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1. N-terminal protein modifications: Bringing back into play the ribosome

Author: Carmela Giglione, Thierry Meinnel, Sonia Fieulaine, Institut des sciences du végétal (ISV), 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), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), 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 )
Subjects: Methionine aminopeptidase, Terminal protein, N-α-acetyltransferase, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Ribosome biogenesis, Biology, Biochemistry, Ribosome, Amidohydrolases, 03 medical and health sciences, chemistry.chemical_compound, Animals, Humans, Methionyl Aminopeptidases, Amino Acid Sequence, N-myristoyltransferase, N-terminal, 030304 developmental biology, 0303 health sciences, Methionine, [ SDV ] Life Sciences [q-bio], 030302 biochemistry & molecular biology, Translation (biology), General Medicine, Cell biology, chemistry, Acetylation, Peptide deformylase, Protein Biosynthesis, Protein Processing, Post-Translational, Ribosomes, Co-translational modifications, Function (biology)
Abstract: International audience; N-terminal protein modifications correspond to the first modifications which in principle any protein may undergo, before translation is completed by the ribosome. This class of essential modifications can have different nature or function and be catalyzed by a variety of dedicated enzymes. Here, we review the current state of the major N-terminal co-translational modifications, with a particular emphasis to their catalysts, which belong to metalloprotease and acyltransferase clans. The earliest of these modifications corresponds to the N-terminal methionine excision, an ubiquitous and essential process leading to the removal of the first methionine. N-alpha acetylation occurs also in all Kingdoms although its extent appears to be significantly increased in higher eukaryotes. Finally, N-myristoylation is a crucial pathway existing only in eukaryotes. Recent studies dealing on how some of these co-translational modifiers might work in close vicinity of the ribosome is starting to provide new information on when these modifications exactly take place on the elongating nascent chain and the interplay with other ribosome biogenesis factors taking in charge the nascent chains. Here a comprehensive overview of the recent advances in the field of N-terminal protein modifications is given.
Published: 2015
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2. Comparative Transcriptomic Analysis of Salt Adaptation in Roots of Contrasting Medicago truncatula Genotypes

Author: Véronique Gruber, Jean-Laurent Ichanté, Axel de Zélicourt, Laura de Lorenzo, Benoit Alunni, Sandrine Imbeaud, Hervé Delacroix, Sandrine Blanchet, Carole Laffont, Mounawer Badri, Anouck Diet, Julie Plet, Esther M. González, Florian Frugier, Ons Zahaf, Martin Crespi, Ana Zabalza, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Génomique Fonctionnelle des Tumeurs Solides (U1162), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de génétique moléculaire (CGM), Université Paris-Sud - Paris 11 (UP11), Laboratoire de physiologie cellulaire végétale ( LPCV ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut National de la Recherche Agronomique ( INRA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Genomique Fonctionnelle des Tumeurs Solides, Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Paris Descartes - Paris 5 ( UPD5 ) -IFR105-Université Paris Diderot - Paris 7 ( UPD7 ), Centre de génétique moléculaire ( CGM ), and Université Paris-Sud - Paris 11 ( UP11 )
Subjects: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Molecular Sequence Data, MESH : Plant Roots, MESH: Plant Roots, MESH : Genotype, Plant Science, Sodium Chloride, 01 natural sciences, Plant Roots, Transcriptome, MESH: Genotype, Gene Expression Regulation, Plant, MESH: Medicago truncatula, MESH : Adaptation, Physiological, Plant Proteins, 2. Zero hunger, Abiotic component, chemistry.chemical_classification, 0303 health sciences, MESH: Plant Proteins, food and beverages, Adaptation, Physiological, Medicago truncatula, MESH : Sodium Chloride, Soil salinity, MESH: Sodium Chloride, Genotype, Molecular Sequence Data, Biology, 03 medical and health sciences, MESH: Gene Expression Profiling, Auxin, MESH : Plant Proteins, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Gene Expression Regulation, Plant, Gene, Molecular Biology, 030304 developmental biology, MESH: Molecular Sequence Data, Abiotic stress, MESH : Gene Expression Profiling, MESH : Medicago truncatula, Gene Expression Profiling, fungi, 15. Life on land, biology.organism_classification, MESH: Adaptation, Physiological, chemistry, Adaptation, MESH : Gene Expression Regulation, Plant, 010606 plant biology & botany
Abstract: International audience; Evolutionary diversity can be driven by the interaction of plants with different environments. Molecular bases involved in ecological adaptations to abiotic constraints can be explored using genomic tools. Legumes are major crops worldwide and soil salinity is a main stress affecting yield in these plants. We analyzed in the Medicago truncatula legume the root transcriptome of two genotypes having contrasting responses to salt stress: TN1.11, sampled in a salty Tunisian soil, and the reference Jemalong A17 genotype. TN1.11 plants show increased root growth under salt stress as well as a differential accumulation of sodium ions when compared to A17. Transcriptomic analysis revealed specific gene clusters preferentially regulated by salt in root apices of TN1.11, notably those related to the auxin pathway and to changes in histone variant isoforms. Many genes encoding transcription factors (TFs) were also differentially regulated between the two genotypes in response to salt. Among those selected for functional studies, overexpression in roots of the A17 genotype of the bHLH-type TF most differentially regulated between genotypes improved significantly root growth under salt stress. Despite the global complexity of the differential transcriptional responses, we propose that an increase in this bHLH TF expression may be linked to the adaptation of M. truncatula to saline soil environments.
Published: 2012
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3. EFD Is an ERF Transcription Factor Involved in the Control of Nodule Number and Differentiation inMedicago truncatula

Author: Françoise de Billy, Andreas Niebel, Tatiana Vernié, Christian Rogers, Florian Frugier, Giles E. D. Oldroyd, Julie Plet, Jean-Philippe Combier, Pascal Gamas, Sandra Moreau, Laboratoire des interactions plantes micro-organismes ( LIPMO ), Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), 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 ( VAS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-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-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), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and 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)
Subjects: MESH: Signal Transduction, 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Cytokinins, MESH : Molecular Sequence Data, MESH : Transcription Factors, MESH: Feedback, Physiological, Regulator, MESH : Gene Deletion, Plant Science, Plant Root Nodulation, 01 natural sciences, Nod factor, chemistry.chemical_compound, MESH : Nitrogen Fixation, MESH: Phylogeny, MESH: Medicago truncatula, Research Articles, Phylogeny, Plant Proteins, Regulator gene, Feedback, Physiological, MESH : Cell Nucleus, 0303 health sciences, MESH: Plant Proteins, food and beverages, MESH: Transcription Factors, MESH : Feedback, Physiological, MESH : Cytokinins, Medicago truncatula, Cell biology, MESH: Root Nodules, Plant, Multigene Family, Cytokinin, RNA Interference, MESH: Cytokinins, Root Nodules, Plant, MESH: Plant Root Nodulation, Signal Transduction, MESH: Cell Nucleus, MESH: Ethylenes, Molecular Sequence Data, MESH: RNA Interference, MESH : Multigene Family, Biology, MESH: Nitrogen Fixation, MESH: Gene Expression Profiling, MESH : Root Nodules, Plant, 03 medical and health sciences, Nitrogen Fixation, MESH : Plant Proteins, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, 030304 developmental biology, Cell Nucleus, MESH : Signal Transduction, MESH: Molecular Sequence Data, Gene Expression Profiling, MESH : Gene Expression Profiling, MESH : Medicago truncatula, fungi, MESH : Phylogeny, MESH : Sinorhizobium meliloti, Cell Biology, Ethylenes, Meristem, biology.organism_classification, Response regulator, chemistry, MESH: Gene Deletion, MESH: Multigene Family, MESH : RNA Interference, MESH: Sinorhizobium meliloti, MESH : Plant Root Nodulation, Gene Deletion, MESH : Ethylenes, Sinorhizobium meliloti, Transcription Factors, 010606 plant biology & botany
Abstract: Mechanisms regulating legume root nodule development are still poorly understood, and very few regulatory genes have been cloned and characterized. Here, we describe EFD (for ethylene response factor required for nodule differentiation), a gene that is upregulated during nodulation in Medicago truncatula. The EFD transcription factor belongs to the ethylene response factor (ERF) group V, which contains ERN1, 2, and 3, three ERFs involved in Nod factor signaling. The role of EFD in the regulation of nodulation was examined through the characterization of a null deletion mutant (efd-1), RNA interference, and overexpression studies. These studies revealed that EFD is a negative regulator of root nodulation and infection by Rhizobium and that EFD is required for the formation of functional nitrogen-fixing nodules. EFD appears to be involved in the plant and bacteroid differentiation processes taking place beneath the nodule meristem. We also showed that EFD activated Mt RR4, a cytokinin primary response gene that encodes a type-A response regulator. We propose that EFD induction of Mt RR4 leads to the inhibition of cytokinin signaling, with two consequences: the suppression of new nodule initiation and the activation of differentiation as cells leave the nodule meristem. Our work thus reveals a key regulator linking early and late stages of nodulation and suggests that the regulation of the cytokinin pathway is important both for nodule initiation and development.
Published: 2008
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4. Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia

Author: Valérie Hocher, Petar Pujic, Lorena Carro, Nicole Alloisio, Pascale Fournier, Séverine Balmand, Franck Poly, Anne E Hay, Philippe Normand, Marjolaine Rey, Philippe François, Hasna Boubakri, Abdelaziz Heddi, Peter Mergaert, 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), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), 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-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, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), 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), 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 National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, ANR ([Sesam ANR-10-BLAN-1708], [BugsInACell ANR-13-BSV7-0013-03]), FR BioEnvironment and Health (Lyon), MEC postdoctoral fellowship from the Spanish government to LC (Programa Nacional de Movilidad de Recursos Humanos del Plan Nacional de I-D+i), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), Ecologie microbienne ( EM ), 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 ( VAS ), Diversité, adaptation, développement des plantes ( DIADE ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Intéractions Plantes-Bactéries ( PBI ), Département Microbiologie ( Dpt Microbio ), 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 ) -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 ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Biologie Fonctionnelle, Insectes et Interactions ( BF2I ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), and Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA )
Subjects: Nitrogen, [SDV]Life Sciences [q-bio], Frankia, Biology, Alnus, Plant Roots, Microbiology, Defensins, 03 medical and health sciences, Symbiosis, Ammonia, Nitrogen Fixation, Nitrogenase, Botany, Ecology, Evolution, Behavior and Systematics, Plant Proteins, 030304 developmental biology, 0303 health sciences, [ SDV ] Life Sciences [q-bio], 030306 microbiology, Vesicle, Cell Membrane, fungi, Microarray Analysis, biology.organism_classification, Plant cell, Glutamine, Alnus glutinosa, Biochemistry, Nitrogen fixation, Original Article, Actinorhizal plant, Porosity
Abstract: International audience; Actinorhizal plant growth in pioneer ecosystems depends on the symbiosis with the nitrogen-fixing actinobacterium Frankia cells that are housed in special root organs called nodules. Nitrogen fixation occurs in differentiated Frankia cells known as vesicles. Vesicles lack a pathway for assimilating ammonia beyond the glutamine stage and are supposed to transfer reduced nitrogen to the plant host cells. However, a mechanism for the transfer of nitrogen-fixation products to the plant cells remains elusive. Here, new elements for this metabolic exchange are described. We show that Alnus glutinosa nodules express defensin-like peptides, and one of these, Ag5, was found to target Frankia vesicles. In vitro and in vivo analyses showed that Ag5 induces drastic physiological changes in Frankia, including an increased permeability of vesicle membranes. A significant release of nitrogen-containing metabolites, mainly glutamine and glutamate, was found in N2-fixing cultures treated with Ag5. This work demonstrates that the Ag5 peptide is central for Frankia physiology in nodules and uncovers a novel cellular function for this large and widespread defensin peptide family.
Published: 2015
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5. Characterization of Arabidopsis thaliana mutants affected in seed iron storage

Author: Mary , Viviane, 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), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Université Paris Sud - Paris XI, Sébastien Thomine, 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 ), Institut des sciences du végétal ( ISV ), and Centre National de la Recherche Scientifique ( CNRS )
Subjects: Graine, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Isv mutants, Seed, Iron, Stockage, Storage, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Fer, Mutants isv, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Nramp3nramp4, Biofortification
Abstract: Over 30% of the world population is iron deficient (WHO resources). One strategy proposed to fight iron deficiency is to improve iron (Fe) content and availability in crops, especially in seeds. To address this challenge, it is crucial to decipher the mechanisms that control Fe storage during seed development. In Arabidopsis thaliana seeds, iron is stored in the vacuoles of cells surrounding the vasculature of the embryo. The AtVIT1 transporter is involved in Fe influx into vacuoles. The vit1-1 mutant displays an altered Fe pattern: Fe is accumulated in abaxial cells of the cotyledons and radicle peripheral cells. AtNRAMP3 and AtNRAMP4 function redundantly in Fe retrieval from vacuoles during germination. When germinated under iron deficient conditions, nramp3nramp4 double mutant development is altered as a consequence of impaired Fe mobilization. To identify novel genes involved in seed Fe homeostasis, we screened an EMS mutagenized population of nramp3nramp4 for mutations restoring the growth of nramp3nramp4 on low Fe. We named these mutants isv for “bypass iron storage in vacuoles”. The 29 confirmed isv mutants identified by the screen have been classified according to the iron localization pattern in their embryo after Perls/DAB staining: 20 display a wild type pattern, 3 display a pattern of Fe localization similar to vit1-1 mutant and 6 do not show any staining in most embryos. The three isv mutants displaying a vit1-1 like pattern were further investigated. In two of them, mutations in the AtVIT1 gene were shown to be responsible for the suppressor phenotype. This result establishes a genetic and functional link between Fe loading in endodermal vacuoles by AtVIT1 and its retrieval by AtNRAMP3 and AtNRAMP4. The third isv mutant with a vit1-1 like iron localization pattern does not carry any mutation in AtVIT1 coding sequence. Identification of the mutated gene will likely uncover molecular mechanisms regulating VIT1 action. For seven other confirmed isv mutants, F2 populations are available. High-throughput sequencing of batched segregants from these F2 populations will allow to map and identify the mutations causing the suppression.; Selon l’Organisation Mondiale de la Santé, environ 30% de la population mondiale souffre de carence en fer. Une des stratégies proposées afin d’endiguer l’anémie due à cette carence est d’augmenter le contenu en fer et sa disponibilité dans les parties consommées des plantes, en particulier les graines. Pour répondre à ce défi, il est important de comprendre les mécanismes de stockage du fer dans la graine. Chez la plante modèle Arabidopsis thaliana, le fer est stocké au sein des vacuoles des cellules entourant les tissus vasculaires de l’embryon. Le transporteur AtVIT1 est impliqué dans l’entrée de fer au sein de ces vacuoles. Le mutant vit1-1 présente un patron de distribution du fer modifié : le fer est accumulé dans les cellules sous épidermiques abaxiales des cotylédons et les cellules corticales de la radicule. AtNRAMP3 et AtNRAMP4 fonctionnent de manière redondante permettant la sortie du fer vacuolaire lors de la germination. En conditions de carence en fer, le double mutant nramp3nramp4 présente un arrêt développemental associé à une forte chlorose dus à son incapacité à utiliser ses stocks de fer vacuolaire. Pour identifier de nouveaux gènes impliqués dans l’homéostasie du fer au sein de la graine, nous avons criblé une population de double mutant nramp3nramp4 mutagénisé à l’EMS à la recherche de suppresseurs du phénotype du double mutant sur un milieu carencé en fer. Nous avons nommés ces mutants isv pour “bypass iron storage in vacuoles”. Nous avons confirmé et classifié 29 candidats selon le patron de distribution du fer de leurs embryons : 20 présentent un patron similaire au type sauvage, 3 dont le patron est semblable à celui du mutant vit1-1 et enfin 6 ne présentent pas de colorations dans la plupart de leurs embryons. Les 3 mutants isv présentant un patron similaire à vit1-1ont été caractérisés de manière plus approfondie. Chez deux d’entre eux, nous avons démontré que des mutations dans le gène AtVIT1 sont responsables du phénotype suppresseur. Ce résultat établit un lien génétique et fonctionnel entre le stockage du fer dans les vacuoles endodermiques par AtVIT1 et sa libération par AtNRAMP3 et AtNRAMP4. Le troisième mutant isv au patron semblable à vit1-1 ne porte pas de mutations dans la séquence codante d’AtVIT1. L’identification du gène affecté apportera sans doute des informations sur la régulation de VIT1. Enfin, pour sept autres mutants isv, nous disposons actuellement des populations F2 dont l’analyse par séquençage haut débit permettra de déterminer la mutation responsable du phénotype suppresseur.
Published: 2015

6. Draft Genome Sequences of the Three Pectobacterium-Antagonistic Bacteria Pseudomonas brassicacearum PP1-210F and PA1G7 and Bacillus simplex BA2H3

