93 results on '"Ollagnier-de Choudens S"'
Search Results
2. SufA/IscA: reactivity studies of a class of scaffold proteins involved in [Fe-S] cluster assembly
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Ollagnier-de-Choudens, S., Sanakis, Y., and Fontecave, M.
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- 2004
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- View/download PDF
3. Iron-sulfur interconversions in the anaerobic ribonucleotide reductase from Escherichia coli
- Author
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Mulliez, E., Ollagnier-de Choudens, S., Meier, C., Cremonini, M., Luchinat, C., Trautwein, A. X., and Fontecave, M.
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- 1999
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4. Iron–Sulfur cluster assembly in bacteria and eukarya using the ISC biosynthesis machinery
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Ollagnier de Choudens, S., Puccio, H., Biocatalyse (BIOCAT ), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), edited by Michael K. Johnson and Robert A. Scott, and GON, Nathalie
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[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,[SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2017
5. Mechanisms of iron–sulfur cluster assembly: the SUF machinery
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Fontecave, M., Ollagnier de Choudens, S., Py, B., and Barras, F.
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- 2006
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- View/download PDF
6. Crystal structure of the apo-form of the CO dehydrogenase accessory protein CooT from Rhodospirillum rubrum
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Timm, J., primary, Brochier-Armanet, C., additional, Perard, J., additional, Zambelli, B., additional, Ollagnier-de-Choudens, S., additional, Ciurli, S., additional, and Cavazza, C., additional
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- 2017
- Full Text
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7. The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein
- Author
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Timm, J., primary, Brochier-Armanet, C., additional, Perard, J., additional, Zambelli, B., additional, Ollagnier-de-Choudens, S., additional, Ciurli, S., additional, and Cavazza, C., additional
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- 2017
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8. Assembly of Fe/S proteins in bacterial systems: Biochemistry of the bacterial ISC system
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Blanc, B., Gerez, C., Ollagnier de Choudens, S., Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
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Protein–protein interaction ,Fe/S transfer ,Frataxin ,Iron–sulfur ,Protein complex ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Fe/S assembly ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology - Abstract
International audience; Iron/sulfur clusters are key cofactors in proteins involved in a large number of conserved cellular processes, including gene expression, DNA replication and repair, ribosome biogenesis, tRNA modification, central metabolism and respiration. Fe/S proteins can perform a wide range of functions, from electron transfer to redox and non-redox catalysis. In all living organisms, Fe/S proteins are first synthesized in an apo-form. However, as the Fe/S prosthetic group is required for correct folding and/or protein stability, Fe/S clusters are inserted co-translationally or immediately after translation by specific assembly machineries. These systems have been extensively studied over the last decade, both in prokaryotes and eukaryotes. The present review covers the basic principles of the bacterial housekeeping Fe/S biogenesis ISC system, and related recent molecular advances. Some of the most exciting recent highlights relating to this system include structural and functional characterization of binary and ternary complexes involved in Fe/S cluster formation on the scaffold protein IscU. These advances enhance our understanding of the Fe/S cluster assembly mechanism by revealing essential interactions that could never be determined with isolated proteins and likely are closer to an in vivo situation. Much less is currently known about the molecular mechanism of the Fe/S transfer step, but a brief account of the protein-protein interactions involved is given. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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- 2015
9. Iron-Sulfur Center of Biotin Synthase and Lipoate Synthase
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Hewitson Ks, Baldwin Je, Peter L. Roach, Yiannis Sanakis, Ollagnier-De Choudens S, Marc Fontecave, and Eckard Münck
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Binding Sites ,ATP synthase ,biology ,Stereochemistry ,Iron ,Dimer ,chemistry.chemical_element ,Biotin synthase ,Photochemistry ,Dithionite ,Biochemistry ,Sulfur ,Substrate Specificity ,chemistry.chemical_compound ,Lipoic acid ,Bacterial Proteins ,Biosynthesis ,chemistry ,Biotin ,Sulfurtransferases ,Escherichia coli ,biology.protein - Abstract
Biotin synthase and lipoate synthase are homodimers that are required for the C-S bond formation at nonactivated carbon in the biosynthesis of biotin and lipoic acid, respectively. Aerobically isolated monomers were previously shown to contain a (2Fe-2S) cluster, however, after incubation with dithionite one (4Fe-4S) cluster per dimer was obtained, suggesting that two (2Fe-2S) clusters had combined at the interface of the subunits to form the (4Fe-4S) cluster. Here we report Mössbauer studies of (57)Fe-reconstituted biotin synthase showing that anaerobically prepared enzyme can accommodate two (4Fe-4S) clusters per dimer. The (4Fe-4S) cluster is quantitatively converted into a (2Fe-2S)(2+) cluster upon exposure to air. Reduction of the air-exposed enzyme with dithionite or photoreduced deazaflavin yields again (4Fe-4S) clusters. The (4Fe-4S) cluster is stable in both the 2+ and 1+ oxidation states. The Mössbauer and EPR parameters were DeltaE(q) = 1.13 mm/s and delta = 0.44 mm/s for the diamagnetic (4Fe-4S)(2+) and DeltaE(q) = 0.51 mm/s, delta = 0.85 mm/s, g(par) = 2.035, and g(perp) = 1.93 for the S = (1)/(2) state of (4Fe-4S)(1+). Considering that we find two (4Fe-4S) clusters per dimer, our studies argue against the early proposal that the enzyme contains one (4Fe-4S) cluster bridging the two subunits. Our study of lipoate synthase gave results similar to those obtained for BS: under strict anaerobiosis, lipoate synthase can accommodate a (4Fe-4S) cluster per subunit [DeltaE(q) = 1.20 mm/s and delta = 0.44 mm/s for the diamagnetic (4Fe-4S)(2+) and g(par) = 2.039 and g(perp) = 1.93 for the S = (1)/(2) state of (4Fe-4S)(1+)], which reacts with oxygen to generate a (2Fe-2S)(2+) center.
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- 2000
10. Structure of E.coli inducible lysine decarboxylase at active pH
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Kandiah, E., primary, Carriel, D., additional, Perard, J., additional, Malet, H., additional, Bacia, M., additional, Liu, K., additional, Chan, S.W.S., additional, Houry, W.A., additional, Ollagnier de Choudens, S., additional, Elsen, S., additional, and Gutsche, I., additional
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- 2016
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11. Structure of E.coli Constitutive lysine decarboxylase
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Kandiah, E., primary, Carriel, D., additional, Perard, J., additional, Malet, H., additional, Bacia, M., additional, Liu, K., additional, Chan, S.W.S., additional, Houry, W.A., additional, Ollagnier de Choudens, S., additional, Elsen, S., additional, and Gutsche, I., additional
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- 2016
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12. Revisited cryo-EM structure of Inducible lysine decarboxylase complexed with LARA domain of RavA ATPase
- Author
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Kandiah, E., primary, Carriel, D., additional, Perard, J., additional, Malet, H., additional, Bacia, M., additional, Liu, K., additional, Chan, S.W.S., additional, Houry, W.A., additional, Ollagnier de Choudens, S., additional, Elsen, S., additional, and Gutsche, I., additional
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- 2016
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13. Interference between titanium from TiO2 nanoparticles and iron homeostasis in E. coli
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Michaud-Soret , I., Fauquant , C., Sageot , C., Chan , A., Petit , A., Chevallet , M., Ollagnier De Choudens , S., Herlin-Boime , Nathalie, Jouneau , P., Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Francis PERRIN (LFP - URA 2453), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Edifices Nanométriques (LEDNA), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Etude des Matériaux par Microscopie Avancée (LEMMA ), Modélisation et Exploration des Matériaux (MEM), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Rabilloud, Thierry, Laboratoire de Chimie et Biologie des Métaux ( LCBM - UMR 5249 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Laboratoire Francis PERRIN ( LFP - URA 2453 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Edifices Nanométriques ( LEDNA ), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) ( NIMBE UMR 3685 ), Institut Rayonnement Matière de Saclay ( IRAMIS ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut Rayonnement Matière de Saclay ( IRAMIS ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Etude des Matériaux par Microscopie Avancée ( LEMMA ), Modélisation et Exploration des Matériaux ( MEM ), Institut Nanosciences et Cryogénie ( INAC ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Institut Nanosciences et Cryogénie ( INAC ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Grenoble Alpes ( UGA ), and Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
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[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,[CHIM.THEO] Chemical Sciences/Theoretical and/or physical chemistry ,[ CHIM.THEO ] Chemical Sciences/Theoretical and/or physical chemistry ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2013
14. ErpA, an iron sulfur (Fe S) protein of the A-type essential for respiratory metabolism in E.coli
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Loiseau, L., Gerez, C., Bekker, M., Ollagnier-de Choudens, S., Py, B., Sanakis, Y., Teixeira De Mattos, M.J., Fontecave, M., Barras, F., and Molecular Microbial Physiology (SILS, FNWI)
- Abstract
Understanding the biogenesis of iron-sulfur (Fe-S) proteins is relevant to many fields, including bioenergetics, gene regulation, and cancer research. Several multiprotein complexes assisting Fe-S assembly have been identified in both prokaryotes and eukaryotes. Here, we identify in Escherichia coli an A-type Fe-S protein that we named ErpA. Remarkably, erpA was found essential for growth of E. coli in the presence of oxygen or alternative electron acceptors. It was concluded that isoprenoid biosynthesis was impaired by the erpA mutation. First, the eukaryotic mevalonate-dependent pathway for biosynthesis of isopentenyl diphosphate restored the respiratory defects of an erpA mutant. Second, the erpA mutant contained a greatly reduced amount of ubiquinone and menaquinone. Third, ErpA bound Fe-S clusters and transferred them to apo-IspG, a protein catalyzing isopentenyl diphosphate biosynthesis in E. coli. Surprisingly, the erpA gene maps at a distance from any other Fe-S biogenesis-related gene. ErpA is an A-type Fe-S protein that is characterized by an essential role in cellular metabolism.
