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Muramoto K, Shinzawa-Itoh K. Calcium-bound structure of bovine cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148956. [PMID: 36708913 DOI: 10.1016/j.bbabio.2023.148956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
The crystal structure of bovine cytochrome c oxidase (CcO) shows a sodium ion (Na+) bound to the surface of subunit I. Changes in the absorption spectrum of heme a caused by calcium ions (Ca2+) are detected as small red shifts, and inhibition of enzymatic activity under low turnover conditions is observed by addition of Ca2+ in a competitive manner with Na+. In this study, we determined the crystal structure of Ca2+-bound bovine CcO in the oxidized and reduced states at 1.7 Å resolution. Although Ca2+ and Na+ bound to the same site of oxidized and reduced CcO, they led to different coordination geometries. Replacement of Na+ with Ca2+ caused a small structural change in the loop segments near the heme a propionate and formyl groups, resulting in spectral changes in heme a. Redox-coupled structural changes observed in the Ca2+-bound form were the same as those previously observed in the Na+-bound form, suggesting that binding of Ca2+ does not severely affect enzymatic function, which depends on these structural changes. The relation between the Ca2+ binding and the inhibitory effect during slow turnover, as well as the possible role of bound Ca2+ are discussed.
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Affiliation(s)
- Kazumasa Muramoto
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.
| | - Kyoko Shinzawa-Itoh
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.
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2
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Coastal Transient Niches Shape the Microdiversity Pattern of a Bacterioplankton Population with Reduced Genomes. mBio 2022; 13:e0057122. [PMID: 35880883 PMCID: PMC9426536 DOI: 10.1128/mbio.00571-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Globally dominant marine bacterioplankton lineages are often limited in metabolic versatility, owing to their extensive genome reductions, and thus cannot take advantage of transient nutrient patches. It is therefore perplexing how the nutrient-poor bulk seawater sustains the pelagic streamlined lineages, each containing numerous populations. Here, we sequenced the genomes of 33 isolates of the recently discovered CHUG lineage (~2.6 Mbp), which have some of the smallest genomes in the globally abundant Roseobacter group (commonly over 4 Mbp). These genome-reduced bacteria were isolated from a transient habitat: seawater surrounding the brown alga, Sargassum hemiphyllum. Population genomic analyses showed that: (i) these isolates, despite sharing identical 16S rRNA genes, were differentiated into several genetically isolated populations through successive speciation events; (ii) only the first speciation event led to the genetic separation of both core and accessory genomes; and (iii) populations resulting from this event are differentiated at many loci involved in carbon utilization and oxygen respiration, corroborated by BiOLOG phenotype microarray assays and oxygen uptake kinetics experiments, respectively. These differentiated traits match well with the dynamic nature of the macroalgal seawater, in which the quantity and quality of carbon sources and the concentration of oxygen likely vary spatially and temporally, though other habitats, like fresh organic aggregates, cannot be ruled out. Our study implies that transient habitats in the overall nutrient-poor ocean can shape the microdiversity and population structure of genome-reduced bacterioplankton lineages.
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Zhang SN, Wang JG, Wang DQ, Jiang QY, Quan ZX. Abundance and Niche Differentiation of Comammox in the Sludges of Wastewater Treatment Plants That Use the Anaerobic-Anoxic-Aerobic Process. Life (Basel) 2022; 12:life12070954. [PMID: 35888046 PMCID: PMC9322089 DOI: 10.3390/life12070954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022] Open
Abstract
Complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate, were recently identified and found to be ubiquitous in artificial systems. Research on the abundance and niche differentiation of comammox in the sludges of wastewater treatment plants (WWTPs) would be useful for improving the nitrogen removal efficiency of WWTPs. Here, we investigated the relative abundance and diversity of comammox in fifteen sludges of five WWTPs that use the anaerobic−anoxic−aerobic process in Jinan, China, via quantitative polymerase chain reaction and high-throughput sequencing of the 16S rRNA gene and ammonia monooxygenase gene. In the activated sludges in the WWTPs, comammox clade A.1 was widely distributed and mostly comprised Candidatus Nitrospira nitrosa-like comammox (>98% of all comammox). The proportion of this clade was negatively correlated (p < 0.01) with the dissolved oxygen (DO) level (1.7−8 mg/L), and slight pH changes (7.20−7.70) affected the structure of the comammox populations. Nitrospira lineage I frequently coexisted with Nitrosomonas, which generally had a significant positive correlation (p < 0.05) with the DO level. Our study provided an insight into the structure of comammox and other nitrifier populations in WWTPs that use the anaerobic−anoxic−aerobic process, broadening the knowledge about the effects of DO on comammox and other nitrifiers.
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Affiliation(s)
| | | | | | - Qiu-Yue Jiang
- Correspondence: (Q.-Y.J.); (Z.-X.Q.); Tel.: +86-21-3124-0665 (Z.-X.Q.)
| | - Zhe-Xue Quan
- Correspondence: (Q.-Y.J.); (Z.-X.Q.); Tel.: +86-21-3124-0665 (Z.-X.Q.)
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Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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5
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Fedotovskaya O, Albertsson I, Nordlund G, Hong S, Gennis RB, Brzezinski P, Ädelroth P. Identification of a cytochrome bc 1-aa 3 supercomplex in Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148433. [PMID: 33932366 DOI: 10.1016/j.bbabio.2021.148433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Respiration is carried out by a series of membrane-bound complexes in the inner mitochondrial membrane or in the cytoplasmic membrane of bacteria. Increasing evidence shows that these complexes organize into larger supercomplexes. In this work, we identified a supercomplex composed of cytochrome (cyt.) bc1 and aa3-type cyt. c oxidase in Rhodobacter sphaeroides. We purified the supercomplex using a His-tag on either of these complexes. The results from activity assays, native and denaturing PAGE, size exclusion chromatography, electron microscopy, optical absorption spectroscopy and kinetic studies on the purified samples support the formation and coupled quinol oxidation:O2 reduction activity of the cyt. bc1-aa3 supercomplex. The potential role of the membrane-anchored cyt. cy as a component in supercomplexes was also investigated.
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Affiliation(s)
- Olga Fedotovskaya
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ingrid Albertsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Gustav Nordlund
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Sangjin Hong
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Robert B Gennis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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Baserga F, Dragelj J, Kozuch J, Mohrmann H, Knapp EW, Stripp ST, Heberle J. Quantification of Local Electric Field Changes at the Active Site of Cytochrome c Oxidase by Fourier Transform Infrared Spectroelectrochemical Titrations. Front Chem 2021; 9:669452. [PMID: 33987170 PMCID: PMC8111224 DOI: 10.3389/fchem.2021.669452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/24/2021] [Indexed: 11/30/2022] Open
Abstract
Cytochrome c oxidase (CcO) is a transmembrane protein complex that reduces molecular oxygen to water while translocating protons across the mitochondrial membrane. Changes in the redox states of its cofactors trigger both O2 reduction and vectorial proton transfer, which includes a proton-loading site, yet unidentified. In this work, we exploited carbon monoxide (CO) as a vibrational Stark effect (VSE) probe at the binuclear center of CcO from Rhodobacter sphaeroides. The CO stretching frequency was monitored as a function of the electrical potential, using Fourier transform infrared (FTIR) absorption spectroelectrochemistry. We observed three different redox states (R4CO, R2CO, and O), determined their midpoint potential, and compared the resulting electric field to electrostatic calculations. A change in the local electric field strength of +2.9 MV/cm was derived, which was induced by the redox transition from R4CO to R2CO. We performed potential jump experiments to accumulate the R2CO and R4CO species and studied the FTIR difference spectra in the protein fingerprint region. The comparison of the experimental and computational results reveals that the key glutamic acid residue E286 is protonated in the observed states, and that its hydrogen-bonding environment is disturbed upon the redox transition of heme a3. Our experiments also suggest propionate A of heme a3 changing its protonation state in concert with the redox state of a second cofactor, heme a. This supports the role of propionic acid side chains as part of the proton-loading site.
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Affiliation(s)
- Federico Baserga
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Jovan Dragelj
- Macromolecular Modelling Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.,Modeling of Biomolecular Systems, Technische Universität Berlin, Berlin, Germany
| | - Jacek Kozuch
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Hendrik Mohrmann
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ernst-Walter Knapp
- Macromolecular Modelling Group, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
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7
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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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8
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Zhu X, Aoyama E, Birk AV, Onasanya O, Carr WH, Mourokh L, Minteer SD, Vittadello M. Cytochrome c oxidase oxygen reduction reaction induced by cytochrome c on nickel-coordination surfaces based on graphene oxide in suspension. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148262. [PMID: 32673675 DOI: 10.1016/j.bbabio.2020.148262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND The electrochemical and spectroscopic investigation of bacterial electron-transfer proteins stabilized on solid state electrodes has provided an effective approach for functional respiratory enzyme studies. METHODS We assess the biocompatibility of carboxylated graphene oxide (CGO) functionalized with Nickel nitrilotriacetic groups (CGO-NiNTA) ccordinating His-tagged cytochrome c oxidase (CcO) from Rhodobacter sphaeroides. RESULTS Kinetic studies employing UV-visible absorption spectroscopy confirmed that the immobilized CcO oxidized horse-heart cytochrome c (Cyt c) albeit at a slower rate than isolated CcO. The oxygen reduction reaction as catalyzed by immobilized CcO could be clearly distinguished from that arising from CGO-NiNTA in the presence of Cyt c and dithiothreitol (DTT) as a sacrificial reducing agent. Our findings indicate that while the protein content is about 3.7‰ by mass with respect to the support, the contribution to the oxygen consumption activity averaged at 56.3%. CONCLUSIONS The CGO-based support stabilizes the free enzyme which, while capable of Cyt c oxidation, is unable to carry out oxygen consumption in solution on its own under our conditions. The turnover rate for the immobilized CcO was as high as 240 O2 molecules per second per CcO unit. GENERAL SIGNIFICANCE In vitro investigations of electron flow on isolated components of bacterial electron-transfer enzymes immobilized on the surface of CGO in suspension are expected to shed new light on microbial bioenergetic functions, that could ultimately contribute toward the improvement of performance in living organisms.
