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Riepl D, Gamiz-Hernandez AP, Kovalova T, Król SM, Mader SL, Sjöstrand D, Högbom M, Brzezinski P, Kaila VRI. Long-range charge transfer mechanism of the III 2IV 2 mycobacterial supercomplex. Nat Commun 2024; 15:5276. [PMID: 38902248 DOI: 10.1038/s41467-024-49628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
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Affiliation(s)
- Daniel Riepl
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Terezia Kovalova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sylwia M Król
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Dan Sjöstrand
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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2
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Degli Esposti M, Guerrero G, Rogel MA, Issotta F, Rojas-Villalobos C, Quatrini R, Martinez-Romero E. The phylogeny of Acetobacteraceae: photosynthetic traits and deranged respiratory enzymes. Microbiol Spectr 2023; 11:e0057523. [PMID: 37975678 PMCID: PMC10715153 DOI: 10.1128/spectrum.00575-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/21/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Acetobacteraceae are one of the best known and most extensively studied groups of bacteria, which nowadays encompasses a variety of taxa that are very different from the vinegar-producing species defining the family. Our paper presents the most detailed phylogeny of all current taxa classified as Acetobacteraceae, for which we propose a taxonomic revision. Several of such taxa inhabit some of the most extreme environments on the planet, from the deserts of Antarctica to the Sinai desert, as well as acidic niches in volcanic sites like the one we have been studying in Patagonia. Our work documents the progressive variation of the respiratory chain in early branching Acetobacteraceae into the different respiratory chains of acidophilic taxa such as Acidocella and acetous taxa such as Acetobacter. Remarkably, several genomes retain remnants of ancestral photosynthetic traits and functional bc 1 complexes. Thus, we propose that the common ancestor of Acetobacteraceae was photosynthetic.
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Affiliation(s)
- Mauro Degli Esposti
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Gabriela Guerrero
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Marco A. Rogel
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
| | - Francisco Issotta
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, P. Universidad Católica, Santiago, Chile
| | - Camila Rojas-Villalobos
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Raquel Quatrini
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia y Vida, Huechuraba, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Providencia, Santiago, Chile
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3
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Tsutsumi E, Niwa S, Takeda R, Sakamoto N, Okatsu K, Fukai S, Ago H, Nagao S, Sekiguchi H, Takeda K. Structure of a putative immature form of a Rieske-type iron-sulfur protein in complex with zinc chloride. Commun Chem 2023; 6:190. [PMID: 37689761 PMCID: PMC10492824 DOI: 10.1038/s42004-023-01000-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023] Open
Abstract
Iron-sulfur clusters are prosthetic groups of proteins involved in various biological processes. However, details of the immature state of the iron-sulfur cluster into proteins have not yet been elucidated. We report here the first structural analysis of the Zn-containing form of a Rieske-type iron-sulfur protein, PetA, from Thermochromatium tepidum (TtPetA) by X-ray crystallography and small-angle X-ray scattering analysis. The Zn-containing form of TtPetA was indicated to be a dimer in solution. The zinc ion adopts a regular tetra-coordination with two chloride ions and two cysteine residues. Only a histidine residue in the cluster-binding site exhibited a conformational difference from the [2Fe-2S] containing form. The Zn-containing structure indicates that the conformation of the cluster binding site is already constructed and stabilized before insertion of [2Fe-2S]. The binding mode of ZnCl2, similar to the [2Fe-2S] cluster, suggests that the zinc ions might be involved in the insertion of the [2Fe-2S] cluster.
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Affiliation(s)
- Erika Tsutsumi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Satomi Niwa
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ryota Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Natsuki Sakamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kei Okatsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shuya Fukai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Satoshi Nagao
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
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4
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Kishimoto H, Azai C, Yamamoto T, Mutoh R, Nakaniwa T, Tanaka H, Miyanoiri Y, Kurisu G, Oh-oka H. Soluble domains of cytochrome c-556 and Rieske iron-sulfur protein from Chlorobaculum tepidum: Crystal structures and interaction analysis. Curr Res Struct Biol 2023; 5:100101. [PMID: 37180033 PMCID: PMC10172866 DOI: 10.1016/j.crstbi.2023.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
In photosynthetic green sulfur bacteria, the electron transfer reaction from menaquinol:cytochrome c oxidoreductase to the P840 reaction center (RC) complex occurs directly without any involvement of soluble electron carrier protein(s). X-ray crystallography has determined the three-dimensional structures of the soluble domains of the CT0073 gene product and Rieske iron-sulfur protein (ISP). The former is a mono-heme cytochrome c with an α-absorption peak at 556 nm. The overall fold of the soluble domain of cytochrome c-556 (designated as cyt c-556sol) consists of four α-helices and is very similar to that of water-soluble cyt c-554 that independently functions as an electron donor to the P840 RC complex. However, the latter's remarkably long and flexible loop between the α3 and α4 helices seems to make it impossible to be a substitute for the former. The structure of the soluble domain of the Rieske ISP (Rieskesol protein) shows a typical β-sheets-dominated fold with a small cluster-binding and a large subdomain. The architecture of the Rieskesol protein is bilobal and belongs to those of b6f-type Rieske ISPs. Nuclear magnetic resonance (NMR) measurements revealed weak non-polar but specific interaction sites on Rieskesol protein when mixed with cyt c-556sol. Therefore, menaquinol:cytochrome c oxidoreductase in green sulfur bacteria features a Rieske/cytb complex tightly associated with membrane-anchored cyt c-556.
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Affiliation(s)
- Hiraku Kishimoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Chihiro Azai
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoya Yamamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Risa Mutoh
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tetsuko Nakaniwa
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hideaki Tanaka
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
- Corresponding author.