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- 2007
15. Structure of the Fe4S4 quinolinate synthase NadA from Thermotoga maritima
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Cherrier, M.V., primary, Chan, A., additional, Darnault, C., additional, Reichmann, D., additional, Amara, P., additional, Ollagnier de Choudens, S., additional, and Fontecilla-Camps, J.C., additional
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- 2014
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16. Insights into the Function of YciM, a Heat Shock Membrane Protein Required To Maintain Envelope Integrity in Escherichia coli
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Nicolaes, V., primary, El Hajjaji, H., additional, Davis, R. M., additional, Van der Henst, C., additional, Depuydt, M., additional, Leverrier, P., additional, Aertsen, A., additional, Haufroid, V., additional, Ollagnier de Choudens, S., additional, De Bolle, X., additional, Ruiz, N., additional, and Collet, J.-F., additional
- Published
- 2013
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17. Mechanisms of iron–sulfur cluster assembly: the SUF machinery
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Fontecave, M., primary, Ollagnier de Choudens, S., additional, Py, B., additional, and Barras, F., additional
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- 2005
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18. The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein
- Author
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S. Ollagnier-de-Choudens, Céline Brochier-Armanet, Barbara Zambelli, Christine Cavazza, Julien Pérard, Jennifer Timm, Stefano Ciurli, Timm, J., Brochier-Armanet, C., Perard, J., Zambelli, B., Ollagnier-De-Choudens, S., Ciurli, S., Cavazza, C., Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), ANR-10-BINF-0001,ANCESTROME,Approche de phylogénie intégrative pour la reconstruction de génomes ancestraux(2010), European Project: 283570,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2011-1,BIOSTRUCT-X(2011), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin, 40, 40127 Bologna, Italy
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0301 basic medicine ,Models, Molecular ,Circular dichroism ,Protein family ,Stereochemistry ,Dimer ,NICKEL ,Biophysics ,CARBON-MONOXIDE DEHYDROGENASE ,Biology ,010402 general chemistry ,Crystallography, X-Ray ,Rhodospirillum rubrum ,01 natural sciences ,Biochemistry ,Biomaterials ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Multienzyme Complexes ,Coot ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Amino Acid Sequence ,METAL-BINDING ,RHODOSPIRILLUM-RUBRUM ,Metals and Alloys ,Active site ,Isothermal titration calorimetry ,biology.organism_classification ,Aldehyde Oxidoreductases ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,0104 chemical sciences ,030104 developmental biology ,chemistry ,Chemistry (miscellaneous) ,biology.protein ,Protein Conformation, beta-Strand ,Protein Multimerization ,Carrier Proteins ,Carbon monoxide dehydrogenase ,Protein Binding - Abstract
International audience; In Rhodospirillum rubrum, maturation of Carbon Monoxide Dehydrogenase (CODH) requires three accessory proteins, CooC, CooT and CooJ, dedicated to nickel insertion into the active site, which is constituted by a distorted [NiFe$_3$S$_4$] cubane coordinated with a mononuclear Fe site. CooC is an ATPase proposed to provide the energy required for the maturation process, while CooJ is described as a metallochaperone with 16 histidines and 2 cysteines at the C-terminus, likely involved in metal binding and/or storage. Prior to the present study, no information was available on CooT at the molecular level. Here, the X-ray structure of RrCooT was obtained, which revealed that this protein is a homodimer featuring a fold that resembles an Sm-like domain, suggesting a role in RNA metabolism that was however not supported by experimental observations. Biochemical and biophysical evidence based on circular dichroism spectroscopy, light scattering, isothermal titration calorimetry and site-directed mutagenesis showed that RrCooT specifically binds a single Ni(ii) per dimer, with a dissociation constant of 9 nM, through the pair of Cys2, highly conserved residues, located at the dimer interface. Despite its role in the activation of RrCODH in vivo, CooT was thought to be a unique protein, found only in R. rubrum, with an unclear function. In this study, we extended the biological impact of CooT, establishing that this protein is a member of a novel Ni(ii)-binding protein family with 111 homologues, linked to anaerobic metabolism in bacteria and archaea, and in most cases to the presence of CODH.
- Published
- 2017
19. Fe-S biogenesis by SMS and SUF pathways: A focus on the assembly step.
- Author
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Dussouchaud M, Barras F, and Ollagnier de Choudens S
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- Phylogeny, Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism, Iron-Sulfur Proteins genetics, Iron-Sulfur Proteins metabolism
- Abstract
FeS clusters are prosthetic groups present in all organisms. Proteins with FeS centers are involved in most cellular processes. ISC and SUF are machineries necessary for the formation and insertion of FeS in proteins. Recently, a phylogenetic analysis on more than 10,000 genomes of prokaryotes have uncovered two new systems, MIS and SMS, which were proposed to be ancestral to ISC and SUF. SMS is composed of SmsBC, two homologs of SufBC(D), the scaffolding complex of SUF. In this review, we will specifically focus on the current knowledge of the SUF system and on the new perspectives given by the recent discovery of its ancestor, the SMS system., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests. Ollagnier Sandrine reports was provided by National Centre for Scientific Research. Ollagnier Sandrine reports a relationship with National Centre for Scientific Research that includes: employment, funding grants, and non-financial support. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
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- 2024
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20. Multimodal Spectroscopic Analysis of the Fe-S Clusters of the as-Isolated Escherichia coli SufBC 2 D Complex.
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Veronesi G, Pérard J, Clémancey M, Gerez C, Duverger Y, Kieffer I, Barras F, Gambarelli S, Blondin G, and Ollagnier de Choudens S
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- Electron Spin Resonance Spectroscopy, Spectroscopy, Mossbauer, X-Ray Absorption Spectroscopy, Carrier Proteins, Iron-Sulfur Proteins chemistry, Iron-Sulfur Proteins metabolism, Escherichia coli Proteins chemistry, Escherichia coli Proteins metabolism, Escherichia coli metabolism
- Abstract
Iron-sulfur (Fe-S) clusters are essential inorganic cofactors dedicated to a wide range of biological functions, including electron transfer and catalysis. Specialized multiprotein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein, on which Fe-S clusters are assembled before being transferred to cellular targets. Here, we describe the first characterization of the native Fe-S cluster of the anaerobically purified SufBC
2 D scaffold from Escherichia coli by XAS and Mössbauer, UV-visible absorption, and EPR spectroscopies. Interestingly, we propose that SufBC2 D harbors two iron-sulfur-containing species, a [2Fe-2S] cluster and an as-yet unidentified species. Mutagenesis and biochemistry were used to propose amino acid ligands for the [2Fe-2S] cluster, supporting the hypothesis that both SufB and SufD are involved in the Fe-S cluster ligation. The [2Fe-2S] cluster can be transferred to ferredoxin in agreement with the SufBC2 D scaffold function. These results are discussed in the context of Fe-S cluster biogenesis.- Published
- 2024
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21. Structural and Biochemical Characterization of Mycobacterium tuberculosis Zinc SufU-SufS Complex.