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Affiliation(s)
- Xiaoping Zhu
- Department of Chemistry and Environmental Science, Medgar Evers College of the City University of New York (CUNY), Brooklyn, NY 11225, USA
| | - Erika Aoyama
- Department of Chemistry, The University of Utah, Salt Lake City, UT 84112, USA
| | - Alexander V Birk
- Department of Chemistry and Environmental Science, Medgar Evers College of the City University of New York (CUNY), Brooklyn, NY 11225, USA; Department of Biology, York College of CUNY, Jamaica, NY 11451, USA
| | - Oladapo Onasanya
- Department of Chemistry and Environmental Science, Medgar Evers College of the City University of New York (CUNY), Brooklyn, NY 11225, USA
| | - William H Carr
- Department of Biology, Medgar Evers College of the City University of New York (CUNY), Brooklyn, NY 11225, USA
| | - Lev Mourokh
- Department of Physics, Queens College of CUNY, Queens, NY 11367, USA; The Graduate Center of CUNY, New York, NY 10016, USA
| | - Shelley D Minteer
- Department of Chemistry, The University of Utah, Salt Lake City, UT 84112, USA
| | - Michele Vittadello
- Department of Chemistry and Environmental Science, Medgar Evers College of the City University of New York (CUNY), Brooklyn, NY 11225, USA; The Graduate Center of CUNY, New York, NY 10016, USA.
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9
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Kinetic advantage of forming respiratory supercomplexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148193. [PMID: 32201307 DOI: 10.1016/j.bbabio.2020.148193] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/11/2020] [Accepted: 03/16/2020] [Indexed: 11/22/2022]
Abstract
Components of respiratory chains in mitochondria and some aerobic bacteria assemble into larger, multiprotein membrane-bound supercomplexes. Here, we address the functional significance of supercomplexes composed of respiratory-chain complexes III and IV. Complex III catalyzes oxidation of quinol and reduction of water-soluble cytochrome c (cyt c), while complex IV catalyzes oxidation of the reduced cyt c and reduction of dioxygen to water. We focus on two questions: (i) under which conditions does diffusion of cyt c become rate limiting for electron transfer between these two complexes? (ii) is there a kinetic advantage of forming a supercomplex composed of complexes III and IV? To answer these questions, we use a theoretical approach and assume that cyt c diffuses in the water phase while complexes III and IV either diffuse independently in the two dimensions of the membrane or form supercomplexes. The analysis shows that the electron flux between complexes III and IV is determined by the equilibration time of cyt c within the volume of the intermembrane space, rather than the cyt c diffusion time constant. Assuming realistic relative concentrations of membrane-bound components and cyt c and that all components diffuse independently, the data indicate that electron transfer between complexes III and IV can become rate limiting. Hence, there is a kinetic advantage of bringing complexes III and IV together in the membrane to form supercomplexes.
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Berg J, Liu J, Svahn E, Ferguson-Miller S, Brzezinski P. Structural changes at the surface of cytochrome c oxidase alter the proton-pumping stoichiometry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148116. [PMID: 31733183 DOI: 10.1016/j.bbabio.2019.148116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/22/2019] [Accepted: 11/08/2019] [Indexed: 10/25/2022]
Abstract
Data from earlier studies showed that minor structural changes at the surface of cytochrome c oxidase, in one of the proton-input pathways (the D pathway), result in dramatically decreased activity and a lower proton-pumping stoichiometry. To further investigate how changes around the D pathway orifice influence functionality of the enzyme, here we modified the nearby C-terminal loop of subunit I of the Rhodobacter sphaeroides cytochrome c oxidase. Removal of 16 residues from this flexible surface loop resulted in a decrease in the proton-pumping stoichiometry to <50% of that of the wild-type enzyme. Replacement of the protonatable residue Glu552, part of the same loop, by an Ala, resulted in a similar decrease in the proton-pumping stoichiometry without loss of the O2-reduction activity or changes in the proton-uptake kinetics. The data show that minor structural changes at the orifice of the D pathway, at a distance of ~40 Å from the proton gate of cytochrome c oxidase, may alter the proton-pumping stoichiometry of the enzyme.
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Affiliation(s)
- Johan Berg
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jian Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Emelie Svahn
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States.
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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11
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Wikström M, Sharma V. Proton pumping by cytochrome c oxidase – A 40 year anniversary. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:692-698. [DOI: 10.1016/j.bbabio.2018.03.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 12/21/2022]
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Hiser C, Liu J, Ferguson-Miller S. The K-path entrance in cytochrome c oxidase is defined by mutation of E101 and controlled by an adjacent ligand binding domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:725-733. [PMID: 29626419 DOI: 10.1016/j.bbabio.2018.03.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 11/19/2022]
Abstract
Three mutant forms of Rhodobacter sphaeroides cytochrome c oxidase (RsCcO) were created to test for multiple K-path entry sites (E101W), the existence of an "upper ligand site" (M350 W), and the nature and binding specificity of the "lower ligand site" (P315W/E101A) in the region of a crystallographically-defined deoxycholate at the K-path entrance. The effects of inhibitory and stimulatory detergents (dodecyl maltoside and Tween20) on these mutants are presented, as well as competition with other ligands, including the potentially physiologically relevant ligands cholesterol and retinoic acid. Ligands are shown to be able to compete with natural lipids to affect the activity of membrane-bound RsCcO. Results point to a single K-path entrance site at E101, with a single ligand binding pocket proximal to the entrance. The affinity of this pocket for amphipathic ligands is enhanced by removal of the E101 carboxyl and blocked by substituting a tryptophan in this area. A new crystal structure of the E101A mutant of RsCcO is presented that illustrates the structural basis of these results, showing that the loss of the E101 carboxyl creates a more hydrophobic groove consistent with altered ligand affinities.
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Affiliation(s)
- Carrie Hiser
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States.
| | - Jian Liu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States.
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States.
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13
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Widespread Distribution and Functional Specificity of the Copper Importer CcoA: Distinct Cu Uptake Routes for Bacterial Cytochrome c Oxidases. mBio 2018; 9:mBio.00065-18. [PMID: 29487231 PMCID: PMC5829832 DOI: 10.1128/mbio.00065-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cytochrome c oxidases are members of the heme-copper oxidase superfamily. These enzymes have different subunits, cofactors, and primary electron acceptors, yet they all contain identical heme-copper (CuB) binuclear centers within their catalytic subunits. The uptake and delivery pathways of the CuB atom incorporated into this active site, where oxygen is reduced to water, are not well understood. Our previous work with the facultative phototrophic bacterium Rhodobacter capsulatus indicated that the copper atom needed for the CuB site of cbb3-type cytochrome c oxidase (cbb3-Cox) is imported to the cytoplasm by a major facilitator superfamily-type transporter, CcoA. In this study, a comparative genomic analysis of CcoA orthologs in alphaproteobacterial genomes showed that CcoA is widespread among organisms and frequently co-occurs with cytochrome c oxidases. To define the specificity of CcoA activity, we investigated its function in Rhodobacter sphaeroides, a close relative of R. capsulatus that contains both cbb3- and aa3-Cox. Phenotypic, genetic, and biochemical characterization of mutants lacking CcoA showed that in its absence, or even in the presence of its bypass suppressors, only the production of cbb3-Cox and not that of aa3-Cox was affected. We therefore concluded that CcoA is dedicated solely to cbb3-Cox biogenesis, establishing that distinct copper uptake systems provide the CuB atoms to the catalytic sites of these two similar cytochrome c oxidases. These findings illustrate the large variety of strategies that organisms employ to ensure homeostasis and fine control of copper trafficking and delivery to the target cuproproteins under different physiological conditions.IMPORTANCE The cbb3- and aa3-type cytochrome c oxidases belong to the widespread heme-copper oxidase superfamily. They are membrane-integral cuproproteins that catalyze oxygen reduction to water under hypoxic and normoxic growth conditions. These enzymes diverge in terms of subunit and cofactor composition, yet they all share a conserved heme-copper binuclear site within their catalytic subunit. In this study, we show that the copper atoms of the catalytic center of two similar cytochrome c oxidases from this superfamily are provided by different copper uptake systems during their biogenesis. This finding illustrates different strategies by which organisms fine-tune the trafficking of copper, which is an essential but toxic micronutrient.
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14
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Shirey K, Stover KR, Cleary J, Hoang N, Hosler J. Membrane-Anchored Cyclic Peptides as Effectors of Mitochondrial Oxidative Phosphorylation. Biochemistry 2016; 55:2100-11. [PMID: 26985698 DOI: 10.1021/acs.biochem.5b01368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The echinocandins are membrane-anchored, cyclic lipopeptides (CLPs) with antifungal activity due to their ability to inhibit a glucan synthase located in the plasma membrane of fungi such as Candida albicans. A hydrophobic tail of an echinocandin CLP inserts into a membrane, placing a six-amino acid cyclic peptide near the membrane surface. Because processes critical for the function of the electron transfer complexes of mitochondria, such as proton uptake and release, take place near the surface of the membrane, we have tested the ability of two echinocandin CLPs, caspofungin and micafungin, to affect the activity of electron transfer complexes in isolated mammalian mitochondria. Indeed, caspofungin and micafungin both inhibit whole chain electron transfer in isolated mitochondria at low micromolar concentrations. The effects of the CLPs are fully reversible, in some cases simply via the addition of bovine serum albumin to bind the CLPs via their hydrophobic tails. Each CLP affects more than one complex, but they still exhibit specificity of action. Only caspofungin inhibits complex I, and the CLP inhibits liver but not heart complex I. Both CLPs inhibit heart and liver complex III. Caspofungin inhibits complex IV activity, while, remarkably, micafungin stimulates complex IV activity nearly 3-fold. Using a variety of assays, we have developed initial hypotheses for the mechanisms by which caspofungin and micafungin alter the activities of complexes IV and III. The dication caspofungin partially inhibits cytochrome c binding at the low-affinity binding site of complex IV, while it also appears to inhibit the release of protons from the outer surface of the complex, similar to Zn(2+). Anionic micafungin appears to stimulate complex IV activity by enhancing the transfer of protons to the O2 reduction site. For complex III, we hypothesize that each CLP binds to the cytochrome b subunit and the Fe-S subunit to inhibit the required rotational movement of the latter.