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
- Corresponding author.
| | - Hirozo Oh-oka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
- Center for Education in Liberal Arts and Sciences, Osaka University, Toyonaka, Osaka, 560-0043, Japan
- Corresponding author. Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
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5
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Amporndanai K, Pinthong N, O’Neill PM, Hong WD, Amewu RK, Pidathala C, Berry NG, Leung SC, Ward SA, Biagini GA, Hasnain SS, Antonyuk SV. Targeting the Ubiquinol-Reduction (Q i) Site of the Mitochondrial Cytochrome bc1 Complex for the Development of Next Generation Quinolone Antimalarials. BIOLOGY 2022; 11:biology11081109. [PMID: 35892964 PMCID: PMC9330653 DOI: 10.3390/biology11081109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
Abstract
Antimalarials targeting the ubiquinol-oxidation (Qo) site of the Plasmodium falciparum bc1 complex, such as atovaquone, have become less effective due to the rapid emergence of resistance linked to point mutations in the Qo site. Recent findings showed a series of 2-aryl quinolones mediate inhibitions of this complex by binding to the ubiquinone-reduction (Qi) site, which offers a potential advantage in circumventing drug resistance. Since it is essential to understand how 2-aryl quinolone lead compounds bind within the Qi site, here we describe the co-crystallization and structure elucidation of the bovine cytochrome bc1 complex with three different antimalarial 4(1H)-quinolone sub-types, including two 2-aryl quinolone derivatives and a 3-aryl quinolone analogue for comparison. Currently, no structural information is available for Plasmodial cytochrome bc1. Our crystallographic studies have enabled comparison of an in-silico homology docking model of P. falciparum with the mammalian's equivalent, enabling an examination of how binding compares for the 2- versus 3-aryl analogues. Based on crystallographic and computational modeling, key differences in human and P. falciparum Qi sites have been mapped that provide new insights that can be exploited for the development of next-generation antimalarials with greater selective inhibitory activity against the parasite bc1 with improved antimalarial properties.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Nattapon Pinthong
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
| | - W. David Hong
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Richard K. Amewu
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Department of Chemistry, School of Physical and Mathematical Sciences, University of Ghana, Accra P.O. Box LG 586, Ghana
| | - Chandrakala Pidathala
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Composite Interceptive Med-Science Laboratories Pvt. Ltd., Bengaluru 60099, Karnataka, India
| | - Neil G. Berry
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Suet C. Leung
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Stephen A. Ward
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - Giancarlo A. Biagini
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
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6
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Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy. Biochem Soc Trans 2022; 50:877-893. [PMID: 35356963 PMCID: PMC9162462 DOI: 10.1042/bst20190963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022]
Abstract
Cytochrome (cyt) bc1, bcc and b6f complexes, collectively referred to as cyt bc complexes, are homologous isoprenoid quinol oxidising enzymes present in diverse phylogenetic lineages. Cyt bc1 and bcc complexes are constituents of the electron transport chain (ETC) of cellular respiration, and cyt b6f complex is a component of the photosynthetic ETC. Cyt bc complexes share in general the same Mitchellian Q cycle mechanism, with which they accomplish proton translocation and thus contribute to the generation of proton motive force which drives ATP synthesis. They therefore require a quinol oxidation (Qo) and a quinone reduction (Qi) site. Yet, cyt bc complexes evolved to adapt to specific electrochemical properties of different quinone species and exhibit structural diversity. This review summarises structural information on native quinones and quinone-like inhibitors bound in cyt bc complexes resolved by X-ray crystallography and cryo-EM structures. Although the Qi site architecture of cyt bc1 complex and cyt bcc complex differs considerably, quinone molecules were resolved at the respective Qi sites in very similar distance to haem bH. In contrast, more diverse positions of native quinone molecules were resolved at Qo sites, suggesting multiple quinone binding positions or captured snapshots of trajectories toward the catalytic site. A wide spectrum of inhibitors resolved at Qo or Qi site covers fungicides, antimalarial and antituberculosis medications and drug candidates. The impact of these structures for characterising the Q cycle mechanism, as well as their relevance for the development of medications and agrochemicals are discussed.
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7
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Zhou L, Maldonado M, Padavannil A, Guo F, Letts JA. Structures of Tetrahymena's respiratory chain reveal the diversity of eukaryotic core metabolism. Science 2022; 376:831-839. [PMID: 35357889 DOI: 10.1126/science.abn7747] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate Tetrahymena thermophila (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt-complex I (CI) and Tt-CIII2 (Tt-SC I+III2) and a structure of Tt-CIV2. Tt-SC I+III2 (~2.3 MDa) is a curved assembly with structural and functional symmetry breaking. Tt-CIV2 is a ~2.7 MDa dimer with over 52 subunits per protomer, including mitochondrial carriers and a TIM83-TIM133-like domain. Our structural and functional study of the T. thermophila respiratory chain reveals divergence in key components of eukaryotic respiration, expanding our understanding of core metabolism.
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Affiliation(s)
- Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - María Maldonado
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Abhilash Padavannil
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Fei Guo
- BIOEM Facility, University of California, Davis, CA 95616, USA
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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8
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Modularity of membrane-bound charge-translocating protein complexes. Biochem Soc Trans 2021; 49:2669-2685. [PMID: 34854900 DOI: 10.1042/bst20210462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023]
Abstract
Energy transduction is the conversion of one form of energy into another; this makes life possible as we know it. Organisms have developed different systems for acquiring energy and storing it in useable forms: the so-called energy currencies. A universal energy currency is the transmembrane difference of electrochemical potential (Δμ~). This results from the translocation of charges across a membrane, powered by exergonic reactions. Different reactions may be coupled to charge-translocation and, in the majority of cases, these reactions are catalyzed by modular enzymes that always include a transmembrane subunit. The modular arrangement of these enzymes allows for different catalytic and charge-translocating modules to be combined. Thus, a transmembrane charge-translocating module can be associated with different catalytic subunits to form an energy-transducing complex. Likewise, the same catalytic subunit may be combined with a different membrane charge-translocating module. In this work, we analyze the modular arrangement of energy-transducing membrane complexes and discuss their different combinations, focusing on the charge-translocating module.