- Author
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Elchennawi I, Carpentier P, Caux C, Ponge M, and Ollagnier de Choudens S
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- Cysteine metabolism, Zinc metabolism, Carbon-Sulfur Lyases chemistry, Carbon-Sulfur Lyases genetics, Carbon-Sulfur Lyases metabolism, Sulfur metabolism, Iron metabolism, Escherichia coli metabolism, Mycobacterium tuberculosis metabolism
- Abstract
Iron-sulfur (Fe-S) clusters are inorganic prosthetic groups in proteins composed exclusively of iron and inorganic sulfide. These cofactors are required in a wide range of critical cellular pathways. Iron-sulfur clusters do not form spontaneously in vivo; several proteins are required to mobilize sulfur and iron, assemble and traffic-nascent clusters. Bacteria have developed several Fe-S assembly systems, such as the ISC, NIF, and SUF systems. Interestingly, in Mycobacterium tuberculosis ( Mtb ), the causative agent of tuberculosis (TB), the SUF machinery is the primary Fe-S biogenesis system. This operon is essential for the viability of Mtb under normal growth conditions, and the genes it contains are known to be vulnerable, revealing the Mtb SUF system as an interesting target in the fight against tuberculosis. In the present study, two proteins of the Mtb SUF system were characterized for the first time: Rv1464( sufS ) and Rv1465( sufU ). The results presented reveal how these two proteins work together and thus provide insights into Fe-S biogenesis/metabolism by this pathogen. Combining biochemistry and structural approaches, we showed that Rv1464 is a type II cysteine-desulfurase enzyme and that Rv1465 is a zinc-dependent protein interacting with Rv1464. Endowed with a sulfurtransferase activity, Rv1465 significantly enhances the cysteine-desulfurase activity of Rv1464 by transferring the sulfur atom from persulfide on Rv1464 to its conserved Cys40 residue. The zinc ion is important for the sulfur transfer reaction between SufS and SufU, and His354 in SufS plays an essential role in this reaction. Finally, we showed that Mtb SufS-SufU is more resistant to oxidative stress than E. coli SufS-SufE and that the presence of zinc in SufU is likely responsible for this improved resistance. This study on Rv1464 and Rv1465 will help guide the design of future anti-tuberculosis agents.
- Published
- 2023
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22. An early origin of iron-sulfur cluster biosynthesis machineries before Earth oxygenation.
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Garcia PS, D'Angelo F, Ollagnier de Choudens S, Dussouchaud M, Bouveret E, Gribaldo S, and Barras F
- Subjects
- Genome, Bacterial, Iron, Phylogeny, Sulfur metabolism, Iron-Sulfur Proteins genetics
- Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors essential for life. It is largely thought that the emergence of oxygenic photosynthesis and progressive oxygenation of the atmosphere led to the origin of multiprotein machineries (ISC, NIF and SUF) assisting Fe-S cluster synthesis in the presence of oxidative stress and shortage of bioavailable iron. However, previous analyses have left unclear the origin and evolution of these systems. Here, we combine exhaustive homology searches with genomic context analysis and phylogeny to precisely identify Fe-S cluster biogenesis systems in over 10,000 archaeal and bacterial genomes. We highlight the existence of two additional and clearly distinct 'minimal' Fe-S cluster assembly machineries, MIS (minimal iron-sulfur) and SMS (SUF-like minimal system), which we infer in the last universal common ancestor (LUCA) and we experimentally validate SMS as a bona fide Fe-S cluster biogenesis system. These ancestral systems were kept in archaea whereas they went through stepwise complexification in bacteria to incorporate additional functions for higher Fe-S cluster synthesis efficiency leading to SUF, ISC and NIF. Horizontal gene transfers and losses then shaped the current distribution of these systems, driving ecological adaptations such as the emergence of aerobic lifestyles in archaea. Our results show that dedicated machineries were in place early in evolution to assist Fe-S cluster biogenesis and that their origin is not directly linked to Earth oxygenation., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)
- Published
- 2022
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23. Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host.
- Author
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D'Angelo F, Fernández-Fueyo E, Garcia PS, Shomar H, Pelosse M, Manuel RR, Büke F, Liu S, van den Broek N, Duraffourg N, de Ram C, Pabst M, Bouveret E, Gribaldo S, Py B, Ollagnier de Choudens S, Barras F, and Bokinsky G
- Subjects
- Escherichia coli genetics, Escherichia coli metabolism, Iron metabolism, Phylogeny, Sulfur metabolism, Escherichia coli Proteins metabolism, Iron-Sulfur Proteins genetics, Iron-Sulfur Proteins metabolism
- Abstract
Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and highly versatile. However, Fe-S proteins and enzymes are often inactive outside their native host species. We sought to systematically investigate the compatibility of Fe-S networks with non-native Fe-S enzymes. By using collections of Fe-S enzyme orthologs representative of the entire range of prokaryotic diversity, we uncovered a striking correlation between phylogenetic distance and probability of functional expression. Moreover, coexpression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be supported by the foreign host. We also find that Fe-S enzymes that require specific electron carrier proteins are rarely functionally expressed unless their taxon-specific reducing partners are identified and co-expressed. We demonstrate how these principles can be applied to improve the activity of a radical S -adenosyl methionine(rSAM) enzyme from a Streptomyces antibiotic biosynthesis pathway in Escherichia coli . Our results clarify how oxygen sensitivity and incompatibilities with foreign Fe-S and electron transfer networks each impede heterologous activity. In particular, identifying compatible electron transfer proteins and heterologous Fe-S biogenesis pathways may prove essential for engineering functional Fe-S enzyme-dependent pathways., Competing Interests: FD, EF, PG, HS, MP, RM, FB, SL, Nv, ND, Cd, MP, EB, SG, BP, SO, FB, GB No competing interests declared, (© 2022, D'Angelo et al.)
- Published
- 2022
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24. Transient Formation of a Second Active Site Cavity during Quinolinic Acid Synthesis by NadA.
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Basbous H, Volbeda A, Amara P, Rohac R, Martin L, Ollagnier de Choudens S, and Fontecilla-Camps JC
- Subjects
- Catalysis, Catalytic Domain, Crystallography, X-Ray, Dihydroxyacetone Phosphate chemistry, Models, Molecular, Multienzyme Complexes metabolism, Protein Conformation, Substrate Specificity, Multienzyme Complexes chemistry, Quinolinic Acid chemistry
- Abstract
Quinolinate synthase, also called NadA, is a [4Fe-4S]-containing enzyme that uses what is probably the oldest pathway to generate quinolinic acid (QA), the universal precursor of the biologically essential cofactor nicotinamide adenine dinucleotide (NAD). Its synthesis comprises the condensation of dihydroxyacetone phosphate (DHAP) and iminoaspartate (IA), which involves dephosphorylation, isomerization, cyclization, and two dehydration steps. The convergence of the three homologous domains of NadA defines a narrow active site that contains a catalytically essential [4Fe-4S] cluster. A tunnel, which can be opened or closed depending on the nature (or absence) of the bound ligand, connects this cofactor to the protein surface. One outstanding riddle has been the observation that the so far characterized active site is too small to bind IA and DHAP simultaneously. Here, we have used site-directed mutagenesis, X-ray crystallography, functional analyses, and molecular dynamics simulations to propose a condensation mechanism that involves the transient formation of a second active site cavity to which one of the substrates can migrate before this reaction takes place.
- Published
- 2021
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25. Design of specific inhibitors of quinolinate synthase based on [4Fe-4S] cluster coordination.
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Saez Cabodevilla J, Volbeda A, Hamelin O, Latour JM, Gigarel O, Clémancey M, Darnault C, Reichmann D, Amara P, Fontecilla-Camps JC, and Ollagnier de Choudens S
- Abstract
Quinolinate synthase (NadA) is a [4Fe-4S] cluster-containing enzyme involved in the formation of quinolinic acid, the precursor of the essential NAD coenzyme. Here, we report the synthesis and activity of derivatives of the first inhibitor of NadA. Using multidisciplinary approaches we have investigated their action mechanism and discovered additional specific inhibitors of this enzyme.
- Published
- 2019
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26. Correction to: Iron-sulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding.
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Pérard J and Ollagnier de Choudens S
- Abstract
The article "Iron-sulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding", written by J. Pérard, Sandrine Ollagnier de Choudens was originally published electronically on the publisher's internet portal (currently SpringerLink) 26 December, 2017 without open access.
- Published
- 2018
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27. Iron-sulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding.