Author: Denis Faure, Valérie Hélias, Yannick Raoul des Essarts, Samuel Mondy, Mohieddine Moumni, Slimane Khayi, Amélie Beury-Cirou, Intéractions Plantes-Bactéries ( PBI ), Département Microbiologie ( Dpt Microbio ), 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 ) -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 ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Université de Moulay Ismail ( UMI ), Fédération Nationale des Producteurs de Plants de Pomme de Terre-Recherche, Développement, Promotion du Plant de Pommes de Terre (FN3PT-RD3PT), COMITE NORD Plants de Pomme de Terre / SIPRE, ANR-11-IDEX-02/10-LABX-0040,SPS,Saclay Plant Sciences ( 2011 ), 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), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Université Moulay Ismail (UMI), Fédération Nationale des Producteurs de Plants de Pomme de Terre (FN3PT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Comité Nord Plants de Pommes de Terre, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0303 health sciences, Pectobacterium, biology, [ SDV ] Life Sciences [q-bio], 030306 microbiology, [SDV]Life Sciences [q-bio], fungi, food and beverages, Bacillus simplex, biology.organism_classification, Genome, DNA sequencing, Microbiology, 03 medical and health sciences, Genetics, Pseudomonas brassicacearum, Natural enemies, Prokaryotes, Molecular Biology, Gene, Bacteria, 030304 developmental biology
Abstract: Pectobacterium spp. are bacterial pathogens causing soft rot diseases on a wide range of plants and crops. We present in this paper the draft genome sequences of three bacterial strains, Pseudomonas brassicacearum PP1-210F and PA1G7 and Bacillus simplex BA2H3, which exhibit antagonistic activities against the Pectobacterium plant pathogens.
Published: 2015
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7. Draft Genome Sequences of Pseudomonas fluorescens Strains PA4C2 and PA3G8 and Pseudomonas putida PA14H7, Three Biocontrol Bacteria against Dickeya Phytopathogens

Author: Denis Faure, Yannick Raoul des Essarts, Samuel Mondy, Amélie Beury-Cirou, Jérémy Cigna, Valérie Hélias, Intéractions Plantes-Bactéries ( PBI ), Département Microbiologie ( Dpt Microbio ), 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 ) -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 ), COMITE NORD Plants de Pomme de Terre / SIPRE, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Fédération Nationale des Producteurs de Plants de Pomme de Terre-Recherche, Développement, Promotion du Plant de Pommes de Terre (FN3PT-RD3PT), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, ANR-11-IDEX-02/10-LABX-0040,SPS,Saclay Plant Sciences ( 2011 ), Intéractions Plantes-Bactéries (PBI), Département Microbiologie (Dpt Microbio), 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-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, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Fédération Nationale des Producteurs de Plants de Pomme de Terre (FN3PT), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), ANR-11-IDEX-02/10-LABX-0040,SPS,Saclay Plant Sciences(2011), 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 National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Comité Nord Plants de Pommes de Terre, and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST
Subjects: Rhizosphere, biology, Strain (chemistry), [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], Antibiosis, Pseudomonas fluorescens, Dickeya, biology.organism_classification, Genome, Pseudomonas putida, Microbiology, Genetics, Prokaryotes, Molecular Biology, Bacteria
Abstract: Pseudomonas fluorescens strains PA4C2 and PA3G8 and Pseudomonas putida strain PA14H7 were isolated from potato rhizosphere and show an ability to inhibit the growth of Dickeya phytopathogens. Here, we report their draft genome sequences, which provide a basis for understanding the molecular mechanisms involved in antibiosis against Dickeya.
Published: 2015
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8. Genotypic variations in the dynamics of metal concentrations in poplar leaves: A field study with a perspective on phytoremediation

Author: Michel Chalot, Cindy Victor, Mathieu Pottier, Laure C. David, Sébastien Thomine, Vanesa S. García de la Torre, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Polluted soils, Health, Toxicology and Mutagenesis, Biology, Toxicology, Positive correlation, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Metal, Soil, Abscission, Botany, Genotype, Gene expression, Soil Pollutants, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, fungi, Trace element, food and beverages, General Medicine, Pollution, Trace Elements, Plant Leaves, Zinc, Phytoremediation, Biodegradation, Environmental, Populus, Metals, visual_art, visual_art.visual_art_medium, Environmental Pollution, Cadmium
Abstract: International audience; a b s t r a c t Poplar is commonly used for phytoremediation of metal polluted soils. However, the high concentrations of trace elements present in leaves may return to soil upon leaf abscission. To investigate the mechanisms controlling leaf metal content, metal concentrations and expression levels of genes involved in metal transport were monitored at different developmental stages on leaves from different poplar genotypes growing on a contaminated field. Large differences in leaf metal concentrations were observed among genotypes. Whereas Mg was remobilized during senescence, Zn and Cd accumulation continued until leaf abscission in all genotypes. A positive correlation between Natural Resistance Associated Macrophage Protein 1 (NRAMP1) expres-sion levels and Zn bio-concentration factors was observed. Principal component analyses of metal concentrations and gene expression levels clearly discriminated poplar genotypes. This study highlights a general absence of trace element remobilization from poplar leaves despite genotype specificities in the control of leaf metal homeostasis.
Published: 2015
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9. Function of glutathione peroxidases in legume root nodules

Author: Maria V. Barja, Marten Moore, Manuel A. Matamoros, Karl-Josef Dietz, Euan K. James, Pilar Bustos-Sanmamed, Nicolas Rouhier, María Peñuelas, José M. Mulet, Ana Saiz, Manuel Becana, Spanish National Research Council (CSIC), UPR2355 Institut des Sciences du Végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Universitat Politecnica de Valencia (UPV), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Universität Bielefeld = Bielefeld University, The James Hutton Institute, ANR (ANR-11-LABX-0002-01), Ministerio de Economia y Competitividad-Fondo Europeo de Desarrollo Regional (AGL2011-24524, AGL2014-53717-R), SPP1710, PT13/0001, Institut des sciences du végétal (ISV), Universitat Politècnica de València (UPV), and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: 0106 biological sciences, Physiology, Legume nodules, [SDV]Life Sciences [q-bio], Glutathione peroxidases, Plant Science, 01 natural sciences, Antioxidants, chemistry.chemical_compound, Gene Expression Regulation, Plant, Gene expression, Protein Isoforms, Plant Proteins, reactive oxygen species, 0303 health sciences, biology, glutathione peroxidases, Nitrosylation, 3. Good health, Complementation, Biochemistry, Lotus japonicus, Root Nodules, Plant, CIENCIAS NATURALES Y EXACTAS, Research Paper, Peroxidase, Otras Ciencias Biológicas, Immunoelectron microscopy, Saccharomyces cerevisiae, Ciencias Biológicas, 03 medical and health sciences, nitric oxide, BIOQUIMICA Y BIOLOGIA MOLECULAR, S-nitrosylation, 030304 developmental biology, Glutathione Peroxidase, Organisms, Genetically Modified, Endoplasmic reticulum, Nitric oxide, Glutathione, biology.organism_classification, chemistry, S-Nitrosoglutathione, Lotus, biology.protein, Reactive oxygen species, legume nodules, 010606 plant biology & botany
Abstract: 39 Pags.- 3 Tabls.- 10 Figs.- The definitive version is available at: http://jxb.oxfordjournals.org/, Glutathione peroxidases (Gpxs) are antioxidant enzymes not studied so far in legume nodules, despite the fact that reactive oxygen species are produced at different steps of the symbiosis. The function of two Gpxs that are highly expressed in nodules of the model legume Lotus japonicus was examined. Gene expression analysis, enzymatic and nitrosylation assays, yeast cell complementation, in situ mRNA hybridization, immunoelectron microscopy, and LjGpx-green fluorescent protein (GFP) fusions were used to characterize the enzymes and to localize each transcript and isoform in nodules. The LjGpx1 and LjGpx3 genes encode thioredoxin-dependent phospholipid hydroperoxidases and are differentially regulated in response to nitric oxide (NO) and hormones. LjGpx1 and LjGpx3 are nitrosylated in vitro or in plants treated with S-nitrosoglutathione (GSNO). Consistent with the modification of the peroxidatic cysteine of LjGpx3, in vitro assays demonstrated that this modification results in enzyme inhibition. The enzymes are highly expressed in the infected zone, but the LjGpx3 mRNA is also detected in the cortex and vascular bundles. LjGpx1 is localized to the plastids and nuclei, and LjGpx3 to the cytosol and endoplasmic reticulum. Based on yeast complementation experiments, both enzymes protect against oxidative stress, salt stress, and membrane damage. It is concluded that both LjGpxs perform major antioxidative functions in nodules, preventing lipid peroxidation and other oxidative processes at different subcellular sites of vascular and infected cells. The enzymes are probably involved in hormone and NO signalling, and may be regulated through nitrosylation of the peroxidatic cysteine essential for catalytic function., AS and PBS were the recipients of predoctoral (Formación de Personal Investigador) and postdoctoral (Marie Curie) contracts, respectively. We thank Martin Crespi for help with in situ RNA hybridization and Simon Avery for sharing the yeast mutant and for helpful advice. This work was supported by Ministerio de Economía y Competitividad-Fondo Europeo de Desarrollo Regional (AGL2011-24524 and AGL2014-53717-R). The UMR1136 is supported by a grant overseen by the French National Research Agency (ANR) as part of the "Investissements d'Avenir" program (ANR-11-LABX-0002-01, Lab of Excellence ARBRE). MM and KJD acknowledge support within SPP1710. The proteomic analysis was performed in the CSIC/UAB Proteomics Facility of IIBB-CSIC that belongs to ProteoRed, PRB2-ISCIII, supported by grant PT13/0001.
Published: 2015
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10. Acetylated 1,3-diaminopropane antagonizes abscisic acid-mediated stomatal closing in Arabidopsis

Author: Jean-Pierre Renou, June M. Kwak, Nathalie Leonhardt, Hervé Sentenac, Daniel Tran, Fabien Jammes, Hadjira Bousserouel, François Bouteau, Anne-Aliénor Véry, Alain Vavasseur, Jeffrey Leung, UPR2355 Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Department of Biology, Pomona College, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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 Interdisciplinaire des Energies de Demain (LIED (UMR_8236)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Institut de Chimie des Substances Naturelles (ICSN), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génétique et Horticulture (GenHort), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Center for Plant Aging Research, Institute for Basic Science, Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Institut des sciences du végétal (ISV), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Arabidopsis thaliana, guard cells, Arabidopsis, Plant Science, drought, Biology, Diamines, Photosynthesis, abscisic acid, chemistry.chemical_compound, Gene Expression Regulation, Plant, Acetyltransferase, Genetics, Polyamines, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Abscisic acid, Ion transporter, Transpiration, Arabidopsis Proteins, fungi, food and beverages, Cell Biology, biology.organism_classification, Cell biology, Droughts, Spermidine, Biochemistry, chemistry, Plant Stomata, 3-diaminopropane, Signal Transduction
Abstract: International audience; Faced with declining soil-water potential, plants synthesize abscisic acid (ABA), which then triggers stomatal closure to conserve tissue moisture. Closed stomates, however, also create several physiological dilemmas. Among these, the large CO2 influx required for net photosynthesis will be disrupted. Depleting CO2 in the plant will in turn bias stomatal opening by suppressing ABA sensitivity, which then aggravates transpiration further. We have investigated the molecular basis of how C3 plants resolve this H2 O-CO2 conflicting priority created by stomatal closure. Here, we have identified in Arabidopsis thaliana an early drought-induced spermidine spermine-N(1) -acetyltransferase homolog, which can slow ABA-mediated stomatal closure. Evidence from genetic, biochemical and physiological analyses has revealed that this protein does so by acetylating the metabolite 1,3-diaminopropane (DAP), thereby turning on the latter's intrinsic activity. Acetylated DAP triggers plasma membrane electrical and ion transport properties in an opposite way to those by ABA. Thus in adapting to low soil-water availability, acetyl-DAP could refrain stomates from complete closure to sustain CO2 diffusion to photosynthetic tissues.
Published: 2014
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11. Les variétés végétales tolérantes aux herbicides, un outil de désherbage durable ? : Expertise scientifique collective

Author: Gérard Arnold, Marc Barbier, Michel Beckert, Christophe Charlier, Nathalie Colbach, François Coleno, Henri Darmency, Yves Dessaux, Christian Gauvrit, Jane Lecomte, Stephane Lemarie, Thierry Marteu, Patrick Mazellier, Isabelle Navarro, Mai-Anh Ngo, Francis Quetier, Claire Richard, Sciences en Société, Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Groupe de Recherche en Droit, Economie et Gestion (GREDEG), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biologie et Gestion des Adventices (BGA), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Economie Appliquée de Grenoble (GAEL), Université Pierre Mendès France - Grenoble 2 (UPMF)-Institut National de la Recherche Agronomique (INRA), Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Clermont-Ferrand (ICCF), Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Sigma CLERMONT (Sigma CLERMONT), Expertise collective INRA CNRS, Bertrand Schmitt, SMDE, Sciences en Société (SenS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Economie Appliquée = Grenoble Applied Economics Laboratory (GAEL), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Université Sciences et Technologies - Bordeaux 1-Université Montesquieu - Bordeaux 4-Institut de Chimie du CNRS (INC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de Chimie du CNRS (INC)-SIGMA Clermont (SIGMA Clermont)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Université Pierre Mendès France - Grenoble 2 (UPMF)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique ( INRA ), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Institut National de la Recherche Agronomique ( INRA ) -Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ), Groupe de Recherche en Droit, Economie et Gestion ( GREDEG ), Centre National de la Recherche Scientifique ( CNRS ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Sciences pour l'Action et le Développement : Activités, Produits, Territoires ( SADAPT ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Biologie et Gestion des Adventices ( BGA ), Etablissement National d'Enseignement Supérieur Agronomique de Dijon ( ENESAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Economie Appliquée de Grenoble ( GAEL ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Institut National de la Recherche Agronomique ( INRA ), Institut des Sciences Moléculaires ( ISM ), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Centre National de la Recherche Scientifique ( CNRS ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Chimie de Clermont-Ferrand ( ICCF ), and Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Sigma CLERMONT ( Sigma CLERMONT ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: variétés végétales tolérantes aux herbicide, [SHS.DROIT]Humanities and Social Sciences/Law, [ SHS.DROIT ] Humanities and Social Sciences/Law
Abstract: Depuis 2009, des variétés de tournesol et de colza, dites « tolérantes aux herbicides » (TH), font leur apparition en France. Destinées à faciliter le désherbage, ces variétés résistent à un herbicide donné ce qui permet a priori d’appliquer l’herbicide sans risque pour la culture. La culture de telles variétés a suscité une contestation sociale se traduisant par l’arrachage de tournesols TH dénoncés comme « OGM cachés ». Dans ce contexte, les ministères chargés de l’Agriculture et de l’Environnement ont demandé à l’Inra et au CNRS de réaliser un bilan des connaissances disponibles sur l’ensemble des impacts de la culture de ces variétés.
Published: 2014

12. Analyzing protein distribution in plant tissues using 'whole-mount' immunolocalization

Author: Pilar, Bustos-Sanmamed, Carole, Laffont, Florian, Frugier, Christine, Lelandais-Brière, Martin, Crespi, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, RNA, Untranslated, animal structures, MESH : RNA, Untranslated, MESH : Ribonucleoproteins, Small Nuclear, MESH: Plant Proteins, MESH: Ribonucleoproteins, Small Nuclear, MESH : Medicago truncatula, Ribonucleoproteins, Small Nuclear, MESH: RNA, Untranslated, MESH: Ribonucleoproteins, Ribonucleoproteins, MESH : Spliceosomes, MESH : Plant Proteins, Medicago truncatula, Spliceosomes, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH : Ribonucleoproteins, MESH: Medicago truncatula, MESH: Spliceosomes, Plant Proteins
Abstract: International audience; Proteins are distributed in different cellular compartments. Our group studies the role of non-coding RNAs and associated RNPs in the development and stress response in legumes. Ribonucleoproteins (RNPs) are RNA-protein complexes that play different roles in many cellular processes. Long and small non-coding RNAs determine the specificity of action of several RNPs as the RNA Induced Silencing Complex (RISC), or affect mRNA translation, splicing and stability by interacting with other RNPs such as P-bodies, spliceosome or polysomes. Together with small and long RNAs (Chapter 20), the precise localization of the associated RNPs or the translational products regulated by small RNAs (ie target proteins regulated by miRNAs, or translationally-regulated products) by immunocytochemistry could bring novel insights into these regulatory processes. The protocol described is currently used for detection of RNP associated proteins in nodules and roots of Medicago truncatula but could be extended to any other protein. The critical points, as the choice of the antibody and the fixation and permeabilization steps, that allow preservation of tissue and cell integrity and increase the accessibility to epitopes, will be discussed.
Published: 2013
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13. Analyzing small and long RNAs in plant development using non-radioactive in situ hybridization

