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Zorova LD, Pevzner IB, Khailova LS, Korshunova GA, Kovaleva MA, Kovalev LI, Serebryakova MV, Silachev DN, Sudakov RV, Zorov SD, Rokitskaya TI, Popkov VA, Plotnikov EY, Antonenko YN, Zorov DB. Mitochondrial ATP Synthase and Mild Uncoupling by Butyl Ester of Rhodamine 19, C4R1. Antioxidants (Basel) 2023; 12:antiox12030646. [PMID: 36978894 PMCID: PMC10044837 DOI: 10.3390/antiox12030646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The homeostasis of the transmembrane potential of hydrogen ions in mitochondria is a prerequisite for the normal mitochondrial functioning. However, in different pathological conditions it is advisable to slightly reduce the membrane potential, while maintaining it at levels sufficient to produce ATP that will ensure the normal functioning of the cell. A number of chemical agents have been found to provide mild uncoupling; however, natural proteins residing in mitochondrial membrane can carry this mission, such as proteins from the UCP family, an adenine nucleotide translocator and a dicarboxylate carrier. In this study, we demonstrated that the butyl ester of rhodamine 19, C4R1, binds to the components of the mitochondrial ATP synthase complex due to electrostatic interaction and has a good uncoupling effect. The more hydrophobic derivative C12R1 binds poorly to mitochondria with less uncoupling activity. Mass spectrometry confirmed that C4R1 binds to the β-subunit of mitochondrial ATP synthase and based on molecular docking, a C4R1 binding model was constructed suggesting the binding site on the interface between the α- and β-subunits, close to the anionic amino acid residues of the β-subunit. The association of the uncoupling effect with binding suggests that the ATP synthase complex can provide induced uncoupling.
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Affiliation(s)
- Ljubava D. Zorova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Irina B. Pevzner
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Ljudmila S. Khailova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Galina A. Korshunova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Marina A. Kovaleva
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Leonid I. Kovalev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Marina V. Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Denis N. Silachev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Roman V. Sudakov
- N.N. Blokhin Russian Cancer Research Center, 115478 Moscow, Russia
| | - Savva D. Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Tatyana I. Rokitskaya
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Vasily A. Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Egor Y. Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
- Correspondence: (E.Y.P.); (Y.N.A.); (D.B.Z.); Tel.: +7-495-939-5944 (E.Y.P.)
| | - Yuri N. Antonenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (E.Y.P.); (Y.N.A.); (D.B.Z.); Tel.: +7-495-939-5944 (E.Y.P.)
| | - Dmitry B. Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
- Correspondence: (E.Y.P.); (Y.N.A.); (D.B.Z.); Tel.: +7-495-939-5944 (E.Y.P.)
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Bogachev AV, Baykov AA, Bertsova YV, Mamedov MD. Mechanism of Ion Translocation by Na+-Rhodopsin. BIOCHEMISTRY (MOSCOW) 2022; 87:731-741. [DOI: 10.1134/s0006297922080053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Tuz K, Yuan M, Hu Y, Do TTT, Willow SY, DePaolo-Boisvert JA, Fuller JR, Minh DDL, Juárez O. Identification of the riboflavin-cofactor binding site in the Vibrio cholerae ion-pumping NQR complex: A novel structural motif in redox enzymes. J Biol Chem 2022; 298:102182. [PMID: 35752362 PMCID: PMC9293633 DOI: 10.1016/j.jbc.2022.102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/18/2022] Open
Abstract
The ion-pumping NQR complex is an essential respiratory enzyme in the physiology of many pathogenic bacteria. This enzyme transfers electrons from NADH to ubiquinone through several cofactors, including riboflavin (vitamin B2). NQR is the only enzyme reported that is able to use riboflavin as a cofactor. Moreover, the riboflavin molecule is found as a stable neutral semiquinone radical. The otherwise highly reactive unpaired electron is stabilized via an unknown mechanism. Crystallographic data suggested that riboflavin might be found in a superficially located site in the interface of NQR subunits B and E. However, this location is highly problematic, as the site does not have the expected physiochemical properties. In this work, we have located the riboflavin-binding site in an amphipathic pocket in subunit B, previously proposed to be the entry site of sodium. Here, we show that this site contains absolutely conserved residues, including N200, N203, and D346. Mutations of these residues decrease enzymatic activity and specifically block the ability of NQR to bind riboflavin. Docking analysis and molecular dynamics simulations indicate that these residues participate directly in riboflavin binding, establishing hydrogen bonds that stabilize the cofactor in the site. We conclude that riboflavin is likely bound in the proposed pocket, which is consistent with enzymatic characterizations, thermodynamic studies, and distance between cofactors.
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Affiliation(s)
- Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago IL
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago IL
| | - Yuyao Hu
- Department of Biological Sciences, Illinois Institute of Technology, Chicago IL
| | - Tien T T Do
- Department of Chemistry, Illinois Institute of Technology, Chicago IL
| | | | | | - James R Fuller
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago IL
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago IL.
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4
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Bordel S, Pérez R, Rodríguez E, Cantera S, Fernández-González N, Martínez MA, Muñoz R. Halotolerance mechanisms of the methanotroph Methylomicrobium alcaliphilum. Biotechnol Bioeng 2020; 117:3459-3474. [PMID: 32672837 DOI: 10.1002/bit.27506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/18/2020] [Accepted: 07/15/2020] [Indexed: 11/12/2022]
Abstract
Methylomicrobium alcaliphilum is an alkaliphilic and halotolerant methanotroph. The physiological responses of M. alcaliphilum to high NaCl concentrations, were studied using RNA sequencing and metabolic modeling. This study revealed that M. alcaliphilum possesses an unusual respiratory chain, in which complex I is replaced by a Na+ extruding NQR complex (highly upregulated under high salinity conditions) and a Na+ driven adenosine triphosphate (ATP) synthase coexists with a conventional H+ driven ATP synthase. A thermodynamic and metabolic model showing the interplay between these different components is presented. Ectoine is the main osmoprotector used by the cells. Ectoine synthesis is activated by the transcription of an ect operon that contains five genes, including the ectoine hydroxylase coding ectD gene. Enzymatic tests revealed that the product of ectD does not have catalytic activity. A new Genome Scale Metabolic Model for M. alcaliphilum revealed a higher flux in the oxidative branch of the pentose phosphate pathway leading to NADPH production and contributing to resistance to oxidative stress.
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Affiliation(s)
- Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Rebeca Pérez
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Elisa Rodríguez
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - Sara Cantera
- Laboratory of Microbiology, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Nuria Fernández-González
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
| | - María A Martínez
- Institute of Sustainable Processes, Valladolid, Spain.,PROIMI Planta Piloto de Procesos Industriales Microbiológicos, CONICET, San Miguel de Tucumán, Argentina.,Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Insdustrial Engineering, University of Valladolid, Valladolid, Spain.,Institute of Sustainable Processes, Valladolid, Spain
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5
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Maynard A, Butler NL, Ito T, da Silva AJ, Murai M, Chen T, Koffas MAG, Miyoshi H, Barquera B. Antibiotic Korormicin A Kills Bacteria by Producing Reactive Oxygen Species. J Bacteriol 2019; 201:e00718-18. [PMID: 30858300 PMCID: PMC6509656 DOI: 10.1128/jb.00718-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/07/2019] [Indexed: 11/20/2022] Open
Abstract
Korormicin is an antibiotic produced by some pseudoalteromonads which selectively kills Gram-negative bacteria that express the Na+-pumping NADH:quinone oxidoreductase (Na+-NQR.) We show that although korormicin is an inhibitor of Na+-NQR, the antibiotic action is not a direct result of inhibiting enzyme activity. Instead, perturbation of electron transfer inside the enzyme promotes a reaction between O2 and one or more redox cofactors in the enzyme (likely the flavin adenine dinucleotide [FAD] and 2Fe-2S center), leading to the production of reactive oxygen species (ROS). All Pseudoalteromonas contain the nqr operon in their genomes, including Pseudoalteromonas strain J010, which produces korormicin. We present activity data indicating that this strain expresses an active Na+-NQR and that this enzyme is not susceptible to korormicin inhibition. On the basis of our DNA sequence data, we show that the Na+-NQR of Pseudoalteromonas J010 carries an amino acid substitution (NqrB-G141A; Vibrio cholerae numbering) that in other Na+-NQRs confers resistance against korormicin. This is likely the reason that a functional Na+-NQR is able to exist in a bacterium that produces a compound that typically inhibits this enzyme and causes cell death. Korormicin is an effective antibiotic against such pathogens as Vibrio cholerae, Aliivibrio fischeri, and Pseudomonas aeruginosa but has no effect on Bacteroides fragilis and Bacteroides thetaiotaomicron, microorganisms that are important members of the human intestinal microflora.IMPORTANCE As multidrug antibiotic resistance in pathogenic bacteria continues to rise, there is a critical need for novel antimicrobial agents. An essential requirement for a useful antibiotic is that it selectively targets bacteria without significant effects on the eukaryotic hosts. Korormicin is an excellent candidate in this respect because it targets a unique respiratory enzyme found only in prokaryotes, the Na+-pumping NADH:quinone oxidoreductase (Na+-NQR). Korormicin is synthesized by some species of the marine bacterium Pseudoalteromonas and is a potent and specific inhibitor of Na+-NQR, an enzyme that is essential for the survival and proliferation of many Gram-negative human pathogens, including Vibrio cholerae and Pseudomonas aeruginosa, among others. Here, we identified how korormicin selectively kills these bacteria. The binding of korormicin to Na+-NQR promotes the formation of reactive oxygen species generated by the reaction of the FAD and the 2Fe-2S center cofactors with O2.