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Pérard J and Ollagnier de Choudens S
- Subjects
- Bacterial Proteins genetics, Humans, Operon genetics, Bacterial Proteins metabolism, Iron-Sulfur Proteins biosynthesis
- Abstract
Iron-sulfur clusters (Fe-S) are amongst the most ancient and versatile inorganic cofactors in nature which are used by proteins for fundamental biological processes. Multiprotein machineries (NIF, ISC, SUF) exist for Fe-S cluster biogenesis which are mainly conserved from bacteria to human. SUF system (sufABCDSE operon) plays a general role in many bacteria under conditions of iron limitation or oxidative stress. In this mini-review, we will summarize the current understanding of the molecular mechanism of Fe-S biogenesis by SUF. The advances in our understanding of the molecular aspects of SUF originate from biochemical, biophysical and recent structural studies. Combined with recent in vivo experiments, the understanding of the Fe-S biogenesis mechanism considerably moved forward.
- Published
- 2018
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28. The ErpA/NfuA complex builds an oxidation-resistant Fe-S cluster delivery pathway.
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Py B, Gerez C, Huguenot A, Vidaud C, Fontecave M, Ollagnier de Choudens S, and Barras F
- Subjects
- Gene Expression Regulation, Bacterial, Oxidation-Reduction, Escherichia coli metabolism, Escherichia coli Proteins metabolism, Iron-Sulfur Proteins metabolism, Metabolic Networks and Pathways, Oxidative Stress, Oxygen metabolism
- Abstract
Fe-S cluster-containing proteins occur in most organisms, wherein they assist in myriad processes from metabolism to DNA repair via gene expression and bioenergetic processes. Here, we used both in vitro and in vivo methods to investigate the capacity of the four Fe-S carriers, NfuA, SufA, ErpA, and IscA, to fulfill their targeting role under oxidative stress. Likewise, Fe-S clusters exhibited varying half-lives, depending on the carriers they were bound to; an NfuA-bound Fe-S cluster was more stable ( t
½ = 100 min) than those bound to SufA ( t½ = 55 min), ErpA ( t = 90 min. Using genetic and plasmon surface resonance analyses, we showed that NfuA and ErpA interacted directly with client proteins, whereas IscA or SufA did not. Moreover, NfuA and ErpA interacted with one another. Given all of these observations, we propose an architecture of the Fe-S delivery network in which ErpA is the last factor that delivers cluster directly to most if not all client proteins. NfuA is proposed to assist ErpA under severely unfavorable conditions. A comparison with the strategy employed in yeast and eukaryotes is discussed.½ = 54 min), or IscA ( t½ = 45 min). Surprisingly, the presence of NfuA further enhanced stability of the ErpA-bound cluster to t½ = 90 min. Using genetic and plasmon surface resonance analyses, we showed that NfuA and ErpA interacted directly with client proteins, whereas IscA or SufA did not. Moreover, NfuA and ErpA interacted with one another. Given all of these observations, we propose an architecture of the Fe-S delivery network in which ErpA is the last factor that delivers cluster directly to most if not all client proteins. NfuA is proposed to assist ErpA under severely unfavorable conditions. A comparison with the strategy employed in yeast and eukaryotes is discussed., (© 2018 Py et al.)- Published
- 2018
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29. Crystallographic Trapping of Reaction Intermediates in Quinolinic Acid Synthesis by NadA.
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Volbeda A, Saez Cabodevilla J, Darnault C, Gigarel O, Han TH, Renoux O, Hamelin O, Ollagnier-de-Choudens S, Amara P, and Fontecilla-Camps JC
- Subjects
- Crystallography, X-Ray, Molecular Docking Simulation, Multienzyme Complexes metabolism, NAD metabolism, Protein Conformation, Multienzyme Complexes chemistry, Quinolinic Acid metabolism, Thermotoga maritima enzymology
- Abstract
NadA is a multifunctional enzyme that condenses dihydroxyacetone phosphate (DHAP) with iminoaspartate (IA) to generate quinolinic acid (QA), the universal precursor of the nicotinamide adenine dinucleotide (NAD(P)) cofactor. Using X-ray crystallography, we have (i) characterized two of the reaction intermediates of QA synthesis using a "pH-shift" approach and a slowly reacting Thermotoga maritima NadA variant and (ii) observed the QA product, resulting from the degradation of an intermediate analogue, bound close to the entrance of a long tunnel leading to the solvent medium. We have also used molecular docking to propose a condensation mechanism between DHAP and IA based on two previously published Pyrococcus horikoshi NadA structures. The combination of reported data and our new results provide a structure-based complete catalytic sequence of QA synthesis by NadA.
- Published
- 2018
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30. ISCA1 is essential for mitochondrial Fe 4 S 4 biogenesis in vivo.
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Beilschmidt LK, Ollagnier de Choudens S, Fournier M, Sanakis I, Hograindleur MA, Clémancey M, Blondin G, Schmucker S, Eisenmann A, Weiss A, Koebel P, Messaddeq N, Puccio H, and Martelli A
- Subjects
- Aconitate Hydratase genetics, Animals, Binding Sites, Cloning, Molecular, Escherichia coli genetics, Escherichia coli metabolism, Female, Gene Expression, Genetic Vectors chemistry, Genetic Vectors metabolism, Iron-Sulfur Proteins genetics, Male, Mice, Mice, Inbred C57BL, Mitochondrial Proteins genetics, Primary Cell Culture, Protein Binding, Protein Interaction Domains and Motifs, Protein Multimerization, Recombinant Proteins genetics, Recombinant Proteins metabolism, Sensory Receptor Cells cytology, Spectroscopy, Mossbauer, Aconitate Hydratase metabolism, Iron-Sulfur Proteins metabolism, Mitochondrial Proteins metabolism, Muscle, Skeletal enzymology, Sensory Receptor Cells enzymology
- Abstract
Mammalian A-type proteins, ISCA1 and ISCA2, are evolutionarily conserved proteins involved in iron-sulfur cluster (Fe-S) biogenesis. Recently, it was shown that ISCA1 and ISCA2 form a heterocomplex that is implicated in the maturation of mitochondrial Fe
4 S4 proteins. Here we report that mouse ISCA1 and ISCA2 are Fe2 S2 -containing proteins that combine all features of Fe-S carrier proteins. We use biochemical, spectroscopic and in vivo approaches to demonstrate that despite forming a complex, ISCA1 and ISCA2 establish discrete interactions with components of the late Fe-S machinery. Surprisingly, knockdown experiments in mouse skeletal muscle and in primary cultures of neurons suggest that ISCA1, but not ISCA2, is required for mitochondrial Fe4 S4 proteins biogenesis. Collectively, our data suggest that cellular processes with different requirements for ISCA1, ISCA2 and ISCA1-ISCA2 complex seem to exist.- Published
- 2017
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31. Genetic, Biochemical, and Biophysical Methods for Studying FeS Proteins and Their Assembly.
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Ollagnier de Choudens S and Barras F
- Subjects
- Alleles, Animals, Bacteria genetics, Bacteria metabolism, Humans, Iron chemistry, Iron Deficiencies, Iron-Binding Proteins chemistry, Mice, Mice, Knockout, Models, Biological, Models, Chemical, Mutation, Organelle Biogenesis, Oxidative Stress, Sulfides metabolism, Frataxin, Iron-Sulfur Proteins genetics, Iron-Sulfur Proteins metabolism, Spectrum Analysis methods, Sulfides chemistry
- Abstract
FeS clusters containing proteins are structurally and functionally diverse and present in most organisms. Our understanding of FeS cluster production and insertion into polypeptides has benefited from collaborative efforts between in vitro and in vivo studies. The former allows a detailed description of FeS-containing protein and a deep understanding of the molecular mechanisms catalyzing FeS cluster assembly. The second allows to include metabolic and environmental constraints within the analysis of FeS homeostasis. The interplay and the cross talk between the two approaches have been a key strategy to reach a multileveled integrated understanding of FeS cluster homeostasis. In this chapter, we describe the genetic and biochemical/biophysical strategies that were used in the field of FeS cluster biogenesis, with the aim of providing the reader with a critical view of both approaches. In addition to the description of classic tricks and a series of recommendations, we will also discuss models as well as spectroscopic techniques useful to characterize FeS clusters such as UV-visible, Mössbauer, electronic paramagnetic resonance, resonance Raman, circular dichroism, and nuclear magnetic resonance., (© 2017 Elsevier Inc. All rights reserved.)
