1
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Amarnath K, Narla AV, Pontrelli S, Dong J, Reddan J, Taylor BR, Caglar T, Schwartzman J, Sauer U, Cordero OX, Hwa T. Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance. Nat Commun 2023; 14:3165. [PMID: 37258505 PMCID: PMC10232422 DOI: 10.1038/s41467-023-38913-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving the extensive cross-feeding needed to support the coexistence of free-living microbes are poorly understood. Here we characterize bacterial physiology under self-acidification and establish that extensive excretion of key metabolites following growth arrest provides a collaborative, inter-species mechanism of stress resistance. This collaboration occurs not only between species isolated from the same community, but also between unrelated species with complementary (glycolytic vs. gluconeogenic) modes of metabolism. Cultures of such communities progress through distinct phases of growth-dilution cycles, comprising of exponential growth, acidification-triggered growth arrest, collaborative deacidification, and growth recovery, with each phase involving different combinations of physiological states of individual species. Our findings challenge the steady-state view of ecosystems commonly portrayed in ecological models, offering an alternative dynamical view based on growth advantages of complementary species in different phases.
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Affiliation(s)
- Kapil Amarnath
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Avaneesh V Narla
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Sammy Pontrelli
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Jiajia Dong
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
- Department of Physics and Astronomy, Bucknell University, Lewisburg, PA, 17837, USA
| | - Jack Reddan
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA
| | - Brian R Taylor
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Tolga Caglar
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Uwe Sauer
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Terence Hwa
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA.
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA.
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2
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Karavaeva V, Sousa FL. Modular structure of complex II: An evolutionary perspective. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148916. [PMID: 36084748 DOI: 10.1016/j.bbabio.2022.148916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/21/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022]
Abstract
Succinate dehydrogenases (SDHs) and fumarate reductases (FRDs) catalyse the interconversion of succinate and fumarate, a reaction highly conserved in all domains of life. The current classification of SDH/FRDs is based on the structure of the membrane anchor subunits and their cofactors. It is, however, unknown whether this classification would hold in the context of evolution. In this work, a large-scale comparative genomic analysis of complex II addresses the questions of its taxonomic distribution and phylogeny. Our findings report that for types C, D, and F, structural classification and phylogeny go hand in hand, while for types A, B and E the situation is more complex, highlighting the possibility for their classification into subgroups. Based on these findings, we proposed a revised version of the evolutionary scenario for these enzymes in which a primordial soluble module, corresponding to the cytoplasmatic subunits, would give rise to the current diversity via several independent membrane anchor attachment events.
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Affiliation(s)
- Val Karavaeva
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Filipa L Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.
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3
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Cauilan A, Ruiz C. Sodium Malonate Inhibits the AcrAB-TolC Multidrug Efflux Pump of Escherichia coli and Increases Antibiotic Efficacy. Pathogens 2022; 11:1409. [PMID: 36558743 PMCID: PMC9781404 DOI: 10.3390/pathogens11121409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
There is an urgent need to find novel treatments for combating multidrug-resistant bacteria. Multidrug efflux pumps that expel antibiotics out of cells are major contributors to this problem. Therefore, using efflux pump inhibitors (EPIs) is a promising strategy to increase antibiotic efficacy. However, there are no EPIs currently approved for clinical use especially because of their toxicity. This study investigates sodium malonate, a natural, non-hazardous, small molecule, for its use as a novel EPI of AcrAB-TolC, the main multidrug efflux pump of the Enterobacteriaceae family. Using ethidium bromide accumulation experiments, we found that 25 mM sodium malonate inhibited efflux by the AcrAB-TolC and other MDR pumps of Escherichia coli to a similar degree than 50 μΜ phenylalanine-arginine-β-naphthylamide, a well-known EPI. Using minimum inhibitory concentration assays and molecular docking to study AcrB-ligand interactions, we found that sodium malonate increased the efficacy of ethidium bromide and the antibiotics minocycline, chloramphenicol, and ciprofloxacin, possibly via binding to multiple AcrB locations, including the AcrB proximal binding pocket. In conclusion, sodium malonate is a newly discovered EPI that increases antibiotic efficacy. Our findings support the development of malonic acid/sodium malonate and its derivatives as promising EPIs for augmenting antibiotic efficacy when treating multidrug-resistant bacterial infections.
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Affiliation(s)
| | - Cristian Ruiz
- Department of Biology, California State University Northridge, Northridge, CA 91330, USA
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4
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Kumar R, Jafri MS. Computational Modeling of Mitochondria to Understand the Dynamics of Oxidative Stress. Methods Mol Biol 2022; 2497:363-422. [PMID: 35771458 PMCID: PMC9811848 DOI: 10.1007/978-1-0716-2309-1_27] [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] [Indexed: 01/14/2023]
Abstract
Mitochondria are complex organelles that use catabolic metabolism to produce ATP which is the critical energy source for cell function. Oxidative phosphorylation by the electron transport chain, which receives reducing equivalents (NADH and FADH2) from the tricarboxylic acid cycle, also produces reactive oxygen species (ROS) as a by-product at complex I and III. ROS play a significant role in health and disease. In order to better understand this process, a computational model of mitochondrial energy metabolism and the production of ROS has been developed. The model demonstrates the process regulating ROS production and removal and how different energy substrates can affect ROS production.
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Affiliation(s)
- Rashmi Kumar
- School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Mohsin S Jafri
- School of Systems Biology, George Mason University, Fairfax, VA, USA.
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA.
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5
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Huang LS, Lümmen P, Berry EA. Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2021; 1869:140679. [PMID: 34089891 PMCID: PMC8516616 DOI: 10.1016/j.bbapap.2021.140679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/15/2021] [Accepted: 05/24/2021] [Indexed: 01/01/2023]
Abstract
The quinone binding site (Q-site) of Mitochondrial Complex II (succinate-ubiquinone oxidoreductase) is the target for a number of inhibitors useful for elucidating the mechanism of the enzyme. Some of these have been developed as fungicides or pesticides, and species-specific Q-site inhibitors may be useful against human pathogens. We report structures of chicken Complex II with six different Q-site inhibitors bound, at resolutions 2.0-2.4 Å. These structures show the common interactions between the inhibitors and their binding site. In every case a carbonyl or hydroxyl oxygen of the inhibitor is H-bonded to Tyr58 in subunit SdhD and Trp173 in subunit SdhB. Two of the inhibitors H-bond Ser39 in subunit SdhC directly, while two others do so via a water molecule. There is a distinct cavity that accepts the 2-substituent of the carboxylate ring in flutolanil and related inhibitors. A hydrophobic "tail pocket" opens to receive a side-chain of intermediate-length inhibitors. Shorter inhibitors fit entirely within the main binding cleft, while the long hydrophobic side chains of ferulenol and atpenin A5 protrude out of the cleft into the bulk lipid region, as presumably does that of ubiquinone. Comparison of mitochondrial and Escherichia coli Complex II shows a rotation of the membrane-anchor subunits by 7° relative to the iron‑sulfur protein. This rotation alters the geometry of the Q-site and the H-bonding pattern of SdhB:His216 and SdhD:Asp57. This conformational difference, rather than any active-site mutation, may be responsible for the different inhibitor sensitivity of the bacterial enzyme.
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Affiliation(s)
- Li-Shar Huang
- Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams Street, Syracuse, N.Y 13210, USA
| | - Peter Lümmen
- Bayer AG, Crop Science Division, Industrial Park Höchst, Frankfurt/Main, Germany
| | - Edward A Berry
- Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 E. Adams Street, Syracuse, N.Y 13210, USA.
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6
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Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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7
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McKinlay JB, Cook GM, Hards K. Microbial energy management-A product of three broad tradeoffs. Adv Microb Physiol 2020; 77:139-185. [PMID: 34756210 DOI: 10.1016/bs.ampbs.2020.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Wherever thermodynamics allows, microbial life has evolved to transform and harness energy. Microbial life thus abounds in the most unexpected places, enabled by profound metabolic diversity. Within this diversity, energy is transformed primarily through variations on a few core mechanisms. Energy is further managed by the physiological processes of cell growth and maintenance that use energy. Some aspects of microbial physiology are streamlined for energetic efficiency while other aspects seem suboptimal or even wasteful. We propose that the energy that a microbe harnesses and devotes to growth and maintenance is a product of three broad tradeoffs: (i) economic, trading enzyme synthesis or operational cost for functional benefit, (ii) environmental, trading optimization for a single environment for adaptability to multiple environments, and (iii) thermodynamic, trading energetic yield for forward metabolic flux. Consideration of these tradeoffs allows one to reconcile features of microbial physiology that seem to opposingly promote either energetic efficiency or waste.
