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178 results on '"Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3)"'

1. Mere end lugtesans - COVID-19 er associeret med svær påvirkning af lugtesansen, smagssansen og mundfølelsen

Author: Parma, Valentina, Ohla, Kathrin, Veldhuizen, Maria G, Niv, Masha Y, Kelly, Christine E, Bakke, Alyssa J, Cooper, Keiland W, Bouysset, Cédric, Pirastu, Nicola, Dibattista, Michele, Kaur, Rishemjit, Liuzza, Marco Tullio, Pepino, Marta Y, Schöpf, Veronika, Pereda-Loth, Veronica, Olsson, Shannon B, Gerkin, Richard C, Rohlfs Domínguez, Paloma, Albayay, Javier, Farruggia, Michael C, Bhutani, Surabhi, Fjaeldstad, Alexander W, Kumar, Ritesh, Menini, Anna, Bensafi, Moustafa, Sandell, Mari, Konstantinidis, Iordanis, Di Pizio, Antonella, Genovese, Federica, Öztürk, Lina, Thomas-Danguin, Thierry, Frasnelli, Johannes, Boesveldt, Sanne, Saatci, Özlem, Saraiva, Luis R, Lin, Cailu, Golebiowski, Jérôme, Hwang, Liang-Dar, Ozdener, Mehmet Hakan, Guàrdia, Maria Dolors, Laudamiel, Christophe, Ritchie, Marina, Havlícek, Jan, Pierron, Denis, Roura, Eugeni, Navarro, Marta, Nolden, Alissa A, Lim, Juyun, Whitcroft, Katherine L, Colquitt, Lauren R, Ferdenzi, Camille, Brindha, Evelyn V, Altundag, Aytug, Macchi, Alberto, Nunez-Parra, Alexia, Patel, Zara M, Fiorucci, Sébastien, Philpott, Carl M, Smith, Barry C, Lundström, Johan N, Mucignat, Carla, Parker, Jane K, van den Brink, Mirjam, Schmuker, Michael, Fischmeister, Florian Ph S, Heinbockel, Thomas, Shields, Vonnie D C, Faraji, Farhoud, Santamaría, Enrique, Fredborg, William E A, Morini, Gabriella, Olofsson, Jonas K, Jalessi, Maryam, Karni, Noam, D’Errico, Anna, Alizadeh, Rafieh, Pellegrino, Robert, Meyer, Pablo, Huart, Caroline, Chen, Ben, Soler, Graciela M, Alwashahi, Mohammed K, Welge-Lüssen, Antje, Freiherr, Jessica, de Groot, Jasper H B, Klein, Hadar, Okamoto, Masako, Singh, Preet Bano, Hsieh, Julien W, Abdulrahman, Olagunju, Dalton, Pamela, Yan, Carol H, Voznessenskaya, Vera V, Chen, Jingguo, Sell, Elizabeth A, Walsh-Messinger, Julie, Archer, Nicholas S, Koyama, Sachiko, Deary, Vincent, Roberts, S Craig, Yanık, Hüseyin, Albayrak, Samet, Nováková, Lenka Martinec, Croijmans, Ilja, Mazal, Patricia Portillo, Moein, Shima T, Margulis, Eitan, Mignot, Coralie, Mariño, Sajidxa, Georgiev, Dejan, Kaushik, Pavan K, Malnic, Bettina, Wang, Hong, Seyed-Allaei, Shima, Yoluk, Nur, Razzaghi-Asl, Sara, Justice, Jeb M, Restrepo, Diego, Reed, Danielle R, Hummel, Thomas, Munger, Steven D, Hayes, John E, Indústries Alimentàries, Qualitat i Tecnologia Alimentària, Tecnologia Alimentària, Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Mersin University, The Hebrew University of Jerusalem (HUJ), AbScent, Pennsylvania State University (Penn State), Penn State System, University of California [Irvine] (UC Irvine), University of California (UC), Université Côte d'Azur (UCA), University of Edinburgh, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Central Scientific Instruments Organisation (CSIR), Università degli Studi 'Magna Graecia' di Catanzaro = University of Catanzaro (UMG), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Medizinische Universität Wien = Medical University of Vienna, Groupement scientifique de Biologie et de Medecine Spatiale (GSBMS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES), Tata Institute for Fundamental Research (TIFR), Arizona State University [Tempe] (ASU), Universidad de Extremadura - University of Extremadura (UEX), Università degli Studi di Padova = University of Padua (Unipd), Yale School of Medicine [New Haven, Connecticut] (YSM), San Diego State University (SDSU), Aarhus University [Aarhus], University of Hertfordshire [Hatfield] (UH), Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), Neurosciences Sensorielles Comportement Cognition, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Turku, Aristotle University of Thessaloniki, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Monell Chemical Senses Center, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), Université de Montréal (UdeM), Wageningen University and Research Centre (WUR), Medical Science University, Sidra Medicine [Doha, Qatar], Institut de Chimie de Nice (ICN), 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)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), University of Southern Queensland (USQ), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), DreamAir Llc, Charles University [Prague] (CU), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Massachusetts System (UMASS), Oregon State University (OSU), Ear Institute, UCL, Lyon Neuroscience Research center, Karunya University, Biruni University, Assi Sette Llaghi Varese, Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, University of East Anglia [Norwich] (UEA), California Department of Food and Agriculture (CDFA), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Maastricht University [Maastricht], Institute for Biology - Neurobiology, Freie Universität Berlin, Karl-Franzens-Universität Graz, Howard University College of Medicine, Towson University, University of California [San Diego] (UC San Diego), Proteomics, Center for Applied Medical Research (CIMA), Stockholm University, University of Gastronomic Sciences, Iran University of Medical Sciences, Goethe Universität Frankfurt, University of Tennessee, IBM T.J. Watson Research Center, Université libre de Bruxelles (ULB), Guangzhou Medical University, Buenos Aires University and GEOG (Grupo de Estudio de Olfato y Gusto), Sultan Qaboos University (SQU), Federal University of Technology of Akure (FUTA), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Hospital of Xi'an Jiaotong University, University of Pennsylvania, University of Dayton, CSIRO Agriculture and Food (CSIRO), Indiana University [Bloomington], Indiana University System, University of Northumbria at Newcastle [United Kingdom], University of Stirling, Middle East Technical University [Ankara] (METU), Utrecht University [Utrecht], Instituto Universitario del Hospital Italiano [Buenos Aires, Argentina], Institute for Research in Fundamental Sciences [Tehran] (IPM), Hebrew University of Jerusalem, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Terrazas del Club Hipico, University Medical Centre Ljubljana [Ljubljana, Slovenia] (UMCL), Tata Institute of Fundamental Research [Bangalore], Universidade de São Paulo = University of São Paulo (USP), University of Florida [Gainesville] (UF), University of Colorado Anschutz [Aurora], Center for Smell and Taste, Department of Food Science, Pennsylvania State University., Julien, Sabine, Tıp Fakültesi, UCL - SSS/IONS/NEUR - Clinical Neuroscience, UCL - (SLuc) Service d'oto-rhino-laryngologie, Department of Food and Nutrition, Senses and Food, Research Center Jülich, University of California [Irvine] (UCI), University of California, Università degli studi di Bari Aldo Moro (UNIBA), Università degli Studi 'Magna Graecia' di Catanzaro [Catanzaro, Italie] (UMG), University of Extremadura, University of Padova, Yale University School of Medicine, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, University of Helsinki, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-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), Institute of Agrifood Research and Technology (IRTA), Universita degli Studi di Padova, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Karl-Franzens-Universität [Graz, Autriche], University of California San Diego Health, University of Brussels, University of Pennsylvania [Philadelphia], Tata Institute of Fundamental Research, University of São Paulo (USP), UCL - SSS/IONS - Institute of NeuroScience, FSE Campus Venlo, and RS: FSE UCV
Subjects: Male, Taste, Physiology, Smagstab, Audiology, AcademicSubjects/SCI01180, Settore BIO/09 - Fisiologia, Behavioral Neuroscience, chemistry.chemical_compound, Olfaction Disorders, Taste Disorders, 0302 clinical medicine, RATINGS, Hyposmia, Surveys and Questionnaires, CHEMOSENSITIVITY, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Viral, PALADAR, 030223 otorhinolaryngology, Sensory Science and Eating Behaviour, media_common, TASTE, US NATIONAL-HEALTH, [SDV.IDA] Life Sciences [q-bio]/Food engineering, Middle Aged, Biological Sciences, 16. Peace & justice, Sensory Systems, 3. Good health, Smell, GCCR Group Author, ddc:540, Smell loss, Female, Original Article, medicine.symptom, Corrigendum, Coronavirus Infections, olfaction, Adult, somatosensation, medicine.medical_specialty, 663/664, Coronavirus disease 2019 (COVID-19), OLFACTORY DISORDERS, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, Pneumonia, Viral, head and neck surgery, Aged, Betacoronavirus, COVID-19, Humans, Pandemics, SARS-CoV-2, Self Report, Somatosensory Disorders, Young Adult, Anosmia, Sensory system, Olfaction, 03 medical and health sciences, Chemesthesis, Physiology (medical), Perception, medicine, Neurology & Neurosurgery, Behaviour Change and Well-being, business.industry, R-PACKAGE, 3112 Neurosciences, Pneumonia, Parosmia, COMPONENT, Smagssans, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Sensoriek en eetgedrag, chemistry, Lugtetab, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Lugtesans
Abstract: Correction: Chemical Senses, Volume 46, 2021, bjab050, https://doi.org/10.1093/chemse/bjab050 Published: 08 December 2021 Recent anecdotal and scientific reports have provided evidence of a link between COVID-19 and chemosensory impairments, such as anosmia. However, these reports have downplayed or failed to distinguish potential effects on taste, ignored chemesthesis, and generally lacked quantitative measurements. Here, we report the development, implementation, and initial results of a multilingual, international questionnaire to assess self-reported quantity and quality of perception in 3 distinct chemosensory modalities (smell, taste, and chemesthesis) before and during COVID-19. In the first 11 days after questionnaire launch, 4039 participants (2913 women, 1118 men, and 8 others, aged 19-79) reported a COVID-19 diagnosis either via laboratory tests or clinical assessment. Importantly, smell, taste, and chemesthetic function were each significantly reduced compared to their status before the disease. Difference scores (maximum possible change +/- 100) revealed a mean reduction of smell (-79.7 +/- 28.7, mean +/- standard deviation), taste (-69.0 +/- 32.6), and chemesthetic (-37.3 +/- 36.2) function during COVID-19. Qualitative changes in olfactory ability (parosmia and phantosmia) were relatively rare and correlated with smell loss. Importantly, perceived nasal obstruction did not account for smell loss. Furthermore, chemosensory impairments were similar between participants in the laboratory test and clinical assessment groups. These results show that COVID-19-associated chemosensory impairment is not limited to smell but also affects taste and chemesthesis.The multimodal impact of COVID-19 and the lack of perceived nasal obstruction suggest that severe acute respiratory syndrome coronavirus strain 2 (SARS-CoV-2) infection may disrupt sensory-neural mechanisms.
Published: 2020

2. Experimental system and image analysis software for high throughput phenotyping of mycorrhizal growth response inBrachypodium distachyon

