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Aldinio-Colbachini A, Grossi A, Duarte AG, Daurelle JV, Fourmond V. Combining a Commercial Mixer with a Wall-Tube Electrode Allows the Arbitrary Control of Concentrations in Protein Film Electrochemistry. Anal Chem 2024; 96:4868-4875. [PMID: 38466774 DOI: 10.1021/acs.analchem.3c05293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Protein film electrochemistry is a technique in which an enzyme is immobilized on an electrode in a configuration that allows following the changes in turnover frequency as a response to changes in the experimental conditions. Insights into the reactivity of the enzyme can be obtained by quantitatively modeling such responses. As a consequence, the more the technique allows flexibility in changing conditions, the more useful it becomes. The most commonly used setup, based on the rotating disc electrode, allows easy stepwise increases in the concentration of nongaseous substrates, or exposure to constant concentration of dissolved gas, but does not permit to easily decrease the concentration of nongaseous substrates, or to change the concentration of dissolved gas in a stepwise fashion. To overcome the limitation by mass transport of the substrate toward the electrode when working with fast enzymes, we have designed another kind of electrochemical cell based on the wall-tube electrode (WTE). We demonstrate here that by using a system combining two syringe pumps, a commercial mixer, and the WTE, it is possible to change the concentration of species in a stepwise fashion in all directions, opening new possibilities to study redox enzymes. As a proof of concept, this device was applied to the study of the electrochemical response of the cytochrome c nitrite reductase of Desulfovibrio desulfuricans.
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Affiliation(s)
- Anna Aldinio-Colbachini
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
- Laboratoire IUSTI (UMR AMU-CNRS 7343) Polytech Marseille, Dpt Mécanique Energétique (ME), Technopôle de Château Gombert, 5 rue Enrico Fermi, Marseille cedex 13 13453, France
| | - Alain Grossi
- Aix-Marseille Université, CNRS, IMM FR3479, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Jean-Vincent Daurelle
- Laboratoire IUSTI (UMR AMU-CNRS 7343) Polytech Marseille, Dpt Mécanique Energétique (ME), Technopôle de Château Gombert, 5 rue Enrico Fermi, Marseille cedex 13 13453, France
| | - Vincent Fourmond
- Aix-Marseille Université, CNRS, BIP UMR 7281, 31 Chemin J. AIGUIER, CS70071, Marseille Cedex 20 F-13402, France
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2
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Na S, Bauß A, Langenmaier M, Koslowski T. Thermodynamic integration network study of electron transfer: from proteins to aggregates. Phys Chem Chem Phys 2017; 19:18938-18947. [DOI: 10.1039/c7cp03030d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe electron transfer through the NrfHA nitrite reductase using a thermodynamic integration scheme. Driving forces are hardly affected by dimerization, but the transport mechanism only emerges simulating the dimer.
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Affiliation(s)
- Sehee Na
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Anna Bauß
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Michael Langenmaier
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
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3
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Bykov D, Neese F. Six-Electron Reduction of Nitrite to Ammonia by Cytochrome c Nitrite Reductase: Insights from Density Functional Theory Studies. Inorg Chem 2015; 54:9303-16. [DOI: 10.1021/acs.inorgchem.5b01506] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dmytro Bykov
- qLEAP Center
for Theoretical Chemistry, Department of Chemistry, Aarhus University, Gustav
Wieds Vej 10A, DK-8000 Aarhus C, Denmark
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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4
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Korte HL, Saini A, Trotter VV, Butland GP, Arkin AP, Wall JD. Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth. Environ Sci Technol 2015; 49:924-931. [PMID: 25534748 DOI: 10.1021/es504484m] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Sulfate-reducing microbes, such as Desulfovibrio vulgaris Hildenborough, cause “souring” of petroleum reservoirs through produced sulfide and precipitate heavy metals, either as sulfides or by alteration of the metal reduction state. Thus, inhibitors of these microbes, including nitrate and nitrite ions, are studied in order to limit their impact. Nitrite is a potent inhibitor of sulfate reducers, and it has been suggested that nitrate does not inhibit these microbes directly but by reduction to nitrite, which serves as the ultimate inhibitor. Here we provide evidence that nitrate inhibition of D. vulgaris can be independent of nitrite production. We also show that D. vulgaris can use nitrite as a nitrogen source or terminal electron acceptor for growth. Moreover, we report that use of nitrite as a terminal electron acceptor requires nitrite reductase (nrfA) as a D. vulgaris nrfA mutant cannot respire nitrite but remains capable of utilizing nitrite as a nitrogen source. These results illuminate previously uncharacterized metabolic abilities of D. vulgaris that may allow niche expansion in low-sulfate environments. Understanding these abilities may lead to better control of sulfate-reducing bacteria in industrial settings and more accurate prediction of their interactions in the environment.