Author: Pilar, Bustos-Sanmamed, Carole, Laffont, Florian, Frugier, Christine, Lelandais-Brière, Martin, Crespi, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : RNA, Messenger, MESH : RNA, Plant, MESH : In Situ Hybridization, MESH: RNA, Plant, MicroRNAs, MESH : MicroRNAs, MESH: In Situ Hybridization, Gene Expression Regulation, Plant, RNA, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, RNA, Messenger, MESH: Gene Expression Regulation, Plant, MESH: MicroRNAs, MESH : Gene Expression Regulation, Plant, In Situ Hybridization, MESH: RNA, Messenger
Abstract: International audience; In the past decade, hundreds of non-coding RNAs (small and long RNAs) have been identified as crucial elements in developmental processes and stress response in plants. Among small RNAs, the microRNAs or miRNAs control levels of specific mRNA by inhibiting translation or reducing the stability of their mRNA targets through integration into different ribonucleoproteins (RNP). Spatio-temporal expression of small and long RNAs, using reporter genes or in situ hybridization, is essential to understand their functions. We are interested in understanding the role of various non-coding RNAs (including miRNAs) in the regulation of root and nodule development in legumes, which are agriculturally important crops. Here, we present the protocol we are currently using for detection of small and long RNA in model legume plants and tissues, like nodules and roots. The probe selection, as well as the fixation and permeabilization steps allowing to preserve tissues and cell integrity and to increase accessibility to RNA targets, will be specifically discussed.
Published: 2013
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14. Mutants impaired in vacuolar metal mobilization identify chloroplasts as a target for cadmium hypersensitivity in Arabidopsis thaliana

Author: Molins, Hélène, Michelet, Laure, Lanquar, Viviane, Agorio, Astrid, Giraudat, Jérôme, Roach, Thomas, Krieger-Liszkay, Anja, Thomine, Sébastien, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Service de Bioénergétique, Biologie Stucturale, et Mécanismes ( SB2SM ), 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 ), Institut de Biologie et de Technologies de Saclay ( IBITECS ), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Service de Bioénergétique, Biologie Stucturale, et Mécanismes (SB2SM), 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 Biologie et de Technologies de Saclay (IBITECS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, 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)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Chlorophyll, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Chloroplasts, Arabidopsis Proteins, Arabidopsis, Biological Transport, Aminoacyltransferases, Plant Roots, Antioxidants, Up-Regulation, Plant Leaves, Oxidative Stress, Gene Expression Regulation, Plant, Seedlings, Mutation, Vacuoles, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Homeostasis, Cation Transport Proteins, Plant Shoots, Cadmium
Abstract: International audience; Cadmium (Cd) is highly toxic to plants causing growth reduction and chlorosis. It binds thiols and competes with essential transition metals. It affects major biochemical processes such as photosynthesis and the redox balance, but the connection between cadmium effects at the biochemical level and its deleterious effect on growth has seldom been established. In this study, two Cd hypersensitive mutants, cad1-3 impaired in phytochelatin synthase (PCS1), and nramp3nramp4 impaired in release of vacuolar metal stores, have been compared. The analysis combines genetics with measurements of photosynthetic and antioxidant functions. Loss of AtNRAMP3 and AtNRAMP4 function or of PCS1 function leads to comparable Cd sensitivity. Root Cd hypersensitivities conferred by cad1-3 and nramp3nramp4 are cumulative. The two mutants contrast in their tolerance to oxidative stress. In nramp3nramp4, the photosynthetic apparatus is severely affected by Cd, whereas it is much less affected in cad1-3. In agreement with chloroplast being a prime target for Cd toxicity in nramp3nramp4, the Cd hypersensitivity of this mutant is alleviated in the dark. The Cd hypersensitivity of nramp3nramp4 mutant highlights the critical role of vacuolar metal stores to supply essential metals to plastids and maintain photosynthetic function under Cd and oxidative stresses.
Published: 2012
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15. Hyaluronic acid-bearing lipoplexes: physico-chemical characterization and in vitro targeting of the CD44 receptor

Author: Valérie Nicolas, Mickael Bourge, Christine Vauthier, Nicolas Tsapis, Myriam Taverna, Elias Fattal, Thais Leite Nascimento, Hervé Hillaireau, Sandy Ribes, Amélie Dufaÿ Wojcicki, Silvia Arpicco, Amélie Bochot, Physico-chimie, pharmacotechnie, biopharmacie (PCPB), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Neuropsychopharmacologie des addictions. Vulnérabilité et variabilité expérimentale et clinique (NAVVEC - UM 81 (UMR 8206/ U705)), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut des sciences du Médicament -Toxicologie - Chimie - Environnement (IFR71), Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Université Paris Diderot - Paris 7 (UPD7), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), IFR 141, Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Paris Descartes - Paris 5 (UPD5)-Université Paris Diderot - Paris 7 (UPD7), Physico-chimie, pharmacotechnie, biopharmacie ( PCPB ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Neuropsychopharmacologie des addictions. Vulnérabilité et variabilité expérimentale et clinique ( NAVVEC (UM 81) ), Université Paris Diderot - Paris 7 ( UPD7 ) -Institut des sciences du Médicament -Toxicologie - Chimie - Environnement ( IFR71 ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), and Centre National de la Recherche Scientifique ( CNRS )
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, lipoplexes, hyaluronic acid, MESH : DNA, Pharmaceutical Science, 02 engineering and technology, MESH : Green Fluorescent Proteins, Green fluorescent protein, MESH : Hyaluronic Acid, chemistry.chemical_compound, MESH : Antigens, CD44, Fluorescence microscope, Cationic liposome, Hyaluronic Acid, 0303 health sciences, Liposome, medicine.diagnostic_test, MESH: DNA, MESH: Complement C3, Transfection, Complement C3, 021001 nanoscience & nanotechnology, Ligand (biochemistry), Endocytosis, Hyaluronan Receptors, Biochemistry, MESH: Endocytosis, lipids (amino acids, peptides, and proteins), MESH : Complement C3, 0210 nano-technology, MESH: Cell Line, Tumor, MESH : Endocytosis, Green Fluorescent Proteins, MESH: Phosphatidylethanolamines, Biology, MESH: Antigens, CD44, Flow cytometry, 03 medical and health sciences, MESH: Green Fluorescent Proteins, Cell Line, Tumor, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Humans, 030304 developmental biology, MESH: Humans, MESH: Hyaluronic Acid, MESH : Cell Line, Tumor, MESH : Phosphatidylethanolamines, Phosphatidylethanolamines, MESH : Humans, DNA, chemistry, MESH : Liposomes, Liposomes, MESH: Liposomes
Abstract: International audience; The mechanism by which hyaluronic acid (HA)-bearing lipoplexes target the A549 lung cancer cell line was evaluated. For this purpose, cationic liposomes targeting the CD44 receptor were designed thanks to the incorporation in their composition of a conjugate between high molecular weight HA and the lipid DOPE (HA-DOPE). Liposomes containing HA-DOPE were complexed at different lipids:DNA ratios with a reporter plasmid encoding the green fluorescent protein (GFP). Diameter, zeta potential, lipoplex stability and DNA protection from nucleases have been determined. Lipids:DNA ratios of 2, 4 and 6 provided a diameter around 250 nm with a zeta potential of -30 mV. The strength of lipids:DNA interaction and the fraction of DNA protected from enzymatic degradation increased with the lipids:DNA ratio. 2D-immunoelectrophoresis demonstrated the low capacity to activate the C3 fraction of the complement system of any of these three ratios, with and without HA-DOPE. Transfection efficiency in the presence of 0, 10 and 15% of HA-DOPE or unconjugated HA, was determined on the CD44-expressing A549 cells by flow cytometry. Lipoplexes at a lipids:DNA ratio of 2 containing 10% (w/w) of HA-DOPE were the most efficient for transfection. The maximal level of GFP expression was obtained after 6h of incubation demonstrating a slow transfection kinetics of lipoplexes. Finally, lipoplex cellular uptake, measured indirectly by the level of transfection using flow cytometry and validated by fluorescence microscopy, was shown to be mediated by the CD44 receptor and caveolae. These results demonstrate the strong specificity of DNA targeting through the CD44 receptor using HA of high molecular weight as a ligand.
Published: 2012
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16. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments

Author: Jon S. Robertson, Claire Prigent-Combaret, Alexandra Calteau, Kristin Wuichet, Ivan R. Kennedy, Zoé Rouy, Ganisan Krishnen, W. Hayes McDonald, Sophie Mangenot, Gladys Alexandre, Gurusahai Khalsa-Moyers, Víctor González, Andrew H. Paterson, Kirill Borziak, Yves Dessaux, Claudine Elmerich, Gregory B. Hurst, Philippe Normand, Valérie Barbe, Guy Condemine, Leonid O. Sukharnikov, Patricia Siguier, Florence Wisniewski-Dyé, Igor B. Zhulin, Mickaël Boyer, Patrick Mavingui, 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), BioEnergy Science Center, The University of Tennessee [Knoxville], Genome Science and Technology, Department of Biochemistry & Cellular & Molecular Biology and the Genome Science & Technology Program, Department of Microbiology, Chemical Sciences Division, Plant Genome Mapping Laboratory, University of Georgia [USA], Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Trafic et signalisation membranaires chez les bactéries (MTSB), Microbiologie, adaptation et pathogénie (MAP), 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)-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)-Centre National de la Recherche Scientifique (CNRS), Faculty of Agriculture, Food, and Natural Resources, The University of Sydney, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), 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), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Universidad Nacional Autónoma de México (UNAM), 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon, Ecologie microbienne ( EM ), 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 ( VAS ), University of Georgia, Institut de Génomique d'Evry ( IG ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de microbiologie et génétique moléculaires ( LMGM ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Biologie Moléculaire du Gène chez les Extrêmophiles ( BMGE ), Microbiologie, adaptation et pathogénie ( MAP ), 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 ) -Centre National de la Recherche Scientifique ( CNRS ), The University of Sydney [Sydney], Universidad Nacional Autónoma de México ( UNAM ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cancer Research, Aquatic Organisms, Lineage (evolution), ved/biology.organism_classification_rank.species, Terrabacteria, Genome, Plant Roots, RNA, Ribosomal, 16S, Genome Sequencing, Clade, Genome Evolution, Genetics (clinical), Phylogeny, 0303 health sciences, Genes, Essential, biology, Genomics, Biological Evolution, Horizontal gene transfer, Terrestrial ecosystem, Research Article, lcsh:QH426-470, Gene Transfer, Horizontal, Glycoside Hydrolases, Genome Complexity, Microbiology, 03 medical and health sciences, Phylogenetics, Terrestrial plant, Botany, Genetics, 14. Life underwater, Molecular Biology, Biology, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Base Sequence, 030306 microbiology, ved/biology, 15. Life on land, Comparative Genomics, biology.organism_classification, Rhodospirillaceae, lcsh:Genetics, Microbial Evolution, Azospirillum, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial
Abstract: Fossil records indicate that life appeared in marine environments ∼3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that “hydrobacteria” and “terrabacteria” might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land., Author Summary Genome sequencing and analysis of plant-associated beneficial soil bacteria Azospirillum spp. reveals that these organisms transitioned from aquatic to terrestrial environments significantly later than the suggested major Precambrian divergence of aquatic and terrestrial bacteria. Separation of Azospirillum from their close aquatic relatives coincided with the emergence of vascular plants on land. Nearly half of the Azospirillum genome has been acquired horizontally, from distantly related terrestrial bacteria. The majority of horizontally acquired genes encode functions that are critical for adaptation to the rhizosphere and interaction with host plants.
Published: 2011
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17. Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis

Author: Sonia Fieulaine, Isabelle Artaud, Carmela Giglione, Michel Desmadril, Frédéric Dardel, Thierry Meinnel, Adrien Boularot, Institut de biologie structurale (IBS - UMR 5075 ), 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 des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de biochimie et biophysique moléculaire et cellulaire (IBBMC), Université Paris-Sud - Paris 11 (UP11)-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)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), 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 (UGA)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale ( IBS - UMR 5075 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Joseph Fourier - Grenoble 1 ( UJF ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques ( LCBPT - UMR 8601 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de biochimie et biophysique moléculaire et cellulaire ( IBBMC ), and Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: Models, Molecular, MESH: Amidohydrolases, MESH: Hydroxamic Acids, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Amino Acid Motifs, Arabidopsis, MESH: Catalytic Domain, Crystallography, X-Ray, Hydroxamic Acids, Biochemistry, MESH : Arabidopsis Proteins, Peptide deformylase, MESH: Amino Acid Motifs, MESH : Arabidopsis, Catalytic Domain, MESH: Arabidopsis, Enzyme Inhibitors, Biology (General), 0303 health sciences, MESH: Kinetics, General Neuroscience, 030302 biochemistry & molecular biology, MESH : Catalytic Domain, MESH : Protein Binding, Enzyme structure, MESH : Mutagenesis, Site-Directed, Enzymes, MESH: Mutagenesis, Site-Directed, MESH : Amidohydrolases, MESH: Enzyme Inhibitors, Thermodynamics, MESH : Kinetics, MESH: Thermodynamics, General Agricultural and Biological Sciences, MESH: Models, Molecular, Protein Binding, Research Article, MESH : Amino Acid Motifs, MESH : Models, Molecular, QH301-705.5, Mutation, Missense, MESH: Arabidopsis Proteins, Biology, Protein Chemistry, General Biochemistry, Genetics and Molecular Biology, Enzyme catalysis, Amidohydrolases, 03 medical and health sciences, Molecular recognition, Hydrolase, MESH : Hydrogen Bonding, MESH: Protein Binding, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Enzyme kinetics, MESH: Hydrogen Bonding, 030304 developmental biology, MESH : Thermodynamics, Enzyme Kinetics, MESH : Enzyme Inhibitors, MESH: Mutation, Missense, MESH : Hydroxamic Acids, General Immunology and Microbiology, Arabidopsis Proteins, Substrate (chemistry), Active site, Proteins, Hydrogen Bonding, MESH: Crystallography, X-Ray, Kinetics, Small Molecules, Enzyme Structure, biology.protein, Biophysics, Mutagenesis, Site-Directed, Biocatalysis, MESH : Crystallography, X-Ray, MESH : Mutation, Missense
Abstract: For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally “zipped up” by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A “movie” that reconstructs this entire process can be further extrapolated to catalysis., Author Summary The notion of induced fit when a protein binds its ligand—like a glove adapting to the shape of a hand—is a central concept of structural biochemistry introduced over 50 years ago. A detailed molecular demonstration of this phenomenon has eluded biochemists, however, largely due to the difficulty of capturing the steps of this very transient process: the “conformational change.” In this study, we were able to see this process by using X-ray diffraction to determine more than 10 distinct structures adopted by a single enzyme when it binds a ligand. To do this, we took advantage of the “slow, tight-binding” of a potent inhibitor to its specific target enzyme to trap intermediates in the binding process, which allowed us to monitor the action of an enzyme in real-time at atomic resolution. We showed the kinetics of the conformational change from an initial open state, including the encounter complex, to the final closed state of the enzyme. From these data and other biochemical and biophysical analyses, we make a coherent causal reconstruction of the sequence of events leading to inhibition of the enzyme's activity. We also generated a movie that reconstructs the sequence of events during the encounter. Our data provide new insights into how enzymes achieve a catalytically competent conformation in which the reactive groups are brought into close proximity, resulting in catalysis.
Published: 2011
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18. New ABA-Hypersensitive Arabidopsis Mutants Are Affected in Loci Mediating Responses to Water Deficit and Dickeya dadantii Infection

Author: Jérôme Giraudat, Yvan Kraepiel, Viridiana Silva Pérez, Helen M. North, Gabriel Cornic, Jeffrey Leung, Raphael Cournol, Lucy Botran, Delphine Effroy, Anne Plessis, Annie Marion-Poll, Bruno Sotta, Anne Frey, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Interactions Plantes Pathogènes (IPP), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National Agronomique Paris-Grignon (INA P-G), UR5, Laboratoire de Physiologie Cellulaire et Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), UPR2355 Institut des sciences du végétal (ISV), and Institut des sciences du végétal (ISV)
Subjects: 0106 biological sciences, mutation, Mutant, Arabidopsis, lcsh:Medicine, Plant Science, drought, Plant Genetics, Plant Roots, 01 natural sciences, nac transcription factors, chemistry.chemical_compound, Gene Expression Regulation, Plant, Gene expression, abscisic-acid biosynthesis, lcsh:Science, Abscisic acid, Plant Growth and Development, Regulation of gene expression, 0303 health sciences, Multidisciplinary, biology, Reverse Transcriptase Polymerase Chain Reaction, plant-pathogen interactions, Temperature, Gene Expression Regulation, Developmental, food and beverages, Phenotype, Dickeya dadantii, Cell biology, protein, Plant Physiology, Host-Pathogen Interactions, Research Article, agent pathogène, signal-transduction, déficience, Arabidopsis Thaliana, Plant Pathogens, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Genes, Plant, cis-acting elements, traitement, 03 medical and health sciences, Model Organisms, Enterobacteriaceae, Plant and Algal Models, eau, Botany, thaliana, Biology, Gene, Plant Diseases, 030304 developmental biology, salt stress, Arabidopsis Proteins, organic chemicals, lcsh:R, fungi, Water, Plant Pathology, biology.organism_classification, gene-expression, Plant Leaves, racine, chemistry, 13. Climate action, Mutation, lcsh:Q, production, Abscisic Acid, 010606 plant biology & botany
Abstract: On water deficit, abscisic acid (ABA) induces stomata closure to reduce water loss by transpiration. To identify Arabidopsis thaliana mutants which transpire less on drought, infrared thermal imaging of leaf temperature has been used to screen for suppressors of an ABA-deficient mutant (aba3-1) cold-leaf phenotype. Three novel mutants, called hot ABA-deficiency suppressor (has), have been identified with hot-leaf phenotypes in the absence of the aba3 mutation. The defective genes imparted no apparent modification to ABA production on water deficit, were inherited recessively and enhanced ABA responses indicating that the proteins encoded are negative regulators of ABA signalling. All three mutants showed ABA-hypersensitive stomata closure and inhibition of root elongation with little modification of growth and development in non-stressed conditions. The has2 mutant also exhibited increased germination inhibition by ABA, while ABA-inducible gene expression was not modified on dehydration, indicating the mutated gene affects early ABA-signalling responses that do not modify transcript levels. In contrast, weak ABA-hypersensitivity relative to mutant developmental phenotypes suggests that HAS3 regulates drought responses by both ABA-dependent and independent pathways. has1 mutant phenotypes were only apparent on stress or ABA treatments, and included reduced water loss on rapid dehydration. The HAS1 locus thus has the required characteristics for a targeted approach to improving resistance to water deficit. In contrast to has2, has1 exhibited only minor changes in susceptibility to Dickeya dadantii despite similar ABA-hypersensitivity, indicating that crosstalk between ABA responses to this pathogen and drought stress can occur through more than one point in the signalling pathway.
Published: 2011
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19. Genome-wide analysis of plant metal transporters, with an emphasis on poplar