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Affiliation(s)
- Kristin Shirey
- Department of Biochemistry and ‡School of Pharmacy, University of Mississippi Medical Center , 2500 North State Street, Jackson, Mississippi 39216, United States
| | - Kayla R Stover
- Department of Biochemistry and ‡School of Pharmacy, University of Mississippi Medical Center , 2500 North State Street, Jackson, Mississippi 39216, United States
| | - John Cleary
- Department of Biochemistry and ‡School of Pharmacy, University of Mississippi Medical Center , 2500 North State Street, Jackson, Mississippi 39216, United States
| | - Ngoc Hoang
- Department of Biochemistry and ‡School of Pharmacy, University of Mississippi Medical Center , 2500 North State Street, Jackson, Mississippi 39216, United States
| | - Jonathan Hosler
- Department of Biochemistry and ‡School of Pharmacy, University of Mississippi Medical Center , 2500 North State Street, Jackson, Mississippi 39216, United States
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15
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Musatov A, Varhač R, Hosler JP, Sedlák E. Delipidation of cytochrome c oxidase from Rhodobacter sphaeroides destabilizes its quaternary structure. Biochimie 2016; 125:23-31. [PMID: 26923069 DOI: 10.1016/j.biochi.2016.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/23/2016] [Indexed: 11/28/2022]
Abstract
Delipidation of detergent-solubilized cytochrome c oxidase isolated from Rhodobacter sphaeroides (Rbs-CcO) has no apparent structural and/or functional effect on the protein, however affects its resistance against thermal or chemical denaturation. Phospholipase A2 (PLA2) hydrolysis of phospholipids that are co-purified with the enzyme removes all but two tightly bound phosphatidylethanolamines. Replacement of the removed phospholipids with nonionic detergent decreases both thermal stability of the enzyme and its resilience against the effect of chemical denaturants such as urea. In contrast to nondelipidated Rbs-CcO, the enzymatic activity of PLA2-treated Rbs-CcO is substantially diminished after exposure to high (>4 M) urea concentration at room temperature without an alteration of its secondary structure. Absorbance spectroscopy and sedimentation velocity experiments revealed a strong correlation between intact tertiary structure of heme regions and quaternary structure, respectively, and the enzymatic activity of the protein. We concluded that phospholipid environment of Rbs-CcO has the protective role for stability of its tertiary and quaternary structures.
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Affiliation(s)
- Andrej Musatov
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA; Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001 Košice, Slovakia.
| | - Rastislav Varhač
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA; Department of Biochemistry, P.J. Šafárik University, Moyzesova 11, 04001 Košice, Slovakia.
| | - Jonathan P Hosler
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216, USA.
| | - Erik Sedlák
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229-3900, USA; Department of Biochemistry, P.J. Šafárik University, Moyzesova 11, 04001 Košice, Slovakia; Centre for Interdisciplinary Biosciences, P.J. Šafárik University, Jesenná 5, 04001 Košice, Slovakia.
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16
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Alnajjar KS, Cvetkov T, Prochaska L. Role of phospholipids of subunit III in the regulation of structural rearrangements in cytochrome c oxidase of Rhodobacter sphaeroides. Biochemistry 2015; 54:1053-63. [PMID: 25559126 DOI: 10.1021/bi5013657] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Subunit III of cytochrome c oxidase possesses structural domains that contain conserved phospholipid binding sites. Mutations within these domains induce a loss of phospholipid binding, coinciding with decreased electron transfer activity. Functional and structural roles for phospholipids in the enzyme from Rhodobacter sphaeroides have been investigated. Upon the removal of intrinsic lipids using phospholipase A2, electron transfer activity was decreased 30-50%. Moreover, the delipidated enzyme exhibited turnover-induced, suicide inactivation, which was reversed by the addition of exogenous lipids, most specifically by cardiolipin. Cardiolipin exhibited two sites of interaction with the delipidated enzyme, a high-affinity site (Km = 0.14 μM) and a low-affinity site (Km = 26 μM). Subunit I of the delipidated enzyme exhibited a faster digestion rate when it was treated with α-chymotrypsin compared to that of the wild-type enzyme, suggesting that lipid removal induces a conformational change to expose the digestion sites further. Upon reaction of subunit III of the enzyme with a fluorophore (AEDANS), fluorescence anisotropy showed an increased rotational rate of the fluorophore in the absence of lipids, indicating increased flexibility of subunit III within the enzyme's tertiary structure. Additionally, Förster resonance energy transfer between AEDANS and a fluorescently labeled cardiolipin revealed that cardiolipin binds in the v-shaped cleft of subunit III in the delipidated enzyme and that it moves closer to the active site in subunit I upon a change in the redox state of the enzyme. In conclusion, these results show that the phospholipids regulate events occurring during electron transfer activity by maintaining the structural integrity of the enzyme at the active site.
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Affiliation(s)
- Khadijeh S Alnajjar
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine at Wright State University , Dayton, Ohio 45435, United States
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17
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Alnajjar KS, Hosler J, Prochaska L. Role of the N-terminus of subunit III in proton uptake in cytochrome c oxidase of Rhodobacter sphaeroides. Biochemistry 2014; 53:496-504. [PMID: 24397338 DOI: 10.1021/bi401535q] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The catalytic core of cytochrome c oxidase consists of three subunits that are conserved across species. The N-terminus of subunit III contains three histidine residues (3, 7, and 10) that are surface-exposed, have physiologically relevant pKa values, and are in close proximity of the mouth of the D-channel in subunit I. A triple-histidine mutation (to glutamine) was created in Rhodobacter sphaeroides. The mutant enzyme retains 60% of wild-type activity. Absorbance during steady-state turnover indicates that electrons accumulate at heme a in the mutant, accompanied by accumulation of the oxoferryl intermediate. When reconstituted into liposomes, the mutant enzyme pumps protons with an efficiency that is half that of the wild type. Finally, the mutant exhibits a lower cytochrome c peroxidation rate. Our results indicate that the mutation lowers activity indirectly by slowing the uptake of protons through the D-channel and that the three histidine residues stabilize the interactions between subunit I and subunit III.
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Affiliation(s)
- Khadijeh S Alnajjar
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University , Dayton, Ohio 45435, United States
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18
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Buhrow L, Hiser C, Van Voorst JR, Ferguson-Miller S, Kuhn LA. Computational prediction and in vitro analysis of potential physiological ligands of the bile acid binding site in cytochrome c oxidase. Biochemistry 2013; 52:6995-7006. [PMID: 24073649 DOI: 10.1021/bi400674h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A conserved bile acid site has been crystallographically defined in the membrane domain of mammalian and Rhodobacter sphaeroides cytochrome c oxidase (RsCcO). Diverse amphipathic ligands were shown previously to bind to this site and affect the electron transfer equilibrium between heme a and a3 cofactors by blocking the K proton uptake path. Current studies identify physiologically relevant ligands for the bile acid site using a novel three-pronged computational approach: ROCS comparison of ligand shape and electrostatics, SimSite3D comparison of ligand binding site features, and SLIDE screening of potential ligands by docking. Identified candidate ligands include steroids, nicotinamides, flavins, nucleotides, retinoic acid, and thyroid hormones, which are predicted to make key protein contacts with the residues involved in bile acid binding. In vitro oxygen consumption and ligand competition assays on RsCcO wildtype and its Glu101Ala mutant support regulatory activity and specificity of some of these ligands. An ATP analog and GDP inhibit RsCcO under low substrate conditions, while fusidic acid, cholesteryl hemisuccinate, retinoic acid, and T3 thyroid hormone are more potent inhibitors under both high and low substrate conditions. The sigmoidal kinetics of RsCcO inhibition in the presence of certain nucleotides is reminiscent of previously reported ATP inhibition of mammalian CcO, suggesting regulation involving the conserved core subunits of both mammalian and bacterial oxidases. Ligand binding to the bile acid site is noncompetitive with respect to cytochrome c and appears to arrest CcO in a semioxidized state with some resemblance to the "resting" state of the enzyme.
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Affiliation(s)
- Leann Buhrow
- Departments of Biochemistry and Molecular Biology and ¶Computer Science & Engineering, Michigan State University , East Lansing, Michigan 48824, United States
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19
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Hiser C, Buhrow L, Liu J, Kuhn L, Ferguson-Miller S. A conserved amphipathic ligand binding region influences k-path-dependent activity of cytochrome C oxidase. Biochemistry 2013; 52:1385-96. [PMID: 23351100 DOI: 10.1021/bi3014505] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A conserved, crystallographically defined bile acid binding site was originally identified in the membrane domain of mammalian and bacterial cytochrome c oxidase (CcO). Current studies show other amphipathic molecules including detergents, fatty acids, steroids, and porphyrins bind to this site and affect the already 50% inhibited activity of the E101A mutant of Rhodobacter sphaeroides CcO as well as altering the activity of wild-type and bovine enzymes. Dodecyl maltoside, Triton X100, C12E8, lysophophatidylcholine, and CHOBIMALT detergents further inhibit RsCcO E101A, with lesser inhibition observed in wild-type. The detergent inhibition is overcome in the presence of micromolar concentrations of steroids and porphyrin analogues including deoxycholate, cholesteryl hemisuccinate, bilirubin, and protoporphyrin IX. In addition to alleviating detergent inhibition, amphipathic carboxylates including arachidonic, docosahexanoic, and phytanic acids stimulate the activity of E101A to wild-type levels by providing the missing carboxyl group. Computational modeling of dodecyl maltoside, bilirubin, and protoporphyrin IX into the conserved steroid site shows energetically favorable binding modes for these ligands and suggests that a groove at the interface of subunit I and II, including the entrance to the K-path and helix VIII of subunit I, mediates the observed competitive ligand interactions involving two overlapping sites. Spectral analysis indicates that ligand binding to this region affects CcO activity by altering the K-path-dependent electron transfer equilibrium between heme a and heme a(3). The high affinity and specificity of a number of compounds for this region, and its conservation and impact on CcO activity, support its physiological significance.
