1
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Hauschild P, Vogel RF, Hilgarth M. Transcriptomic analysis of the response of Photobacterium phosphoreum and Photobacterium carnosum to co-contaminants on chicken meat. Arch Microbiol 2022; 204:467. [PMID: 35804270 DOI: 10.1007/s00203-022-03059-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/07/2022] [Indexed: 11/02/2022]
Abstract
This study investigated the impact of Brochothrix (B.) thermosphacta and Pseudomonas (Ps.) fragi on the transcriptomes of Photobacterium (P.) phosphoreum and P. carnosum on chicken meat under modified atmosphere (MA) and air atmosphere (AA). P. phosphoreum TMW2.2103 responded to MA with a reduced transcript number related to cell division and an enhanced number related to oxidative stress. Concomitantly, the analysis revealed upregulation of fermentation and downregulation of respiration. It predicts enhanced substrate competition in presence of co-contaminants/MA. In contrast, the strain upregulated the respiration in AA, supposably due to improved substrate accessibility in this situation. For P. carnosum TMW2.2149 the respiration was downregulated, and the pyruvate metabolism upregulated under MA. MA/co-contaminant resulted in multiple upregulated metabolic routes. Conversely, AA/co-contaminant resulted only in minor regulations, showing inability to cope with fast growing competitors. Observations reveal different strategies of photobacteria to react to co-contaminants on meat.
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Affiliation(s)
- Philippa Hauschild
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354, Freising, Germany
| | - Maik Hilgarth
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354, Freising, Germany.
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2
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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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3
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Willow SY, Yuan M, Juárez O, Minh DDL. Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR. Proteins 2021; 89:1376-1385. [PMID: 34091964 DOI: 10.1002/prot.26158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Proteins like NADH:ubiquinone oxidoreductase (NQR), an essential enzyme and ion pump in the physiology of several pathogenic bacteria, tightly regulate the redox properties of their cofactors. Although flavin mononucleotide (FMN) is fully reduced in aqueous solution, FMN in subunits B and C of NQR exclusively undergo one-electron transitions during its catalytic cycle. Here, we perform ab initio calculations and molecular dynamics simulations to elucidate the mechanisms that regulate the redox state of FMN in NQR. QM/MM calculations show that binding site electrostatics disfavor anionic forms of FMNH2 , but permit a neutral form of the fully reduced flavin. The potential energy surface is unaffected by covalent bonding between FMN and threonine. Molecular dynamics simulations show that the FMN binding sites are inaccessible by water, suggesting that further reductions of the cofactors are limited or prohibited by the availability of water and other proton donors. These findings provide a deeper understanding of the mechanisms used by NQR to regulate electron transfer through the cofactors and perform its physiologic role. They also provide the first, to our knowledge, evidence of the simple concept that proteins regulate flavin redox states via water occlusion.
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Affiliation(s)
- Soohaeng Yoo Willow
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, USA
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4
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Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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5
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Raba D, Yuan M, Fang X, Menzer WM, Xie B, Liang P, Tuz K, Minh DDL, Juárez O. Role of Subunit D in Ubiquinone-Binding Site of Vibrio cholerae NQR: Pocket Flexibility and Inhibitor Resistance. ACS OMEGA 2019; 4:19324-19331. [PMID: 31763556 PMCID: PMC6868883 DOI: 10.1021/acsomega.9b02707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
The ion-pumping NADH: ubiquinone dehydrogenase (NQR) is a vital component of the respiratory chain of numerous species of marine and pathogenic bacteria, including Vibrio cholerae. This respiratory enzyme couples the transfer of electrons from NADH to ubiquinone (UQ) to the pumping of ions across the plasma membrane, producing a gradient that sustains multiple homeostatic processes. The binding site of UQ within the enzyme is an important functional and structural motif that could be used to design drugs against pathogenic bacteria. Our group recently located the UQ site in the interface between subunits B and D and identified the residues within subunit B that are important for UQ binding. In this study, we carried out alanine scanning mutagenesis of amino acid residues located in subunit D of V. cholerae NQR to understand their role in UQ binding and enzymatic catalysis. Moreover, molecular docking calculations were performed to characterize the structure of the site at the atomic level. The results show that mutations in these positions, in particular, in residues P185, L190, and F193, decrease the turnover rate and increase the Km for UQ. These mutants also showed an increase in the resistance against the inhibitor HQNO. The data indicate that residues in subunit D fulfill important structural roles, restricting and orienting UQ in a catalytically favorable position. In addition, mutations of these residues open the site and allow the simultaneous binding of substrate and inhibitors, producing partial inhibition, which appears to be a strategy used by Pseudomonas aeruginosa to avoid autopoisoning.