Author: Fabrice Devoilles, Felicia Maviane-Macia, Camille Ribeyre, Benoit Lefebvre, Luis Buendia, Mehdi Khafif, Nemo Peeters, Mégane Gaston, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 2. Zero hunger, 0106 biological sciences, Rhizophagus irregularis, 0303 health sciences, Genetic diversity, biology, fungi, food and beverages, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, Computational biology, biology.organism_classification, Plant phenotyping, 01 natural sciences, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 03 medical and health sciences, Experimental system, Brachypodium distachyon, Image analysis, Arbuscular mycorrhizal, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 030304 developmental biology, 010606 plant biology & botany
Abstract: Plant growth response to Arbuscular Mycorrhizal (AM) fungi is variable and depends on genetic and environment factors that still remain largely unknown. Identification of these factors can be envisaged using high-throughput and accurate plant phenotyping.We setup experimental conditions based on a two-compartment system allowing to measureBrachypodium distachyonmycorhizal growth response (MGR) in an automated phenotyping greenhouse. We developed a new image analysis software“IPSO Phen”to estimate ofB. distachyonaboveground biomass.We found a positive MGR in theB. distachyonBd3-1 genotype inoculated with the AM fungiRhizophagus irregularisonly if nitrogen and phosphorus were added together in the compartment restricted to AM fungi. Using this condition, we found genetic diversity inB. distachyonfor MGR ranging from positive to negative MGR depending on the plant genotype tested.Our result on the interaction between nitrogen and phosphorus for MGR inB. distachyonopens new perspectives about AM functioning. In addition, our open-source software allowing to test and run image analysis parameters on large amount of images generated by automated plant phenotyping facilities, will help to screen large panels of genotypes and environmental conditions to identify the factors controlling the MGR.
Published: 2019

3. A comparative analysis of dispersal syndromes in terrestrial and semi-terrestrial animals

Author: Jean-François Le Galliard, Dries Bonte, Sarah Whitmee, Virginie M. Stevens, Katrin Böhning-Gaese, Christian Hof, D. Matthias Dehling, Michel Baguette, Audrey Trochet, Jean Clobert, Martin Brändle, Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Division of Biology, Imperial College London, International Union for Conservation of Nature, Institute of Zoology, Zoological Society of London, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Goethe-Universität Frankfurt am Main, Biodiversity and Climate Research Centre (BiK-F) (LOEWE), Senckenberg Museum [Frankfurt], Universiteit Gent = Ghent University [Belgium] (UGENT), Philipps University of Marburg, Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), French National Research Agency (ANR) [ANR-13-JSV7-0010-01], BelSpo (IAPproject SPEEDY), FWO Research Network EVENET, Hesse's Ministry of Higher Education, Research, and the Arts, European Project: 226852,EC:FP7:ENV,FP7-ENV-2008-1,SCALES(2009), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Universiteit Gent = Ghent University (UGENT), Philipps Universität Marburg = Philipps University of Marburg, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Range (biology), fecundity, [SDV]Life Sciences [q-bio], Population Dynamics, Zoology, Biology, survival, Age at maturity, Homing Behavior, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Phylogeny, global change, Ecology, Evolution, Behavior and Systematics, Trophic level, thermoregulation, trophic levels, Herbivore, Ecology, life-history trade-offs, phylogenetic signal, Interspecific competition, 15. Life on land, Biological Evolution, Invertebrates, Seed dispersal syndrome, 13. Climate action, Ectotherm, Vertebrates, Linear Models, Biological dispersal, Animal Distribution, dispersal phenotypes, dispersal costs, Landscape connectivity
Abstract: International audience; Dispersal, the behaviour ensuring gene flow, tends to covary with a number of morphological, ecological and behavioural traits. While species-specific dispersal behaviours are the product of each species' unique evolutionary history, there may be distinct interspecific patterns of covariation between dispersal and other traits ('dispersal syndromes') due to their shared evolutionary history or shared environments. Using dispersal, phylogeny and trait data for 15 terrestrial and semi-terrestrial animal Orders (> 700 species), we tested for the existence and consistency of dispersal syndromes across species. At this taxonomic scale, dispersal increased linearly with body size in omnivores, but decreased above a critical length in herbivores and carnivores. Species life history and ecology significantly influenced patterns of covariation, with higher phylogenetic signal of dispersal in aerial dispersers compared with ground dwellers and stronger evidence for dispersal syndromes in aerial dispersers and ectotherms, compared with ground dwellers and endotherms. Our results highlight the complex role of dispersal in the evolution of species life-history strategies: good dispersal ability was consistently associated with high fecundity and survival, and in aerial dispersers it was associated with early maturation. We discuss the consequences of these findings for species evolution and range shifts in response to future climate change.
Published: 2014

4. The Plant Membrane-Associated REMORIN1.3 Accumulates in Discrete Perihaustorial Domains and Enhances Susceptibility to Phytophthora infestans

Author: Sébastien Mongrand, Yasin F. Dagdas, Tolga O. Bozkurt, Sophien Kamoun, A. Richardson, Sylvain Raffaele, The Sainsbury Laboratory [Norwich] (TSL), Department of Life Sciences, Imperial College London, John Innes Centre, Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Gatsby Charitable Foundation, European Research Council, Biotechnology and Biological Sciences Research Council, and Marie Curie Intra European Fellowships [268419, 255104]
Subjects: 0106 biological sciences, Oomycete, 0303 health sciences, Physiology, Effector, [SDV]Life Sciences [q-bio], fungi, food and beverages, Articles, Plant Science, Biology, biology.organism_classification, Plant cell, 01 natural sciences, Microbiology, 03 medical and health sciences, Haustorium, Phytophthora infestans, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Secretion, Extrahaustorial membrane, Biogenesis, 030304 developmental biology, 010606 plant biology & botany
Abstract: Filamentous pathogens such as the oomycete Phytophthora infestans infect plants by developing specialized structures termed haustoria inside the host cells. Haustoria are thought to enable the secretion of effector proteins into the plant cells. Haustorium biogenesis, therefore, is critical for pathogen accommodation in the host tissue. Haustoria are enveloped by a specialized host-derived membrane, the extrahaustorial membrane (EHM), which is distinct from the plant plasma membrane. The mechanisms underlying the biogenesis of the EHM are unknown. Remarkably, several plasma membrane-localized proteins are excluded from the EHM, but the remorin REM1.3 accumulates around P. infestans haustoria. Here, we used overexpression, colocalization with reporter proteins, and superresolution microscopy in cells infected by P. infestans to reveal discrete EHM domains labeled by REM1.3 and the P. infestans effector AVRblb2. Moreover, SYNAPTOTAGMIN1, another previously identified perihaustorial protein, localized to subdomains that are mainly not labeled by REM1.3 and AVRblb2. Functional characterization of REM1.3 revealed that it is a susceptibility factor that promotes infection by P. infestans. This activity, and REM1.3 recruitment to the EHM, require the REM1.3 membrane-binding domain. Our results implicate REM1.3 membrane microdomains in plant susceptibility to an oomycete pathogen.
Published: 2014

5. Polymorphisms in twelve candidate genes are associated with growth, muscle lipid profile and meat quality traits in eleven European cattle breeds

Author: Sevane, Natalia, Armstrong, E., Wiener, P., Pong Wong, R., Dunner, S., Alberti, P., Amarger, Valérie, Delourme, Didier, Levéziel, Hubert, Boitard, Simon, Mangin, Brigitte, Canon, J., Checa, M.L., Dunner, Susana, Garcia, David, Miranda, M.E., Pérez, R., Christensen, M., Crisa, A., Marchitelli, Cinzia, Valentini, A., Failla, S., GIGLI, S., Hocquette, Jean-François, Nute, G., Richardson, I., Olleta, J.L., Panea, Begoña, Sanudo, Carlos, Razzaq, N., Renand, Gilles, Williams, J.L., Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Universidad de la República, University of Edinburgh, Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), Unité de Génétique Moléculaire Animale (UMR GMA), Université de Limoges (UNILIM)-Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-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-Université Fédérale Toulouse Midi-Pyrénées, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Departamento de Producción Animal, Facultad de Veterinaria, University of Copenhagen = Københavns Universitet (KU), Département de Production Animale, Faculté d’Agronomie, Université de Parakou, Istituto Sperimentale per la Zootecnia, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), 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)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Division of Farm Animal Science, University of Bristol [Bristol], University of Zaragoza - Universidad de Zaragoza [Zaragoza], Roslin Institute, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Parco Tecnologico Padano, Polo Universitario, and EC QLK5 - CT2000-0147
Subjects: Genetic Markers, Male, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, Meat, Genetic Linkage, Gene Expression, Muscle Proteins, SNP, Breeding, Quantitative trait locus, Beef cattle, Biology, Polymorphism, Single Nucleotide, meat quality, 03 medical and health sciences, Quantitative Trait, Heritable, beef cattle, Genetic linkage, Genetics, Animals, Molecular Biology, Gene, Genetic Association Studies, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Gene Expression Profiling, Body Weight, 0402 animal and dairy science, 04 agricultural and veterinary sciences, General Medicine, Lipid Metabolism, 040201 dairy & animal science, Europe, Genetic marker, Docosahexaenoic acid, Body Composition, bos taurus, Cattle, Female, candidate genes, Purebred
Abstract: International audience; Current customers' demands focus on the nutritional and sensory quality of cattle meat. Candidate gene approach allows identification of genetic polymorphisms that have a measurable effect on traits of interest. The aim of this work is to identify new molecular markers for beef production through an association study using 27 candidate genes and 314 purebred bulls from 11 European cattle breeds. Twelve genes were found associated with different lipid and meat quality traits, and among these stand out the considerable effect of CAST on fatness score, CGGBP1 on growth traits, HSPB1 on the percentage of lauric acid (12:0) and phospholipid docosahexaenoic acid (DHA 22:6 n - 3), RORA on the ratio of light absorption (K) to light scattering (S) (K/S), and TNFA on lightness (L*). Most of these traits are related to post-mortem muscle biochemical changes, which are key factors controlling meat quality and consumers' acceptance. Also, the variations produced on muscle fatty acid profiles, such as those of AANAT, CRH, CSN3, HSPB1, and TNFA, give insights into the genetic networks controlling these complex traits and the possibility of future improvement of meat nutritional quality.
Published: 2014

6. Muscle lipid composition in bulls from 15 European breeds

Author: Sevane, Natalia, Nute, G., Sanudo, Carlos, Cortes, J., Canon, J., Williams, J.L., Dunner, S., Alberti, P., Amarger, Valérie, Boitard, Simon, Checa, M.L., Christensen, M., Crisa, A., Delourme, Didier, Ertbjerg, Per, Failla, S., Garcia, David, GIGLI, S., Hocquette, Jean-François, Levéziel, Hubert, Mangin, Brigitte, Marchitelli, Cinzia, Miranda, M.E., Olleta, J.L., Panea, Begoña, Pérez, R., Razzaq, N., Renand, Gilles, Valentini, A., Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Division of Farm Animal Science, University of Bristol [Bristol], University of Zaragoza - Universidad de Zaragoza [Zaragoza], Departamento de Producción Animal, Facultad de Veterinaria, Parco Tecnologico Padano, Polo Universitario, Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), Unité de Génétique Moléculaire Animale (UMR GMA), Institut National de la Recherche Agronomique (INRA)-Université de Limoges (UNILIM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-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-Université Fédérale Toulouse Midi-Pyrénées, University of Copenhagen = Københavns Universitet (KU), Department of Food Science, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Istituto Sperimentale per la Zootecnia, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), 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)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Département de Production Animale, Faculté d’Agronomie, Université de Parakou, Roslin Institute, Génétique Animale et Biologie Intégrative (GABI), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: 2. Zero hunger, chemistry.chemical_classification, Taste, General Veterinary, medicine.diagnostic_test, food and beverages, Biology, Beef cattle, Breed, fatty acid profile, Tenderness, beef cattle, Human nutrition, chemistry, medicine, Animal Science and Zoology, Food science, omega-3, medicine.symptom, Lipid profile, Essential nutrient, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, PUFA, Polyunsaturated fatty acid
Abstract: International audience; Cattle meat provides essential nutrients necessary for a balanced diet and health preservation. Besides nutritional quality, consumers' preferences are related to specific attributes such as tenderness, taste and flavour. The present study characterizes the fatty acid composition of beef, which is an important factor in both nutritional and quality values, in 15 European cattle breeds fed a similar diet and reared in five countries (United Kingdom, Denmark, France, Italy and Spain). The effect of possible slight differences on diet composition which might have occurred between countries were included in the breed effect which confounds country, diet, slaughter house and slaughter day as all individuals of a same breed were managed simultaneously. The wide range of breeds studied and the significant differences on lipid profile described here provide a broad characterization of beef meat, which allows giving a better response to the variety of consumers' preferences. Regarding meat health benefits, the groups that stand out are: the double-muscled animals, which displayed lower total fat, lower proportion of saturated (SFA) and monounsaturated (MUFA) fatty acids, and a higher proportion of polyunsaturated (PUFA) fatty acids; and Limousin and Charolais breeds with a significantly higher conversion of 18:3n-3 PUFA to the long chain 22:6n-3 PUFA.
Published: 2014

