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Zeamari K, Gerbaud G, Grosse S, Fourmond V, Chaspoul F, Biaso F, Arnoux P, Sabaty M, Pignol D, Guigliarelli B, Burlat B. Tuning the redox properties of a [4Fe-4S] center to modulate the activity of Mo-bisPGD periplasmic nitrate reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:402-413. [DOI: 10.1016/j.bbabio.2019.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 11/15/2022]
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2
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Miller AF, Duan HD, Varner TA, Mohamed Raseek N. Reduction midpoint potentials of bifurcating electron transfer flavoproteins. Methods Enzymol 2019; 620:365-398. [PMID: 31072494 DOI: 10.1016/bs.mie.2019.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recently, a variety of enzymes have been found to accept electrons from NAD(P)H yet reduce lower-potential carriers such as ferredoxin and flavodoxin semiquinone, in apparent violation of thermodynamics. The reaction is favorable overall, however, because these enzymes couple the foregoing endergonic one-electron transfer to exergonic transfer of the other electron from each NAD(P)H, in a process called "flavin-based electron bifurcation." The reduction midpoint potentials (E°s) of the multiple flavins in these enzymes are critical to their mechanisms. We describe methods we have found to be useful for measuring each of the E°s of each of the flavins in bifurcating electron transfer flavoproteins.
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Affiliation(s)
- A-F Miller
- Department of Chemistry, University of Kentucky, Lexington, KY, United States.
| | - H D Duan
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
| | - T A Varner
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
| | - N Mohamed Raseek
- Department of Chemistry, University of Kentucky, Lexington, KY, United States
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part III. [4Fe-4S], [3Fe-4S] and [2Fe-2S] iron-sulfur proteins. J Struct Biol 2018; 202:264-274. [DOI: 10.1016/j.jsb.2018.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/16/2018] [Indexed: 11/18/2022]
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Ashmore D, Chaudhari A, Barlow B, Barlow B, Harper T, Vig K, Miller M, Singh S, Nelson E, Pillai S. Evaluation of E. coli inhibition by plain and polymer-coated silver nanoparticles. Rev Inst Med Trop Sao Paulo 2018; 60:e18. [PMID: 29694600 PMCID: PMC5956551 DOI: 10.1590/s1678-9946201860018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/15/2018] [Indexed: 11/22/2022] Open
Abstract
Escherichia coli causes various ailments such as septicemia, enteritis, foodborne illnesses, and urinary tract infections which are of concern in the public health field due to antibiotic resistance. Silver nanoparticles (AgNP) are known for their biocompatibility and antibacterial activity, and may prove to be an alternative method of treatment, especially as wound dressings. In this study, we compared the antibacterial efficacy of two polymer-coated silver nanoparticles either containing 10% Ag (Ag 10% + Polymer), or 99% Ag (AgPVP) in relation to plain uncoated silver nanoparticles (AgNP). Atomic force microscopy was used to characterize the nanoparticles, and their antibacterial efficacy was compared by the minimum inhibitory concentration (MIC) and bacterial growth curve assays, followed by molecular studies using scanning electron microscopy (SEM) and (qRT- PCR). AgNP inhibited the growth of E. coli only at 0.621 mg/mL, which was double the concentration required for both coated nanoparticles (0.312 mg/mL). Similarly, bacterial growth was impeded as early as 8 h at 0.156 mg/mL of both coated nanoparticles as compared to 0.312 mg/mL for plain AgNP. SEM data showed that nanoparticles damaged the cell membrane, resulting in bacterial cell lysis, expulsion of cellular contents, and complete disintegration of some cells. The expression of genes associated with the TCA cycle (aceF and frdB) and amino acid metabolism (gadB, metL, argC) were substantially downregulated in E. coli treated with nanoparticles. The reduction in the silver ion (Ag+) concentration of polymer-coated AgNP did not affect their antibacterial efficacy against E. coli.