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Affiliation(s)
- Daniel
A. Raba
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Ming Yuan
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Xuan Fang
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - William M. Menzer
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Bing Xie
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Pingdong Liang
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Karina Tuz
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - David D. L. Minh
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Oscar Juárez
- Department
of Biological Sciences and Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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6
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Mezic KG, Juárez O, Neehaul Y, Cho J, Cook D, Hellwig P, Barquera B. Glutamate 95 in NqrE Is an Essential Residue for the Translocation of Cations in Na +-NQR. Biochemistry 2019; 58:2167-2175. [PMID: 30907577 DOI: 10.1021/acs.biochem.8b01294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The sodium-pumping NADH:quinone oxidoreductase (Na+-NQR) is a bacterial enzyme that oxidizes NADH, reduces ubiquinone, and translocates Na+ across the membrane. We previously identified three acidic residues in the membrane-spanning helices, near the cytosol, NqrB-D397, NqrD-D133, and NqrE-E95, as candidates likely to be involved in Na+ uptake, and replacement of any one of them by a non-acidic residue affects the Na+-dependent kinetics of the enzyme. Here, we have inquired further into the role of the NqrE-E95 residue by constructing a series of mutants in which this residue is replaced by amino acids with charges and/or sizes different from those of the glutamate of the wild-type enzyme. All of the mutants showed altered steady-state kinetics with the acceleration of turnover by Na+ greatly diminished. Selected mutants were studied by other physical methods. Membrane potential measurements showed that NqrE-E95D and A are significantly less efficient in ion transport. NqrE-E95A, Q, and D were studied by transient kinetic measurements of the reduction of the enzyme by NADH. In all three cases, the results indicated inhibition of the electron-transfer step in which the FMNC becomes reduced. This is the first Na+-dependent step and is associated with Na+ uptake by the enzyme. Electrochemical measurements on NqrE-E95Q showed that the Na+ dependence of the redox potential of the FMN cofactors has been lost. The fact that the mutations at the NqrE-E95 site have specific effects related to translocation of Na+ and Li+ strongly indicates a definite role for NqrE-E95 in the cation transport process of Na+-NQR.
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Affiliation(s)
- Katherine G Mezic
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Oscar Juárez
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Yashvin Neehaul
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe , Université de Strasbourg-CNRS , 1 rue Blaise Pascal , 67000 Strasbourg , France
| | - Jonathan Cho
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Darcie Cook
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe , Université de Strasbourg-CNRS , 1 rue Blaise Pascal , 67000 Strasbourg , France
| | - Blanca Barquera
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
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7
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Raba DA, Rosas-Lemus M, Menzer WM, Li C, Fang X, Liang P, Tuz K, Minh DDL, Juárez O. Characterization of the Pseudomonas aeruginosa NQR complex, a bacterial proton pump with roles in autopoisoning resistance. J Biol Chem 2018; 293:15664-15677. [PMID: 30135204 DOI: 10.1074/jbc.ra118.003194] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/13/2018] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium responsible for a large number of nosocomial infections. The P. aeruginosa respiratory chain contains the ion-pumping NADH:ubiquinone oxidoreductase (NQR). This enzyme couples the transfer of electrons from NADH to ubiquinone to the pumping of sodium ions across the cell membrane, generating a gradient that drives essential cellular processes in many bacteria. In this study, we characterized P. aeruginosa NQR (Pa-NQR) to elucidate its physiologic function. Our analyses reveal that Pa-NQR, in contrast with NQR homologues from other bacterial species, is not a sodium pump, but rather a completely new form of proton pump. Homology modeling and molecular dynamics simulations suggest that cation selectivity could be determined by the exit ion channels. We also show that Pa-NQR is resistant to the inhibitor 2-n-heptyl-4-hydroxyquinoline N-oxide (HQNO). HQNO is a quinolone secreted by P. aeruginosa during infection that acts as a quorum sensing agent and also has bactericidal properties against other bacteria. Using comparative analysis and computational modeling of the ubiquinone-binding site, we identified the specific residues that confer resistance toward this inhibitor. In summary, our findings indicate that Pa-NQR is a proton pump rather than a sodium pump and is highly resistant against the P. aeruginosa-produced compound HQNO, suggesting an important role in the adaptation against autotoxicity. These results provide a deep understanding of the metabolic role of NQR in P. aeruginosa and provide insight into the structural factors that determine the functional specialization in this family of respiratory complexes.