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Affiliation(s)
- Carrie Hiser
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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20
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Lin MT, Gennis RB. Product-controlled steady-state kinetics between cytochrome aa(3) from Rhodobacter sphaeroides and equine ferrocytochrome c analyzed by a novel spectrophotometric approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1894-900. [PMID: 22516686 DOI: 10.1016/j.bbabio.2012.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase (CcO) catalyzes the reduction of molecular oxygen to water using ferrocytochrome c (cyt c(2+)) as the electron donor. In this study, the oxidation of horse cyt c(2+) by CcO from Rhodobacter sphaeroides, was monitored using stopped-flow spectrophotometry. A novel analytic procedure was applied in which the spectra were deconvoluted into the reduced and oxidized forms of cyt c by a least-squares fitting method, yielding the reaction rates at various concentrations of cyt c(2+) and cyt c(3+). This allowed an analysis of the effects of cyt c(3+) on the steady-state kinetics between CcO and cyt c(2+). The results show that cyt c(3+) exhibits product inhibition by two mechanisms: competition with cyt c(2+) at the catalytic site and, in addition, an interaction at a second site which further modulates the reaction of cyt c(2+) at the catalytic site. These results are generally consistent with previous reports, indicating the reliability of the new procedure. We also find that a 6×His-tag at the C-terminus of the subunit II of CcO affects the binding of cyt c at both sites. The approach presented here should be generally useful in spectrophotometric studies of complex enzyme kinetics. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Myat T Lin
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
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21
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Proton transfer in ba3 cytochrome c oxidase from Thermus thermophilus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:650-7. [DOI: 10.1016/j.bbabio.2011.11.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 11/15/2011] [Accepted: 11/16/2011] [Indexed: 11/23/2022]
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22
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Thompson AK, Gray J, Liu A, Hosler JP. The roles of Rhodobacter sphaeroides copper chaperones PCu(A)C and Sco (PrrC) in the assembly of the copper centers of the aa(3)-type and the cbb(3)-type cytochrome c oxidases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:955-64. [PMID: 22248670 DOI: 10.1016/j.bbabio.2012.01.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/30/2011] [Accepted: 01/02/2012] [Indexed: 11/28/2022]
Abstract
The α proteobacter Rhodobacter sphaeroides accumulates two cytochrome c oxidases (CcO) in its cytoplasmic membrane during aerobic growth: a mitochondrial-like aa(3)-type CcO containing a di-copper Cu(A) center and mono-copper Cu(B), plus a cbb(3)-type CcO that contains Cu(B) but lacks Cu(A). Three copper chaperones are located in the periplasm of R. sphaeroides, PCu(A)C, PrrC (Sco) and Cox11. Cox11 is required to assemble Cu(B) of the aa(3)-type but not the cbb(3)-type CcO. PrrC is homologous to mitochondrial Sco1; Sco proteins are implicated in Cu(A) assembly in mitochondria and bacteria, and with Cu(B) assembly of the cbb(3)-type CcO. PCu(A)C is present in many bacteria, but not mitochondria. PCu(A)C of Thermus thermophilus metallates a Cu(A) center in vitro, but its in vivo function has not been explored. Here, the extent of copper center assembly in the aa(3)- and cbb(3)-type CcOs of R. sphaeroides has been examined in strains lacking PCu(A)C, PrrC, or both. The absence of either chaperone strongly lowers the accumulation of both CcOs in the cells grown in low concentrations of Cu(2+). The absence of PrrC has a greater effect than the absence of PCu(A)C and PCu(A)C appears to function upstream of PrrC. Analysis of purified aa(3)-type CcO shows that PrrC has a greater effect on the assembly of its Cu(A) than does PCu(A)C, and both chaperones have a lesser but significant effect on the assembly of its Cu(B) even though Cox11 is present. Scenarios for the cellular roles of PCu(A)C and PrrC are considered. The results are most consistent with a role for PrrC in the capture and delivery of copper to Cu(A) of the aa(3)-type CcO and to Cu(B) of the cbb(3)-type CcO, while the predominant role of PCu(A)C may be to capture and deliver copper to PrrC and Cox11. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.
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Affiliation(s)
- Audie K Thompson
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS 39216, USA.
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23
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Zhang X, Hiser C, Tamot B, Benning C, Reid GE, Ferguson-Miller SM. Combined genetic and metabolic manipulation of lipids in Rhodobacter sphaeroides reveals non-phospholipid substitutions in fully active cytochrome c oxidase. Biochemistry 2011; 50:3891-902. [PMID: 21476580 DOI: 10.1021/bi1017039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A specific requirement for lipids, particularly cardiolipin (CL), in cytochrome c oxidase (CcO) has been reported in many previous studies using mainly in vitro lipid removal approaches in mammalian systems. Our accompanying paper shows that CcO produced in markedly CL-depleted Rhodobacter sphaeroides displays wild-type properties in all respects, likely allowed by quantitative substitution with other negatively charged lipids. To further examine the structural basis for the lipid requirements of R. sphaeroides CcO and the extent of interchangeability between lipids, we employed a metabolic approach to enhance the alteration of the lipid profiles of the CcO-expressing strains of R. sphaeroides in vivo using a phosphate-limiting growth medium in addition to the CL-deficient mutation. Strikingly, the purified CcO produced under these conditions still maintained wild-type function and characteristics, in spite of even greater depletion of cardiolipin compared to that of the CL-deficient mutant alone (undetectable by MS) and drastically altered profiles of all the phospholipids and non-phospholipids. The lipids in the membrane and in the purified CcO were identified and quantified by ESI and MALDI mass spectrometry and tandem mass spectrometry. Comparison between the molecular structures of those lipids that showed major changes provides new insight into the structural rationale for the flexible lipid requirements of CcO from R. sphaeroides and reveals a more comprehensive interchangeability network between different phospholipids and non-phospholipids.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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24
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Zhang X, Tamot B, Hiser C, Reid GE, Benning C, Ferguson-Miller S. Cardiolipin deficiency in Rhodobacter sphaeroides alters the lipid profile of membranes and of crystallized cytochrome oxidase, but structure and function are maintained. Biochemistry 2011; 50:3879-90. [PMID: 21476578 DOI: 10.1021/bi101702c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many recent studies highlight the importance of lipids in membrane proteins, including in the formation of well-ordered crystals. To examine the effect of changes in one lipid, cardiolipin, on the lipid profile and the production, function, and crystallization of an intrinsic membrane protein, cytochrome c oxidase, we mutated the cardiolipin synthase (cls) gene of Rhodobacter sphaeroides, causing a >90% reduction in cardiolipin content in vivo and selective changes in the abundances of other lipids. Under these conditions, a fully native cytochrome c oxidase (CcO) was produced, as indicated by its activity, spectral properties, and crystal characteristics. Analysis by MALDI tandem mass spectrometry (MS/MS) revealed that the cardiolipin level in CcO crystals, as in the membranes, was greatly decreased. Lipid species present in the crystals were directly analyzed for the first time using MS/MS, documenting their identities and fatty acid chain composition. The fatty acid content of cardiolipin in R. sphaeroides CcO (predominantly 18:1) differs from that in mammalian CcO (18:2). In contrast to the cardiolipin dependence of mammalian CcO activity, major depletion of cardiolipin in R. sphaeroides did not impact any aspect of CcO structure or behavior, suggesting a greater tolerance of interchange of cardiolipin with other lipids in this bacterial system.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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25
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Thompson AK, Smith D, Gray J, Carr HS, Liu A, Winge DR, Hosler JP. Mutagenic analysis of Cox11 of Rhodobacter sphaeroides: insights into the assembly of Cu(B) of cytochrome c oxidase. Biochemistry 2010; 49:5651-61. [PMID: 20524628 DOI: 10.1021/bi1003876] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Cu(I) chaperone Cox11 is required for the insertion of Cu(B) into cytochrome c oxidase (CcO) of mitochondria and many bacteria, including Rhodobacter sphaeroides. Exploration of the copper binding stoichiometry of R. sphaeroides Cox11 led to the finding that an apparent tetramer of both mitochondrial and bacterial Cox11 binds more copper than the sum of the dimers, providing another example of the flexibility of copper binding by Cu(I)-S clusters. Site-directed mutagenesis has been used to identify components of Cox11 that are not required for copper binding but are absolutely required for the assembly of Cu(B), including conserved Cys-35 and Lys-123. In contrast to earlier proposals, Cys-35 is not required for dimerization of Cox11 or for copper binding. These findings, and the location of Cys-35 at the C-terminus of the predicted transmembrane helix and thereby close to the surface of the membrane, allow a proposal that Cys-35 is involved in the transfer of copper from the Cu(I) cluster of Cox11 to the Cu(B) ligands His-333 and His-334 during the folding of CcO subunit I. Lys-123 is located near the Cu(I) cluster of Cox11, in an area otherwise devoid of charged residues. From the analysis of several Cox11 mutants, including K123E, -L, and -R, we conclude that a previous proposal that Lys-123 provides charge balance for the stabilization of the Cu(I) cluster is unlikely to account for its absolute requirement for Cox11 function. Rather, consideration of the properties of Lys-123 and the apparent specificity of Cox11 suggest that Lys-123 plays a role in the interaction of Cox11 with its target.
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Affiliation(s)
- Audie K Thompson
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
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26
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Sedlák E, Robinson NC. Sequential dissociation of subunits from bovine heart cytochrome C oxidase by urea. Biochemistry 2009; 48:8143-50. [PMID: 19663452 DOI: 10.1021/bi900773r] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The quaternary stability of purified, detergent-solubilized, cytochrome c oxidase (CcO) was probed using two chemical denaturants, urea and guanidinium chloride (GdmCl). Each chaotrope induces dissociation of five subunits in a concentration-dependent manner. These five subunits are not scattered over the surface of CcO but are clustered together in close contact at the dimer interface. Increasing the concentration of urea selectively dissociates subunits from CcO in the following order: VIa and VIb, followed by III and VIIa, and finally Vb. After incubation in urea for 10 min at room temperature, the sigmoidal dissociation transitions were centered at 3.7, 4.6, and 7.0 M urea, respectively. The secondary structure of CcO was only minimally perturbed, indicating that urea causes disruption of subunit interactions without urea-induced conformational changes. Incubation of CcO in urea for 120 min produced similar results but shifted the sigmoidal dissociation curves to lower urea concentrations. Incubation of CcO with increasing concentrations of GdmCl produces an analogous effect; however, the GdmCl-induced dissociation of subunits occurs at lower concentrations and with a narrower concentration range. Thermodynamic parameters for each subunit dissociation were evaluated from the sigmoidal dissociation data by assuming a single transition from bound to dissociated subunit. The free energy change accompanying urea-induced dissociation of each subunit ranged from 18.0 to 29.7 kJ/mol, which corresponds to 0.32-0.59 kJ/mol per 100 A(2) of newly exposed solvent-accessible surface area. These values are 30-50-fold smaller than previously reported for the unfolding of soluble or membrane proteins.