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9
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Abstract
Bacteria power their energy metabolism using membrane-bound respiratory enzymes that capture chemical energy and transduce it by pumping protons or Na+ ions across their cell membranes. Recent breakthroughs in molecular bioenergetics have elucidated the architecture and function of many bacterial respiratory enzymes, although key mechanistic principles remain debated. In this Review, we present an overview of the structure, function and bioenergetic principles of modular bacterial respiratory chains and discuss their differences from the eukaryotic counterparts. We also discuss bacterial supercomplexes, which provide central energy transduction systems in several bacteria, including important pathogens, and which could open up possible avenues for treatment of disease.
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10
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Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
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Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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11
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Calisto F, Sousa FM, Sena FV, Refojo PN, Pereira MM. Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins. Chem Rev 2021; 121:1804-1844. [PMID: 33398986 DOI: 10.1021/acs.chemrev.0c00830] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.
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Affiliation(s)
- Filipa Calisto
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
| | - Patricia N Refojo
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Campo Grande, 1749-016 Lisboa, Portugal
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12
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Zhu G, Zeng H, Zhang S, Juli J, Pang X, Hoffmann J, Zhang Y, Morgner N, Zhu Y, Peng G, Michel H, Sun F. A 3.3 Å‐Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guoliang Zhu
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100101 China
| | - Hui Zeng
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Shuangbo Zhang
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Jana Juli
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Strasse 3 60438 Frankfurt am Main Germany
| | | | - Jan Hoffmann
- Institute of Physical and Theoretical Chemistry Goethe University Max-von Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Yan Zhang
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry Goethe University Max-von Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Yun Zhu
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
| | - Guohong Peng
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology Max Planck Institute of Biophysics Max-von Laue-Strasse 3 60438 Frankfurt am Main Germany
| | - Fei Sun
- National Laboratory of Biomacromolecules Institute of Biophysics (IBP) Chinese Academy of Sciences 15 Datun Road, Chaoyang District Beijing 100101 China
- University of Chinese Academy of Sciences Beijing 100101 China
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13
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Zhu G, Zeng H, Zhang S, Juli J, Pang X, Hoffmann J, Zhang Y, Morgner N, Zhu Y, Peng G, Michel H, Sun F. A 3.3 Å-Resolution Structure of Hyperthermophilic Respiratory Complex III Reveals the Mechanism of Its Thermal Stability. Angew Chem Int Ed Engl 2019; 59:343-351. [PMID: 31778296 PMCID: PMC7004027 DOI: 10.1002/anie.201911554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/06/2019] [Indexed: 01/01/2023]
Abstract
Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc1 complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc1 complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Å resolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N‐terminus of cyt. c1 was found to greatly enhance the interaction between cyt. b and cyt. c1, and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc1 complex in an extreme thermal environment.
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Affiliation(s)
- Guoliang Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui Zeng
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von Laue-Strasse 3, 60438, Frankfurt am Main, Germany
| | - Shuangbo Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Jana Juli
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von Laue-Strasse 3, 60438, Frankfurt am Main, Germany
| | | | - Jan Hoffmann
- Institute of Physical and Theoretical Chemistry, Goethe University, Max-von Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Yan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University, Max-von Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Yun Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Guohong Peng
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.,Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von Laue-Strasse 3, 60438, Frankfurt am Main, Germany
| | - Hartmut Michel
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von Laue-Strasse 3, 60438, Frankfurt am Main, Germany
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
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14
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Refojo PN, Sena FV, Calisto F, Sousa FM, Pereira MM. The plethora of membrane respiratory chains in the phyla of life. Adv Microb Physiol 2019; 74:331-414. [PMID: 31126533 DOI: 10.1016/bs.ampbs.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.
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Affiliation(s)
- Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa Calisto
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal; University of Lisboa, Faculty of Sciences, BIOISI- Biosystems & Integrative Sciences Institute, Lisboa, Portugal
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15
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Speijer D. Can All Major ROS Forming Sites of the Respiratory Chain Be Activated By High FADH 2 /NADH Ratios?: Ancient evolutionary constraints determine mitochondrial ROS formation. Bioessays 2018; 41:e1800180. [PMID: 30512221 DOI: 10.1002/bies.201800180] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/30/2018] [Indexed: 01/20/2023]
Abstract
Aspects of peroxisome evolution, uncoupling, carnitine shuttles, supercomplex formation, and missing neuronal fatty acid oxidation (FAO) are linked to reactive oxygen species (ROS) formation in respiratory chains. Oxidation of substrates with high FADH2 /NADH (F/N) ratios (e.g., FAs) initiate ROS formation in Complex I due to insufficient availability of its electron acceptor (Q) and reverse electron transport from QH2 , e.g., during FAO or glycerol-3-phosphate shuttle use. Here it is proposed that the Q-cycle of Complex III contributes to enhanced ROS formation going from low F/N ratio substrates (glucose) to high F/N substrates. This contribution is twofold: 1) Complex III uses Q as substrate, thus also competing with Complex I; 2) Complex III itself will produce more ROS under these conditions. I link this scenario to the universally observed Complex III dimerization. The Q-cycle of Complex III thus again illustrates the tension between efficient ATP generation and endogenous ROS formation. This model can explain recent findings concerning succinate and ROS-induced uncoupling.
