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Ernst C, Kayastha K, Koch T, Venceslau SS, Pereira IAC, Demmer U, Ermler U, Dahl C. Structural and spectroscopic characterization of a HdrA-like subunit from Hyphomicrobium denitrificans. FEBS J 2020; 288:1664-1678. [PMID: 32750208 DOI: 10.1111/febs.15505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 07/03/2020] [Accepted: 07/31/2020] [Indexed: 02/01/2023]
Abstract
Many bacteria and archaea employ a novel pathway of sulfur oxidation involving an enzyme complex that is related to the heterodisulfide reductase (Hdr or HdrABC) of methanogens. As a first step in the biochemical characterization of Hdr-like proteins from sulfur oxidizers (sHdr), we structurally analyzed the recombinant sHdrA protein from the Alphaproteobacterium Hyphomicrobium denitrificans at 1.4 Å resolution. The sHdrA core structure is similar to that of methanogenic HdrA (mHdrA) which binds the electron-bifurcating flavin adenine dinucleotide (FAD), the heart of the HdrABC-[NiFe]-hydrogenase catalyzed reaction. Each sHdrA homodimer carries two FADs and two [4Fe-4S] clusters being linked by electron conductivity. Redox titrations monitored by electron paramagnetic resonance and visible spectroscopy revealed a redox potential between -203 and -188 mV for the [4Fe-4S] center. The potentials for the FADH•/FADH- and FAD/FADH• pairs reside between -174 and -156 mV and between -81 and -19 mV, respectively. The resulting stable semiquinone FADH• species already detectable in the visible and electron paramagnetic resonance spectra of the as-isolated state of sHdrA is incompatible with basic principles of flavin-based electron bifurcation such that the sHdr complex does not apply this new mode of energy coupling. The inverted one-electron FAD redox potentials of sHdr and mHdr are clearly reflected in the different FAD-polypeptide interactions. According to this finding and the assumption that the sHdr complex forms an asymmetric HdrAA'B1C1B2C2 hexamer, we tentatively propose a mechanism that links protein-bound sulfane oxidation to sulfite on HdrB1 with NAD+ reduction via lipoamide disulfide reduction on HdrB2. The FAD of HdrA thereby serves as an electron storage unit. DATABASE: Structural data are available in PDB database under the accession number 6TJR.
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Affiliation(s)
- Corvin Ernst
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Tobias Koch
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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Valette O, Tran TTT, Cavazza C, Caudeville E, Brasseur G, Dolla A, Talla E, Pieulle L. Biochemical Function, Molecular Structure and Evolution of an Atypical Thioredoxin Reductase from Desulfovibrio vulgaris. Front Microbiol 2017; 8:1855. [PMID: 29033913 PMCID: PMC5627308 DOI: 10.3389/fmicb.2017.01855] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/11/2017] [Indexed: 11/19/2022] Open
Abstract
Thioredoxin reductase (TR) regulates the intracellular redox environment by reducing thioredoxin (Trx). In anaerobes, recent findings indicate that the Trx redox network is implicated in the global redox regulation of metabolism but also actively participates in protecting cells against O2. In the anaerobe Desulfovibrio vulgaris Hildenborough (DvH), there is an intriguing redundancy of the Trx system which includes a classical system using NADPH as electron source, a non-canonical system using NADH and an isolated TR (DvTRi). The functionality of DvTRi was questioned due to its lack of reactivity with DvTrxs. Structural analysis shows that DvTRi is a NAD(P)H-independent TR but its reducer needs still to be identified. Moreover, DvTRi reduced by an artificial electron source is able to reduce in turn DvTrx1 and complexation experiments demonstrate a direct interaction between DvTRi and DvTrx1. The deletion mutant tri exhibits a higher sensitivity to disulfide stress and the gene tri is upregulated by O2 exposure. Having DvTRi in addition to DvTR1 as electron source for reducing DvTrx1 must be an asset to combat oxidative stress. Large-scale phylogenomics analyses show that TRi homologs are confined within the anaerobes. All TRi proteins displayed a conserved TQ/NGK motif instead of the HRRD motif, which is selective for the binding of the 2′-phosphate group of NADPH. The evolutionary history of TRs indicates that tr1 is the common gene ancestor in prokaryotes, affected by both gene duplications and horizontal gene events, therefore leading to the appearance of TRi through subfunctionalization over the evolutionary time.