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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6
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Youngblut M, Pauly DJ, Stein N, Walters D, Conrad JA, Moran GR, Bennett B, Pacheco AA. Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) does not disproportionate hydroxylamine to ammonia and nitrite, despite a strongly favorable driving force. Biochemistry 2014; 53:2136-44. [PMID: 24645742 DOI: 10.1021/bi401705d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c nitrite reductase (ccNiR) from Shewanella oneidensis, which catalyzes the six-electron reduction of nitrite to ammonia in vivo, was shown to oxidize hydroxylamine in the presence of large quantities of this substrate, yielding nitrite as the sole free nitrogenous product. UV-visible stopped-flow and rapid-freeze-quench electron paramagnetic resonance data, along with product analysis, showed that the equilibrium between hydroxylamine and nitrite is fairly rapidly established in the presence of high initial concentrations of hydroxylamine, despite said equilibrium lying far to the left. By contrast, reduction of hydroxylamine to ammonia did not occur, even though disproportionation of hydroxylamine to yield both nitrite and ammonia is strongly thermodynamically favored. This suggests a kinetic barrier to the ccNiR-catalyzed reduction of hydroxylamine to ammonia. A mechanism for hydroxylamine reduction is proposed in which the hydroxide group is first protonated and released as water, leaving what is formally an NH2(+) moiety bound at the heme active site. This species could be a metastable intermediate or a transition state but in either case would exist only if it were stabilized by the donation of electrons from the ccNiR heme pool into the empty nitrogen p orbital. In this scenario, ccNiR does not catalyze disproportionation because the electron-donating hydroxylamine does not poise the enzyme at a sufficiently low potential to stabilize the putative dehydrated hydroxylamine; presumably, a stronger reductant is required for this.
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Affiliation(s)
- Matthew Youngblut
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53211, United States
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7
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Abstract
The human gut microbiota plays a key role in pharmacology, yet the mechanisms responsible remain unclear, impeding efforts toward personalized medicine. We recently identified a cytochrome-encoding operon in the common gut Actinobacterium Eggerthella lenta that is transcriptionally activated by the cardiac drug digoxin. These genes represent a predictive microbial biomarker for the inactivation of digoxin. Gnotobiotic mouse experiments revealed that increased protein intake can limit microbial drug inactivation. Here, we present a biochemical rationale for how the proteins encoded by this operon might inactivate digoxin through substrate promiscuity. We discuss digoxin signaling in eukaryotic systems, and consider the possibility that endogenous digoxin-like molecules may have selected for microbial digoxin inactivation. Finally, we highlight the diverse contributions of gut microbes to drug metabolism, present a generalized approach to studying microbe-drug interactions, and argue that mechanistic studies will pave the way for the clinical application of this work.
