57 results on '"Myriam Brugna"'
Search Results
2. An essential role of the reversible electron-bifurcating hydrogenase Hnd for ethanol oxidation in Solidesulfovibrio fructosivorans
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Arlette Kpebe, Chloé Guendon, Natalie Payne, Julien Ros, Manel Khelil Berbar, Régine Lebrun, Carole Baffert, Laetitia Shintu, and Myriam Brugna
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hydrogenase ,Hnd ,Desulfovibrio ,Solidesulfovibrio ,ethanol ,alcohol dehydrogenase ,Microbiology ,QR1-502 - Abstract
The tetrameric cytoplasmic FeFe hydrogenase Hnd from Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans) catalyses H2 oxidation and couples the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin by using a flavin-based electron-bifurcating mechanism. Regarding its implication in the bacterial physiology, we previously showed that Hnd, which is non-essential when bacteria grow fermentatively on pyruvate, is involved in ethanol metabolism. Under these conditions, it consumes H2 to produce reducing equivalents for ethanol production as a fermentative product. In this study, the approach implemented was to compare the two S. fructosivorans WT and the hndD deletion mutant strains when grown on ethanol as the sole carbon and energy source. Based on the determination of bacterial growth, metabolite consumption and production, gene expression followed by RT-q-PCR, and Hnd protein level followed by mass spectrometry, our results confirm the role of Hnd hydrogenase in the ethanol metabolism and furthermore uncover for the first time an essential function for a Desulfovibrio hydrogenase. Hnd is unequivocally required for S. fructosivorans growth on ethanol, and we propose that it produces H2 from NADH and reduced ferredoxin generated by an alcohol dehydrogenase and an aldehyde ferredoxin oxidoreductase catalyzing the conversion of ethanol into acetate. The produced H2 could then be recycled and used for sulfate reduction. Hnd is thus a reversible hydrogenase that operates in H2-consumption by an electron-bifurcating mechanism during pyruvate fermentation and in H2-production by an electron-confurcating mechanism when the bacterium uses ethanol as electron donor.
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- 2023
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3. Transport limited adsorption experiments give a new lower estimate of the turnover frequency of Escherichia coli hydrogenase 1
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Anna Aldinio-Colbachini, Andrea Fasano, Chloé Guendon, Aurore Jacq-Bailly, Jérémy Wozniak, Carole Baffert, Arlette Kpebe, Christophe Léger, Myriam Brugna, and Vincent Fourmond
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Hydrogenase ,Metalloenzyme ,Protein film electrochemistry ,Bioinorganic chemistry ,Biochemistry ,QD415-436 ,Genetics ,QH426-470 - Abstract
Protein Film Electrochemistry is a technique in which a redox enzyme is directly wired to an electrode, which substitutes for the natural redox partner. In this technique, the electrical current flowing through the electrode is proportional to the catalytic activity of the enzyme. However, in most cases, the amount of enzyme molecules contributing to the current is unknown and the absolute turnover frequency cannot be determined. Here, we observe the formation of electrocatalytically active films of E. coli hydrogenase 1 by rotating an electrode in a sub-nanomolar solution of enzyme. This process is slow, and we show that it is mass-transport limited. Measuring the rate of the immobilization allows the determination of an estimation of the turnover rate of the enzyme, which appears to be much greater than that deduced from solution assays under the same conditions.
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- 2023
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4. Overproduction of the Flv3B flavodiiron, enhances the photobiological hydrogen production by the nitrogen-fixing cyanobacterium Nostoc PCC 7120
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Baptiste Roumezi, Luisana Avilan, Véronique Risoul, Myriam Brugna, Sophie Rabouille, and Amel Latifi
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Cyanobacteria ,Flavodiiron ,Heterocyte ,Hydrogen ,Hydrogenase ,Microbiology ,QR1-502 - Abstract
Abstract Background The ability of some photosynthetic microorganisms, particularly cyanobacteria and microalgae, to produce hydrogen (H2) is a promising alternative for renewable, clean-energy production. However, the most recent, related studies point out that much improvement is needed for sustainable cyanobacterial-based H2 production to become economically viable. In this study, we investigated the impact of induced O2-consumption on H2 photoproduction yields in the heterocyte-forming, N2-fixing cyanobacterium Nostoc PCC7120. Results The flv3B gene, encoding a flavodiiron protein naturally expressed in Nostoc heterocytes, was overexpressed. Under aerobic and phototrophic growth conditions, the recombinant strain displayed a significantly higher H2 production than the wild type. Nitrogenase activity assays indicated that flv3B overexpression did not enhance the nitrogen fixation rates. Interestingly, the transcription of the hox genes, encoding the NiFe Hox hydrogenase, was significantly elevated, as shown by the quantitative RT-PCR analyses. Conclusion We conclude that the overproduced Flv3B protein might have enhanced O2-consumption, thus creating conditions inducing hox genes and facilitating H2 production. The present study clearly demonstrates the potential to use metabolic engineered cyanobacteria for photosynthesis driven H2 production.
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- 2020
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5. Electrochemical Characterization of a Complex FeFe Hydrogenase, the Electron-Bifurcating Hnd From Desulfovibrio fructosovorans
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Aurore Jacq-Bailly, Martino Benvenuti, Natalie Payne, Arlette Kpebe, Christina Felbek, Vincent Fourmond, Christophe Léger, Myriam Brugna, and Carole Baffert
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direct electrochemistry ,FeFe hydrogenase ,electron bifurcation ,Desulfovibrio fructosovorans ,inactivation ,Chemistry ,QD1-999 - Abstract
Hnd, an FeFe hydrogenase from Desulfovibrio fructosovorans, is a tetrameric enzyme that can perform flavin-based electron bifurcation. It couples the oxidation of H2 to both the exergonic reduction of NAD+ and the endergonic reduction of a ferredoxin. We previously showed that Hnd retains activity even when purified aerobically unlike other electron-bifurcating hydrogenases. In this study, we describe the purification of the enzyme under O2-free atmosphere and its biochemical and electrochemical characterization. Despite its complexity due to its multimeric composition, Hnd can catalytically and directly exchange electrons with an electrode. We characterized the catalytic and inhibition properties of this electron-bifurcating hydrogenase using protein film electrochemistry of Hnd by purifying Hnd aerobically or anaerobically, then comparing the electrochemical properties of the enzyme purified under the two conditions via protein film electrochemistry. Hydrogenases are usually inactivated under oxidizing conditions in the absence of dioxygen and can then be reactivated, to some extent, under reducing conditions. We demonstrate that the kinetics of this high potential inactivation/reactivation for Hnd show original properties: it depends on the enzyme purification conditions and varies with time, suggesting the coexistence and the interconversion of two forms of the enzyme. We also show that Hnd catalytic properties (Km for H2, diffusion and reaction at the active site of CO and O2) are comparable to those of standard hydrogenases (those which cannot catalyze electron bifurcation). These results suggest that the presence of the additional subunits, needed for electron bifurcation, changes neither the catalytic behavior at the active site, nor the gas diffusion kinetics but induces unusual rates of high potential inactivation/reactivation.
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- 2021
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6. On the Natural History of Flavin-Based Electron Bifurcation
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Frauke Baymann, Barbara Schoepp-Cothenet, Simon Duval, Marianne Guiral, Myriam Brugna, Carole Baffert, Michael J. Russell, and Wolfgang Nitschke
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electron bifurcation ,redox cooperativity ,flavoenzymes ,emergence of life ,redox enzyme construction kit ,bioenergetics ,Microbiology ,QR1-502 - Abstract
Electron bifurcation is here described as a special case of the continuum of electron transfer reactions accessible to two-electron redox compounds with redox cooperativity. We argue that electron bifurcation is foremost an electrochemical phenomenon based on (a) strongly inverted redox potentials of the individual redox transitions, (b) a high endergonicity of the first redox transition, and (c) an escapement-type mechanism rendering completion of the first electron transfer contingent on occurrence of the second one. This mechanism is proposed to govern both the traditional quinone-based and the newly discovered flavin-based versions of electron bifurcation. Conserved and variable aspects of the spatial arrangement of electron transfer partners in flavoenzymes are assayed by comparing the presently available 3D structures. A wide sample of flavoenzymes is analyzed with respect to conserved structural modules and three major structural groups are identified which serve as basic frames for the evolutionary construction of a plethora of flavin-containing redox enzymes. We argue that flavin-based and other types of electron bifurcation are of primordial importance to free energy conversion, the quintessential foundation of life, and discuss a plausible evolutionary ancestry of the mechanism.
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- 2018
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7. A biochemical approach to study the role of the terminal oxidases in aerobic respiration in Shewanella oneidensis MR-1.
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Sébastien Le Laz, Arlette Kpebe, Marielle Bauzan, Sabrina Lignon, Marc Rousset, and Myriam Brugna
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Medicine ,Science - Abstract
The genome of the facultative anaerobic γ-proteobacterium Shewanella oneidensis MR-1 encodes for three terminal oxidases: a bd-type quinol oxidase and two heme-copper oxidases, a A-type cytochrome c oxidase and a cbb 3-type oxidase. In this study, we used a biochemical approach and directly measured oxidase activities coupled to mass-spectrometry analysis to investigate the physiological role of the three terminal oxidases under aerobic and microaerobic conditions. Our data revealed that the cbb 3-type oxidase is the major terminal oxidase under aerobic conditions while both cbb 3-type and bd-type oxidases are involved in respiration at low-O2 tensions. On the contrary, the low O2-affinity A-type cytochrome c oxidase was not detected in our experimental conditions even under aerobic conditions and would therefore not be required for aerobic respiration in S. oneidensis MR-1. In addition, the deduced amino acid sequence suggests that the A-type cytochrome c oxidase is a ccaa 3-type oxidase since an uncommon extra-C terminal domain contains two c-type heme binding motifs. The particularity of the aerobic respiratory pathway and the physiological implication of the presence of a ccaa 3-type oxidase in S. oneidensis MR-1 are discussed.
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- 2014
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8. The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus.