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Affiliation(s)
| | - Tam T T Tran
- Aix-Marseille Univ, CNRS, LCB, Marseille, France
| | - Christine Cavazza
- Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, Grenoble, France.,UMR 5249, Laboratoire de Chimie et Biologie des Métaux, Centre National de la Recherche Scientifique, Grenoble, France.,DRF/BIG/CBM, CEA-Grenoble, Grenoble, France
| | | | | | - Alain Dolla
- Aix-Marseille Univ, CNRS, LCB, Marseille, France
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Susanti D, Loganathan U, Compton A, Mukhopadhyay B. A Reexamination of Thioredoxin Reductase from Thermoplasma acidophilum, a Thermoacidophilic Euryarchaeon, Identifies It as an NADH-Dependent Enzyme. ACS OMEGA 2017; 2:4180-4187. [PMID: 28884159 PMCID: PMC5579543 DOI: 10.1021/acsomega.7b00640] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/18/2017] [Indexed: 06/07/2023]
Abstract
Flavin-containing Trx reductase (TrxR) of Thermoplasma acidophilum (Ta), a thermoacidophilic facultative anaerobic archaeon, lacks the structural features for the binding of 2'-phosphate of nicotinamide adenine dinucleotide phosphate (NADPH), and this feature has justified the observed lack of activity with NADPH; NADH has also been reported to be ineffective. Our recent phylogenetic analysis identified Ta-TrxR as closely related to the NADH-dependent enzymes of Thermotoga maritima and Desulfovibrio vulgaris, both being anaerobic bacteria. This observation instigated a reexamination of the activity of the enzyme, which showed that Ta-TrxR is NADH dependent; the apparent Km for NADH was 3.1 μM, a physiologically relevant value. This finding is consistent with the observation that NADH:TrxR has thus far been found primarily in anaerobic bacteria and archaea.
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Affiliation(s)
- Dwi Susanti
- Department
of Biochemistry, Biocomplexity Institute, and Virginia Tech Carilion School of
Medicine, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Usha Loganathan
- Department
of Biochemistry, Biocomplexity Institute, and Virginia Tech Carilion School of
Medicine, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Austin Compton
- Department
of Biochemistry, Biocomplexity Institute, and Virginia Tech Carilion School of
Medicine, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Biswarup Mukhopadhyay
- Department
of Biochemistry, Biocomplexity Institute, and Virginia Tech Carilion School of
Medicine, Virginia Tech, Blacksburg, Virginia 24061, United States
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Adamson H, Robinson M, Bond PS, Soboh B, Gillow K, Simonov AN, Elton DM, Bond AM, Sawers RG, Gavaghan DJ, Parkin A. Analysis of HypD Disulfide Redox Chemistry via Optimization of Fourier Transformed ac Voltammetric Data. Anal Chem 2017; 89:1565-1573. [PMID: 28029041 DOI: 10.1021/acs.analchem.6b03589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Rapid disulfide bond formation and cleavage is an essential mechanism of life. Using large amplitude Fourier transformed alternating current voltammetry (FTacV) we have measured previously uncharacterized disulfide bond redox chemistry in Escherichia coli HypD. This protein is representative of a class of assembly proteins that play an essential role in the biosynthesis of the active site of [NiFe]-hydrogenases, a family of H2-activating enzymes. Compared to conventional electrochemical methods, the advantages of the FTacV technique are the high resolution of the faradaic signal in the higher order harmonics and the fact that a single electrochemical experiment contains all the data needed to estimate the (very fast) electron transfer rates (both rate constants ≥ 4000 s-1) and quantify the energetics of the cysteine disulfide redox-reaction (reversible potentials for both processes approximately -0.21 ± 0.01 V vs SHE at pH 6). Previously, deriving such data depended on an inefficient manual trial-and-error approach to simulation. As a highly advantageous alternative, we describe herein an automated multiparameter data optimization analysis strategy where the simulated and experimental faradaic current data are compared for both the real and imaginary components in each of the 4th to 12th harmonics after quantifying the charging current data using the time-domain response.