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Affiliation(s)
- Adam Maynard
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Nicole L Butler
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Takeshi Ito
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Adilson José da Silva
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
- Chemical Engineering Department, Federal University of Sao Carlos, Sao Paulo, Brazil
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tsute Chen
- The Forsyth Institute, Cambridge, Massachusetts, USA
- School of Dental Medicine, Harvard University, Boston, Massachusetts, USA
| | - Mattheos A G Koffas
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York, USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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Moradali MF, Ghods S, Angelini TE, Davey ME. Amino acids as wetting agents: surface translocation by Porphyromonas gingivalis. THE ISME JOURNAL 2019; 13:1560-1574. [PMID: 30783212 PMCID: PMC6775972 DOI: 10.1038/s41396-019-0360-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 02/06/2023]
Abstract
Our understanding of how oral microbiota adapt in response to changes in their surroundings remains limited. This is particularly true of the slow-growing anaerobes that persist below the gum line. Here, we report that the oral anaerobe Porphyromonas gingivalis strain 381 can surface translocate when sandwiched between two surfaces. We show that during movement, this bacterium alters its metabolism, specifically side products of arginine utilization including citrulline and ornithine accumulated in the translocating cells; while arginine, N-acetyl-arginine, and the polyamine putrescine, which is produced from arginine were consumed. In addition, our results indicate that movement requires modification of the surrounding environment via proteolysis, cell dispersion, cell-on-cell rolling, and sub-diffusive cell-driven motility. We also show that production of fimbriae and fimbriae-associated proteins; as well as the regulation of contact-dependent growth inhibition genes, which are known to be involved in self-nonself discrimination, and the type IX secretion system are central to surface translocation. These studies provide a first glimpse into P. gingivalis motility and its relationship to ecological variables.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA
| | - Shirin Ghods
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA
| | - Thomas E Angelini
- Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL, 32610, USA
| | - Mary Ellen Davey
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32610, USA.
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Ball J, Salvi F, Gadda G. Functional Annotation of a Presumed Nitronate Monoxygenase Reveals a New Class of NADH:Quinone Reductases. J Biol Chem 2016; 291:21160-21170. [PMID: 27502282 PMCID: PMC5076524 DOI: 10.1074/jbc.m116.739151] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 12/12/2022] Open
Abstract
The protein PA1024 from Pseudomonas aeruginosa PAO1 is currently classified as 2-nitropropane dioxygenase, the previous name for nitronate monooxygenase in the GenBankTM and PDB databases, but the enzyme was not kinetically characterized. In this study, PA1024 was purified to high levels, and the enzymatic activity was investigated by spectroscopic and polarographic techniques. Purified PA1024 did not exhibit nitronate monooxygenase activity; however, it displayed NADH:quinone reductase and a small NADH:oxidase activity. The enzyme preferred NADH to NADPH as a reducing substrate. PA1024 could reduce a broad spectrum of quinone substrates via a Ping Pong Bi Bi steady-state kinetic mechanism, generating the corresponding hydroquinones. The reductive half-reaction with NADH showed a kred value of 24 s-1 and an apparent Kd value estimated in the low micromolar range. The enzyme was not able to reduce the azo dye methyl red, routinely used in the kinetic characterization of azoreductases. Finally, we revisited and modified the existing six conserved motifs of PA1024, which define a new class of NADH:quinone reductases and are present in more than 490 hypothetical proteins in the GenBankTM, the vast majority of which are currently misannotated as nitronate monooxygenase.
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Affiliation(s)
| | | | - Giovanni Gadda
- From the Departments of Chemistry and Biology, Center for Biotechnology and Drug Design, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965
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NqrM (DUF539) Protein Is Required for Maturation of Bacterial Na+-Translocating NADH:Quinone Oxidoreductase. J Bacteriol 2015; 198:655-63. [PMID: 26644436 DOI: 10.1128/jb.00757-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/24/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) catalyzes electron transfer from NADH to ubiquinone in the bacterial respiratory chain, coupled with Na(+) translocation across the membrane. Na(+)-NQR maturation involves covalent attachment of flavin mononucleotide (FMN) residues, catalyzed by flavin transferase encoded by the nqr-associated apbE gene. Analysis of complete bacterial genomes has revealed another putative gene (duf539, here renamed nqrM) that usually follows the apbE gene and is present only in Na(+)-NQR-containing bacteria. Expression of the Vibrio harveyi nqr operon alone or with the associated apbE gene in Escherichia coli, which lacks its own Na(+)-NQR, resulted in an enzyme incapable of Na(+)-dependent NADH or reduced nicotinamide hypoxanthine dinucleotide (dNADH) oxidation. However, fully functional Na(+)-NQR was restored when these genes were coexpressed with the V. harveyi nqrM gene. Furthermore, nqrM lesions in Klebsiella pneumoniae and V. harveyi prevented production of functional Na(+)-NQR, which could be recovered by an nqrM-containing plasmid. The Na(+)-NQR complex isolated from the nqrM-deficient strain of V. harveyi lacks several subunits, indicating that nqrM is necessary for Na(+)-NQR assembly. The protein product of the nqrM gene, NqrM, contains a single putative transmembrane α-helix and four conserved Cys residues. Mutating one of these residues (Cys33 in V. harveyi NqrM) to Ser completely prevented Na(+)-NQR maturation, whereas mutating any other Cys residue only decreased the yield of the mature protein. These findings identify NqrM as the second specific maturation factor of Na(+)-NQR in proteobacteria, which is presumably involved in the delivery of Fe to form the (Cys)4[Fe] center between subunits NqrD and NqrE. IMPORTANCE Na(+)-translocating NADH:quinone oxidoreductase complex (Na(+)-NQR) is a unique primary Na(+) pump believed to enhance the vitality of many bacteria, including important pathogens such as Vibrio cholerae, Vibrio parahaemolyticus, Haemophilus influenzae, Neisseria gonorrhoeae, Pasteurella multocida, Porphyromonas gingivalis, Enterobacter aerogenes, and Yersinia pestis. Production of Na(+)-NQR in bacteria requires Na(+)-NQR-specific maturation factors. We earlier identified one such factor (ApbE) that covalently attaches flavin residues to Na(+)-NQR. Here we identify the other protein factor, designated NqrM, and show that NqrM and ApbE suffice to produce functional Na(+)-NQR from the Vibrio harveyi nqr operon. NqrM may be involved in Fe delivery to a unique Cys4[Fe] center during Na(+)-NQR assembly. Besides highlighting Na(+)-NQR biogenesis, these findings suggest a novel drug target to combat Na(+)-NQR-containing bacteria.
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Shea ME, Mezic KG, Juárez O, Barquera B. A mutation in Na(+)-NQR uncouples electron flow from Na(+) translocation in the presence of K(+). Biochemistry 2014; 54:490-6. [PMID: 25486106 DOI: 10.1021/bi501266e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The sodium-pumping NADH:ubiquinone oxidoreductase (Na(+)-NQR) is a bacterial respiratory enzyme that obtains energy from the redox reaction between NADH and ubiquinone and uses this energy to create an electrochemical Na(+) gradient across the cell membrane. A number of acidic residues in transmembrane helices have been shown to be important for Na(+) translocation. One of these, Asp-397 in the NqrB subunit, is a key residue for Na(+) uptake and binding. In this study, we show that when this residue is replaced with asparagine, the enzyme acquires a new sensitivity to K(+); in the mutant, K(+) both activates the redox reaction and uncouples it from the ion translocation reaction. In the wild-type enzyme, Na(+) (or Li(+)) accelerates turnover while K(+) alone does not activate. In the NqrB-D397N mutant, K(+) accelerates the same internal electron transfer step (2Fe-2S → FMNC) that is accelerated by Na(+). This is the same step that is inhibited in mutants in which Na(+) uptake is blocked. NqrB-D397N is able to translocate Na(+) and Li(+), but when K(+) is introduced, no ion translocation is observed, regardless of whether Na(+) or Li(+) is present. Thus, this mutant, when it turns over in the presence of K(+), is the first, and currently the only, example of an uncoupled Na(+)-NQR. The fact the redox reaction and ion pumping become decoupled from each other only in the presence of K(+) provides a switch that promises to be a useful experimental tool.