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Affiliation(s)
- D'Andrea Ashmore
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | | | - Brandi Barlow
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | - Brett Barlow
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | - Talia Harper
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | - Komal Vig
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | - Michael Miller
- AU Research Instrumentation Facility, Harrison School of Pharmacy, Auburn University, Auburn, Alabama, USA
| | - Shree Singh
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
| | | | - Shreekumar Pillai
- Center for Nanobiotechnology Research, Alabama State University, Montgomery, Alabama, USA
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Lu Y, Qiao F, Li Y, Sang XH, Li CR, Jiang JD, Yang XY, You XF. Recombinant expression and biochemical characterization of Mycobacterium tuberculosis 3Fe-4S ferredoxin Rv1786. Appl Microbiol Biotechnol 2017; 101:7201-7212. [DOI: 10.1007/s00253-017-8454-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 07/26/2017] [Indexed: 11/25/2022]
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6
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Benjdia A, Decamps L, Guillot A, Kubiak X, Ruffié P, Sandström C, Berteau O. Insights into the catalysis of a lysine-tryptophan bond in bacterial peptides by a SPASM domain radical S-adenosylmethionine (SAM) peptide cyclase. J Biol Chem 2017; 292:10835-10844. [PMID: 28476884 PMCID: PMC5491770 DOI: 10.1074/jbc.m117.783464] [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: 02/27/2017] [Revised: 04/26/2017] [Indexed: 11/06/2022] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes are emerging as a major superfamily of biological catalysts involved in the biosynthesis of the broad family of bioactive peptides called ribosomally synthesized and post-translationally modified peptides (RiPPs). These enzymes have been shown to catalyze unconventional reactions, such as methyl transfer to electrophilic carbon atoms, sulfur to Cα atom thioether bonds, or carbon-carbon bond formation. Recently, a novel radical SAM enzyme catalyzing the formation of a lysine-tryptophan bond has been identified in Streptococcus thermophilus, and a reaction mechanism has been proposed. By combining site-directed mutagenesis, biochemical assays, and spectroscopic analyses, we show here that this enzyme, belonging to the emerging family of SPASM domain radical SAM enzymes, likely contains three [4Fe-4S] clusters. Notably, our data support that the seven conserved cysteine residues, present within the SPASM domain, are critical for enzyme activity. In addition, we uncovered the minimum substrate requirements and demonstrate that KW cyclic peptides are more widespread than anticipated, notably in pathogenic bacteria. Finally, we show a strict specificity of the enzyme for lysine and tryptophan residues and the dependence of an eight-amino acid leader peptide for activity. Altogether, our study suggests novel mechanistic links among SPASM domain radical SAM enzymes and supports the involvement of non-cysteinyl ligands in the coordination of auxiliary clusters.
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Affiliation(s)
- Alhosna Benjdia
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Laure Decamps
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Alain Guillot
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Xavier Kubiak
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Pauline Ruffié
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
| | - Corine Sandström
- the Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P. O. Box 7015, Uppsala 750-07, Sweden
| | - Olivier Berteau
- From the Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France and
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Molle T, Moreau Y, Clemancey M, Forouhar F, Ravanat JL, Duraffourg N, Fourmond V, Latour JM, Gambarelli S, Mulliez E, Atta M. Redox Behavior of the S-Adenosylmethionine (SAM)-Binding Fe-S Cluster in Methylthiotransferase RimO, toward Understanding Dual SAM Activity. Biochemistry 2016; 55:5798-5808. [PMID: 27677419 DOI: 10.1021/acs.biochem.6b00597] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RimO, a radical-S-adenosylmethionine (SAM) enzyme, catalyzes the specific C3 methylthiolation of the D89 residue in the ribosomal S12 protein. Two intact iron-sulfur clusters and two SAM cofactors both are required for catalysis. By using electron paramagnetic resonance, Mössbauer spectroscopies, and site-directed mutagenesis, we show how two SAM molecules sequentially bind to the unique iron site of the radical-SAM cluster for two distinct chemical reactions in RimO. Our data establish that the two SAM molecules bind the radical-SAM cluster to the unique iron site, and spectroscopic evidence obtained under strongly reducing conditions supports a mechanism in which the first molecule of SAM causes the reoxidation of the reduced radical-SAM cluster, impeding reductive cleavage of SAM to occur and allowing SAM to methylate a HS- ligand bound to the additional cluster. Furthermore, by using density functional theory-based methods, we provide a description of the reaction mechanism that predicts the attack of the carbon radical substrate on the methylthio group attached to the additional [4Fe-4S] cluster.