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Affiliation(s)
- Hope Adamson
- Department of Chemistry, University of York , Heslington, York, YO10 5DD, United Kingdom
| | - Martin Robinson
- Department of Computer Science, University of Oxford , Wolfson Building, Parks Road, Oxford, OX1 3QD, United Kingdom
| | - Paul S Bond
- Department of Chemistry, University of York , Heslington, York, YO10 5DD, United Kingdom
| | - Basem Soboh
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
| | - Kathryn Gillow
- Mathematical Institute, Andrew Wiles Building, University of Oxford , Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom
| | - Alexandr N Simonov
- School of Chemistry and the ARC Centre of Excellence for Electromaterials Science, Monash University , Clayton, Victoria 3800, Australia
| | - Darrell M Elton
- School of Engineering and Mathematical Sciences, La Trobe University , Bundoora, Victoria 3086, Australia
| | - Alan M Bond
- School of Chemistry and the ARC Centre of Excellence for Electromaterials Science, Monash University , Clayton, Victoria 3800, Australia
| | - R Gary Sawers
- Institute for Biology/Microbiology, Martin Luther University Halle-Wittenberg , Halle (Saale), Germany
| | - David J Gavaghan
- Department of Computer Science, University of Oxford , Wolfson Building, Parks Road, Oxford, OX1 3QD, United Kingdom
| | - Alison Parkin
- Department of Chemistry, University of York , Heslington, York, YO10 5DD, United Kingdom
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Susanti D, Loganathan U, Mukhopadhyay B. A Novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD: A TOOL FOR REDOX REGULATION IN AN ANAEROBE. J Biol Chem 2016; 291:23084-23100. [PMID: 27590343 DOI: 10.1074/jbc.m116.750208] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Indexed: 12/18/2022] Open
Abstract
A recent report suggested that the thioredoxin-dependent metabolic regulation, which is widespread in all domains of life, existed in methanogenic archaea about 3.5 billion years ago. We now show that the respective electron delivery enzyme (thioredoxin reductase, TrxR), although structurally similar to flavin-containing NADPH-dependent TrxRs (NTR), lacked an NADPH-binding site and was dependent on reduced coenzyme F420 (F420H2), a stronger reductant with a mid-point redox potential (E'0) of -360 mV; E'0 of NAD(P)H is -320 mV. Because F420 is a deazaflavin, this enzyme was named deazaflavin-dependent flavin-containing thioredoxin reductase (DFTR). It transferred electrons from F420H2 to thioredoxin via protein-bound flavin; Km values for thioredoxin and F420H2 were 6.3 and 28.6 μm, respectively. The E'0 of DFTR-bound flavin was approximately -389 mV, making electron transfer from NAD(P)H or F420H2 to flavin endergonic. However, under high partial pressures of hydrogen prevailing on early Earth and present day deep-sea volcanoes, the potential for the F420/F420H2 pair could be as low as -425 mV, making DFTR efficient. The presence of DFTR exclusively in ancient methanogens and mostly in the early Earth environment of deep-sea volcanoes and DFTR's characteristics suggest that the enzyme developed on early Earth and gave rise to NTR. A phylogenetic analysis revealed six more novel-type TrxR groups and suggested that the broader flavin-containing disulfide oxidoreductase family is more diverse than previously considered. The unprecedented structural similarities between an F420-dependent enzyme (DFTR) and an NADPH-dependent enzyme (NTR) brought new thoughts to investigations on F420 systems involved in microbial pathogenesis and antibiotic production.
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Affiliation(s)
| | | | - Biswarup Mukhopadhyay
- From the Department of Biochemistry, .,Biocomplexity Institute, and.,Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, Virginia 24061
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Duarte AG, Santos AA, Pereira IAC. Electron transfer between the QmoABC membrane complex and adenosine 5'-phosphosulfate reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:380-6. [PMID: 26768116 DOI: 10.1016/j.bbabio.2016.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/30/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
The dissimilatory adenosine 5'-phosphosulfate reductase (AprAB) is a key enzyme in the sulfate reduction pathway that catalyzes the reversible two electron reduction of adenosine 5'-phosphosulfate (APS) to sulfite and adenosine monophosphate (AMP). The physiological electron donor for AprAB is proposed to be the QmoABC membrane complex, coupling the quinone-pool to sulfate reduction. However, direct electron transfer between these two proteins has never been observed. In this work we demonstrate for the first time direct electron transfer between the Desulfovibrio desulfuricans ATCC 27774 QmoABC complex and AprAB. Cyclic voltammetry conducted with the modified Qmo electrode and AprAB in the electrolyte solution presented the Qmo electrochemical signature with two additional well-defined one electron redox processes, attributed to the AprAB FAD redox behavior. Moreover, experiments performed under catalytic conditions using the QmoABC modified electrode, with AprAB and APS in solution, show a catalytic current peak develop in the cathodic wave, attributed to substrate reduction, and which is not observed in the absence of QmoABC. Substrate dependence conducted with different electrode preparations (with and without immobilized Qmo) demonstrated that the QmoABC complex is essential for efficient electron delivery to AprAB, in order to sustain catalysis. These results confirm the role of Qmo in electron transfer to AprAB.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal.
| | - André A Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal.