7. The symbiotic transcription factor<scp>M</scp>t<scp>EFD</scp>and cytokinins are positively acting in the<scp>M</scp>edicago truncatulaand<scp>R</scp>alstonia solanacearumpathogenic interaction

Author: Justine Fromentin, Florian Frugier, Tatiana Vernié, Sandrine Balzergue, Marie-Françoise Jardinaud, Stéphanie Huguet, Pascal Gamas, Sandra Moreau, Fabienne Vailleau, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche [ANR-08-PXXX-0-03], EU-CNRS (Fonds Social Europeen), INRA-CJS, Ecole Nationale Superieure d'Agronomie part of the Institut National Polytechnique de Toulouse (ENSAT-INP), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Transcription, Genetic, Physiology, [SDV]Life Sciences [q-bio], Colony Count, Microbial, root pathogen, Plant Science, Models, Biological, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, pathogenesis-symbiosis crosstalk, Gene Expression Regulation, Plant, Medicago truncatula, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, RNA, Messenger, Symbiosis, Transcription factor, Gene, Plant Diseases, Plant Proteins, 030304 developmental biology, 0303 health sciences, Sinorhizobium meliloti, Ralstonia solanacearum, biology, Bacterial wilt, fungi, food and beverages, biology.organism_classification, Up-Regulation, Cell biology, cytokinins, Response regulator, chemistry, Mutation, Cytokinin, Root Nodules, Plant, transcriptome, Signal Transduction, Transcription Factors, 010606 plant biology & botany
Abstract: International audience; • A plant-microbe dual biological system was set up involving the model legume Medicago truncatula and two bacteria, the soil-borne root pathogen Ralstonia solanacearum and the beneficial symbiont Sinorhizobium meliloti. • Comparison of transcriptomes under symbiotic and pathogenic conditions highlighted the transcription factor MtEFD (Ethylene response Factor required for nodule Differentiation) as being upregulated in both interactions, together with a set of cytokinin-related transcripts involved in metabolism, signaling and response. MtRR4 (Response Regulator), a cytokinin primary response gene negatively regulating cytokinin signaling and known as a target of MtEFD in nodulation processes, was retrieved in this set of transcripts. • Refined studies of MtEFD and MtRR4 expression during M. truncatula and R. solanacearum interaction indicated differential kinetics of induction and requirement of central regulators of bacterial pathogenicity, HrpG and HrpB. Similar to MtRR4, MtEFD upregulation during the pathogenic interaction was dependent on cytokinin perception mediated by the MtCRE1 (Cytokinin REsponse 1) receptor. • The use of M. truncatula efd-1 and cre1-1 mutants evidenced MtEFD and cytokinin perception as positive factors for bacterial wilt development. These factors therefore play an important role in both root nodulation and root disease development.
Published: 2013

8. Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles

Author: Claire Lurin, Clément Bernard, Laure Heurtevin, Jean Colcombet, Richard Berthomé, Mauricio Lopez-Obando, Karine Martin, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GAFL), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Arabidopsis thaliana, Arabidopsis, Computational biology, Biology, Bioinformatics, 01 natural sciences, Genome, PPR proteins, 03 medical and health sciences, Organelle, subcellular localization, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plastids, Molecular Biology, Gene, 030304 developmental biology, Organelles, 0303 health sciences, Arabidopsis Proteins, RNA-Binding Proteins, Cell Biology, Subcellular localization, biology.organism_classification, High-Throughput Screening Assays, Mitochondria, targeting peptide, Pentatricopeptide repeat, organelle genome expression, Function (biology), 010606 plant biology & botany, Research Paper
Abstract: International audience; Four hundred and fifty-eight genes coding for PentatricoPeptide Repeat (PP R) proteins are annotated in the Arabidopsis thaliana genome. Over the past 10 years, numerous reports have shown that many of these proteins function in organelles to target specific transcripts and are involved in post-transcriptional regulation. Therefore, they are thought to be important players in the coordination between nuclear and organelle genome expression. Only four of these proteins have been described to be addressed outside organelles, indicating that some PP Rs could function in posttranscriptional regulations of nuclear genes. In this work, we updated and improved our current knowledge on the localization of PP R proteins of Arabidopsis within the plant cell. We particularly investigated the subcellular localization of 166 PP R proteins whose targeting predictions were ambiguous, using a combination of high-throughput cloning and microscopy. Through systematic localization experiments and data integration, we confirmed that PP R proteins are largely targeted to organelles and showed that dual targeting to both the mitochondria and plastid occurs more frequently than expected. These results allow us to speculate that dual-targeted PP R proteins could be important for the fine coordination of gene expressions in both organelles.
Published: 2013

9. Plant-activated bacterial receptor adenylate cyclases modulate epidermal infection in the Sinorhizobium meliloti–Medicago symbiosis

Author: Céline Mathieu-Demazière, Jacques Batut, Catherine Masson-Boivin, A. M. Garnerone, Chang Fu Tian, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), China Agricultural University (CAU), China Scholarship Council, China Postdoctoral Science Foundation [20100480377], National Basic Research Program of China ('973') [2010CB126500], French Agence Nationale de la Recherche (ANR) [ANR-2010-BLAN-1719-01], and Laboratoire d'Excellence [ANR-10-LABX-41]
Subjects: NODULATION, [SDV]Life Sciences [q-bio], ALFALFA, Organogenesis, Root hair, OXYGEN, Rhizobia, Microbiology, 03 medical and health sciences, Symbiosis, Cyclic AMP, Medicago, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, GENE-EXPRESSION, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Sinorhizobium meliloti, Multidisciplinary, biology, 030306 microbiology, fungi, food and beverages, Plants, Biological Sciences, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, ABSENCE, DIFFERENTIATION, RHIZOBIUM-LEGUME SYMBIOSIS, ESCHERICHIA-COLI, Nitrogen fixation, REGULATOR, NODULE, Bacteria, Adenylyl Cyclases, Signal Transduction
Abstract: Legumes and soil bacteria called rhizobia have coevolved a facultative nitrogen-fixing symbiosis. Establishment of the symbiosis requires bacterial entry via root hair infection threads and, in parallel, organogenesis of nodules that subsequently are invaded by bacteria. Tight control of nodulation and infection is required to maintain the mutualistic character of the interaction. Available evidence supports a passive bacterial role in nodulation and infection after the microsymbiont has triggered the symbiotic plant developmental program. Here we identify in Sinorhizobium meliloti , the Medicago symbiont, a cAMP-signaling regulatory cascade consisting of three receptor-like adenylate cyclases, a Crp-like regulator, and a target gene of unknown function. The cascade is activated specifically by a plant signal during nodule organogenesis. Cascade inactivation results in a hyperinfection phenotype consisting of abortive epidermal infection events uncoupled from nodulation. These findings show that, in response to a plant signal, rhizobia play an active role in the control of infection. We suggest that rhizobia may modulate the plant’s susceptibility to infection. This regulatory loop likely aims at optimizing legume infection.
Published: 2012

10. Progress towards a reference genome for sunflower

Author: N.C. Kane, N. Gill, M.G. King, J.E. Bowers, H. Berges, J. Gouzy, E. Bachlava, N.B. Langlade, Z. Lai, M. Stewart, J.M. Burke, P. Vincourt, S.J. Knapp, L.H. Rieseberg, Dept Bot, University of British Columbia (UBC), Dept Plant Biol, University of Georgia [USA], Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Monsanto Company, Indiana University, Indiana University System, Dept Biol, Indiana University [Bloomington], Indiana University System-Indiana University System, Genome Canada, Genome British Columbia, French National Institute for Agricultural Research (INRA), US National Science Foundation [0421630], and US Department of Agriculture [2008-35300-19263, 2008-35300-04579]
Subjects: 0106 biological sciences, Compositae, sunflower, HELIANTHUS-ANNUUS L, [SDV]Life Sciences [q-bio], Horticultural crops, physical map, Plant Science, CULTIVATED SUNFLOWER, Biology, RFLP LINKAGE MAP, SEQUENCE, 01 natural sciences, DNA sequencing, 03 medical and health sciences, Helianthus annuus, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, reference genome, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, next generation sequencing, 2. Zero hunger, 0303 health sciences, IDENTIFICATION, Ecology, MAIZE GENOME, Noxious weed, business.industry, food and beverages, Sunflower, EVOLUTION, WILD SUNFLOWERS, Biotechnology, ARABIDOPSIS-THALIANA, business, GENUS HELIANTHUS, 010606 plant biology & botany, Reference genome
Abstract: International audience; The Compositae is one of the largest and most economically important families of flowering plants and includes a diverse array of food crops, horticultural crops, medicinals, and noxious weeds. Despite its size and economic importance, there is no reference genome sequence for the Compositae, which impedes research and improvement efforts. We report on progress toward sequencing the 3.5 Gb genome of cultivated sunflower (Helianthus annuus), the most important crop in the family. Our sequencing strategy combines whole-genome shotgun sequencing using the Solexa and 454 platforms with the generation of high-density genetic and physical maps that serve as scaffolds for the linear assembly of whole-genome shotgun sequences. The performance of this approach is enhanced by the construction of a sequence-based physical map, which provides unique sequence-based tags every 5-6 kb across the genome. Thus far, our physical map covers similar to 85% of the sunflower genome, and we have generated similar to 80x genome coverage with Solexa reads and 15.5x with 454 reads. Preliminary analyses indicated that similar to 78% of the sunflower genome consists of repetitive sequences. Nonetheless, similar to 76% of contigs >5 kb in size can be assigned to either the physical or genetic map or to both, suggesting that our approach is likely to deliver a highly accurate and contiguous reference genome for sunflower.
Published: 2011

11. Targeted mRNA Oxidation Regulates Sunflower Seed Dormancy Alleviation during Dry After-Ripening

Author: Nicolas B. Langlade, Hayat El-Maarouf-Bouteau, Christophe Bailly, Sandrine Balzergue, Sandrine Arribat, Patrick Vincourt, Jérémie Bazin, Université Pierre et Marie Curie - Paris 6 (UPMC), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, abscisic acid, alzheimer disease, Protein biosynthesis, Research Articles, Plant Proteins, 2. Zero hunger, 0303 health sciences, food and beverages, vitamin e, Plant Dormancy, Biochemistry, 8-Hydroxy-2'-Deoxyguanosine, Germination, gene expression, arabidopsis thaliana, signal transduction, processing bodies, stress granules, cdna aflp, germination, Seeds, Helianthus, Sunflower seed, Oxidation-Reduction, Polymorphism, Restriction Fragment Length, Molecular Sequence Data, Phosphatase, Biology, 03 medical and health sciences, Helianthus annuus, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, RNA, Messenger, 030304 developmental biology, Polymorphism, Genetic, Gene Expression Profiling, Deoxyguanosine, Cell Biology, Microarray Analysis, Lyase, Protein Biosynthesis, Dormancy, Imbibition, Transcriptome, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; International audience; After-ripening is the mechanism by which dormant seeds become nondormant during their dry storage after harvest. The absence of free water in mature seeds does not allow detectable metabolism; thus, the processes associated with dormancy release under these conditions are largely unknown. We show here that sunflower (Helianthus annuus) seed alleviation of dormancy during after-ripening is associated with mRNA oxidation and that this oxidation is prevented when seeds are maintained dormant. In vitro approaches demonstrate that mRNA oxidation results in artifacts in cDNA-amplified fragment length polymorphim analysis and alters protein translation. The oxidation of transcripts is not random but selective, and, using microarrays, we identified 24 stored mRNAs that became highly oxidized during after-ripening. Oxidized transcripts mainly correspond to genes involved in responses to stress and in cell signaling. Among them, protein phosphatase 2C PPH1, mitogen-activated protein kinase phosphatase 1, and phenyl ammonia lyase 1 were identified. We propose that targeted mRNA oxidation during dry after-ripening of dormant seeds could be a process that governs cell signaling toward germination in the early steps of seed imbibition.
Published: 2011