Author: Malcolm M. Campbell, Barbara Montanini, Pierre Richaud, Aude Migeon, Damien Blaudez, Olivia Wilkins, Sébastien Thomine, Michel Chalot, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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 Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Biologie végétale et microbiologie environnementale - UMR7265 ( BVME ), Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Aix Marseille Université ( AMU ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), and Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC )
Subjects: 0106 biological sciences, Populus trichocarpa, MESH: Genome, Plant, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Populus, MESH : Saccharomyces cerevisiae, MESH: Plants, Chlamydomonas reinhardtii, MESH: Carrier Proteins, Saccharomyces cerevisiae, MESH : Plants, Physcomitrella patens, 01 natural sciences, Genome, Fungal Proteins, 03 medical and health sciences, Cellular and Molecular Neuroscience, Selaginella moellendorffii, Botany, Arabidopsis thaliana, Gene family, MESH : Fungal Proteins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Phylogeny, Molecular Biology, Gene, Phylogeny, 030304 developmental biology, Pharmacology, 0303 health sciences, MESH: Metals, biology, MESH : Metals, MESH : Phylogeny, food and beverages, Cell Biology, Plants, biology.organism_classification, MESH: Saccharomyces cerevisiae, MESH : Genome, Plant, MESH: Populus, Populus, Metals, Molecular Medicine, MESH: Fungal Proteins, MESH : Carrier Proteins, Carrier Proteins, Genome, Plant, 010606 plant biology & botany
Abstract: International audience; The specific transport of metal ions, mediated by membrane-localized metal transporters, is of fundamental importance in all eukaryotes. Genome-wide analysis of metal transporters was undertaken, making use of whole genome sequences of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, as well as of the yeast Saccharomyces cerevisiae. A repertoire of 430 metal transporters was found in total across eight photosynthetic plants, as well as in S. cerevisiae. Seventy-two full-length metal transporter genes were identified in the Populus genome alone, which is the largest number of metal transporters genes identified in any single species to date. Diversification of some transporter family gene clusters appears to have occurred in a lineage-specific manner. Expression analysis of Populus metal transporters indicates that some family members show tissue-specific transcript abundance. Taken together, the data provide a picture into the diversification of these important gene families.
Published: 2010
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20. Export of vacuolar manganese by AtNRAMP3 and AtNRAMP4 is required for optimal photosynthesis and growth under manganese deficiency

Author: Françoise Lelièvre, Magali Schnell Ramos, Hélène Barbier-Brygoo, Viviane Lanquar, Ute Krämer, Sébastien Thomine, Anja Krieger-Liszkay, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Service de Bioénergétique, Biologie Stucturale, et Mécanismes (SB2SM), 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 Biologie et de Technologies de Saclay (IBITECS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Service de Bioénergétique, Biologie Stucturale, et Mécanismes ( SB2SM ), 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 ), Institut de Biologie et de Technologies de Saclay ( IBITECS ), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Max Planck Institute of Molecular Plant Physiology, Max-Planck-Institut, 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)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Photosystem II, Physiology, MESH: Biological Transport, MESH: Manganese, Plant Science, Vacuole, MESH: Arabidopsis Proteins, Manganese deficiency (plant), Photosynthesis, 01 natural sciences, MESH : Cation Transport Proteins, MESH : Arabidopsis Proteins, MESH: Vacuoles, Superoxide dismutase, MESH : Protoplasts, 03 medical and health sciences, MESH : Plant Leaves, MESH: Cation Transport Proteins, MESH : Arabidopsis, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Arabidopsis, MESH : Superoxide Dismutase, MESH: Photosynthesis, MESH: Superoxide Dismutase, 030304 developmental biology, 0303 health sciences, biology, Wild type, food and beverages, MESH: Protoplasts, MESH : Photosynthesis, Chloroplast, MESH: Plant Leaves, MESH : Biological Transport, Biochemistry, biology.protein, MESH : Manganese, Plant nutrition, MESH : Vacuoles, 010606 plant biology & botany
Abstract: International audience; Manganese (Mn) is an essential element, acting as cofactor in numerous enzymes. In particular, a Mn cluster is indispensable for the function of the oxygen-evolving complex of photosystem II. Metal transporters of the Natural Resistance-Associated Macrophage Protein (NRAMP) family have the ability to transport both iron and Mn. AtNRAMP3 and AtNRAMP4 are required for iron mobilization in germinating seeds. The results reported here show that, in adult Arabidopsis (Arabidopsis thaliana) plants, AtNRAMP3 and AtNRAMP4 have an important role in Mn homeostasis. Vacuolar Mn accumulation in mesophyll cells of rosette leaves of adult nramp3nramp4 double mutant plants was dramatically increased when compared with the wild type. This suggests that a considerable proportion of the cellular Mn pool passes through the vacuole and is retrieved in an AtNRAMP3/AtNRAMP4-dependent manner. The impaired Mn release from mesophyll vacuoles of nramp3nramp4 double mutant plants is associated with reduced growth under Mn deficiency. However, leaf AtNRAMP3 and AtNRAMP4 protein levels are unaffected by Mn supply. Under Mn deficiency, nramp3nramp4 plants contain less functional photosystem II than the wild type. These data are consistent with a shortage of Mn to produce functional photosystem II, whereas mitochondrial Mn-dependent superoxide dismutase activity is maintained under Mn deficiency in both genotypes. The results presented here suggest an important role for AtNRAMP3/AtNRAMP4-dependent Mn transit through the vacuole prior to the import into chloroplasts of mesophyll cells.
Published: 2010
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21. Des modèles pour les sciences du végétal et à vocation agronomique

Author: Mieulet, Delphine, Meyer, Christian, Ratet, Pascal, Pean, Michel, Sormani, Rodnay, Couzigou, Jean-Malo, Philibert, Michel, Guiderdoni, Emmanuel, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, UPR2355 Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Université de la Méditerranée - Aix-Marseille 2, Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut des sciences du végétal (ISV)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, mécanisme génétique, RIZ
Abstract: La compréhension des mécanismes génétiques, moléculaires et physiologiques sous-tendant les grandes fonctions biologiques et les caractères d’intérêt agronomique chez les plantes à fleur représente un enjeu considérable. Les efforts se concentrent sur un nombre réduit de modèles présentant des caractéristiques favorables et réunissant une masse critique de chercheurs et de moyens. Arabidopsis thaliana, le riz et Medicago truncatula sont ces modèles.
Published: 2010

22. Rapid and Efficient Identification of Agrobacterium Species by recA Allele Analysis

Author: Costechareyre, Denis, Rhouma, Ali, Lavire, Céline, Portier, Perrine, Chapulliot, David, Bertolla, Franck, Boubaker, Ali, Dessaux, Yves, Nesme, Xavier, 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), Protection des plantes cultivées et environnement, Institut de l'Olivier, Pathologie Végétale (PaVé), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire de Phytopathologie, Institut National Agronomique de Tunisie, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), CMCU/PHC Utique 0900923, 'Institut de l'Olivier' in Tunisia, Universite Lyon I, 'Institut des Sciences du Vegetal-CNRS' in France, 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), Ecologie microbienne ( EM ), 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 ( VAS ), Pathologie Végétale ( PaVé ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Institut des sciences du végétal ( ISV ), and Centre National de la Recherche Scientifique ( CNRS )
Subjects: [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, AGROBACTERIUM LARRYMOOREI, food and beverages, bacteria, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, AGROBACTERIUM SPP, [SDV.BID]Life Sciences [q-bio]/Biodiversity, biochemical phenomena, metabolism, and nutrition, AGROBACTERIUM RUBI, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, GENOMIQUE
Abstract: International audience; The analysis of housekeeping recA gene sequences from 138 strains from 13 species or genomic species of Agrobacterium, nine being biovar 1 genomospecies, and the others Agrobacterium larrymoorei, Agrobacterium rubi, Agrobacterium sp. NCPPB 1650, and Agrobacterium vitis and one “former” Agrobacterium species, Rhizobium rhizogenes, led to the identification of 50 different recA alleles and to a clear delineation of the 14 species or genomospecies entirely consistent with that obtained by amplified fragment length polymorphism (AFLP) analysis. The relevance of a recA sequencing approach for epidemiological analyses was next assessed on agrobacterial Tunisian isolates. All Tunisian isolates were found to belong to the Agrobacterium tumefaciens/ biovar 1 species complex by both biochemical tests and rrs sequencing. recA sequence analysis further permitted their unambiguous assignment to A. tumefaciens genomospecies G4, G6, G7, and G8 in total agreement with the results of an AFLP-based analysis. At subspecific level, several Tunisian recA alleles were novel, indicating the power and accuracy of recA-based typing for studies of Agrobacterium spp.
Published: 2010
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23. Structure-activity relationship analysis of the peptide deformylase inhibitor 5-bromo-1H-indole-3-acetohydroxamic acid

Author: Frédéric Dardel, Valéry Larue, Thierry Meinnel, Coralie Soulama, Carmela Giglione, Isabelle Artaud, Yann Duroc, Alexis Denis, Sylvain Petit, Carole Léon, Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), CNRS Region Ile-de-France Agence Nationale de la Recherche (ANR, France) ANR-06-MIME-010, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Laboratoire Léon Brillouin ( LLB - UMR 12 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut Jean-Pierre Bourgin ( IJPB ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Laboratoire de cristallographie et RMN biologiques ( LCRB - UMR 8015 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques ( LCBPT - UMR 8601 ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, MESH: Amidohydrolases, MESH: Hydroxamic Acids, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Magnetic Resonance Spectroscopy, Peptide, Hydroxamic Acids, 01 natural sciences, Biochemistry, antibiotics, chemistry.chemical_compound, Peptide deformylase, MESH: Structure-Activity Relationship, MESH : Indoles, Drug Discovery, MESH : Structure-Activity Relationship, inhibitors, Enzyme Inhibitors, General Pharmacology, Toxicology and Pharmaceutics, MESH : Anti-Bacterial Agents, Actinonin, chemistry.chemical_classification, MESH: Indoles, 0303 health sciences, peptide deformylase, MESH: Microbial Sensitivity Tests, Chemistry, MESH : Spectrometry, Mass, Electrospray Ionization, Anti-Bacterial Agents, MESH : Amidohydrolases, MESH: Enzyme Inhibitors, Molecular Medicine, Antibacterial activity, Lead compound, MESH: Models, Molecular, Spectrometry, Mass, Electrospray Ionization, Stereochemistry, MESH : Models, Molecular, Microbial Sensitivity Tests, MESH: Spectrometry, Mass, Electrospray Ionization, Amidohydrolases, Structure-Activity Relationship, 03 medical and health sciences, NMR spectroscopy, MESH: Anti-Bacterial Agents, Structure–activity relationship, Potency, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Pharmacology, Indole test, MESH : Enzyme Inhibitors, MESH : Hydroxamic Acids, 010405 organic chemistry, MESH: Magnetic Resonance Spectroscopy, Organic Chemistry, indoles, 0104 chemical sciences, MESH : Magnetic Resonance Spectroscopy, MESH : Microbial Sensitivity Tests
Abstract: International audience; The lead compound 5-bromoindolyl-3-acetohydroxamic acid (10) was recently identified as a potent inhibitor of bacterial peptide deformylases (PDFs). The synthesis and associated activities of new variants were investigated at position 5 to optimize the fit at the S1' subsite and at position 1 to improve both potency and antibacterial activity. A morphomimetic series, termed "reverse-indole" was synthesized. The indole derivatives remain selective in vitro inhibitors of PDF2 over PDF1. Bromide is the best group at position 5 and cannot be replaced by bulkier substituents. In this series, an N-benzyl group at position 1 in 19 e improves the potency relative to 10. In the case of PDF1, and unlike PDF2, potency is increased as the alkyl chain becomes longer and more ramified. These data support the results of NMR footprinting experiments that were performed with (15)N-labeled Ni-PDF and the corresponding 3-acetic acid derivatives. Most of the compounds have antibacterial activities toward B. subtilis, but are inefficient toward E. coli owing to active removal by the major efflux pumps. Among the reverse-indole derivatives, 23 c, which is the exact mirror image of 19 e, shows strong potency in vitro against PDF2, but little against PDF1, although this compound displays significant antibacterial activity toward an efflux-minus mutant of E. coli. All the compounds were assessed with major pathogenic bacteria, but most of them are inefficient antibacterial agents. The reverse-indole compounds 23 a and 23 c have potency against S. pneumoniae that is similar to that of actinonin.
Published: 2009
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24. New antibiotic molecules: bypassing the membrane barrier of gram negative bacteria increases the activity of peptide deformylase inhibitors

Author: Jacqueline Chevalier, Carmela Giglione, Isabelle Artaud, Thierry Meinnel, Aurélie Lieutaud, Jean-Marie Pagès, Laurent Mamelli, Sylvain Petit, Transporteurs membranaires, chimioresistance et drug-design (TMCD2), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), ANR-06-MIME-0010,Def-Inhib,Les inhibiteurs de peptide deformylase, une nouvelle classe d'antibiotique: Conception, spectre d'action et mécanismes de résistance(2006), Laboratoire Léon Brillouin ( LLB - UMR 12 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de chimie bactérienne ( LCB ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques ( LCBPT - UMR 8601 ), Université Paris Descartes - Paris 5 ( UPD5 ) -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 Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Amidohydrolases, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Cell Membrane Permeability, Antibiotic resistance, Polymyxin, lcsh:Medicine, Antimicrobial resistance, chemistry.chemical_compound, Peptide deformylase, Antibiotics, MESH: Gram-Negative Bacteria, MESH: Cell Membrane Permeability, Enzyme Inhibitors, MESH : Anti-Bacterial Agents, Actinonin, lcsh:Science, 0303 health sciences, Multidisciplinary, biology, MESH : Gram-Negative Bacteria, Anti-Bacterial Agents, Infectious Diseases, MESH : Amidohydrolases, Biochemistry, MESH: Enzyme Inhibitors, Pseudomonas aeruginosa, Microbiology/Microbial Physiology and Metabolism, Efflux, Antibacterial activity, Gram negative bacteria, Research Article, Gram-negative bacteria, medicine.drug_class, Microbiology, Permeability, Amidohydrolases, 03 medical and health sciences, MESH: Anti-Bacterial Agents, Gram-Negative Bacteria, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Polymyxins, 030304 developmental biology, MESH : Enzyme Inhibitors, Infectious Diseases/Antimicrobials and Drug Resistance, 030306 microbiology, lcsh:R, Microbiology/Medical Microbiology, biology.organism_classification, Cytosol, chemistry, MESH : Cell Membrane Permeability, Antibacterials, lcsh:Q, Bacteria
Abstract: International audience; BACKGROUND : Multi-drug resistant (MDR) bacteria have become a major concern in hospitals worldwide and urgently require the development of new antibacterial molecules. Peptide deformylase is an intracellular target now well-recognized for the design of new antibiotics. The bacterial susceptibility to such a cytoplasmic target primarily depends on the capacity of the compound to reach and accumulate in the cytosol. METHODOLOGY/PRINCIPAL FINDINGS : To determine the respective involvement of penetration (influx) and pumping out (efflux) mechanisms to peptide deformylase inhibitors (PDF-I) activity, the potency of various series was determined using various genetic contexts (efflux overproducers or efflux-deleted strains) and membrane permeabilizers. Depending on the structure of the tested molecules, two behaviors could be observed: (i) for actinonin the first PDF-I characterized, the AcrAB efflux system was the main parameter involved in the bacterial susceptibility, and (ii), for the latest PDF-Is such as the derivatives of 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide, the penetration through the membrane was a important limiting step CONCLUSIONS/SIGNIFICANCE : Our results clearly show that the bacterial membrane plays a key role in modulating the antibacterial activity of PDF-Is. The bacterial susceptibility for these new antibacterial molecules can be improved by two unrelated ways in MDR strains: by collapsing the Acr efflux activity or by increasing the uptake rate through the bacterial membrane. The efficiency of the second method is associated with the nature of the compound.
Published: 2009
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25. Functional characterization of NRAMP3 and NRAMP4 from the metal hyperaccumulator Thlaspi caerulescens