- Published
- 2017
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32. Crystal Structures of Quinolinate Synthase in Complex with a Substrate Analogue, the Condensation Intermediate, and Substrate-Derived Product.
- Author
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Volbeda A, Darnault C, Renoux O, Reichmann D, Amara P, Ollagnier de Choudens S, and Fontecilla-Camps JC
- Subjects
- Alkyl and Aryl Transferases genetics, Crystallography, X-Ray, Dihydroxyacetone Phosphate metabolism, Molecular Docking Simulation, Mutation, Protein Conformation, Thermotoga maritima enzymology, Alkyl and Aryl Transferases chemistry, Alkyl and Aryl Transferases metabolism, Quinolinic Acid metabolism
- Abstract
The enzyme NadA catalyzes the synthesis of quinolinic acid (QA), the precursor of the universal nicotinamide adenine dinucleotide (NAD) cofactor. Here, we report the crystal structures of complexes between the Thermotoga maritima (Tm) NadA K219R/Y107F variant and (i) the first intermediate (W) resulting from the condensation of dihydroxyacetone phosphate (DHAP) with iminoaspartate and (ii) the DHAP analogue and triose-phosphate isomerase inhibitor phosphoglycolohydroxamate (PGH). In addition, using the TmNadA K219R/Y21F variant, we have reacted substrates and obtained a crystalline complex between this protein and the QA product. We also show that citrate can bind to both TmNadA K219R and its Y21F variant. The W structure indicates that condensation causes dephosphorylation. We propose that catalysis by the K219R/Y107F variant is arrested at the W intermediate because the mutated protein is unable to catalyze its aldo-keto isomerization and/or cyclization that ultimately lead to QA formation. Intriguingly, PGH binds to NadA with its phosphate group at the site where the carboxylate groups of W also bind. Our results shed significant light on the mechanism of the reaction catalyzed by NadA.
- Published
- 2016
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33. Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA.
- Author
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Kandiah E, Carriel D, Perard J, Malet H, Bacia M, Liu K, Chan SW, Houry WA, Ollagnier de Choudens S, Elsen S, and Gutsche I
- Subjects
- Adenosine Triphosphatases chemistry, Amino Acid Sequence, Carboxy-Lyases chemistry, Catalytic Domain, Cryoelectron Microscopy, Enzyme Activation, Escherichia coli Proteins chemistry, Hydrogen-Ion Concentration, Models, Molecular, Protein Binding, Adenosine Triphosphatases metabolism, Carboxy-Lyases metabolism, Escherichia coli enzymology, Escherichia coli Proteins metabolism
- Abstract
The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation. Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer. We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity. Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.
- Published
- 2016
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34. Dual activity of quinolinate synthase: triose phosphate isomerase and dehydration activities play together to form quinolinate.
- Author
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Reichmann D, Couté Y, and Ollagnier de Choudens S
- Subjects
- Aspartic Acid analogs & derivatives, Aspartic Acid metabolism, Bacterial Proteins chemistry, Bacterial Proteins metabolism, Dihydroxyacetone Phosphate metabolism, Metabolic Networks and Pathways, Models, Chemical, NAD biosynthesis, Quinolinic Acid metabolism, Thermotoga maritima enzymology, Multienzyme Complexes chemistry, Multienzyme Complexes metabolism, Triose-Phosphate Isomerase chemistry, Triose-Phosphate Isomerase metabolism
- Abstract
Quinolinate synthase (NadA) is an Fe4S4 cluster-containing dehydrating enzyme involved in the synthesis of quinolinic acid (QA), the universal precursor of the essential coenzyme nicotinamide adenine dinucleotide. The reaction catalyzed by NadA is not well understood, and two mechanisms have been proposed in the literature that differ in the nature of the molecule (DHAP or G-3P) that condenses with iminoaspartate (IA) to form QA. In this article, using biochemical approaches, we demonstrate that DHAP is the triose that condenses with IA to form QA. The capacity of NadA to use G-3P is due to its previously unknown triose phosphate isomerase activity.
- Published
- 2015
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35. Assembly of Fe/S proteins in bacterial systems: Biochemistry of the bacterial ISC system.
- Author
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Blanc B, Gerez C, and Ollagnier de Choudens S
- Subjects
- Escherichia coli metabolism, Escherichia coli Proteins chemistry, Escherichia coli Proteins metabolism, Iron chemistry, Iron metabolism, Iron-Sulfur Proteins chemistry, Iron-Sulfur Proteins metabolism, Models, Molecular, Protein Binding, Protein Structure, Tertiary, Escherichia coli genetics, Escherichia coli Proteins genetics, Gene Order, Iron-Sulfur Proteins genetics, Operon
- Abstract
Iron/sulfur clusters are key cofactors in proteins involved in a large number of conserved cellular processes, including gene expression, DNA replication and repair, ribosome biogenesis, tRNA modification, central metabolism and respiration. Fe/S proteins can perform a wide range of functions, from electron transfer to redox and non-redox catalysis. In all living organisms, Fe/S proteins are first synthesized in an apo-form. However, as the Fe/S prosthetic group is required for correct folding and/or protein stability, Fe/S clusters are inserted co-translationally or immediately after translation by specific assembly machineries. These systems have been extensively studied over the last decade, both in prokaryotes and eukaryotes. The present review covers the basic principles of the bacterial housekeeping Fe/S biogenesis ISC system, and related recent molecular advances. Some of the most exciting recent highlights relating to this system include structural and functional characterization of binary and ternary complexes involved in Fe/S cluster formation on the scaffold protein IscU. These advances enhance our understanding of the Fe/S cluster assembly mechanism by revealing essential interactions that could never be determined with isolated proteins and likely are closer to an in vivo situation. Much less is currently known about the molecular mechanism of the Fe/S transfer step, but a brief account of the protein-protein interactions involved is given. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases., (Copyright © 2014 Elsevier B.V. All rights reserved.)
- Published
- 2015
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36. Turning Escherichia coli into a Frataxin-Dependent Organism.
- Author
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Roche B, Agrebi R, Huguenot A, Ollagnier de Choudens S, Barras F, and Py B
- Subjects
- Computational Biology, Escherichia coli metabolism, Escherichia coli Proteins metabolism, Gene Deletion, Iron-Binding Proteins genetics, Iron-Sulfur Proteins metabolism, Microbial Viability, Mutation, Phylogeny, Succinate Dehydrogenase genetics, Succinate Dehydrogenase metabolism, Frataxin, Escherichia coli genetics, Escherichia coli Proteins genetics, Iron-Binding Proteins metabolism, Iron-Sulfur Proteins genetics
- Abstract
Fe-S bound proteins are ubiquitous and contribute to most basic cellular processes. A defect in the ISC components catalyzing Fe-S cluster biogenesis leads to drastic phenotypes in both eukaryotes and prokaryotes. In this context, the Frataxin protein (FXN) stands out as an exception. In eukaryotes, a defect in FXN results in severe defects in Fe-S cluster biogenesis, and in humans, this is associated with Friedreich's ataxia, a neurodegenerative disease. In contrast, prokaryotes deficient in the FXN homolog CyaY are fully viable, despite the clear involvement of CyaY in ISC-catalyzed Fe-S cluster formation. The molecular basis of the differing importance in the contribution of FXN remains enigmatic. Here, we have demonstrated that a single mutation in the scaffold protein IscU rendered E. coli viability strictly dependent upon a functional CyaY. Remarkably, this mutation changed an Ile residue, conserved in prokaryotes at position 108, into a Met residue, conserved in eukaryotes. We found that in the double mutant IscUIM ΔcyaY, the ISC pathway was completely abolished, becoming equivalent to the ΔiscU deletion strain and recapitulating the drastic phenotype caused by FXN deletion in eukaryotes. Biochemical analyses of the "eukaryotic-like" IscUIM scaffold revealed that it exhibited a reduced capacity to form Fe-S clusters. Finally, bioinformatic studies of prokaryotic IscU proteins allowed us to trace back the source of FXN-dependency as it occurs in present-day eukaryotes. We propose an evolutionary scenario in which the current mitochondrial Isu proteins originated from the IscUIM version present in the ancestor of the Rickettsiae. Subsequent acquisition of SUF, the second Fe-S cluster biogenesis system, in bacteria, was accompanied by diminished contribution of CyaY in prokaryotic Fe-S cluster biogenesis, and increased tolerance to change in the amino acid present at the 108th position of the scaffold.
- Published
- 2015
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37. Molecular investigation of iron-sulfur cluster assembly scaffolds under stress.