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Affiliation(s)
- Erik Sedlák
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA
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27
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Mills DA, Xu S, Geren L, Hiser C, Qin L, Sharpe MA, McCracken J, Durham B, Millett F, Ferguson-Miller S. Proton-dependent electron transfer from CuA to heme a and altered EPR spectra in mutants close to heme a of cytochrome oxidase. Biochemistry 2008; 47:11499-509. [PMID: 18847227 PMCID: PMC2659347 DOI: 10.1021/bi801156s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eukaryotic cytochrome c oxidase (CcO) and homologous prokaryotic forms of Rhodobacter and Paraccocus differ in the EPR spectrum of heme a. It was noted that a histidine ligand of heme a (H102) is hydrogen bonded to serine in Rhodobacter (S44) and Paraccocus CcOs, in contrast to glycine in the bovine enzyme. Mutation of S44 to glycine shifts the heme a EPR signal from g(z) = 2.82 to 2.86, closer to bovine heme a at 3.03, without modifying other properties. Mutation to aspartate, however, results in an oppositely shifted and split heme a EPR signal of g(z) = 2.72/2.78, accompanied by lower activity and drastically inhibited intrinsic electron transfer from CuA to heme a. This intrinsic rate is biphasic; the proportion that is slow is pH dependent, as is the relative intensity of the two EPR signal components. At pH 8, the heme a EPR signal at 2.72 is most intense, and the electron transfer rate (CuA to heme a) is 10-130 s(-1), compared to wild-type at 90,000 s(-1). At pH 5.5, the signal at 2.78 is intensified, and a biphasic rate is observed, 50% fast (approximately wild type) and 50% slow (90 s(-1)). The data support the prediction that the hydrogen-bonding partner of the histidine ligand of heme a is one determinant of the EPR spectral difference between bovine and bacterial CcO. We further demonstrate that the heme a redox potential can be dramatically altered by a nearby carboxyl, whose protonation leads to a proton-coupled electron transfer process.
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Affiliation(s)
- Denise A. Mills
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Shujuan Xu
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Lois Geren
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Carrie Hiser
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Ling Qin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Martyn A. Sharpe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - John McCracken
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
| | - Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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28
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Electronic wiring of a multi-redox site membrane protein in a biomimetic surface architecture. Biophys J 2008; 94:3698-705. [PMID: 18222995 DOI: 10.1529/biophysj.107.117846] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bioelectronic coupling of multi-redox-site membrane proteins was accomplished with cytochrome c oxidase (CcO) as an example. A biomimetic membrane system was used for the oriented immobilization of the CcO oxidase on a metal electrode. When the protein is immobilized with the CcO binding side directed toward the electrode and reconstituted in situ into a lipid bilayer, it is addressable by direct electron transfer to the redox centers. Electron transfer to the enzyme via the spacer, referred to as electronic wiring, shows an exceptionally high rate constant. This allows a kinetic analysis of all four consecutive electron transfer steps within the enzyme to be carried out. Electron transfer followed by rapid scan cyclic voltammetry in combination with surface-enhanced resonance Raman spectroscopy provides mechanistic and structural information about the heme centers. Probing the enzyme under turnover conditions showed mechanistic insights into proton translocation coupled to electron transfer. This bioelectronic approach opens a new field of activity to investigate complex processes in a wide variety of membrane proteins.
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29
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Szundi I, Ray J, Pawate A, Gennis RB, Einarsdóttir Ó. Flash-Photolysis of Fully Reduced and Mixed-Valence CO-Bound Rhodobacter sphaeroides Cytochrome c Oxidase: Heme Spectral Shifts. Biochemistry 2007; 46:12568-78. [DOI: 10.1021/bi700728g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, and Department of Biochemistry, University of Illinois, Urbana Champaign, Illinois 61801
| | - Jayashree Ray
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, and Department of Biochemistry, University of Illinois, Urbana Champaign, Illinois 61801
| | - Ashtamurthy Pawate
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, and Department of Biochemistry, University of Illinois, Urbana Champaign, Illinois 61801
| | - Robert B. Gennis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, and Department of Biochemistry, University of Illinois, Urbana Champaign, Illinois 61801
| | - Ólöf Einarsdóttir
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, and Department of Biochemistry, University of Illinois, Urbana Champaign, Illinois 61801
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Cvetkov TL, Prochaska LJ. Biophysical and biochemical characterization of reconstituted and purified Rhodobacter sphaeroides cytochrome c oxidase in phospholipid vesicles sheds insight into its functional oligomeric structure. Protein Expr Purif 2007; 56:189-96. [PMID: 17910921 DOI: 10.1016/j.pep.2007.07.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Revised: 07/16/2007] [Accepted: 07/17/2007] [Indexed: 11/18/2022]
Abstract
Discontinuous sucrose gradient ultracentrifugation was used to separate liposomes containing Rhodobacter sphaeroides cytochrome c oxidase (pCOV) from liposomes devoid of the enzyme, and the biophysical and biochemical properties of pCOV were compared to unpurified liposomes containing cytochrome c oxidase (COV). Isolated and purified R. sphaeroides cytochrome c oxidase (COX) was reconstituted into asolectin phospholipid vesicles by cholate dialysis, and this preparation was purified further on a discontinuous sucrose gradient to isolate only those vesicles which contained the enzyme (pCOV). After centrifugation at 300,000g for 22h, 80% of the enzyme recovered was in a single band. The number of COX molecules per pCOV liposome was estimated by measuring the visible absorbance spectrum of cytochrome c oxidase (for heme aa(3)) and inorganic phosphate concentration (for phospholipid). The number of COX molecules incorporated per pCOV was estimated to be approximately one (0.72+/-0.19-1.09+/-0.28). The pCOV exhibited similar physical properties as COV; respiratory control ratios (indicators of endogenous proton permeability) and maximum enzymatic turnover number at pH 7.4 were comparable (6.0+/-1.3 and 535+/-130s(-1)). Furthermore, proton pumping activities of the pCOV were at least 70% of COV, indicating that discontinuous sucrose gradient centrifugation is a useful technique for functional experiments in R. sphaeroides cytochrome c oxidase. Our results suggest that the monomeric form of R. sphaeroides COX when reconstituted into a phospholipid bilayer is completely functionally active in its ability to perform electron transfer and proton pumping activities of the enzyme.
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Affiliation(s)
- Teresa L Cvetkov
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine and College of Science and Mathematics, Wright State University, Dayton, OH 45435, USA
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Brändén G, Gennis RB, Brzezinski P. Transmembrane proton translocation by cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1052-63. [PMID: 16824482 DOI: 10.1016/j.bbabio.2006.05.020] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 05/11/2006] [Accepted: 05/12/2006] [Indexed: 10/24/2022]
Abstract
Respiratory heme-copper oxidases are integral membrane proteins that catalyze the reduction of molecular oxygen to water using electrons donated by either quinol (quinol oxidases) or cytochrome c (cytochrome c oxidases, CcOs). Even though the X-ray crystal structures of several heme-copper oxidases and results from functional studies have provided significant insights into the mechanisms of O2 -reduction and, electron and proton transfer, the design of the proton-pumping machinery is not known. Here, we summarize the current knowledge on the identity of the structural elements involved in proton transfer in CcO. Furthermore, we discuss the order and timing of electron-transfer reactions in CcO during O2 reduction and how these reactions might be energetically coupled to proton pumping across the membrane.
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Affiliation(s)
- Gisela Brändén
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
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32
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Megehee JA, Hosler JP, Lundrigan MD. Evidence for a cytochrome bcc–aa 3 interaction in the respiratory chain of Mycobacterium smegmatis. Microbiology (Reading) 2006; 152:823-829. [PMID: 16514162 DOI: 10.1099/mic.0.28723-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spectroscopic analysis of membranes isolated fromMycobacterium smegmatis, along with analysis of its genome, indicates that the cytochromecbranch of its respiratory pathway consists of a modifiedbc1complex that contains two cytochromescin itsc1subunit, similar to other acid-fast bacteria, and anaa3-type cytochromecoxidase. A functional association of the cytochromebccandaa3complexes was indicated by the findings that levels of detergent sufficient to completely disrupt isolated membranes failed to inhibit quinol-driven O2reduction, but known inhibitors of thebc1complex did inhibit quinol-driven O2reduction. The gene for subunit II of theaa3-type oxidase indicates the presence of additional charged residues in a predicted extramembrane domain, which could mediate an intercomplex association. However, high concentrations of monovalent salts had no effect on O2reduction, suggesting that ionic interactions between extramembrane domains do not play the major role in stabilizing thebcc–aa3interaction. Divalent cations did inhibit electron transfer, likely by distorting the electron-transfer interface between cytochromec1and subunit II. Soluble cytochromeccannot donate electrons to theaa3-type oxidase, even though key cytochromec-binding residues are conserved, probably because the additional residues of subunit II prevent the binding of soluble cytochromec. The results indicate that hydrophobic interactions are the primary forces maintaining thebcc–aa3interaction, but ionic interactions may assist in aligning the two complexes for efficient electron transfer.
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Affiliation(s)
- James A Megehee
- Department of Microbiology, The University of Mississippi Medical Center, Jackson, 2500 North State Street, MS 39216-4505, USA
| | - Jonathan P Hosler
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, 2500 North State Street, MS 39216-4505, USA
| | - Michael D Lundrigan
- Department of Microbiology, The University of Mississippi Medical Center, Jackson, 2500 North State Street, MS 39216-4505, USA
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Mills DA, Geren L, Hiser C, Schmidt B, Durham B, Millett F, Ferguson-Miller S. An arginine to lysine mutation in the vicinity of the heme propionates affects the redox potentials of the hemes and associated electron and proton transfer in cytochrome c oxidase. Biochemistry 2005; 44:10457-65. [PMID: 16060654 PMCID: PMC2533729 DOI: 10.1021/bi050283d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome c oxidase pumps protons across a membrane using energy from electron transfer and reduction of oxygen to water. It is postulated that an element of the energy transduction mechanism is the movement of protons to the vicinity of the hemes upon reduction, to favor charge neutrality. Possible sites on which protons could reside, in addition to the conserved carboxylate E286, are the propionate groups of heme a and/or heme a(3). A highly conserved pair of arginines (R481 and R482) interact with these propionates through ionic and hydrogen bonds. This study shows that the conservative mutant, R481K, although as fully active as the wild type under many conditions, exhibits a significant decrease in the midpoint redox potential of heme a relative to Cu(A) (DeltaE(m)) of approximately equal 40 mV, has lowered activity under conditions of high pH or in the presence of a membrane potential, and has a slowed heme a(3) reduction with dithionite. Another mutant, D132A, which strongly inhibits proton uptake from the internal side of the membrane, has <4% of the activity of the wild type and appears to be dependent on proton uptake from the outside. A double mutation, D132A/R481K, is even more strongly inhibited ( approximately 1% of that of the wild type). The more-than-additive effect supports the concept that R481K not only lowers the midpoint potential of heme a but also limits a supply route for protons from the outside of the membrane used by the D132 mutant. The results are consistent with an important role of R481 and heme a/a(3) propionates in proton movement in a reversible exit path.