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Affiliation(s)
- Dave Speijer
- Academic Medical Center (AMC), University of Amsterdam, Medical Biochemistry, Room K1-257, 1105, AZ Amsterdam, The Netherlands
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16
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Shimada S, Maeda S, Hikita M, Mieda-Higa K, Uene S, Nariai Y, Shinzawa-Itoh K. Solubilization conditions for bovine heart mitochondrial membranes allow selective purification of large quantities of respiratory complexes I, III, and V. Protein Expr Purif 2018; 150:33-43. [PMID: 29702187 DOI: 10.1016/j.pep.2018.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 11/28/2022]
Abstract
Ascertaining the structure and functions of mitochondrial respiratory chain complexes is essential to understanding the biological mechanisms of energy conversion; therefore, numerous studies have examined these complexes. A fundamental part of that research involves devising a method for purifying samples with good reproducibility; the samples obtained need to be stable and their constituents need to retain the same structure and functions they possess when in mitochondrial membranes. Submitochondrial bovine heart particles were isolated using differential centrifugation to adjust to a membrane concentration of 46.0% (w/v) or 31.5% (w/v) based on weight. After 0.7% (w/v) deoxycholic acid, 0.4% (w/v) decyl maltoside, and 7.2% (w/v) potassium chloride were added to the mitochondrial membranes, those membranes were solubilized. At a membrane concentration of 46%, complex V was selectively solubilized, whereas at a concentration of 31.5% (w/v), complexes I and III were solubilized. Two steps-sucrose density gradient centrifugation and anion-exchange chromatography on a POROS HQ 20 μm column-enabled selective purification of samples that retained their structure and functions. These two steps enabled complexes I, III, and V to be purified in two days with a high yield. Complexes I, III, and V were stabilized with n-decyl-β-D-maltoside. A total of 200 mg-300 mg of those complexes from one bovine heart (1.1 kg muscle) was purified with good reproducibility, and the complexes retained the same functions they possessed while in mitochondrial membranes.
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Affiliation(s)
- Satoru Shimada
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Shintaro Maeda
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Masahide Hikita
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Kaoru Mieda-Higa
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Shigefumi Uene
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Yukiko Nariai
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan
| | - Kyoko Shinzawa-Itoh
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Koto 3-2-1, Kamighori, Ako, Hyogo, 678-1297, Japan.
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17
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Mendoza-Hoffmann F, Pérez-Oseguera Á, Cevallos MÁ, Zarco-Zavala M, Ortega R, Peña-Segura C, Espinoza-Simón E, Uribe-Carvajal S, García-Trejo JJ. The Biological Role of the ζ Subunit as Unidirectional Inhibitor of the F 1F O-ATPase of Paracoccus denitrificans. Cell Rep 2018; 22:1067-1078. [PMID: 29386127 DOI: 10.1016/j.celrep.2017.12.106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/09/2017] [Accepted: 12/28/2017] [Indexed: 11/16/2022] Open
Abstract
The biological roles of the three natural F1FO-ATPase inhibitors, ε, ζ, and IF1, on cell physiology remain controversial. The ζ subunit is a useful model for deletion studies since it mimics mitochondrial IF1, but in the F1FO-ATPase of Paracoccus denitrificans (PdF1FO), it is a monogenic and supernumerary subunit. Here, we constructed a P. denitrificans 1222 derivative (PdΔζ) with a deleted ζ gene to determine its role in cell growth and bioenergetics. The results show that the lack of ζ in vivo strongly restricts respiratory P. denitrificans growth, and this is restored by complementation in trans with an exogenous ζ gene. Removal of ζ increased the coupled PdF1FO-ATPase activity without affecting the PdF1FO-ATP synthase turnover, and the latter was not affected at all by ζ reconstitution in vitro. Therefore, ζ works as a unidirectional pawl-ratchet inhibitor of the PdF1FO-ATPase nanomotor favoring the ATP synthase turnover to improve respiratory cell growth and bioenergetics.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México
| | - Ángeles Pérez-Oseguera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, U.N.A.M., Cuernavaca, Morelos, México
| | - Miguel Ángel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, U.N.A.M., Cuernavaca, Morelos, México
| | | | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México
| | | | | | | | - José J García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Delegación Coyoacán, Ciudad de México (CDMX) 04510, México.
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18
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Bown L, Srivastava SK, Piercey BM, McIsaac CK, Tahlan K. Mycobacterial Membrane Proteins QcrB and AtpE: Roles in Energetics, Antibiotic Targets, and Associated Mechanisms of Resistance. J Membr Biol 2017; 251:105-117. [DOI: 10.1007/s00232-017-9997-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/20/2017] [Indexed: 02/08/2023]
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19
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Papa S, Capitanio G, Papa F. The mechanism of coupling between oxido-reduction and proton translocation in respiratory chain enzymes. Biol Rev Camb Philos Soc 2017. [DOI: 10.1111/brv.12347] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sergio Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs (BMSNSO), Section of Medical Biochemistry; University of Bari ‘Aldo Moro’; Piazza G. Cesare 11 70124 Bari Italy
- Institute of Biomembranes and Bioenergetics; National Research Council at BMSNSO; Piazza G. Cesare 11 70124 Bari Italy
| | - Giuseppe Capitanio
- Department of Basic Medical Sciences, Neurosciences and Sense Organs (BMSNSO), Section of Medical Biochemistry; University of Bari ‘Aldo Moro’; Piazza G. Cesare 11 70124 Bari Italy
| | - Francesco Papa
- Department of Basic Medical Sciences, Neurosciences and Sense Organs (BMSNSO), Section of Medical Biochemistry; University of Bari ‘Aldo Moro’; Piazza G. Cesare 11 70124 Bari Italy
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20
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Esser L, Zhou F, Zhou Y, Xiao Y, Tang WK, Yu CA, Qin Z, Xia D. Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III. J Biol Chem 2016; 291:25019-25031. [PMID: 27758861 DOI: 10.1074/jbc.m116.744391] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/05/2016] [Indexed: 11/06/2022] Open
Abstract
Complex III or the cytochrome (cyt) bc1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc1 is to couple the reaction of electron transfer from ubiquinol to cytochrome c to proton pumping across the membrane. Mechanistically, the electron transfer reaction requires docking of its Rieske iron-sulfur protein (ISP) subunit to the quinol oxidation site (QP) of the complex. Formation of an H-bond between the ISP and the bound substrate was proposed to mediate the docking. Here we show that the binding of oxazolidinedione-type inhibitors famoxadone, jg144, and fenamidone induces docking of the ISP to the QP site in the absence of the H-bond formation both in mitochondrial and bacterial cyt bc1 complexes, demonstrating that ISP docking is independent of the proposed direct ISP-inhibitor interaction. The binding of oxazolidinedione-type inhibitors to cyt bc1 of different species reveals a toxophore that appears to interact optimally with residues in the QP site. The effect of modifications or additions to the toxophore on the binding to cyt bc1 from different species could not be predicted from structure-based sequence alignments, as demonstrated by the altered binding mode of famoxadone to bacterial cyt bc1.