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Affiliation(s)
| | | | - William M Menzer
- From the Departments of Biological Sciences and.,Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Chen Li
- Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Xuan Fang
- From the Departments of Biological Sciences and
| | | | - Karina Tuz
- From the Departments of Biological Sciences and
| | - David D L Minh
- Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
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8
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Tuz K, Li C, Fang X, Raba DA, Liang P, Minh DDL, Juárez O. Identification of the Catalytic Ubiquinone-binding Site of Vibrio cholerae Sodium-dependent NADH Dehydrogenase: A NOVEL UBIQUINONE-BINDING MOTIF. J Biol Chem 2017; 292:3039-3048. [PMID: 28053088 DOI: 10.1074/jbc.m116.770982] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 12/29/2016] [Indexed: 11/06/2022] Open
Abstract
The sodium-dependent NADH dehydrogenase (Na+-NQR) is a key component of the respiratory chain of diverse prokaryotic species, including pathogenic bacteria. Na+-NQR uses the energy released by electron transfer between NADH and ubiquinone (UQ) to pump sodium, producing a gradient that sustains many essential homeostatic processes as well as virulence factor secretion and the elimination of drugs. The location of the UQ binding site has been controversial, with two main hypotheses that suggest that this site could be located in the cytosolic subunit A or in the membrane-bound subunit B. In this work, we performed alanine scanning mutagenesis of aromatic residues located in transmembrane helices II, IV, and V of subunit B, near glycine residues 140 and 141. These two critical glycine residues form part of the structures that regulate the site's accessibility. Our results indicate that the elimination of phenylalanine residue 211 or 213 abolishes the UQ-dependent activity, produces a leak of electrons to oxygen, and completely blocks the binding of UQ and the inhibitor HQNO. Molecular docking calculations predict that UQ interacts with phenylalanine 211 and pinpoints the location of the binding site in the interface of subunits B and D. The mutagenesis and structural analysis allow us to propose a novel UQ-binding motif, which is completely different compared with the sites of other respiratory photosynthetic complexes. These results are essential to understanding the electron transfer pathways and mechanism of Na+-NQR catalysis.
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Affiliation(s)
- Karina Tuz
- From the Departments of Biological Sciences and
| | - Chen Li
- Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Xuan Fang
- From the Departments of Biological Sciences and
| | | | | | - David D L Minh
- Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
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9
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Tuz K, Mezic KG, Xu T, Barquera B, Juárez O. The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase. J Biol Chem 2015; 290:20009-21. [PMID: 26004776 DOI: 10.1074/jbc.m115.658773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 11/06/2022] Open
Abstract
The sodium-dependent NADH dehydrogenase (Na(+)-NQR) is the main ion transporter in Vibrio cholerae. Its activity is linked to the operation of the respiratory chain and is essential for the development of the pathogenic phenotype. Previous studies have described different aspects of the enzyme, including the electron transfer pathways, sodium pumping structures, cofactor and subunit composition, among others. However, the mechanism of the enzyme remains to be completely elucidated. In this work, we have studied the kinetic mechanism of Na(+)-NQR with the use of steady state kinetics and stopped flow analysis. Na(+)-NQR follows a hexa-uni ping-pong mechanism, in which NADH acts as the first substrate, reacts with the enzyme, and the oxidized NAD leaves the catalytic site. In this conformation, the enzyme is able to capture two sodium ions and transport them to the external side of the membrane. In the last step, ubiquinone is bound and reduced, and ubiquinol is released. Our data also demonstrate that the catalytic cycle involves two redox states, the three- and five-electron reduced forms. A model that gathers all available information is proposed to explain the kinetic mechanism of Na(+)-NQR. This model provides a background to understand the current structural and functional information.