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Affiliation(s)
- Denise A. Mills
- Biochemistry and Molecular Biology Department, Michigan State University, East Lansing, MI 48814, U.S.A
| | - Lois Geren
- Department of Chemistry, University of Arkansas, Fayetteville, AR 72701
| | - Carrie Hiser
- Biochemistry and Molecular Biology Department, Michigan State University, East Lansing, MI 48814, U.S.A
| | - Bryan Schmidt
- Biochemistry and Molecular Biology Department, Michigan State University, East Lansing, MI 48814, U.S.A
| | - Bill Durham
- Department of Chemistry, University of Arkansas, Fayetteville, AR 72701
| | - Francis Millett
- Department of Chemistry, University of Arkansas, Fayetteville, AR 72701
- Authors to whom the correspondence should be addressed. F.M. Telephone 479-575-4049. Fax 479-575-4999; E-mail . S. F-M. Telephone 517-353-0199. Fax 517-353-9334; E-mail:
| | - Shelagh Ferguson-Miller
- Biochemistry and Molecular Biology Department, Michigan State University, East Lansing, MI 48814, U.S.A
- Authors to whom the correspondence should be addressed. F.M. Telephone 479-575-4049. Fax 479-575-4999; E-mail . S. F-M. Telephone 517-353-0199. Fax 517-353-9334; E-mail:
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Lucioli S, Hoffmeier K, Carrozzo R, Tessa A, Ludwig B, Santorelli FM. Introducing a novel human mtDNA mutation into the Paracoccus denitrificans COX I gene explains functional deficits in a patient. Neurogenetics 2005; 7:51-7. [PMID: 16284789 DOI: 10.1007/s10048-005-0015-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2005] [Accepted: 08/22/2005] [Indexed: 10/25/2022]
Abstract
We identified a novel mutation (S142F) in the human mtDNA CO I gene in a patient with a clinical phenotype resembling mitochondrial cardioencephalomyopathy. To substantiate pathogenicity, we modeled the identified mutation in the homologous gene in Paracoccus denitrificans and analyzed the biochemical consequences. We observed a deleterious effect on enzyme activity, with a lack of heme a3. Taking advantage of the extensive structural homology between the bacterial enzyme and the mammalian core complex, we conclude that the novel S142F mutation is disease-related. This approach can be used in other cases to support the pathogenicity of novel variants in the mitochondrial genome.
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Affiliation(s)
- Simona Lucioli
- Molecular Medicine, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
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35
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Smith D, Gray J, Mitchell L, Antholine WE, Hosler JP. Assembly of cytochrome-c oxidase in the absence of assembly protein Surf1p leads to loss of the active site heme. J Biol Chem 2005; 280:17652-6. [PMID: 15764605 DOI: 10.1074/jbc.c500061200] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Surf1p is a protein of the inner membrane of mitochondria that functions in the assembly of cytochrome-c oxidase. The specifics of the role of Surf1p have remained unresolved. Numerous mutations in human Surf1p lead to severe mitochondrial disease. A homolog of human Surf1p is encoded by the genome of the alpha-proteobacterium Rhodobacter sphaeroides, which synthesizes a mitochondrial-like aa(3)-type cytochrome-c oxidase. The gene for Surf1p was deleted from the genome of R. sphaeroides. The resulting aa(3)-type oxidase was purified and analyzed by biochemical methods plus optical and EPR spectroscopy. The oxidase that assembled in the absence of Surf1p was composed of three subpopulations with structurally distinct heme a(3)-Cu active sites. 50% of the oxidase lacked heme a(3), 10-15% contained heme a(3) but lacked Cu(BB), and 35-40% had a normal heme a(3) -Cu(B) active site with normal activity. Cu(A) assembly was unaffected. All of the oxidase contained low-spin heme a, but the environment of the heme a center was slightly altered in the 50% of the enzyme that lacked heme a(3). Introduction of a normal copy of the gene for Surf1p on an exogenous plasmid resulted in a single population of normally assembled, highly active enzyme. The data indicate that Surf1p plays a role in facilitating the insertion of heme a(3) into the active site of cytochrome-c oxidase. The results suggest that maturation of the heme a(3)-Cu(B) center is a step that limits the association of subunits I and II in the assembly of mitochondrial cytochrome oxidase.
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Affiliation(s)
- Daniel Smith
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216-4505, USA
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Siletsky SA, Pawate AS, Weiss K, Gennis RB, Konstantinov AA. Transmembrane Charge Separation during the Ferryl-oxo → Oxidized Transition in a Nonpumping Mutant of Cytochrome c Oxidase. J Biol Chem 2004; 279:52558-65. [PMID: 15385565 DOI: 10.1074/jbc.m407549200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The N139D mutant of cytochrome c oxidase from Rhodobacter sphaeroides retains full steady state oxidase activity but completely lacks proton translocation coupled to turnover in reconstituted liposomes (Pawate, A. S., Morgan, J., Namslauer, A., Mills, D., Brzezinski, P., Ferguson-Miller, S., and Gennis, R. B. (2002) Biochemistry 41, 13417-13423). Here, time-resolved electron transfer and vectorial charge translocation in the ferryl-oxo --> oxidized transition (transfer of the 4th electron in the catalytic cycle) have been studied with the N139D mutant using ruthenium(II)-tris-bipyridyl complex as a photoactive single-electron donor. With the wild type oxidase, the flash-induced generation of Deltaphi in the ferryl-oxo --> oxidized transition begins with rapid vectorial electron transfer from CuA to heme a (tau approximately 15 micros), followed by two protonic phases, referred to as the intermediate (0.4 ms) and slow electrogenic phases (1.5 ms). In the N139D mutant, only a single protonic phase (tau approximately 0.6 ms) is observed, which was associated with electron transfer from heme a to the heme a3/CuB site and decelerates approximately 4-fold in D2O. With the wild type oxidase, such a high H2O/D2O solvent isotope effect is characteristic of only the slow (1.5 ms) phase. Presumably, the 0.6-ms electrogenic phase in the N139D mutant reports proton transfer from the inner aqueous phase to Glu-286, replacing the "chemical" proton transferred from Glu-286 to the heme a3/CuB site. The transfer occurs through the D-channel, because it is observed also in the N139D/K362M double mutant in which the K-channel is blocked. It is concluded that the intermediate electrogenic phase observed in the wild type enzyme is missing in the N139D mutant and is because of translocation of the "pumped" proton from Glu-286 to the D-ring propionate of heme a3 or to release of this proton to the outer aqueous phase. Significantly, with the wild type oxidase, the protonic electrogenic phase associated with proton pumping (approximately 0.4 ms) precedes the electrogenic phase associated with the oxygen chemistry (approximately 1.5 ms).
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Affiliation(s)
- Sergey A Siletsky
- AN Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119 992, Russia
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37
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Pinakoulaki E, Vamvouka M, Varotsis C. Resonance Raman detection of the Fe2+-C-N modes in heme-copper oxidases: a probe of the active site. Inorg Chem 2004; 43:4907-10. [PMID: 15285666 DOI: 10.1021/ic035216r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Resonance Raman spectroscopy has been employed to investigate the reduced cyano complexes of cytochrome aa(3) from bovine heart and Rhodobacter sphaeroides and of cytochrome bo(3) from E. coli. In the aa(3)-type oxidases, the frequency of the Fe-CN stretching mode is located at 468 cm(-1), and the bending Fe-C-N vibration, at 500 cm(-1). The fully reduced cytochrome bo(3)-CN complex gives rise to a stretching vibration at 468 cm(-1), a bending vibration at 491 cm(-1), and a stretching C-N vibration at 2037 cm(-1). The observed differences between aa(3) and bo(3) oxidases in the frequencies of the Fe-C-N group suggest a quantitative difference in the structure of the His-heme a(3)(2+)/Cu(B)(1+) and His-heme o(3)(2+)/Cu(B)(1+) binuclear pockets upon CN- binding.
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38
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Qian J, Mills DA, Geren L, Wang K, Hoganson CW, Schmidt B, Hiser C, Babcock GT, Durham B, Millett F, Ferguson-Miller S. Role of the Conserved Arginine Pair in Proton and Electron Transfer in Cytochrome c Oxidase. Biochemistry 2004; 43:5748-56. [PMID: 15134449 DOI: 10.1021/bi036279o] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A hydrogen-bonded network is observed above the hemes in all of the high-resolution crystal structures of cytochrome oxidases. It includes water and a pair of arginines, R481 and R482 (Rhodobacter sphaeroides numbering), that interact directly with heme a and the heme a(3) propionates. The hydrogen-bonded network provides potential pathways for proton release. The arginines, and the backbone peptide bond between them, have also been proposed to form part of a facilitated electron transfer route between Cu(A) and heme a. Our studies show that mutations of R482 (K, Q, and A) and R481 (K) retain substantial activity and are able to pump protons, but at somewhat reduced rates and stoichiometries. A slowed rate of electron transfer from cytochrome c to Cu(A) suggests a change in the orientation of cytochrome c binding in all but the R to K mutants. The mutant R482P is more perturbed in its structure and is altered in the redox potential difference between heme a and Cu(A): +18 mV for R482P and +46 mV for the wild type (heme a - Cu(A)). The electron transfer rate between Cu(A) and heme a is also altered from 93000 s(-1) in the wild type to 50 s(-1) in the oxidized R482P mutant, reminiscent of changes observed in a Cu(A)-ligand mutant, H260N. In neither case is the approximately 2000-fold change in the rate accounted for by the altered redox potentials, suggesting that both cause a major modification in the path or reorganization energy of electron transfer.