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Affiliation(s)
- Thibaut Molle
- Laboratoire de Chimie et Biologie des Métaux, team "Biocatalyse", Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/Biocat, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Yohann Moreau
- Laboratoire de Chimie et Biologie des Métaux, team "MCT" Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/MCT, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Martin Clemancey
- Laboratoire de Chimie et Biologie des Métaux, team "PMB" Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/PMB, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Farhad Forouhar
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University , New York, New York 10027, United States
| | - Jean-Luc Ravanat
- University Grenoble Alpes , INAC-SCIB, F-38000 Grenoble, France.,CEA , INAC-SyMMES, F-38000 Grenoble, France
| | - Nicolas Duraffourg
- Laboratoire de Chimie et Biologie des Métaux, team "Affond" Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/Affond, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Vincent Fourmond
- Aix-Marseille University , CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France
| | - Jean-Marc Latour
- Laboratoire de Chimie et Biologie des Métaux, team "PMB" Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/PMB, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Serge Gambarelli
- University Grenoble Alpes, INAC, SCIB/LRM , F-38000 Grenoble, France.,CEA, INAC, SCIB/LRM, F-38054 Grenoble, France
| | - Etienne Mulliez
- Laboratoire de Chimie et Biologie des Métaux, team "Biocatalyse", Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/Biocat, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux, team "Biocatalyse", Biosciences & Biotechnology Institute of Grenoble (BIG), BIG/LCBM/Biocat, UMR 5249 CEA/CNRS/UGA, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
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Cheng VWT, Piragasam RS, Rothery RA, Maklashina E, Cecchini G, Weiner JH. Redox state of flavin adenine dinucleotide drives substrate binding and product release in Escherichia coli succinate dehydrogenase. Biochemistry 2015; 54:1043-52. [PMID: 25569225 DOI: 10.1021/bi501350j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The Complex II family of enzymes, comprising respiratory succinate dehydrogenases and fumarate reductases, catalyzes reversible interconversion of succinate and fumarate. In contrast to the covalent flavin adenine dinucleotide (FAD) cofactor assembled in these enzymes, soluble fumarate reductases (e.g., those from Shewanella frigidimarina) that assemble a noncovalent FAD cannot catalyze succinate oxidation but retain the ability to reduce fumarate. In this study, an SdhA-H45A variant that eliminates the site of the 8α-N3-histidyl covalent linkage between the protein and FAD was examined. Variants SdhA-R286A/K/Y and -H242A/Y that target residues thought to be important for substrate binding and catalysis were also studied. The variants SdhA-H45A and -R286A/K/Y resulted in the assembly of a noncovalent FAD cofactor, which led to a significant decrease (-87 mV or more) in its reduction potential. The variant enzymes were studied by electron paramagnetic resonance spectroscopy following stand-alone reduction and potentiometric titrations. The "free" and "occupied" states of the active site were linked to the reduced and oxidized states of FAD, respectively. Our data allow for a proposed model of succinate oxidation that is consistent with tunnel diode effects observed in the succinate dehydrogenase enzyme and a preference for fumarate reduction catalysis in fumarate reductase homologues that assemble a noncovalent FAD.
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Affiliation(s)
- Victor W T Cheng
- Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G 2H7, Canada
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