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Affiliation(s)
- Michael E Shea
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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10
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Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton ILG, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 2014; 15:924. [PMID: 25342549 PMCID: PMC4287430 DOI: 10.1186/1471-2164-15-924] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Symbioses between chemoautotrophic bacteria and marine invertebrates are rare examples of living systems that are virtually independent of photosynthetic primary production. These associations have evolved multiple times in marine habitats, such as deep-sea hydrothermal vents and reducing sediments, characterized by steep gradients of oxygen and reduced chemicals. Due to difficulties associated with maintaining these symbioses in the laboratory and culturing the symbiotic bacteria, studies of chemosynthetic symbioses rely heavily on culture independent methods. The symbiosis between the coastal bivalve, Solemya velum, and its intracellular symbiont is a model for chemosynthetic symbioses given its accessibility in intertidal environments and the ability to maintain it under laboratory conditions. To better understand this symbiosis, the genome of the S. velum endosymbiont was sequenced. RESULTS Relative to the genomes of obligate symbiotic bacteria, which commonly undergo erosion and reduction, the S. velum symbiont genome was large (2.7 Mb), GC-rich (51%), and contained a large number (78) of mobile genetic elements. Comparative genomics identified sets of genes specific to the chemosynthetic lifestyle and necessary to sustain the symbiosis. In addition, a number of inferred metabolic pathways and cellular processes, including heterotrophy, branched electron transport, and motility, suggested that besides the ability to function as an endosymbiont, the bacterium may have the capacity to live outside the host. CONCLUSIONS The physiological dexterity indicated by the genome substantially improves our understanding of the genetic and metabolic capabilities of the S. velum symbiont and the breadth of niches the partners may inhabit during their lifecycle.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jonathan A Eisen
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, 4081 Biological Laboratories, Cambridge, MA 02138, USA.
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Dittami SM, Barbeyron T, Boyen C, Cambefort J, Collet G, Delage L, Gobet A, Groisillier A, Leblanc C, Michel G, Scornet D, Siegel A, Tapia JE, Tonon T. Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae. Front Genet 2014; 5:241. [PMID: 25120558 PMCID: PMC4110880 DOI: 10.3389/fgene.2014.00241] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022] Open
Abstract
Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The “Ca. P. ectocarpi” genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, “Ca. P. ectocarpi” has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus “Phaeomarinobacter” may comprise several species, which may colonize different niches.
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Affiliation(s)
- Simon M Dittami
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Tristan Barbeyron
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Catherine Boyen
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Jeanne Cambefort
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Guillaume Collet
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Ludovic Delage
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Angélique Gobet
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Agnès Groisillier
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Catherine Leblanc
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Delphine Scornet
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Anne Siegel
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Javier E Tapia
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Thierry Tonon
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
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12
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Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase. PLoS One 2014; 9:e96696. [PMID: 24809444 PMCID: PMC4014512 DOI: 10.1371/journal.pone.0096696] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/11/2014] [Indexed: 11/27/2022] Open
Abstract
The sodium -pumping NADH: ubiquinone oxidoreductase (Na+-NQR) is the main ion pump and the primary entry site for electrons into the respiratory chain of many different types of pathogenic bacteria. This enzymatic complex creates a transmembrane gradient of sodium that is used by the cell to sustain ionic homeostasis, nutrient transport, ATP synthesis, flagellum rotation and other essential processes. Comparative genomics data demonstrate that the nqr operon, which encodes all Na+-NQR subunits, is found in a large variety of bacterial lineages with different habitats and metabolic strategies. Here we studied the distribution, origin and evolution of this enzymatic complex. The molecular phylogenetic analyses and the organizations of the nqr operon indicate that Na+-NQR evolved within the Chlorobi/Bacteroidetes group, after the duplication and subsequent neofunctionalization of the operon that encodes the homolog RNF complex. Subsequently, the nqr operon dispersed through multiple horizontal transfer events to other bacterial lineages such as Chlamydiae, Planctomyces and α, β, γ and δ -proteobacteria. Considering the biochemical properties of the Na+-NQR complex and its physiological role in different bacteria, we propose a detailed scenario to explain the molecular mechanisms that gave rise to its novel redox- dependent sodium -pumping activity. Our model postulates that the evolution of the Na+-NQR complex involved a functional divergence from its RNF homolog, following the duplication of the rnf operon, the loss of the rnfB gene and the recruitment of the reductase subunit of an aromatic monooxygenase.
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13
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Localization-controlled specificity of FAD:threonine flavin transferases in Klebsiella pneumoniae and its implications for the mechanism of Na(+)-translocating NADH:quinone oxidoreductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:1122-9. [PMID: 24361839 DOI: 10.1016/j.bbabio.2013.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/04/2013] [Accepted: 12/13/2013] [Indexed: 12/22/2022]
Abstract
The Klebsiella pneumoniae genome contains genes for two putative flavin transferase enzymes (ApbE1 and ApbE2) that add FMN to protein Thr residues. ApbE1, but not ApbE2, has a periplasm-addressing signal sequence. The genome also contains genes for three target proteins with the Dxx(s/t)gAT flavinylation motif: two subunits of Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR), and a 99.5kDa protein, KPK_2907, with a previously unknown function. We show here that KPK_2907 is an active cytoplasmically-localized fumarate reductase. K. pneumoniae cells with an inactivated kpk_2907 gene lack cytoplasmic fumarate reductase activity, while retaining this activity in the membrane fraction. Complementation of the mutant strain with a kpk_2907-containing plasmid resulted in a complete recovery of cytoplasmic fumarate reductase activity. KPK_2907 produced in Escherichia coli cells contains 1mol/mol each of covalently bound FMN, noncovalently bound FMN and noncovalently bound FAD. Lesion in the ApbE1 gene in K. pneumoniae resulted in inactive Na(+)-NQR, but cytoplasmic fumarate reductase activity remained unchanged. On the contrary, lesion in the ApbE2 gene abolished the fumarate reductase but not the Na(+)-NQR activity. Both activities could be restored by transformation of the ApbE1- or ApbE2-deficient K. pneumoniae strains with plasmids containing the Vibrio cholerae apbE gene with or without the periplasm-directing signal sequence, respectively. Our data thus indicate that ApbE1 and ApbE2 bind FMN to Na(+)-NQR and fumarate reductase, respectively, and that, contrary to the presently accepted view, the FMN residues are on the periplasmic side of Na(+)-NQR. A new, "electron loop" mechanism is proposed for Na(+)-NQR, involving an electroneutral Na(+)/electron symport. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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14
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Shea ME, Juárez O, Cho J, Barquera B. Aspartic acid 397 in subunit B of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae forms part of a sodium-binding site, is involved in cation selectivity, and affects cation-binding site cooperativity. J Biol Chem 2013; 288:31241-9. [PMID: 24030824 DOI: 10.1074/jbc.m113.510776] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+)-pumping NADH:quinone complex is found in Vibrio cholerae and other marine and pathogenic bacteria. NADH:ubiquinone oxidoreductase oxidizes NADH and reduces ubiquinone, using the free energy released by this reaction to pump sodium ions across the cell membrane. In a previous report, a conserved aspartic acid residue in the NqrB subunit at position 397, located in the cytosolic face of this protein, was proposed to be involved in the capture of sodium. Here, we studied the role of this residue through the characterization of mutant enzymes in which this aspartic acid was substituted by other residues that change charge and size, such as arginine, serine, lysine, glutamic acid, and cysteine. Our results indicate that NqrB-Asp-397 forms part of one of the at least two sodium-binding sites and that both size and charge at this position are critical for the function of the enzyme. Moreover, we demonstrate that this residue is involved in cation selectivity, has a critical role in the communication between sodium-binding sites, by promoting cooperativity, and controls the electron transfer step involved in sodium uptake (2Fe-2S → FMNC).
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Affiliation(s)
- Michael E Shea
- From the Department of Biology and Center of Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 121801
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15
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Bertsova YV, Fadeeva MS, Kostyrko VA, Serebryakova MV, Baykov AA, Bogachev AV. Alternative pyrimidine biosynthesis protein ApbE is a flavin transferase catalyzing covalent attachment of FMN to a threonine residue in bacterial flavoproteins. J Biol Chem 2013; 288:14276-14286. [PMID: 23558683 DOI: 10.1074/jbc.m113.455402] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) contains two flavin residues as redox-active prosthetic groups attached by a phosphoester bond to threonine residues in subunits NqrB and NqrC. We demonstrate here that flavinylation of truncated Vibrio harveyi NqrC at Thr-229 in Escherichia coli cells requires the presence of a co-expressed Vibrio apbE gene. The apbE genes cluster with genes for Na(+)-NQR and other FMN-binding flavoproteins in bacterial genomes and encode proteins with previously unknown function. Experiments with isolated NqrC and ApbE proteins confirmed that ApbE is the only protein factor required for NqrC flavinylation and also indicated that the reaction is Mg(2+)-dependent and proceeds with FAD but not FMN. Inactivation of the apbE gene in Klebsiella pneumoniae, wherein the nqr operon and apbE are well separated in the chromosome, resulted in a complete loss of the quinone reductase activity of Na(+)-NQR, consistent with its dependence on covalently bound flavin. Our data thus identify ApbE as a novel modifying enzyme, flavin transferase.