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Affiliation(s)
- Jie Qian
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824-1319, USA
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39
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Distler AM, Allison J, Hiser C, Qin L, Hilmi Y, Ferguson-Miller S. Mass spectrometric detection of protein, lipid and heme components of cytochrome c oxidase from R. sphaeroides and the stabilization of non-covalent complexes from the enzyme. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2004; 10:295-308. [PMID: 15103107 DOI: 10.1255/ejms.594] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The cytochrome c oxidase enzyme from the Rhodobacter sphaeroides bacteria exists as a complex of four peptide subunits, two hemes, and a variety of lipids and metal ions held together by non-covalent forces. While the native enzyme functions as an associated unit, this complex usually dissociates during MALDI- TOF analysis. Through the use of matrix additives such as sucrose, the complete complex and partial complexes can be stabilized in the MALDI-TOF experiment. The dissociation of the complex allows for the detection of the components of the enzyme. The direct detection of associated lipids from an aqueous solution of the intact enzyme may eliminate the need for enzyme disruption and lipid extraction. The partial dissociation of multisubunit enzymes in such experiments may allow for the determination of subunit-subunit and subunit-lipid interactions
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Affiliation(s)
- Anne M Distler
- Department of Chemistry, Michigan State University, East Lansing, MI 48824-1322, USA
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40
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Mills DA, Tan Z, Ferguson-Miller S, Hosler J. A role for subunit III in proton uptake into the D pathway and a possible proton exit pathway in Rhodobacter sphaeroides cytochrome c oxidase. Biochemistry 2003; 42:7410-7. [PMID: 12809496 DOI: 10.1021/bi0341307] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protons are transferred from the inner surface of cytochrome c oxidase to the active site by the D and K pathways, as well as from the D pathway to the outer surface by a largely undefined proton exit route. Alteration of the initial proton acceptor of the D pathway, D132, to alanine has previously been shown to greatly inhibit oxidase turnover and slow proton uptake into the D pathway. Here it is shown that the removal of subunit III restores a substantial rate of O(2) reduction to D132A. Presumably an alternative proton acceptor for the D pathway becomes active in the absence of subunit III and D132. Thus, in the absence of subunit III cytochrome oxidase shows greater flexibility in terms of proton entry into the D pathway. In the presence of DeltaPsi and DeltapH, turnover of the wild-type oxidase or D132A is slower in the absence of subunit III. Comparison of the turnover rates of subunit III-depleted wild-type oxidase to those of the zinc-inhibited wild-type oxidase containing subunit III, both reconstituted into vesicles, leads to the hypothesis that the absence of subunit III inhibits the ability of the normal proton exit pathway to take up protons from the outside in the presence of DeltaPsi and DeltapH. Thus, subunit III appears to affect the transfer of protons from both the inner and outer surfaces of cytochrome oxidase, perhaps accounting for the long-observed lower efficiency of proton pumping by the subunit III-depleted oxidase.
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Affiliation(s)
- Denise A Mills
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824, USA
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41
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Gilderson G, Salomonsson L, Aagaard A, Gray J, Brzezinski P, Hosler J. Subunit III of cytochrome c oxidase of Rhodobacter sphaeroides is required to maintain rapid proton uptake through the D pathway at physiologic pH. Biochemistry 2003; 42:7400-9. [PMID: 12809495 DOI: 10.1021/bi0341298] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The catalytic core of cytochrome c oxidase is composed of three subunits where subunits I and II contain all of the redox-active metal centers and subunit III is a seven transmembrane helix protein that binds to subunit I. The N-terminal region of subunit III is adjacent to D132 of subunit I, the initial proton acceptor of the D pathway that transfers protons from the protein surface to the buried active site approximately 30 A distant. The absence of subunit III only slightly alters the initial steady-state activity of the oxidase at pH 6.5, but activity declines sharply with increasing pH, yielding an apparent pK(a) of 7.2 for steady-state O(2) reduction. When subunit III is present, cytochrome oxidase is more active at higher pH, and the apparent pK(a) of steady-state O(2) reduction is 8.5. Single-turnover experiments show that proton uptake through the D pathway at pH 8 slows from >10000 s(-1) in the presence of subunit III to 350 s(-1) in its absence. At low pH (5.5) the D pathway of the oxidase lacking subunit III regains its capacity for rapid proton uptake. Analysis of the F --> O transition indicates that the apparent pK(a) of the D pathway in the absence of subunit III is 6.8, similar to that of steady-state O(2) reduction (7.2). The pK(a) of D132 itself may decline in the absence of subunit III since its carboxylate group will be more exposed to solvent water. Alternatively, part of a proton antenna for the D pathway may be lost upon removal of subunit III. It is proposed that one role of subunit III in the normal oxidase is to maintain rapid proton uptake through the D pathway at physiologic pH.
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Affiliation(s)
- Gwen Gilderson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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Bratton M, Mills D, Castleden CK, Hosler J, Meunier B. Disease-related mutations in cytochrome c oxidase studied in yeast and bacterial models. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1222-30. [PMID: 12631280 DOI: 10.1046/j.1432-1033.2003.03482.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mitochondrial cytochrome c oxidase is a key protonmotive component of the respiratory chain. Mutations in the mitochondrially-encoded subunits of the complex have been reported in association with a range of diseases. In this work we used yeast and bacterial mutants to assess the effect of human mutations in subunit 1 (L196I) and subunit 3 (G78S, A200T, Delta F94-F98, F251L and W249Stop). While the stop mutation at the C-terminus of subunit 3 and the short deletion were highly deleterious and abolished the assembly of the mitochondrial enzyme, the four missense mutations caused little or no effect on the respiratory function. Detailed analysis of G78S, A200T and Delta F94-F98 in Rhodobacter sphaeroides confirmed and extended these observations. We show in this study that the combination of yeast and bacterial models is a useful tool to elucidate the effect of mutations in the catalytic core of cytochrome oxidase. The yeast enzyme is highly similar to the human enzyme and provides a good model to assess the deleterious effect of reported mutations. The bacterial system allows detailed biochemical analysis of the effect of the mutations on the function and assembly of the catalytic core of the enzyme.
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Affiliation(s)
- Melyssa Bratton
- Department of Biochemistry, University of Mississippi Medical Center, USA
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43
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Pawate AS, Morgan J, Namslauer A, Mills D, Brzezinski P, Ferguson-Miller S, Gennis RB. A mutation in subunit I of cytochrome oxidase from Rhodobacter sphaeroides results in an increase in steady-state activity but completely eliminates proton pumping. Biochemistry 2002; 41:13417-23. [PMID: 12416987 DOI: 10.1021/bi026582+] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heme-copper oxidases convert the free energy liberated in the reduction of O(2) to water into a transmembrane proton electrochemical potential (protonmotive force). One of the essential structural elements of the enzyme is the D-channel, which is thought to be the input pathway, both for protons which go to form H(2)O ("chemical protons") and for protons that get translocated across the lipid membrane ("pumped protons"). The D-channel contains a chain of water molecules extending about 25 A from an aspartic acid (D132 in the Rhodobacter sphaeroides oxidase) near the cytoplasmic ("inside") enzyme surface to a glutamic acid (E286) in the protein interior. Mutations in which either of these acidic residues is replaced by their corresponding amides (D132N or E286Q) result in severe inhibition of enzyme activity. In the current work, an asparagine located in the D-channel has been replaced by the corresponding acid (N139 to D; N98 in bovine enzyme) with dramatic consequences. The N139D mutation not only completely eliminates proton pumping but, at the same time, confers a substantial increase (150-300%) in the steady-state cytochrome oxidase activity. The N139D mutant of the R. sphaeroides oxidase was further characterized by examining the rates of individual steps in the catalytic cycle. Under anaerobic conditions, the rate of reduction of heme a(3) in the fully oxidized enzyme, prior to the reaction with O(2), is identical to that of the wild-type oxidase and is not accelerated. However, the rate of reaction of the fully reduced enzyme with O(2) is accelerated by the N139D mutation, as shown by a more rapid F --> O transition. Whereas the rates of formation and decay of the oxygenated intermediates are altered, the nature of the oxygenated intermediates is not perturbed by the N139D mutation.
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Affiliation(s)
- Ashtamurthy S Pawate
- Center for Biophysics and Computational Biology and Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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44
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Mills DA, Ferguson-Miller S. Influence of structure, pH and membrane potential on proton movement in cytochrome oxidase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1555:96-100. [PMID: 12206898 DOI: 10.1016/s0005-2728(02)00261-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cytochrome c oxidase (CcO) reconstituted into phospholipid vesicles and subject to a membrane potential, exhibits different characteristics than the free enzyme, with respect to effects of mutations, pH, inhibitors, and native structural differences between CcO from different species. The results indicate that the membrane potential influences the conformation of CcO and the direction of proton movement in the exit path. The importance of the protein structure above the hemes in proton exit, back leak and respiratory control is discussed.
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Affiliation(s)
- Denise A Mills
- Biochemistry and Molecular Biology Department, Michigan State University, East Lansing 48824, USA.
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McEwan AG, Lewin A, Davy SL, Boetzel R, Leech A, Walker D, Wood T, Moore GR. PrrC from Rhodobacter sphaeroides, a homologue of eukaryotic Sco proteins, is a copper-binding protein and may have a thiol-disulfide oxidoreductase activity. FEBS Lett 2002; 518:10-6. [PMID: 11997009 DOI: 10.1016/s0014-5793(02)02532-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PrrC from Rhodobacter sphaeroides provides the signal input to a two-component signal transduction system that senses changes in oxygen tension and regulates expression of genes involved in photosynthesis (Eraso, J.M. and Kaplan, S. (2000) Biochemistry 39, 2052-2062; Oh, J.-I. and Kaplan, S. (2000) EMBO J. 19, 4237-4247). It is also a homologue of eukaryotic Sco proteins and each has a C-x-x-x-C-P sequence. In mitochondrial Sco proteins these cysteines appear to be essential for the biogenesis of the CuA centre of respiratory cytochrome oxidase. Overexpression and purification of a water-soluble and monomeric form of PrrC has provided sufficient material for a chemical and spectroscopic study of the properties of the four cysteine residues of PrrC, and its ability to bind divalent cations, including copper. PrrC expressed in the cytoplasm of Escherichia coli binds Ni2+ tightly and the data are consistent with a mononuclear metal site. Following removal of Ni2+ and formation of renatured metal-free rPrrC (apo-PrrC), Cu2+ could be loaded into the reduced form of PrrC to generate a protein with a distinctive UV-visible spectrum, having absorbance with a lambda(max) of 360 nm. The copper:PrrC ratio is consistent with the presence of a mononuclear metal centre. The cysteines of metal-free PrrC oxidise in the presence of air to form two intramolecular disulfide bonds, with one pair being extremely reactive. The cysteine thiols with extreme O2 sensitivity are involved in copper binding in reduced PrrC since the same copper-loaded protein could not be generated using oxidised PrrC. Thus, it appears that PrrC, and probably Sco proteins in general, could have both a thiol-disulfide oxidoreductase function and a copper-binding role.
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Affiliation(s)
- Alastair G McEwan
- School of Molecular and Microbial Sciences, The University of Queensland, 4072, Brisbane, Qld, Australia.