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Affiliation(s)
- James B McKinlay
- Department of Biology, Indiana University, Bloomington, IN, United States.
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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8
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Hards K, Rodriguez SM, Cairns C, Cook GM. Alternate quinone coupling in a new class of succinate dehydrogenase may potentiate mycobacterial respiratory control. FEBS Lett 2019; 593:475-486. [DOI: 10.1002/1873-3468.13330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 01/16/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Kiel Hards
- Department of Microbiology and Immunology University of Otago Dunedin New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery The University of Auckland New Zealand
| | | | - Charlotte Cairns
- Department of Microbiology and Immunology University of Otago Dunedin New Zealand
| | - Gregory M. Cook
- Department of Microbiology and Immunology University of Otago Dunedin New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery The University of Auckland New Zealand
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9
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Starbird CA, Maklashina E, Sharma P, Qualls-Histed S, Cecchini G, Iverson TM. Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase. J Biol Chem 2017; 292:12921-12933. [PMID: 28615448 DOI: 10.1074/jbc.m117.795120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/07/2017] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a ΔsdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdAE245 residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdAE245Q have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdAE245 variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdAE245 residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.
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Affiliation(s)
- C A Starbird
- Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Elena Maklashina
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - Susan Qualls-Histed
- Departments of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Gary Cecchini
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121; Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158.
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232.
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10
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Jeschek M, Bahls MO, Schneider V, Marlière P, Ward TR, Panke S. Biotin-independent strains of Escherichia coli for enhanced streptavidin production. Metab Eng 2017; 40:33-40. [DOI: 10.1016/j.ymben.2016.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/13/2016] [Accepted: 12/26/2016] [Indexed: 11/16/2022]
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11
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Creation of a gold nanoparticle based electrochemical assay for the detection of inhibitors of bacterial cytochrome bd oxidases. Bioelectrochemistry 2016; 111:109-14. [DOI: 10.1016/j.bioelechem.2016.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 12/23/2022]
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12
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Zhang Y, Qadri A, Weiner JH. The quinone-binding site ofAcidithiobacillus ferrooxidanssulfide: quinone oxidoreductase controls both sulfide oxidation and quinone reduction. Biochem Cell Biol 2016; 94:159-66. [DOI: 10.1139/bcb-2015-0097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sulfide:quinone oxidoreductase (SQR) is a peripheral membrane enzyme that catalyzes the oxidation of sulfide and the reduction of ubiquinone. Ubiquinone binds to a conserved hydrophobic domain and shuttles electrons from a noncovalent flavin adenine dinucleotide cofactor to the membrane-bound quinone pool. Utilizing the structure of decylubiquinone bound to Acidithiobacillus ferrooxidans SQR, we combined site-directed mutagenesis and kinetic approaches to analyze quinone binding. SQR can reduce both benzoquinones and naphthoquinones. The alkyl side-chain of ubiquinone derivatives enhances binding to SQR but limits the enzyme turnover. Pentachlorophenol and 2-n-heptyl-4-hydroxyquinoline-N-oxide are potent inhibitors of SQR with apparent inhibition constants (Ki) of 0.46 μmol·L−1and 0.58 μmol·L−1, respectively. The highly conserved amino acids surrounding the quinone binding site play an important role in quinone reduction. The phenyl side-chains of Phe357 and Phe391 sandwich the benzoquinone head group and are critical for quinone binding. Importantly, conserved amino acids that define the ubiquinone-binding site also play an important role in sulfide oxidation/flavin reduction.
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Affiliation(s)
- Yanfei Zhang
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ali Qadri
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Joel H. Weiner
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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13
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Hellwig P. Infrared spectroscopic markers of quinones in proteins from the respiratory chain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:126-33. [PMID: 25026472 DOI: 10.1016/j.bbabio.2014.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 01/12/2023]
Abstract
In bioenergetic systems quinones play a central part in the coupling of electron and proton transfer. The specific function of each quinone binding site is based on the protein-quinone interaction that can be described by means of reaction induced FTIR difference spectroscopy, induced for example by light or electrochemically. The identification of sites in enzymes from the respiratory chain is presented together with the analysis of the accommodation of different types of quinones to the same enzyme and the possibility to monitor the interaction with inhibitors. Reaction induced FTIR difference spectroscopy is shown to give an essential information on the general geometry of quinone binding sites, the conformation of the ring and of the substituents as well as essential structural information on the identity of the amino-acid residues lining this site. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Petra Hellwig
- Laboratoire de bioélectrochimie et spectroscopie, UMR 7140, Chimie de la matière complexe, Université de Strasbourg, 1, rue Blaise Pascal, 67008 Strasbourg, France.
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14
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Nordlund G, Brzezinski P, von Ballmoos C. SNARE-fusion mediated insertion of membrane proteins into native and artificial membranes. Nat Commun 2014; 5:4303. [DOI: 10.1038/ncomms5303] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/04/2014] [Indexed: 11/09/2022] Open
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15
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Anderson RF, Shinde SS, Hille R, Rothery RA, Weiner JH, Rajagukguk S, Maklashina E, Cecchini G. Electron-transfer pathways in the heme and quinone-binding domain of complex II (succinate dehydrogenase). Biochemistry 2014; 53:1637-46. [PMID: 24559074 PMCID: PMC3985935 DOI: 10.1021/bi401630m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Single electron transfers have been
examined in complex II (succinate:ubiquinone
oxidoreductase) by the method of pulse radiolysis. Electrons are introduced
into the enzyme initially at the [3Fe–4S] and ubiquinone sites
followed by intramolecular equilibration with the b heme of the enzyme. To define thermodynamic and other controlling
parameters for the pathways of electron transfer in complex II, site-directed
variants were constructed and analyzed. Variants at SdhB-His207 and
SdhB-Ile209 exhibit significantly perturbed electron transfer between
the [3Fe–4S] cluster and ubiquinone. Analysis of the data using
Marcus theory shows that the electronic coupling constants for wild-type
and variant enzyme are all small, indicating that electron transfer
occurs by diabatic tunneling. The presence of the ubiquinone is necessary
for efficient electron transfer to the heme, which only slowly equilibrates
with the [3Fe–4S] cluster in the absence of the quinone.
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Affiliation(s)
- Robert F Anderson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland , Auckland 1142, New Zealand
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16
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Biochemical analysis of recombinant AlkJ from Pseudomonas putida reveals a membrane-associated, flavin adenine dinucleotide-dependent dehydrogenase suitable for the biosynthetic production of aliphatic aldehydes. Appl Environ Microbiol 2014; 80:2468-77. [PMID: 24509930 DOI: 10.1128/aem.04297-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The noncanonical alcohol dehydrogenase AlkJ is encoded on the alkane-metabolizing alk operon of the mesophilic bacterium Pseudomonas putida GPo1. To gain insight into the enzymology of AlkJ, we have produced the recombinant protein in Escherichia coli and purified it to homogeneity using His6 tag affinity and size exclusion chromatography (SEC). Despite synthesis in the cytoplasm, AlkJ was associated with the bacterial cell membrane, and solubilization with n-dodecyl-β-D-maltoside was necessary to liberate the enzyme. SEC and spectrophotometric analysis revealed a dimeric quaternary structure with stoichiometrically bound reduced flavin adenine dinucleotide (FADH2). The holoenzyme showed thermal denaturation at moderate temperatures around 35°C, according to both activity assay and temperature-dependent circular dichroism spectroscopy. The tightly bound coenzyme was released only upon denaturation with SDS or treatment with urea-KBr and, after air oxidation, exhibited the characteristic absorption spectrum of FAD. The enzymatic activity of purified AlkJ for 1-butanol, 1-hexanol, and 1-octanol as well as the n-alkanol derivative ω-hydroxy lauric acid methyl ester (HLAMe) was quantified in the presence of the artificial electron acceptors phenazine methosulfate (PMS) and 2,6-dichlorophenolindophenol (DCPIP), indicating broad substrate specificity with the lowest activity on the shortest alcohol, 1-butanol. Furthermore, AlkJ was able to accept as cosubstrates/oxidants the ubiquinone derivatives Q0 and Q1, also in conjunction with cytochrome c, which suggests coupling to the bacterial respiratory chain of this membrane-associated enzyme in its physiological environment. Using gas chromatographic analysis, we demonstrated specific biocatalytic conversion by AlkJ of the substrate HLAMe to the industrially relevant aldehyde, thus enabling the biotechnological production of 12-amino lauric acid methyl ester via subsequent enzymatic transamination.