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Laurence Prunetti, Myriam Brugna, Régine Lebrun, Marie-Thérèse Giudici-Orticoni, and Marianne Guiral
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Medicine ,Science - Abstract
The reduction of molecular oxygen to water is catalyzed by complicated membrane-bound metallo-enzymes containing variable numbers of subunits, called cytochrome c oxidases or quinol oxidases. We previously described the cytochrome c oxidase II from the hyperthermophilic bacterium Aquifex aeolicus as a ba(3)-type two-subunit (subunits I and II) enzyme and showed that it is included in a supercomplex involved in the sulfide-oxygen respiration pathway. It belongs to the B-family of the heme-copper oxidases, enzymes that are far less studied than the ones from family A. Here, we describe the presence in this enzyme of an additional transmembrane helix "subunit IIa", which is composed of 41 amino acid residues with a measured molecular mass of 5105 Da. Moreover, we show that subunit II, as expected, is in fact longer than the originally annotated protein (from the genome) and contains a transmembrane domain. Using Aquifex aeolicus genomic sequence analyses, N-terminal sequencing, peptide mass fingerprinting and mass spectrometry analysis on entire subunits, we conclude that the B-type enzyme from this bacterium is a three-subunit complex. It is composed of subunit I (encoded by coxA(2)) of 59000 Da, subunit II (encoded by coxB(2)) of 16700 Da and subunit IIa which contain 12, 1 and 1 transmembrane helices respectively. A structural model indicates that the structural organization of the complex strongly resembles that of the ba(3) cytochrome c oxidase from the bacterium Thermus thermophilus, the IIa helical subunit being structurally the lacking N-terminal transmembrane helix of subunit II present in the A-type oxidases. Analysis of the genomic context of genes encoding oxidases indicates that this third subunit is present in many of the bacterial oxidases from B-family, enzymes that have been described as two-subunit complexes.
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- 2011
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9. NMR-based metabolomic analysis of the physiological role of the electron-bifurcating FeFe-hydrogenase Hnd in Solidesulfovibrio fructosivorans under pyruvate fermentation
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Natalie Payne, Arlette Kpebe, Chloé Guendon, Carole Baffert, Matthieu Maillot, Typhaine Haurogné, Fabrice Tranchida, Myriam Brugna, and Laetitia Shintu
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Microbiology - Abstract
Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans), an anaerobic sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of hydrogen gas (H
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- 2022
10. The electron-bifurcating FeFe-hydrogenase Hnd is involved in ethanol metabolism in Desulfovibrio fructosovorans grown on pyruvate
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Natalie Payne, Arlette Kpebe, Chloé Guendon, Carole Baffert, Julien Ros, Régine Lebrun, Yann Denis, Laetitia Shintu, Myriam Brugna, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Plateforme Protéomique [Marseille], Institut de Microbiologie de la Méditerranée (IMM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Plate-forme Transcriptome FR3479, MM-CNRS, Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), and European Project: 7137500(1971)
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Ethanol ,Alcohol dehydrogenase ,Electron bifurcation ,Electrons ,NAD ,Microbiology ,Hydrogenase ,Pyruvic Acid ,Ferredoxins ,Aldehyde ferredoxin oxidoreductase ,Desulfovibrio ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Molecular Biology ,Oxidation-Reduction ,Hydrogen - Abstract
International audience; Desulfovibrio fructosovorans, a sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of H2 into protons and electrons. Among them, Hnd is an electron-bifurcating hydrogenase, coupling the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2. It was previously hypothesized that its biological function involves the production of NADPH necessary for biosynthetic purposes. However, it was subsequently demonstrated that Hnd is instead a NAD+-reducing enzyme, thus its specific function has yet to be established. To understand the physiological role of Hnd in D. fructosovorans, we compared the hnd deletion mutant with the wild-type strain grown on pyruvate. Growth, metabolites production and comsumption, and gene expression were compared under three different growth conditions. Our results indicate that hnd is strongly regulated at the transcriptional level and that its deletion has a drastic effect on the expression of genes for two enzymes, an aldehyde ferredoxin oxidoreductase and an alcohol dehydrogenase. We demonstrated here that Hnd is involved in ethanol metabolism when bacteria grow fermentatively and proposed that Hnd might oxidize part of the H2 produced during fermentation generating both NADH and reduced ferredoxin for ethanol production via its electron bifurcation mechanism.
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- 2022
11. First steps in the characterization of cytochrome bd oxidase from Solidesulfovibrio fructosovorans
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Arlette Kpebe, Stéphane Grimaldi, Myriam Brugna, and Eric Pilet
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Biophysics ,Cell Biology ,Biochemistry - Published
- 2022
12. The physiological role of the electron-bifurcating FeFe-hydrogenase Hnd in Solidesulfovibrio fructosivorans
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Natalie Payne, Arlette Kpebe, Chloé Guendon, Carole Baffert, Julien Ros, Laetitia Shintu, and Myriam Brugna
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Biophysics ,Cell Biology ,Biochemistry - Published
- 2022
13. Clostridial whole cell and enzyme systems for hydrogen production: current state and perspectives
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Luisana Avilan, Amel Latifi, Myriam Brugna, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Bioénergétique et Ingénierie des Protéines (BIP ), and ANR-13-BIME-0001,CYANHY,Exploitation de l'énergie solaire pour une production de Bio-Hydrogène dans un environnement naturellement micro-oxique chez la Cyanobactérie Anabaena PCC 7120.(2013)
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[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,Hydrogenase ,Hydrogen ,[SDV]Life Sciences [q-bio] ,Industrial Waste ,chemistry.chemical_element ,Metabolic engineering ,Applied Microbiology and Biotechnology ,Industrial waste ,03 medical and health sciences ,Anaerobiosis ,030304 developmental biology ,Hydrogen production ,Clostridium ,0303 health sciences ,030306 microbiology ,General Medicine ,Dark fermentation ,Clostridia ,chemistry ,Fermentation ,Biochemical engineering ,Anaerobic bacteria ,Biotechnology - Abstract
International audience; Strictly anaerobic bacteria of the Clostridium genus have attracted great interest as potential cell factories for molecular hydrogen production purposes. In addition to being a useful approach to this process, dark fermentation has the advantage of using the degradation of cheap agricultural residues and industrial wastes for molecular hydrogen production. However, many improvements are still required before large-scale hydrogen production from clostridial metabolism is possible. Here we review the literature on the basic biological processes involved in clostridial hydrogen production, and present the main advances obtained so far in order to enhance the hydrogen productivity, as well as suggesting some possible future prospects.
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- 2018
14. Electrochemical characterization of a complex FeFe hydrogenase, the electron-bifurcating Hnd from Desulfovibrio fructosovorans
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Carole Baffert, Christophe Léger, Vincent Fourmond, Natalie Payne, Martino Benvenuti, Christina Felbek, Aurore Jacq-Bailly, Arlette Kpebe, Myriam Brugna, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
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Hydrogenase ,[SDV]Life Sciences [q-bio] ,Kinetics ,Desulfovibrio fructosovorans ,Flavin group ,direct electrochemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,lcsh:Chemistry ,03 medical and health sciences ,inactivation ,Ferredoxin ,030304 developmental biology ,Exergonic reaction ,0303 health sciences ,biology ,Chemistry ,Active site ,General Chemistry ,Combinatorial chemistry ,0104 chemical sciences ,lcsh:QD1-999 ,FeFe hydrogenase ,electron bifurcation ,biology.protein ,NAD+ kinase - Abstract
Hnd, an FeFe hydrogenase from Desulfovibrio fructosovorans, is a tetrameric enzyme that can perform flavin-based electron bifurcation. It couples the oxidation of H2 to both the exergonic reduction of NAD+ and the endergonic reduction of a ferredoxin. We previously showed that Hnd retains activity even when purified aerobically unlike other electron-bifurcating hydrogenases. In this study, we describe the purification of the enzyme under O2-free atmosphere and its biochemical and electrochemical characterization. Despite its complexity due to its multimeric composition, Hnd can catalytically and directly exchange electrons with an electrode. We characterized the catalytic and inhibition properties of this electron-bifurcating hydrogenase using protein film electrochemistry of Hnd by purifying Hnd aerobically or anaerobically, then comparing the electrochemical properties of the enzyme purified under the two conditions via protein film electrochemistry. Hydrogenases are usually inactivated under oxidizing conditions in the absence of dioxygen and can then be reactivated, to some extent, under reducing conditions. We demonstrate that the kinetics of this high potential inactivation/reactivation for Hnd show original properties: it depends on the enzyme purification conditions and varies with time, suggesting the coexistence and the interconversion of two forms of the enzyme. We also show that Hnd catalytic properties (Km for H2, diffusion and reaction at the active site of CO and O2) are comparable to those of standard hydrogenases (those which cannot catalyze electron bifurcation). These results suggest that the presence of the additional subunits, needed for electron bifurcation, changes neither the catalytic behavior at the active site, nor the gas diffusion kinetics but induces unusual rates of high potential inactivation/reactivation.
- Published
- 2021
15. The dyad of the Y-junction- and a flavin module unites diverse redox enzymes
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Frauke Baymann, Kilian Zuchan, Myriam Brugna, Carole Baffert, Wolfgang Nitschke, Bioénergétique et Ingénierie des Protéines (BIP ), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
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Stereochemistry ,[PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] ,Biophysics ,formate dehydrogenase ,Electrons ,Flavin group ,Formate dehydrogenase ,Biochemistry ,Redox ,Electron Transport ,03 medical and health sciences ,Electron transfer ,Bacterial Proteins ,Flavins ,evolution ,Moiety ,hydrogenase ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Peptide sequence ,Phylogeny ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,030306 microbiology ,Chemistry ,complex I ,Cell Biology ,flavin ,Formate Dehydrogenases ,Enzyme ,electron bifurcation ,NAD+ kinase - Abstract
International audience; The concomitant presence of two distinctive polypeptide modules, which we have chosen to denominate as the “Y-junction” and the “flavin” module, is observed in 3D structures of enzymes as functionally diverse as complex I, NAD(P)-dependent [NiFe]-hydrogenases and NAD(P)-dependent formate dehydrogenases. Amino acid sequence conservation furthermore suggests that both modules are also part of NAD(P)-dependent [FeFe]-hydrogenases for which no 3D structure model is available yet. The flavin module harbours the site of interaction with the substrate NAD(P) which exchanges two electrons with a strictly conserved flavin moiety. The Y-junction module typically contains four iron-sulphur centres arranged to form a Y-shaped electron transfer conduit and mediates electron transfer between the flavin module and the catalytic units of the respective enzymes. The Y-junction module represents an electron transfer hub with three potential electron entry/exit sites. The pattern of specific redox centres present both in the Y-junction and the flavin module is correlated to present knowledge of these enzymes' functional properties. We have searched publicly accessible genomes for gene clusters containing both the Y-junction and the flavin module to assemble a comprehensive picture of the diversity of enzymes harbouring this dyad of modules and to reconstruct their phylogenetic relationships. These analyses indicate the presence of the dyad already in the last universal common ancestor and the emergence of complex I's EFG-module out of a subgroup of NAD(P)- dependent formate dehydrogenases.