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Affiliation(s)
- Lothar Esser
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Fei Zhou
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Yihui Zhou
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.,the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Yumei Xiao
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.,the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Wai-Kwan Tang
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Chang-An Yu
- the Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Zhaohai Qin
- the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Di Xia
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
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21
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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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22
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Ko Y, Choi I. Putative 3D Structure of QcrB fromMycobacterium tuberculosisCytochromebc1 Complex, a Novel Drug-Target for New Series of Antituberculosis Agent Q203. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10765] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoonae Ko
- Cheminformatics Group; Institut Pasteur Korea; Gyeonggi-do 13488 Republic of Korea
| | - Inhee Choi
- Cheminformatics Group; Institut Pasteur Korea; Gyeonggi-do 13488 Republic of Korea
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23
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Khare S, Roach SL, Barnes SW, Hoepfner D, Walker JR, Chatterjee AK, Neitz RJ, Arkin MR, McNamara CW, Ballard J, Lai Y, Fu Y, Molteni V, Yeh V, McKerrow JH, Glynne RJ, Supek F. Utilizing Chemical Genomics to Identify Cytochrome b as a Novel Drug Target for Chagas Disease. PLoS Pathog 2015; 11:e1005058. [PMID: 26186534 PMCID: PMC4506092 DOI: 10.1371/journal.ppat.1005058] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 06/30/2015] [Indexed: 11/19/2022] Open
Abstract
Unbiased phenotypic screens enable identification of small molecules that inhibit pathogen growth by unanticipated mechanisms. These small molecules can be used as starting points for drug discovery programs that target such mechanisms. A major challenge of the approach is the identification of the cellular targets. Here we report GNF7686, a small molecule inhibitor of Trypanosoma cruzi, the causative agent of Chagas disease, and identification of cytochrome b as its target. Following discovery of GNF7686 in a parasite growth inhibition high throughput screen, we were able to evolve a GNF7686-resistant culture of T. cruzi epimastigotes. Clones from this culture bore a mutation coding for a substitution of leucine by phenylalanine at amino acid position 197 in cytochrome b. Cytochrome b is a component of complex III (cytochrome bc1) in the mitochondrial electron transport chain and catalyzes the transfer of electrons from ubiquinol to cytochrome c by a mechanism that utilizes two distinct catalytic sites, QN and QP. The L197F mutation is located in the QN site and confers resistance to GNF7686 in both parasite cell growth and biochemical cytochrome b assays. Additionally, the mutant cytochrome b confers resistance to antimycin A, another QN site inhibitor, but not to strobilurin or myxothiazol, which target the QP site. GNF7686 represents a promising starting point for Chagas disease drug discovery as it potently inhibits growth of intracellular T. cruzi amastigotes with a half maximal effective concentration (EC50) of 0.15 µM, and is highly specific for T. cruzi cytochrome b. No effect on the mammalian respiratory chain or mammalian cell proliferation was observed with up to 25 µM of GNF7686. Our approach, which combines T. cruzi chemical genetics with biochemical target validation, can be broadly applied to the discovery of additional novel drug targets and drug leads for Chagas disease. Chagas Disease, or American trypanosomiasis, is caused by the kinetoplastid protozoan Trypanosoma cruzi and is primarily transmitted to a mammalian host via a triatomine insect vector (the “kissing bug”) infected with T. cruzi parasites. Although discovered in 1909 by the physician Dr. Carlos Chagas, the disease gained recognition by the public health community only following a major outbreak in Brazil during the 1960s. Approximately eight million people (primarily in Central and South America) are infected with T. cruzi and cases are becoming more widespread due to migration out of the endemic regions. Current treatment options have severe problems with toxicity, limited efficacy, and long administration. Hence, discovery of new drugs for treatment of Chagas disease has become of prime interest to the biomedical research community. In this study, we report identification of a potent inhibitor of T. cruzi growth and use a chemical genetics-based approach to elucidate the associated mechanism of action. We found that this compound, GNF7686, targets cytochrome b, a component of the mitochondrial electron transport chain crucial for ATP generation. Our study provides new insights into the use of phenotypic screening to identify novel targets for kinetoplastid drug discovery.
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Affiliation(s)
- Shilpi Khare
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Steven L. Roach
- Department of Medicinal Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - S. Whitney Barnes
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - John R. Walker
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Arnab K. Chatterjee
- Department of Medicinal Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - R. Jeffrey Neitz
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Michelle R. Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Case W. McNamara
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Jaime Ballard
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yin Lai
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yue Fu
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Valentina Molteni
- Department of Medicinal Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Vince Yeh
- Department of Medicinal Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Richard J. Glynne
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Frantisek Supek
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * E-mail:
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Vladkova R. Chlorophyllais the crucial redox sensor and transmembrane signal transmitter in the cytochromeb6fcomplex. Components and mechanisms of state transitions from the hydrophobic mismatch viewpoint. J Biomol Struct Dyn 2015; 34:824-54. [DOI: 10.1080/07391102.2015.1056551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Agarwal R, Hasan SS, Jones LM, Stofleth JT, Ryan CM, Whitelegge JP, Kehoe DM, Cramer WA. Role of domain swapping in the hetero-oligomeric cytochrome b6f lipoprotein complex. Biochemistry 2015; 54:3151-63. [PMID: 25928281 DOI: 10.1021/acs.biochem.5b00279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Domain swapping that contributes to the stability of biologically crucial multisubunit complexes has been implicated in protein oligomerization. In the case of membrane protein assemblies, domain swapping of the iron-sulfur protein (ISP) subunit occurs in the hetero-oligomeric cytochrome b6f and bc1 complexes, which are organized as symmetric dimers that generate the transmembrane proton electrochemical gradient utilized for ATP synthesis. In these complexes, the ISP C-terminal predominantly β-sheet extrinsic domain containing the redox-active [2Fe-2S] cluster resides on the electrochemically positive side of each monomer in the dimeric complex. This domain is bound to the membrane sector of the complex through an N-terminal transmembrane α-helix that is "swapped' to the other monomer of the complex where it spans the complex and the membrane. Detailed analysis of the function and structure of the b6f complex isolated from the cyanobacterium Fremyella diplosiphon SF33 shows that the domain-swapped ISP structure is necessary for function but is not necessarily essential for maintenance of the dimeric structure of the complex. On the basis of crystal structures of the cytochrome complex, the stability of the cytochrome dimer is attributed to specific intermonomer protein-protein and protein-lipid hydrophobic interactions. The geometry of the domain-swapped ISP structure is proposed to be a consequence of the requirement that the anchoring helix of the ISP not perturb the heme organization or quinone channel in the conserved core of each monomer.