12. Structure-Function Similarities between a Plant Receptor-like Kinase and the Human Interleukin-1 Receptor-associated Kinase-4

Author: Carole Pichereaux, Ton Timmers, Michel Rossignol, Doerte Klaus-Heisen, Sylvie Camut, Benoit Lefebvre, Theodorus W. J. Gadella, Anne Imberty, Alessandra Nurisso, Julie V. Cullimore, Anna Pietraszewska-Bogiel, Malick Mbengue, inconnu, Inconnu, Centre de Recherches sur les Macromolécules Végétales (CERMAV), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Swammerdam Institute for Life Sciences, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, European Community : MRTN-CT-2006-035546, Fondation pour la Recherche Medicale, Toulouse Midi-Pyrenees Genopole, Midi-Pyrenees Regional Council : CR07003760, French National Research Agency, Faculty of Science, and Molecular Cytology (SILS, FNWI)
Subjects: Models, Molecular, 0106 biological sciences, kinase, Plant Biology, RECEPTOR-LIKE KINASE, Biology, Plant Roots, légumineuse, 01 natural sciences, Biochemistry, Protein Structure, Secondary, SH3 domain, MAP2K7, RECEPTOR SERINE / THREONINE KINASE, Structure-Activity Relationship, 03 medical and health sciences, Receptor Serine/Threonine Kinase, Medicago truncatula, Humans, c-Raf, PLANT, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Kinase activity, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 030304 developmental biology, Serine/threonine-specific protein kinase, 0303 health sciences, PROTEIN KINASES, SYMBIOSIS, Autophosphorylation, PROTEIN STRUCTURE, Cell Biology, MOLECULAR DYNAMICS, LEGUME, Enzyme Activation, Interleukin-1 Receptor-Associated Kinases, Structural Homology, Protein, Casein kinase 2, symbiose, 010606 plant biology & botany
Abstract: International audience; Phylogenetic analysis has previously shown that plant receptor-like kinases (RLKs) are monophyletic with respect to the kinase domain and share an evolutionary origin with the animal interleukin-1 receptor-associated kinase/Pelle-soluble kinases. The lysin motif domain-containing receptor-like kinase-3 (LYK3) of the legume Medicago truncatula shows 33% amino acid sequence identity with human IRAK-4 over the kinase domain. Using the structure of this animal kinase as a template, homology modeling revealed that the plant RLK contains structural features particular to this group of kinases, including the tyrosine gatekeeper and the N-terminal extension α-helix B. Functional analysis revealed the importance of these conserved features for kinase activity and suggests that kinase activity is essential for the biological role of LYK3 in the establishment of the root nodule nitrogen-fixing symbiosis with rhizobia bacteria. The kinase domain of LYK3 has dual serine/threonine and tyrosine specificity, and mass spectrometry analysis identified seven serine, eight threonine, and one tyrosine residue as autophosphorylation sites in vitro. Three activation loop serine/threonine residues are required for biological activity, and molecular dynamics simulations suggest that Thr-475 is the prototypical phosphorylated residue that interacts with the conserved arginine in the catalytic loop, whereas Ser-471 and Thr-472 may be secondary sites. A threonine in the juxtamembrane region and two threonines in the C-terminal lobe of the kinase domain are important for biological but not kinase activity. We present evidence that the structure-function similarities that we have identified between LYK3 and IRAK-4 may be more widely applicable to plant RLKs in general.
Published: 2011

13. Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza

Author: Fabienne Maillet, Hugues Driguez, Véréna Poinsot, Guillaume Bécard, Andreas Niebel, Laurence Cromer, Damien Formey, Jean Dénarié, Olivier André, Virginie Puech-Pagès, Eduardo Andres Martinez, Delphine Giraudet, Monique Gueunier, Alexandra Haouy, inconnu, Inconnu, Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), 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), Metatoul - Agromix, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-MetaToul-MetaboHUB, 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), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), 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), Centre de Recherches sur les Macromolécules Végétales, Centre National de la Recherche Scientifique (CNRS), EMD Crop BioScience, Charles-Leopold Mayer Prize, French Academy of Sciences, Institut National de la Recherche Agronomique, Carret, Michèle, 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), and 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)-Ecole Nationale Vétérinaire de Toulouse (ENVT)
Subjects: Lipopolysaccharides, EXTRACTS CHEMISTRY METABOLISM, 0106 biological sciences, ved/biology.organism_classification_rank.species, Plant Roots, 01 natural sciences, CHOMATOGRAPHY HIGH PRESSURE LIQUID, LIPOPOLYSACCHARIDES CHEMISTRY METABOLISM, Glomeromycota, Mycorrhizae, Mycorrhiza, Chromatography, High Pressure Liquid, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Multidisciplinary, Endosymbiosis, Ecology, SIGNAL TRANSDUCTION, SYMBIOSIS, food and beverages, SPORES FUNGAL CHEMISTRY METABOLISM SYMBIOSIS, Spores, Fungal, GLOMEROMYCOTA METABOLISM, MEDICAGO TRUNCATULA CHEMISTRY GROWTH & DEVELOPMENT METABOLISM MICROBIOLOBY, Medicago truncatula, Daucus carota, Arbuscular mycorrhiza, MYCORRHIZAE METABOLISM, PLANT ROOTS CHEMISTRY GROWTH & DEVELOPMENT METABOLISM MICROBIOLOGY, CARBOHYDRATE SEQUENCE, CAROTA CHEMISTRY METABOLISM MICROBIOLOGY, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, 03 medical and health sciences, Symbiosis, Terrestrial plant, Botany, MOLECULAR SEQUENCE DATA, PLANT, 030304 developmental biology, Plant Extracts, ved/biology, fungi, Fabaceae, 15. Life on land, biology.organism_classification, DAUCUS, AM, SUSTAINABLE DEVELOPMENT, 010606 plant biology & botany
Abstract: International audience; Arbuscular mycorrhiza (AM) is a root endosymbiosis between plants and glomeromycete fungi. It is the most widespread terrestrial plant symbiosis, improving plant uptake of water and mineral nutrients. Yet, despite its crucial role in land ecosystems, molecular mechanisms leading to its formation are just beginning to be unravelled. Recent evidence suggests that AM fungi produce diffusible symbiotic signals. Here we show that Glomus intraradices secretes symbiotic signals that are a mixture of sulphated and non-sulphated simple lipochitooligosaccharides (LCOs), which stimulate formation of AM in plant species of diverse families (Fabaceae, Asteraceae and Umbelliferae). In the legume Medicago truncatula these signals stimulate root growth and branching by the symbiotic DMI signalling pathway. These findings provide a better understanding of the evolution of signalling mechanisms involved in plant root endosymbioses and will greatly facilitate their molecular dissection. They also open the way to using these natural and very active molecules in agriculture.
Published: 2011

14. TheMedicago truncatulaE3 Ubiquitin Ligase PUB1 Interacts with the LYK3 Symbiotic Receptor and Negatively Regulates Infection and Nodulation

Author: Susana Rivas, Benoit Lefebvre, Ton Timmers, Dörte Klaus-Heisen, Laurent Deslandes, Christine Hervé, Malick Mbengue, Fernanda de Carvalho-Niebel, Julie V. Cullimore, Solène Froidure, Sylvie Camut, Sandra Moreau, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), European Community funded Research Training Network 'NODPERCEPTION', French Ministry for Higher Education and Research, and ANR-05-BLAN-0243,NodBindsLysM,Etude multidisciplinaire des Interactions signal Nod / LysM récepteurs kinases dans la symbiose Rhizobia-Légumineuses(2005)
Subjects: 0106 biological sciences, symbiotic receptor, Plant Science, luzerne, Plant Root Nodulation, 01 natural sciences, nitrogen, Nod factor, Ubiquitin, Gene Expression Regulation, Plant, medicago trunculata, Génétique des plantes, sinorhizobium meliloti, nodulation, Research Articles, Plant Proteins, azote, 0303 health sciences, Sinorhizobium meliloti, fourrage, biology, Kinase, ubiquitin ligase, fabaceae, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Plants, Genetically Modified, Medicago truncatula, Ubiquitin ligase, Cell biology, Biochemistry, RNA Interference, Signal transduction, symbiose, récepteur, Signal Transduction, Ubiquitin-Protein Ligases, Molecular Sequence Data, Plants genetics, légumineuse, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Two-Hybrid System Techniques, Tobacco, Symbiosis, 030304 developmental biology, fungi, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, infection, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Protein kinase domain, biology.protein, bacteria, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; International audience; LYK3 is a lysin motif receptor-like kinase of Medicago truncatula, which is essential for the establishment of the nitrogenfixing, root nodule symbiosis with Sinorhizobium meliloti. LYK3 is a putative receptor of S. meliloti Nod factor signals, but little is known of how it is regulated and how it transduces these symbiotic signals. In a screen for LYK3-interacting proteins, we identified M. truncatula Plant U-box protein 1 (PUB1) as an interactor of the kinase domain. In planta, both proteins are localized and interact in the plasma membrane. In M. truncatula, PUB1 is expressed specifically in symbiotic conditions, is induced by Nod factors, and shows an overlapping expression pattern with LYK3 during nodulation. Biochemical studies show that PUB1 has a U-box–dependent E3 ubiquitin ligase activity and is phosphorylated by the LYK3 kinase domain. Overexpression and RNA interference studies in M. truncatula show that PUB1 is a negative regulator of the LYK3 signaling pathway leading to infection and nodulation and is important for the discrimination of rhizobia strains producing variant Nod factors. The potential role of PUB E3 ubiquitin ligases in controlling plant–microbe interactions and development through interacting with receptor-like kinases is discussed.
Published: 2010

15. A remorin protein interacts with symbiotic receptors and regulates bacterial infection

Author: Jeremy D. Murray, Sylvain Raffaele, Sandra Moreau, Laurence Godiard, Thomas Ott, Michael K. Udvardi, Joana Bittencourt-Silvestre, Dörte Klaus, Pascal Gamas, Laurent Deslandes, Andreas Niebel, Katalin Tóth, Benoit Lefebvre, Sébastien Mongrand, Julie V. Cullimore, Ton Timmers, Christine Hervé, Malick Mbengue, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Ludwig Maximilians University of Munich, Plant Biology Division, The Samuel Roberts Noble Foundation, Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Marie-Curie Intra-European Fellowship : 024587, French Agence National de la Recherche : ANR-05-BLAN-0243-01, European Community's Sixth Framework Programme, MRTN-CT-2006-035546, German Academic exchange service, German Research Council (DFG) : OT 423/1-1, and Biotechnology and Biological Sciences Research Council : BB/G023832/1
Subjects: 0106 biological sciences, Scaffold protein, Cell signaling, Root nodule, Molecular Sequence Data, SCAFFOLDING PROTEIN, REMORINE, RECEPTOR-LIKE KINASE, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 01 natural sciences, Rhizobia, 03 medical and health sciences, Transformation, Genetic, Medicago truncatula, Symbiosis, DNA Primers, Plant Proteins, 030304 developmental biology, Genetics, 0303 health sciences, Sinorhizobium meliloti, Multidisciplinary, Base Sequence, biology, fungi, REMORIN, food and beverages, Biological Sciences, Phosphoproteins, Plants, Genetically Modified, biology.organism_classification, Cell biology, INTERACTION PLANTE MICROORGANISME, SIGNALING, Cytoplasm, Mutation, RNA Interference, Signal transduction, PLANT PROTEIN, Carrier Proteins, NODULE, Rhizobium, Signal Transduction, 010606 plant biology & botany
Abstract: Remorin proteins have been hypothesized to play important roles during cellular signal transduction processes. Induction of some members of this multigene family has been reported during biotic interactions. However, no roles during host-bacteria interactions have been assigned to remorin proteins until now. We used root nodule symbiosis between Medicago truncatula and Sinorhizobium meliloti to study the roles of a remorin that is specifically induced during nodulation. Here we show that this oligomeric remorin protein attaches to the host plasma membrane surrounding the bacteria and controls infection and release of rhizobia into the host cytoplasm. It interacts with the core set of symbiotic receptors that are essential for perception of bacterial signaling molecules, and thus might represent a plant-specific scaffolding protein.
Published: 2010