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- 2021
16. Overproduction of the Flv3B flavodiiron, enhances the photobiological hydrogen production by the nitrogen-fixing cyanobacterium Nostoc PCC 7120
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Luisana Avilan, Amel Latifi, Véronique Risoul, Sophie Rabouille, Baptiste Roumezi, Myriam Brugna, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ANR-18-CE05-0029,OtolHyd,Hydrogénases cyanobactériennes tolérantes à l'Oxygène: caractérisation fonctionnelle et ingénierie(2018), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
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0106 biological sciences ,Cyanobacteria ,Nostoc ,Hydrogenase ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,flavodiiron ,Nitrogen ,lcsh:QR1-502 ,Bioengineering ,Photosynthesis ,01 natural sciences ,Applied Microbiology and Biotechnology ,lcsh:Microbiology ,03 medical and health sciences ,Bacterial Proteins ,Nitrogen Fixation ,heterocyte ,hydrogenase ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Overproduction ,Hox gene ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,biology ,Chemistry ,Research ,Genes, Homeobox ,Nitrogenase ,biology.organism_classification ,Heterocyte ,Oxygen ,Biochemistry ,Metabolic Engineering ,hydrogen ,Nitrogen fixation ,Flavodiiron ,010606 plant biology & botany ,Biotechnology ,Hydrogen - Abstract
Background The ability of some photosynthetic microorganisms, particularly cyanobacteria and microalgae, to produce hydrogen (H2) is a promising alternative for renewable, clean-energy production. However, the most recent, related studies point out that much improvement is needed for sustainable cyanobacterial-based H2 production to become economically viable. In this study, we investigated the impact of induced O2-consumption on H2 photoproduction yields in the heterocyte-forming, N2-fixing cyanobacterium Nostoc PCC7120. Results The flv3B gene, encoding a flavodiiron protein naturally expressed in Nostoc heterocytes, was overexpressed. Under aerobic and phototrophic growth conditions, the recombinant strain displayed a significantly higher H2 production than the wild type. Nitrogenase activity assays indicated that flv3B overexpression did not enhance the nitrogen fixation rates. Interestingly, the transcription of the hox genes, encoding the NiFe Hox hydrogenase, was significantly elevated, as shown by the quantitative RT-PCR analyses. Conclusion We conclude that the overproduced Flv3B protein might have enhanced O2-consumption, thus creating conditions inducing hox genes and facilitating H2 production. The present study clearly demonstrates the potential to use metabolic engineered cyanobacteria for photosynthesis driven H2 production.
- Published
- 2020
17. Hydrogenases and H
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Carole, Baffert, Arlette, Kpebe, Luisana, Avilan, and Myriam, Brugna
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Bacterial Proteins ,Hydrogenase ,Biocatalysis ,Genetic Variation ,Desulfovibrio ,Electrons ,Gene Expression Regulation, Bacterial ,Models, Biological ,Hydrogen - Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H
- Published
- 2019
18. Hydrogenases and H2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus
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Carole Baffert, Myriam Brugna, Luisana Avilan, Arlette Kpebe, Bioénergétique et Ingénierie des Protéines (BIP ), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and AZZOPARDI, LAURE
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[CHIM.INOR] Chemical Sciences/Inorganic chemistry ,inorganic chemicals ,H2 metabolism ,Hydrogenase ,Microorganism ,[SDV]Life Sciences [q-bio] ,[CHIM.INOR]Chemical Sciences/Inorganic chemistry ,environment and public health ,03 medical and health sciences ,[CHIM] Chemical Sciences ,energy metabolism ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,[CHIM]Chemical Sciences ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,hydrogenase ,Sulfate-reducing bacteria ,bacteria ,electron-bifurcation ,chemistry.chemical_classification ,0303 health sciences ,biology ,030306 microbiology ,Chemistry ,organic chemicals ,Metabolism ,biology.organism_classification ,equipment and supplies ,Desulfovibrio ,[SDV] Life Sciences [q-bio] ,Enzyme ,Biochemistry ,Sulfate-reducing ,Bacteria ,Hydrogen - Abstract
International audience; Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
- Published
- 2019
19. A new mechanistic model for an O 2-protected electron-bifurcating hydrogenase, Hnd from Desulfovibrio fructosovorans
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Amani Rebai, Myriam Brugna, Sébastien Le Laz, Gabriel García-Molina, Antonio L. De Lacey, Emilien Etienne, Bruno Guigliarelli, Chloé Guendon, Martino Benvenuti, Arlette Kpebe, Victoria Isabel Fernandez, Carole Baffert, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), instituto de Catalysis y Petroleoquimica (ICP), and Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)
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0301 basic medicine ,Hydrogenase ,Stereochemistry ,[SDV]Life Sciences [q-bio] ,030106 microbiology ,Biophysics ,Flavin group ,7. Clean energy ,Biochemistry ,Redox ,03 medical and health sciences ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Ferredoxin ,chemistry.chemical_classification ,Exergonic reaction ,biology ,Chemistry ,Cell Biology ,[CHIM.CATA]Chemical Sciences/Catalysis ,biology.organism_classification ,flavin ,ferredoxin ,Desulfovibrio ,030104 developmental biology ,Enzyme ,electron bifurcation ,NAD+ kinase - Abstract
International audience; The genome of the sulfate-reducing and anaerobic bacterium Desulfovibrio fructosovorans encodes different hydrogenases. Among them is Hnd, a tetrameric cytoplasmic [FeFe] hydrogenase that has previously been described as an NADP-specific enzyme (Malki et al., 1995). In this study, we purified and characterized a recombinant Strep-tagged form of Hnd and demonstrated that it is an electron-bifurcating enzyme. Flavin-based electron-bifurcation is a mechanism that couples an exergonic redox reaction to an endergonic one allowing energy conservation in anaerobic microorganisms. One of the three ferredoxins of the bacterium, that was named FdxB, was also purified and characterized. It contains a low-potential (E m =-450 mV) [4Fe4S] cluster. We found that Hnd was not able to reduce NADP + , and that it catalyzes the simultaneous reduction of FdxB and NAD +. Moreover, Hnd is the first electron-bifurcating hydrogenase that retains activity when purified aerobically due to formation of an inactive state of its catalytic site protecting against O 2 damage (H inact). Hnd is highly active with the artificial redox partner (methyl viologen) and can perform the electron-bifurcation reaction to oxidize H 2 with a specific activity of 10 µmol of NADH/min/mg of enzyme. Surprisingly, the ratio between NADH and reduced FdxB varies over the reaction 2 with a decreasing amount of FdxB reduced per NADH produced, indicating a more complex mechanism than previously described. We proposed a new mechanistic model in which the ferredoxin is recycled at the hydrogenase catalytic subunit.
- Published
- 2018
20. A new mechanistic model for an O
- Author
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Arlette, Kpebe, Martino, Benvenuti, Chloé, Guendon, Amani, Rebai, Victoria, Fernandez, Sébastien, Le Laz, Emilien, Etienne, Bruno, Guigliarelli, Gabriel, García-Molina, Antonio L, de Lacey, Carole, Baffert, and Myriam, Brugna
- Subjects
Oxygen ,Hydrogenase ,Spectroscopy, Fourier Transform Infrared ,Biocatalysis ,Ferredoxins ,Desulfovibrio ,Electrons ,Spectrophotometry, Ultraviolet ,Amino Acid Sequence ,NAD ,Models, Biological - Abstract
The genome of the sulfate-reducing and anaerobic bacterium Desulfovibrio fructosovorans encodes different hydrogenases. Among them is Hnd, a tetrameric cytoplasmic [FeFe] hydrogenase that has previously been described as an NADP-specific enzyme (Malki et al., 1995). In this study, we purified and characterized a recombinant Strep-tagged form of Hnd and demonstrated that it is an electron-bifurcating enzyme. Flavin-based electron-bifurcation is a mechanism that couples an exergonic redox reaction to an endergonic one allowing energy conservation in anaerobic microorganisms. One of the three ferredoxins of the bacterium, that was named FdxB, was also purified and characterized. It contains a low-potential (E
- Published
- 2018
21. The electron-bifurcating hydrogenase Hnd from Desulfovibrio fructosovorans
- Author
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Chloé Guendon, Martino Benvenuti, Arlette Kpebe, Myriam Brugna, Carole Baffert, Amani Rebai, Victoria Isabel Fernandez, Emilien Etienne, and Bruno Guigliarelli
- Subjects
Hydrogenase ,Stereochemistry ,Chemistry ,Biophysics ,Desulfovibrio fructosovorans ,Cell Biology ,Biochemistry - Published
- 2018
22. In vivo production of catalase containing haem analogues
- Author
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Myriam Brugna, Lars Hederstedt, and Lena Tasse
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chemistry.chemical_classification ,biology ,Protoporphyrin IX ,Cell growth ,Stereochemistry ,digestive, oral, and skin physiology ,Haem peroxidase ,Cell Biology ,biology.organism_classification ,Biochemistry ,Cofactor ,Enterococcus faecalis ,chemistry.chemical_compound ,Enzyme ,chemistry ,In vivo ,Catalase ,polycyclic compounds ,biology.protein ,Molecular Biology - Abstract
Haem (protohaem IX) analogues are toxic compounds and have been considered for use as antibacterial agents, but the primary mechanism behind their toxicity has not been demonstrated. Using the haem protein catalase in the Gram-positive bacterium Enterococcus faecalis as an experimental system, we show that a variety of haem analogues can be taken up by bacterial cells and incorporated into haem-dependent enzymes. The resulting cofactor-substituted proteins are dysfunctional, generally resulting in arrested cell growth or death. This largely explains the cell toxicity of haem analogues. In contrast to many other organisms, E. faecalis does not depend on haem for growth, and therefore resists the toxicity of many haem analogues. We have exploited this feature to establish a bacterial in vivo system for the production of cofactor-substituted haem protein variants. As a pilot study, we produced, isolated and analysed novel catalase variants in which the iron atom of the haem prosthetic group is replaced by other metals, i.e. cobalt, gallium, tin, and zinc, and also variants containing meso-protoheme IX, ruthenium meso-protoporphyrin IX and (metal-free) protoporphyrin IX. Engineered haem proteins of this type are of potential use within basic research and the biotechnical industry.