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Affiliation(s)
- Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Maria S Fadeeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Vitaly A Kostyrko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
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16
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Matallana-Surget S, Joux F, Wattiez R, Lebaron P. Proteome analysis of the UVB-resistant marine bacterium Photobacterium angustum S14. PLoS One 2012; 7:e42299. [PMID: 22870314 PMCID: PMC3411663 DOI: 10.1371/journal.pone.0042299] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 07/03/2012] [Indexed: 12/22/2022] Open
Abstract
The proteome of the marine bacterium Photobacterium angustum S14 was exposed to UVB and analyzed by the implementation of both the post-digest ICPL labeling method and 2D-DIGE technique using exponentially growing cells. A total of 40 and 23 proteins were quantified in all replicates using either the ICPL or 2D-DIGE methods, respectively. By combining both datasets from 8 biological replicates (4 biological replicates for each proteomics technique), 55 proteins were found to respond significantly to UVB radiation in P. angustum. A total of 8 UVB biomarkers of P. angustum were quantified in all replicates using both methods. Among them, the protein found to present the highest increase in abundance (almost a 3-fold change) was RecA, which is known to play a crucial role in the so-called recombinational repair process. We also observed a high number of antioxidants, transport proteins, metabolism-related proteins, transcription/translation regulators, chaperonins and proteases. We also discuss and compare the UVB response and global protein expression profiles obtained for two different marine bacteria with trophic lifestyles: the copiotroph P. angustum and oligotroph Sphingopyxis alaskensis.
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Affiliation(s)
- Sabine Matallana-Surget
- UPMC Univ Paris 06, UMR7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls/mer, France.
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17
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Verkhovsky MI, Bogachev AV, Pivtsov AV, Bertsova YV, Fedin MV, Bloch DA, Kulik LV. Sodium-dependent movement of covalently bound FMN residue(s) in Na(+)-translocating NADH:quinone oxidoreductase. Biochemistry 2012; 51:5414-21. [PMID: 22697411 DOI: 10.1021/bi300322n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) is a component of respiratory electron-transport chain of various bacteria generating redox-driven transmembrane electrochemical Na(+) potential. We found that the change in Na(+) concentration in the reaction medium has no effect on the thermodynamic properties of prosthetic groups of Na(+)-NQR from Vibrio harveyi, as was revealed by the anaerobic equilibrium redox titration of the enzyme's EPR spectra. On the other hand, the change in Na(+) concentration strongly alters the EPR spectral properties of the radical pair formed by the two anionic semiquinones of FMN residues bound to the NqrB and NqrC subunits (FMN(NqrB) and FMN(NqrC)). Using data obtained by pulse X- and Q-band EPR as well as by pulse ENDOR and ELDOR spectroscopy, the interspin distance between FMN(NqrB) and FMN(NqrC) was found to be 15.3 Å in the absence and 20.4 Å in the presence of Na(+), respectively. Thus, the distance between the covalently bound FMN residues can vary by about 5 Å upon changes in Na(+) concentration. Using these results, we propose a scheme of the sodium potential generation by Na(+)-NQR based on the redox- and sodium-dependent conformational changes in the enzyme.
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Affiliation(s)
- Michael I Verkhovsky
- Department of Molecular Energetics of Microorganisms, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
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18
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Neehaul Y, Juárez O, Barquera B, Hellwig P. Thermodynamic contribution to the regulation of electron transfer in the Na(+)-pumping NADH:quinone oxidoreductase from Vibrio cholerae. Biochemistry 2012; 51:4072-7. [PMID: 22533880 DOI: 10.1021/bi300343u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Na(+)-pumping NADH:quinone oxidoreductase (Na(+)-NQR) is a fundamental enzyme of the oxidative phosphorylation metabolism and ionic homeostasis in several pathogenic and marine bacteria. To understand the mechanism that couples electron transfer with sodium translocation in Na(+)-NQR, the ion dependence of the redox potential of the individual cofactors was studied using a spectroelectrochemical approach. The redox potential of one of the FMN cofactors increased 90 mV in the presence of Na(+) or Li(+), compared to the redox potentials measured in the presence of other cations that are not transported by the enzyme, such as K(+), Rb(+), and NH(4)(+). This shift in redox potential of one FMN confirms the crucial role of the FMN anionic radicals in the Na(+) pumping mechanism and demonstrates that the control of the electron transfer rate has both kinetic (via conformational changes) and thermodynamic components.
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Affiliation(s)
- Yashvin Neehaul
- Laboratoire de spectroscopie vibrationnelle et electrochimie des biomolecules, Institut de Chimie, UMR 7177, Université de Strasbourg-CNRS, 67070 Strasbourg, France
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19
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Penn K, Jensen PR. Comparative genomics reveals evidence of marine adaptation in Salinispora species. BMC Genomics 2012; 13:86. [PMID: 22401625 PMCID: PMC3314556 DOI: 10.1186/1471-2164-13-86] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 03/08/2012] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. RESULTS Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. CONCLUSIONS The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed.
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Affiliation(s)
- Kevin Penn
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0204, USA
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20
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Fadeeva MS, Bertsova YV, Euro L, Bogachev AV. Cys377 residue in NqrF subunit confers Ag(+) sensitivity of Na+-translocating NADH:quinone oxidoreductase from Vibrio harveyi. BIOCHEMISTRY (MOSCOW) 2011; 76:186-95. [PMID: 21568851 DOI: 10.1134/s0006297911020040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) is a component of the respiratory chain of various bacteria that generates a redox-driven transmembrane electrochemical Na(+) potential. The Na(+)-NQR activity is known to be specifically inhibited by low concentrations of silver ions. Replacement of the conserved Cys377 residue with alanine in the NqrF subunit of Na(+)-NQR from Vibrio harveyi resulted in resistance of the enzyme to Ag(+) and to other heavy metal ions. Analysis of the catalytic activity also showed that the rate of electron input into the mutant Na(+)-NQR decreased by about 14-fold in comparison to the wild type enzyme, whereas all other properties of (NqrF)C377A Na(+)-NQR including its stability remained unaffected.
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Affiliation(s)
- M S Fadeeva
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
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21
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Juárez O, Shea ME, Makhatadze GI, Barquera B. The role and specificity of the catalytic and regulatory cation-binding sites of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae. J Biol Chem 2011; 286:26383-90. [PMID: 21652714 DOI: 10.1074/jbc.m111.257873] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+)-translocating NADH:quinone oxidoreductase is the entry site for electrons into the respiratory chain and the main sodium pump in Vibrio cholerae and many other pathogenic bacteria. In this work, we have employed steady-state and transient kinetics, together with equilibrium binding measurements to define the number of cation-binding sites and characterize their roles in the enzyme. Our results show that sodium and lithium ions stimulate enzyme activity, and that Na(+)-NQR enables pumping of Li(+), as well as Na(+) across the membrane. We also confirm that the enzyme is not able to translocate other monovalent cations, such as potassium or rubidium. Although potassium is not used as a substrate, Na(+)-NQR contains a regulatory site for this ion, which acts as a nonessential activator, increasing the activity and affinity for sodium. Rubidium can bind to the same site as potassium, but instead of being activated, enzyme turnover is inhibited. Activity measurements in the presence of both sodium and lithium indicate that the enzyme contains at least two functional sodium-binding sites. We also show that the binding sites are not exclusively responsible for ion selectivity, and other steps downstream in the mechanism also play a role. Finally, equilibrium-binding measurements with (22)Na(+) show that, in both its oxidized and reduced states, Na(+)-NQR binds three sodium ions, and that the affinity for sodium is the same for both of these states.
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Affiliation(s)
- Oscar Juárez
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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22
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Isabella VM, Clark VL. Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae. BMC Genomics 2011; 12:51. [PMID: 21251255 PMCID: PMC3032703 DOI: 10.1186/1471-2164-12-51] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 01/20/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maintenance of an anaerobic denitrification system in the obligate human pathogen, Neisseria gonorrhoeae, suggests that an anaerobic lifestyle may be important during the course of infection. Furthermore, mounting evidence suggests that reduction of host-produced nitric oxide has several immunomodulary effects on the host. However, at this point there have been no studies analyzing the complete gonococcal transcriptome response to anaerobiosis. Here we performed deep sequencing to compare the gonococcal transcriptomes of aerobically and anaerobically grown cells. Using the information derived from this sequencing, we discuss the implications of the robust transcriptional response to anaerobic growth. RESULTS We determined that 198 chromosomal genes were differentially expressed (~10% of the genome) in response to anaerobic conditions. We also observed a large induction of genes encoded within the cryptic plasmid, pJD1. Validation of RNA-seq data using translational-lacZ fusions or RT-PCR demonstrated the RNA-seq results to be very reproducible. Surprisingly, many genes of prophage origin were induced anaerobically, as well as several transcriptional regulators previously unknown to be involved in anaerobic growth. We also confirmed expression and regulation of a small RNA, likely a functional equivalent of fnrS in the Enterobacteriaceae family. We also determined that many genes found to be responsive to anaerobiosis have also been shown to be responsive to iron and/or oxidative stress. CONCLUSIONS Gonococci will be subject to many forms of environmental stress, including oxygen-limitation, during the course of infection. Here we determined that the anaerobic stimulon in gonococci was larger than previous studies would suggest. Many new targets for future research have been uncovered, and the results derived from this study may have helped to elucidate factors or mechanisms of virulence that may have otherwise been overlooked.