16. Ten things to know about oomycete effectors

Author: Sylvain Raffaele, Ricardo Oliva, Tolga O. Bozkurt, Jorunn I. B. Bos, Angela Chaparro-Garcia, Marco Thines, Joe Win, Rhys A. Farrer, Mireille van Damme, Sebastian Schornack, Michael C. Zody, Edgar Huitema, Sophien Kamoun, Brian J. Haas, Chad Nusbaum, María Eugenia Segretin, Simon Schwizer, Liliana M. Cano, The Sainsbury Laboratory [Norwich] (TSL), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], University of Hohenheim, and Gatsby Charitable Foundation, Biotechnology and Biological Sciences Research Council (BBSRC) BASF Plant Sciences Deutsche Forschungsgemeinschaft (DFG) fellowship Marie Curie Intra-European fellowship Max Planck Society German Science foundation (DFG)
Subjects: [SDV]Life Sciences [q-bio], Reviews, Soil Science, Plant Science, Computational biology, Biology, Models, Biological, Fungal Proteins, 03 medical and health sciences, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Plant Diseases, 030304 developmental biology, Oomycete, 0303 health sciences, 030306 microbiology, Effector, Agricultura, biology.organism_classification, Oomycetes, CIENCIAS AGRÍCOLAS, Host-Pathogen Interactions, purl.org/becyt/ford/4.1 [https], Phytophthora infestans, Agricultura, Silvicultura y Pesca, Agronomy and Crop Science, purl.org/becyt/ford/4 [https]
Abstract: Long considered intractable organisms by fungal genetic research standards, the oomycetes have recently moved to the centre stage of research on plant-microbe interactions. Recent work on oomycete effector evolution, trafficking and function has led to major conceptual advances in the science of plant pathology. In this review, we provide a historical perspective on oomycete genetic research and summarize the state of the art in effector biology of plant pathogenic oomycetes by describing what we consider to be the 10 most important concepts about oomycete effectors. Fil: Schornack, Sebastian. The Sainsbury Laboratory; Reino Unido Fil: Huitema, Edgar. The Sainsbury Laboratory; Reino Unido Fil: Cano, Liliana M.. The Sainsbury Laboratory; Reino Unido Fil: Bozkurt, Tolga O.. The Sainsbury Laboratory; Reino Unido Fil: Oliva, Ricardo. The Sainsbury Laboratory; Reino Unido Fil: Van Damme, Mireille. The Sainsbury Laboratory; Reino Unido Fil: Schwizer, Simon. The Sainsbury Laboratory; Reino Unido Fil: Raffaele, Sylvain. The Sainsbury Laboratory; Reino Unido Fil: Chaparro Garcia, Angela. The Sainsbury Laboratory; Reino Unido Fil: Farrer, Rhys. The Sainsbury Laboratory; Reino Unido Fil: Segretin, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. The Sainsbury Laboratory; Reino Unido Fil: Bos, Jorunn. The Sainsbury Laboratory; Reino Unido Fil: Haas, Brian J.. Harvard University; Estados Unidos. Massachusetts Institute of Technology; Estados Unidos Fil: Zody, Michael C.. Massachusetts Institute of Technology; Estados Unidos. Harvard University; Estados Unidos Fil: Nusbaum, Chad. Massachusetts Institute of Technology; Estados Unidos. Harvard University; Estados Unidos Fil: Win, Joe. The Sainsbury Laboratory; Reino Unido Fil: Thines, Marco. The Sainsbury Laboratory; Reino Unido. Universidad de Hohenheim; Alemania Fil: Kamoun, Sophien. The Sainsbury Laboratory; Reino Unido
Published: 2009

17. Altered expression of cytosolic/nuclear HSC70-1 molecular chaperone affects development and abiotic stress tolerance in Arabidopsis thaliana

Author: Marie-Anne Roncato, Serge Chiarenza, Nathalie Pochon, Nathalie Leonhardt, Mathilde Clément, Audrey Creff, Anne-Claire Cazalé, Elena Marin, Laurent D. Noël, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie cellulaire et moléculaire des plantes et des bactéries (BCMPB), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université de la Méditerranée - Aix-Marseille 2, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de la Méditerranée - Aix-Marseille 2, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, SGT1, Physiology, Mutant, Arabidopsis, Y-RAY, AUXIN, Plant Science, 01 natural sciences, DnaK, Cytosol, Gene Expression Regulation, Plant, UV-C, HSP70, 2. Zero hunger, Abiotic component, 0303 health sciences, biology, Salt Tolerance, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cell biology, Co-chaperone, Glucosyltransferases, embryonic structures, ARSENIC, Signal Transduction, HEAT SHOCK, animal structures, HSC70, Ultraviolet Rays, macromolecular substances, CADMIUM, 03 medical and health sciences, Stress, Physiological, Botany, 030304 developmental biology, Cell Nucleus, Indoleacetic Acids, Arabidopsis Proteins, Abiotic stress, HSC70 Heat-Shock Proteins, ARABIDOPSIS THALIANA, Meristem, biology.organism_classification, MERSITEM, Hsp70, Gamma Rays, Chaperone (protein), biology.protein, CO-CHAPERONE, 010606 plant biology & botany
Abstract: International audience; Molecular chaperones of the heat shock cognate 70 kDa (HSC70) family are highly conserved in all living organisms and assist nascent protein folding in normal physiological conditions as well as in biotic and abiotic stress conditions. In the absence of specific inhibitors or viable knockout mutants, cytosolic/nuclear HSC70-1 overexpression (OE) and mutants in the HSC70 co-chaperone SGT1 (suppressor of G2/M allele of skp1) were used as genetic tools to identify HSC70/SGT1 functions in Arabidopsis development and abiotic stress responses. HSC70-1 OE caused a reduction in root and shoot meristem activities, thus explaining the dwarfism of those plants. In addition, HSC70-1 OE did not impair auxin-dependent phenotypes, suggesting that SGT1 functions previously identified in auxin signalling are HSC70 independent. While responses to abiotic stimuli such as UV-C exposure, phosphate starvation, or seedling de-etiolation were not perturbed by HSC70-1 OE, it specifically conferred γ-ray hypersensitivity and tolerance to salt, cadmium (Cd), and arsenic (As). Cd and As perception was not perturbed, but plants overexpressing HSC70-1 accumulated less Cd, thus providing a possible molecular explanation for their tolerance phenotype. In summary, genetic evidence is provided for HSC70-1 involvement in a limited set of physiological processes, illustrating the essential and yet specific functions of this chaperone in development and abiotic stress responses in Arabidopsis.
Published: 2009

18. ABA-Mediated Inhibition of Germination Is Related to the Inhibition of Genes Encoding Cell-Wall Biosynthetic and Architecture: Modifying Enzymes and Structural Proteins in Medicago truncatula Embryo Axis

Author: Anis M. Limami, Laure Viau, Claudie Ricoult, Mustafa Malik-Ghulam, Nathalie Leduc, Christine Gimeno-Gilles, Eric Lelièvre, Andreas Niebel, Physiologie Moléculaire des Semences (PMS), Institut National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Sciences Agronomiques Appliquées à l'Horticulture (SAGAH), and Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-Institut National d'Horticulture
Subjects: 0106 biological sciences, Cell division, [SDV]Life Sciences [q-bio], Germination, Plant Science, Genes, Plant, Polymerase Chain Reaction, 01 natural sciences, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Cell Wall, Medicago truncatula, Botany, Gene expression, Radicle, Molecular Biology, Abscisic acid, Research Articles, CELL-WALL EXPANSION, Plant Proteins, 030304 developmental biology, 0303 health sciences, biology, food and beverages, Embryo, biology.organism_classification, CONTROLE DE LA GERMINATION, RADICLE EMERGENCE, Cell biology, ABA, chemistry, [SDE]Environmental Sciences, XET, Abscisic Acid, 010606 plant biology & botany
Abstract: International audience; Radicle emergence and reserves mobilization are two distinct programmes that are thought to control germination. Both programs are influenced by abscissic acid (ABA) but how this hormone controls seed germination is still poorly known. Phenotypic and microscopic observations of the embryo axis of Medicago truncatula during germination in mitotic inhibition condition triggered by 10 mu M oryzalin showed that cell division was not required to allow radicle emergence. A suppressive subtractive hybridization showed that more than 10% of up-regulated genes in the embryo axis encoded proteins related to cell-wall biosynthesis. The expression of alpha-expansins, pectin-esterase, xylogucan-endotransglycosidase, cellulose synthase, and extensins was monitored in the embryo axis of seeds germinated on water, constant and transitory ABA. These genes were overexpressed before completion of germination in the control and strongly inhibited by ABA. The expression was re-established in the ABA transitory-treatment after the seeds were transferred back on water and proceeded to germination. This proves these genes as contributors to the completion of germination and strengthen the idea that cell-wall loosening and remodeling in relation to cell expansion in the embryo axis is a determinant feature in germination. Our results also showed that ABA controls germination through the control of radicle emergence, namely by inhibiting cell-wall loosening and expansion
Published: 2009

19. Genome Annotation in Plants and Fungi: EuGene as a Model Platform

Author: Pierre Rouzé, Joelle Amselem, Stephane Rombauts, Jérôme Gouzy, Sylvain Foissac, Catherine Mathé, Yves Van de Peer, Thomas Schiex, Lieven Sterck, Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Department of plant systems biology, Flanders Institute for Biotechnology, Department of Molecular Genetics, Universiteit Gent = Ghent University [Belgium] (UGENT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité associée au Département Biologie et Amélioration des Plantes (Associée BAP), Institut National de la Recherche Agronomique (INRA), Laboratoire Associé de l'INRA, and Unité de Biométrie et Intelligence Artificielle (UBIA)
Subjects: 0106 biological sciences, GENE FINDING, Gene prediction, Computational biology, Vertebrate and Genome Annotation Project, Biology, GENOME ANNOTATION, 01 natural sciences, Biochemistry, Genome, 03 medical and health sciences, Annotation, Genetics, [INFO]Computer Science [cs], PLANT, [MATH]Mathematics [math], Molecular Biology, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Genome project, Computational Mathematics, FUNGUS, Proteome, Identification (biology), 010606 plant biology & botany
Abstract: International audience; In this era of whole genome sequencing, reliable genome annotations (identification of functional regions) are the cornerstones for many subsequent analyses. Not only is careful annotation important for studying the gene and gene family content of a genome and its host, but also for wide-scale transcriptome and proteome analyses attempting to describe a certain biological process or to get a global picture of a cell's behavior. Although the number of sequenced genomes is increasing thanks to the application of new technologies, genome-wide analyses will critically depend on the quality of the genome annotations. However, the annotation process is more complicated in the plant field than in the animal field because of the limited funding that leads to much fewer experimental data and less annotation expertise. This situation calls for highly automated annotation platforms that can make the best use of all available data, experimental or not. We discuss how the gene prediction (the process of predicting protein gene structures in genomic sequences) research field increasingly shifts from methods that typically exploited one or two types of data to more integrative approaches that simultaneously deal with various experimental, statistical, or other in silico evidence. We illustrate the importance of integrative approaches for producing high-quality automatic annotations of genomes of plants and algae as well as of fungi that live in close association with plants using the platform EuGène as an example.
Published: 2008