Author: Pierre Richaud, Ronald Oomen, Hélène Barbier-Brygoo, Jian Wu, Sébastien Thomine, Françoise Lelièvre, Mark G. M. Aarts, Sandrine Blanchet, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratory of Genetics, Wageningen University and Research [Wageningen] (WUR), Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS), Bioénergie et Microalgues (EBM), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), UMR Biolologie Végétale & Microbiologie Environementale, Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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 National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Environnement, Bioénergie, Microalgues et Plantes (EBMP), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Wageningen University and Research Centre [Wageningen] ( WUR ), Institute of Vegetables and Flowers ( IVF ), Chinese Academy of Agricultural Sciences ( CAAS ), Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues ( L3BM ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Biologie végétale et microbiologie environnementale - UMR7265 ( BVME ), and Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Aix Marseille Université ( AMU )
Subjects: 0106 biological sciences, iron transport, Mutant, Arabidopsis, Plant Science, MESH : Green Fluorescent Proteins, 01 natural sciences, Laboratorium voor Plantenveredeling, Arabidopsis thaliana, MESH : Cadmium, transporter genes, 0303 health sciences, food and beverages, NRAMP, Zinc, Laboratory of Genetics, MESH : Vacuoles, MESH : Cloning, Molecular, zinc transporter, Recombinant Fusion Proteins, Molecular Sequence Data, Saccharomyces cerevisiae, Laboratorium voor Erfelijkheidsleer, MESH: Vacuoles, 03 medical and health sciences, MESH: Green Fluorescent Proteins, Thlaspi caerulescens, Botany, MESH: Recombinant Fusion Proteins, MESH: Cloning, Molecular, MESH: DNA, Plant, MESH: Metals, MESH: Molecular Sequence Data, MESH : Metals, fungi, Plant Breeding, Mutation, MESH : Gene Expression Regulation, Plant, MESH: Genome, Plant, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Molecular Sequence Data, MESH : DNA, Complementary, Physiology, MESH : Saccharomyces cerevisiae, MESH : Thlaspi, medicine.disease_cause, MESH: Zinc, expression differences, MESH : Arabidopsis, Gene Expression Regulation, Plant, MESH: Arabidopsis, Cloning, Molecular, Plant Proteins, metal transport, zinc (Zn), MESH: Genetic Complementation Test, biology, MESH: Plant Proteins, EPS-3, MESH: Saccharomyces cerevisiae, MESH : Genome, Plant, MESH: Intracellular Membranes, MESH : DNA, Plant, Biochemistry, Metals, saccharomyces-cerevisiae, MESH : Mutation, hyperaccumulator, Genome, Plant, DNA, Complementary, MESH: Mutation, MESH : Recombinant Fusion Proteins, DNA, Plant, cadmium, heavy-metal, MESH: Biological Transport, Green Fluorescent Proteins, MESH: Cadmium, MESH: Thlaspi, arabidopsis-thaliana, MESH : Plant Proteins, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Hyperaccumulator, MESH: Gene Expression Regulation, Plant, 030304 developmental biology, MESH : Genetic Complementation Test, cadmium (Cd), ACL, Genetic Complementation Test, Biological Transport, MESH : Zinc, Intracellular Membranes, MESH: DNA, Complementary, biology.organism_classification, Yeast, Thlaspi, MESH : Biological Transport, MESH : Intracellular Membranes, Vacuoles, Zinc toxicity, gene encodes, Heterologous expression, protein, 010606 plant biology & botany
Abstract: International audience; The ability of metal hyperaccumulating plants to tolerate and accumulate heavy metals results from adaptations of metal homeostasis. NRAMP metal transporters were found to be highly expressed in some hyperaccumulating plant species. Here, we identified TcNRAMP3 and TcNRAMP4, the closest homologues to AtNRAMP3 and AtNRAMP4 in Thlaspi caerulescens and characterized them by expression analysis, confocal imaging and heterologous expression in yeast and Arabidopsis thaliana. TcNRAMP3 and TcNRAMP4 are expressed at higher levels than their A. thaliana homologues. When expressed in yeast TcNRAMP3 and TcNRAMP4 transport the same metals as their respective A. thaliana orthologues: iron (Fe), manganese (Mn) and cadmium (Cd) but not zinc (Zn) for NRAMP3; Fe, Mn, Cd and Zn for NRAMP4. They also localize at the vacuolar membrane in A. thaliana protoplasts. Inactivation of AtNRAMP3 and AtNRAMP4 in A. thaliana results in strong Cd and Zn hypersensitivity, which is fully rescued by TcNRAMP3 or TcNRAMP4 expression. However, metal tolerance conferred by TcNRAMP expression in nramp3nramp4 mutant does not exceed that of wild-type A. thaliana. Our data indicate that the difference between TcNRAMP3 and TcNRAMP4 and their A. thaliana orthologues does not lie in a different protein function, but probably resides in a different expression level or expression pattern.
Published: 2009
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26. MicroRNA166 controls root and nodule development in Medicago truncatula

Author: Carole Laffont, Martin Crespi, Andreas Niebel, Julie Plet, Philippe Laporte, Jean-Philippe Combier, Mariana Jovanovic, Florian Frugier, Adnane Boualem, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Nouveaux Outils pour La Coopération et l'Education (NOCE), Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-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-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), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 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), 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), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Nouveaux Outils pour La Coopération et l'Education ( NOCE ), Laboratoire d'Informatique Fondamentale de Lille ( LIFL ), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique ( CNRS ) -Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique ( CNRS ), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), 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 ( VAS ), Laboratoire des interactions plantes micro-organismes ( LIPMO ), and Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: 0106 biological sciences, MESH : Plant Roots, MESH : Brain Chemistry, MESH: Plant Roots, clustered miRNA, Plant Science, MESH: Amino Acid Sequence, MESH: Base Sequence, 01 natural sciences, MESH : Cattle, MESH: Cattle Diseases, MESH: Animals, In Situ Hybridization, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Reverse Transcriptase Polymerase Chain Reaction, MESH : In Situ Hybridization, Medicago truncatula, Cell biology, MESH : Proton-Translocating ATPases, MESH : DNA Primers, MESH: Proteolipids, MESH: DNA Primers, MESH: Mitochondria, Organogenesis, MESH: Microscopy, Electron, MESH : Electrophoresis, Polyacrylamide Gel, 03 medical and health sciences, MESH: In Situ Hybridization, microRNA, Botany, Genetics, MESH: Blotting, Northern, MESH: Mass Spectrometry, MESH : Cattle Diseases, MESH: Molecular Sequence Data, MESH : Medicago truncatula, Lateral root, HD ZIP III transcription factors, MESH : Pigments, Biological, MESH: Neuronal Ceroid-Lipofuscinoses, MESH : Brain, MESH : Amino Acids, MESH : Gene Expression Regulation, Plant, MESH: MicroRNAs, MESH: Female, MESH: Liver, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Molecular Sequence Data, MESH: Amino Acids, Plant Roots, lateral root, MESH: Proton-Translocating ATPases, Gene Expression Regulation, Plant, MESH: Reverse Transcriptase Polymerase Chain Reaction, MESH : Female, MESH: Brain Chemistry, MESH : Pancreas, MESH: Medicago truncatula, biology, Reverse Transcriptase Polymerase Chain Reaction, MESH : Blotting, Northern, MESH: Pancreas, MESH: Lipoproteins, MESH : Kidney, MESH: Cattle, MESH : Mitochondria, Rhizobium, MESH: Pigments, Biological, Transgene, MESH : Lipoproteins, MESH: Brain, MESH : Mass Spectrometry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Gene Expression Regulation, Plant, Transcription factor, Gene, 030304 developmental biology, DNA Primers, Base Sequence, polycistronic miRNA, MESH : Liver, MESH : Lipids, Cell Biology, MESH: Kidney, Meristem, biology.organism_classification, Blotting, Northern, symbiotic nodulation, MESH: Lipids, MESH : Microscopy, Electron, MESH : MicroRNAs, MicroRNAs, MESH : Proteolipids, MESH : Base Sequence, MESH : Animals, MESH : Neuronal Ceroid-Lipofuscinoses, 010606 plant biology & botany, MESH: Electrophoresis, Polyacrylamide Gel
Abstract: International audience; Legume root architecture is characterized by the development of two de novo meristems, leading to the formation of lateral roots or symbiotic nitrogen-fixing nodules. Organogenesis involves networks of transcription factors, the encoding mRNAs of which are frequently targets of microRNA (miRNA) regulation. Most plant miRNAs, in contrast with animal miRNAs, are encoded as single entities in an miRNA precursor. In the model legume Medicago truncatula, we have identified the MtMIR166a precursor containing tandem copies of MIR166 in a single transcriptional unit. These miRNAs post-transcriptionally regulate a new family of transcription factors associated with nodule development, the class-III homeodomain-leucine zipper (HD-ZIP III) genes. In situ expression analysis revealed that these target genes are spatially co-expressed with MIR166 in vascular bundles, and in apical regions of roots and nodules. Overexpression of the tandem miRNA precursor correlated with MIR166 accumulation and the downregulation of several class-III HD-ZIP genes, indicating its functionality. MIR166 overexpression reduced the number of symbiotic nodules and lateral roots, and induced ectopic development of vascular bundles in these transgenic roots. Hence, plant polycistronic miRNA precursors, although rare, can be processed, and MIR166-mediated post-transcriptional regulation is a new regulatory pathway involved in the regulation of legume root architecture.
Published: 2008
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27. Detection of potential transgenic plant DNA recipients among soil bacteria

Author: Elizabeth Kay, Yves Dessaux, Oleksandra Rybalka, Dominique Bernillon, Timothy M. Vogel, Aurélie Faugier, Pascal Simonet, Jean-Michel Monier, 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), Ampère, École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), 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)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 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), Ampère (AMPERE), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie microbienne ( EM ), 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 ( VAS ), École Centrale de Lyon ( ECL ), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 ( UCBL ), 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 ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), and Centre National de la Recherche Scientifique ( CNRS )
Subjects: DNA, Plant, Gene Transfer, Horizontal, Transgene, Biomedical Engineering, Ralstonia, Biology, Genome, natural transformation, tobacco, DNA sequencing, soil, 03 medical and health sciences, chemistry.chemical_compound, Plasmid, Transgenes, Safety, Risk, Reliability and Quality, antibiotic resistance gene, bacteria, Gene, hybridization, Soil Microbiology, 030304 developmental biology, General Environmental Science, Genetics, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, transplastomic, Acinetobacter, 030306 microbiology, GMO, transgene, food and beverages, DNA, Plants, Genetically Modified, recombination, Transformation (genetics), chemistry, Transformation, Bacterial, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Safety Research, Biotechnology, Transplastomic plant, Plasmids
Abstract: International audience; The likelihood of gene transfer from transgenic plants to bacteria is dependent on gene number and the presence of homologous sequences. The large number of transgene copies in transplastomic (transgenes contained in the chloroplast genome) plant cells as well as the prokaryotic origin of the transgene, may thus significantly increase the likelihood of gene transfer to bacteria that colonize plant tissues. In order to assess the probability of such transfer, the length of homologous DNA sequences required between the transgene and the genome of the bacterial host was assessed. In addition, the probability that bacteria, which co-infect diseased plants, are transformable and have sequences similar to the flanking regions of the transgene was evaluated. Using Acinetobacter baylyi strain BD143 and transplastomic tobacco plants harboring the aadA gene (streptomycin and spectinomycin resistance), we found that sequences identical to the flanking regions containing as few as 55 nucleotides were sufficient for recombination to occur. Consequently, a collection of bacterial isolates able to colonize tobacco plant tissue infected by Ralstonia solanacearum strain K60 was obtained, screened for DNA sequence similarity with the chloroplastic genes accD and rbcL flanking the transgene, and tested for their ability to uptake extracellular DNA (broad host-range pBBR1MCS plasmids) by natural or electro-transformation. Results showed that among the 288 bacterial isolates tested, 8% presented DNA sequence similarity with one or both chloroplastic regions flanking the transgene. Two isolates, identified as Pseudomonas sp. and Acinetobacter sp., were able to integrate exogenous plasmid DNA by electro-transformation and natural transformation, respectively. Our data suggest that transplastomic plant DNA recipients might be present in soil bacterial communities.
Published: 2007
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28. Eucalyptus occidentalis plantlets are naturally infected by pathogenic Agrobacterium tumefaciens

Author: Zoulikha Krimi, Yves Dessaux, Xavier Nesme, Aida Raio, Annik Petit, Laboratoire de Phytobactériologie, Faculté des Sciences Agronomiques et Vétérinaires, Université de Saâd Dahlab [Blida] (USDB ), Instituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche [Roma] (CNR), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), 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), Université de Blida, Consiglio Nazionale delle Ricerche [Roma] ( CNR ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), 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 ( VAS ), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), 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: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, food.ingredient, Agrobacterium, Ti plasmid, agrocin 84 : opine, Opine, Plant Science, Horticulture, Biology, 01 natural sciences, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, food, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 16S rRNA, 0303 health sciences, 030306 microbiology, Eucalyptus occidentalis, Agrobacterium tumefaciens, 15. Life on land, biology.organism_classification, plant pathogen, Eucalyptus camaldulensis, chemistry, Chromosomal region, Nopaline, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: In the Sidi M'djahed nursery (Algeria), over 60,000 eucalyptus (Eucalyptus occidentalis) plantlets exhibited tumour-like growths localized at the crown of the plants that resembled crown galls caused by Agrobacterium tumefaciens. Bacteria colonizing the galls were isolated and purified. Most (22 out of 24) of the isolates had cultural and biochemical characteristics similar to those of strains of the biovar 1 of A. tumefaciens. Twenty out of 22 Agrobacterium isolates induced tumour formation on various test plants. In PCR experiments, DNA extracted from these virulent strains yielded an amplification signal corresponding to a 247-bp fragment located within the virulence region of nopaline type Ti plasmid. Consistent with this, the opine nopaline was detected in the tumours induced on test plants – but not on eucalyptus plants. Nopaline was degraded by the 20 pathogenic isolates that were also sensitive to agrocin 84, indicating the presence of a nopaline-type pTi in these strains. The chromosomal region encoding the 16S rRNA was analyzed in a sub-population of the pathogenic agrobacterial isolates. The analyzed strains were found to belong to the ribogroup of the reference strain B6. Interestingly, Eucalyptus camaldulensis and Eucalyptus cladocalyx grown in the same nursery and in the same soil substrate developed no galls.
Published: 2006
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29. Medicago truncatula transformation using leaf explants

Author: Cosson, Viviane, Durand, Patricia, D'Erfurth, Isabelle, Kondorosi, Adam, Ratet, Pascal, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Rhizobium radiobacter, MESH : Medicago truncatula, fungi, Gene Transfer Techniques, MESH: Regeneration, Embryonic Development, food and beverages, MESH: Gene Transfer Techniques, MESH : Regeneration, MESH: Transformation, Genetic, Plant Leaves, MESH: Plant Leaves, MESH : Plant Leaves, Transformation, Genetic, MESH : Embryonic Development, Agrobacterium tumefaciens, MESH: Rhizobium radiobacter, Medicago truncatula, Regeneration, MESH: Embryonic Development, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH : Gene Transfer Techniques, MESH : Transformation, Genetic, MESH: Medicago truncatula
Abstract: Legumes have long been recalcitrant to efficient Agrobacterium tumefaciens-mediated transformation. The choice and use of model legume plants (Medicago truncatula and Lotus japonicus) for molecular studies has triggered extensive studies devoted to the development of efficient Agrobacterium-mediated transformation protocols for these two plants. In M. truncatula, transformation protocols rely on the use of highly regenerable lines obtained by recurrent in vitro culture selection. These protocols are based on Agrobacterium-mediated transformation of M. truncatula followed by somatic embryogenesis-mediated plant regeneration. We describe here the protocol developed for M. truncatula R108-1 (c3).
Published: 2006

30. The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines for the Design of Inhibitors Specific for the Bacterial Forms

Author: Jean-Luc Ferrer, Frédéric Dardel, Sonia Fieulaine, Alexandre Serero, Thierry Meinnel, Céline Juillan-Binard, Carmela Giglione, Institut de biologie structurale (IBS - UMR 5075 ), 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)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), 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 (UGA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Institut de biologie structurale ( IBS - UMR 5075 ), 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 ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de cristallographie et RMN biologiques ( LCRB - UMR 8015 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Models, Molecular, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Protein Conformation, Stereochemistry, Dimer, Molecular Sequence Data, Arabidopsis, chemistry.chemical_element, Substrate analog, Zinc, Mitochondrion, Crystallography, X-Ray, Biochemistry, Amidohydrolases, 03 medical and health sciences, chemistry.chemical_compound, Peptide deformylase, Hydrolase, Amino Acid Sequence, Enzyme Inhibitors, [ SDV.OT ] Life Sciences [q-bio]/Other [q-bio.OT], Protein Structure, Quaternary, Molecular Biology, 030304 developmental biology, Leptospira, 0303 health sciences, Sequence Homology, Amino Acid, biology, 030302 biochemistry & molecular biology, fungi, Active site, Substrate (chemistry), Cell Biology, Mitochondria, chemistry, Drug Design, biology.protein
Abstract: Peptide deformylase (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1' binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3' pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.
Published: 2005
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31. Engineering root exudation of Lotus towards the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere