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17
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Singh PK, Sarwar M, Maklashina E, Kotlyar V, Rajagukguk S, Tomasiak TM, Cecchini G, Iverson TM. Plasticity of the quinone-binding site of the complex II homolog quinol:fumarate reductase. J Biol Chem 2013; 288:24293-301. [PMID: 23836905 DOI: 10.1074/jbc.m113.487082] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Respiratory processes often use quinone oxidoreduction to generate a transmembrane proton gradient, making the 2H(+)/2e(-) quinone chemistry important for ATP synthesis. There are a variety of quinones used as electron carriers between bioenergetic proteins, and some respiratory proteins can functionally interact with more than one quinone type. In the case of complex II homologs, which couple quinone chemistry to the interconversion of succinate and fumarate, the redox potentials of the biologically available ubiquinone and menaquinone aid in driving the chemical reaction in one direction. In the complex II homolog quinol:fumarate reductase, it has been demonstrated that menaquinol oxidation requires at least one proton shuttle, but many of the remaining mechanistic details of menaquinol oxidation are not fully understood, and little is known about ubiquinone reduction. In the current study, structural and computational studies suggest that the sequential removal of the two menaquinol protons may be accompanied by a rotation of the naphthoquinone ring to optimize the interaction with a second proton shuttling pathway. However, kinetic measurements of site-specific mutations of quinol:fumarate reductase variants show that ubiquinone reduction does not use the same pathway. Computational docking of ubiquinone followed by mutagenesis instead suggested redundant proton shuttles lining the ubiquinone-binding site or from direct transfer from solvent. These data show that the quinone-binding site provides an environment that allows multiple amino acid residues to participate in quinone oxidoreduction. This suggests that the quinone-binding site in complex II is inherently plastic and can robustly interact with different types of quinones.
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Affiliation(s)
- Prashant K Singh
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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Defining a direction: electron transfer and catalysis in Escherichia coli complex II enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:668-78. [PMID: 23396003 DOI: 10.1016/j.bbabio.2013.01.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/23/2013] [Accepted: 01/23/2013] [Indexed: 11/24/2022]
Abstract
There are two homologous membrane-bound enzymes in Escherichia coli that catalyze reversible conversion between succinate/fumarate and quinone/quinol. Succinate:ubiquinone reductase (SQR) is a component of aerobic respiratory chains, whereas quinol:fumarate reductase (QFR) utilizes menaquinol to reduce fumarate in a final step of anaerobic respiration. Although, both protein complexes are capable of supporting bacterial growth on either minimal succinate or fumarate media, the enzymes are more proficient in their physiological directions. Here we evaluate factors that may underlie this catalytic bias. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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20
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Harada S, Inaoka DK, Ohmori J, Kita K. Diversity of parasite complex II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:658-67. [PMID: 23333273 DOI: 10.1016/j.bbabio.2013.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 10/27/2022]
Abstract
Parasites have developed a variety of physiological functions necessary for completing at least part of their life cycles in the specialized environments of surrounding the parasites in the host. Regarding energy metabolism, which is essential for survival, parasites adapt to the low oxygen environment in mammalian hosts by using metabolic systems that are very different from those of the hosts. In many cases, the parasite employs aerobic metabolism during the free-living stage outside the host but undergoes major changes in developmental control and environmental adaptation to switch to anaerobic energy metabolism. Parasite mitochondria play diverse roles in their energy metabolism, and in recent studies of the parasitic nematode, Ascaris suum, the mitochondrial complex II plays an important role in anaerobic energy metabolism of parasites inhabiting hosts by acting as a quinol-fumarate reductase. In Trypanosomes, parasite complex II has been found to have a novel function and structure. Complex II of Trypanosoma cruzi is an unusual supramolecular complex with a heterodimeric iron-sulfur subunit and seven additional non-catalytic subunits. The enzyme shows reduced binding affinities for both substrates and inhibitors. Interestingly, this structural organization is conserved in all trypanosomatids. Since the properties of complex II differ across a wide range of parasites, this complex is a potential target for the development of new chemotherapeutic agents. In this regard, structural information on the target enzyme is essential for the molecular design of drugs. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- Shigeharu Harada
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.
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21
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Iverson TM. Catalytic mechanisms of complex II enzymes: a structural perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:648-57. [PMID: 22995215 DOI: 10.1016/j.bbabio.2012.09.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 11/25/2022]
Abstract
Over a decade has passed since the elucidation of the first X-ray crystal structure of any complex II homolog. In the intervening time, the structures of five additional integral-membrane complex II enzymes and three homologs of the soluble domain have been determined. These structures have provided a framework for the analysis of enzymological studies of complex II superfamily enzymes, and have contributed to detailed proposals for reaction mechanisms at each of the two enzyme active sites, which catalyze dicarboxylate and quinone oxidoreduction, respectively. This review focuses on how structural data have augmented our understanding of catalysis by the superfamily. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- T M Iverson
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232-6600, USA.
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22
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van Lis R, Nitschke W, Duval S, Schoepp-Cothenet B. Arsenics as bioenergetic substrates. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:176-88. [PMID: 22982475 DOI: 10.1016/j.bbabio.2012.08.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 08/28/2012] [Accepted: 08/31/2012] [Indexed: 01/24/2023]
Abstract
Although at low concentrations, arsenic commonly occurs naturally as a local geological constituent. Whereas both arsenate and arsenite are strongly toxic to life, a number of prokaryotes use these compounds as electron acceptors or donors, respectively, for bioenergetic purposes via respiratory arsenate reductase, arsenite oxidase and alternative arsenite oxidase. The recent burst in discovered arsenite oxidizing and arsenate respiring microbes suggests the arsenic bioenergetic metabolisms to be anything but exotic. The first goal of the present review is to bring to light the widespread distribution and diversity of these metabolizing pathways. The second goal is to present an evolutionary analysis of these diverse energetic pathways. Taking into account not only the available data on the arsenic metabolizing enzymes and their phylogenetical relatives but also the palaeogeochemical records, we propose a crucial role of arsenite oxidation via arsenite oxidase in primordial life. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Robert van Lis
- Laboratoire de Bioénergétique et Ingénierie des Protéines UMR 7281 CNRS/AMU, FR3479, F-13402 Marseille Cedex 20, France
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23
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Schütz B, Seidel J, Sturm G, Einsle O, Gescher J. Investigation of the electron transport chain to and the catalytic activity of the diheme cytochrome c peroxidase CcpA of Shewanella oneidensis. Appl Environ Microbiol 2011; 77:6172-80. [PMID: 21742904 PMCID: PMC3165401 DOI: 10.1128/aem.00606-11] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/30/2011] [Indexed: 11/20/2022] Open
Abstract
Bacterial diheme c-type cytochrome peroxidases (BCCPs) catalyze the periplasmic reduction of hydrogen peroxide to water. The gammaproteobacterium Shewanella oneidensis produces the peroxidase CcpA under a number of anaerobic conditions, including dissimilatory iron-reducing conditions. We wanted to understand the function of this protein in the organism and its putative connection to the electron transport chain to ferric iron. CcpA was isolated and tested for peroxidase activity, and its structural conformation was analyzed by X-ray crystallography. CcpA exhibited in vitro peroxidase activity and had a structure typical of diheme peroxidases. It was produced in almost equal amounts under anaerobic and microaerophilic conditions. With 50 mM ferric citrate and 50 μM oxygen in the growth medium, CcpA expression results in a strong selective advantage for the cell, which was detected in competitive growth experiments with wild-type and ΔccpA mutant cells that lack the entire ccpA gene due to a markerless deletion. We were unable to reduce CcpA directly with CymA, MtrA, or FccA, which are known key players in the chain of electron transport to ferric iron and fumarate but identified the small monoheme ScyA as a mediator of electron transport between CymA and BCCP. To our knowledge, this is the first detailed description of a complete chain of electron transport to a periplasmic c-type cytochrome peroxidase. This study furthermore reports the possibility of establishing a specific electron transport chain using c-type cytochromes.