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Affiliation(s)
- Karina Tuz
- From the Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616 and
| | - Katherine G Mezic
- the Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Tianhao Xu
- From the Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616 and
| | - Blanca Barquera
- the Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Oscar Juárez
- From the Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616 and
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10
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Hreha TN, Mezic KG, Herce HD, Duffy EB, Bourges A, Pryshchep S, Juarez O, Barquera B. Complete topology of the RNF complex from Vibrio cholerae. Biochemistry 2015; 54:2443-55. [PMID: 25831459 DOI: 10.1021/acs.biochem.5b00020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNF is a redox-driven ion (Na(+) and in one case possibly H(+)) transporter present in many prokaryotes. It has been proposed that RNF performs a variety of reactions in different organisms, delivering low-potential reducing equivalents for specific cellular processes. RNF shares strong homology with the Na(+)-pumping respiratory enzyme Na(+)-NQR, although there are significant differences in subunit and redox cofactor composition. Here we report a topological analysis of the six subunits of RNF from Vibrio cholerae. Although individual subunits from other organisms have previously been studied, this is the first complete, experimentally derived, analysis of RNF from any one source. This has allowed us to identify and confirm key properties of RNF. The putative NADH binding site in RnfC is located on the cytoplasmic side of the membrane. FeS centers in RnfB and RnfC are also located on the cytoplasmic side. However, covalently attached FMNs in RnfD and RnfG are both located in the periplasm. RNF also contains a number of acidic residues that correspond to functionally important groups in Na(+)-NQR. The acidic residues involved in Na(+) uptake and many of those implicated in Na(+) translocation are topologically conserved. The topology of RNF closely matches the topology represented in the newly published structure of Na(+)-NQR, consistent with the close relation between the two enzymes. The topology of RNF is discussed in the context of the current structural model of Na(+)-NQR, and the proposed functionality of the RNF complex itself.
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11
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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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12
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Steuber J, Halang P, Vorburger T, Steffen W, Vohl G, Fritz G. Central role of the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) in sodium bioenergetics of Vibrio cholerae. Biol Chem 2014; 395:1389-99. [DOI: 10.1515/hsz-2014-0204] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 07/09/2014] [Indexed: 11/15/2022]
Abstract
Abstract
Vibrio cholerae is a Gram-negative bacterium that lives in brackish or sea water environments. Strains of V. cholerae carrying the pathogenicity islands infect the human gut and cause the fatal disease cholera. Vibrio cholerae maintains a Na+ gradient at its cytoplasmic membrane that drives substrate uptake, motility, and efflux of antibiotics. Here, we summarize the major Na+-dependent transport processes and describe the central role of the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR), a primary Na+ pump, in maintaining a Na+-motive force. The Na+-NQR is a membrane protein complex with a mass of about 220 kDa that couples the exergonic oxidation of NADH to the transport of Na+ across the cytoplasmic membrane. We describe the molecular architecture of this respiratory complex and summarize the findings how electron transport might be coupled to Na+-translocation. Moreover, recent advances in the determination of the three-dimensional structure of this complex are reported.
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13
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The sodium pumping NADH:quinone oxidoreductase (Na⁺-NQR), a unique redox-driven ion pump. J Bioenerg Biomembr 2014; 46:289-98. [PMID: 25052842 DOI: 10.1007/s10863-014-9565-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 07/03/2014] [Indexed: 12/15/2022]
Abstract
The Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) is a unique Na(+) pumping respiratory complex found only in prokaryotes, that plays a key role in the metabolism of marine and pathogenic bacteria, including Vibrio cholerae and other human pathogens. Na(+)-NQR is the main entrance for reducing equivalents into the respiratory chain of these bacteria, catalyzing the oxidation of NADH and the reduction of quinone, the free energy of this redox reaction drives the selective translocation of Na(+) across the cell membrane, which energizes key cellular processes. In this review we summarize the unique properties of Na(+)-NQR in terms of its redox cofactor composition, electron transfer reactions and a possible mechanism of coupling and pumping.
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14
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Strickland M, Juárez O, Neehaul Y, Cook DA, Barquera B, Hellwig P. The conformational changes induced by ubiquinone binding in the Na+-pumping NADH:ubiquinone oxidoreductase (Na+-NQR) are kinetically controlled by conserved glycines 140 and 141 of the NqrB subunit. J Biol Chem 2014; 289:23723-33. [PMID: 25006248 DOI: 10.1074/jbc.m114.574640] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Na(+)-pumping NADH:ubiquinone oxidoreductase (Na(+)-NQR) is responsible for maintaining a sodium gradient across the inner bacterial membrane. This respiratory enzyme, which couples sodium pumping to the electron transfer between NADH and ubiquinone, is not present in eukaryotes and as such could be a target for antibiotics. In this paper it is shown that the site of ubiquinone reduction is conformationally coupled to the NqrB subunit, which also hosts the final cofactor in the electron transport chain, riboflavin. Previous work showed that mutations in conserved NqrB glycine residues 140 and 141 affect ubiquinone reduction and the proper functioning of the sodium pump. Surprisingly, these mutants did not affect the dissociation constant of ubiquinone or its analog HQNO (2-n-heptyl-4-hydroxyquinoline N-oxide) from Na(+)-NQR, which indicates that these residues do not participate directly in the ubiquinone binding site but probably control its accessibility. Indeed, redox-induced difference spectroscopy showed that these mutations prevented the conformational change involved in ubiquinone binding but did not modify the signals corresponding to bound ubiquinone. Moreover, data are presented that demonstrate the NqrA subunit is able to bind ubiquinone but with a low non-catalytically relevant affinity. It is also suggested that Na(+)-NQR contains a single catalytic ubiquinone binding site and a second site that can bind ubiquinone but is not active.