- Author
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Blanc B, Clémancey M, Latour JM, Fontecave M, and Ollagnier de Choudens S
- Subjects
- Carrier Proteins genetics, Escherichia coli genetics, Escherichia coli Proteins genetics, Hydrogen Peroxide metabolism, Iron-Sulfur Proteins genetics, Oxygen metabolism, Carrier Proteins metabolism, Escherichia coli metabolism, Escherichia coli Proteins metabolism, Iron-Sulfur Proteins metabolism, Stress, Physiological physiology
- Abstract
Fe/S biosynthesis is controlled in Escherichia coli by two machineries, the housekeeping ISC machinery and the SUF system that is functional under stress conditions. Despite many in vivo studies showing that SUF is more adapted for Fe/S assembly under stress, no molecular data supporting this concept have been provided so far. This work focuses on molecular studies of key actors in Fe/S assembly, the SufB and IscU scaffolds under oxidative stress and iron limitation. We show that the IscU Fe2S2 cluster is less stable than the SufB Fe2S2 cluster in the presence of hydrogen peroxide, oxygen, and an iron chelator.
- Published
- 2014
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38. An integrative computational model for large-scale identification of metalloproteins in microbial genomes: a focus on iron-sulfur cluster proteins.
- Author
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Estellon J, Ollagnier de Choudens S, Smadja M, Fontecave M, and Vandenbrouck Y
- Subjects
- Artificial Intelligence, Computer Simulation, Databases, Protein, Iron-Sulfur Proteins chemistry, Iron-Sulfur Proteins genetics, Markov Chains, Models, Biological, Genome, Microbial, Iron-Sulfur Proteins metabolism
- Abstract
Metalloproteins represent a ubiquitous group of molecules which are crucial to the survival of all living organisms. While several metal-binding motifs have been defined, it remains challenging to confidently identify metalloproteins from primary protein sequences using computational approaches alone. Here, we describe a comprehensive strategy based on a machine learning approach to design and assess a penalized generalized linear model. We used this strategy to detect members of the iron-sulfur cluster protein family. A new category of descriptors, whose profile is based on profile hidden Markov models, encoding structural information was combined with public descriptors into a linear model. The model was trained and tested on distinct datasets composed of well-characterized iron-sulfur protein sequences, and the resulting model provided higher sensitivity compared to a motif-based approach, while maintaining a good level of specificity. Analysis of this linear model allows us to detect and quantify the contribution of each descriptor, providing us with a better understanding of this complex protein family along with valuable indications for further experimental characterization. Two newly-identified proteins, YhcC and YdiJ, were functionally validated as genuine iron-sulfur proteins, confirming the prediction. The computational model was then applied to over 550 prokaryotic genomes to screen for iron-sulfur proteomes; the results are publicly available at: . This study represents a proof-of-concept for the application of a penalized linear model to identify metalloprotein superfamilies on a large-scale. The application employed here, screening for iron-sulfur proteomes, provides new candidates for further biochemical and structural analysis as well as new resources for an extensive exploration of iron-sulfuromes in the microbial world.
- Published
- 2014
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39. The crystal structure of Fe₄S₄ quinolinate synthase unravels an enzymatic dehydration mechanism that uses tyrosine and a hydrolase-type triad.
- Author
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Cherrier MV, Chan A, Darnault C, Reichmann D, Amara P, Ollagnier de Choudens S, and Fontecilla-Camps JC
- Subjects
- Crystallography, X-Ray, Dehydration, Hydrolases metabolism, Models, Molecular, Molecular Structure, Multienzyme Complexes metabolism, Tyrosine metabolism, Hydrolases chemistry, Multienzyme Complexes chemistry, Tyrosine chemistry
- Abstract
Quinolinate synthase (NadA) is a Fe4S4 cluster-containing dehydrating enzyme involved in the synthesis of quinolinic acid (QA), the universal precursor of the essential nicotinamide adenine dinucleotide (NAD) coenzyme. A previously determined apo NadA crystal structure revealed the binding of one substrate analog, providing partial mechanistic information. Here, we report on the holo X-ray structure of NadA. The presence of the Fe4S4 cluster generates an internal tunnel and a cavity in which we have docked the last precursor to be dehydrated to form QA. We find that the only suitably placed residue to initiate this process is the conserved Tyr21. Furthermore, Tyr21 is close to a conserved Thr-His-Glu triad reminiscent of those found in proteases and other hydrolases. Our mutagenesis data show that all of these residues are essential for activity and strongly suggest that Tyr21 deprotonation, to form the reactive nucleophilic phenoxide anion, is mediated by the triad. NadA displays a dehydration mechanism significantly different from the one found in archetypical dehydratases such as aconitase, which use a serine residue deprotonated by an oxyanion hole. The X-ray structure of NadA will help us unveil its catalytic mechanism, the last step in the understanding of NAD biosynthesis.
- Published
- 2014
- Full Text
- View/download PDF
40. Insights into the function of YciM, a heat shock membrane protein required to maintain envelope integrity in Escherichia coli.
- Author
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Nicolaes V, El Hajjaji H, Davis RM, Van der Henst C, Depuydt M, Leverrier P, Aertsen A, Haufroid V, Ollagnier de Choudens S, De Bolle X, Ruiz N, and Collet JF
- Subjects
- Amino Acid Motifs, Amino Acid Sequence, Bacteriolysis, Culture Media chemistry, Endopeptidases metabolism, Escherichia coli cytology, Escherichia coli growth & development, Escherichia coli radiation effects, Escherichia coli Proteins genetics, Gene Deletion, Hot Temperature, Iron metabolism, Membrane Proteins genetics, Microscopy, Molecular Sequence Data, Osmotic Pressure, Protein Binding, Protein Interaction Mapping, Sequence Alignment, Cell Membrane metabolism, Escherichia coli physiology, Escherichia coli Proteins metabolism, Membrane Proteins metabolism
- Abstract
The cell envelope of Gram-negative bacteria is an essential organelle that is important for cell shape and protection from toxic compounds. Proteins involved in envelope biogenesis are therefore attractive targets for the design of new antibacterial agents. In a search for new envelope assembly factors, we screened a collection of Escherichia coli deletion mutants for sensitivity to detergents and hydrophobic antibiotics, a phenotype indicative of defects in the cell envelope. Strains lacking yciM were among the most sensitive strains of the mutant collection. Further characterization of yciM mutants revealed that they display a thermosensitive growth defect on low-osmolarity medium and that they have a significantly altered cell morphology. At elevated temperatures, yciM mutants form bulges containing cytoplasmic material and subsequently lyse. We also discovered that yciM genetically interacts with envC, a gene encoding a regulator of the activity of peptidoglycan amidases. Altogether, these results indicate that YciM is required for envelope integrity. Biochemical characterization of the protein showed that YciM is anchored to the inner membrane via its N terminus, the rest of the protein being exposed to the cytoplasm. Two CXXC motifs are present at the C terminus of YciM and serve to coordinate a redox-sensitive iron center of the rubredoxin type. Both the N-terminal membrane anchor and the C-terminal iron center of YciM are important for function.
- Published
- 2014
- Full Text
- View/download PDF
41. In vivo [Fe-S] cluster acquisition by IscR and NsrR, two stress regulators in Escherichia coli.
- Author
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Vinella D, Loiseau L, Ollagnier de Choudens S, Fontecave M, and Barras F
- Subjects
- Protein Processing, Post-Translational, DNA-Binding Proteins metabolism, Escherichia coli genetics, Escherichia coli metabolism, Escherichia coli Proteins metabolism, Gene Expression Regulation, Bacterial, Iron metabolism, Sulfur metabolism, Transcription Factors metabolism
- Abstract
The multi-proteins Isc and Suf systems catalyse the biogenesis of [Fe-S] proteins. Here we investigate how NsrR and IscR, transcriptional regulators that sense NO and [Fe-S] homeostasis, acquire their [Fe-S] clusters under both normal and iron limitation conditions. Clusters directed at the apo-NsrR and apo-IscR proteins are built on either of the two scaffolds, IscU or SufB. However, differences arise in [Fe-S] delivery steps. In the case of NsrR, scaffolds deliver clusters to either one of the two ATCs, IscA and SufA, and, subsequently, to the 'non-Isc non-Suf' ATC, ErpA. Nevertheless, a high level of SufA can bypass the requirement for ErpA. In the case of IscR, several routes occur. One does not include assistance of any ATC. Others implicate ATCs IscA or ErpA, but, surprisingly, SufA was totally absent from any IscR maturation pathways. Both IscR and NsrR have the intrinsic capacity to sense iron limitation. However, NsrR appeared to be efficiently matured by Isc and Suf, thereby preventing NsrR to act as a physiologically relevant iron sensor. This work emphasizes that different maturation pathways arise as a function of the apo-target considered, possibly in relation with the type of cluster, [2Fe-2S] versus [4Fe-4S], it binds., (© 2013 Blackwell Publishing Ltd.)