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Affiliation(s)
- Björn Schütz
- Institut für Biologie II, Mikrobiologie, Universität Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Julian Seidel
- Institut für organische Chemie und Biochemie, Biochemie, Universität Freiburg, Albertstr. 21, D-79104 Freiburg, Germany
| | - Gunnar Sturm
- Institut für angewandte Biowissenschaften, Angewandte Biologie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
| | - Oliver Einsle
- Institut für organische Chemie und Biochemie, Biochemie, Universität Freiburg, Albertstr. 21, D-79104 Freiburg, Germany
| | - Johannes Gescher
- Institut für angewandte Biowissenschaften, Angewandte Biologie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 2, D-76131 Karlsruhe, Germany
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24
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Zhou Q, Zhai Y, Lou J, Liu M, Pang X, Sun F. Thiabendazole inhibits ubiquinone reduction activity of mitochondrial respiratory complex II via a water molecule mediated binding feature. Protein Cell 2011; 2:531-42. [PMID: 21822798 DOI: 10.1007/s13238-011-1079-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022] Open
Abstract
The mitochondrial respiratory complex II or succinate: ubiquinone oxidoreductase (SQR) is a key membrane complex in both the tricarboxylic acid cycle and aerobic respiration. Five disinfectant compounds were investigated with their potent inhibition effects on the ubiquinone reduction activity of the porcine mitochondrial SQR by enzymatic assay and crystallography. Crystal structure of the SQR bound with thiabendazole (TBZ) reveals a different inhibitor-binding feature at the ubiquinone binding site where a water molecule plays an important role. The obvious inhibitory effect of TBZ based on the biochemical data (IC(50) ~100 μmol/L) and the significant structure-based binding affinity calculation (~94 μmol/L) draw the suspicion of using TBZ as a good disinfectant compound for nematode infections treatment and fruit storage.
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Affiliation(s)
- Qiangjun Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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25
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Ruprecht J, Iwata S, Rothery RA, Weiner JH, Maklashina E, Cecchini G. Perturbation of the quinone-binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster. J Biol Chem 2011; 286:12756-65. [PMID: 21310949 DOI: 10.1074/jbc.m110.209874] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones; however, SQR preferentially reacts with higher potential ubiquinones, and QFR preferentially reacts with lower potential naphthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones, a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His-207 by threonine (as found in QFR) resulted in a 70-mV lowering of the redox potential of the cluster as measured by EPR. The converse substitution in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster have only a minor effect on catalysis.
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Affiliation(s)
- Jonathan Ruprecht
- Membrane Protein Crystallography Group, Molecular Biosciences Division, Imperial College, London SW7 2AZ, United Kingdom
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26
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Supramolecular organizations in the aerobic respiratory chain of Escherichia coli. Biochimie 2010; 93:418-25. [PMID: 21040753 DOI: 10.1016/j.biochi.2010.10.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 10/20/2010] [Indexed: 12/26/2022]
Abstract
The organization of respiratory chain complexes in supercomplexes has been shown in the mitochondria of several eukaryotes and in the cell membranes of some bacteria. These supercomplexes are suggested to be important for oxidative phosphorylation efficiency and to prevent the formation of reactive oxygen species. Here we describe, for the first time, the identification of supramolecular organizations in the aerobic respiratory chain of Escherichia coli, including a trimer of succinate dehydrogenase. Furthermore, two heterooligomerizations have been shown: one resulting from the association of the NADH:quinone oxidoreductases NDH-1 and NDH-2, and another composed by the cytochrome bo(3) quinol:oxygen reductase, cytochrome bd quinol:oxygen reductase and formate dehydrogenase (fdo). These results are supported by blue native-electrophoresis, mass spectrometry and kinetic data of wild type and mutant E . coli strains.
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27
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Choi SB, Normi YM, Wahab HA. Why hypothetical protein KPN00728 of Klebsiella pneumoniae should be classified as chain C of succinate dehydrogenase? Protein J 2010; 28:415-27. [PMID: 19859792 PMCID: PMC2785890 DOI: 10.1007/s10930-009-9209-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Twenty percent of genes that encode for hypothetical proteins from Klebsiella pneumoniae MGH78578 were identified, leading to KPN00728 and KPN00729 after bioinformatics analysis. Both open reading frames showed high sequence homology to Succinate dehydrogenase Chain C (SdhC) and D (SdhD) from Escherichia coli. Recently, KPN00729 was assigned as SdhD. KPN00728 thus remains of particular interest as no annotated genes from the complete genome sequence encode for SdhC. We discovered KPN00728 has a missing region with conserved residues important for ubiquinone (UQ) and heme group binding. Structure and function prediction of KPN00728 coupled with secondary structure analysis and transmembrane topology showed KPN00728 adopts SDH-(subunit C)-like structure. To further probe its functionality, UQ was docked on the built model (consisting KPN00728 and KPN00729) and formation of hydrogen bonds between UQ and Ser27, Arg31 (KPN00728) and Tyr84 (KPN00729) further reinforces and supports that KPN00728 is indeed SDH. This is the first report on the structural and function prediction of KPN00728 of K. pneumoniae MGH78578 as SdhC.
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Affiliation(s)
- Sy Bing Choi
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang Malaysia
| | - Yahaya M. Normi
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang Malaysia
| | - Habibah A. Wahab
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang Malaysia
- Centre for Advanced Drug Delivery, Malaysian Institute of Pharmaceuticals and Nutraceuticals, Ministry of Science, Technology and Innovation, SAINS@USM, No 10, 11900 Persiaran Bukit Jambul, Pulau Pinang Malaysia
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28
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Maklashina E, Cecchini G. The quinone-binding and catalytic site of complex II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1877-82. [PMID: 20175986 DOI: 10.1016/j.bbabio.2010.02.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Revised: 02/08/2010] [Accepted: 02/16/2010] [Indexed: 10/19/2022]
Abstract
The complex II family of proteins includes succinate:quinone oxidoreductase (SQR) and quinol:fumarate oxidoreductase (QFR). In the facultative bacterium Escherichia coli both are expressed as part of the aerobic (SQR) and anaerobic (QFR) respiratory chains. SQR from E. coli is homologous to mitochondrial complex II and has proven to be an excellent model system for structure/function studies of the enzyme. Both SQR and QFR from E. coli are tetrameric membrane-bound enzymes that couple succinate/fumarate interconversion with quinone/quinol reduction/oxidation. Both enzymes are capable of binding either ubiquinone or menaquinone, however, they have adopted different quinone binding sites where catalytic reactions with quinones occur. A comparison of the structures of the quinone binding sites in SQR and QFR reveals how the enzymes have adapted in order to accommodate both benzo- and napthoquinones. A combination of structural, computational, and kinetic studies of members of the complex II family of enzymes has revealed that the catalytic quinone adopts different positions in the quinone-binding pocket. These data suggest that movement of the quinone within the quinone-binding pocket is essential for catalysis.
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Affiliation(s)
- Elena Maklashina
- Molecular Biology Division, VA Medical Center, San Francisco, CA 94121, USA
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Maklashina E, Rajagukguk S, McIntire WS, Cecchini G. Mutation of the heme axial ligand of Escherichia coli succinate-quinone reductase: implications for heme ligation in mitochondrial complex II from yeast. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:747-54. [PMID: 20100456 DOI: 10.1016/j.bbabio.2010.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 01/15/2010] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
Abstract
A b-type heme is conserved in membrane-bound complex II enzymes (SQR, succinate-ubiquinone reductase). The axial ligands for the low spin heme b in Escherichia coli complex II are SdhC His84 and SdhD His71. E. coli SdhD His71 is separated by 10 residues from SdhD Asp82 and Tyr83 which are essential for ubiquinone catalysis. The same His-10x-AspTyr motif dominates in homologous SdhD proteins, except for Saccharomyces cerevisiae where a tyrosine is at the axial position (Tyr-Cys-9x-AspTyr). Nevertheless, the yeast enzyme was suggested to contain a stoichiometric amount of heme, however, with the Cys ligand in the aforementioned motif acting as heme ligand. In this report, the role of Cys residues for heme coordination in the complex II family of enzymes is addressed. Cys was substituted to the SdhD-71 position and the yeast Tyr71Cys72 motif was also recreated. The Cys71 variant retained heme, although it was high spin, while the Tyr71Cys72 mutant lacked heme. Previously the presence of heme in S. cerevisiae was detected by a spectral peak in fumarate-oxidized, dithionite-reduced mitochondria. Here it is shown that this method must be used with caution. Comparison of bovine and yeast mitochondrial membranes shows that fumarate induced reoxidation of cytochromes in both SQR and the bc1 complex (ubiquinol-cytochrome c reductase). Thus, this report raises a concern about the presence of low spin heme b in S. cerevisiae complex II.