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Affiliation(s)
- Vincent M Isabella
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Box 672, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Virginia L Clark
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Box 672, 601 Elmwood Avenue, Rochester, NY 14642, USA
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Fadeeva MS, Bertsova YV, Verkhovsky MI, Bogachev AV. Site-directed mutagenesis of conserved cysteine residues in NqrD and NqrE subunits of Na+-translocating NADH:quinone oxidoreductase. BIOCHEMISTRY (MOSCOW) 2011; 73:123-9. [DOI: 10.1134/s0006297908020028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Casutt MS, Huber T, Brunisholz R, Tao M, Fritz G, Steuber J. Localization and function of the membrane-bound riboflavin in the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae. J Biol Chem 2010; 285:27088-27099. [PMID: 20558724 PMCID: PMC2930708 DOI: 10.1074/jbc.m109.071126] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 06/16/2010] [Indexed: 12/29/2022] Open
Abstract
The sodium ion-translocating NADH:quinone oxidoreductase (Na(+)-NQR) from the human pathogen Vibrio cholerae is a respiratory membrane protein complex that couples the oxidation of NADH to the transport of Na(+) across the bacterial membrane. The Na(+)-NQR comprises the six subunits NqrABCDEF, but the stoichiometry and arrangement of these subunits are unknown. Redox-active cofactors are FAD and a 2Fe-2S cluster on NqrF, covalently attached FMNs on NqrB and NqrC, and riboflavin and ubiquinone-8 with unknown localization in the complex. By analyzing the cofactor content and NADH oxidation activity of subcomplexes of the Na(+)-NQR lacking individual subunits, the riboflavin cofactor was unequivocally assigned to the membrane-bound NqrB subunit. Quantitative analysis of the N-terminal amino acids of the holo-complex revealed that NqrB is present in a single copy in the holo-complex. It is concluded that the hydrophobic NqrB harbors one riboflavin in addition to its covalently attached FMN. The catalytic role of two flavins in subunit NqrB during the reduction of ubiquinone to ubiquinol by the Na(+)-NQR is discussed.
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Affiliation(s)
- Marco S Casutt
- Department of Neuropathology, Breisacherstrasse 64, University of Freiburg, 79106 Freiburg, Germany
| | - Tamara Huber
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - René Brunisholz
- Functional Genomics Centre Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Minli Tao
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Günter Fritz
- Department of Neuropathology, Breisacherstrasse 64, University of Freiburg, 79106 Freiburg, Germany
| | - Julia Steuber
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
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Energy transducing redox steps of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae. Proc Natl Acad Sci U S A 2010; 107:12505-10. [PMID: 20616050 DOI: 10.1073/pnas.1002866107] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Na(+)-NQR is a unique respiratory enzyme that couples the free energy of electron transfer reactions to electrogenic pumping of sodium across the cell membrane. This enzyme is found in many marine and pathogenic bacteria where it plays an analogous role to the H(+)-pumping complex I. It has generally been assumed that the sodium pump of Na(+)-NQR operates on the basis of thermodynamic coupling between reduction of a single redox cofactor and the binding of sodium at a nearby site. In this study, we have defined the coupling to sodium translocation of individual steps in the redox reaction of Na(+)-NQR. Sodium uptake takes place in the reaction step in which an electron moves from the 2Fe-2S center to FMN(C), while the translocation of sodium across the membrane dielectric (and probably its release into the external medium) occurs when an electron moves from FMN(B) to riboflavin. This argues against a single-site coupling model because the redox steps that drive these two parts of the sodium pumping process do not have any redox cofactor in common. The significance of these results for the mechanism of coupling is discussed, and we proposed that Na(+)-NQR operates through a novel mechanism based on kinetic coupling, mediated by conformational changes.
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26
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Sodium-translocating NADH:quinone oxidoreductase as a redox-driven ion pump. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:738-46. [PMID: 20056102 DOI: 10.1016/j.bbabio.2009.12.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 12/17/2009] [Accepted: 12/24/2009] [Indexed: 11/20/2022]
Abstract
The Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) is a component of the respiratory chain of various bacteria. This enzyme is an analogous but not homologous counterpart of mitochondrial Complex I. Na+-NQR drives the same chemistry and also uses released energy to translocate ions across the membrane, but it pumps Na+ instead of H+. Most likely the mechanism of sodium pumping is quite different from that of proton pumping (for example, it could not accommodate the Grotthuss mechanism of ion movement); this is why the enzyme structure, subunits and prosthetic groups are completely special. This review summarizes modern knowledge on the structural and catalytic properties of bacterial Na+-translocating NADH:quinone oxidoreductases. The sequence of electron transfer through the enzyme cofactors and thermodynamic properties of those cofactors is discussed. The resolution of the intermediates of the catalytic cycle and localization of sodium-dependent steps are combined in a possible molecular mechanism of sodium transfer by the enzyme.
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27
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Juárez O, Athearn K, Gillespie P, Barquera B. Acid residues in the transmembrane helices of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae involved in sodium translocation. Biochemistry 2009; 48:9516-24. [PMID: 19694431 DOI: 10.1021/bi900845y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vibrio cholerae and many other marine and pathogenic bacteria possess a unique respiratory complex, the Na(+)-pumping NADH:quinone oxidoreductase (Na(+)-NQR), which pumps Na(+) across the cell membrane using the energy released by the redox reaction between NADH and ubiquinone. To function as a selective sodium pump, Na(+)-NQR must contain structures that (1) allow the sodium ion to pass through the hydrophobic core of the membrane and (2) provide cation specificity to the translocation system. In other sodium-transporting proteins, the structures that carry out these roles frequently include aspartate and glutamate residues. The negative charge of these residues facilitates binding and translocation of sodium. In this study, we have analyzed mutants of acid residues located in the transmembrane helices of subunits B, D, and E of Na(+)-NQR. The results are consistent with the participation of seven of these residues in the translocation process of sodium. Mutations at NqrB-D397, NqrD-D133, and NqrE-E95 produced a decrease of approximately >or=10-fold in the apparent affinity of the enzyme for sodium (Km(app)(Na+)), which suggests that these residues may form part of a sodium-binding site. Mutation at other residues, including NqrB-E28, NqrB-E144, NqrB-E346, and NqrD-D88, had a strong effect on the quinone reductase activity of the enzyme and its sodium sensitivity, but a weaker effect on the apparent sodium affinity, consistent with a possible role in sodium conductance pathways.
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Affiliation(s)
- Oscar Juárez
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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28
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Bogachev AV, Kulik LV, Bloch DA, Bertsova YV, Fadeeva MS, Verkhovsky MI. Redox properties of the prosthetic groups of Na(+)-translocating nadh:quinone oxidoreductase. 1. Electron paramagnetic resonance study of the enzyme. Biochemistry 2009; 48:6291-8. [PMID: 19496621 DOI: 10.1021/bi900524m] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Redox properties of all EPR-detectable prosthetic groups of Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) from Vibrio harveyi were studied at pH 7.5 using cryo-EPR spectroelectrochemistry. Titration shows five redox transitions. One with E(m) = -275 mV belongs to the reduction of the [2Fe-2S] cluster, and the four others reflect redox transitions of flavin cofactors. Two transitions (E(m)(1) = -190 mV and E(m)(2) = -275 mV) originate from the formation of FMN anion radical, covalently bound to the NqrC subunit, and its subsequent reduction. The remaining two transitions arise from the two other flavin cofactors. A high potential (E(m) = -10 mV) transition corresponds to the reduction of riboflavin neutral radical, which is stable at rather high redox potentials. An E(m) = -130 mV transition reflects the formation of FMN anion radical from a flavin covalently bound to the NqrB subunit, which stays as a radical down to very low potentials. Taking into account the EPR-silent, two-electron transition of noncovalently bound FAD located in the NqrF subunit, there are four flavins in Na(+)-NQR all together. Defined by dipole-dipole magnetic interaction measurements, the interspin distance between the [2Fe-2S](+) cluster and the NqrB subunit-bound FMN anion radical is found to be 22.5 +/- 1.5 A, which means that for the functional electron transfer between these two centers another cofactor, most likely FMN bound to the NqrC subunit, should be located.