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Affiliation(s)
- Rachna Agarwal
- †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - S Saif Hasan
- †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - LaDonna M Jones
- ‡Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Jason T Stofleth
- †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Christopher M Ryan
- §Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, University of California, Los Angeles, California 90095, United States
| | - Julian P Whitelegge
- §Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, University of California, Los Angeles, California 90095, United States
| | - David M Kehoe
- ‡Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - William A Cramer
- †Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
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Schöttler MA, Tóth SZ, Boulouis A, Kahlau S. Photosynthetic complex stoichiometry dynamics in higher plants: biogenesis, function, and turnover of ATP synthase and the cytochrome b6f complex. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2373-400. [PMID: 25540437 DOI: 10.1093/jxb/eru495] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
During plant development and in response to fluctuating environmental conditions, large changes in leaf assimilation capacity and in the metabolic consumption of ATP and NADPH produced by the photosynthetic apparatus can occur. To minimize cytotoxic side reactions, such as the production of reactive oxygen species, photosynthetic electron transport needs to be adjusted to the metabolic demand. The cytochrome b6f complex and chloroplast ATP synthase form the predominant sites of photosynthetic flux control. Accordingly, both respond strongly to changing environmental conditions and metabolic states. Usually, their contents are strictly co-regulated. Thereby, the capacity for proton influx into the lumen, which is controlled by electron flux through the cytochrome b6f complex, is balanced with proton efflux through ATP synthase, which drives ATP synthesis. We discuss the environmental, systemic, and metabolic signals triggering the stoichiometry adjustments of ATP synthase and the cytochrome b6f complex. The contribution of transcriptional and post-transcriptional regulation of subunit synthesis, and the importance of auxiliary proteins required for complex assembly in achieving the stoichiometry adjustments is described. Finally, current knowledge on the stability and turnover of both complexes is summarized.
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Affiliation(s)
- Mark Aurel Schöttler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Szilvia Z Tóth
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alix Boulouis
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Sabine Kahlau
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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28
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Zhu X, Zhang M, Liu J, Ge J, Yang G. Ametoctradin is a potent Qo site inhibitor of the mitochondrial respiration complex III. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3377-3386. [PMID: 25784492 DOI: 10.1021/acs.jafc.5b00228] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ametoctradin is a new Oomycete-specific fungicide under development by BASF. It is a potent inhibitor of the bc1 complex in mitochondrial respiration. However, its detailed action mechanism remains unknown. In the present work, the binding mode of ametoctradin was first uncovered by integrating molecular docking, MD simulations, and MM/PBSA calculations, which showed that ametoctradin should be a Q(o) site inhibitor of bc1 complex. Subsequently, a series of new 1,2,4-triazolo[1,5-a]pyrimidine derivatives were designed and synthesized to further understand the substituent effects on the 5- and 6-position of 1,2,4-triazolo[1,5-a]pyrimidine. The calculated binding free energies (ΔG(cal)) of newly synthesized analogues as Qo site inhibitors correlated very well (R(2) = 0.96) with their experimental binding free energies (ΔG(exp)). Two compounds (4a and 4c) with higher inhibitory activity against porcine SQR than ametoctradin were successfully identified. The structural and mechanistic insights obtained from the present study will provide a valuable clue for future designing of a new promising bc1 inhibitor.
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Affiliation(s)
- Xiaolei Zhu
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Mengmeng Zhang
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Jingjing Liu
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Jingming Ge
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Guangfu Yang
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
- ‡Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 30071, P.R.China
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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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30
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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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31
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Vitale R, Angelini R, Lobasso S, Capitanio G, Ludwig B, Corcelli A. MALDI-TOF MS lipid profiles of cytochrome c oxidases: cardiolipin is not an essential component of the Paracoccus denitrificans oxidase. Biochemistry 2015; 54:1144-50. [PMID: 25565128 DOI: 10.1021/bi5008468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lipids of cytochrome c oxidase (COX) of Paracoccus denitrificans have been identified by MALDI-TOF MS direct analyses of isolated protein complexes, avoiding steps of lipid extraction or chromatographic separation. Two different COX preparations have been considered in this study: the enzyme core consisting of subunits I and II (COX 2-SU) and the complete complex comprising all four subunits (COX 4-SU). In addition, MALDI-TOF MS lipid profiles of bacterial COX are also compared with those of the isolated mitochondrial COX and bacterial bc1 complex. We show that the main lipids associated with bacterial COX 4-SU are phosphatidylglycerol (PG) and phosphatidylcholine (PC), and minor amounts of cardiolipin (CL). PG and PC are absent in the COX 2-SU preparation lacking subunits III and IV, whereas CL is still present. Quantitative analyses indicate that at variance from mitochondrial COX, cardiolipin is present in substoichiometric amounts in bacterial COX, at a CL:COX molar ratio of ∼1:10. We conclude that bacterial COX does not require CL for structure or its activity.
