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9 results on '"Microbiologie et enzymologie structurale (MESB3S)"'

1. Fitness costs restrict niche expansion by generalist niche-constructing pathogens

Author

Abbas El Sahili, Yves Dessaux, Denis Faure, Magali Aumont-Nicaise, Solange Moréra, Julien Lang, Armelle Vigouroux, Jacqui A. Shykoff, Anthony Kwasiborski, Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Mesures d'interactions protéine-protéine (PIM), Département Plateforme (PF I2BC), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), ANRBlanc SENSOR (ANR-12-BSV8-0003-01/02/03), Intéractions Plantes-Bactéries ( PBI ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Microbiologie et enzymologie structurale ( MESB3S ), Département Biochimie, Biophysique et Biologie Structurale ( B3S ), Mesures d'interactions protéine-protéine ( PIM ), Département Plateforme ( PF I2BC ), Ecologie Systématique et Evolution ( ESE ), and Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS )

Subjects
0301 basic medicine, Models, Molecular, [SDV]Life Sciences [q-bio], Niche, Opine, Generalist and specialist species, Arginine, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Octopine, Ecological niche, biology, [ SDV ] Life Sciences [q-bio], Ecology, Agrobacterium tumefaciens, Plants, biology.organism_classification, Plants, Genetically Modified, 030104 developmental biology, chemistry, Evolutionary biology, Sympatric speciation, Original Article, Nopaline, Carrier Proteins
Abstract

International audience; We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant hosts that provide different nutrients: nopaline or octopine, respectively. Previous studies revealed that nopaline-type pathogens may expand their niche to also assimilate octopine in the presence of nopaline, but consequences of this phenomenon on pathogen dynamics in planta were not known. Here, we provided molecular insight into how the transport protein NocT can bind octopine as well as nopaline, contributing to niche expansion. We further showed that despite the ability for niche expansion, nopaline-type pathogens had no competitive advantage over octopine-type pathogens in co-infected plants. We also demonstrated that a single nucleotide polymorphism in the nocR gene was sufficient to allow octopine assimilation by nopaline-type strains even in absence of nopaline. The evolved nocR bacteria had higher fitness than their ancestor in octopine-rich transgenic plants but lower fitness in tumors induced by octopine-type pathogens. Overall, this work elucidates the specialization of A. tumefaciens to particular opine niches and explains why generalists do not always spread despite the advantage associated with broader nutritional niches.The ISME Journal advance online publication, 1 November 2016; doi:10.1038/ismej.2016.137.

Published
2016
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2. Kinetic and structural investigation of the cytokinin oxidase/dehydrogenase active site

Author

Pierre Briozzo, Solange Moréra, David Zalabák, Jana Skopalová, David Kopečný, Armelle Vigouroux, Marek Šebela, Ivo Frébort, Martina Kopečná, Radka Končitíková, Hana Popelka, Faculty of Science, Department of Biochemistry, Palacky University, Department of Molecular, Cellular and Developmental Biology, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Centre of the Region Hana for Biotechnological and Agricultural Research, Fac Sci, Dept Analyt Chem, Palacky University Olomouc, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Institut Jean-Pierre Bourgin ( IJPB ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Microbiologie et enzymologie structurale ( MESB3S ), Département Biochimie, Biophysique et Biologie Structurale ( B3S ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), and Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 )

Subjects
0106 biological sciences, 0301 basic medicine, crystal structure, Cytokinins, Protein Conformation, [SDV]Life Sciences [q-bio], Flavoprotein, Dehydrogenase, plant hormone, Crystallography, X-Ray, maize, Zea mays, 01 natural sciences, Biochemistry, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, Oxidoreductase, flavoprotein, Catalytic Domain, Site-directed mutagenesis, Molecular Biology, chemistry.chemical_classification, biology, [ SDV ] Life Sciences [q-bio], fungi, Active site, food and beverages, Cell Biology, Electron acceptor, biology.organism_classification, Kinetics, 030104 developmental biology, chemistry, Flavin-Adenine Dinucleotide, Mutagenesis, Site-Directed, biology.protein, Plant hormone, Zeatin, site-directed mutagenesis, Oxidoreductases, cytokinin oxidase/dehydrogenase, 010606 plant biology & botany
Abstract