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Affiliation(s)
- Henry J Haiser
- Faculty of Arts and Sciences (FAS) Center for Systems Biology; Harvard University; Cambridge, MA USA
| | - Kristen L Seim
- Department of Chemistry and Chemical Biology; Harvard University; Cambridge, MA USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology; Harvard University; Cambridge, MA USA
| | - Peter J Turnbaugh
- Faculty of Arts and Sciences (FAS) Center for Systems Biology; Harvard University; Cambridge, MA USA,Correspondence to: Peter J Turnbaugh,
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Bykov D, Plog M, Neese F. Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study. J Biol Inorg Chem 2014; 19:97-112. [DOI: 10.1007/s00775-013-1065-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/05/2013] [Indexed: 11/25/2022]
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9
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Heylen K, Keltjens J. Redundancy and modularity in membrane-associated dissimilatory nitrate reduction in Bacillus. Front Microbiol 2012; 3:371. [PMID: 23087684 PMCID: PMC3475470 DOI: 10.3389/fmicb.2012.00371] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/28/2012] [Indexed: 11/13/2022] Open
Abstract
The genomes of two phenotypically denitrifying type strains of the genus Bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed. Results suggest that denitrification proceeds in the periplasmic space and in an analogous fashion as in Gram-negative organisms, yet with the participation of proteins that tend to be membrane-bound or membrane-associated. A considerable degree of functional redundancy was observed with marked differences between B. azotoformans LMG 9581(T) and B. bataviensis LMG 21833(T). In addition to the already characterized menaquinol/cyt c-dependent nitric oxide reductase (Suharti et al., 2001, 2004) of which the encoding genes could be identified now, evidence for another novel nitric oxide reductase (NOR) was found. Also, our analyses confirm earlier findings on branched electron transfer with both menaquinol and cytochrome c as reductants. Quite unexpectedly, both bacilli have the disposal of two parallel pathways for nitrite reduction enabling a life style as a denitrifier and as an ammonifying bacterium.
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Affiliation(s)
- Kim Heylen
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, University of Ghent Gent, Belgium
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Youngblut M, Judd ET, Srajer V, Sayyed B, Goelzer T, Elliott SJ, Schmidt M, Pacheco AA. Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system. J Biol Inorg Chem 2012; 17:647-62. [PMID: 22382353 PMCID: PMC3412176 DOI: 10.1007/s00775-012-0885-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
Abstract
The high-yield expression and purification of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) and its characterization by a variety of methods, notably Laue crystallography, are reported. A key component of the expression system is an artificial ccNiR gene in which the N-terminal signal peptide from the highly expressed S. oneidensis protein "small tetraheme c" replaces the wild-type signal peptide. This gene, inserted into the plasmid pHSG298 and expressed in S. oneidensis TSP-1 strain, generated approximately 20 mg crude ccNiR per liter of culture, compared with 0.5-1 mg/L for untransformed cells. Purified ccNiR has nitrite and hydroxylamine reductase activities comparable to those previously reported for Escherichia coli ccNiR, and is stable for over 2 weeks in pH 7 solution at 4 °C. UV/vis spectropotentiometric titrations and protein film voltammetry identified five independent one-electron reduction processes. Global analysis of the spectropotentiometric data also allowed determination of the extinction coefficient spectra for the five reduced ccNiR species. The characteristics of the individual extinction coefficient spectra suggest that, within each reduced species, the electrons are distributed among the various hemes, rather than being localized on specific heme centers. The purified ccNiR yielded good-quality crystals, with which the 2.59-Å-resolution structure was solved at room temperature using the Laue diffraction method. The structure is similar to that of E. coli ccNiR, except in the region where the enzyme interacts with its physiological electron donor (CymA in the case of S. oneidensis ccNiR, NrfB in the case of the E. coli protein).
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Affiliation(s)
- Matthew Youngblut
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Evan T. Judd
- Department of Chemistry, 590 Commonwealth Ave., Boston, MA 02215
| | - Vukica Srajer
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Bilal Sayyed
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Tyler Goelzer
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Sean J. Elliott
- Department of Chemistry, 590 Commonwealth Ave., Boston, MA 02215
| | - Marius Schmidt
- Department of Physics, 1900 E. Kenwood Blvd, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - A. Andrew Pacheco
- Department of Chemistry and Biochemistry, 3210 N. Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
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11
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Bykov D, Neese F. Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study. J Biol Inorg Chem 2012; 17:741-60. [DOI: 10.1007/s00775-012-0893-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/05/2012] [Indexed: 01/08/2023]
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12
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Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A. Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biol 2011; 12:R99. [PMID: 21992415 PMCID: PMC3333781 DOI: 10.1186/gb-2011-12-10-r99] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 07/23/2011] [Accepted: 10/12/2011] [Indexed: 01/26/2023] Open
Abstract
Background Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems. Results We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study. Conclusions The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms.