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Affiliation(s)
- Rita Vitale
- Department of Basic Medical Sciences, Neuroscience and Sensory Organs, University of Bari "A. Moro" , 70124 Bari, Italy
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32
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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: 97] [Impact Index Per Article: 10.8] [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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33
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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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Xiao YM, Esser L, Zhou F, Li C, Zhou YH, Yu CA, Qin ZH, Xia D. Studies on inhibition of respiratory cytochrome bc1 complex by the fungicide pyrimorph suggest a novel inhibitory mechanism. PLoS One 2014; 9:e93765. [PMID: 24699450 PMCID: PMC3974799 DOI: 10.1371/journal.pone.0093765] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 03/05/2014] [Indexed: 11/29/2022] Open
Abstract
The respiratory chain cytochrome bc1 complex (cyt bc1) is a major target of numerous antibiotics and fungicides. All cyt bc1 inhibitors act on either the ubiquinol oxidation (QP) or ubiquinone reduction (QN) site. The primary cause of resistance to bc1 inhibitors is target site mutations, creating a need for novel agents that act on alternative sites within the cyt bc1 to overcome resistance. Pyrimorph, a synthetic fungicide, inhibits the growth of a broad range of plant pathogenic fungi, though little is known concerning its mechanism of action. In this study, using isolated mitochondria from pathogenic fungus Phytophthora capsici, we show that pyrimorph blocks mitochondrial electron transport by affecting the function of cyt bc1. Indeed, pyrimorph inhibits the activities of both purified 11-subunit mitochondrial and 4-subunit bacterial bc1 with IC50 values of 85.0 μM and 69.2 μM, respectively, indicating that it targets the essential subunits of cyt bc1 complexes. Using an array of biochemical and spectral methods, we show that pyrimorph acts on an area near the QP site and falls into the category of a mixed-type, noncompetitive inhibitor with respect to the substrate ubiquinol. In silico molecular docking of pyrimorph to cyt b from mammalian and bacterial sources also suggests that pyrimorph binds in the vicinity of the quinol oxidation site.
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Affiliation(s)
- Yu-Mei Xiao
- Department of Applied Chemistry, China Agricultural University, Beijing, China
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Lothar Esser
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Fei Zhou
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Chang Li
- Department of Applied Chemistry, China Agricultural University, Beijing, China
| | - Yi-Hui Zhou
- Department of Applied Chemistry, China Agricultural University, Beijing, China
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Chang-An Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Zhao-Hai Qin
- Department of Applied Chemistry, China Agricultural University, Beijing, China
- * E-mail: (ZQ); (DX)
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
- * E-mail: (ZQ); (DX)
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35
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Xia D, Esser L, Tang WK, Zhou F, Zhou Y, Yu L, Yu CA. Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1278-94. [PMID: 23201476 PMCID: PMC3593749 DOI: 10.1016/j.bbabio.2012.11.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/13/2012] [Accepted: 11/19/2012] [Indexed: 01/18/2023]
Abstract
The cytochrome bc1 complex (bc1) is the mid-segment of the cellular respiratory chain of mitochondria and many aerobic prokaryotic organisms; it is also part of the photosynthetic apparatus of non-oxygenic purple bacteria. The bc1 complex catalyzes the reaction of transferring electrons from the low potential substrate ubiquinol to high potential cytochrome c. Concomitantly, bc1 translocates protons across the membrane, contributing to the proton-motive force essential for a variety of cellular activities such as ATP synthesis. Structural investigations of bc1 have been exceedingly successful, yielding atomic resolution structures of bc1 from various organisms and trapped in different reaction intermediates. These structures have confirmed and unified results of decades of experiments and have contributed to our understanding of the mechanism of bc1 functions as well as its inactivation by respiratory inhibitors. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Pethe K, Bifani P, Jang J, Kang S, Park S, Ahn S, Jiricek J, Jung J, Jeon HK, Cechetto J, Christophe T, Lee H, Kempf M, Jackson M, Lenaerts AJ, Pham H, Jones V, Seo MJ, Kim YM, Seo M, Seo JJ, Park D, Ko Y, Choi I, Kim R, Kim SY, Lim S, Yim SA, Nam J, Kang H, Kwon H, Oh CT, Cho Y, Jang Y, Kim J, Chua A, Tan BH, Nanjundappa MB, Rao SPS, Barnes WS, Wintjens R, Walker JR, Alonso S, Lee S, Kim J, Oh S, Oh T, Nehrbass U, Han SJ, No Z, Lee J, Brodin P, Cho SN, Nam K, Kim J. Discovery of Q203, a potent clinical candidate for the treatment of tuberculosis. Nat Med 2013; 19:1157-60. [PMID: 23913123 DOI: 10.1038/nm.3262] [Citation(s) in RCA: 433] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/04/2013] [Indexed: 11/09/2022]
Abstract
New therapeutic strategies are needed to combat the tuberculosis pandemic and the spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) forms of the disease, which remain a serious public health challenge worldwide. The most urgent clinical need is to discover potent agents capable of reducing the duration of MDR and XDR tuberculosis therapy with a success rate comparable to that of current therapies for drug-susceptible tuberculosis. The last decade has seen the discovery of new agent classes for the management of tuberculosis, several of which are currently in clinical trials. However, given the high attrition rate of drug candidates during clinical development and the emergence of drug resistance, the discovery of additional clinical candidates is clearly needed. Here, we report on a promising class of imidazopyridine amide (IPA) compounds that block Mycobacterium tuberculosis growth by targeting the respiratory cytochrome bc1 complex. The optimized IPA compound Q203 inhibited the growth of MDR and XDR M. tuberculosis clinical isolates in culture broth medium in the low nanomolar range and was efficacious in a mouse model of tuberculosis at a dose less than 1 mg per kg body weight, which highlights the potency of this compound. In addition, Q203 displays pharmacokinetic and safety profiles compatible with once-daily dosing. Together, our data indicate that Q203 is a promising new clinical candidate for the treatment of tuberculosis.