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Affiliation(s)
- Alexander V Bogachev
- Department of Molecular Energetics of Microorganisms, A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
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29
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Bogachev AV, Bloch DA, Bertsova YV, Verkhovsky MI. Redox properties of the prosthetic groups of Na(+)-translocating NADH:quinone oxidoreductase. 2. Study of the enzyme by optical spectroscopy. Biochemistry 2009; 48:6299-304. [PMID: 19496622 DOI: 10.1021/bi900525v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Redox titration of the electronic spectra of the prosthetic groups of the Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) from Vibrio harveyi at different pH values showed five redox transitions corresponding to the four flavin cofactors of the enzyme and one additional transition reflecting oxidoreduction of the [2Fe-2S] cluster. The pH dependence of the measured midpoint redox potentials showed that the two-electron reduction of the FAD located in the NqrF subunit was coupled with the uptake of only one H(+). The one-electron reduction of neutral semiquinone of riboflavin and the formation of anion flavosemiquinone from the oxidized FMN bound to the NqrB subunit were not coupled to any proton uptake. The two sequential one-electron reductions of the FMN residue bound to the NqrC subunit showed pH-independent formation of anion radical in the first step and the formation of fully reduced flavin coupled to the uptake of one H(+) in the second step. All four flavins stayed in the anionic form in the fully reduced enzyme. None of the six redox transitions in Na(+)-NQR showed dependence of its midpoint redox potential on the concentration of sodium ions. A model of the sequence of electron transfer steps in the enzyme is suggested.
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Affiliation(s)
- Alexander V Bogachev
- Department of Molecular Energetics of Microorganisms, A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
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30
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Juárez O, Morgan JE, Barquera B. The Electron Transfer Pathway of the Na+-pumping NADH:Quinone Oxidoreductase from Vibrio cholerae. J Biol Chem 2009; 284:8963-72. [PMID: 19155212 PMCID: PMC2659253 DOI: 10.1074/jbc.m809395200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/12/2009] [Indexed: 12/16/2022] Open
Abstract
The Na(+)-pumping NADH:quinone oxidoreductase (Na(+)-NQR) is the only respiratory enzyme that operates as a Na(+) pump. This redox-driven Na(+) pump is amenable to experimental approaches not available for H(+) pumps, providing an excellent system for mechanistic studies of ion translocation. An understanding of the internal electron transfer steps and their Na(+) dependence is an essential prerequisite for such studies. To this end, we analyzed the reduction kinetics of the wild type Na(+)-NQR, as well as site-directed mutants of the enzyme, which lack specific cofactors. NADH and ubiquinol were used as reductants in separate experiments, and a full spectrum UV-visible stopped flow kinetic method was employed. The results make it possible to define the complete sequence of redox carriers in the electrons transfer pathway through the enzyme. Electrons flow from NADH to quinone through the FAD in subunit F, the 2Fe-2S center, the FMN in subunit C, the FMN in subunit B, and finally riboflavin. The reduction of the FMN(C) to its anionic flavosemiquinone state is the first Na(+)-dependent process, suggesting that reduction of this site is linked to Na(+) uptake. During the reduction reaction, two FMNs are transformed to their anionic flavosemiquinone in a single kinetic step. Subsequently, FMN(C) is converted to the flavohydroquinone, accounting for the single anionic flavosemiquinone radical in the fully reduced enzyme. A model of the electron transfer steps in the catalytic cycle of Na(+)-NQR is presented to account for the kinetic and spectroscopic data.
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Affiliation(s)
- Oscar Juárez
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
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31
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Mulkidjanian AY, Galperin MY, Koonin EV. Co-evolution of primordial membranes and membrane proteins. Trends Biochem Sci 2009; 34:206-15. [PMID: 19303305 DOI: 10.1016/j.tibs.2009.01.005] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 01/20/2009] [Accepted: 01/21/2009] [Indexed: 01/14/2023]
Abstract
Studies of the past several decades have provided major insights into the structural organization of biological membranes and mechanisms of many membrane molecular machines. However, the origin(s) of the membrane(s) and membrane proteins remains enigmatic. We discuss different concepts of the origin and early evolution of membranes with a focus on the evolution of the (im)permeability to charged molecules such as proteins, nucleic acids and small ions. Reconstruction of the evolution of F-type and A/V-type membrane ATPases (ATP synthases), which are either proton- or sodium-dependent, might help us to understand not only the origin of membrane bioenergetics but also of membranes themselves. We argue that evolution of biological membranes occurred as a process of co-evolution of lipid bilayers, membrane proteins and membrane bioenergetics.
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32
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Schmidt S, Biegel E, Müller V. The ins and outs of Na(+) bioenergetics in Acetobacterium woodii. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:691-6. [PMID: 19167341 DOI: 10.1016/j.bbabio.2008.12.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 12/30/2008] [Accepted: 12/30/2008] [Indexed: 12/15/2022]
Abstract
The acetogenic bacterium Acetobacterium woodii uses a transmembrane electrochemical sodium ion potential for bioenergetic reactions. A primary sodium ion potential is established during carbonate (acetogenesis) as well as caffeate respiration. The electrogenic Na(+) pump connected to the Wood-Ljungdahl pathway (acetogenesis) still remains to be identified. The pathway of caffeate reduction with hydrogen as electron donor was investigated and the only membrane-bound activity was found to be a ferredoxin-dependent NAD(+) reduction. This exergonic electron transfer reaction may be catalyzed by the membrane-bound Rnf complex that was discovered recently and is suggested to couple exergonic electron transfer from ferredoxin to NAD(+) to the vectorial transport of Na(+) across the cytoplasmic membrane. Rnf may also be involved in acetogenesis. The electrochemical sodium ion potential thus generated is used to drive endergonic reactions such as flagellar rotation and ATP synthesis. The ATP synthase is a member of the F(1)F(O) class of enzymes but has an unusual and exceptional feature. Its membrane-embedded rotor is a hybrid made of F(O) and V(O)-like subunits in a stoichiometry of 9:1. This stoichiometry is apparently not variable with the growth conditions. The structure and function of the Rnf complex and the Na(+) F(1)F(O) ATP synthase as key elements of the Na(+) cycle in A. woodii are discussed.
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Affiliation(s)
- Silke Schmidt
- Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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33
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Bogachev AV, Belevich NP, Bertsova YV, Verkhovsky MI. Primary steps of the Na+-translocating NADH:ubiquinone oxidoreductase catalytic cycle resolved by the ultrafast freeze-quench approach. J Biol Chem 2008; 284:5533-8. [PMID: 19117949 DOI: 10.1074/jbc.m808984200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+)-translocating NADH:ubiquinone oxidoreductase (Na(+)-NQR) is a component of respiratory chain of various bacteria, and it generates a redox-driven transmembrane electrochemical Na(+) potential. Primary steps of the catalytic cycle of Na(+)-NQR from Vibrio harveyi were followed by the ultrafast freeze-quench approach in combination with conventional stopped-flow technique. The obtained sequence of events includes NADH binding ( approximately 1.5 x 10(7) m(-1) s(-1)), hydride ion transfer from NADH to FAD ( approximately 3.5 x 10(3) s(-1)), and partial electron separation and formation of equivalent fractions of reduced 2Fe-2S cluster and neutral semiquinone of FAD ( approximately 0.97 x 10(3) s(-1)). In the last step, a quasi-equilibrium is approached between the two states of FAD: two-electron reduced (50%) and one-electron reduced (the other 50%) species. The latter, neutral semiquinone of FAD, shares the second electron with the 2Fe-2S center. The transient midpoint redox potentials for the cofactors obtained during the fast kinetics measurements are very different from ones achieved during equilibrium redox titration and show that the functional states of the enzyme realized during its turning over cannot be modeled by the equilibrium approach.
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Affiliation(s)
- Alexander V Bogachev
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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34
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Backiel J, Juárez O, Zagorevski DV, Wang Z, Nilges MJ, Barquera B. Covalent binding of flavins to RnfG and RnfD in the Rnf complex from Vibrio cholerae. Biochemistry 2008; 47:11273-84. [PMID: 18831535 DOI: 10.1021/bi800920j] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes of the Rnf family are believed to be bacterial redox-driven ion pumps, coupling an oxidoreduction process to the translocation of Na+ across the cell membrane. Here we show for the first time that Rnf is a flavoprotein, with FMN covalently bound to threonine-175 in RnfG and a second flavin bound to threonine-187 in RnfD. Rnf subunits D and G are homologous to subunits B and C of Na+-NQR, respectively. Each of these Na+-NQR subunits includes a conserved S(T)GAT motif, with FMN covalently bound to the final threonine. RnfD and RnfG both contain the same motif, suggesting that they bind flavins in a similar way. In order to investigate this, the genes for RnfD and RnfG from Vibrio cholerae were cloned and expressed individually in that organism. In both cases the produced protein fluoresced under UV illumination on an SDS gel, further indicating the presence of flavin. However, analysis of the mutants RnfG-T175L, RnfD-T278L, and RnfD-T187V showed that RnfG-T175 and RnfD-T187 are the likely flavin ligands. This indicates that, in the case of RnfD, the flavin is bound, not to the SGAT sequence but to the final residues of a TMAT sequence, a novel variant of the flavin binding motif. In the case of RnfG, flavin analysis, followed by MALDI-TOF-TOF mass spectrometry, showed that an FMN is covalently attached to threonine-175, the final threonine of the S(T)GAT sequence. Studies by visible, EPR, and ENDOR spectroscopy showed that, upon partial reduction, the isolated RnfG produces a neutral semiquinone intermediate. The semiquinone species disappeared upon full reduction and was not observed in the denatured protein. A topological analysis combining reporter protein fusion and computer predictions indicated that the flavins in RnfG and RnfD are localized in the periplasmic space. In contrast, in NqrC and NqrB the flavins are located in a cytoplasmic loop. This topological analysis suggests that there may be mechanistic differences between the Rnf and Na+-NQR complexes.