International audience; Cytokinins are hormones that regulate plant development and their environmental responses. Their levels are mainly controlled by the cytokinin oxidase/dehydrogenase (CKO), which oxidatively cleaves cytokinins using redox-active electron acceptors. CKO belongs to the group of flavoproteins with an 8α-N1-histidyl FAD covalent linkage. Here, we investigated the role of seven active site residues, H105, D169, E288, V378, E381, P427 and L492, in substrate binding and catalysis of the CKO1 from maize (Zea mays, ZmCKO1) combining site-directed mutagenesis with kinetics and X-ray crystallography. We identify E381 as a key residue for enzyme specificity that restricts substrate binding as well as quinone electron acceptor binding. We show that D169 is important for catalysis and that H105 covalently linked to FAD maintains the enzyme's structural integrity, stability and high rates with electron acceptors. The L492A mutation significantly modulates the cleavage of aromatic cytokinins and zeatin isomers. The high resolution X-ray structures of ZmCKO1 and the E381S variant in complex with N6-(2-isopentenyl)adenosine reveal the binding mode of cytokinin ribosides. Those of ZmCKO2 and ZmCKO4a contain a mobile domain, which might contribute to binding of the N9 substituted cytokinins.

Published
2016
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3. Role and structural characterization of plant aldehyde dehydrogenases from family 2 and family 7

Author

Marek Šebela, Martina Kopečná, David Kopečný, Jan Bartoš, Armelle Vigouroux, Radka Končitíková, Solange Moréra, Tomáš Andree, Faculty of Science, Department of Biochemistry, Palacky University, Microbiologie et enzymologie structurale ( MESB3S ), Département Biochimie, Biophysique et Biologie Structurale ( B3S ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique ( CNRS ), Ctr Reg Hana Biotechnol & Agr Res, Inst Expt Bot, Palacky University Olomouc, Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Models, Molecular, Sinapaldehyde, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Aldehyde dehydrogenase, Phenylalanine, Biology, Crystallography, X-Ray, 01 natural sciences, Biochemistry, Zea mays, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, Oxidoreductase, Catalytic Domain, Amino Acid Sequence, Molecular Biology, Phylogeny, 030304 developmental biology, ALDH2, Plant Proteins, chemistry.chemical_classification, 0303 health sciences, Phenylpropanoid, [ SDV ] Life Sciences [q-bio], Models, Genetic, Gene Expression Profiling, Peas, Cell Biology, Aldehyde Dehydrogenase, Plants, NAD, Isoenzymes, Kinetics, Enzyme, chemistry, Osmolyte, biology.protein, 010606 plant biology & botany
Abstract

International audience; Aldehyde dehydrogenases (ALDHs) are responsible for oxidation of biogenic aldehyde intermediates as well as for cell detoxification of aldehydes generated during lipid peroxidation. So far, 13 ALDH families have been described in plants. In the present study, we provide a detailed biochemical characterization of plant ALDH2 and ALDH7 families by analysing maize and pea ALDH7 (ZmALDH7 and PsALDH7) and four maize cytosolic ALDH(cALDH)2 isoforms RF2C, RF2D, RF2E and RF2F [the first maize ALDH2 was discovered as a fertility restorer (RF2A)]. We report the crystal structures of ZmALDH7, RF2C and RF2F at high resolution. The ZmALDH7 structure shows that the three conserved residues Glu(120), Arg(300) and Thr(302) in the ALDH7 family are located in the substrate-binding site and are specific to this family. Our kinetic analysis demonstrates that α-aminoadipic semialdehyde, a lysine catabolism intermediate, is the preferred substrate for plant ALDH7. In contrast, aromatic aldehydes including benzaldehyde, anisaldehyde, cinnamaldehyde, coniferaldehyde and sinapaldehyde are the best substrates for cALDH2. In line with these results, the crystal structures of RF2C and RF2F reveal that their substrate-binding sites are similar and are formed by an aromatic cluster mainly composed of phenylalanine residues and several nonpolar residues. Gene expression studies indicate that the RF2C gene, which is strongly expressed in all organs, appears essential, suggesting that the crucial role of the enzyme would certainly be linked to the cell wall formation using aldehydes from phenylpropanoid pathway as substrates. Finally, plant ALDH7 may significantly contribute to osmoprotection because it oxidizes several aminoaldehydes leading to products known as osmolytes.