- Published
- 2010
23. Immobilization of the hyperthermophilic hydrogenase from Aquifex aeolicus bacterium onto gold and carbon nanotube electrodes for efficient H2 oxidation
- Author
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Marie-Thérèse Giudici-Orticoni, Pascale Tron-Infossi, Xiaojun Luo, Elisabeth Lojou, and Myriam Brugna
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Models, Molecular ,Hydrogenase ,Protein Conformation ,Aerobic bacteria ,Molecular Sequence Data ,Inorganic chemistry ,Carbon nanotube ,Electrochemistry ,Biochemistry ,Catalysis ,law.invention ,Inorganic Chemistry ,Electron transfer ,Bacterial Proteins ,law ,Amino Acid Sequence ,Enzyme Inhibitors ,Electrodes ,Aquifex aeolicus ,Bacteria ,biology ,Nanotubes, Carbon ,Chemistry ,Electrochemical Techniques ,Enzymes, Immobilized ,biology.organism_classification ,Chemical engineering ,Electrode ,Adsorption ,Gold ,Oxidation-Reduction ,Sequence Alignment - Abstract
The electrochemistry of membrane-bound [NiFe] hydrogenase I ([NiFe]-hase I) from the hyperthermophilic bacterium Aquifex aeolicus was investigated at gold and graphite electrodes. Direct and mediated H(2) oxidation were proved to be efficient in a temperature range of 25-70 degrees C, describing a potential window for H(2) oxidation similar to that of O(2)-tolerant hydrogenases. Search for enhancement of current densities and enzyme stability was achieved by the use of carbon nanotube coatings. We report high catalytic currents for H(2) oxidation up to 1 mA cm(-2), 10 times higher than at the bare electrode. Interestingly, high stability of the direct catalytic process was observed when encapsulating A. aeolicus [NiFe]-hase I into a carboxylic functionalized single walled carbon nanotube network. This suggests a peculiar interaction between the enzyme and the electrode material. The parameters that governed the orientation of the enzyme before electron transfer were thus investigated using self-assembled-monolayer gold electrodes. No control of the orientation by the charge or the hydrophobicity of the interface was demonstrated. This behavior was explained on the basis of a structural comparison between A. aeolicus [NiFe]-hase I and Desulfovibrio fructosovorans [NiFe] hydrogenase, which revealed the absence of acidic residues and an additional loop in the environment of the [4Fe-4S] distal cluster in A. aeolicus [NiFe]-hase I. Finally, the effect of inhibitors on the direct oxidation of H(2) by A. aeolicus [NiFe]-hase I encapsulated in a single walled carbon nanotube network was investigated. No inhibition by CO and tolerance toward O(2) were observed. Discussion of the reasons for such tolerance was undertaken on the basis of structural comparison with hydrogenases from aerobic bacteria.
- Published
- 2009
24. A New Iron-oxidizing/O2-reducing Supercomplex Spanning Both Inner and Outer Membranes, Isolated from the Extreme Acidophile Acidithiobacillus ferrooxidans
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Cindy J. Castelle, Marie-Thérèse Giudici-Orticoni, Guillaume Malarte, Gisèle Leroy, Myriam Brugna, Marianne Guiral, and Fouzia Ledgham
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Cytochrome ,Acidithiobacillus ,Iron ,Respiratory chain ,Models, Biological ,Biochemistry ,Ferrous ,Electron Transport ,Cytochrome c oxidase ,Cloning, Molecular ,Molecular Biology ,Oxidase test ,biology ,Chemistry ,Cytochrome c ,Cell Membrane ,Electron Spin Resonance Spectroscopy ,Cell Biology ,Carbon Dioxide ,biology.organism_classification ,Recombinant Proteins ,Oxygen ,Metabolism and Bioenergetics ,Multiprotein Complexes ,Acidophile ,biology.protein ,Oxidoreductases ,Oxidation-Reduction ,NADP - Abstract
The iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans involves various metalloenzymes. Here we demonstrate that the oxygen reduction pathway from ferrous iron (named downhill pathway) is organized as a supercomplex constituted of proteins located in the outer and inner membranes as well as in the periplasm. For the first time, the outer membrane-bound cytochrome c Cyc2 was purified, and we showed that it is responsible for iron oxidation and determined that its redox potential is the highest measured to date for a cytochrome c. The organization of metalloproteins inside the supramolecular structure was specified by protein-protein interaction experiments. The isolated complex spanning the two membranes had iron oxidase as well as oxygen reductase activities, indicating functional electron transfer between the first iron electron acceptor, Cyc2, and the CuA center of cytochrome c oxidase aa3. This is the first characterization of a respirasome from an acidophilic bacterium. In Acidithiobacillus ferrooxidans,O2 reduction from ferrous iron must be coupled to the energy-consuming reduction of NAD+(P) from ferrous iron (uphill pathway) required for CO2 fixation and other anabolic processes. Besides the proteins involved in the O2 reduction, there were additional proteins in the supercomplex, involved in uphill pathway (bc complex and cytochrome Cyc42), suggesting a possible physical link between these two pathways.
- Published
- 2008
25. Expression of terminal oxidases under nutrient-starved conditions in Shewanella oneidensis: detection of the A-type cytochrome c oxidase
- Author
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Sébastien Le Laz, Myriam Brugna, Marielle Bauzan, Marc Rousset, Sabrina Lignon, Arlette Kpebe, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Microbiologie de la Méditerranée (IMM), Plateforme Protéomique [Marseille], and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,Shewanella ,[SDV]Life Sciences [q-bio] ,Gene Expression Regulation, Enzymologic ,Article ,Electron Transport Complex IV ,03 medical and health sciences ,Nutrient ,Oxygen Consumption ,MESH: Bacterial physiology Enzymes ,Bacterial Proteins ,Respiration ,Cytochrome c oxidase ,Shewanella oneidensis ,Gene ,chemistry.chemical_classification ,Oxidase test ,Multidisciplinary ,biology ,Cytochrome c ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,030104 developmental biology ,Enzyme ,Biochemistry ,chemistry ,biology.protein - Abstract
Shewanella species are facultative anaerobic bacteria that colonize redox-stratified habitats where O2 and nutrient concentrations fluctuate. The model species Shewanella oneidensis MR-1 possesses genes coding for three terminal oxidases that can perform O2 respiration: a bd-type quinol oxidase and cytochrome c oxidases of the cbb3-type and the A-type. Whereas the bd- and cbb3-type oxidases are routinely detected, evidence for the expression of the A-type enzyme has so far been lacking. Here, we investigated the effect of nutrient starvation on the expression of these terminal oxidases under different O2 tensions. Our results reveal that the bd-type oxidase plays a significant role under nutrient starvation in aerobic conditions. The expression of the cbb3-type oxidase is also modulated by the nutrient composition of the medium and increases especially under iron-deficiency in exponentially growing cells. Most importantly, under conditions of carbon depletion, high O2 and stationary-growth, we report for the first time the expression of the A-type oxidase in S. oneidensis, indicating that this terminal oxidase is not functionally lost. The physiological role of the A-type oxidase in energy conservation and in the adaptation of S. oneidensis to redox-stratified environments is discussed.
- Published
- 2015
26. The aerobic respiratory chain of the acidophilic archaeon Ferroplasma acidiphilum: A membrane-bound complex oxidizing ferrous iron
- Author
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Magali Roger, Sabrina Lignon, Marielle Bauzan, Marianne Guiral, Olga V. Golyshina, Myriam Brugna, Manfred Nimtz, Marie-Thérèse Giudici-Orticoni, Cindy J. Castelle, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Microbiologie de la Méditerranée (IMM), Plateforme Protéomique [Marseille], Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Centre for Infection Research (HZI), School of Biological Sciences [Bangor], and Bangor University
- Subjects
Cytochrome ,Ferroplasma ,Archaeal Proteins ,[SDV]Life Sciences [q-bio] ,Biophysics ,Respiratory chain ,Biomining ,Thermoplasmales ,Iron oxidation pathway ,Biochemistry ,Cytochrome oxidase ,Ferrous ,Sulfocyanin ,Electron Transport ,Electron Transport Complex IV ,Acidophilic archaea ,Operon ,Cytochrome c oxidase ,Cytochrome ba complex ,Ferrous Compounds ,biology ,Ferroplasma acidiphilum ,Cell Membrane ,Cell Biology ,biology.organism_classification ,Aerobiosis ,Oxygen ,Multiprotein Complexes ,Rieske protein ,biology.protein ,Acids ,Oxidation-Reduction - Abstract
International audience; The extremely acidophilic archaeon Ferroplasma acidiphilum is found in iron-rich biomining environments and is an important micro-organism in naturally occurring microbial communities in acid mine drainage. F. acidiphilum is an iron oxidizer that belongs to the order Thermoplasmatales (Euryarchaeota), which harbors the most extremely acidophilic micro-organisms known so far. At present, little is known about the nature or the structural and functional organization of the proteins in F. acidiphilum that impact the iron biogeochemical cycle. We combine here biochemical and biophysical techniques such as enzyme purification, activity measurements, proteomics and spectroscopy to characterize the iron oxidation pathway(s) in F. acidiphilum. We isolated two respiratory membrane protein complexes: a 850 kDa complex containing an aa3-type cytochrome oxidase and a blue copper protein, which directly oxidizes ferrous iron and reduces molecular oxygen, and a 150 kDa cytochrome ba complex likely composed of a di-heme cytochrome and a Rieske protein. We tentatively propose that both of these complexes are involved in iron oxidation respiratory chains, functioning in the so-called uphill and downhill electron flow pathways, consistent with autotrophic life. The cytochrome ba complex could possibly play a role in regenerating reducing equivalents by a reverse (‘uphill’) electron flow. This study constitutes the first detailed biochemical investigation of the metalloproteins that are potentially directly involved in iron-mediated energy conservation in a member of the acidophilic archaea of the genus Ferroplasma
- Published
- 2015
27. The NADP-dependent [FeFe] hydrogenase Hnd from Desulfovibrio fructosovorans
- Author
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Carole Baffert, Arlette Kpebe, Sébastien Le Laz, Myriam Brugna, Chloé Guendon, Martino Benvenuti, Luisana Avilan, and Marc Rousset
- Subjects
Hydrogenase ,Chemistry ,Stereochemistry ,Biophysics ,Desulfovibrio fructosovorans ,Cell Biology ,Biochemistry - Published
- 2016
28. The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes
- Author
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Barbara Schoepp-Cothenet, Marie-Thérèse Giudici-Orticoni, Evelyne Lebrun, Myriam Brugna, Wolfgang Nitschke, and Frauke Baymann
- Subjects
Protein Conformation ,Coenzymes ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Cofactor ,Evolution, Molecular ,03 medical and health sciences ,Protein structure ,Bacterial Proteins ,Hydrogenase ,Species Specificity ,Phylogenetics ,Metalloproteins ,Phylogeny ,030304 developmental biology ,chemistry.chemical_classification ,Genetics ,0303 health sciences ,Bacteria ,biology ,Phylogenetic tree ,Pteridines ,Last universal ancestor ,030302 biochemistry & molecular biology ,Cytochrome b Group ,biology.organism_classification ,Archaea ,Enzymes ,Enzyme ,chemistry ,Evolutionary biology ,Ferritins ,biology.protein ,Energy Metabolism ,Oxidoreductases ,General Agricultural and Biological Sciences ,Molybdenum Cofactors ,Oxidation-Reduction ,Research Article - Abstract
Genome analyses and the resolution of three–dimensional structures have provided evidence in recent years for hitherto unexpected family relationships between redox proteins of very diverse enzymes involved in bioenergetic electron transport. Many of these enzymes appear in fact to be constructed from only a limited set of building blocks. Phylogenetic analysis of selected units from this ‘redox enzyme construction kit’ indicates an origin for several prominent bioenergetic enzymes that is very early, lying before the divergence of Bacteria and Archaea. Possible scenarios for the early evolution of selected complexes are proposed based on the obtained tree topologies.