- Published
- 2013
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42. Mammalian frataxin controls sulfur production and iron entry during de novo Fe4S4 cluster assembly.
- Author
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Colin F, Martelli A, Clémancey M, Latour JM, Gambarelli S, Zeppieri L, Birck C, Page A, Puccio H, and Ollagnier de Choudens S
- Subjects
- Animals, Coordination Complexes chemistry, Humans, Models, Molecular, Frataxin, Iron metabolism, Iron-Binding Proteins physiology, Iron-Sulfur Proteins chemistry, Sulfur metabolism
- Abstract
Iron-sulfur (Fe-S) cluster-containing proteins are essential components of cells. In eukaryotes, Fe-S clusters are synthesized by the mitochondrial iron-sulfur cluster (ISC) machinery and the cytosolic iron-sulfur assembly (CIA) system. In the mammalian ISC machinery, preassembly of the Fe-S cluster on the scaffold protein (ISCU) involves a cysteine desulfurase complex (NFS1/ISD11) and frataxin (FXN), the protein deficient in Friedreich's ataxia. Here, by comparing the biochemical and spectroscopic properties of quaternary (ISCU/NFS1/ISD11/FXN) and ternary (ISCU/NFS1/ISD11) complexes, we show that FXN stabilizes the quaternary complex and controls iron entry to the complex through activation of cysteine desulfurization. Furthermore, we show for the first time that in the presence of iron and L-cysteine, an [Fe(4)S(4)] cluster is formed within the quaternary complex that can be transferred to mammalian aconitase (mACO2) to generate an active enzyme. In the absence of FXN, although the ternary complex can assemble an Fe-S cluster, the cluster is inefficiently transferred to ACO2. Taken together, these data help to unravel further the Fe-S cluster assembly process and the molecular basis of Friedreich's ataxia.
- Published
- 2013
- Full Text
- View/download PDF
43. Molecular organization, biochemical function, cellular role and evolution of NfuA, an atypical Fe-S carrier.
- Author
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Py B, Gerez C, Angelini S, Planel R, Vinella D, Loiseau L, Talla E, Brochier-Armanet C, Garcia Serres R, Latour JM, Ollagnier-de Choudens S, Fontecave M, and Barras F
- Subjects
- Aconitate Hydratase metabolism, Electron Transport Complex I metabolism, Escherichia coli genetics, Escherichia coli metabolism, Phylogeny, Protein Binding, Protein Interaction Mapping, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Escherichia coli enzymology, Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism, Iron-Sulfur Proteins genetics, Iron-Sulfur Proteins metabolism
- Abstract
Biosynthesis of iron-sulphur (Fe-S) proteins is catalysed by multi-protein systems, ISC and SUF. However, 'non-ISC, non-SUF' Fe-S biosynthesis factors have been described, both in prokaryotes and eukaryotes. Here we report in vitro and in vivo investigations of such a 'non-ISC, non SUF' component, the Nfu proteins. Phylogenomic analysis allowed us to define four subfamilies. Escherichia coli NfuA is within subfamily II. Most members of this subfamily have a Nfu domain fused to a 'degenerate' A-type carrier domain (ATC*) lacking Fe-S cluster co-ordinating Cys ligands. The Nfu domain binds a [4Fe-4S] cluster while the ATC* domain interacts with NuoG (a complex I subunit) and aconitase B (AcnB). In vitro, holo-NfuA promotes maturation of AcnB. In vivo, NfuA is necessary for full activity of complex I under aerobic growth conditions, and of AcnB in the presence of superoxide. NfuA receives Fe-S clusters from IscU/HscBA and SufBCD scaffolds and eventually transfers them to the ATCs IscA and SufA. This study provides significant information on one of the Fe-S biogenesis factors that has been often used as a building block by ISC and/or SUF synthesizing organisms, including bacteria, plants and animals., (© 2012 Blackwell Publishing Ltd.)
- Published
- 2012
- Full Text
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44. Studies of inhibitor binding to the [4Fe-4S] cluster of quinolinate synthase.
- Author
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Chan A, Clémancey M, Mouesca JM, Amara P, Hamelin O, Latour JM, and Ollagnier de Choudens S
- Subjects
- Alkyl and Aryl Transferases metabolism, Binding Sites drug effects, Dihydroxyacetone Phosphate chemistry, Dose-Response Relationship, Drug, Enzyme Inhibitors chemistry, Escherichia coli Proteins metabolism, Iron-Sulfur Proteins metabolism, Models, Molecular, Molecular Structure, Structure-Activity Relationship, Alkyl and Aryl Transferases antagonists & inhibitors, Dihydroxyacetone Phosphate pharmacology, Enzyme Inhibitors pharmacology, Escherichia coli Proteins antagonists & inhibitors, Iron-Sulfur Proteins antagonists & inhibitors
- Abstract
Stop for NadA! A [4Fe-4S] enzyme, NadA, catalyzes the formation of quinolinic acid in de novo nicotinamide adenine dinucleotide (NAD) biosynthesis. A structural analogue of an intermediate, 4,5-dithiohydroxyphthalic acid (DTHPA), has an in vivo NAD biosynthesis inhibiting activity in E. coli. The inhibitory effect can be explained by the coordination of DTHPA thiolate groups to a unique Fe site of the NadA [4Fe-4S] cluster., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2012
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45. Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis.
- Author
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Tsaousis AD, Ollagnier de Choudens S, Gentekaki E, Long S, Gaston D, Stechmann A, Vinella D, Py B, Fontecave M, Barras F, Lukeš J, and Roger AJ
- Subjects
- Anaerobiosis, Animals, Molecular Sequence Data, Phylogeny, Biological Evolution, Blastocystis metabolism, Iron-Sulfur Proteins metabolism
- Abstract
Iron/sulfur cluster (ISC)-containing proteins are essential components of cells. In most eukaryotes, Fe/S clusters are synthesized by the mitochondrial ISC machinery, the cytosolic iron/sulfur assembly system, and, in photosynthetic species, a plastid sulfur-mobilization (SUF) system. Here we show that the anaerobic human protozoan parasite Blastocystis, in addition to possessing ISC and iron/sulfur assembly systems, expresses a fused version of the SufC and SufB proteins of prokaryotes that it has acquired by lateral transfer from an archaeon related to the Methanomicrobiales, an important lineage represented in the human gastrointestinal tract microbiome. Although components of the Blastocystis ISC system function within its anaerobic mitochondrion-related organelles and can functionally replace homologues in Trypanosoma brucei, its SufCB protein has similar biochemical properties to its prokaryotic homologues, functions within the parasite's cytosol, and is up-regulated under oxygen stress. Blastocystis is unique among eukaryotic pathogens in having adapted to its parasitic lifestyle by acquiring a SUF system from nonpathogenic Archaea to synthesize Fe/S clusters under oxygen stress.
- Published
- 2012
- Full Text
- View/download PDF
46. Iron-sulfur (Fe-S) cluster assembly: the SufBCD complex is a new type of Fe-S scaffold with a flavin redox cofactor.
- Author
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Wollers S, Layer G, Garcia-Serres R, Signor L, Clemancey M, Latour JM, Fontecave M, and Ollagnier de Choudens S
- Subjects
- Adenosine Triphosphatases chemistry, Adenosine Triphosphatases metabolism, Amino Acid Sequence, Anaerobiosis, Carrier Proteins chemistry, Carrier Proteins metabolism, Escherichia coli metabolism, Flavin-Adenine Dinucleotide metabolism, Molecular Sequence Data, Oxidants metabolism, Oxidation-Reduction, Escherichia coli Proteins chemistry, Escherichia coli Proteins metabolism, Flavin-Adenine Dinucleotide analogs & derivatives, Iron-Sulfur Proteins chemistry, Iron-Sulfur Proteins metabolism
- Abstract
Assembly of iron-sulfur (Fe-S) clusters and maturation of Fe-S proteins in vivo require complex machineries. In Escherichia coli, under adverse stress conditions, this process is achieved by the SUF system that contains six proteins as follows: SufA, SufB, SufC, SufD, SufS, and SufE. Here, we provide a detailed characterization of the SufBCD complex whose function was so far unknown. Using biochemical and spectroscopic analyses, we demonstrate the following: (i) the complex as isolated exists mainly in a 1:2:1 (B:C:D) stoichiometry; (ii) the complex can assemble a [4Fe-4S] cluster in vitro and transfer it to target proteins; and (iii) the complex binds one molecule of flavin adenine nucleotide per SufBC(2)D complex, only in its reduced form (FADH(2)), which has the ability to reduce ferric iron. These results suggest that the SufBC(2)D complex functions as a novel type of scaffold protein that assembles an Fe-S cluster through the mobilization of sulfur from the SufSE cysteine desulfurase and the FADH(2)-dependent reductive mobilization of iron.