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Affiliation(s)
- Elena Maklashina
- Molecular Biology Division, VA Medical Center, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
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Berry EA, Huang LS, Lee DW, Daldal F, Nagai K, Minagawa N. Ascochlorin is a novel, specific inhibitor of the mitochondrial cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:360-70. [PMID: 20025846 DOI: 10.1016/j.bbabio.2009.12.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 12/03/2009] [Accepted: 12/08/2009] [Indexed: 11/24/2022]
Abstract
Ascochlorin is an isoprenoid antibiotic that is produced by the phytopathogenic fungus Ascochyta viciae. Similar to ascofuranone, which specifically inhibits trypanosome alternative oxidase by acting at the ubiquinol binding domain, ascochlorin is also structurally related to ubiquinol. When added to the mitochondrial preparations isolated from rat liver, or the yeast Pichia (Hansenula) anomala, ascochlorin inhibited the electron transport via CoQ in a fashion comparable to antimycin A and stigmatellin, indicating that this antibiotic acted on the cytochrome bc(1) complex. In contrast to ascochlorin, ascofuranone had much less inhibition on the same activities. On the one hand, like the Q(i) site inhibitors antimycin A and funiculosin, ascochlorin induced in H. anomala the expression of nuclear-encoded alternative oxidase gene much more strongly than the Q(o) site inhibitors tested. On the other hand, it suppressed the reduction of cytochrome b and the generation of superoxide anion in the presence of antimycin A(3) in a fashion similar to the Q(o) site inhibitor myxothiazol. These results suggested that ascochlorin might act at both the Q(i) and the Q(o) sites of the fungal cytochrome bc(1) complex. Indeed, the altered electron paramagnetic resonance (EPR) lineshape of the Rieske iron-sulfur protein, and the light-induced, time-resolved cytochrome b and c reduction kinetics of Rhodobacter capsulatus cytochrome bc(1) complex in the presence of ascochlorin demonstrated that this inhibitor can bind to both the Q(o) and Q(i) sites of the bacterial enzyme. Additional experiments using purified bovine cytochrome bc(1) complex showed that ascochlorin inhibits reduction of cytochrome b by ubiquinone through both Q(i) and Q(o) sites. Moreover, crystal structure of chicken cytochrome bc(1) complex treated with excess ascochlorin revealed clear electron densities that could be attributed to ascochlorin bound at both the Q(i) and Q(o) sites. Overall findings clearly show that ascochlorin is an unusual cytochrome bc(1) inhibitor that acts at both of the active sites of this enzyme.
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Affiliation(s)
- Edward A Berry
- SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
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31
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Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, Cecchini G. Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site. J Biol Chem 2009; 284:29836-46. [PMID: 19710024 PMCID: PMC2785614 DOI: 10.1074/jbc.m109.010058] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 07/20/2009] [Indexed: 11/06/2022] Open
Abstract
Three new structures of Escherichia coli succinate-quinone oxidoreductase (SQR) have been solved. One with the specific quinone-binding site (Q-site) inhibitor carboxin present has been solved at 2.4 A resolution and reveals how carboxin inhibits the Q-site. The other new structures are with the Q-site inhibitor pentachlorophenol and with an empty Q-site. These structures reveal important details unresolved in earlier structures. Comparison of the new SQR structures shows how subtle rearrangements of the quinone-binding site accommodate the different inhibitors. The position of conserved water molecules near the quinone binding pocket leads to a reassessment of possible water-mediated proton uptake networks that complete reduction of ubiquinone. The dicarboxylate-binding site in the soluble domain of SQR is highly similar to that seen in high resolution structures of avian SQR (PDB 2H88) and soluble flavocytochrome c (PDB 1QJD) showing mechanistically significant structural features conserved across prokaryotic and eukaryotic SQRs.
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Affiliation(s)
- Jonathan Ruprecht
- From the Membrane Protein Crystallography Group, Molecular Biosciences Division, Imperial College, London SW7 2AZ, United Kingdom
| | - Victoria Yankovskaya
- the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, and
| | - Elena Maklashina
- the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, and
- the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - So Iwata
- From the Membrane Protein Crystallography Group, Molecular Biosciences Division, Imperial College, London SW7 2AZ, United Kingdom
| | - Gary Cecchini
- the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, and
- the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
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Singh R, Lemire J, Mailloux RJ, Chénier D, Hamel R, Appanna VD. An ATP and oxalate generating variant tricarboxylic acid cycle counters aluminum toxicity in Pseudomonas fluorescens. PLoS One 2009; 4:e7344. [PMID: 19809498 PMCID: PMC2752808 DOI: 10.1371/journal.pone.0007344] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 09/11/2009] [Indexed: 01/05/2023] Open
Abstract
Although the tricarboxylic acid (TCA) cycle is essential in almost all aerobic organisms, its precise modulation and integration in global cellular metabolism is not fully understood. Here, we report on an alternative TCA cycle uniquely aimed at generating ATP and oxalate, two metabolites critical for the survival of Pseudomonas fluorescens. The upregulation of isocitrate lyase (ICL) and acylating glyoxylate dehydrogenase (AGODH) led to the enhanced synthesis of oxalate, a dicarboxylic acid involved in the immobilization of aluminum (Al). The increased activity of succinyl-CoA synthetase (SCS) and oxalate CoA-transferase (OCT) in the Al-stressed cells afforded an effective route to ATP synthesis from oxalyl-CoA via substrate level phosphorylation. This modified TCA cycle with diminished efficacy in NADH production and decreased CO(2)-evolving capacity, orchestrates the synthesis of oxalate, NADPH, and ATP, ingredients pivotal to the survival of P. fluorescens in an Al environment. The channeling of succinyl-CoA towards ATP formation may be an important function of the TCA cycle during anaerobiosis, Fe starvation and O(2)-limited conditions.
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Affiliation(s)
- Ranji Singh
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Joseph Lemire
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Ryan J. Mailloux
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Daniel Chénier
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Robert Hamel
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Vasu D. Appanna
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
- * E-mail:
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Assembly of a chimeric respiratory chain from bovine heart submitochondrial particles and cytochrome bd terminal oxidase of Escherichia coli. FEBS Lett 2009; 583:1287-91. [PMID: 19303413 DOI: 10.1016/j.febslet.2009.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 03/04/2009] [Accepted: 03/12/2009] [Indexed: 11/23/2022]
Abstract
Cytochrome bd is a terminal quinol oxidase in Escherichia coli. Mitochondrial respiration is inhibited at cytochrome bc(1) (complex III) by myxothiazol. Mixing purified cytochrome bd oxidase with myxothiazol-inhibited bovine heart submitochondrial particles (SMP) restores up to 50% of the original rotenone-sensitive NADH oxidase and succinate oxidase activities in the absence of exogenous ubiquinone analogs. Complex III bypassed respiration and is saturated at amounts of added cytochrome bd similar to that of other natural respiratory components in SMP. The cytochrome bd tightly binds to the mitochondrial membrane and operates as an intrinsic component of the chimeric respiratory chain.