- Published
- 2003
29. The cytoplasmic NADP-dependent [FeFe] hydrogenase Hnd from the sulfate-reducing bacterium Desulfovibrio fructosovorans: Study of the hnd operon expression
- Author
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Sébastien Le Laz, Myriam Brugna, Laure Fousson, Marc Rousset, and Arlette Kpebe
- Subjects
Hydrogenase ,biology ,Operon ,Chemistry ,Biophysics ,Desulfovibrio fructosovorans ,Cell Biology ,biology.organism_classification ,Biochemistry ,chemistry.chemical_compound ,Cytoplasm ,Sulfate ,Bacteria - Published
- 2014
- Full Text
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30. H2-dependent azoreduction by Shewanella oneidensis MR-1: involvement of secreted flavins and both [Ni–Fe] and [Fe–Fe] hydrogenases
- Author
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Arlette Kpebe, Jean Lorquin, Myriam Brugna, Sébastien Le Laz, Marc Rousset, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), MEB, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
- Subjects
Hydrogenase ,Flavin mononucleotide ,Amaranth ,Flavin group ,Applied Microbiology and Biotechnology ,03 medical and health sciences ,chemistry.chemical_compound ,Hyda ,[CHIM.ANAL]Chemical Sciences/Analytical chemistry ,Flavins ,Extracellular ,Shewanella oneidensis ,030304 developmental biology ,0303 health sciences ,biology ,030306 microbiology ,MR-1 ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,General Medicine ,Periplasmic space ,biology.organism_classification ,chemistry ,Biochemistry ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Biotechnology ,Hydrogen ,Azo dye - Abstract
International audience; In this paper, the hydrogen (H2)-dependent discoloration of azo dye amaranth by Shewanella oneidensis MR-1 was investigated. Experiments with hydrogenase-deficient strains demonstrated that periplasmic [Ni–Fe] hydrogenase (HyaB) and periplasmic [Fe–Fe] hydrogenase (HydA) are both respiratory hydrogenases of dissimilatory azoreduction in S. oneidensis MR-1. These findings suggest that HyaB and HydA can function as uptake hydrogenases that couple the oxidation of H2 to the reduction of amaranth to sustain cellular growth. This constitutes to our knowledge the first report of the involvement of [Fe-Fe] hydrogenase in a bacterial azoreduction process. Assays with respiratory inhibitors indicated that a menaquinone pool and different cytochromes were involved in the azoreduction process. High-performance liquid chromatography analysis revealed that flavin mononucleotide and riboflavin were secreted in culture supernatant by S. oneidensis MR-1 under H2-dependent conditions with concentration of 1.4 and 2.4 μmol g protein-1, respectively. These endogenous flavins were shown to significantly accelerate the reduction of amaranth at micromolar concentrations acting as electron shuttles between the cell surface and the extracellular azo dye. This work may facilitate a better understanding of the mechanisms of azoreduction by S. oneidensis MR-1 and may have practical applications for microbiological treatments of dye-polluted industrial effluents.
- Published
- 2014
31. A Biochemical Approach to Study the Role of the Terminal Oxidases in Aerobic Respiration in Shewanella oneidensis MR-1
- Author
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Arlette Kpebe, Sébastien Le Laz, Sabrina Lignon, Marc Rousset, Marielle Bauzan, Myriam Brugna, Bioénergétique et Ingénierie des Protéines (BIP ), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut de Microbiologie de la Méditerranée (IMM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Plateforme Protéomique [Marseille], Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and ANR-09-BIOE-0002,EngineeringH2Cyano,Ingénierie de la cyanobactérie modèle Synechocystis pour une meilleure photoproduction d'hydrogène(2009)
- Subjects
Shewanella ,Enzyme Metabolism ,lcsh:Medicine ,Biochemistry ,Plastid terminal oxidase ,chemistry.chemical_compound ,Microbial Physiology ,Gene Order ,Membrane proteins ,Shewanella oneidensis ,lcsh:Science ,Heme ,Oxidase test ,Hemoproteins ,Multidisciplinary ,biology ,Enzyme Classes ,Deletion mutagenesis ,Aerobiosis ,Oxygen Metabolism ,Enzymes ,[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,Multigene Family ,Oxidoreductases ,Research Article ,Heme binding ,Cell Respiration ,Electron donors ,Bioenergetics ,Microbiology ,Electron Transport Complex IV ,Absorption spectroscopy ,Cytochrome c oxidase ,Protein sequencing ,Biology ,Microbial Metabolism ,Enzyme Kinetics ,lcsh:R ,Cell Membrane ,Proteins ,Oxidoreductases, N-Demethylating ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,biology.organism_classification ,Enzyme Activation ,Transmembrane Proteins ,Oxygen ,Metabolism ,chemistry ,Sequence motif analysis ,biology.protein ,lcsh:Q ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Gene Deletion - Abstract
International audience; The genome of the facultative anaerobic γ-proteobacterium Shewanella oneidensis MR-1 encodes for three terminal oxidases: a bd-type quinol oxidase and two heme-copper oxidases, a A-type cytochrome c oxidase and a cbb3-type oxidase. In this study, we used a biochemical approach and directly measured oxidase activities coupled to mass-spectrometry analysis to investigate the physiological role of the three terminal oxidases under aerobic and microaerobic conditions. Our data revealed that the cbb3-type oxidase is the major terminal oxidase under aerobic conditions while both cbb3-type and bd-type oxidases are involved in respiration at low-O2 tensions. On the contrary, the low O2-affinity A-type cytochrome c oxidase was not detected in our experimental conditions even under aerobic conditions and would therefore not be required for aerobic respiration in S. oneidensis MR-1. In addition, the deduced amino acid sequence suggests that the A-type cytochrome c oxidase is a ccaa3-type oxidase since an uncommon extra-C terminal domain contains two c-type heme binding motifs. The particularity of the aerobic respiratory pathway and the physiological implication of the presence of a ccaa3-type oxidase in S. oneidensis MR-1 are discussed.
- Published
- 2014
32. Daddy, where did (PS)I come from?
- Author
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Frauke Baymann, Myriam Brugna, Ulrich Mühlenhoff, and Wolfgang Nitschke
- Subjects
Photosystem I ,Cyanobacteria ,Evolution ,Molecular Sequence Data ,Photosynthetic Reaction Center Complex Proteins ,Biophysics ,Bioenergetics ,Biology ,Biochemistry ,Protein Structure, Secondary ,Chlorobi ,Evolution, Molecular ,Botany ,Amino Acid Sequence ,RCI type reaction centre ,Photosynthesis ,Phylogeny ,Photosystem ,Bacteria ,Photosystem I Protein Complex ,Phylogenetic tree ,Electron transport ,Cell Biology ,biology.organism_classification ,Green Sulphur Bacteria ,Energy Metabolism ,Sequence Alignment ,Phylogenetic relationship - Abstract
The reacton centre I (RCI)-type photosystems from plants, cyano-, helio- and green sulphur bacteria are compared and the essential properties of an archetypal RCI are deduced. Species containing RCI-type photosystems most probably cluster together on a common branch of the phylogenetic tree. The predicted branching order is green sulphur, helio- and cyanobacteria. Striking similarities between RCI- and RCII-type photosystems recently became apparent in the three-dimensional structures of photosystem I (PSI), PSII and RCII. The phylogenetic relationship between all presently known photosystems is analysed suggesting (a) RCI as the ancestral photosystem and (b) the descendence of PSII from RCI via gene duplication and gene splitting. An evolutionary model trying to rationalise available data is presented.
- Published
- 2001
33. Redox Components of Cytochrome bc-type Enzymes in Acidophilic Prokaryotes
- Author
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Wolfgang Nitschke, Bruno Guigliarelli, Myriam Brugna, Marcel Asso, Christian L. Schmidt, and Danielle Lemesle-Meunier
- Subjects
chemistry.chemical_classification ,Cytochrome ,biology ,Acid resistance ,Cell Biology ,Biochemistry ,Redox ,law.invention ,Enzyme ,Membrane ,chemistry ,law ,Redox titration ,biology.protein ,Rieske protein ,Electron paramagnetic resonance ,Molecular Biology - Abstract
The Rieske proteins of two phylogenetically distant acidophilic organisms, i.e. the proteobacteriumThiobacillus ferrooxidans and the crenarchaeonSulfolobus acidocaldarius, were studied by EPR. Redox titrations at a range of pH values showed that the Rieske centers of both organisms are characterized by redox midpoint potential-versus-pH curves featuring a common pK value of 6.2. This pK value is significantly more acidic (by almost 2 pH units) than that of Rieske proteins in neutrophilic species. The orientations of the Rieske center’s g tensors with respect to the plane of the membrane were studied between pH 4 and 8 using partially ordered samples. At pH 4, theSulfolobus Rieske cluster was found in the “typical” orientation of chemically reduced Rieske centers, whereas this orientation changed significantly on going toward high pH values. TheThiobacillus protein, by contrast, appeared to be in the “standard” orientation at both low and high pH values. The results are discussed with respect to the molecular parameters conveying acid resistance and in light of the recently demonstrated long-range conformational movement of the Rieske protein during enzyme turnover in cytochrome bc 1 complexes.