Author: Xavier Nesme, Yves Dessaux, Philippe Oger, H. Mansouri, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Sciences de la Terre (LST), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS 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), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Sciences de la Terre ( LST ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), 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 ( 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.BV ] Life Sciences [q-bio]/Vegetal Biology, food.ingredient, Agrobacterium, Lotus, Sequence Homology, Soil Science, Opine, Biology, Arginine, Plant Roots, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, food, RNA, Ribosomal, 16S, Botany, Duganella, Cluster Analysis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Mannitol, Phyllobacterium, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Rhizosphere, Bacteria, Ecology, 030306 microbiology, fungi, Genetic Variation, food and beverages, Sequence Analysis, DNA, Agrobacterium tumefaciens, 15. Life on land, Plants, Genetically Modified, biology.organism_classification, chemistry, France, Nopaline, Polymorphism, Restriction Fragment Length
Abstract: The culture of opine-producing transgenic Lotus plants induces the increase in the rhizosphere of bacterial communities that are able to utilize these molecules as sole carbon source. We used transgenic Lotus plants producing two opines, namely mannopine and nopaline, to characterize the microbial communities directly influenced by the modification of root exudation. We showed that opine-utilizers represent a large community in the rhizosphere of opine-producing transgenic Lotus. This community is composed of at least 12 different bacterial species, one third of which are able to utilize the opine mannopine and two thirds the opine nopaline. Opine utilizers are diverse, belonging to the Gram-positive and -negative bacteria. We described two novel mannopine-utilizing species, Rhizobium and Duganella spp., and five novel nopaline-utilizing species, Duganella, Afipia, Phyllobacterium, Arthrobacter, and Bosea spp. Although opine utilizers mostly belong to the α-Proteobacteria, Rhizobiaceae family, there is little overlap between the populations able to utilize each of the two opines produced by the plants. Noticeably, in the rhizosphere of transgenic Lotus, only the opine mannopine favors the growth of Agrobacterium tumefaciens, the bacterium from which opines have been characterized. The diversity of opine utilizers from the rhizosphere of Lotus plants is greater than that observed from any other environment. Therefore, transgenic plants with engineered exudation constitute an excellent tool to isolate and characterize specific microbial populations.
Published: 2004
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32. The Arabidopsis GNOM ARF-GEF mediates endosomal recycling, auxin transport, and auxin-dependent plant growth

Author: Philippe Muller, Nadine Anders, Takashi Ueda, Hanno Wolters, Gerd Jürgens, Akihiko Nakano, Niko Geldner, Alain Delbarre, Wolfgang Kornberger, Jutta Keicher, Zentrum für Molekularbiologie der Pflanzen ( ZMBP ), Eberhard Karls Universität Tübingen, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Molecular Membrane Biology Laboratory, RIKEN, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), and RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)
Subjects: 0106 biological sciences, Auxin efflux, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Molecular Sequence Data, Arabidopsis, Drug Resistance, MESH: Amino Acid Sequence, 01 natural sciences, MESH : Arabidopsis Proteins, MESH: Membrane Transport Proteins, chemistry.chemical_compound, MESH : Arabidopsis, MESH : Membrane Transport Proteins, Plant Growth Regulators, MESH: Microscopy, Confocal, MESH: Guanine Nucleotide Exchange Factors, Guanine Nucleotide Exchange Factors, MESH: Arabidopsis, MESH : Brefeldin A, PIN proteins, chemistry.chemical_classification, 0303 health sciences, Microscopy, Confocal, biology, Membrane transport protein, MESH : Amino Acid Sequence, food and beverages, Brefeldin A, MESH : Indoleacetic Acids, Cell biology, MESH : Guanine Nucleotide Exchange Factors, MESH: Drug Resistance, MESH: Genetic Engineering, MESH: Membrane Proteins, MESH : Mutation, Genetic Engineering, Auxin influx, MESH: Indoleacetic Acids, MESH: Mutation, Molecular Sequence Data, Biological Transport, Active, MESH: Arabidopsis Proteins, Endosomes, General Biochemistry, Genetics and Molecular Biology, MESH : Genetic Engineering, 03 medical and health sciences, Auxin, MESH : Plant Growth Regulators, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, MESH: Plant Growth Regulators, MESH : Microscopy, Confocal, MESH : Biological Transport, Active, 030304 developmental biology, MESH : Drug Resistance, MESH: Molecular Sequence Data, MESH: Brefeldin A, Indoleacetic Acids, Biochemistry, Genetics and Molecular Biology(all), Arabidopsis Proteins, fungi, Membrane Proteins, Membrane Transport Proteins, biology.organism_classification, chemistry, MESH: Endosomes, MESH : Membrane Proteins, Mutation, biology.protein, MESH: Biological Transport, Active, MESH : Endosomes, Polar auxin transport, 010606 plant biology & botany
Abstract: Exchange factors for ARF GTPases (ARF-GEFs) regulate vesicle trafficking in a variety of organisms. The Arabidopsis protein GNOM is a brefeldin A (BFA) sensitive ARF-GEF that is required for the proper polar localization of PIN1, a candidate transporter of the plant hormone auxin. Mutations in GNOM lead to developmental defects that resemble those caused by interfering with auxin transport. Both PIN1 localization and auxin transport are also sensitive to BFA. In this paper, we show that GNOM localizes to endosomes and is required for their structural integrity. We engineered a BFA-resistant version of GNOM. In plants harboring this fully functional GNOM variant, PIN1 localization and auxin transport are no longer sensitive to BFA, while trafficking of other proteins is still affected by the drug. Our results demonstrate that GNOM is required for the recycling of auxin transport components and suggest that ARF-GEFs regulate specific endosomal trafficking pathways.
Published: 2003
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33. AtMYB92 enhances fatty acid synthesis and suberin deposition in leaves of Nicotiana benthamiana

Author: Loïc Lepiniec, Sami Kazaz, Jean Thueux, Jérôme Joubès, Sébastien Baud, Alexandra To, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), IJPB's Plant Observatory technological platforms, ANR-10-GENM-0009,SOLAR,Développer et tester de nouveaux outils biotechnologiques pour accroître la teneur en huile de la graine : une clé pour la production de chaînes hydrocarbonées chez les oléagineux.(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Unité associée au Département Biologie et Amélioration des Plantes (Associée BAP), Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Arabidopsis, Nicotiana benthamiana, Plant Science, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, MYB92, suberin, Suberin, Tobacco, Genetics, MYB, Transcription factor, ComputingMilieux_MISCELLANEOUS, transcription factor, Fatty acid synthesis, Plant Proteins, chemistry.chemical_classification, biology, Arabidopsis Proteins, Activator (genetics), Fatty Acids, Fatty acid, Lipid metabolism, Cell Biology, Plants, Genetically Modified, biology.organism_classification, Lipids, Plant Leaves, 030104 developmental biology, chemistry, Biochemistry, fatty acid, Transcription Factors, 010606 plant biology & botany
Abstract: International audience; Acyl lipids are important constituents of the plant cell. Depending on the cell type, requirements in acyl lipids vary greatly, implying a tight regulation of fatty acid and lipid metabolism. The discovery of the WRINKLED1 (WRI1) transcription factors, members of the AP2-EREBP (APETALA2-ethylene-responsive element binding protein) family, has emphasized the importance of transcriptional regulation for adapting the rate of acyl chain production to cell requirements. Here, we describe the identification of another activator of the fatty acid biosynthetic pathway, the Arabidopsis MYB92 transcription factor. This MYB and all the members of the subgroups S10 and S24 of MYB transcription factors can directly activate the promoter of BCCP2 that encodes a component of the fatty acid biosynthetic pathway. Two adjacent MYB cis-regulatory elements are essential for the binding and activation of the BCCP2 promoter by MYB92. Overexpression of MYB92 or WRI1 in Nicotiana benthamiana induces the expression of fatty acid biosynthetic genes but results in the accumulation of different types of acyl lipids. In the presence of WRI1, triacylglycerol biosynthetic enzymes coded by constitutively expressed genes efficiently channel the excess fatty acids toward reserve lipid accumulation. By contrast, MYB92 activates both fatty acid and suberin biosynthetic genes; hence, the remarkable increase in suberin monomers measured in leaves expressing MYB92. These results provide additional insight into the molecular mechanisms that control the biosynthesis of an important cell wall-associated acylglycerol polymer playing critical roles in plants.
Published: 2020
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34. Nitrate efflux is an essential component of the cryptogein signaling pathway leading to defense responses and hypersensitive cell death in tobacco

Author: David Wendehenne, Alain Pugin, Olivier Lamotte, Jean-Marie Frachisse, Hélène Barbier-Brygoo, Plante - microbe - environnement : biochimie, biologie cellulaire et écologie ( PMEBBCE ), Etablissement National d'Enseignement Supérieur Agronomique de Dijon ( ENESAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), and Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, MESH: Signal Transduction, MESH: Algal Proteins, MESH: Hydrogen-Ion Concentration, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Reactive Oxygen Species, Apoptosis, MESH : Immunity, Natural, Plant Science, 01 natural sciences, Ion Channels, MESH : Phosphorylation, MESH: Plant Diseases, MESH : Anions, Plant defense against herbivory, MESH: Protein Kinase Inhibitors, Phosphorylation, MESH: Tobacco, 0303 health sciences, Fungal protein, MESH : Plant Diseases, food and beverages, MESH: Reactive Oxygen Species, MESH : Nitrates, Hydrogen-Ion Concentration, Cell biology, Elicitor, Respiratory burst, MESH: Nitrates, MESH: Calcium, Natural, Efflux, MESH : Algal Proteins, Signal transduction, MESH : Ion Channels, MESH: Anions, Research Article, Signal Transduction, Anions, Programmed cell death, MESH: Enzyme Activation, MESH : Tobacco, Biology, MESH : Protein Kinases, Fungal Proteins, 03 medical and health sciences, MESH : Hydrogen-Ion Concentration, Tobacco, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Protein kinase A, MESH : Calcium, Protein Kinase Inhibitors, MESH: Protein Kinases, 030304 developmental biology, Plant Diseases, MESH: Immunity, Natural, MESH : Signal Transduction, Nitrates, MESH: Phosphorylation, MESH: Apoptosis, Algal Proteins, Immunity, Cell Biology, MESH : Protein Kinase Inhibitors, Immunity, Innate, Enzyme Activation, MESH: Ion Channels, Calcium, Reactive Oxygen Species, MESH : Enzyme Activation, Protein Kinases, MESH : Apoptosis, 010606 plant biology & botany
Abstract: There is much interest in the transduction pathways by which avirulent pathogens or derived elicitors activate plant defense responses. However, little is known about anion channel functions in this process. The aim of this study was to reveal the contribution of anion channels in the defense response triggered in tobacco by the elicitor cryptogein. Cryptogein induced a fast nitrate (NO(3)(-)) efflux that was sensitive to anion channel blockers and regulated by phosphorylation events and Ca(2+) influx. Using a pharmacological approach, we provide evidence that NO(3)(-) efflux acts upstream of the cryptogein-induced oxidative burst and a 40-kD protein kinase whose activation seems to be controlled by the duration and intensity of anion efflux. Moreover, NO(3)(-) efflux inhibitors reduced and delayed the hypersensitive cell death triggered by cryptogein in tobacco plants. This was accompanied by a delay or a complete suppression of the induction of several defense-related genes, including hsr203J, a gene whose expression is correlated strongly with programmed cell death in plants. Our results indicate that anion channels are involved intimately in mediating defense responses and hypersensitive cell death.
Published: 2002
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35. Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils

Author: Yves Dessaux, Zoulikha Krimi, Christophe Mougel, Xavier Nesme, Annik Petit, Département de Foresterie, Faculté des Sciences, Université de Tlemcen, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie ( PMEBBCE ), Etablissement National d'Enseignement Supérieur Agronomique de Dijon ( ENESAD ) -Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), 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 ( VAS ), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), 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-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), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-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 ProdInra, Migration
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Biovar, Applied Microbiology and Biotechnology, Polymerase Chain Reaction, Ti plasmid, chemistry.chemical_compound, Plant Microbiology, MESH : Ecosystem, MESH : DNA, Bacterial, MESH: Ecosystem, MESH : Polymerase Chain Reaction, ComputingMilieux_MISCELLANEOUS, Soil Microbiology, 2. Zero hunger, Octopine, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Rhizosphere, education.field_of_study, Ecology, biology, Bacterial, Horticulture, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, POUVOIR PATHOGENE, Seasons, Soil microbiology, Biotechnology, Plasmids, Rhizobium, MESH: Rhizobium, DNA, Bacterial, Agrobacterium, Population, MESH : Soil Microbiology, Bulk soil, MESH : Rhizobium, 03 medical and health sciences, MESH: Plasmids, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, Ecosystem, 030304 developmental biology, MESH : Seasons, 030306 microbiology, MESH: Polymerase Chain Reaction, DNA, biology.organism_classification, MESH: DNA, Bacterial, chemistry, MESH: Soil Microbiology, MESH : Plasmids, MESH: Seasons, Food Science
Abstract: Short- and long-term persistence of pathogenic (i.e., tumor forming) agrobacteria in soil was investigated in six nursery plots with a history of high crown gall incidence. No pathogenic Agrobacterium strains were isolated in soil samples taken in fall and winter in any plots, but such strains were isolated from both bulk soils and weed rhizospheres (over 0.5 × 10 5 pathogenic CFU/g of bulk soil or rhizosphere) in three out of six plots in spring and summer. PCR amplifications of a vir sequence from DNA extracted from soil confirmed the presence of Ti plasmids in summer and their absence in fall and winter. The results indicate that strains that harbor a Ti plasmid had an unforeseen positive fitness versus Ti plasmid-free strains in soil and rhizosphere in spring and summer in spite of the apparent absence of tumor, and hence of opines. The gain of fitness occurred during a bloom of all cultivable agrobacteria observed only in conducive soils. An evolution of the pathogenic population was recorded during a 4-year period in one particularly conducive soil. In 1990, the pathogenic population in this soil consisted of only biovar 1 strains harboring both octopine- and nopaline-type Ti plasmids. In 1994, it consisted of only nopaline-type Ti plasmids equally distributed among biovar 1 and 2 strains. These results suggest that nopaline-type Ti plasmids conferred a better survival ability than octopine-type Ti plasmids to biovar 2 agrobacteria under the present field conditions.
Published: 2002
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36. Acyl-homoserine lactone production is more common among plant-associated Pseudomonas spp. than among soilborne Pseudomonas spp

Author: Yves Dessaux, Phil M. Oger, Bridget E. Laue, Miena Elasri, Sandrine Delorme, Eric Glickmann, Gordon S. A. B. Stewart, Philippe Lemanceau, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), University of Nottingham, UK (UON), Plante - microbe - environnement : biochimie, biologie cellulaire et écologie (PMEBBCE), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD), ProdInra, Migration, Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Microbiologie du Sol et de l'Environnement ( MSE ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), and University of Nottingham, UK ( UON )
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH: Sequence Analysis, DNA, MESH : Molecular Sequence Data, MESH: Plants, MESH: Amino Acid Sequence, Erwinia, MESH: Base Sequence, Applied Microbiology and Biotechnology, chemistry.chemical_compound, Plant Microbiology, MESH: Plant Diseases, 4-Butyrolactone, Chromobacterium, Pseudomonas syringae, MESH : Bacterial Proteins, MESH : DNA, Bacterial, Cloning, Molecular, MESH: Bacterial Proteins, ComputingMilieux_MISCELLANEOUS, Soil Microbiology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, MESH: Gene Expression Regulation, Bacterial, MESH: Genetic Complementation Test, Ecology, biology, MESH : Amino Acid Sequence, MESH : Plant Diseases, Pseudomonas, Bacterial, MESH : 4-Butyrolactone, Plants, N-ACYL-HOMOSERINE LACTONE, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Pseudomonadales, Sequence Analysis, Biotechnology, Pseudomonadaceae, MESH : Gene Expression Regulation, Bacterial, DNA, Bacterial, MESH : Cloning, Molecular, MESH : Soil Microbiology, Carbon-Oxygen Lyases, Molecular Sequence Data, Homoserine, MESH : Plants, Microbiology, MESH: Carbon-Oxygen Lyases, 03 medical and health sciences, Bacterial Proteins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Cloning, Molecular, Amino Acid Sequence, MESH : Carbon-Oxygen Lyases, 030304 developmental biology, Plant Diseases, MESH: Molecular Sequence Data, MESH : Genetic Complementation Test, Base Sequence, 030306 microbiology, Pantoea, Genetic Complementation Test, Molecular, MESH: Pseudomonas, Gene Expression Regulation, Bacterial, Sequence Analysis, DNA, DNA, biology.organism_classification, MESH: DNA, Bacterial, chemistry, Gene Expression Regulation, MESH: Soil Microbiology, MESH: 4-Butyrolactone, MESH : Base Sequence, Food Science, MESH : Pseudomonas, MESH : Sequence Analysis, DNA, Cloning
Abstract: A total of 137 soilborne and plant-associated bacterial strains belonging to different Pseudomonas species were tested for their ability to synthesize N -acyl-homoserine lactones (NAHL). Fifty-four strains synthesized NAHL. Interestingly, NAHL production appears to be more common among plant-associated than among soilborne Pseudomonas spp. Indeed, 40% of the analyzed Pseudomonas syringae strains produced NAHL which were identified most often as the short-chain NAHL, N -hexanoyl- l -homoserine lactone, N -(3-oxo-hexanoyl)-homoserine lactone, and N -(3-oxo-octanoyl)- l -homoserine lactone (no absolute correlation between genomospecies of P. syringae and their ability to produce NAHL could be found). Six strains of fluorescent pseudomonads, belonging to the species P. chlororaphis , P. fluorescens , and P. putida , isolated from the plant rhizosphere produced different types of NAHL. In contrast, none of the strains isolated from soil samples were shown to produce NAHL. The gene encoding the NAHL synthase in P. syringae pv. maculicola was isolated by complementation of an NAHL-deficient Chromobacterium mutant. Sequence analysis revealed the existence of a luxI homologue that we named psmI . This gene is sufficient to confer NAHL synthesis upon its bacterial host and has strong homology to psyI and ahlI , two genes involved in NAHL production in P. syringae pv. tabaci and P. syringae pv. syringae, respectively. We identified another open reading frame that we termed psmR , transcribed convergently in relation to psmI and partly overlapping psmI ; this gene encodes a putative LuxR regulatory protein. This gene organization, with luxI and luxR homologues facing each other and overlapping, has been found so far only in the enteric bacteria Erwinia and Pantoea and in the related species P. syringae pv. tabaci.
Published: 2001
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37. Blast-furnace slag cement and metakaolin based geopolymer as construction materials for liquid anaerobic digestion structures: Interactions and biodeterioration mechanisms