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Bartnikas TB, Wang Y, Bobo T, Veselov A, Scholes CP, Shapleigh JP. Characterization of a member of the NnrR regulon in Rhodobacter sphaeroides 2.4.3 encoding a haem-copper protein. MICROBIOLOGY (READING, ENGLAND) 2002; 148:825-833. [PMID: 11882718 DOI: 10.1099/00221287-148-3-825] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Upstream of the nor and nnrR cluster in Rhodobacter sphaeroides 2.4.3 is a previously uncharacterized gene that has been designated nnrS. nnrS is only expressed when 2.4.3 is grown under denitrifying conditions. Expression of nnrS is dependent on the transcriptional regulator NnrR, which also regulates expression of genes required for the reduction of nitrite to nitrous oxide, including nirK and nor. Deletion analysis indicated the sequence 5'-TTGCG(N4)CACAA-3', which is similar to sequences found in nirK and nor, is required for nnrS expression. Mutation of this sequence to the consensus Fnr-binding sequence by changing two bases in each half site caused nnrS expression to become nitrate independent. Inactivation of nnrS did not affect nitric oxide metabolism, nor did it affect expression of any of the genes involved in nitric oxide metabolism. However, taxis towards nitrate and nitrite was affected by nnrS inactivation. Purification of a histidine-tagged NnrS demonstrated that NnrS is a haem- and copper-containing membrane protein. Genes encoding putative orthologues of NnrS are sometimes but not always found in bacteria encoding nitrite and/or nitric oxide reductase.
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Affiliation(s)
- Thomas B Bartnikas
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853-8101, USA1
| | - Yousheng Wang
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853-8101, USA1
| | - Tanya Bobo
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853-8101, USA1
| | - Andrei Veselov
- Department of Chemistry, Center of Biophysics and Biochemistry, University at Albany, SUNY, Albany, NY 12222, USA2
| | - Charles P Scholes
- Department of Chemistry, Center of Biophysics and Biochemistry, University at Albany, SUNY, Albany, NY 12222, USA2
| | - James P Shapleigh
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853-8101, USA1
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Zhen Y, Schmidt B, Kang UG, Antholine W, Ferguson-Miller S. Mutants of the CuA site in cytochrome c oxidase of Rhodobacter sphaeroides: I. Spectral and functional properties. Biochemistry 2002; 41:2288-97. [PMID: 11841221 DOI: 10.1021/bi0114628] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To study the functional significance of the unusual bimetallic Cu(A) center of cytochrome c oxidase, the direct ligands of the Cu(A) center in subunit II of the holoenzyme were mutated. Two of the mutant forms, M263L and H260N, exhibit major changes in activity (10% and 1% of wild-type, respectively) and in near-infrared and EPR spectra, but metal analysis shows that both mutants retain two coppers in the Cu(A) center and both retain proton pumping activity. In M263L, multifrequency EPR studies indicate the coppers are still electronically coupled, while all the other metal centers in M263L appear unchanged, by visible, EPR, and FTIR spectroscopy. Nevertheless, heme a3 is very slow to reduce with cytochrome c or dithionite under stopped-flow and steady-state conditions. This effect appears to be secondary to the change in redox equilibrium between Cu(A) and heme a. The studies reported here and in Wang et al. [Wang, K., Geren, L., Zhen, Y., Ma, L., Ferguson-Miller, S., Durham, B., and Millett, F. (2002) Biochemistry 41, 2298-2304] demonstrate that altering the ligands of Cu(A) can influence the rate and equilibrium of electron transfer between Cu(A) and heme a, but that the native ligation state is not essential for proton pumping.
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Affiliation(s)
- Yuejun Zhen
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824, USA
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Hiser L, Hosler JP. Heme A is not essential for assembly of the subunits of cytochrome c oxidase of Rhodobacter sphaeroides. J Biol Chem 2001; 276:45403-7. [PMID: 11574544 DOI: 10.1074/jbc.m107016200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aa(3)-type cytochrome c oxidase of Rhodobacter sphaeroides, a proteobacterium of the alpha subgroup, is structurally similar to the core subunits of the terminal oxidase in the mitochondrial electron transport chain. Subunit I, the product of the coxI gene, normally binds two heme A molecules. A deletion of cox10, the gene for the farnesyltransferase required for heme A synthesis, did not prevent high level accumulation of subunit I in the cytoplasmic membrane. Thus, subunit I can be expressed and stably inserted into the cytoplasmic membrane in the absence of heme A. Aposubunit I was purified via affinity chromatography to a polyhistidine tag. Copurification of subunits II and III with aposubunit I indicated that assembly of the core oxidase complex occurred without the binding of heme A. In addition to formation of the apooxidase containing all three large structural proteins, CoxI-II and CoxI-III heterodimers were isolated from cox10 deletion strains harboring expression plasmids with coxI and coxII or with coxI and coxIII, respectively. This demonstrated that subunit assembly of the apoenzyme was not an inherently ordered or sequential process. Thus, multiple paths must be considered for understanding the assembly of this integral membrane metalloprotein complex.
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Affiliation(s)
- L Hiser
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, Mississippi 39216, USA
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Gibney BR, Huang SS, Skalicky JJ, Fuentes EJ, Wand AJ, Dutton PL. Hydrophobic modulation of heme properties in heme protein maquettes. Biochemistry 2001; 40:10550-61. [PMID: 11523997 DOI: 10.1021/bi002806h] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the properties of the two hemes bound to histidine in the H10 positions of the uniquely structured apo form of the heme binding four-helix bundle protein maquette [H10H24-L6I,L13F](2), here called [I(6)F(13)H(24)](2) for the amino acids at positions 6 (I), 13 (F) and 24 (H), respectively. The primary structure of each alpha-helix, alpha-SH, in [I(6)F(13)H(24)](2) is Ac-CGGGEI(6)WKL.H(10)EEF(13)LKK.FEELLKL.H(24)EERLKK.L-CONH(2). In our nomenclature, [I(6)F(13)H(24)] represents the disulfide-bridged di-alpha-helical homodimer of this sequence, i.e., (alpha-SS-alpha), and [I(6)F(13)H(24)](2) represents the dimeric four helix bundle composed of two di-alpha-helical subunits, i.e., (alpha-SS-alpha)(2). We replaced the histidines at positions H24 in [I(6)F(13)H(24)](2) with hydrophobic amino acids incompetent for heme ligation. These maquette variants, [I(6)F(13)I(24)](2), [I(6)F(13)A(24)](2), and [I(6)F(13)F(24)](2), are distinguished from the tetraheme binding parent peptide, [I(6)F(13)H(24)](2), by a reduction in the heme:four-helix bundle stoichiometry from 4:1 to 2:1. Iterative redesign has identified phenylalanine as the optimal amino acid replacement for H24 in the context of apo state conformational specificity. Furthermore, the novel second generation diheme [I(6)F(13)F(24)](2) maquette was related to the first generation diheme [H10A24](2) prototype, [L(6)L(13)A(24)](2) in the present nomenclature, via a sequential path in sequence space to evaluate the effects of conservative hydrophobic amino acid changes on heme properties. Each of the disulfide-linked dipeptides studied was highly helical (>77% as determined from circular dichroism spectroscopy), self-associates in solution to form a dimer (as determined by size exclusion chromatography), is thermodynamically stable (-DeltaG(H)2(O) >18 kcal/mol), and possesses conformational specificity that NMR data indicate can vary from multistructured to single structured. Each peptide binds one heme with a dissociation constant, K(d1) value, tighter than 65 nM forming a series of monoheme maquettes. Addition of a second equivalent of heme results in heme binding with a K(d2) in the range of 35-800 nM forming the diheme maquette state. Single conservative amino acid changes between peptide sequences are responsible for up to 10-fold changes in K(d) values. The equilibrium reduction midpoint potential (E(m7.5)) determined in the monoheme state ranges from -156 to -210 mV vs SHE and in the diheme state ranges from -144 to -288 mV. An observed heme-heme electrostatic interaction (>70 mV) in the diheme state indicates a syn global topology of the di-alpha-helical monomers. The heme affinity and electrochemistry of the three H24 variants studied identify the tight binding sites (K(d1) and K(d2) values <200 nM) having the lower reduction midpoint potentials (E(m7.5) values of -155 and -260 mV) with the H10 bound hemes in the parent tetraheme state of [H10H24-L6I,L13F](2), here called [I(6)F(13)H(24)](2). The results of this study illustrate that conservative hydrophobic amino acid changes near the heme binding site can modulate the E(m) by up to +/-50 mV and the K(d) by an order of magnitude. Furthermore, the effects of multiple single amino acid changes on E(m) and K(d) do not appear to be additive.
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Affiliation(s)
- B R Gibney
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Daldal F, Mandaci S, Winterstein C, Myllykallio H, Duyck K, Zannoni D. Mobile cytochrome c2 and membrane-anchored cytochrome cy are both efficient electron donors to the cbb3- and aa3-type cytochrome c oxidases during respiratory growth of Rhodobacter sphaeroides. J Bacteriol 2001; 183:2013-24. [PMID: 11222600 PMCID: PMC95097 DOI: 10.1128/jb.183.6.2013-2024.2001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have recently established that the facultative phototrophic bacterium Rhodobacter sphaeroides, like the closely related Rhodobacter capsulatus species, contains both the previously characterized mobile electron carrier cytochrome c2 (cyt c2) and the more recently discovered membrane-anchored cyt cy. However, R. sphaeroides cyt cy, unlike that of R. capsulatus, is unable to function as an efficient electron carrier between the photochemical reaction center and the cyt bc1 complex during photosynthetic growth. Nonetheless, R. sphaeroides cyt cy can act at least in R. capsulatus as an electron carrier between the cyt bc1 complex and the cbb3-type cyt c oxidase (cbb3-Cox) to support respiratory growth. Since R. sphaeroides harbors both a cbb3-Cox and an aa3-type cyt c oxidase (aa3-Cox), we examined whether R. sphaeroides cyt cy can act as an electron carrier to either or both of these respiratory terminal oxidases. R. sphaeroides mutants which lacked either cyt c2 or cyt cy and either the aa3-Cox or the cbb3-Cox were obtained. These double mutants contained linear respiratory electron transport pathways between the cyt bc1 complex and the cyt c oxidases. They were characterized with respect to growth phenotypes, contents of a-, b-, and c-type cytochromes, cyt c oxidase activities, and kinetics of electron transfer mediated by cyt c2 or cyt cy. The findings demonstrated that both cyt c2 and cyt cy are able to carry electrons efficiently from the cyt bc1 complex to either the cbb3-Cox or the aa3-Cox. Thus, no dedicated electron carrier for either of the cyt c oxidases is present in R. sphaeroides. However, under semiaerobic growth conditions, a larger portion of the electron flow out of the cyt bc1 complex appears to be mediated via the cyt c2-to-cbb3-Cox and cyt cy-to-cbb3-Cox subbranches. The presence of multiple electron carriers and cyt c oxidases with different properties that can operate concurrently reveals that the respiratory electron transport pathways of R. sphaeroides are more complex than those of R. capsulatus.
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Affiliation(s)
- F Daldal
- Department of Biology, Plant Science Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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