20. Narcisse: a mirror view of conserved syntenies

Author: Sébastien Letort, Olivier Stahl, Yoann Beausse, Emmanuel Courcelle, Jérôme Gouzy, Catherine Ngom-Bru, Romain Fremez, Thomas Faraut, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP)
Subjects: Sequence alignment, Genomics, Computational biology, Genome browser, syntenie, Biology, Genome, Synteny, DNA sequencing, Conserved sequence, 03 medical and health sciences, User-Computer Interface, 0302 clinical medicine, Genetics, Animals, Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Conserved Sequence, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Internet, Base Sequence, génome, food and beverages, Chromosome Mapping, Articles, Rats, 030220 oncology & carcinogenesis, BASE DE DONNEES NARCISSE, Databases, Nucleic Acid, Sequence Alignment, Genome, Bacterial, Genome, Plant
Abstract: International audience; New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr.
Published: 2007

21. Stat-mediated Signaling Induced by Type I and Type II Interferons (IFNs) Is Differentially Controlled through Lipid Microdomain Association and Clathrin-dependent Endocytosis of IFN Receptors

Author: Ludger Johannes, Pierre Eid, Keith Mitchell, Christophe Lamaze, Marie-Noëlle Monier, Florence Baychelier, Alexandre Fradagrada, Marta Marchetti, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut Curie [Paris], Oncologie virale (OV), and Centre National de la Recherche Scientifique (CNRS)
Subjects: Transcription, Genetic, [SDV]Life Sciences [q-bio], Active Transport, Cell Nucleus, Receptor, Interferon alpha-beta, Response Elements, stat, Interferon-gamma, 03 medical and health sciences, Membrane Microdomains, 0302 clinical medicine, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, STAT1, Receptor, Molecular Biology, Receptors, Interferon, 030304 developmental biology, 0303 health sciences, biology, Cell Membrane, Lipid microdomain, Interferon-alpha, Membrane Proteins, STAT2 Transcription Factor, Articles, Cell Biology, Receptor-mediated endocytosis, Clathrin, Endocytosis, Cell biology, Protein Transport, STAT1 Transcription Factor, [SDE]Environmental Sciences, STAT protein, biology.protein, 030217 neurology & neurosurgery
Abstract: International audience; Type I (alpha/beta) and type II (gamma) interferons (IFNs) bind to distinct receptors, although they activate the same signal transducer and activator of transcription, Stat1, raising the question of how signal specificity is maintained. Here, we have characterized the sorting of IFN receptors (IFN-Rs) at the plasma membrane and the role it plays in IFN-dependent signaling and biological activities. We show that both IFN-alpha and IFN-gamma receptors are internalized by a classical clathrin- and dynamin-dependent endocytic pathway. Although inhibition of clathrin-dependent endocytosis blocked the uptake of IFN-alpha and IFN-gamma receptors, this inhibition only affected IFN-alpha-induced Stat1 and Stat2 signaling. Furthermore, the antiviral and antiproliferative activities induced by IFN-alpha but not IFN-gamma were also affected. Finally, we show that, unlike IFN-alpha receptors, activated IFN-gamma receptors rapidly become enriched in plasma membrane lipid microdomains. We conclude that IFN-R compartmentalization at the plasma membrane, through clathrin-dependent endocytosis and lipid-based microdomains, plays a critical role in the signaling and biological responses induced by IFNs and contributes to establishing specificity within the Jak/Stat signaling pathway.
Published: 2006

22. Pea in the genomic era

Author: Alves Carvalho, Susete, Aluome, Christelle, Aubert, Gregoire, Cruaud, Corinne, Klein, Anthony, Jacquin, Françoise, Carrere, Sebastien, Brochot, Anne-Lise, Kreplak, Jonathan, Martin, Chantal, Boucherot, Karen, Da Silva, Corinne, Gamas, Pascal, Wincker, Patrick, Brunel, Dominique, Le Paslier, Marie-Christine, Gouzy, Jerome, Burstin, Judith, 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, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), 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), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2014

23. The Medicago truncatula SUNN Gene Encodes a CLV1-like Leucine-rich Repeat Receptor Kinase that Regulates Nodule Number and Root Length

Author: Fernanda de Carvalho-Niebel, Elise Schnabel, Gérard Duc, Etienne-Pascal Journet, Julia Frugoli, Clemson University, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, USDA Grant (2002-35319-12529), CREES SC-1700150 to JF, ACI Ministère de la Recherche (2001-03) (02N60/0546), INRA-SPE Grant (0441-01) (2002-03) to EPJ, and Technical Contribution No. 5054 of the Clemson University Experiment Station
Subjects: 0106 biological sciences, Mutant, Lotus japonicus, Plant Science, Leucine-rich repeat, Biology, Genes, Plant, Plant Roots, Synteny, 01 natural sciences, Gene Expression Regulation, Enzymologic, 03 medical and health sciences, SUNN, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Arabidopsis, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, GENETIQUE VEGETALE, RLP1, Gene, Phylogeny, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Nitrates, fungi, Receptor Protein-Tyrosine Kinases, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Medicago truncatula, NODULE REGULATION, Phenotype, SUPERNODULATION, Mutation, MEDICAGO TRUNCATULA, Agronomy and Crop Science, Plant Shoots, 010606 plant biology & botany
Abstract: International audience; Four Medicago truncatula sunn mutants displayed shortened roots and hypernodulation under all conditions examined. The mutants, recovered in three independent genetic screens, all contained lesions in a leucine-rich repeat (LRR) receptor kinase. Although the molecular defects among alleles varied, root length and the extent of nodulation were not significantly different between the mutants. SUNN is expressed in shoots, flowers and roots. Although previously reported grafting experiments showed that the presence of the mutated SUNN gene in roots does not confer an obvious phenotype, expression levels of SUNN mRNA were reduced in sunn-1 roots. SUNN and the previously identified genes HAR1 (Lotus japonicus) and NARK (Glycine max) are orthologs based on gene sequence and synteny between flanking sequences. Comparison of related LRR receptor kinases determined that all nodulation autoregulation genes identified to date are the closest legume relatives of AtCLV1 by sequence, yet sunn, har and nark mutants do not display the fasciated clv phenotype. The M. truncatula region is syntenic with duplicated regions of Arabidopsis chromosomes 2 and 4, none of which harbor CLV1 or any other LRR receptor kinase genes. A novel truncated copy of the SUNN gene lacking a kinase domain, RLP1, is found immediately upstream of SUNN and like SUNN is expressed at a reduced level in sunn-1 roots.
Published: 2005

24. ERECTA, an LRR receptor-like kinase protein controlling development pleiotropically affects resistance to bacterial wilt

Author: Laurent Sauviac, Olivier Grenon, Yves Marco, Keiko U. Torii, Brigitte Mangin, Laurence Godiard, Nigel Grimsley, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Agrosystèmes Cultivés et Herbagers (ARCHE), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Unité de Biométrie et Intelligence Artificielle (UBIA), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Hypersensitive response, Population, Arabidopsis, Locus (genetics), Plant Science, Biology, Plant disease resistance, 01 natural sciences, Genetic analysis, Chromosomes, Plant, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, RALSTONIA SOLANACEARUM, 03 medical and health sciences, Inbred strain, Genetics, Serotyping, education, Plant Diseases, 030304 developmental biology, 0303 health sciences, Ralstonia solanacearum, education.field_of_study, Arabidopsis Proteins, Bacterial wilt, fungi, Chromosome Mapping, food and beverages, Cell Biology, biology.organism_classification, Immunity, Innate, Protein Kinases, Genome, Plant, 010606 plant biology & botany
Abstract: Bacterial wilt, one of the most devastating bacterial diseases of plants worldwide, is caused by Ralstonia solanacearum and affects many important crop species. We show that several strains isolated from solanaceous crops in Europe are pathogenic in different accessions of Arabidopsis thaliana. One of these strains, 14.25, causes wilting symptoms in A. thaliana accession Landsberg erecta (Ler) and no apparent symptoms in accession Columbia (Col-0). Disease development and bacterial multiplication in the susceptible Ler accession depend on functional hypersensitive response and pathogenicity (hrp) genes, key elements for bacterial pathogenicity. Genetic analysis using Ler x Col-0 recombinant inbred lines showed that resistance is governed by at least three loci: QRS1 (Quantitative Resistance to R. solanacearum) and QRS2 on chromosome 2, and QRS3 on chromosome 5. These loci explain about 90% of the resistance carried by the Col-0 accession. The ERECTA gene, which encodes a leucine-rich repeat receptor-like kinase (LRR-RLK) and affects development of aerial organs, is dimorphic in our population and lies close to QRS1. Susceptible Ler plants transformed with a wild-type ERECTA gene, and the LER line showed increased disease resistance to R. solanacearum as indicated by reduced wilt symptoms and impaired bacterial growth, suggesting unexpected cross-talk between resistance and developmental pathways.
Published: 2003

25. Chronic acid exposure leads to activation of thecdx2intestinal homeobox gene in a long-term culture of mouse esophageal keratinocytes

Author: Marta Marchetti, Eric Pringault, Elise Caliot, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Institut Pasteur [Paris]
Subjects: Adult, Keratinocytes, Time Factors, [SDV]Life Sciences [q-bio], Recombinant Fusion Proteins, Green Fluorescent Proteins, Cell, Biology, Epithelium, Barrett Esophagus, Mice, Esophagus, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animals, Humans, CDX2 Transcription Factor, Promoter Regions, Genetic, CDX2, Cells, Cultured, Homeodomain Proteins, Mice, Inbred BALB C, Microscopy, Confocal, Cell growth, Intestinal metaplasia, Cell Differentiation, Cell Biology, Transfection, Hydrogen-Ion Concentration, medicine.disease, Molecular biology, Luminescent Proteins, Microscopy, Electron, medicine.anatomical_structure, Gene Expression Regulation, Cell culture, [SDE]Environmental Sciences, Trans-Activators, Homeobox, Hydrochloric Acid, Caco-2 Cells, Cell Division
Abstract: International audience; To explore mechanisms whereby Malpighian keratinocytes can transdifferentiate into an intestinal-like epithelium, as observed in the early steps of Barrett's esophagus (BE) development, long-standing cultures of esophageal keratinocytes derived from normal mouse esophageal explants were developed. These cells were able to form multilayers and to differentiate on filter support by the formation of differentiated layers of basal cells (cytokeratine 14 positive) on which secondary suprabasal cell layers (cytokeratine 4 positive) spontaneously developed. Thus, these cultured cells, referred to as P3E6, reproduced, at least in part, the proliferation and stratification pattern existing in the normal esophagus. Because chronic exposure to acid pH is known to be a critical factor for BE development, culture medium at pH 3.5 was added into the apical chamber of cell cultures. This led to a decrease in the overall number of cells but it did not affect cell proliferation. Furthermore, external acid environment triggered expression of the GFP reporter gene fused downstream of the cdx2 intestinal homeogene regulatory sequences in P3E6 transfected cells. Expression of the endogenous CDX2 protein, detected by western blot and immunocytochemical analysis, correlated with promoter activation. These findings demonstrate that chronic exposure of esophageal keratinocytes to acid pH induces transcription of cdx2, an intestinal specific homeobox gene known to play a critical role in the differentiation and maintenance of intestinal epithelial functions. The results suggest that chronic acid exposure can modify the fate of P3E6 esophageal keratinocytes towards an intestinal program. This can be a key step in the development of intestinal metaplasia often observed in esophagus-cardia junction.
Published: 2003