- Published
- 1999
34. The Qo-site inhibitor DBMIB favours the proximal position of the chloroplast Rieske protein and induces a pK-shift of the redox-linked proton
- Author
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Astrid Riedel, Barbara Schoepp, Wolfgang Nitschke, Myriam Brugna, and David Kramer
- Subjects
Iron-Sulfur Proteins ,Chloroplasts ,Cytochrome ,Stereochemistry ,Biophysics ,Ascorbic Acid ,Biochemistry ,Redox ,law.invention ,Electron Transport Complex III ,chemistry.chemical_compound ,Rieske ,Structural Biology ,law ,Genetics ,Electron paramagnetic resonance ,Molecular Biology ,Heme ,Rieske protein’s domain movement ,Binding Sites ,biology ,Chemistry ,Electron Spin Resonance Spectroscopy ,Substrate (chemistry) ,Cell Biology ,Cytochrome b Group ,Quinone ,Chloroplast ,Crystallography ,Cytochrome b6f Complex ,Dibromothymoquinone ,Redox-linked proton ,DBMIB ,biology.protein ,Rieske protein ,EPR ,Protons ,Oxidation-Reduction - Abstract
The interaction of the inhibitor 2,5-dibromo-3-methyl-6-isopropylbenzoquinone (DBMIB) with the Rieske protein of the chloroplast b6f complex has been studied by EPR. All three redox states of DBMIB were found to interact with the iron-sulphur cluster. The presence of the oxidised form of DBMIB altered the equilibrium distribution of the Rieske protein’s conformational substates, strongly favouring the proximal position close to heme bL. In addition to this conformational effect, DBMIB shifted the pK-value of the redox-linked proton involved in the iron-sulphur cluster’s redox transition by about 1.5 pH units towards more acidic values. The implications of these results with respect to the interaction of the native quinone substrate and the Rieske cluster in cytochrome bc complexes are discussed.
- Published
- 1999
35. H₂-dependent azoreduction by Shewanella oneidensis MR-1: involvement of secreted flavins and both [Ni-Fe] and [Fe-Fe] hydrogenases
- Author
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Sébastien, Le Laz, Arlette, Kpebe, Jean, Lorquin, Myriam, Brugna, and Marc, Rousset
- Subjects
Iron-Sulfur Proteins ,Shewanella ,Amaranth Dye ,Amaranthus ,Hydrogenase ,Flavins ,Electrons ,Oxidation-Reduction ,Chromatography, High Pressure Liquid - Abstract
In this paper, the hydrogen (H2)-dependent discoloration of azo dye amaranth by Shewanella oneidensis MR-1 was investigated. Experiments with hydrogenase-deficient strains demonstrated that periplasmic [Ni-Fe] hydrogenase (HyaB) and periplasmic [Fe-Fe] hydrogenase (HydA) are both respiratory hydrogenases of dissimilatory azoreduction in S. oneidensis MR-1. These findings suggest that HyaB and HydA can function as uptake hydrogenases that couple the oxidation of H2 to the reduction of amaranth to sustain cellular growth. This constitutes to our knowledge the first report of the involvement of [Fe-Fe] hydrogenase in a bacterial azoreduction process. Assays with respiratory inhibitors indicated that a menaquinone pool and different cytochromes were involved in the azoreduction process. High-performance liquid chromatography analysis revealed that flavin mononucleotide and riboflavin were secreted in culture supernatant by S. oneidensis MR-1 under H2-dependent conditions with concentration of 1.4 and 2.4 μmol g protein(-1), respectively. These endogenous flavins were shown to significantly accelerate the reduction of amaranth at micromolar concentrations acting as electron shuttles between the cell surface and the extracellular azo dye. This work may facilitate a better understanding of the mechanisms of azoreduction by S. oneidensis MR-1 and may have practical applications for microbiological treatments of dye-polluted industrial effluents.
- Published
- 2013
36. Hydrogen metabolism in the sulfate-reducing bacterium Desulfovibrio fructosovorans : Involvement of an alcohol dehydrogenase
- Author
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Laure Fousson, Arlette Kpebe, Julien Ros, Myriam Brugna, Chloé Guendon, and Marc Rousset
- Subjects
biology ,Hydrogen ,020209 energy ,Biophysics ,chemistry.chemical_element ,Desulfovibrio fructosovorans ,02 engineering and technology ,Cell Biology ,Metabolism ,biology.organism_classification ,Biochemistry ,chemistry.chemical_compound ,chemistry ,0202 electrical engineering, electronic engineering, information engineering ,biology.protein ,Sulfate ,Bacteria ,Alcohol dehydrogenase - Published
- 2016
37. The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus
- Author
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Marianne Guiral, Régine Lebrun, Marie-Thérèse Giudici-Orticoni, Myriam Brugna, Laurence Prunetti, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Plateforme Protéomique [Marseille], Institut de Microbiologie de la Méditerranée (IMM), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Proteomics ,Enzyme Metabolism ,lcsh:Medicine ,sequence motif analysis ,Biochemistry ,Energy-Producing Processes ,Sequence alignment ,Sequencing ,lcsh:Science ,Peptide sequence ,0303 health sciences ,Multidisciplinary ,biology ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Enzyme Classes ,Cytochrome c ,030302 biochemistry & molecular biology ,Sequence analysis ,Thermus thermophilus ,Oxygen Metabolism ,Enzymes ,Transmembrane domain ,Multiple alignment calculation ,Oxidoreductases ,Research Article ,Protein subunit ,Molecular Sequence Data ,Heme ,Bioenergetics ,Microbiology ,Cytochrome oxidase ,03 medical and health sciences ,Bacterial Proteins ,Cytochrome c oxidase ,Amino Acid Sequence ,Biology ,030304 developmental biology ,Microbial Metabolism ,Aquifex aeolicus ,lcsh:R ,Proteins ,biology.organism_classification ,Hyperthermophile ,Transmembrane Proteins ,Protein Subunits ,Metabolism ,Enzyme Structure ,biology.protein ,lcsh:Q ,Genome annotation - Abstract
International audience; The reduction of molecular oxygen to water is catalyzed by complicated membrane-bound metallo-enzymes containing variable numbers of subunits, called cytochrome c oxidases or quinol oxidases. We previously described the cytochrome c oxidase II from the hyperthermophilic bacterium Aquifex aeolicus as a ba3-type two-subunit (subunits I and II) enzyme and showed that it is included in a supercomplex involved in the sulfide-oxygen respiration pathway. It belongs to the B-family of the heme-copper oxidases, enzymes that are far less studied than the ones from family A. Here, we describe the presence in this enzyme of an additional transmembrane helix “subunit IIa”, which is composed of 41 amino acid residues with a measured molecular mass of 5105 Da. Moreover, we show that subunit II, as expected, is in fact longer than the originally annotated protein (from the genome) and contains a transmembrane domain. Using Aquifex aeolicus genomic sequence analyses, N-terminal sequencing, peptide mass fingerprinting and mass spectrometry analysis on entire subunits, we conclude that the B-type enzyme from this bacterium is a three-subunit complex. It is composed of subunit I (encoded by coxA2) of 59000 Da, subunit II (encoded by coxB2) of 16700 Da and subunit IIa which contain 12, 1 and 1 transmembrane helices respectively. A structural model indicates that the structural organization of the complex strongly resembles that of the ba3 cytochrome c oxidase from the bacterium Thermus thermophilus, the IIa helical subunit being structurally the lacking N-terminal transmembrane helix of subunit II present in the A-type oxidases. Analysis of the genomic context of genes encoding oxidases indicates that this third subunit is present in many of the bacterial oxidases from B-family, enzymes that have been described as two-subunit complexes.
- Published
- 2011
38. Original Design of an Oxygen-Tolerant [NiFe] Hydrogenase: Major Effect of a Valine-to-Cysteine Mutation near the Active Site
- Author
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Sébastien Dementin, Pierre Richaud, Antonio L. De Lacey, Victor M. Fernandez, Christophe Léger, Bruno Guigliarelli, Bénédicte Burlat, Pierre-Pol Liebgott, Myriam Brugna, Laurent Cournac, Marc Rousset, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), instituto de Catalysis y Petroleoquimica (ICP), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Biologie cellulaire et moléculaire des plantes et des bactéries (BCMPB), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Environnement, Bioénergie, Microalgues et Plantes (EBMP), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de la Méditerranée - Aix-Marseille 2, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Bioénergie et Microalgues (EBM), and Azzopardi, Laure
- Subjects
Models, Molecular ,Mutant ,01 natural sciences ,Biochemistry ,Colloid and Surface Chemistry ,Catalytic Domain ,Electrochemistry ,Anaerobiosis ,ComputingMilieux_MISCELLANEOUS ,chemistry.chemical_classification ,Carbon Monoxide ,0303 health sciences ,biology ,Valine ,Aerobiosis ,Thermodynamics ,Desulfovibrio ,Oxidation-Reduction ,[CHIM.INOR] Chemical Sciences/Inorganic chemistry ,Hydrogenase ,Stereochemistry ,Inorganic chemistry ,Protonation ,[CHIM.INOR]Chemical Sciences/Inorganic chemistry ,010402 general chemistry ,Catalysis ,03 medical and health sciences ,Gram-Negative Bacteria ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Cysteine ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,030304 developmental biology ,Aquifex aeolicus ,Spectrum Analysis ,Cell Membrane ,Deuterium Exchange Measurement ,Active site ,General Chemistry ,biology.organism_classification ,0104 chemical sciences ,Enzyme Activation ,Oxygen ,Kinetics ,Enzyme ,chemistry ,Mutation ,biology.protein ,Hydrogen - Abstract
Hydrogenases are efficient biological catalysts of H(2) oxidation and production. Most of them are inhibited by O(2), and a prerequisite for their use in biotechnological applications under air is to improve their oxygen tolerance. We have previously shown that exchanging the residue at position 74 in the large subunit of the oxygen-sensitive [NiFe] hydrogenase from Desulfovibrio fructosovorans could impact the reaction of the enzyme with O(2) (Dementin, S.; J. Am. Chem. Soc. 2009, 131, 10156-10164; Liebgott, P. P.; Nat. Chem. Biol. 2010, 6, 63-70). This residue, a valine in the wild-type enzyme, located at the bottleneck of the gas channel near the active site, has here been exchanged with a cysteine. A thorough characterization using a combination of kinetic, spectroscopic (EPR, FTIR), and electrochemical studies demonstrates that the V74C mutant has features of the naturally occurring oxygen-tolerant membrane-bound hydrogenases (MBH). The mutant is functional during several minutes under O(2), has impaired H(2)-production activity, and has a weaker affinity for CO than the WT. Upon exposure to O(2), it is converted into the more easily reactivatable inactive form, Ni-B, and this inactive state reactivates about 20 times faster than in the WT enzyme. Control experiments carried out with the V74S and V74N mutants indicate that protonation of the position 74 residue is not the reason the mutants reactivate faster than the WT enzyme. The electrochemical behavior of the V74C mutant toward O(2) is intermediate between that of the WT enzyme from D. fructosovorans and the oxygen-tolerant MBH from Aquifex aeolicus.