Published
2015
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4. Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture

Author

Zdeněk Wimmer, David Zalabák, Nino Murvanidze, Pierre Briozzo, David Kopečný, Martina Kopečná, Stefaan Werbrouck, Solange Moréra, Jaroslav Nisler, Zuzana Pěkná, Radoslav Koprna, Nuria De Diego, Miroslav Strnad, Radka Končitíková, Libor Havlíček, Lukáš Spíchal, University of Chemistry and Technology Prague (UCT Prague), Palacky University Olomouc, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Universiteit Gent = Ghent University (UGENT), Grant Agency of the Czech Republic 18-07563S, ERDF from the Ministry of Education, Youth and Sports, Czech Republic CZ.02.1.01/0.0/0.0/16_019/000 0827CZ.02.2.69/0.0/0.0/16_027/0008482, Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Faculty of Science, Department of Biochemistry, Grant Agency of the Czech Republic18-07563S, ERDF from the Ministry of Education, Youth and Sports, Czech RepublicCZ.02.1.01/0.0/0.0/16_019/000 0827, and CZ.02.2.69/0.0/0.0/16_027/0008482

Subjects
0106 biological sciences, BIOCHEMICAL-CHARACTERIZATION, Cytokinins, Rapeseed, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Dehydrogenase, Plant Science, THIDIAZURON, 01 natural sciences, CKX inhibitor, stress, chemistry.chemical_compound, Arabidopsis thaliana, ZEA-MAYS, 2. Zero hunger, 0303 health sciences, Oxidase test, biology, Chemistry, food and beverages, Agriculture, Cytokinin, Plant hormone, Oxidoreductases, biotechnology, EXPRESSION, crystal structure, Plant tissue culture, OXIDASE, cytokinin, 03 medical and health sciences, DEHYDROGENASE, 030304 developmental biology, diphenylurea, PURIFICATION, business.industry, fungi, Biology and Life Sciences, yield, biology.organism_classification, Biotechnology, ARABIDOPSIS-THALIANA, plant tissue culture, business, SEED YIELD, MAIZE, cytokinin oxidase/dehydrogenase, 010606 plant biology & botany
Abstract

Increasing crop productivity is our major challenge if we are to meet global needs for food, fodder and fuel. Controlling the content of the plant hormone cytokinin is a method of improving plant productivity. Cytokinin oxidase/dehydrogenase (CKO/CKX) is a major target in this regard because it degrades cytokinins. Here, we describe the synthesis and biological activities of new CKX inhibitors derived mainly from diphenylurea. They were tested on four CKX isoforms from maize and Arabidopsis, where the best compounds showed IC50 values in the 10–8 M concentration range. The binding mode of the most efficient inhibitors was characterized from high-resolution crystal complexed structures. Although these compounds do not possess intrinsic cytokinin activity, we have demonstrated their tremendous potential for use in the plant tissue culture industry as well as in agriculture. We have identified a key substance, compound 19, which not only increases stress resistance and seed yield in Arabidopsis, but also improves the yield of wheat, barley and rapeseed grains under field conditions. Our findings reveal that modulation of cytokinin levels via CKX inhibition can positively affect plant growth, development and yield, and prove that CKX inhibitors can be an attractive target in plant biotechnology and agriculture.

Published
2020
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5. A unique ferrous iron binding mode is associated with large conformational changes for the transport protein FpvC of Pseudomonas aeruginosa