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Affiliation(s)
- Lara Rajeev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Tikhonova TV, Slutskaya ES, Filimonenkov AA, Boyko KM, Kleimenov SY, Konarev PV, Polyakov KM, Svergun DI, Trofimov AA, Khomenkov VG, Zvyagilskaya RA, Popov VO. Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Biochemistry Moscow 2011; 73:164-70. [DOI: 10.1134/s0006297908020077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bykov D, Neese F. Substrate binding and activation in the active site of cytochrome c nitrite reductase: a density functional study. J Biol Inorg Chem 2010; 16:417-30. [DOI: 10.1007/s00775-010-0739-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 11/19/2010] [Indexed: 10/18/2022]
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Silveira CM, Besson S, Moura I, Moura JJ, Almeida MG. Measuring the cytochrome C nitrite reductase activity-practical considerations on the enzyme assays. Bioinorg Chem Appl 2010:634597. [PMID: 20689707 DOI: 10.1155/2010/634597] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Accepted: 05/03/2010] [Indexed: 11/20/2022] Open
Abstract
The cytochrome c nitrite reductase (ccNiR) from Desulfovibrio desulfuricans ATCC 27774 is
able to reduce nitrite to ammonia in a six-electron transfer reaction. Although extensively
characterized from the spectroscopic and structural points-of-view, some of its kinetic aspects
are still under explored. In this work the kinetic behaviour of ccNiR has been evaluated in a
systematic manner using two different spectrophotometric assays carried out in the presence of
different redox mediators and a direct electrochemical approach. Solution assays have proved
that the specific activity of ccNiR decreases with the reduction potential of the electronic carriers
and ammonium is always the main product of nitrite reduction. The catalytic parameters were
discussed on the basis of the mediator reducing power and also taking into account the location
of their putative docking sites with ccNiR. Due to the fast kinetics of ccNiR, electron delivering
from reduced electron donors is rate-limiting in all spectrophotometric assays, so the estimated
kinetic constants are apparent only. Nevertheless, this limitation could be overcome by using a
direct electrochemical approach which shows that the binding affinity for nitrite decreases whilst
turnover increases with the reductive driving force.
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16
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Polyakov KM, Boyko KM, Tikhonova TV, Slutsky A, Antipov AN, Zvyagilskaya RA, Popov AN, Bourenkov GP, Lamzin VS, Popov VO. High-Resolution Structural Analysis of a Novel Octaheme Cytochrome c Nitrite Reductase from the Haloalkaliphilic Bacterium Thioalkalivibrio nitratireducens. J Mol Biol 2009; 389:846-62. [DOI: 10.1016/j.jmb.2009.04.037] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 04/15/2009] [Accepted: 04/20/2009] [Indexed: 11/19/2022]
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Klotz MG, Schmid MC, Strous M, op den Camp HJM, Jetten MSM, Hooper AB. Evolution of an octahaem cytochromecprotein family that is key to aerobic and anaerobic ammonia oxidation by bacteria. Environ Microbiol 2008; 10:3150-63. [DOI: 10.1111/j.1462-2920.2008.01733.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rodrigues ML, Scott KA, Sansom MS, Pereira IA, Archer M. Quinol Oxidation by c-Type Cytochromes: Structural Characterization of the Menaquinol Binding Site of NrfHA. J Mol Biol 2008; 381:341-50. [DOI: 10.1016/j.jmb.2008.05.066] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/15/2008] [Accepted: 05/20/2008] [Indexed: 11/18/2022]
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Barton LL, Goulhen F, Bruschi M, Woodards NA, Plunkett RM, Rietmeijer FJM. The bacterial metallome: composition and stability with specific reference to the anaerobic bacterium Desulfovibrio desulfuricans. Biometals 2007; 20:291-302. [PMID: 17216357 DOI: 10.1007/s10534-006-9059-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 11/28/2006] [Indexed: 10/23/2022]
Abstract
In bacteria, the intracellular metal content or metallome reflects the metabolic requirements of the cell. When comparing the composition of metals in phytoplankton and bacteria that make up the macronutrients and the trace elements, we have determined that the content of trace elements in both of these microorganisms is markedly similar. The trace metals consisting of transition metals plus zinc are present in a stoichometric molar formula that we have calculated to be as follows: Fe(1)Mn(0.3)Zn(0.26)Cu(0.03)Co(0.03)Mo(0.03). Under conditions of routine cultivation, trace metal homeostasis may be maintained by a series of transporter systems that are energized by the cell. In specific environments where heavy metals are present at toxic levels, some bacteria have developed a detoxification strategy where the metallic ion is reduced outside of the cell. The result of this extracellular metabolism is that the bacterial metallome specific for trace metals is not disrupted. One of the microorganisms that reduces toxic metals outside of the cell is the sulfate-reducing bacterium Desulfovibrio desulfuricans. While D. desulfuricans reduces metals by enzymatic processes involving polyhemic cytochromes c3 and hydrogenases, which are all present inside the cell; we report the presence of chain B cytochrome c nitrite reductase, NrfA, in the outer membrane fraction of D. desulfuricans ATCC 27774 and discuss its activity as a metal reductase.