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Affiliation(s)
- Julianne Backiel
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eight Street, Troy, New York 12180, USA
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35
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Müller V, Imkamp F, Biegel E, Schmidt S, Dilling S. Discovery of a ferredoxin:NAD+-oxidoreductase (Rnf) in Acetobacterium woodii: a novel potential coupling site in acetogens. Ann N Y Acad Sci 2008; 1125:137-46. [PMID: 18378592 DOI: 10.1196/annals.1419.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Acetogens use the Wood-Ljungdahl pathway for reduction of carbon dioxide to acetate. This pathway not only allows reoxidation of reducing equivalents during heterotrophic growth but also supports chemolithoautotrophic growth on H(2) + CO(2). The latter argues for this pathway being a source for net energy conservation, but the mechanism involved remains unknown. In addition to CO(2), acetogens can use alternative electron acceptors, such as nitrate or caffeate. Caffeate respiration in the model acetogen Acetobacterium woodii is coupled to energy conservation via a chemiosmotic mechanism, with Na(+) as coupling ion. The pathway and its bioenergetics were solved in some detail very recently. This review focuses on the regulation of caffeate respiration, describes the enyzmes involved, summarizes the evidence for a potential Na(+)-translocating ferredoxin:NAD(+)-oxidoreductase (Rnf complex) as a new coupling site, and hypothesizes on the role of this Rnf complex in the Wood-Ljungdahl pathway.
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Affiliation(s)
- Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany.
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36
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Mulkidjanian AY, Dibrov P, Galperin MY. The past and present of sodium energetics: may the sodium-motive force be with you. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:985-92. [PMID: 18485887 DOI: 10.1016/j.bbabio.2008.04.028] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 04/18/2008] [Accepted: 04/18/2008] [Indexed: 10/22/2022]
Abstract
All living cells routinely expel Na(+) ions, maintaining lower concentration of Na(+) in the cytoplasm than in the surrounding milieu. In the vast majority of bacteria, as well as in mitochondria and chloroplasts, export of Na(+) occurs at the expense of the proton-motive force. Some bacteria, however, possess primary generators of the transmembrane electrochemical gradient of Na(+) (sodium-motive force). These primary Na(+) pumps have been traditionally seen as adaptations to high external pH or to high temperature. Subsequent studies revealed, however, the mechanisms for primary sodium pumping in a variety of non-extremophiles, such as marine bacteria and certain bacterial pathogens. Further, many alkaliphiles and hyperthermophiles were shown to rely on H(+), not Na(+), as the coupling ion. We review here the recent progress in understanding the role of sodium-motive force, including (i) the conclusion on evolutionary primacy of the sodium-motive force as energy intermediate, (ii) the mechanisms, evolutionary advantages and limitations of switching from Na(+) to H(+) as the coupling ion, and (iii) the possible reasons why certain pathogenic bacteria still rely on the sodium-motive force.
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37
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Tao M, Casutt MS, Fritz G, Steuber J. Oxidant-induced formation of a neutral flavosemiquinone in the Na+-translocating NADH:Quinone oxidoreductase (Na+-NQR) from Vibrio cholerae. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:696-702. [PMID: 18454933 DOI: 10.1016/j.bbabio.2008.04.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 03/31/2008] [Accepted: 04/05/2008] [Indexed: 10/22/2022]
Abstract
The Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) from the human pathogen Vibrio cholerae is a respiratory flavo-FeS complex composed of the six subunits NqrA-F. The Na(+)-NQR was produced as His(6)-tagged protein by homologous expression in V. cholerae. The isolated complex contained near-stoichiometric amounts of non-covalently bound FAD (0.78 mol/mol Na(+)-NQR) and riboflavin (0.70 mol/mol Na(+)-NQR), catalyzed NADH-driven Na(+) transport (40 nmol Na(+)min(-1) mg(-1)), and was inhibited by 2-n-heptyl-4-hydroxyquinoline-N-oxide. EPR spectroscopy showed that Na(+)-NQR as isolated contained very low amounts of a neutral flavosemiquinone (10(-3) mol/mol Na(+)-NQR). Reduction with NADH resulted in the formation of an anionic flavosemiquinone (0.10 mol/mol Na(+)-NQR). Subsequent oxidation of the Na(+)-NQR with ubiquinone-1 or O(2) led to the formation of a neutral flavosemiquinone (0.24 mol/mol Na(+)-NQR). We propose that the Na(+)-NQR is fully oxidized in its resting state, and discuss putative schemes of NADH-triggered redox transitions.
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Affiliation(s)
- Minli Tao
- Biochemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland
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Yamada H, Takashima E, Konishi K. Molecular characterization of the membrane-bound quinol peroxidase functionally connected to the respiratory chain. FEBS J 2007; 274:853-66. [PMID: 17288564 DOI: 10.1111/j.1742-4658.2006.05637.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report for the first time quinol peroxidase (QPO), an enzyme that uses ubiquinol-1 as an electron donor for the reduction of H(2)O(2) to water. We purified QPO to > 90% purity from the membrane fraction of Actinobacillus actinomycetemcomitans. QPO is a 53.6-kDa protein that contains three heme c molecules. The qpo gene was predicted to encode a putative bacterial cytochrome c peroxidase with N-terminal extensions containing an additional potential heme c-binding motif. Although qpo has high sequence homology to bacterial cytochrome c peroxidases, QPO did not catalyze peroxidation in the presence of horse heart cytochrome c. In addition, the cytoplasmic membrane of A. actinomycetemcomitans had apparent QPO-dependent peroxidase activity in the presence of NADH or succinate, which are substrates for the respiratory chain. Based on these findings, we present a new mechanism for the scavenging of reactive oxygen species in which quinol in the respiratory chain is consumed.
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Affiliation(s)
- Hiroyuki Yamada
- Department of Microbiology, School of Life Dentistry at Tokyo, Nippon Dental University, Tokyo, Japan
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Fadeeva MS, Yakovtseva EA, Belevich GA, Bertsova YV, Bogachev AV. Regulation of expression of Na+ -translocating NADH:quinone oxidoreductase genes in Vibrio harveyi and Klebsiella pneumoniae. Arch Microbiol 2007; 188:341-8. [PMID: 17551713 DOI: 10.1007/s00203-007-0254-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 03/16/2007] [Accepted: 04/28/2007] [Indexed: 10/23/2022]
Abstract
The expression of genes encoding sodium-translocating NADH:quinone oxidoreductase (Na(+)-NQR) was studied in the marine bacterium Vibrio harveyi and in the enterobacterium Klebsiella pneumoniae. It has been shown that such parameters as NaCl concentration, pH value, and presence of an uncoupler in the growth media do not influence significantly the level of nqr expression. However, nqr expression depends on the growth substrates used by these bacteria. Na(+)-NQR is highly repressed in V. harveyi during anaerobic growth, and nqr expression is modulated by electron acceptors and values of their redox potentials. The latter effect was shown to be independent of the ArcAB regulatory system.
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Affiliation(s)
- Maria S Fadeeva
- Department of Molecular Energetics of Microorganisms, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory, Moscow 119992, Russia
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Kerscher S, Dröse S, Zickermann V, Brandt U. The three families of respiratory NADH dehydrogenases. Results Probl Cell Differ 2007; 45:185-222. [PMID: 17514372 DOI: 10.1007/400_2007_028] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Most reducing equivalents extracted from foodstuffs during oxidative metabolism are fed into the respiratory chains of aerobic bacteria and mitochondria by NADH:quinone oxidoreductases. Three families of enzymes can perform this task and differ remarkably in their complexity and role in energy conversion. Alternative or NDH-2-type NADH dehydrogenases are simple one subunit flavoenzymes that completely dissipate the redox energy of the NADH/quinone couple. Sodium-pumping NADH dehydrogenases (Nqr) that are only found in procaryotes contain several flavins and are integral membrane protein complexes composed of six different subunits. Proton-pumping NADH dehydrogenases (NDH-1 or complex I) are highly complicated membrane protein complexes, composed of up to 45 different subunits, that are found in bacteria and mitochondria. This review gives an overview of the origin, structural and functional properties and physiological significance of these three types of NADH dehydrogenase.