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Bewley KD, Dey M, Bjork RE, Mitra S, Chobot SE, Drennan CL, Elliott SJ. Rheostat re-wired: alternative hypotheses for the control of thioredoxin reduction potentials. PLoS One 2015; 10:e0122466. [PMID: 25874934 PMCID: PMC4395160 DOI: 10.1371/journal.pone.0122466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 02/11/2015] [Indexed: 11/19/2022] Open
Abstract
Thioredoxins are small soluble proteins that contain a redox-active disulfide (CXXC). These disulfides are tuned to oxidizing or reducing potentials depending on the function of the thioredoxin within the cell. The mechanism by which the potential is tuned has been controversial, with two main hypotheses: first, that redox potential (Em) is specifically governed by a molecular 'rheostat'-the XX amino acids, which influence the Cys pKa values, and thereby, Em; and second, the overall thermodynamics of protein folding stability regulates the potential. Here, we use protein film voltammetry (PFV) to measure the pH dependence of the redox potentials of a series of wild-type and mutant archaeal Trxs, PFV and glutathionine-equilibrium to corroborate the measured potentials, the fluorescence probe BADAN to measure pKa values, guanidinium-based denaturation to measure protein unfolding, and X-ray crystallography to provide a structural basis for our functional analyses. We find that when these archaeal thioredoxins are probed directly using PFV, both the high and low potential thioredoxins display consistent 2H+:2e- coupling over a physiological pH range, in conflict with the conventional 'rheostat' model. Instead, folding measurements reveals an excellent correlation to reduction potentials, supporting the second hypothesis and revealing the molecular mechanism of reduction potential control in the ubiquitous Trx family.
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Affiliation(s)
- Kathryn D. Bewley
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
| | - Mishtu Dey
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rebekah E. Bjork
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sangha Mitra
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
| | - Sarah E. Chobot
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
| | - Catherine L. Drennan
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sean J. Elliott
- Department of Chemistry, Boston University, Boston, Massachusetts, United States of America
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Cheng Z, Zhang J, Ballou DP, Williams CH. Reactivity of thioredoxin as a protein thiol-disulfide oxidoreductase. Chem Rev 2011; 111:5768-83. [PMID: 21793530 DOI: 10.1021/cr100006x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhiyong Cheng
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-5606, USA
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Hernandez HH, Jaquez OA, Hamill MJ, Elliott SJ, Drennan CL. Thioredoxin reductase from Thermoplasma acidophilum: a new twist on redox regulation. Biochemistry 2008; 47:9728-37. [PMID: 18717593 DOI: 10.1021/bi8006753] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thioredoxin reductases (TrxRs) regulate the intracellular redox environment by using NADPH to provide reducing equivalents for thioredoxins (Trxs). Here we present the cloning and biochemical characterization of a putative TrxR (Ta0984) and a putative Trx (Ta0866) from Thermoplasma acidophilum. Our data identify Ta0866 as a Trx through its capacity to reduce insulin and be reduced by Escherichia coli TrxR in a NADPH-dependent manner. Our data also establish Ta0984 as a TrxR due to its ability to reduce T. acidophilum Trx ( taTrx), although not in a NADPH- or NADH-dependent manner. To explore the apparent inability of taTrxR to use NADPH or NADH as a reductant, we carried out a complete electrochemical characterization, which suggests that redox potential is not the source of this nonreactivity [Hamill et al. (2008) Biochemistry 47, 9738-9746]. Turning to crystallographic analysis, a 2.35 A resolution structure of taTrxR, also presented here, shows that despite the overall structural similarity to the well-characterized TrxR from E. coli (RMSD 1.30 A (2) for chain A), the "NADPH binding pocket" is not conserved. E. coli TrxR residues implicated in NADPH binding, H175, R176, R177, and R181, have been substituted with E185, Y186, M187, and M191 in the ta protein. Thus, we have identified a Trx and TrxR protein system from T. acidophilum for which the TrxR shares overall structural and redox properties with other TrxRs but lacks the appropriate binding motif to use the standard NADPH reductant. Our discovery of a TrxR that does not use NADPH provides a new twist in redox regulation.
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Affiliation(s)
- Hector H Hernandez
- Department of Chemistry, Massachusetts Institute of Technology, 16-573, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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