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Morales J, Mogi T, Mineki S, Takashima E, Mineki R, Hirawake H, Sakamoto K, Omura S, Kita K. Novel mitochondrial complex II isolated from Trypanosoma cruzi is composed of 12 peptides including a heterodimeric Ip subunit. J Biol Chem 2009; 284:7255-63. [PMID: 19122194 PMCID: PMC2652292 DOI: 10.1074/jbc.m806623200] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 01/02/2009] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial respiratory enzymes play a central role in energy production in aerobic organisms. They differentiated from the alpha-proteobacteria-derived ancestors by adding noncatalytic subunits. An exception is Complex II (succinate: ubiquinone reductase), which is composed of four alpha-proteobacteria-derived catalytic subunits (SDH1-SDH4). Complex II often plays a pivotal role in adaptation of parasites in host organisms and would be a potential target for new drugs. We purified Complex II from the parasitic protist Trypanosoma cruzi and obtained the unexpected result that it consists of six hydrophilic (SDH1, SDH2N, SDH2C, and SDH5-SDH7) and six hydrophobic (SDH3, SDH4, and SDH8-SDH11) nucleus-encoded subunits. Orthologous genes for each subunit were identified in Trypanosoma brucei and Leishmania major. Notably, the iron-sulfur subunit was heterodimeric; SDH2N and SDH2C contain the plant-type ferredoxin domain in the N-terminal half and the bacterial ferredoxin domain in the C-terminal half, respectively. Catalytic subunits (SDH1, SDH2N plus SDH2C, SDH3, and SDH4) contain all key residues for binding of dicarboxylates and quinones, but the enzyme showed the lower affinity for both substrates and inhibitors than mammalian enzymes. In addition, the enzyme binds protoheme IX, but SDH3 lacks a ligand histidine. These unusual features are unique in the Trypanosomatida and make their Complex II a target for new chemotherapeutic agents.
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Affiliation(s)
- Jorge Morales
- Department of Biomedical Chemistry, Graduate School of Medicine, the University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, USA
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Sonck KAJ, Kint G, Schoofs G, Vander Wauven C, Vanderleyden J, De Keersmaecker SCJ. The proteome of Salmonella Typhimurium grown under in vivo-mimicking conditions. Proteomics 2009; 9:565-79. [DOI: 10.1002/pmic.200700476] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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36
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Quinol Oxidation by c-Type Cytochromes: Structural Characterization of the Menaquinol Binding Site of NrfHA. J Mol Biol 2008; 381:341-50. [DOI: 10.1016/j.jmb.2008.05.066] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/15/2008] [Accepted: 05/20/2008] [Indexed: 11/18/2022]
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Tomasiak TM, Maklashina E, Cecchini G, Iverson TM. A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II. J Biol Chem 2008; 283:15460-8. [PMID: 18385138 PMCID: PMC2397489 DOI: 10.1074/jbc.m801372200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 03/26/2008] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, the complex II superfamily members succinate:ubiquinone oxidoreductase (SQR) and quinol:fumarate reductase (QFR) participate in aerobic and anaerobic respiration, respectively. Complex II enzymes catalyze succinate and fumarate interconversion at the interface of two domains of the soluble flavoprotein subunit, the FAD binding domain and the capping domain. An 11-amino acid loop in the capping domain (Thr-A234 to Thr-A244 in quinol:fumarate reductase) begins at the interdomain hinge and covers the active site. Amino acids of this loop interact with both the substrate and a proton shuttle, potentially coordinating substrate binding and the proton shuttle protonation state. To assess the loop's role in catalysis, two threonine residues were mutated to alanine: QFR Thr-A244 (act-T; Thr-A254 in SQR), which hydrogen-bonds to the substrate at the active site, and QFR Thr-A234 (hinge-T; Thr-A244 in SQR), which is located at the hinge and hydrogen-bonds the proton shuttle. Both mutations impair catalysis and decrease substrate binding. The crystal structure of the hinge-T mutation reveals a reorientation between the FAD-binding and capping domains that accompanies proton shuttle alteration. Taken together, hydrogen bonding from act-T to substrate may coordinate with interdomain motions to twist the double bond of fumarate and introduce the strain important for attaining the transition state.
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Affiliation(s)
- Thomas M. Tomasiak
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, and the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Elena Maklashina
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, and the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Gary Cecchini
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, and the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Tina M. Iverson
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, the Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, and the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
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Escherichia coli succinate dehydrogenase variant lacking the heme b. Proc Natl Acad Sci U S A 2007; 104:18007-12. [PMID: 17989224 DOI: 10.1073/pnas.0707732104] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Escherichia coli enzyme succinate:ubiquinone oxidoreductase [(succinate dehydrogenase (SdhCDAB)] couples succinate oxidation to ubiquinone reduction and is structurally and functionally equivalent to mitochondrial complex II, an essential component of the aerobic respiratory chain and tricarboxylic acid cycle. All such enzymes contain a heme within their membrane anchor domain with a highly contentious, but as-yet-undetermined, function. Here, we report the generation of a complex II that lacks heme, which is confirmed by both optical and EPR spectroscopy. Despite the absence of heme, this mutant still assembles properly and retains physiological activity. However, the mutants lacking heme are highly sensitive to the presence of detergent. In addition, the heme does not appear to be involved in reactive oxygen species suppression. Our results indicate that redox cycling of the heme in complex II is not essential for the enzyme's ubiquinol reductase activity.
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Effects of the deletion of the Escherichia coli frataxin homologue CyaY on the respiratory NADH:ubiquinone oxidoreductase. BMC BIOCHEMISTRY 2007; 8:13. [PMID: 17650323 PMCID: PMC1959517 DOI: 10.1186/1471-2091-8-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Accepted: 07/24/2007] [Indexed: 11/30/2022]
Abstract
Background Frataxin is discussed as involved in the biogenesis of iron-sulfur clusters. Recently it was discovered that a frataxin homologue is a structural component of the respiratory NADH:ubiquinone oxidoreductase (complex I) in Thermus thermophilus. It was not clear whether frataxin is in general a component of complex I from bacteria. The Escherichia coli homologue of frataxin is coined CyaY. Results We report that complex I is completely assembled to a stable and active enzyme complex equipped with all known iron-sulfur clusters in a cyaY mutant of E. coli. However, the amount of complex I is reduced by one third compared to the parental strain. Western blot analysis and live cell imaging of CyaY engineered with a GFP demonstrated that CyaY is located in the cytoplasm and not attached to the membrane as to be expected if it were a component of complex I. Conclusion CyaY plays a non-essential role in the assembly of complex I in E. coli. It is not a structural component but may transiently interact with the complex.
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Mailloux RJ, Hamel R, Appanna VD. Aluminum toxicity elicits a dysfunctional TCA cycle and succinate accumulation in hepatocytes. J Biochem Mol Toxicol 2007; 20:198-208. [PMID: 16906525 DOI: 10.1002/jbt.20137] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Aluminum (Al), a known environmental toxicant, has been linked to a variety of pathological conditions such as dialysis dementia, osteomalacia, Alzheimer's disease, and Parkinson's disease. However, its precise role in the pathogenesis of these disorders is not fully understood. Using hepatocytes as a model system, we have probed the impact of this trivalent metal on the aerobic energy-generating machinery. Here we show that Al-exposed hepatocytes were characterized by lipid and protein oxidation and a dysfunctional tricarboxylic acid (TCA) cycle. BN-PAGE, SDS-PAGE, and Western blot analyses revealed a marked decrease in activity and expression of succinate dehydrogenase (SDH), alpha-ketoglutarate dehydrogenase (KGDH), isocitrate dehydrogenase-NAD+ (IDH), fumarase (FUM), aconitase (ACN), and cytochrome c oxidase (Cyt C Ox). 13C-NMR and HPLC studies further confirmed the disparate metabolism operative in control and Al-stressed cells and provided evidence for the accumulation of succinate in the latter cultures. In conclusion, these results suggest that Al toxicity promotes a dysfunctional TCA cycle and impedes ATP production, events that may contribute to various Al-induced abnormalities.
