2)/Q transfer may be hindered by lipid acyl chains; (ii) the shorter less hindered inter-monomer pathway across the complex would not pass through the center of the cavity, as inferred from the n-side antimycin site on one monomer and the p-side stigmatellin site on the other residing on the same surface of the complex. (V) Narrow p-side portal for QH(2)/Q passage. The [2Fe-2S] cluster that serves as oxidant, and whose histidine ligand serves as a H(+) acceptor in the oxidation of QH(2), is connected to the inter-monomer cavity by a narrow extended portal, which is also occupied in the b(6)f complex by the 20 carbon phytyl chain of the bound chlorophyll.
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Affiliation(s)
- William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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Bcs1p can rescue a large and productive cytochrome bc1 complex assembly intermediate in the inner membrane of yeast mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:91-101. [DOI: 10.1016/j.bbamcr.2010.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 06/15/2010] [Accepted: 08/11/2010] [Indexed: 11/23/2022]
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26
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Mulkidjanian AY. Activated Q-cycle as a common mechanism for cytochrome bc1 and cytochrome b6f complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1858-68. [DOI: 10.1016/j.bbabio.2010.07.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 03/14/2010] [Accepted: 07/13/2010] [Indexed: 10/19/2022]
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Zara V, Conte L, Trumpower BL. Evidence that the assembly of the yeast cytochrome bc1 complex involves the formation of a large core structure in the inner mitochondrial membrane. FEBS J 2009; 276:1900-14. [PMID: 19236481 DOI: 10.1111/j.1742-4658.2009.06916.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The assembly status of the cytochrome bc(1) complex has been analyzed in distinct yeast deletion strains in which genes for one or more of the bc(1) subunits were deleted. In all the yeast strains tested, a bc(1) sub-complex of approximately 500 kDa was found when the mitochondrial membranes were analyzed by blue native electrophoresis. The subsequent molecular characterization of this sub-complex, carried out in the second dimension by SDS/PAGE and immunodecoration, revealed the presence of the two catalytic subunits, cytochrome b and cytochrome c(1), associated with the noncatalytic subunits core protein 1, core protein 2, Qcr7p and Qcr8p. Together, these bc(1) subunits build up the core structure of the cytochrome bc(1) complex, which is then able to sequentially bind the remaining subunits, such as Qcr6p, Qcr9p, the Rieske iron-sulfur protein and Qcr10p. This bc(1) core structure may represent a true assembly intermediate during the maturation of the bc(1) complex; first, because of its wide distribution in distinct yeast deletion strains and, second, for its characteristics of stability, which resemble those of the intact homodimeric bc(1) complex. By contrast, the bc(1) core structure is unable to interact with the cytochrome c oxidase complex to form respiratory supercomplexes. The characterization of this novel core structure of the bc(1) complex provides a number of new elements clarifying the molecular events leading to the maturation of the yeast cytochrome bc(1) complex in the inner mitochondrial membrane.
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Affiliation(s)
- Vincenzo Zara
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Lecce, Italy.
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