26. The E3 Ubiquitin Ligase PUB1 negatively regulates both nodulation and mycorrhization in Medicago truncatula

Author: Vernié, Tatiana, Camut, Sylvie, Rembliere, Celine, Thompson, Richard, Lesignor, C., Mbengue, Malick, Gasciolli, Virginie, Camps, Céline, Timmers, Ton, Lefebvre, Benoît, Gough, Clare, Cullimore, Julie Vera, Hervé, Christine, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-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), 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, ANR, and ProdInra, Migration
Subjects: [SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [INFO] Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2014

27. The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome

Author: Andreas Niebel, Damien Formey, Patrick Wincker, Julie Poulain, Christophe Roux, Laurent Gentzbittel, Christine Lelandais-Brière, Caroline Hartmann, Cécile Ben, Pilar Bustos-Sanmamed, Florian Frugier, Erika Sallet, Martin Crespi, Frédérick Gavory, Jean Combier, Frédéric Debellé, Jérôme Gouzy, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Peptides et petits ARN, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), 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), Interactions Microbiennes dans la Rhizosphère et les Racines, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, Small RNA, [SDV]Life Sciences [q-bio], Computational biology, Biology, 01 natural sciences, MiRBase, Conserved sequence, purl.org/becyt/ford/1 [https], Transcriptome, Ciencias Biológicas, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, purl.org/becyt/ford/1.6 [https], Gene, 030304 developmental biology, miRNA, 2. Zero hunger, Genetics, Regulation of gene expression, 0303 health sciences, Ecotype, 15. Life on land, Bioquímica y Biología Molecular, biology.organism_classification, Legumes, Abiotic stress, Medicago truncatula, CIENCIAS NATURALES Y EXACTAS, 010606 plant biology & botany
Abstract: Background: Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. Results: In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. Conclusions: We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops. Fil: Formey, Damien. Centre National de la Recherche Scientifique; Francia. Université de Toulouse; Francia Fil: Sallet, Erika. Institut National de la Recherche Agronomique; Francia Fil: Lelandais Brière, Christine. Université Paris Diderot - Paris 7; Francia Fil: Ben, Cécile. Université de Toulouse; Francia Fil: Bustos Sanmamed, Maria del Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentina. Université Paris Diderot - Paris 7; Francia Fil: Niebel, Andreas. Institut National de la Recherche Agronomique; Francia Fil: Frugier, Florian. Centre National de la Recherche Scientifique; Francia Fil: Combier, Jean Philippe. Centre National de la Recherche Scientifique; Francia Fil: Debellé, Frédéric. Institut National de la Recherche Agronomique; Francia Fil: Hartmann, Caroline. Université Paris Diderot - Paris 7; Francia Fil: Poulain, Julie. Commissariat A Energie Atomique; Francia Fil: Gavory, Frédérick. Commissariat A Energie Atomique; Francia Fil: Wincker, Patrick. Commissariat A Energie Atomique; Francia Fil: Roux, Christophe. Centre National de la Recherche Scientifique; Francia Fil: Gentzbittel, Laurent. Université de Toulouse; Francia Fil: Gouzy, Jérôme. Institut National de la Recherche Agronomique; Francia Fil: Crespi, Martin. Université Paris Diderot - Paris 7; Francia
Published: 2014

28. Root functional traits and their plasticity drive grasslands' Fabaceae capacities to face phosphorus shortage

Author: Florian Fort, Pablo Cruz, Olivier Catrice, Stroia Ciprian, Claire Jouany, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), University of Agricultural Sciences and Veterinary Medicine, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD). FRA., Institut de Recherche pour le Développement (IRD). FRA., and Institut National d'Etudes Supérieures Agronomiques de Montpellier (Montpellier SupAgro). FRA.
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, complex mixtures, Sciences agricoles, Agricultural sciences
Abstract: National audience; Fabaceae performances in low fertility agro systems rely on their capacity to acquire phosphorus (P) since their growth is highly limited by P shortage. Recent work conducted on grassland’s legumes demonstrated, that different roots strategies exist within fabaceae family resulting in a large range of responses to P stress. Our objective is to evaluate to what extend rhizospheric soil phosphatase activity is related to Fabaceae response to P limitation. In that purpose, we grew in a green house, 13 grassland Fabaceae species under two levels of P availability for more than 100 days. At harvest, rhizospheric soil were sampled then analysed for alkaline phospho-monoesterase activity together with bulk soil (control). Results show a significant effect of plant on species identity on rhizospheric phosphatase activity, Anthylis vulneraria and Vicia cracca induce high phosphatase activity in their rhizsospheric soil while Securigera varia and Trifolium pratense induce low phosphatase activity. There is also a significant and negative effect of P supply on phosphatase activity of rhizospheric soil. The activity measured for the bulk soil is always significantly lower than the one measured for the rhizospheric soil. It was interesting to notice that phosphatase activities measured for Fabaceae are not different from those obtained for Poaceae grown under similar conditions. We showed that Fabaceae species induce au strong increase of the phosphatase activity in their rhizospheric soil in comparison to bulk soil. However, further work is needed to understand the link between rhizospheric soil activity and P stress tolerance.
Published: 2014

29. Recent pea genomic resources will enhance complementary improvement strategies in this crop

Author: Burstin, Judith, Alves Carvalho, Susete, Tayeh, Nadim, Aluome, Christelle, Bourion, Virginie, Klein, Anthony, Carrere, Sebastien, Brochot, Anne-Lise, Salloignon, P., Siol, Mathieu, Delaitre, Catherine, Cruaud, C, Kreplak, Jonathan, Truntzer, C., Balzergue, Sandrine, Wincker, P., Le Paslier, Marie-Christine, Brunel, Dominique, Gouzy, Jerome, Lejeune-Henaut, Isabelle, Duc, Gérard, Aubert, Gregoire, 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, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB), 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), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), Institut National de la Recherche Agronomique (INRA)-Université de Lille, Sciences et Technologies, University of Saskatchewan. CAN., Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, pea genomic ressources, improvement, high density marker genotypes, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract: BAP GEAPSI BAP CT2 Événement(s) lié(s) : - 7. International Conference on Legume Genetics and Genomics (ICLGG VII); Saskatoon (CAN) - (2014-07-07 - 2014-07-11); International audience; The recent development of high-throughput sequencing and genotyping technologies has permitted pea genomics to catch up and enter into the genomic era. We will present the development of functional and structural genomic resources in pea and their application in pea breeding. We developed a pea Unigene expression atlas that allows visualization of expression profiles for any gene of interest in various tissues subjected to different conditions. This was the basis for generating a high density microarray for functional genomics and a high-throughput genotyping BeadChip array for genotyping. These tools will be extremely useful in three breeding strategies followed by the team: (i) ideotype breeding, which pursue an ideal plant model that is expected to meet the desired yield and quality requirements of producers and users; (ii) targeted breeding, which chase the good combinations of genetic factors controlling traits of interest; and (iii) genome-wide breeding, which models phenotypes from high density marker genotypes.
Published: 2014

30. Secretome analysis reveals effector candidates associated with broad host range necrotrophy in the fungal plant pathogen Sclerotinia sclerotiorum

Author: Dominique Roby, Koanna Guyon, Sylvain Raffaele, Claudine Balagué, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Marie Curie CIG grant [334036], European Research Council [336808], and French Laboratory of Excellence project 'TULIP' [ANR-10-LABX-41, ANR-11-IDEX-0002-02]
Subjects: 0106 biological sciences, effecteur, Candidate gene, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], Plant disease resistance, 01 natural sciences, Microbiology, Fungal Proteins, secrétome, 03 medical and health sciences, Sclerotinia sclerotiorum. Effectors, Ascomycota, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Sclerotinia sclerotiorum, Effectors, Gene expression, Secretome, Necrotrophic fungal, Pathogen, sclerotinia sclérotiorum, Gene, 030304 developmental biology, parasite nécrotrophe, 0303 health sciences, Fungal protein, biology, Effector, Plants, biology.organism_classification, 3. Good health, DNA microarray, agent pathogène, expression des gènes, Research Article, 010606 plant biology & botany, Biotechnology
Abstract: Background The white mold fungus Sclerotinia sclerotiorum is a devastating necrotrophic plant pathogen with a remarkably broad host range. The interaction of necrotrophs with their hosts is more complex than initially thought, and still poorly understood. Results We combined bioinformatics approaches to determine the repertoire of S. sclerotiorum effector candidates and conducted detailed sequence and expression analyses on selected candidates. We identified 486 S. sclerotiorum secreted protein genes expressed in planta, many of which have no predicted enzymatic activity and may be involved in the interaction between the fungus and its hosts. We focused on those showing (i) protein domains and motifs found in known fungal effectors, (ii) signatures of positive selection, (iii) recent gene duplication, or (iv) being S. sclerotiorum-specific. We identified 78 effector candidates based on these properties. We analyzed the expression pattern of 16 representative effector candidate genes on four host plants and revealed diverse expression patterns. Conclusions These results reveal diverse predicted functions and expression patterns in the repertoire of S. sclerotiorum effector candidates. They will facilitate the functional analysis of fungal pathogenicity determinants and should prove useful in the search for plant quantitative disease resistance components active against the white mold. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-336) contains supplementary material, which is available to authorized users.
Published: 2014

31. Regulation of plant stem cell quiescence by a brassinosteroid signaling module

Author: Norma Fàbregas, Jan U. Lohmann, Philip N. Benfey, Marta Ibañes, Josep Vilarrasa-Blasi, Konstantinos G. Alexiou, David Frigola, Alain Jauneau, Susana Rivas, Mary Paz González-García, Ana I. Caño-Delgado, Nuria Lopez-Bigas, Generalitat de Catalunya, German Research Foundation, Ministerio de Economía y Competitividad (España), Agence Nationale de la Recherche (France), Ministerio de Ciencia e Innovación (España), National Science Foundation (US), European Commission, Centre de Recerca en Agrigenòmica - Center for Research in Agricultural Genomics, Partenaires INRAE, University of Barcelona, Barcelona Biomedical Research Park (PRBB), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Heidelberg University, Duke University [Durham], FI PhD fellowship from the Generalitat de Catalunya (GC), DFG [BE1-00924, SFB873], Spanish Ministry de Economy and Competitiveness [FIS2012-37655-C02-02], GC [2009SGR14], Laboratoire d'Excellence (LABEX) TULIP [ANR-10-LABX-41], 'Juan de la Cierva' post-doctoral contract from the Spanish Ministry of Science HFSP short-term fellowship, NSF Arabidopsis grant, Spanish Ministry of Innovation and Science [BIO2010/007], and Marie-Curie Initial Training Network 'BRAVISSIMO' [PITN-GA-2008-215118, FPU-AP2009-3736]
Subjects: Cell division, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Roots, chemistry.chemical_compound, 0302 clinical medicine, Plant Growth Regulators, Gene Expression Regulation, Plant, Brassinosteroid, Stem Cell Niche, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, 0303 health sciences, Reverse Transcriptase Polymerase Chain Reaction, Stem Cells, Plants, Genetically Modified, Cell biology, Signal transduction, Stem cell, Cell Division, Signal Transduction, Plant stem cell, Chromatin Immunoprecipitation, animal structures, Blotting, Western, Enzyme-Linked Immunosorbent Assay, Biology, Real-Time Polymerase Chain Reaction, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Brassinosteroids, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Immunoprecipitation, RNA, Messenger, Molecular Biology, Transcription factor, 030304 developmental biology, Cell Proliferation, Cell growth, Arabidopsis Proteins, Gene Expression Profiling, Cell Biology, Models, Theoretical, biology.organism_classification, chemistry, Mutation, 030217 neurology & neurosurgery, Biomarkers, Developmental Biology
Abstract: Referred to by: Josep Vilarrasa-Blasi, Mary-Paz González-García, David Frigola, Norma Fàbregas-Vallvé, Konstantinos G. Alexiou, Nuria López-Bigas, Susana Rivas, Alain Jauneau, Jan U. Lohmann, Philip N. Benfey, Marta Ibañes, Ana I. Caño-Delgado Regulation of Plant Stem Cell Quiescence by a Brassinosteroid Signaling Module Developmental Cell, Volume 33, Issue 2, 20 April 2015, Pages 238., The quiescent center (QC) maintains the activity of the surrounding stem cells within the root stem cell niche, yet specific molecular players sustaining the low rate of QC cell division remain poorly understood. Here, we identified a R2R3-MYB transcription factor, BRAVO (BRASSINOSTEROIDS AT VASCULAR AND ORGANIZING CENTER), acting as a cell-specific repressor of QC divisions in the primary root of Arabidopsis. Ectopic BRAVO expression restricts overall root growth and ceases root regeneration upon damage of the stem cells, demonstrating the role of BRAVO in counteracting Brassinosteroid (BR)-mediated cell division in the QC cells. Interestingly, BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo, creating a switch that modulates QC divisions at the root stem cell niche. Together, our results define a mechanism for BR-mediated regulation of stem cell quiescence in plants., J.V.-B. and N.F.-V. are funded by FI PhD fellowship from the Generalitat de Catalunya (GC) in the A.I.C.-D. laboratory. J.V.-B. received a short-term fellowship (BE1-00924) in the Lohmann (J.U.L.) laboratory supported by the SFB873 of the DFG. Research by D.F and M.I. is funded by FIS2012-37655-C02-02 by the Spanish Ministry de Economy and Competitiveness and 2009SGR14 from GC, and D.F. has a PhD fellowship (FPU-AP2009-3736). S.R. is funded by the Laboratoire d’Excellence (LABEX) TULIP (ANR-10-LABX-41). M.-P.G.-G. received a “Juan de la Cierva” postdoctoral contract from the Spanish Ministry of Science in the Ana Caño (A.I.C.-D.) laboratory, and an HFSP short-term fellowship in the Benfey (P.N.B.) laboratory. P.N.B. is funded by NSF Arabidopsis 2010 grant. Work in the Ana Caño (A.I.C.-D.) laboratory is funded by a BIO2010/007 grant from the Spanish Ministry of Innovation and Science and a Marie-Curie Initial Training Network “BRAVISSIMO” (grant no. PITN-GA-2008-215118).
Published: 2014