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Affiliation(s)
- Ryan J Mailloux
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada, P3E 2C6
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41
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Tomasiak TM, Cecchini G, Iverson TM. Succinate as Donor; Fumarate as Acceptor. EcoSal Plus 2007; 2. [PMID: 26443593 DOI: 10.1128/ecosal.3.2.6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Indexed: 06/05/2023]
Abstract
Succinate and fumarate are four-carbon dicarboxylates that differ in the identity of their central bond (single or double). The oxidoreduction of these small molecules plays a central role in both aerobic and anaerobic respiration. During aerobic respiration, succinate is oxidized, donating two reducing equivalents, while in anaerobic respiration, fumarate is reduced, accepting two reducing equivalents. Two related integral membrane Complex II superfamily members catalyze these reactions, succinate:ubiquinone oxidoreductase (SQR) and fumarate:menaquinol oxidoreductase (QFR). The structure, function, and regulation of these integral-membrane enzymes are summarized here. The overall architecture of these Complex II enzymes has been found to consist of four subunits: two integral membrane subunits, and a soluble domain consisting of an iron-sulfur protein subunit, and a flavoprotein subunit. This architecture provides a scaffold that houses one active site in the membrane and another in the soluble milieu, making a linear electron transfer chain that facilities shuttling of reducing equivalents between the two active sites. A combination of kinetic measurements, mutagenesis, electron paramagnetic resonance spectroscopy, UV/Vis spectroscopy, and x-ray crystallography have suggested mechanisms for succinate:fumarate interconversion, electron transfer, and quinone:quinol interconversion. Of particular interest are the structural details that control directionality and make SQR and QFR primed for preferential catalysis each in different favored directions.
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Tran QM, Rothery RA, Maklashina E, Cecchini G, Weiner JH. The Quinone Binding Site in Escherichia coli Succinate Dehydrogenase Is Required for Electron Transfer to the Heme b. J Biol Chem 2006; 281:32310-7. [PMID: 16950775 DOI: 10.1074/jbc.m607476200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have examined the role of the quinone-binding (Q(P)) site of Escherichia coli succinate:ubiquinone oxidoreductase (succinate dehydrogenase) in heme reduction and reoxidation during enzyme turnover. The SdhCDAB electron transfer pathway leads from a cytosolically localized flavin adenine dinucleotide cofactor to a Q(P) site located within the membrane-intrinsic domain of the enzyme. The Q(P) site is sandwiched between the [3Fe-4S] cluster of the SdhB subunit and the heme b(556) that is coordinated by His residues from the SdhC and SdhD subunits. The intercenter distances between the cluster, heme, and Q(P) site are all within the theoretical 14 A limit proposed for kinetically competent intercenter electron transfer. Using EPR spectroscopy, we have demonstrated that the Q(P) site of SdhCDAB stabilized a ubisemiquinone radical intermediate during enzyme turnover. Potentiometric titrations indicate that this species has an E(m,8) of approximately 60 mV and a stability constant (K(STAB)) of approximately 1.0. Mutants of the following conserved Q(P) site residues, SdhC-S27, SdhC-R31, and SdhD-D82, have severe consequences on enzyme function. Mutation of the conserved SdhD-Y83 suggested to hydrogen bond to the ubiquinone cofactor had a less severe but still significant effect on function. In addition to loss of overall catalysis, these mutants also affect the rate of succinate-dependent heme reduction, indicating that the Q(P) site is an essential stepping stone on the electron transfer pathway from the [3Fe-4S] cluster to the heme. Furthermore, the mutations result in the elimination of EPR-visible ubisemiquinone during potentiometric titrations. Overall, these results demonstrate the importance of a functional, semiquinone-stabilizing Q(P) site for the observation of rapid succinate-dependent heme reduction.
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Affiliation(s)
- Quang M Tran
- Membrane Protein Research Group, Department of Biochemistry, University of Alberta, 473 Medical Sciences Building, Edmonton, Alberta T6G 2H7, Canada
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43
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Maklashina E, Hellwig P, Rothery RA, Kotlyar V, Sher Y, Weiner JH, Cecchini G. Differences in protonation of ubiquinone and menaquinone in fumarate reductase from Escherichia coli. J Biol Chem 2006; 281:26655-64. [PMID: 16829675 DOI: 10.1074/jbc.m602938200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli quinol-fumarate reductase operates with both natural quinones, ubiquinone (UQ) and menaquinone (MQ), at a single quinone binding site. We have utilized a combination of mutagenesis, kinetic, EPR, and Fourier transform infrared methods to study the role of two residues, Lys-B228 and Glu-C29, at the quinol-fumarate reductase quinone binding site in reactions with MQ and UQ. The data demonstrate that Lys-B228 provides a strong hydrogen bond to MQ and is essential for reactions with both quinone types. Substitution of Glu-C29 with Leu and Phe caused a dramatic decrease in enzymatic reactions with MQ in agreement with previous studies, however, the succinate-UQ reductase reaction remains unaffected. Elimination of a negative charge in Glu-C29 mutant enzymes resulted in significantly increased stabilization of both UQ-* and MQ-* semiquinones. The data presented here suggest similar hydrogen bonding of the C1 carbonyl of both MQ and UQ, whereas there is different hydrogen bonding for their C4 carbonyls. The differences are shown by a single point mutation of Glu-C29, which transforms the enzyme from one that is predominantly a menaquinol-fumarate reductase to one that is essentially only functional as a succinate-ubiquinone reductase. These findings represent an example of how enzymes that are designed to accommodate either UQ or MQ at a single Q binding site may nevertheless develop sufficient plasticity at the binding pocket to react differently with MQ and UQ.
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Affiliation(s)
- Elena Maklashina
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California, 94121, USA
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44
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Maklashina E, Iverson TM, Sher Y, Kotlyar V, Andréll J, Mirza O, Hudson JM, Armstrong FA, Rothery RA, Weiner JH, Cecchini G. Fumarate Reductase and Succinate Oxidase Activity of Escherichia coli Complex II Homologs Are Perturbed Differently by Mutation of the Flavin Binding Domain. J Biol Chem 2006; 281:11357-65. [PMID: 16484232 DOI: 10.1074/jbc.m512544200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli complex II homologues succinate:ubiquinone oxidoreductase (SQR, SdhCDAB) and menaquinol:fumarate oxidoreductase (QFR, FrdABCD) have remarkable structural homology at their dicarboxylate binding sites. Although both SQR and QFR can catalyze the interconversion of fumarate and succinate, QFR is a much better fumarate reductase, and SQR is a better succinate oxidase. An exception to the conservation of amino acids near the dicarboxylate binding sites of the two enzymes is that there is a Glu (FrdA Glu-49) near the covalently bound FAD cofactor in most QFRs, which is replaced with a Gln (SdhA Gln-50) in SQRs. The role of the amino acid side chain in enzymes with Glu/Gln/Ala substitutions at FrdA Glu-49 and SdhA Gln-50 has been investigated in this study. The data demonstrate that the mutant enzymes with Ala substitutions in either QFR or SQR remain functionally similar to their wild type counterparts. There were, however, dramatic changes in the catalytic properties when Glu and Gln were exchanged for each other in QFR and SQR. The data show that QFR and SQR enzymes are more efficient succinate oxidases when Gln is in the target position and a better fumarate reductase when Glu is present. Overall, structural and catalytic analyses of the FrdA E49Q and SdhA Q50E mutants suggest that coulombic effects and the electronic state of the FAD are critical in dictating the preferred directionality of the succinate/fumarate interconversions catalyzed by the complex II superfamily.
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Affiliation(s)
- Elena Maklashina
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California 94121, USA
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45
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Castro-Guerrero NA, Jasso-Chávez R, Moreno-Sánchez R. Physiological role of rhodoquinone in Euglena gracilis mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1710:113-21. [PMID: 16325648 DOI: 10.1016/j.bbabio.2005.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Revised: 09/21/2005] [Accepted: 10/11/2005] [Indexed: 11/24/2022]
Abstract
Rhodoquinone (RQ) participates in fumarate reduction under anaerobiosis in some bacteria and some primitive eukaryotes. Euglena gracilis, a facultative anaerobic protist, also possesses significant rhodoquinone-9 (RQ9) content. Growth under low oxygen concentration induced a decrease in cytochromes and ubiquinone-9 (UQ9) content, while RQ9 and fumarate reductase (FR) activity increased. However, in cells cultured under aerobic conditions, a relatively high RQ9 content was also attained together with significant FR activity. In addition, RQ9 purified from E. gracilis mitochondria was able to trigger the activities of cytochrome bc1 complex, bc1-like alternative component and alternative oxidase, although with lower efficiency (higher Km, lower Vm) than UQ9. Moreover, purified E. gracilis mitochondrial NAD+-independent D-lactate dehydrogenase (D-iLDH) showed preference for RQ9 as electron acceptor, whereas L-iLDH and succinate dehydrogenase preferred UQ9. These results indicated a physiological role for RQ9 under aerobiosis and microaerophilia in E. gracilis mitochondria, in which RQ9 mediates electron transfer between D-iLDH and other respiratory chain components, including FR.