Author: Couzigou, Jean-Malo, Mondy, Samuel, Sahl, Lucien, Gourion, Benjamin, Ratet, Pascal, Laboratoire Matériaux et Durabilité des constructions (LMDC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-16-CE22-0001,GELULE,Géopolitique de la lutte contre l'étalement urbain(2016), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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 des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ANR-16-CE22-0011,BIBENdOM,Impact BIochimique des effluents agricoles et agroindustriels sur les ouvrages en BEtOn dans la filière de valorisation par Méthanisation (co-digestion anaérobie)(2016)
Subjects: Environmental Engineering, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 010504 meteorology & atmospheric sciences, 010501 environmental sciences, Alkalies, Geopolymer, 01 natural sciences, 12. Responsible consumption, law.invention, [SPI.MAT]Engineering Sciences [physics]/Materials, Bioreactors, law, Anaerobic digestion, Environmental Chemistry, Animals, Anaerobiosis, Waste Management and Disposal, Metakaolin, 0105 earth and related environmental sciences, Cement, Slag cement, Chemistry, Construction Materials, Slag, Pulp and paper industry, Pollution, 6. Clean water, Portland cement, [SPI.GCIV]Engineering Sciences [physics]/Civil Engineering, Biodeterioration, Ground granulated blast-furnace slag, visual_art, Biofuels, visual_art.visual_art_medium, Cattle, Cementitious, Ammonium
Abstract: International audience; In order to promote the development of the biogas industry, solutions are needed to improve concrete structures durability in this environment. This multiphysics study aims to analyse the multiphases interactions between the liquid phase of an anaerobic digestion system and cementitious matrices, focusing on (i) the impacts of the binder nature on the anaerobic digestion process at local scale, and (ii) the deterioration mechanisms of the materials. Cementitious pastes made of slag cement (CEM III), innovative metakaolin-based alkali-activated material (MKAA), with compositions presumed to resist chemically aggressive media, and a reference binder, ordinary Portland cement (CEM I), were tested by immersion in inoculated cattle manure in bioreactors for a long period of five digestion cycles. For the first time it was shown that the digestion process was disturbed in the short term by the presence of the materials that increased the pH of the liquid phase and slowed the acids consumption, with much more impact of the MKAA. However, the final total production of biogas was similar in all bioreactors. Material analyses showed that, in this moderately aggressive medium, the biodeterioration of the CEM I and CEM III pastes mainly led to cement matrix leaching (decalcification) and carbonation. MKAA showed a good behaviour with very low degraded depths. In addition, the material was found to have interesting ammonium adsorption properties in the chemical conditions (notably the pH range) of anaerobic digestion.
Published: 2021
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38. Introduction

Author: ULLA NEUMANN, BÉATRICE SATIAT‐JEUNEMAITRE, Max Planck Institute for Plant Breeding Research (MPIPZ), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell [Gif-sur-Yvette] (I2BC), Département Plateforme (PF I2BC), 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), École normale supérieure - Paris (ENS-PSL), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0303 health sciences, 03 medical and health sciences, Histology, [SDV]Life Sciences [q-bio], 02 engineering and technology, 021001 nanoscience & nanotechnology, 0210 nano-technology, 030304 developmental biology, Pathology and Forensic Medicine
Abstract: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jmi.12959; International audience
Published: 2020
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39. Involvement of Arabidopsis BIG protein in cell death mediated by Myo- Inositol homeostasis

Author: Frédérique Tellier, Moussa Benhamed, Stéphanie Boutet-Mercey, Catherine Bergounioux, Florence Piron-Prunier, Cécile Raynaud, Quentin Bruggeman, Christelle Mazubert, David Latrasse, Marianne Delarue, Raphaël Lugan, Sylvie Citerne, Jean-Denis Faure, Deborah Manza-Mianza, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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 moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Centre National de la Recherche Scientifique (CNRS) Universite Paris-sud French National Research Agency (ANR)European CommissionMAPK-IPS ANR-2010-BLAN-1613-02Saclay Plant Sciences-SPS ANR-17-EUR-0007, Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Université d'Évry-Val-d'Essonne (UEVE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Université de Paris-Université Paris-Saclay, and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Mutant, Arabidopsis, lcsh:Medicine, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], medicine.disease_cause, 01 natural sciences, Plant Growth Regulators, Cluster Analysis, Homeostasis, Arabidopsis thaliana, lcsh:Science, Ceramide synthase, Mutation, Multidisciplinary, biology, Phenotype, Cell biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Salicylic Acid, Signal Transduction, Programmed cell death, Plant physiology, Article, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Plant development, medicine, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Sphingolipids, Arabidopsis Proteins, lcsh:R, Epistasis, Genetic, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, biology.organism_classification, Sphingolipid, Plant Leaves, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Plant stress responses, Calmodulin-Binding Proteins, lcsh:Q, Inositol, 010606 plant biology & botany
Abstract: Programmed cell death (PCD) is essential for several aspects of plant life. We previously identified the mips1 mutant of Arabidopsis thaliana, which is deficient for the enzyme catalysing myo-inositol synthesis, and that displays light-dependent formation of lesions on leaves due to Salicylic Acid (SA) over-accumulation. Rationale of this work was to identify novel regulators of plant PCD using a genetic approach. A screen for secondary mutations that abolish the mips1 PCD phenotype identified a mutation in the BIG gene, encoding a factor of unknown molecular function that was previously shown to play pleiotropic roles in plant development and defence. Physiological analyses showed that BIG is required for lesion formation in mips1 via SA-dependant signalling. big mutations partly rescued transcriptomic and metabolomics perturbations as stress-related phytohormones homeostasis. In addition, since loss of function of the ceramide synthase LOH2 was not able to abolish cell death induction in mips1, we show that PCD induction is not fully dependent of sphingolipid accumulation as previously suggested. Our results provide further insights into the role of the BIG protein in the control of MIPS1-dependent cell death and also into the impact of sphingolipid homeostasis in this pathway.
Published: 2020
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40. Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation

Author: Chica, Claudia, Louis, Alexandra, Roest Crollius, Hugues, Colot, Vincent, Roudier, François, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie moléculaire des organismes photosynthétiques (UMR8186), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), ANR Investissements d'Avenir [ ANR-10-LABX-54MEMOLIFE], [ANR-11-IDEX-0001-02], [ANR-12-ADAP-0020-01], [ ANR-10-BINF-01-03], European Project: 257082,EC:FP7:HEALTH,FP7-HEALTH-2010-two-stage,EPIGENESYS(2010), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris
Subjects: Chromosome architecture, lcsh:QH426-470, [SDV]Life Sciences [q-bio], H3K27me3, Arabidopsis, macromolecular substances, Chromosomes, Plant, Epigenesis, Genetic, Evolution, Molecular, Arabis, Gene Expression Regulation, Plant, Gene Duplication, Gene orthologs, evolution, Promoter Regions, Genetic, lcsh:QH301-705.5, Conserved Sequence, Arabis alpina, Base Sequence, Comparative epigenomics, Research, Polycomb Repressive Complex 2, PRC2, Chromatin, Histone Code, lcsh:Genetics, lcsh:Biology (General), Brassicaceae, Transcriptome, Arabidopsis sp
Abstract: Background Polycomb Repressive Complexes 2 (PRC2) are multi-protein chromatin modifiers that are evolutionarily conserved among eukaryotes and play key roles in the regulation of gene expression, notably through the trimethylation of lysine 27 of histone H3 (H3K27me3). Although PRC2-mediated gene regulation has been studied in many organisms, few studies have explored in depth the evolutionary conservation of PRC2 targets. Results Here, we compare the H3K27me3 epigenomic profiles for the two closely related species Arabidopsis thaliana and Arabidopsis lyrata and the more distant species Arabis alpina, three Brassicaceae that diverged from each other within the past 24 million years. Using a robust set of gene orthologs present in the three species, we identify two classes of evolutionarily conserved PRC2 targets, which are characterized by either developmentally plastic or developmentally constrained H3K27me3 marking across species. Constrained H3K27me3 marking is associated with higher conservation of promoter sequence information content and higher nucleosome occupancy compared to plastic H3K27me3 marking. Moreover, gene orthologs with constrained H3K27me3 marking exhibit a higher degree of tissue specificity and tend to be involved in developmental functions, whereas gene orthologs with plastic H3K27me3 marking preferentially encode proteins associated with metabolism and stress responses. In addition, gene orthologs with constrained H3K27me3 marking are the predominant contributors to higher-order chromosome organization. Conclusions Our findings indicate that developmentally plastic and constrained H3K27me3 marking define two evolutionarily conserved modes of PRC2-mediated gene regulation that are associated with distinct selective pressures operating at multiple scales, from DNA sequence to gene function and chromosome architecture. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1333-9) contains supplementary material, which is available to authorized users.
Published: 2017
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41. Ion Transport at the Vacuole during Stomatal Movements

Author: Cornelia Eisenach, Alexis De Angeli, Inst Plant Biol, Universität Zürich [Zürich] = University of Zurich (UZH), Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, [SDV]Life Sciences [q-bio], Plant Science, Vacuole, Biology, Photosynthesis, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Guard cell, BIOCELL, Botany, Genetics, MINION, Ion transporter, 010606 plant biology & botany, Transpiration
Abstract: Plant gas exchange with the environment is facilitated by stomata, small pores found on most aerial surfaces of land plants. Stomatal pores are formed between a pair of specialized guard cells. In C3 plants, open stomata allow the uptake of CO2 for photosynthesis during the day and at the same time
Published: 2017
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42. Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes

Author: Mathias Brault, Sovanna Tan, Pascal Gamas, Florian Frugier, Frédéric Debellé, École Nationale Supérieure de Techniques Avancées (ENSTA Paris), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Electrophysiologie des Membranes (LEM) EA 3514, Université Paris Diderot - Paris 7 (UPD7), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Paris-Saclay University, Labex 'Saclay Plant Science', and Lidex 'Plant Phenotyping Pipeline' (3P)
Subjects: 0106 biological sciences, Cytokinins, Root nodule, Symbiotic nitrogen-fixing nodulation, lcsh:QH426-470, Phosphorelay, Cytokinin signaling, Histidine kinase, Response regulator, Legumes, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], Lotus japonicus, 01 natural sciences, Rhizobia, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, Gene Expression Regulation, Plant, lcsh:TP248.13-248.65, Medicago truncatula, Genetics, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Phylogeny, Plant Proteins, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Whole Genome Sequencing, biology, fungi, food and beverages, Fabaceae, biology.organism_classification, lcsh:Genetics, chemistry, Cytokinin, Root Nodules, Plant, Research Article, Signal Transduction, Transcription Factors, 010606 plant biology & botany, Biotechnology
Abstract: Background Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering root cortical cell divisions at the onset of nodule initiation. Cytokinin signaling is based on a Two-Component System (TCS) phosphorelay cascade, involving successively Cytokinin-binding Histidine Kinase receptors, phosphorelay proteins shuttling between the cytoplasm and the nucleus, and Type-B Response Regulator (RRB) transcription factors activating the expression of cytokinin primary response genes. Among those, Type-A Response Regulators (RRA) exert a negative feedback on the TCS signaling. To determine whether the legume plant nodulation capacity is linked to specific features of TCS proteins, a genome-wide identification was performed in six legume genomes (Cajanus cajan, pigeonpea; Cicer arietinum, chickpea; Glycine max, soybean; Phaseolus vulgaris, common bean; Lotus japonicus; Medicago truncatula). The diversity of legume TCS proteins was compared to the one found in two non-nodulating species, Arabidopsis thaliana and Vitis vinifera, which are references for functional analyses of TCS components and phylogenetic analyses, respectively. Results A striking expansion of non-canonical RRBs was identified, notably leading to the emergence of proteins where the conserved phosphor-accepting aspartate residue is replaced by a glutamate or an asparagine. M. truncatula genome-wide expression datasets additionally revealed that only a limited subset of cytokinin-related TCS genes is highly expressed in different organs, namely MtCHK1/MtCRE1, MtHPT1, and MtRRB3, suggesting that this “core” module potentially acts in most plant organs including nodules. Conclusions Further functional analyses are required to determine the relevance of these numerous non-canonical TCS RRBs in symbiotic nodulation, as well as of canonical MtHPT1 and MtRRB3 core signaling elements. Electronic supplementary material The online version of this article (10.1186/s12864-019-5724-z) contains supplementary material, which is available to authorized users.
Published: 2019
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43. Arabidopsis LDIP protein locates at a confined area within the lipid droplet surface and favors lipid droplet formation

Author: Lysiane Brocard, Denis Coulon, Claire Bréhélin, Karine Tuphile, Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Bordeaux Imaging Center (BIC), Université de Bordeaux (UB)-Institut François Magendie-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut François Magendie-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Senescence, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Gene Expression, Endoplasmic Reticulum, Biochemistry, Gene Knockout Techniques, 03 medical and health sciences, Lipid droplet, Tobacco, Organelle, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cloning, Molecular, Triglycerides, 030102 biochemistry & molecular biology, biology, Arabidopsis Proteins, Chemistry, Lipid Droplet Associated Proteins, Lipid Droplets, General Medicine, Lipid Metabolism, Plants, Genetically Modified, biology.organism_classification, Recombinant Proteins, Cell biology, Plant Leaves, Neutral lipid, 030104 developmental biology, Seeds, Ultrastructure, Biogenesis
Abstract: International audience; Lipid droplets (LDs) are cell organelles specialized in neutral lipid storage. Extendedly studied in seeds, LDs also accumulate in leaves during senescence or in response to abiotic stresses. However the mechanisms underlying their biogenesis remain relatively unknown. Here, we deciphered the distinct roles of two proteins during LD biogenesis: LD-associated protein 1 (AtLDAP1) and LDAP-interacting protein (AtLDIP). We demonstrated that AtLDIP overexpression favors the neo-formation of small LDs under growing conditions where LD accumulation is usually not observed. In addition, atldip knock-out mutant displayed fewer but larger LDs, confirming a role of AtLDIP in LD biogenesis. Interestingly, a synergistic effect of the overexpression of both AtLDIP and AtLDAP1 was observed, resulting in an increase of LD cluster occurrence and LD abundance within the clusters and the cells. AtLDIP overexpression has no significant impact on triacylglycerol and steryl ester accumulation but AtLDIP inactivation is associated with an increase of neutral lipid content, that is probably a consequence of the enlarged but less abundant LDs present in this line. Our localization study demonstrated that AtLDIP is localized at specific dotted sites within the LD in contrast to AtLDAP1 that covers the whole LD. In addition, AtLDIP sometimes localized away from the LD marker, but always associated with the ER network, suggesting a location at LD nascent sites within the ER. Taken together, our results suggested that AtLDIP promotes the formation of new LDs from ER localized TAG lenses.
Published: 2019
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44. Calibration and evaluation of the STICS soil-crop model for faba bean to explain variability in yield and N2 fixation