- Published
- 2011
39. The aerobic respiratory chain of the extremely acidophilic iron-oxidizing archaeon Ferroplasma acidiphilum
- Author
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Magali Roger, Marianne Guiral, Cindy J. Castelle, Marielle Bauzan, Olga V. Golyshina, Myriam Brugna, and Marie-Thérèse Giudici-Orticoni
- Subjects
biology ,Ferroplasma acidiphilum ,Chemistry ,Oxidizing agent ,Respiratory chain ,Biophysics ,Cell Biology ,biology.organism_classification ,Biochemistry ,Microbiology - Published
- 2014
- Full Text
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40. Expression of terminal oxidases under nutrient-limited conditions in Shewanella oneidensis MR-1
- Author
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Arlette Kpebe, Marielle Bauzan, Sébastien Le Laz, Sabrina Lignon, Marc Rousset, and Myriam Brugna
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Biochemistry ,Terminal (electronics) ,biology ,Chemistry ,Biophysics ,Cell Biology ,Shewanella oneidensis ,biology.organism_classification - Published
- 2014
41. Aerobic respiration in Shewanella oneidensis MR-1
- Author
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Arlette Kpebe, Sébastien Le Laz, Marielle Bauzan, Sabrina Lignon, Marc Rousset, and Myriam Brugna
- Subjects
biology ,Cellular respiration ,Chemistry ,Biophysics ,Cell Biology ,Shewanella oneidensis ,biology.organism_classification ,Biochemistry ,Microbiology - Published
- 2014
42. New Functional Sulfide Oxidase-Oxygen Reductase Supercomplex in the Membrane of the Hyperthermophilic Bacterium Aquifex aeolicus*
- Author
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Marianne Guiral, Pascale Infossi, Christine Ebel, Myriam Brugna, Laurence Prunetti, Marie-Thérèse Giudici-Orticoni, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Azzopardi, Laure
- Subjects
Sulfide ,Sulfur metabolism ,Respiratory chain ,Bioenergetics ,Biochemistry ,Electron Transport ,Electron Transport Complex IV ,03 medical and health sciences ,Quinone Reductases ,Oxygen Consumption ,Bacterial Proteins ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Cytochrome c oxidase ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Oxidoreductases Acting on Sulfur Group Donors ,Hydrogen Sulfide ,Molecular Biology ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Aquifex aeolicus ,biology ,Bacteria ,Chemistry ,030302 biochemistry & molecular biology ,Electron Spin Resonance Spectroscopy ,Cell Biology ,biology.organism_classification ,Oxygen ,Spectrometry, Fluorescence ,Coenzyme Q – cytochrome c reductase ,biology.protein ,Spectrophotometry, Ultraviolet ,Oxidation-Reduction ,Hydrogen - Abstract
Aquifex aeolicus, a hyperthermophilic and microaerophilic bacterium, obtains energy for growth from inorganic compounds alone. It was previously proposed that one of the respiratory pathways in this organism consists of the electron transfer from hydrogen sulfide (H(2)S) to molecular oxygen. H(2)S is oxidized by the sulfide quinone reductase, a membrane-bound flavoenzyme, which reduces the quinone pool. We have purified and characterized a novel membrane-bound multienzyme supercomplex that brings together all the molecular components involved in this bioenergetic chain. Our results indicate that this purified structure consists of one dimeric bc(1) complex (complex III), one cytochrome c oxidase (complex IV), and one or two sulfide quinone reductases as well as traces of the monoheme cytochrome c(555) and quinone molecules. In addition, this work strongly suggests that the cytochrome c oxidase in the supercomplex is a ba(3)-type enzyme. The supercomplex has a molecular mass of about 350 kDa and is enzymatically functional, reducing O(2) in the presence of the electron donor, H(2)S. This is the first demonstration of the existence of such a respirasome carrying a sulfide oxidase-oxygen reductase activity. Moreover, the kinetic properties of the sulfide quinone reductase change slightly when integrated in the supercomplex, compared with the free enzyme. We previously purified a complete respirasome involved in hydrogen oxidation and sulfur reduction from Aquifex aeolicus. Thus, two different bioenergetic pathways (sulfur reduction and sulfur oxidation) are organized in this bacterium as supramolecular structures in the membrane. A model for the energetic sulfur metabolism of Aquifex aeolicus is proposed.
- Published
- 2010
43. Aquifex aeolicus membrane Hydrogenase for hydrogen biooxidation: role of lipids and physiological partners in enzyme stability and activity
- Author
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Myriam Brugna, Pascale Infossi, Jean-Paul Chauvin, Marie-Thérèse Giudici-Orticoni, Gaëtan Herbette, Elisabeth Lojou, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université de la Méditerranée - Aix-Marseille 2, Institut de Biologie du Développement de Marseille (IBDM), Spectropôle - Aix Marseille Université (AMU SPEC), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
- Subjects
Hydrogenase ,Energy Engineering and Power Technology ,Hydrogenase mimic ,010402 general chemistry ,01 natural sciences ,03 medical and health sciences ,Oxidation ,PIEnergie ,Biohydrogen ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Aquifex aeolicus ,biology ,Renewable Energy, Sustainability and the Environment ,Chemistry ,Fuel cell ,Membrane ,Condensed Matter Physics ,biology.organism_classification ,High temperature ,Combinatorial chemistry ,0104 chemical sciences ,Quinone ,Fuel Technology ,Enzyme ,Biochemistry ,Electrochemical properties ,Aquifex ,Oxidoreductases ,Stability ,Hydrogen - Abstract
Hydrogenase I from the hyperthermophilic bacterium Aquifex aeolicus is a good candidate for biotechnological devices thanks to its ability to oxidize hydrogen at high temperature, even in the presence of oxygen and CO. In order to enhance the enzyme stability and the catalytic efficiency, we investigated the hydrogen oxidation process with hydrogenase I embedded in a physiological-like environment. Hydrogenase I partners in the metabolic chain, namely membrane quinone and cytochrome b, were purified and fully characterized. The complex hydrogenase I–cytochrome b was inserted into liposomes. Surface Plasmon Resonance revealed that quinone took part in the stabilization of the complex. By use of molecular modelization and electrochemistry analysis, enzyme stability has been demonstrated to be stronger and enzymatic efficiency to be five times higher when hydrogenase is embedded into the liposomes. This result raises the possibility of using hydrogenases as biocatalysts in fuel cells.
- Published
- 2010
44. Biocatalysts for fuel cells : efficient hydrogenase orientation for H2 oxidation at electrodes modified with carbon nanotubes
- Author
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Myriam Brugna, X. Luo, Sébastien Dementin, Nadine Candoni, Marie-Thérèse Giudici-Orticoni, Elisabeth Lojou, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Cinam, Hal, Centre de recherche de la matière condensée et des nanosciences (CRMCN), and Université de la Méditerranée - Aix-Marseille 2-Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Hydrogenase ,Bioelectric Energy Sources ,Surface Properties ,Inorganic chemistry ,02 engineering and technology ,Carbon nanotube ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Catalysis ,law.invention ,Inorganic Chemistry ,Electron transfer ,Adsorption ,law ,Electrochemistry ,Pyrolytic carbon ,Electrodes ,Voltammetry ,ComputingMilieux_MISCELLANEOUS ,Nanotubes, Carbon ,Chemistry ,Enzymes, Immobilized ,021001 nanoscience & nanotechnology ,Carbon ,0104 chemical sciences ,Chemical engineering ,Electrode ,Biocatalysis ,Desulfovibrio ,Gold ,0210 nano-technology ,Oxidation-Reduction ,Hydrogen - Abstract
We report the modification of gold and graphite electrodes with commercially available carbon nanotubes for immobilization of Desulfovibrio fructosovorans [NiFe] hydrogenase, for hydrogen evolution or consumption. Multiwalled carbon nanotubes, single-walled carbon nanotubes (SWCNs), and amine-modified and carboxyl-functionalized SWCNs were used and compared throughout. Two separate methods were performed: covalent attachment of oriented hydrogenase by controlled architecture of carbon nanotubes at gold electrodes, and adsorption of hydrogenase at carbon-nanotube-coated pyrolytic graphite electrodes. In the case of self-assembled carbon nanotubes at gold electrodes, hydrogenase orientation based on electrostatic interaction with the electrode surface was found to control the electrocatalytic process for H(2) oxidation. In the case of carbon nanotube coatings on pyrolytic graphite electrodes, catalysis was controlled more by the geometry of the nanotubes than by the orientation of the enzyme. Noticeably, shortened SWCNs were demonstrated to allow direct electron transfer and generate high and quite stable current densities for H(2) oxidation via adsorbed hydrogenase, despite having many carboxylic surface functions that could yield unfavorable hydrogenase orientation for direct electron transfer. This result is attributable to the high degree of oxygenated surface functions in addition to the length of shortened SWCNs that yields highly divided materials.
- Published
- 2008
45. The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction
- Author
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Barbara Schoepp-Cothenet, Wolfgang Nitschke, Myriam Brugna, Evelyne Lebrun, Anne-Lise Ducluzeau, Soufian Ouchane, Frauke Baymann, Joanne M. Santini, Institut de biologie structurale et microbiologie (IBSM), Université de la Méditerranée - Aix-Marseille 2-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Biology, University College of London [London] (UCL), Centre de génétique moléculaire (CGM), and Centre National de la Recherche Scientifique (CNRS)
- Subjects
Iron-Sulfur Proteins ,MESH: Protein Structure, Secondary ,MESH: Amino Acid Sequence ,Protein Structure, Secondary ,Electron Transport Complex III ,Protein structure ,MESH: Electron Transport Complex III ,MESH: Phylogeny ,Phylogeny ,Genetics ,0303 health sciences ,biology ,Phylogenetic tree ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,030302 biochemistry & molecular biology ,Cytochromes b ,MESH: Cytochromes b ,MESH: DNA Transposable Elements ,MESH: Sulfolobus ,Horizontal gene transfer ,Rieske protein ,Oxidoreductases ,Algorithms ,Gene Transfer, Horizontal ,Protein family ,Protein domain ,MESH: Sequence Alignment ,Sequence alignment ,MESH: Algorithms ,Computational biology ,Sulfolobus ,03 medical and health sciences ,Phylogenetics ,MESH: Genes, rRNA ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Amino Acid Sequence ,MESH: Oxidoreductases ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Bacteria ,Genes, rRNA ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,MESH: Iron-Sulfur Proteins ,MESH: Gene Transfer, Horizontal ,MESH: Bacteria ,MESH: Gene Deletion ,DNA Transposable Elements ,biology.protein ,Sequence Alignment ,Gene Deletion - Abstract
Previously published phylogenetic trees reconstructed on "Rieske protein" sequences frequently are at odds with each other, with those of other subunits of the parent enzymes and with small-subunit rRNA trees. These differences are shown to be at least partially if not completely due to problems in the reconstruction procedures. A major source of erroneous Rieske protein trees lies in the presence of a large, poorly conserved domain prone to accommodate very long insertions in well-defined structural hot spots substantially hampering multiple alignments. The remaining smaller domain, in contrast, is too conserved to allow distant phylogenies to be deduced with sufficient confidence. Three-dimensional structures of representatives from this protein family are now available from phylogenetically distant species and from diverse enzymes. Multiple alignments can thus be refined on the basis of these structures. We show that structurally guided alignments of Rieske proteins from Rieske-cytochrome b complexes and arsenite oxidases strongly reduce conflicts between resulting trees and those obtained on their companion enzyme subunits. Further problems encountered during this work, mainly consisting in database errors such as wrong annotations and frameshifts, are described. The obtained results are discussed against the background of hypotheses stipulating pervasive lateral gene transfer in prokaryotes.