Author

Isabelle J. Schalk, Pierre Legrand, Karl Brillet, Magali Aumont-Nicaise, Solange Moréra, Léa Lo Bello, Loïc Marty, Alain Boussac, Armelle Vigouroux, Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Cristallisation (CRISTA), Département Plateforme (PF I2BC), Mesures d'interactions protéine-protéine (PIM), Photosystème II (PS2), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Biotechnologie et signalisation cellulaire (BSC), Université de Strasbourg (UNISTRA)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche de l'Ecole de biotechnologie de Strasbourg (IREBS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrochimie Infrarouge et Raman - UMR 8516 (LASIR), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Siderophore, siderophore, Iron, Aucun, Molecular Dynamics Simulation, Biochemistry, Ferrous, Divalent, solute-binding protein, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Nickel, Protein purification, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Solute Carrier Proteins, Pyoverdine, Binding Sites, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], pyoverdine, Cell Biology, Periplasmic space, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Transport protein, 030104 developmental biology, chemistry, 030220 oncology & carcinogenesis, Pseudomonas aeruginosa, Biophysics, Ferrous iron binding, Oligopeptides, Bacterial Outer Membrane Proteins, Protein Binding
Abstract

Pseudomonas aeruginosa secretes pyoverdine, a major siderophore to get access to iron, an essential nutrient. Pyoverdine scavenges ferric iron in the bacterial environment with the resulting complex internalized by bacteria. Iron release from pyoverdine in the periplasm involves an iron reduction by an inner membrane reductase and two solute-binding proteins (SBPs) FpvC and FpvF in association with their ABC transporter. FpvC and FpvF belong to two different subgroups of SBPs within the structural cluster A: FpvC and FpvF were proposed to be a metal-binding protein and a ferrisiderophore binding protein, respectively. Here, we report the redox state and the binding mode of iron to FpvC. We first solved the crystal structure of FpvC bound to a fortuitous Ni2+ by single anomalous dispersion method. Using a different protein purification strategy, we determined the structure of FpvC with manganese and iron, which binds to FpvC in a ferrous state as demonstrated by electron paramagnetic resonance. FpvC is the first example of a hexahistidine metal site among SBPs in which the Fe2+ redox state is stabilized under aerobic conditions. Using biophysics methods, we showed that FpvC reversibly bind a broad range of divalent ions. The structure of a mutant mimicking the apo FpvC reveals a protein in an open state with large conformational changes when compared with the metal-bound FpvC. These results highlight that the canonical metal site in FpvC is distinct from those yet described in SBPs and they provide new insights into the mechanism of PVD-Fe dissociation in P. aeruginosa. This article is protected by copyright. All rights reserved. The following values have no corresponding Zotero field:auth-address: 1 Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France. 2 Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, Gif-sur-Yvette, 91198, France. 3 UMR7242, CNRS, Université de Strasbourg, ESBS, Bd Sébastien Brant, F-67412, Illkirch, Strasbourg, France.accession-num: 31318478

Published
2019
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6. Synthesis of a non-natural glucose-2-phosphate ester able to dupe the acc system of Agrobacterium fabrum

Author

Laila Sago, Armelle Vigouroux, Abbas El Sahili, David Cornu, Laurent Soulère, Si-Zhe Li, Yves Queneau, Solange Moréra, Mohammed Ahmar, Chimie Organique et Bioorganique (COB), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), SICaPS (SICaPS), Département Plateforme (PF I2BC), Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
plasmids, [SDV]Life Sciences [q-bio], Agrobacterium, Crystallography, X-Ray, 01 natural sciences, Biochemistry, Substrate Specificity, 03 medical and health sciences, Residue (chemistry), chemistry.chemical_compound, Hydrolysis, Bacterial Proteins, diesters, Physical and Theoretical Chemistry, 030304 developmental biology, phosphate, 0303 health sciences, opines, biology, Phosphoric Diester Hydrolases, 010405 organic chemistry, Chemistry, Binding protein, Organic Chemistry, Glucosephosphates, Substrate (chemistry), Phosphodiesterase, Esters, Agrobacterium tumefaciens, Periplasmic space, Phosphate, biology.organism_classification, 0104 chemical sciences, hydrolysis, Periplasmic Binding Proteins, glycogen
Abstract

International audience; The first non-natural derivative of the rare D-glucose-2-phosphate (G2P), namely glucose-2-(O-lactic acid phosphate) (G2LP), has been synthesized. When used as sole carbon source, G2LP enables bacterial growth of the plant pathogenic strain Agrobacterium fabrum C58 (formerly referred to as Agrobacterium tumefa-ciens). X-ray crystallography and affinity measurements investigations reveal that G2LP binds the periplasmic binding protein (PBP) AccA similarly to the natural compounds and with the same affinity. Moreover, enzy-matic assays show that it is able to serve as substrate of the phosphodiesterase AccF. The properties found for G2LP demonstrate that the very unusual glucose-2-phosphoryl residue, present in G2LP, can be used as structural feature for designing non-natural systems fully compatible with the Acc cascade of A. fabrum.