Author: Etienne-Pascal Journet, Eric Justes, Florent Chlebowski, Laurent Bedoussac, Anthony Vermue, Gatien N. Falconnier, Nicolas Beaudoin, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), Agroressources et Impacts environnementaux (AgroImpact), Institut National de la Recherche Agronomique (INRA), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), French National Research Agency through the LEGITIMES French project, 7th PIREN-Seine program, Climate-CAFE European project, ANR-13-AGRO-0004,LEGITIMES,Construction et évaluation de scénarios territoriaux d'insertion de légumineuses dans les systèmes de culture pour répondre aux changements globaux(2013), European Project: 613551,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,LEGATO(2014), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, UR 1158 AgroImpact Agroressources et Impacts environnementaux, and Unité d'Agronomie de Laon-Reims-Mons (AGRO-LRM)
Subjects: 0106 biological sciences, Fixation de l'azote, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Soil Science, Growing season, F62 - Physiologie végétale - Croissance et développement, Plant Science, 01 natural sciences, Crop, grain legume, F01 - Culture des plantes, Leaf area index, Cropping system, yield variability, Legume, Pisum sativum, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Phenology, 04 agricultural and veterinary sciences, 15. Life on land, Crop rotation, abiotic stresses, Vicia faba, F61 - Physiologie végétale - Nutrition, Rendement des cultures, Agronomy, 13. Climate action, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, parameter estimation, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Faba bean (Vicia Faba L.) is the second most widely grown grain legume in Europe after pea (Pisum Sativum L.) and presents several agronomic and environmental advantages when inserted in cropping systems (e.g. decreased dependency on synthetic fertilisers and N provision to the subsequent crop). However, yield variability due to several factors including heat and drought impede wide adoption of faba bean by farmers. Soil-crop models provide quantitative information to evaluate these processes and help to design innovative cropping system including legumes. The STICS model was chosen for its agro-environmental purpose and its genericity allowing crop rotation simulation and robustness for a wide range of pedoclimatic conditions. However, there is so far for STICS no parameterization for faba bean. We calibrated 38 crop related parameters based on literature, direct measurements and sequential estimation using the optimisation tool OptimiSTICS and a dataset of winter faba bean grown in two sites in France with contrasting soil conditions over several growing seasons (2002–2015). Data from 22 experimental plots were used for calibration and the remaining independent 13 plots were used for model evaluation. After calibration, the STICS model reproduced adequately phenology, Leaf Area Index and dynamic growth of above ground biomass, uptake of mineral N, N2 fixation and grain yield, with satisfactory model efficiency (0.56 to 0.81) and low relative bias (−7% to 2%). The model adequately reproduced the large observed variation in faba bean grain yield (0.42–4.70 t ha−1) and total N2 fixed at harvest (62–172 kg N ha−1) in the contrasted years and soil conditions of this study. Simulations indicated that water stress was the overriding factor driving yield and N2 fixation variability. Simulation of temporal crop growth and water stresses during grain onset and grain filling allowed a robust and credible agronomic diagnosis of the causes of this variability for faba bean crops not significantly damaged by pests and diseases. Water supply/ demand ratio averaged over a period of six days preceding beginning of grain filling explained 78% of the observed grain yield variability while water deficit factor for N2 fixation averaged over a period of 20 days following the beginning of grain filling explained 83% of the variability of fixed N2 at harvest. Our work provides a first calibration and evaluation of the STICS model for faba bean. It offers the opportunity to quantify the ecosystem services associated with crop rotations including faba bean and the effect of climate change on the performance of such rotations.
Published: 2019
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45. Transformation of floral organs with GFP in Medicago truncatula

Author: Adam Kondorosi, Patricia Durand, Marije Scholte, Ignacio D. Rodríguez-Llorente, K. Kamaté, Pascal Ratet, T. H. Trinh, Eva Kondorosi, Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Somatic embryogenesis, Plant Science, Biology, 01 natural sciences, Green fluorescent protein, 03 medical and health sciences, Medicago truncatula, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, 030304 developmental biology, Southern blot, 0303 health sciences, Reporter gene, fungi, food and beverages, General Medicine, Agrobacterium tumefaciens, biology.organism_classification, gfp, Cell biology, Transformation (genetics), Floral organs, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: A high frequency of embryogenesis and transformation from all parts of flowers of two lines of Medicago truncatula R-108-1 and Jemalong J5 were obtained. Using this flower system, we obtained transgenic plants expressing promoter-uidA gene fusions as well as the gfp living cell color reporter gene. Moreover, this method allows us to save time and to use a smaller greenhouse surface for the culture of donor plants. Southern hybridization showed that the internal gfp fragment had the expected size and the number of T-DNA copies integrated in the plant genome varied between one and three. These data suggest that the presence of the GFP protein has no toxic effects, since no rearrangement of the gfp reporter gene was detected in the regenerated plants.
Published: 2019
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46. CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the {\beta}-globin locus

Author: Ann Dean, Ivan Junier, Ryan K. Dale, Chunhui Hou, François Képès, Institut des Systèmes Complexes - Paris Ile-de-France ( ISC-PIF ), École normale supérieure - Cachan ( ENS Cachan ) -Université Panthéon-Sorbonne ( UP1 ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -École polytechnique ( X ) -INSTITUT CURIE-Centre National de la Recherche Scientifique ( CNRS ), Center for Genomic Regulation ( CRG-UPF ), CIBER de Epidemiología y Salud Pública (CIBERESP), Laboratory of Cellular and Developmental Biology ( LCDB ), NIDDK, NIH, Génopole [Evry], Université d'Évry-Val-d'Essonne ( UEVE ), Epigenomics Project, Université d'Évry-Val-d'Essonne (UEVE), Laboratory of Cellular and Developmental Biology (LCDB), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Institut des Systèmes Complexes - Paris Ile-de-France (ISC-PIF), École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-École polytechnique (X), Center for Genomic Regulation (CRG-UPF), and École normale supérieure - Cachan (ENS Cachan)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École polytechnique (X)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: CCCTC-Binding Factor, [ SDV.BBM.BP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Transcription, Genetic, [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], [SDV]Life Sciences [q-bio], Locus (genetics), beta-Globins, Insulator (genetics), Gene Regulation, Chromatin and Epigenetics, Condensed Matter - Soft Condensed Matter, Cell Line, Chromosome conformation capture, 03 medical and health sciences, 0302 clinical medicine, [ PHYS.PHYS.PHYS-BIO-PH ] Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], Genetics, Humans, Nucleosome, Quantitative Biology - Genomics, Physics - Biological Physics, Gene, ComputingMilieux_MISCELLANEOUS, Locus control region, 030304 developmental biology, 0303 health sciences, Genome, Human, Chemistry, Chromosomes, Human, Pair 11, Locus Control Region, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Chromatin, Cell biology, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Repressor Proteins, Gene Expression Regulation, Quantitative Biology - Biomolecules, Genetic Loci, CTCF, K562 Cells, 030217 neurology & neurosurgery
Abstract: The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the 3-dimensional folding of a 1 Mbp region of human chromosome 11 containing the {\beta}-globin genes by integrating looping interactions of the insulator protein CTCF determined comprehensively by chromosome conformation capture (3C) into a polymer model of chromatin. We find that CTCF-mediated cell type specific interactions in erythroid cells are organized to favor contacts known to occur in vivo between the {\beta}-globin locus control region (LCR) and genes. In these cells, the modeled {\beta}-globin domain folds into a globule with the LCR and the active globin genes on the periphery. By contrast, in non-erythroid cells, the globule is less compact with few but dominant CTCF interactions driving the genes away from the LCR. This leads to a decrease in contact frequencies that can exceed 1000-fold depending on the stiffness of the chromatin and the exact positioning of the genes. Our findings show that an ensemble of CTCF contacts functionally affects spatial distances between control elements and target genes contributing to chromosomal organization required for transcription., Comment: Full article, including Supp. Mat., is available at Nucleic Acids Research, doi: 10.1093/nar/gks536
Published: 2016
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47. Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturiapirina, Venturia aucupariae and Venturia asperata

Author: Mélanie Sannier, Jérôme Collemare, Robert Debuchy, Spencer Brown, Christophe Lemaire, Jérôme Gouzy, Bruno Le Cam, Bouchez Olivier, Jason Shiller, Marie Noëlle Bellanger, Daniel Sargent, Thibaut Payen, Ludovic Duvaux, Joelle Amselem, Marie De Gracia, Valérie Caffier, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Différenciation sexuée et méiose chez les champignons (DSMC), Département Biologie des Génomes (DBG), 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), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Plant Healt Department of INRA (ESCAPADES Project), Agence Nationale pour la Recherche (Bioadapt ANR) : ANR-12-ADAP-0009, ANR-09-GENM-028, French Region Pays de la Loire (ROAD MOVIE project), French Region Pays de la Loire, Angers Loire Metropole, European Regional Development Fund, University of Angers, Plant health Department of INRA, Region Pays de La Loire, France Genomique National infrastructure : ANR-10-INBS-09, France-BioImaging : ANR-10-INBS-04-01, Labex 'Saclay Plant Science' : ANR-11-IDEX-0003-02, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, 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, 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 de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), URA 0083, Wageningen University and Research Centre [Wageningen] (WUR), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Fungal Natural Products, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Population, MRP, apple, Genomics, QH426-470, 01 natural sciences, Genome, Venturia, DNA sequencing, Population genomics, 03 medical and health sciences, Transposable, Genetics, education, Molecular Biology, Gene, Genetics (clinical), 030304 developmental biology, 2. Zero hunger, Whole genome sequencing, 0303 health sciences, education.field_of_study, biology, Fusicladium, Venturia inaequalis, pear, Elements, biology.organism_classification, formae specialis, Apple scab, apple scab, transposable elements, 010606 plant biology & botany, effectors
Abstract: TheVenturiagenus comprises fungal species that are pathogens onRosaceaehost plants, includingV. inaequalisandV. asperataon apple,V. aucupariaeon sorbus andV. pirinaon pear. Although the genetic structure ofV. inaequalispopulations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87Venturiastrains that represent each species and each population withinV. inaequalis. We present a PacBio genome assembly for theV. inaequalisEU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies ofV. inaequalisandV. aucupariaecontain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly ofV. inaequalispresents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research ofVenturiapathogens. Especially, it will help understanding the evolutionary history ofVenturiaspecies that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.
Published: 2019
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48. Prevalence and molecular diversity of the main viruses infecting cucurbit and solanaceous crops in Azerbaijan

Author: A. Kheyr-Pour, Nargiz Sultanova, Irada M. Huseynova, Hervé Lecoq, Cécile Desbiez, Samra Mirzayeva, Benoît Moury, Alamdar Mammadov, G. Balakishiyeva, Pauline Millot, Catherine Wipf-Scheibel, Eric Verdin, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Azerbaijan National Academy of Sciences (ANAS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Science Development Foundation under the President of the Republic of Azerbaijan (EİF-2014-9(24)-KETPL-14/11/3-M-10), and Presidium of Azerbaijan National Academy of Sciences (decision № 7/3 dated on 14.03.2018)
Subjects: 0106 biological sciences, 0301 basic medicine, Pepper mild mottle virus, food.ingredient, viruses, Plant Science, Horticulture, tomato, 01 natural sciences, Cucumber mosaic virus, 03 medical and health sciences, food, pepper, Tomato mosaic virus, Tomato yellow leaf curl virus, Watermelon mosaic virus, 2. Zero hunger, Zucchini yellow mosaic virus, biology, Begomovirus, fungi, food and beverages, genetic diversity, biology.organism_classification, Virology, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, cucurbitaceae, 030104 developmental biology, Alfalfa mosaic virus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, epidemiology, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Two surveys were conducted in September 2014 and July 2015 in important vegetable-growing areas in Azerbaijan. Cucurbit and solanaceous plants exhibiting symptoms of mosaic, yellowing, leaf curl or necrosis were collected and tested serologically and molecularly for the presence of the major viruses infecting these crops. For cucurbits, the most common viruses in both sampling sets were aphid-transmitted ones, including potyviruses (watermelon mosaic virus, WMV, zucchini yellow mosaic virus, ZYMV), cucumoviruses (cucumber mosaic virus, CMV) and poleroviruses (cucurbit aphid-borne yellows virus, CABYV). Eggplant mottled dwarf (EMDV) was also detected for the first time in Azerbaijan on cucumber at a low prevalence. In solanaceous crops, CMV was the most common virus detected, followed by potato virus Y (PVY). Tomato spotted wilt virus (TSWV), alfalfa mosaic virus (AMV) and tobamoviruses (tomato mosaic virus (TMV), pepper mild mottle virus (PMMoV)) were also detected in 2015. The begomovirus tomato yellow leaf curl virus (TYLCV) was present on tomato only in the Absheron area, where it had a high prevalence and induced important losses. TYLCV-like symptoms on tomato in other areas of Azerbaijan were due to phytoplasma diseases.
Published: 2019
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49. Complete Genome Sequence of the Polymyxin E (Colistin)-Producing Paenibacillus sp. Strain B-LR

Author: Salsano, Caroline, Didelot, Sandrine, Tambadou, Fatoumata, Caradec, Thibault, Sopena, Valérie, Barthélémy, Cyrille, Thiéry, Valérie, Chevrot, Romain, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Procédés Biologiques Génie Enzymatique et Microbien (PROBIOGEM), Université de Lille, Sciences et Technologies-Fédération Universitaire et Polytechnique de Lille, Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018
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50. A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses

Author: Eric Giraud, Maria Zabaleta, Heriniaina Ramanankierana, Paul Simion, Herizo Randriambanona, Clémence Chaintreuil, Ronan Rivallan, Mario Gomez-Pacheco, Spencer Brown, Mathieu Gueye, Robin Duponnois, Gwilym P. Lewis, Lionel Moulin, Maitrayee DasGupta, Pierre Mournet, Jean-François Arrighi, Angélique D'Hont, Catherine Hervouet, Hervé Vandrot, Joël Fardoux, Celine Scornavacca, Mickaël Bourges, Laurent Brottier, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Royal Botanic Gardens, Kew, Institut des sciences du végétal (ISV), 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), Transporteurs et Imagerie, Radiothérapie en Oncologie et Mécanismes biologiques des Altérations du Tissu Osseux (TIRO-MATOs - UMR E4320), UMR E4320 (TIRO-MATOs), Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Service Hospitalier Frédéric Joliot (SHFJ), 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)-Université Paris-Saclay-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)-Université Paris-Saclay, Institut Fondamental d'Afrique Noire (IFAN), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Centre National de Recherches sur l'Environnement, Centre National de Recherche sur l'Environnement (CNRE), Institut Agronomique Néo-Calédonien (IAC), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Instituto de Investigaciones Biológicas Clemente Estable [Montevideo] (IIBCE), ANR-14-CE19-0005,AeschyNod,Génétique de la légumineuse Nod-indépendante Aeschynomene evenia pour étudier l'évolution de la symbiose rhizobienne et dans la perspective du transfert de la fixation d'azote aux plantes d'intérêt agronomique(2014), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Côte d'Azur (UCA)-Service Hospitalier Frédéric Joliot (SHFJ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Royal Botanic Gardens [Kew], Service Hospitalier Frédéric Joliot (SHFJ), Université Paris-Saclay-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)-UMR E4320 (TIRO-MATOs), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Côte d'Azur (UCA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Royal Botanic Gardens Kew, 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, Transporteurs en Imagerie et Radiothérapie en Oncologie (TIRO - UMR E4320), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Institut Fondamental d'Afrique Noire - Laboratoire de botanique (IFAN), Institut Fondamental d'Afrique Noire, Centre National de Recherche sur l'Environnement, and Centre National de recherche sur l'environnement
Subjects: 0106 biological sciences, Polytomy, Nuclear gene, F62 - Physiologie végétale - Croissance et développement, Biology, Nodulation, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genetic analysis, Plant Root Nodulation, F30 - Génétique et amélioration des plantes, Aeschynomene, Genetics, Legumes, Phylogenetics, Polyploidy, Symbiosis, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Polyploid, lcsh:Botany, Nitrogen Fixation, Bradyrhizobium, Genome size, Phylogeny, 030304 developmental biology, 0303 health sciences, Ploidies, Phylogenetic tree, P34 - Biologie du sol, Fabaceae, Genomics, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Biological Evolution, lcsh:QK1-989, Agricultural sciences, Evolutionary biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sciences agricoles, 010606 plant biology & botany, Research Article
Abstract: Background Among semi-aquatic species of the legume genus Aeschynomene, some have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the synthesis of Nod factors. Knowledge of the specificities underlying this Nod-independent symbiosis has been gained from the model legume Aeschynomene evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod factor-dependent process. To fill this gap, we combined different approaches to perform a thorough comparative analysis in the genus Aeschynomene. Results This study significantly broadened previous taxon sampling, including in allied genera, in order to construct a comprehensive phylogeny. In the phylogenetic tree, five main lineages were delineated, including a novel lineage, the Nod-independent clade and another one containing a polytomy that comprised several Aeschynomene groups and all the allied genera. This phylogeny was matched with data on chromosome number, genome size and low-copy nuclear gene sequences to reveal the diploid species and a polytomy containing mostly polyploid taxa. For these taxa, a single allopolyploid origin was inferred and the putative parental lineages were identified. Finally, nodulation tests with different Bradyrhizobium strains revealed new nodulation behaviours and the diploid species outside of the Nod-independent clade were compared for their experimental tractability and genetic diversity. Conclusions The extended knowledge of the genetics and biology of the different lineages sheds new light of the evolutionary history of the genus Aeschynomene and they provide a solid framework to exploit efficiently the diversity encountered in Aeschynomene legumes. Notably, our backbone tree contains all the species that are diploid and it clarifies the genetic relationships between the Nod-independent clade and the Nod-dependent lineages. This study enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses. Electronic supplementary material The online version of this article (10.1186/s12870-018-1567-z) contains supplementary material, which is available to authorized users.
Published: 2018
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