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Affiliation(s)
- Larry L Barton
- Department of Biology, Laboratory of Microbial Chemistry, University of New Mexico, MSC03 2020, Albuquerque, NM 87131-0001, USA.
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Almeida MG, Silveira CM, Guigliarelli B, Bertrand P, Moura JJG, Moura I, Léger C. A needle in a haystack: The active site of the membrane-bound complex cytochromecnitrite reductase. FEBS Lett 2006; 581:284-8. [PMID: 17207484 DOI: 10.1016/j.febslet.2006.12.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 12/07/2006] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
Cytochrome c nitrite reductase is a multicenter enzyme that uses a five-coordinated heme to perform the six-electron reduction of nitrite to ammonium. In the sulfate reducing bacterium Desulfovibrio desulfuricans ATCC 27774, the enzyme is purified as a NrfA2NrfH complex that houses 14 hemes. The number of closely-spaced hemes in this enzyme and the magnetic interactions between them make it very difficult to study the active site by using traditional spectroscopic approaches such as EPR or UV-Vis. Here, we use both catalytic and non-catalytic protein film voltammetry to simply and unambiguously determine the reduction potential of the catalytic heme over a wide range of pH and we demonstrate that proton transfer is coupled to electron transfer at the active site.
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Affiliation(s)
- M Gabriela Almeida
- REQUIMTE, CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516, Monte de Caparica, Portugal
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21
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Rodrigues ML, Oliveira TF, Pereira IAC, Archer M. X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination. EMBO J 2006; 25:5951-60. [PMID: 17139260 PMCID: PMC1698886 DOI: 10.1038/sj.emboj.7601439] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 10/10/2006] [Indexed: 11/09/2022] Open
Abstract
Oxidation of membrane-bound quinol molecules is a central step in the respiratory electron transport chains used by biological cells to generate ATP by oxidative phosphorylation. A novel family of cytochrome c quinol dehydrogenases that play an important role in bacterial respiratory chains was recognised in recent years. Here, we describe the first structure of a cytochrome from this family, NrfH from Desulfovibrio vulgaris, which forms a stable complex with its electron partner, the cytochrome c nitrite reductase NrfA. One NrfH molecule interacts with one NrfA dimer in an asymmetrical manner, forming a large membrane-bound complex with an overall alpha(4)beta(2) quaternary arrangement. The menaquinol-interacting NrfH haem is pentacoordinated, bound by a methionine from the CXXCHXM sequence, with an aspartate residue occupying the distal position. The NrfH haem that transfers electrons to NrfA has a lysine residue from the closest NrfA molecule as distal ligand. A likely menaquinol binding site, containing several conserved and essential residues, is identified.
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Affiliation(s)
- Maria Luisa Rodrigues
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, ITQB-UNL, Oeiras, Portugal
| | - Tânia F Oliveira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, ITQB-UNL, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, ITQB-UNL, Oeiras, Portugal
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, ITQB-UNL, Oeiras, Portugal
- Membrane Protein Crystallography, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, ITQB-UNL, Apt. 127, Av. Republica, EAN, Oeiras 2780-157, Portugal. Tel.: +351 214469762; Fax: +351 21433644; E-mail:
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