Published
2019
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7. Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogen Agrobacterium tumefaciens

Author

Céline Lavire, Loïc Marty, Yves Dessaux, Thibault Meyer, Armelle Vigouroux, Magali Aumont-Nicaise, Solange Moréra, Franck Pelissier, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche Centre National de la Recherche Scientifique (CNRS)French National Research Agency (ANR) ANR-12-BSV8-0003-01/02/03FRISBI ANR-10-INSB-05-01I2BC mass spectrometry SICaPS platform, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Bio-inspired Chemistry and Ecological Innovations (ChimEco), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)

Subjects
[SDV]Life Sciences [q-bio], opine, Opine, ATP-binding cassette transporter, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Ti plasmid, crystal structures, octopine, periplasmic binding protein, crown-gall, gene, Molecular Biology, Gene, transformed plants, 030304 developmental biology, degradation, Octopine, 0303 health sciences, region, biology, Catabolism, 030302 biochemistry & molecular biology, catabolism, Cell Biology, Agrobacterium tumefaciens, biology.organism_classification, agrobacterium tumefaciens, cyclase, ti-plasmid, chemistry, mannopinic acid, affinity, Bacteria
Abstract

Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. The mannityl-opine family encompasses mannopine, mannopinic acid, agropine and agropinic acid. These opines serve as nutrients and are imported into bacteria via periplasmic-binding proteins (PBPs) in association with ABC transporters. Structural and affinity data on agropine and agropinic acid opines bound to PBPs are currently lacking. Here, we investigated the molecular basis of AgtB and AgaA, proposed as the specific PBP for agropine and agropinic acid import, respectively. Using genetic approaches and affinity measurements, we identified AgtB and its transporter as responsible for agropine uptake in agropine-assimilating agrobacteria. Nonetheless, we showed that AgtB binds agropinic acid with a higher affinity than agropine, and we structurally characterized the agropinic acid-binding mode through three crystal structures at 1.4, 1.74 and 1.9 Å resolution. In the crystallization time course, obtaining a crystal structure of AgtB with agropine was unsuccessful due to the spontaneous lactamization of agropine into agropinic acid. AgaA binds agropinic acid only with a similar affinity in nanomolar range as AgtB. The structure of AgaA bound to agropinic acid at 1.65 Å resolution defines a different agropinic acid-binding signature. Our work highlights the structural and functional characteristics of two efficient agropinic acid assimilation pathways, of which one is also involved in agropine assimilation.

Published
2019
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8. The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogen Agrobacterium fabrum

Author

Céline Lavire, Magali Aumont-Nicaise, Gilles Comte, Solange Moréra, Thibault Meyer, Ludovic Vial, Armelle Vigouroux, Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Département Biochimie, Biophysique et Biologie Structurale (B3S), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Microbiologie et enzymologie structurale (MESB3S), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Mesures d'interactions protéine-protéine (PIM), Département Plateforme (PF I2BC), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), FRISBI ANR-10-INSB-05-01, and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)

Subjects
0301 basic medicine, Protein Conformation, [SDV]Life Sciences [q-bio], ATP-binding cassette transporter, crystal structure, sugar transport, bacteria, ABC transporter, microbiology, agrobacterium, galactinol, periplasmic binding protein, RFOs, plant defense, Agrobacterium fabrum, Crystallography, X-Ray, Disaccharides, Biochemistry, chemistry.chemical_compound, Plant defense against herbivory, Raffinose, MESB3S, bactérie, Rhizosphere, food and beverages, Plants, Protein Structure and Folding, PF, rhizosphère, B3S, agent pathogène, Agrobacterium, 030106 microbiology, Biology, Stachyose, 03 medical and health sciences, Bacterial Proteins, oligosaccharide, Melibiose, Molecular Biology, fungi, Nutrients, Cell Biology, biology.organism_classification, PIM, chemistry, Agrobacterium tumefaciens, Galactose
Abstract