- Published
- 2006
46. The three-dimensional structure of catalase from Enterococcus faecalis
- Author
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Kjell O. Håkansson, Lena Tasse, and Myriam Brugna
- Subjects
Models, Molecular ,Protein subunit ,Molecular Sequence Data ,Heme ,Crystallography, X-Ray ,Enterococcus faecalis ,Structural Biology ,Oxidoreductase ,Serine ,Molecular replacement ,Amino Acid Sequence ,Protein Structure, Quaternary ,chemistry.chemical_classification ,Binding Sites ,biology ,Chemistry ,Active site ,Hydrogen Bonding ,General Medicine ,biology.organism_classification ,Catalase ,Proteus mirabilis ,Crystallography ,biology.protein ,Solvents ,Peptides ,Sequence Alignment ,Homotetramer - Abstract
Enterococcus faecalis haem catalase was crystallized using lithium sulfate at neutral pH. The crystals belong to space group R3, with unit-cell parameters a = b = 236.9, c = 198.1 A. The three-dimensional structure was determined by molecular replacement using a subunit of the Proteus mirabilis catalase structure. It was refined against 2.3 A synchrotron data to a free R factor of 21.8%. Like other catalases, the E. faecalis catalase is a homotetramer with a fold and structure similar to those of its structurally closest relative P. mirabilis. The solvent structure in the active site is identical in the four subunits but differs from that found in other catalases. The structural consequences of the Ramachandran outlier Ser196 are discussed.
- Published
- 2004
47. Arsenite oxidase, an ancient bioenergetic enzyme
- Author
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Frauke Baymann, Wolfgang Nitschke, Evelyne Lebrun, Didier Lièvremont, Myriam Brugna, Marie-Claire Lett, Daniel Muller, Dynamique, évolution et expression de génomes de microorganismes (DEEGM), and Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Iron-Sulfur Proteins ,Models, Molecular ,MESH: Escherichia coli Proteins ,MESH: Amino Acid Sequence ,Formate dehydrogenase ,MESH: Membrane Transport Proteins ,Electron Transport Complex III ,MESH: Electron Transport Complex III ,Databases, Genetic ,MESH: Databases, Genetic ,Phylogeny ,chemistry.chemical_classification ,0303 health sciences ,biology ,Escherichia coli Proteins ,Chloroflexus aurantiacus ,MESH: Comparative Study ,Amino acid ,Transmembrane domain ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Biochemistry ,MESH: Archaea ,Oxidoreductases ,MESH: Models, Molecular ,Protein subunit ,Molecular Sequence Data ,Chloroflexus ,03 medical and health sciences ,Genetics ,Amino Acid Sequence ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,MESH: Molecular Sequence Data ,Bacteria ,030306 microbiology ,Spectrum Analysis ,MESH: Chloroflexus ,Membrane Transport Proteins ,MESH: Iron-Sulfur Proteins ,biology.organism_classification ,Molecular biology ,Archaea ,MESH: Bacteria ,Enzyme ,chemistry ,MESH: Oxidored ,Sequence Alignment - Abstract
Operons coding for the enzyme arsenite oxidase have been detected in the genomes from Archaea and Bacteria by Blast searches using the amino acid sequences of the respective enzyme characterized in two different beta-proteobacteria as templates. Sequence analyses show that in all these species, arsenite oxidase is transported over the cytoplasmic membrane via the tat system and most probably remains membrane attached by an N-terminal transmembrane helix of the Rieske subunit. The biochemical and biophysical data obtained for arsenite oxidase in the green filamentous bacterium Chloroflexus aurantiacus allow a structural model of the enzyme's membrane association to be proposed. Phylogenies for the two constituent subunits (i.e., the molybdopterin-containing and the Rieske subunit) of the heterodimeric enzyme and their respective homologs in DMSO-reductase, formate dehydrogenase, nitrate reductase, and the Rieske/cytb complexes were calculated from multiple sequence alignments. The obtained phylogenetic trees indicate an early origin of arsenite oxidase before the divergence of Archaea and Bacteria. Evolutionary implications of these phylogenies are discussed.
- Published
- 2003
48. The membrane-extrinsic domain of cytochrome b(558/566) from the archaeon Sulfolobus acidocaldarius performs pivoting movements with respect to the membrane surface
- Author
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Hannu Myllykallio, Frauke Baymann, Barbara Schoepp-Cothenet, Michael Schütz, Wolfgang Nitschke, Myriam Brugna, and Christian L. Schmidt
- Subjects
Sulfolobus acidocaldarius ,Cytochrome ,Protein Conformation ,Molecular Sequence Data ,Biophysics ,Cytochrome cy ,Biochemistry ,Redox ,law.invention ,Sulfolobus ,Electron Transport ,Electron transfer ,Cytochrome C1 ,Structural Biology ,law ,Genetics ,Amino Acid Sequence ,Electron paramagnetic resonance ,Molecular Biology ,biology ,Sequence Homology, Amino Acid ,Chemistry ,Cell Membrane ,Electron Spin Resonance Spectroscopy ,NADPH Oxidases ,Cell Biology ,biology.organism_classification ,Cytochrome b Group ,Protein Structure, Tertiary ,Crystallography ,Membrane ,biology.protein ,Archaeon ,Oxidation-Reduction ,Cytochrome b558/566 - Abstract
The orientation of the membrane-attached cytochrome b(558/566)-haem with respect to the membrane was determined by electron paramagnetic resonance spectroscopy on two-dimensionally ordered oxidised membrane fragments from Sulfolobus acidocaldarius. Unlike the other redox centres in the membrane, the cytochrome b(558/566)-haem was found to cover a range of orientations between 25 degrees and 90 degrees. The described results are reminiscent of those obtained on the Rieske cluster of bc complexes and indicate that the membrane-extrinsic domain of cytochrome b(558/566) can perform pivoting motion between two extreme positions. Such a conformational flexibility is likely to play a role in electron transfer with its redox partners.
- Published
- 2001
49. Enzymatic reduction of chromate: comparative studies using sulfate-reducing bacteria
- Author
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A. Bernadac, Corinne Aubert, Caroline Michel, Mireille Bruschi, Myriam Brugna, Bioénergétique et Ingénierie des Protéines (BIP ), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Hydrogenase ,Cytochrome ,biology ,Chromate conversion coating ,Chemistry ,[SDV]Life Sciences [q-bio] ,Desulfuromonas acetoxidans ,General Medicine ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Desulfovibrio ,Microbiology ,Biochemistry ,biology.protein ,Sulfate-reducing bacteria ,Desulfovibrio vulgaris ,Bacteria ,ComputingMilieux_MISCELLANEOUS ,Biotechnology - Abstract
Various sulfate-reducing bacteria of the genera Desulfovibrio and Desulfomicrobium were tested and compared for enzymatic reduction of chromate. Our study demonstrated that the ability to reduce chromate is widespread among sulfate-reducing bacteria. Among them, Desulfomicrobium norvegicum reduced Cr(VI) with the highest reaction rate. This strain grew in the presence of up to 500 μM chromate, but Cr(VI) reduction in the absence of sulfate was not associated with growth. The presence of chromate induced morphological changes and leakage of periplasmic proteins into the medium. The ability of isolated polyheme cytochromes c from sulfate- and sulfur-reducing bacteria to reduce chromate was also analyzed. Tetraheme cytochrome c3(Mr. 13,000) from Desulfomicrobium norvegicum showed twice as much activity as either tetraheme cytochrome c3 from Desulfovibrio vulgaris strain Hildenborough or triheme cytochrome c7 from Desulfuromonas acetoxidans. Results with cytochromes c3 and other c-type cytochromes altered by site-directed mutagenesis indicated that negative redox potential hemes are crucial for metal reductase activity. The present study also demonstrated that the (Fe) hydrogenase from sulfate-reducing bacteria could reduce chromate.
- Published
- 2001
50. Early evolution of cytochrome bc complexes
- Author
-
Evelyne Lebrun, René Toci, Danielle Lemesle-Meunier, Frauke Baymann, Wolfgang Nitschke, Christian L. Schmidt, Robert Huber, Günter Hauska, Michael Schütz, Myriam Brugna, Karl-Otto Stetter, and Pascale Tron
- Subjects
Cytochrome ,Protein subunit ,Molecular Sequence Data ,Sequence alignment ,Cyanobacteria ,Gram-Positive Bacteria ,Chlorobi ,Evolution, Molecular ,Electron Transport Complex III ,Structural Biology ,Phylogenetics ,Proteobacteria ,Amino Acid Sequence ,Molecular Biology ,Phylogeny ,Recombination, Genetic ,biology ,Phylogenetic tree ,Cytochrome b ,Ribosomal RNA ,Archaea ,Biochemistry ,Evolutionary biology ,Horizontal gene transfer ,biology.protein ,Sequence Alignment - Abstract
Primary structures, functional characteristics and phylogenetic relationships of subunits of cytochrome bc complexes from phylogenetically diverse bacterial and archaeal species were analysed. A single case of lateral gene transfer, i.e. the import of an epsilon-proteobacterial cytochrome bc(1) complex into Aquificales, was identified. For the enzyme in the remainder of the species studied, the obtained phylogenies were globally in line with small subunit rRNA trees. The distribution of a few key phylogenetic markers, such as contiguousness of cytochrome b, nature of the c-type subunit or spacing between b-heme ligands, are discussed. A localised modification of previous tree topologies is proposed on the basis of the obtained data. The comparison of extant enzymes furthermore allowed us to define the minimal functional and evolutionary core of the enzyme. The data furthermore suggest that the ancestral enzyme was put together from subunits that previously had played a role in other electron transfer chains.
- Published
- 2000
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