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Affiliation(s)
- Madeleine Strickland
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
| | - Oscar Juárez
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Yashvin Neehaul
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
| | - Darcie A Cook
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Blanca Barquera
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Petra Hellwig
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
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15
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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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16
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Dupont CL, Larsson J, Yooseph S, Ininbergs K, Goll J, Asplund-Samuelsson J, McCrow JP, Celepli N, Allen LZ, Ekman M, Lucas AJ, Hagström Å, Thiagarajan M, Brindefalk B, Richter AR, Andersson AF, Tenney A, Lundin D, Tovchigrechko A, Nylander JAA, Brami D, Badger JH, Allen AE, Rusch DB, Hoffman J, Norrby E, Friedman R, Pinhassi J, Venter JC, Bergman B. Functional tradeoffs underpin salinity-driven divergence in microbial community composition. PLoS One 2014; 9:e89549. [PMID: 24586863 PMCID: PMC3937345 DOI: 10.1371/journal.pone.0089549] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/23/2014] [Indexed: 11/23/2022] Open
Abstract
Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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Affiliation(s)
- Chris L. Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
- * E-mail: (CLD); (JL)
| | - John Larsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- * E-mail: (CLD); (JL)
| | - Shibu Yooseph
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Karolina Ininbergs
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Johannes Goll
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - John P. McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Narin Celepli
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Lisa Zeigler Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Martin Ekman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Andrew J. Lucas
- Marine Physical Laboratory, Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States of America
| | - Åke Hagström
- Swedish Institute for the Marine Environment (SIME), University of Gothenburg, Gothenburg, Sweden
| | - Mathangi Thiagarajan
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Björn Brindefalk
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Alexander R. Richter
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden
| | - Aaron Tenney
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Daniel Lundin
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna, Sweden
| | - Andrey Tovchigrechko
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Johan A. A. Nylander
- Department of Biodiversity Informatics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Daniel Brami
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Jonathan H. Badger
- Informatics Group, J. Craig Venter Institute, San Diego, California, United States of America
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Douglas B. Rusch
- Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jeff Hoffman
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Erling Norrby
- Center for History of Science, The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Robert Friedman
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - J. Craig Venter
- Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, United States of America
| | - Birgitta Bergman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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17
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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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18
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Neehaul Y, Juárez O, Barquera B, Hellwig P. Infrared Spectroscopic Evidence of a Redox-Dependent Conformational Change Involving Ion Binding Residue NqrB-D397 in the Na+-Pumping NADH:Quinone Oxidoreductase from Vibrio cholerae. Biochemistry 2013; 52:3085-93. [DOI: 10.1021/bi4000386] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yashvin Neehaul
- Laboratoire de bioelectrochimie
et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Oscar Juárez
- Department of Biology, Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United
States
| | - Blanca Barquera
- Department of Biology, Center
for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United
States
| | - Petra Hellwig
- Laboratoire de bioelectrochimie
et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
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19
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Juárez O, Neehaul Y, Turk E, Chahboun N, DeMicco JM, Hellwig P, Barquera B. The role of glycine residues 140 and 141 of subunit B in the functional ubiquinone binding site of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae. J Biol Chem 2012; 287:25678-85. [PMID: 22645140 DOI: 10.1074/jbc.m112.366088] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+)-pumping NADH:quinone oxidoreductase (Na(+)-NQR) is the main entrance for electrons into the respiratory chain of many marine and pathogenic bacteria. The enzyme accepts electrons from NADH and donates them to ubiquinone, and the free energy released by this redox reaction is used to create an electrochemical gradient of sodium across the cell membrane. Here we report the role of glycine 140 and glycine 141 of the NqrB subunit in the functional binding of ubiquinone. Mutations at these residues altered the affinity of the enzyme for ubiquinol. Moreover, mutations in residue NqrB-G140 almost completely abolished the electron transfer to ubiquinone. Thus, NqrB-G140 and -G141 are critical for the binding and reaction of Na(+)-NQR with its electron acceptor, ubiquinone.
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Affiliation(s)
- Oscar Juárez
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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