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Affiliation(s)
- Kevin Pethe
- 1] Institut Pasteur Korea, Sampyeong-dong, Seongnam-si, Gyeonggi-do, Korea. [2]
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37
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Carrasco MP, Gut J, Rodrigues T, Ribeiro MHL, Lopes F, Rosenthal PJ, Moreira R, Dos Santos DJVA. Exploring the Molecular Basis of Qo bc1 Complex Inhibitors Activity to Find Novel Antimalarials Hits. Mol Inform 2013; 32:659-70. [PMID: 27481771 DOI: 10.1002/minf.201300024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/11/2013] [Indexed: 02/01/2023]
Abstract
Cytochrome bc1 complex is a crucial element in the mitochondrial respiratory chain, being indispensable for the survival of several species of Plasmodia that cause malaria and, therefore, it is a promising target for antimalarial drug development. We report a molecular docking study building on the most recently obtained X-ray structure of the Saccharomyces cerevisiae bc1 complex (PDB code: 3CX5) using several reported inhibitors with experimentally determined IC50 values against the Plasmodium falciparum bc1 complex. We produced a molecular docking model that correlated the calculated binding free energy with the experimental inhibitory activity of each compound. This Qo model was used to search the drug-like database included in the MOE package for novel potential bc1 complex inhibitors. Twenty three compounds were chosen to be tested for their antimalarial activity and four of these compounds demonstrated activity against the chloroquine-resistant W2 strain of P. falciparum. The most active compounds were also active against the atovaquone-resistant P. falciparum FCR3 strain and S. cerevisiae. Our study suggests the validity of the yeast bc1 complex structure as a model for the discovery of new antimalarial hits.
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Affiliation(s)
- Marta P Carrasco
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470
| | - Jiri Gut
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, CA 94143-0811, USA
| | - Tiago Rodrigues
- Departement Chemie und Angewandte Biowissenschaften, Eidgenössische Technische Hochschule (ETH), Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Maria H L Ribeiro
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470
| | - Francisca Lopes
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470
| | - Philip J Rosenthal
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, CA 94143-0811, USA
| | - Rui Moreira
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470
| | - Daniel J V A Dos Santos
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal phone/fax: +351217946477/+351217946470. .,REQUIMTE, Department of Chemistry & Biochemistry, Faculty of Sciences, University of Porto, R. do Campo Alegre, 4169-007 Porto, Portugal.
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38
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Berry EA, De Bari H, Huang LS. Unanswered questions about the structure of cytochrome bc1 complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1258-77. [PMID: 23624176 DOI: 10.1016/j.bbabio.2013.04.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/13/2013] [Accepted: 04/16/2013] [Indexed: 11/25/2022]
Abstract
X-ray crystal structures of bc1 complexes obtained over the last 15 years have provided a firm structural basis for our understanding of the complex. For the most part there is good agreement between structures from different species, different crystal forms, and with different inhibitors bound. In this review we focus on some of the remaining unexplained differences, either between the structures themselves or the interpretations of the structural observations. These include the structural basis for the motion of the Rieske iron-sulfur protein in response to inhibitors, a possible conformational change involving tyrosine132 of cytochrome (cyt) b, the presence of cis-peptides at the beginnings of transmembrane helices C, E, and H, the structural insight into the function of the so-called "Core proteins", different modelings of the retained signal peptide, orientation of the low-potential heme b, and chirality of the Met ligand to heme c1. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Edward A Berry
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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39
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Lanciano P, Khalfaoui-Hassani B, Selamoglu N, Ghelli A, Rugolo M, Daldal F. Molecular mechanisms of superoxide production by complex III: a bacterial versus human mitochondrial comparative case study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1332-9. [PMID: 23542447 DOI: 10.1016/j.bbabio.2013.03.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/14/2013] [Accepted: 03/20/2013] [Indexed: 12/23/2022]
Abstract
In this mini review, we briefly survey the molecular processes that lead to reactive oxygen species (ROS) production by the respiratory complex III (CIII or cytochrome bc1). In particular, we discuss the "forward" and "reverse" electron transfer pathways that lead to superoxide generation at the quinol oxidation (Qo) site of CIII, and the components that affect these reactions. We then describe and compare the properties of a bacterial (Rhodobacter capsulatus) mutant enzyme producing ROS with its mitochondrial (human cybrids) counterpart associated with a disease. The mutation under study is located at a highly conserved tyrosine residue of cytochrome b (Y302C in R. capsulatus and Y278C in human mitochondria) that is at the heart of the quinol oxidation (Qo) site of CIII. Similarities of the major findings of bacterial and human mitochondrial cases, including decreased catalytic activity of CIII, enhanced ROS production and ensuing cellular responses and damages, are remarkable. This case illustrates the usefulness of undertaking parallel and complementary studies using biologically different yet evolutionarily related systems, such as α-proteobacteria and human mitochondria. It progresses our understanding of CIII mechanism of function and ROS production, and underlines the possible importance of supra-molecular organization of bacterial and mitochondrial respiratory chains (i.e., respirasomes) and their potential disease-associated protective roles. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Pascal Lanciano
- University of Pennsylvania, Department of Biology, Philadelphia, PA, USA
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40
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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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Abstract
Prokaryotes are characterized by an extreme flexibility of their respiratory systems allowing them to cope with various extreme environments. To date, supramolecular organization of respiratory systems appears as a conserved evolutionary feature as supercomplexes have been isolated in bacteria, archaea, and eukaryotes. Most of the yet identified supercomplexes in prokaryotes are involved in aerobic respiration and share similarities with those reported in mitochondria. Supercomplexes likely reflect a snapshot of the cellular respiration in a given cell population. While the exact nature of the determinants for supramolecular organization in prokaryotes is not understood, lipids, proteins, and subcellular localization can be seen as key players. Owing to the well-reported supramolecular organization of the mitochondrial respiratory chain in eukaryotes, several hypotheses have been formulated to explain the consequences of such arrangement and can be tested in the context of prokaryotes. Considering the inherent metabolic flexibility of a number of prokaryotes, cellular distribution and composition of the supramolecular assemblies should be studied in regards to environmental signals. This would pave the way to new concepts in cellular respiration.
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