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Affiliation(s)
- Norma A Castro-Guerrero
- Departamento de Bioquímica, Instituto Nacional de Cardiología, Juan Badiano No. 1, Col. Sección XVI, Tlalpan, México 14080, D.F., México.
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46
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Abstract
Electron transfer within Escherichia coli succinate:ubiquinone oxidoreductase has been examined by the pulse radiolysis technique using spectrophotometric detection. Electrons have been introduced into the protein by the bimolecular reaction with quantified concentrations of the low potential N-methylnicotinamide radical at a rate constant of 7 x 10(8) M(-1) s(-1). Two redox-active centers in the protein are initially reduced, assigned as the high potential [3Fe-4S] center and the bound ubiquinone, followed by intramolecular equilibration with the b heme in both cases. Electron equilibration at 25 degrees C from the ubisemiquinone proceeds with an observed rate constant of 7,200 s(-1) and from the more distant [3Fe-4S] reduced center at a rate constant of 1,200 s(-1). Temperature dependence studies have revealed that both reactions have large free energies of activation, with deltaG(double dagger) values of +0.53 and +0.58 eV, respectively. Cumulative spectral changes, as well as accompanying decreases in the rates of intramolecular electron transfer, observed upon adding electrons to progressively reduced protein, indicate that 4 electrons must be introduced into the protein before the heme center is fully reduced. Overall, evidence is presented that the heme, far from being a bystander in the efficient transfer of reducing equivalents from succinate to the ubiquinone via the flavin-Fe/S centers, plays a pivotal role in providing a lower energy pathway for the transfer of an electron from the high potential [3Fe-4S] center to ubiquinone.
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Affiliation(s)
- Robert F Anderson
- Department of Chemistry, the University of Auckland, Auckland 1, New Zealand.
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47
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Sevilla A, Schmid JW, Mauch K, Iborra JL, Reuss M, Cánovas M. Model of central and trimethylammonium metabolism for optimizing l-carnitine production by E. coli. Metab Eng 2005; 7:401-25. [PMID: 16098782 DOI: 10.1016/j.ymben.2005.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Revised: 05/27/2005] [Accepted: 06/13/2005] [Indexed: 11/23/2022]
Abstract
The application of metabolic engineering principles to the rational design of microbial production processes crucially depends on the ability to make quantitative descriptions of the systemic ability of the central carbon metabolism to redirect fluxes to the product-forming pathways. The aim of this work was to further our understanding of the steps controlling the biotransformation of trimethylammonium compounds into L-carnitine by Escherichia coli. Despite the importance of L-carnitine production processes, development of a model of the central carbon metabolism linked to the secondary carnitine metabolism of E. coli has been severely hampered by the lack of stoichiometric information on the metabolic reactions taking place in the carnitine metabolism. Here we present the design and experimental validation of a model which, for the first time, links the carnitine metabolism with the reactions of glycolysis, the tricarboxylic acid cycle and the pentose-phosphate pathway. The results demonstrate a need for a high production rate of ATP to be devoted to the biotransformation process. The results demonstrate that ATP is used up in a futile cycle, since both trimethylammonium compound carriers CaiT and ProU operate simultaneously. To improve the biotransformation process, resting processes as well as CaiT or ProU knock out mutants would yield a more efficient system for producing L-carnitine from crotonobetaine or D-carnitine.
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Affiliation(s)
- Angel Sevilla
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Apdo. Correos 4021, 30100 Murcia, Spain
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48
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Sun F, Huo X, Zhai Y, Wang A, Xu J, Su D, Bartlam M, Rao Z. Crystal structure of mitochondrial respiratory membrane protein complex II. Cell 2005; 121:1043-57. [PMID: 15989954 DOI: 10.1016/j.cell.2005.05.025] [Citation(s) in RCA: 592] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 05/05/2005] [Accepted: 05/19/2005] [Indexed: 11/25/2022]
Abstract
The mitochondrial respiratory Complex II or succinate:ubiquinone oxidoreductase (SQR) is an integral membrane protein complex in both the tricarboxylic acid cycle and aerobic respiration. Here we report the first crystal structure of Complex II from porcine heart at 2.4 A resolution and its complex structure with inhibitors 3-nitropropionate and 2-thenoyltrifluoroacetone (TTFA) at 3.5 A resolution. Complex II is comprised of two hydrophilic proteins, flavoprotein (Fp) and iron-sulfur protein (Ip), and two transmembrane proteins (CybL and CybS), as well as prosthetic groups required for electron transfer from succinate to ubiquinone. The structure correlates the protein environments around prosthetic groups with their unique midpoint redox potentials. Two ubiquinone binding sites are discussed and elucidated by TTFA binding. The Complex II structure provides a bona fide model for study of the mitochondrial respiratory system and human mitochondrial diseases related to mutations in this complex.
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Affiliation(s)
- Fei Sun
- Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
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49
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Solntsev KM, Clower CE, Tolbert LM, Huppert D. 6-Hydroxyquinoline-N-oxides: A New Class of “Super” Photoacids1. J Am Chem Soc 2005; 127:8534-44. [PMID: 15941289 DOI: 10.1021/ja0514545] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-Oxidation of hydroxyquinolines leads to a dramatic increase in their excited-state acidity. Time-resolved and steady-state emission characterization of 6-hydroxyquinoline-N-oxide and 2-methyl-6-hydroxyquinoline-N-oxide reveals a rich but less complex proton-transfer behavior than that of its parent hydroxyquinoline. The electronic effect of the oxidized heterocyclic nitrogen atom makes the excited state both less basic and more acidic than the parent and adds hydroxyquinoline N-oxides to the class of high-acidity excited-state proton donors in photochemistry and photobiology. Adiabatic photoinduced proton transfer is accompanied by the efficient nonreversible deoxygenation and 1-2 oxygen migration.
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Affiliation(s)
- Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
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50
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Rothery RA, Seime AM, Spiers AMC, Maklashina E, Schröder I, Gunsalus RP, Cecchini G, Weiner JH. Defining the Q-site of Escherichia coli fumarate reductase by site-directed mutagenesis, fluorescence quench titrations and EPR spectroscopy. FEBS J 2005; 272:313-26. [PMID: 15654871 DOI: 10.1111/j.1742-4658.2004.04469.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have used fluorescence quench titrations, EPR spectroscopy and steady-state kinetics to study the effects of site-directed mutants of FrdB, FrdC and FrdD on the proximal menaquinol (MQH(2)) binding site (Q(P)) of Escherichia coli fumarate reductase (FrdABCD) in cytoplasmic membrane preparations. Fluorescence quench (FQ) titrations with the fluorophore and MQH(2) analog 2-n-heptyl-4-hydroxyquinoline-N-oxide (HOQNO) indicate that the Q(P) site is defined by residues from FrdB, FrdC and FrdD. In FQ titrations, wild-type FrdABCD binds HOQNO with an apparent K(d) of 2.5 nM, and the following mutations significantly increase this value: FrdB-T205H (K(d) = 39 nM); FrdB-V207C (K(d) = 20 nM); FrdC-E29L (K(d) = 25 nM); FrdC-W86R (no detectable binding); and FrdD-H80K (K(d) = 20 nM). In all titrations performed, data were fitted to a monophasic binding equation, indicating that no additional high-affinity HOQNO binding sites exist in FrdABCD. In all cases where HOQNO binding is detectable by FQ titration, it can also be observed by EPR spectroscopy. Steady-state kinetic studies of fumarate-dependent quinol oxidation indicate that there is a correlation between effects on HOQNO binding and effects on the observed K(m) and k(cat) values, except in the FrdC-E29L mutant, in which HOQNO binding is observed, but no enzyme turnover is detected. In this case, EPR studies indicate that the lack of activity arises because the enzyme can only remove one electron from reduced MQH(2), resulting in it being trapped in a form with a bound menasemiquinone radical anion. Overall, the data support a model for FrdABCD in which there is a single redox-active and dissociable Q-site.
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Affiliation(s)
- Richard A Rothery
- Department of Biochemistry, CIHR Membrane Protein Research Group, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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