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Affiliation(s)
- Stefan Kerscher
- Molecular Bioenergetics Group, Centre of Excellence Macromolecular Complexes, Johann Wolfgang Goethe-Universität, 60590, Frankfurt am Main, Germany
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Lin PC, Türk K, Häse CC, Fritz G, Steuber J. Quinone reduction by the Na+-translocating NADH dehydrogenase promotes extracellular superoxide production in Vibrio cholerae. J Bacteriol 2007; 189:3902-8. [PMID: 17322313 PMCID: PMC1913329 DOI: 10.1128/jb.01651-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The pathogenicity of Vibrio cholerae is influenced by sodium ions which are actively extruded from the cell by the Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR). To study the function of the Na(+)-NQR in the respiratory chain of V. cholerae, we examined the formation of organic radicals and superoxide in a wild-type strain and a mutant strain lacking the Na(+)-NQR. Upon reduction with NADH, an organic radical was detected in native membranes by electron paramagnetic resonance spectroscopy which was assigned to ubisemiquinones generated by the Na(+)-NQR. The radical concentration increased from 0.2 mM at 0.08 mM Na(+) to 0.4 mM at 14.7 mM Na(+), indicating that the concentration of the coupling cation influences the redox state of the quinone pool in V. cholerae membranes. During respiration, V. cholerae cells produced extracellular superoxide with a specific activity of 10.2 nmol min(-1) mg(-1) in the wild type compared to 3.1 nmol min(-1) mg(-1) in the NQR deletion strain. Raising the Na(+) concentration from 0.1 to 5 mM increased the rate of superoxide formation in the wild-type V. cholerae strain by at least 70%. Rates of respiratory H(2)O(2) formation by wild-type V. cholerae cells (30.9 nmol min(-1) mg(-1)) were threefold higher than rates observed with the mutant strain lacking the Na(+)-NQR (9.7 nmol min(-1) mg(-1)). Our study shows that environmental Na(+) could stimulate ubisemiquinone formation by the Na(+)-NQR and hereby enhance the production of reactive oxygen species formed during the autoxidation of reduced quinones.
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Affiliation(s)
- Po-Chi Lin
- Biochemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland
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Barquera B, Ramirez-Silva L, Morgan JE, Nilges MJ. A New Flavin Radical Signal in the Na+-pumping NADH:Quinone Oxidoreductase from Vibrio cholerae. J Biol Chem 2006; 281:36482-91. [PMID: 16973619 DOI: 10.1074/jbc.m605765200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+)-pumping NADH-ubiquinone oxidoreductase has six polypeptide subunits (NqrA-F) and a number of redox cofactors, including a noncovalently bound FAD and a 2Fe-2S center in subunit F, covalently bound FMNs in subunits B and C, and a noncovalently bound riboflavin in an undisclosed location. The FMN cofactors in subunits B and C are bound to threonine residues by phosphoester linkages. A neutral flavin-semiquinone radical is observed in the oxidized enzyme, whereas an anionic flavin-semiquinone has been reported in the reduced enzyme. For this work, we have altered the binding ligands of the FMNs in subunits B and C by replacing the threonine ligands with other amino acids, and we studied the resulting mutants by EPR and electron nuclear double resonance spectroscopy. We conclude that the sodium-translocating NADH:quinone oxidoreductase forms three spectroscopically distinct flavin radicals as follows: 1) a neutral radical in the oxidized enzyme, which is observed in all of the mutants and most likely arises from the riboflavin; 2) an anionic radical observed in the fully reduced enzyme, which is present in wild type, and the NqrC-T225Y mutant but not the NqrB-T236Y mutant; 3) a second anionic radical, seen primarily under weakly reducing conditions, which is present in wild type, and the NqrB-T236Y mutant but not the NqrC-T225Y mutant. Thus, we can tentatively assign the first anionic radical to the FMN in subunit B and the second to the FMN in subunit C. The second anionic radical has not been reported previously. In electron nuclear double resonance spectra, it exhibits a larger line width and larger 8alpha-methyl proton splittings, compared with the first anionic radical.
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Affiliation(s)
- Blanca Barquera
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
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Duffy EB, Barquera B. Membrane topology mapping of the Na+-pumping NADH: quinone oxidoreductase from Vibrio cholerae by PhoA-green fluorescent protein fusion analysis. J Bacteriol 2006; 188:8343-51. [PMID: 17041063 PMCID: PMC1698230 DOI: 10.1128/jb.01383-06] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 09/25/2006] [Indexed: 11/20/2022] Open
Abstract
The membrane topologies of the six subunits of Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae were determined by a combination of topology prediction algorithms and the construction of C-terminal fusions. Fusion expression vectors contained either bacterial alkaline phosphatase (phoA) or green fluorescent protein (gfp) genes as reporters of periplasmic and cytoplasmic localization, respectively. A majority of the topology prediction algorithms did not predict any transmembrane helices for NqrA. A lack of PhoA activity when fused to the C terminus of NqrA and the observed fluorescence of the green fluorescent protein C-terminal fusion confirm that this subunit is localized to the cytoplasmic side of the membrane. Analysis of four PhoA fusions for NqrB indicates that this subunit has nine transmembrane helices and that residue T236, the binding site for flavin mononucleotide (FMN), resides in the cytoplasm. Three fusions confirm that the topology of NqrC consists of two transmembrane helices with the FMN binding site at residue T225 on the cytoplasmic side. Fusion analysis of NqrD and NqrE showed almost mirror image topologies, each consisting of six transmembrane helices; the results for NqrD and NqrE are consistent with the topologies of Escherichia coli homologs YdgQ and YdgL, respectively. The NADH, flavin adenine dinucleotide, and Fe-S center binding sites of NqrF were localized to the cytoplasm. The determination of the topologies of the subunits of Na+-NQR provides valuable insights into the location of cofactors and identifies targets for mutagenesis to characterize this enzyme in more detail. The finding that all the redox cofactors are localized to the cytoplasmic side of the membrane is discussed.
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Affiliation(s)
- Ellen B Duffy
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, NY 12180, USA
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Patridge EV, Ferry JG. WrbA from Escherichia coli and Archaeoglobus fulgidus is an NAD(P)H:quinone oxidoreductase. J Bacteriol 2006; 188:3498-506. [PMID: 16672604 PMCID: PMC1482846 DOI: 10.1128/jb.188.10.3498-3506.2006] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
WrbA (tryptophan [W] repressor-binding protein) was discovered in Escherichia coli, where it was proposed to play a role in regulation of the tryptophan operon; however, this has been put in question, leaving the function unknown. Here we report a phylogenetic analysis of 30 sequences which indicated that WrbA is the prototype of a distinct family of flavoproteins which exists in a diversity of cell types across all three domains of life and includes documented NAD(P)H:quinone oxidoreductases (NQOs) from the Fungi and Viridiplantae kingdoms. Biochemical characterization of the prototypic WrbA protein from E. coli and WrbA from Archaeoglobus fulgidus, a hyperthermophilic species from the Archaea domain, shows that these enzymes have NQO activity, suggesting that this activity is a defining characteristic of the WrbA family that we designate a new type of NQO (type IV). For E. coli WrbA, the K(m)(NADH) was 14 +/- 0.43 microM and the K(m)(benzoquinone) was 5.8 +/- 0.12 microM. For A. fulgidus WrbA, the K(m)(NADH) was 19 +/- 1.7 microM and the K(m)(benzoquinone) was 37 +/- 3.6 microM. Both enzymes were found to be homodimeric by gel filtration chromatography and homotetrameric by dynamic light scattering and to contain one flavin mononucleotide molecule per monomer. The NQO activity of each enzyme is retained over a broad pH range, and apparent initial velocities indicate that maximal activities are comparable to the optimum growth temperature for the respective organisms. The results are discussed and implicate WrbA in the two-electron reduction of quinones, protecting against oxidative stress.
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Affiliation(s)
- Eric V Patridge
- Department of Biochemistry and Molecular Biology, Eberly College of Science, The Pennsylvania State University, University Park, 16802-4500, USA
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Tao M, Türk K, Diez J, Grütter MG, Fritz G, Steuber J. Crystallization of the NADH-oxidizing domain of the Na+-translocating NADH:ubiquinone oxidoreductase from Vibrio cholerae. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:110-2. [PMID: 16511277 PMCID: PMC2150961 DOI: 10.1107/s174430910504306x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Accepted: 12/22/2005] [Indexed: 05/06/2023]
Abstract
The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from pathogenic and marine bacteria is a respiratory complex that couples the exergonic oxidation of NADH by quinone to the transport of Na+ across the membrane. The NqrF subunit oxidizes NADH and transfers the electrons to other redox cofactors in the enzyme. The FAD-containing domain of NqrF has been expressed, purified and crystallized. The purified NqrF FAD domain exhibited high rates of NADH oxidation and contained stoichiometric amounts of the FAD cofactor. Initial crystallization of the flavin domain was achieved by the sitting-drop technique using a Cartesian MicroSys4000 robot. Optimization of the crystallization conditions yielded yellow hexagonal crystals with dimensions of 30 x 30 x 70 microm. The protein mainly crystallizes in long hexagonal needles with a diameter of up to 30 microm. Crystals diffract to 2.8 A and belong to space group P622, with unit-cell parameters a = b = 145.3, c = 90.2 A, alpha = beta = 90, gamma = 120 degrees.
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Affiliation(s)
- Minli Tao
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Karin Türk
- School of Engineering and Science, International University Bremen, 28759 Bremen, Germany
| | - Joachim Diez
- Swiss Light Source at Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Markus G. Grütter
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Günter Fritz
- Fachbereich Biologie, Universität Konstanz, Postfach M665, Universitätsstrasse 10, 78457 Konstanz, Germany
- Correspondence e-mail: ,
| | - Julia Steuber
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Correspondence e-mail: ,
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