- Published
- 2010
- Full Text
- View/download PDF
47. The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein.
- Author
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Trotter V, Vinella D, Loiseau L, Ollagnier de Choudens S, Fontecave M, and Barras F
- Subjects
- Adenosine Triphosphatases genetics, Adenosine Triphosphatases metabolism, Artificial Gene Fusion, Biosynthetic Pathways, Carrier Proteins genetics, Carrier Proteins metabolism, DNA Transposable Elements, Escherichia coli Proteins genetics, Gene Deletion, Genes, Reporter, Lyases genetics, Lyases metabolism, Mutagenesis, Insertional, Protein Binding, beta-Galactosidase genetics, beta-Galactosidase metabolism, DEAD-box RNA Helicases metabolism, Escherichia coli metabolism, Escherichia coli Proteins metabolism, Iron metabolism, Protein Interaction Mapping, Sulfur metabolism, Ubiquitin-Activating Enzymes metabolism
- Abstract
Cysteine desulphurases are primary sources of sulphur that can eventually be used for Fe/S biogenesis or thiolation of various cofactors and tRNA. Escherichia coli contains three such enzymes, IscS, SufS and CsdA. The importance of IscS and SufS in Fe/S biogenesis is well established. The physiological role of CsdA in contrast remains uncertain. We provide here additional evidences for a functional redundancy between the three cysteine desulphurases in vivo. In particular, we show that a deficiency in isoprenoid biosynthesis is the unique cause of the lethality of the iscS sufS mutant. Moreover, we show that CsdA is engaged in two separate sulphur transfer pathways. In one pathway, CsdA interacts functionally with SufE-SufBCD proteins to assist Fe/S biogenesis. In another pathway, CsdA interacts with CsdE and a newly discovered protein, which we called CsdL, resembling E1-like proteins found in ubiquitin-like modification systems. We propose this new pathway to allow synthesis of an as yet to be discovered thiolated compound.
- Published
- 2009
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48. Native Escherichia coli SufA, coexpressed with SufBCDSE, purifies as a [2Fe-2S] protein and acts as an Fe-S transporter to Fe-S target enzymes.
- Author
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Gupta V, Sendra M, Naik SG, Chahal HK, Huynh BH, Outten FW, Fontecave M, and Ollagnier de Choudens S
- Subjects
- Aconitate Hydratase chemistry, Carrier Proteins chemistry, Carrier Proteins metabolism, Escherichia coli Proteins chemistry, Escherichia coli Proteins metabolism, Iron-Sulfur Proteins chemistry, Iron-Sulfur Proteins isolation & purification, Membrane Transport Proteins chemistry, Aconitate Hydratase metabolism, Carrier Proteins genetics, Carrier Proteins isolation & purification, Escherichia coli metabolism, Escherichia coli Proteins genetics, Escherichia coli Proteins isolation & purification, Iron-Sulfur Proteins metabolism, Membrane Transport Proteins metabolism
- Abstract
Iron-sulfur (Fe-S) clusters are versatile biological cofactors that require biosynthetic systems in vivo to be assembled. In Escherichia coli, the Isc (iscRSUA-hscBA-fdx-iscX) and Suf (sufABCDSE) pathways fulfill this function. Despite extensive biochemical and genetic analysis of these two pathways, the physiological function of the A-type proteins of each pathway (IscA and SufA) is still unclear. Studies conducted in vitro suggest two possible functions for A-type proteins, as Fe-S scaffold/transfer proteins or as iron donors during cluster assembly. To resolve this issue, SufA was coexpressed in vivo with its cognate partner proteins from the suf operon, SufBCDSE. Native SufA purified anaerobically using this approach was unambiguously demonstrated to be a [2Fe-2S] protein by biochemical analysis and UV-vis, Mossbauer, resonance Raman, and EPR spectroscopy. Furthermore, native [2Fe-2S] SufA can transfer its Fe-S cluster to both [2Fe-2S] and [4Fe-4S] apoproteins. These results clearly show that A-type proteins form Fe-S clusters in vivo and are competent to function as Fe-S transfer proteins as purified. This study resolves the contradictory results from previous in vitro studies and demonstrates the critical importance of providing in vivo partner proteins during protein overexpression to allow correct biochemical maturation of metalloproteins.
- Published
- 2009
- Full Text
- View/download PDF
49. DNA repair and free radicals, new insights into the mechanism of spore photoproduct lyase revealed by single amino acid substitution.
- Author
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Chandor-Proust A, Berteau O, Douki T, Gasparutto D, Ollagnier-de-Choudens S, Fontecave M, and Atta M
- Subjects
- Alanine chemistry, Amino Acids chemistry, Catalysis, Catalytic Domain, Cloning, Molecular, Cysteine chemistry, Models, Chemical, Proteins genetics, Sulfinic Acids chemistry, Thymine chemistry, Ultraviolet Rays, Bacillus subtilis metabolism, DNA Repair, Free Radicals, Iron-Sulfur Proteins chemistry, Proteins metabolism
- Abstract
The major DNA photoproduct in UV-irradiated Bacillus subtilis spores is the thymine dimer named spore photoproduct (SP, 5-(alpha-thyminyl)-5,6-dihydrothymine). The SP lesion has been found to be efficiently repaired by SP lyase (SPL) a very specific enzyme that reverses the SP to two intact thymines, at the origin of the great resistance of the spores to UV irradiation. SPL belongs to a superfamily of [4Fe-4S] iron-sulfur enzymes, called "Radical-SAM." Here, we show that the single substitution of cysteine 141 into alanine, a residue fully conserved in Bacillus species and previously shown to be essential for spore DNA repair in vivo, has a major impact on the outcome of the SPL-dependent repair reaction in vitro. Indeed the modified enzyme catalyzes the almost quantitative conversion of the SP lesion into one thymine and one thymine sulfinic acid derivative. This compound results from the trapping of the allyl-type radical intermediate by dithionite, used as reducing agent in the reaction mixture. Implications of the data reported here regarding the repair mechanism and the role of Cys-141 are discussed.
- Published
- 2008
- Full Text
- View/download PDF
50. From Iron and Cysteine to Iron-Sulfur Clusters: the Biogenesis Protein Machineries.
- Author
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Fontecave M, Py B, Ollagnier de Choudens S, and Barras F
- Abstract
This review describes the two main systems, namely the Isc (iron-sulfur cluster) and Suf (sulfur assimilation) systems, utilized by Escherichia coli and Salmonella for the biosynthesis of iron-sulfur (Fe-S) clusters, as well as other proteins presumably participating in this process. In the case of Fe-S cluster biosynthesis, it is assumed that the sulfur atoms from the cysteine desulfurase end up at cysteine residues of the scaffold protein, presumably waiting for iron atoms for cluster assembly. The review discusses the various potential iron donor proteins. For in vitro experiments, in general, ferrous salts are used during the assembly of Fe-S clusters, even though this approach is unlikely to reflect the physiological conditions. The fact that sulfur atoms can be directly transferred from cysteine desulfurases to scaffold proteins supports a mechanism in which the latter bind sulfur atoms first and iron atoms afterwards. In E. coli, fdx gene inactivation results in a reduced growth rate and reduced Fe-S enzyme activities. Interestingly, the SufE structure resembles that of IscU, strengthening the notion that the two proteins share the property of acting as acceptors of sulfur atoms provided by cysteine desulfurases. Several other factors have been suggested to participate in cluster assembly and repair in E. coli and Salmonella. Most of them were identified by their abilities to act as extragenic and/or multicopy suppressors of mutations in Fe-S cluster metabolism, while others possess biochemical properties that are consistent with a role in Fe-S cluster biogenesis.
- Published
- 2008
- Full Text
- View/download PDF
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