The bacterial plant pathogen Agrobacterium fabrum uses periplasmic-binding proteins (PBPs) along with ABC transporters to import a wide variety of plant molecules as nutrients. Nonetheless, how A. fabrum acquires plant metabolites is incompletely understood. Using genetic approaches and affinity measurements, we identified here the PBP MelB and its transporter as being responsible for the uptake of the raffinose family of oligosaccharides (RFO), which are the most widespread d-galactose–containing oligosaccharides in higher plants. We also found that the RFO precursor galactinol, recently described as a plant defense molecule, is imported into Agrobacterium via MelB with nanomolar range affinity. Structural analyses and binding mode comparisons of the X-ray structures of MelB in complex with raffinose, stachyose, galactinol, galactose, and melibiose (a raffinose degradation product) revealed how MelB recognizes the nonreducing end galactose common to all these ligands and that MelB has a strong preference for a two-unit sugar ligand. Of note, MelB conferred a competitive advantage to A. fabrum in colonizing the rhizosphere of tomato plants. Our integrative work highlights the structural and functional characteristics of melibiose and galactinol assimilation by A. fabrum, leading to a competitive advantage for these bacteria in the rhizosphere. We propose that the PBP MelB, which is highly conserved among both symbionts and pathogens from Rhizobiace family, is a major trait in these bacteria required for early steps of plant colonization.

Published
2018
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9. The ALDH21 gene found in lower plants and some vascular plants codes for a NADP(+) -dependent succinic semialdehyde dehydrogenase

Author

Radka Končitíková, Armelle Vigouroux, David Kopečný, Lenka Jašková, Jan Vilím, Martina Kopečná, Klaus von Schwartzenberg, Eva Hajkova, Solange Moréra, Pierre Briozzo, Marek Šebela, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Microbiologie et enzymologie structurale (MESB3S), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Arginine, [SDV]Life Sciences [q-bio], Aldehyde dehydrogenase, Plant Science, Mitochondrion, Physcomitrella patens, Cofactor, structure-function, Succinic semialdehyde, 03 medical and health sciences, chemistry.chemical_compound, GABA, aldehyde dehydrogenase, Oxidoreductase, Genetics, succinic semialdehyde, ALDH5, x-ray crystallography, chemistry.chemical_classification, biology, ALDH21, Cell Biology, 15. Life on land, biology.organism_classification, 030104 developmental biology, chemistry, Biochemistry, biology.protein, NAD+ kinase, site-directed mutagenesis
Abstract

Lower plant species including some green algae, non-vascular plants (bryophytes) as well as the oldest vascular plants (lycopods) and ferns (monilophytes) possess a unique aldehyde dehydrogenase (ALDH) gene named ALDH21, which is upregulated during dehydration. However, the gene is absent in flowering plants. Here, we show that ALDH21 from the moss Physcomitrella patens codes for a tetrameric NADP(+) -dependent succinic semialdehyde dehydrogenase (SSALDH), which converts succinic semialdehyde, an intermediate of the γ-aminobutyrate (GABA) shunt pathway, into succinate in the cytosol. NAD(+) is a very poor coenzyme for ALDH21 unlike for mitochondrial SSALDHs (ALDH5), which are the closest related ALDH members. Structural comparison between the apoform and the coenzyme complex reveal that NADP(+) binding induces a conformational change of the loop carrying Arg-228, which seals the NADP(+) in the coenzyme cavity via its 2'-phosphate and α-phosphate groups. The crystal structure with the bound product succinate shows that its carboxylate group establishes salt bridges with both Arg-121 and Arg-457 and a hydrogen bond with Tyr-296. While both arginine residues are pre-formed for substrate/product binding, Tyr-296 moves by more than 1 Å. Both R121A and R457A variants are almost inactive demonstrating a key role of each arginine in catalysis. Our study implies that bryophytes but presumably also some green algae, lycopods and ferns, which carry both ALDH21 and ALDH5 genes, can oxidize SSAL to succinate in both cytosol and mitochondria indicating more diverse GABA shunt pathway compared with higher plants carrying only the mitochondrial ALDH5. This article is protected by copyright. All rights reserved.

Published
2017
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