32. Recherche de facteurs génétiques impliqués dans l'élaboration du rendement sous contrainte hydrique chez le tournesol Helianthus annuus par génétique d'association et analyse de liaison dans une population recombinante

Author: Cadic, Eléna, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Université Toulouse III - Paul Sabatier, Brigitte Mangin, and Patrick Vincourt
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], these, [MATH]Mathematics [math]
Abstract: La disponibilité en eau est un facteur essentiel pour le rendement des principales espèces cultivées. Le tournesol figurant parmi les espèces d'importance économique majeure est concerné par cet enjeu. L'objectif de cette thèse est d'identifier les régions génomiques permettant d'expliquer la variabilité du rendement sous contraintes hydriques. Une approche de génétique d'association a été menée sur un panel de 384 lignées cultivées et élites évalué en combinaison hybride sur un réseau expérimental de 17 environnements. L'analyse séparée de chaque environnement a permis d'identifier 157 marqueurs associés avec au moins un caractère grâce à l'utilisation d'un modèle prenant en compte la structuration du panel en deux groupes : restauratrices de fertilité et mainteneuses de stérilité mâle. Parmi ces marqueurs significatifs, 34 étaient associés avec un caractère lié à la productivité, mais ceci, le plus souvent, de manière spécifique à un environnement, soulignant ainsi l'importance de l'interaction génotype-environnement. Un modèle éco-physiologique simulant la performance de génotypes en fonction des conditions environnementales, a permis de caractériser le stress hydrique au sein du réseau. En utilisant des variétés témoins définies dans le modèle, un index de stress a été estimé pour chaque environnement. La réponse du panel à cet index a ensuite été testée en génétique d'association permettant d'identifier de nouveaux loci impliqués dans la tolérance au stress hydrique et la stabilité du rendement. Enfin, La détection de QTL à partir d'une population bi-parentale a permis de confirmer certaines zones détectées en génétique d'association et d'en découvrir de nouvelles.
Published: 2014

33. Genetic control of water use efficiency and leaf carbon isotope discrimination in sunflower (Helianthus annuus L.) subjected to two drought scenarios

Author: Thierry Lamaze, Stéphane Muños, Nicolas B. Langlade, Philippe Grieu, Afifuddin Latif Adiredjo, Olivier Navaud, Centre d'études spatiales de la biosphère (CESBIO), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National d'Études Spatiales - CNES (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut de Recherche pour le Développement - IRD (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Universitas Brawijaya (INDONESIA), and Centre d'Etudes Spatiales de la Biosphère - CESBIO (Toulouse, France)
Subjects: 0106 biological sciences, Environmental Impacts, Water resources, Leaves, Genetic Linkage, [SDV]Life Sciences [q-bio], lcsh:Medicine, Plant Science, Plant Genetics, 01 natural sciences, [SHS]Humanities and Social Sciences, Inbred strain, TRANSPIRATION EFFICIENCY, GENOTYPIC VARIATION, Biomass, ENVIRONMENT INTERACTIONS, lcsh:Science, WHOLE-PLANT, 2. Zero hunger, 0303 health sciences, education.field_of_study, Carbon Isotopes, Multidisciplinary, biology, food and beverages, Chromosome Mapping, Agriculture, Sunflower, Droughts, Phenotypes, Phenotype, Plant Physiology, [SDE]Environmental Sciences, QUANTITATIVE TRAIT LOCI, ARABIDOPSIS-THALIANA, QTL ANALYSIS, PHOTOSYNTHETIC CAPACITY, BIOMASS PRODUCTIVITY, STOMATAL CONDUCTANCE, Helianthus, Research Article, Quantitative trait loci, Genotype, DNA recombination, Population, Quantitative Trait Loci, Crops, Quantitative trait locus, Polymorphism, Single Nucleotide, Chromosomes, Plant, 03 medical and health sciences, Agricultural Production, Genetic variation, Helianthus annuus, Genetics, Inbred strains, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Water-use efficiency, education, Gene mapping, 030304 developmental biology, Crop Genetics, lcsh:R, Ecology and Environmental Sciences, Genetic Variation, Water, Biology and Life Sciences, 15. Life on land, biology.organism_classification, Crop Management, Agronomy, Plant Leaves, Plant Breeding, lcsh:Q, Biologie végétale, 010606 plant biology & botany
Abstract: International audience; High water use efficiency (WUE) can be achieved by coordination of biomass accumulation and water consumption. WUE is physiologically and genetically linked to carbon isotope discrimination (CID) in leaves of plants. A population of 148 recombinant inbred lines (RILs) of sunflower derived from a cross between XRQ and PSC8 lines was studied to identify quantitative trait loci (QTL) controlling WUE and CID, and to compare QTL associated with these traits in different drought scenarios. We conducted greenhouse experiments in 2011 and 2012 by using 100 balances which provided a daily measurement of water transpired, and we determined WUE, CID, biomass and cumulative water transpired by plants. Wide phenotypic variability, significant genotypic effects, and significant negative correlations between WUE and CID were observed in both experiments. A total of nine QTL controlling WUE and eight controlling CID were identified across the two experiments. A QTL for phenotypic response controlling WUE and CID was also significantly identified. The QTL for WUE were specific to the drought scenarios, whereas the QTL for CID were independent of the drought scenarios and could be found in all the experiments. Our results showed that the stable genomic regions controlling CID were located on the linkage groups 06 and 13 (LG06 and LG13). Three QTL for CID were co-localized with the QTL for WUE, biomass and cumulative water transpired. We found that CID and WUE are highly correlated and have common genetic control. Interestingly, the genetic control of these traits showed an interaction with the environment (between the two drought scenarios and control conditions). Our results open a way for breeding higher WUE by using CID and marker-assisted approaches and therefore help to maintain the stability of sunflower crop production.
Published: 2014

34. Genetic variability and identification of quantitative trait loci affecting plant growth and chlorophyll fluorescence parameters in the model legume Medicago truncatula under control and salt stress conditions

Author: Foroozanfar, Maryam, Exbrayat, Sarah, Gentzbittel, Laurent, BERTONI, Georges, Maury, Pierre, Naghavie, Mohamad Reza, Peyghambari, Ali, Badri, Mounavar, Ben, Cécile, Debellé, Frederic, Sarrafi, Ahmad, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), University of Tehran, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, UMR 2594, Centre National de la Recherche Scientifique (CNRS), Dynamiques Forestières dans l'Espace Rural (DYNAFOR), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Centre de Biotechnologie de Borj Cedria (CBBC), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), ANR-10-BLAN-1722,NODON -NODOFF,Nouvelles approches génétiques pour analyser le contrôle du spectre d'hôte dans la symbiose rhizobium-légumineuses(2010), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), and Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP)
Subjects: 0106 biological sciences, Ecophysiology, recombinant inbred lines, [SDV]Life Sciences [q-bio], Population, photosystem II efficiency, Plant Science, Quantitative trait locus, k+ content, 01 natural sciences, Transgressive segregation, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Genetic variation, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genetic variability, education, Chlorophyll fluorescence, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, na+ content, biology, fungi, food and beverages, biology.organism_classification, Medicago truncatula, [SDE]Environmental Sciences, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Salinity is one of the major stresses that limits crop production worldwide and affects most physiological activities in plants. In order to study the genetic control of salt stress in the model legume Medicago truncatula Gaertn., an experiment was undertaken to determine the genetic variability and to identify quantitative trait loci (QTLs) controlling several traits related to plant growth and physiology in a population of recombinant inbred lines. Shoot and root DW, relative water content, leaf area, chlorophyll content, chlorophyll fluorescence parameters, and Na+ and K+ in shoots and roots were measured. The experiment was carried out with three replications. ANOVA showed a large genetic variation and transgressive segregation for the traits studied, suggesting putative complex tolerance mechanisms. A total of 21 QTLs were detected under control conditions and 19 QTLs were identified under 100mm salt stress conditions, with three QTLs being common to both situations. The percentage of total phenotypic variance explained by the QTLs ranged from 4.6% to 23.01%. Overlapping QTLs for different traits were also observed, which enables us to discriminate independent traits from linked ones. The results should be helpful information for further functional analysis of salt tolerance in M. truncatula.
Published: 2014

35. PIRIN2 stabilizes cysteine protease XCP2 and increases susceptibility to the vascular pathogen Ralstonia solanacearum in Arabidopsis

Author: Renier A. L. van der Hoorn, Hannele Tuominen, Anja C. Hörger, Dominique Tremousaygue, Patrick Dabos, Bart P. H. J. Thomma, Nicolas Denancé, Deborah Goffner, Bo Zhang, H. Peter van Esse, Umeå University, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Max Planck Institute for Plant Breeding Research (MPIPZ), The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford [Oxford], Environnement, Santé, Sociétés (ESS), and Centre National de la Recherche Scientifique (CNRS)
Subjects: Arabidopsis thaliana, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Pseudomonas syringae, Plant Science, Verticillium, xylem, Xanthomonas campestris, Gene Knockout Techniques, Cysteine Proteases, PIRIN2, Ralstonia solanacearum, EPS-2, plants, Effector, Biochemistry and Molecular Biology, food and beverages, Cysteine protease, defense, effector, Botrytis, Disease Susceptibility, Rabbits, Proteases, disease resistance, Recombinant Fusion Proteins, phytophthora-infestans, Molecular Sequence Data, vascular pathogen, Biology, Plant disease resistance, Antibodies, Microbiology, Two-Hybrid System Techniques, Tobacco, nf-kappa-b, Genetics, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, thaliana, Amino Acid Sequence, Plant Diseases, programmed cell-death, Arabidopsis Proteins, Original Articles, Cell Biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, gene-expression, XCP2, Laboratorium voor Phytopathologie, Plant Leaves, Mutagenesis, Insertional, papain-like cysteine protease, Laboratory of Phytopathology, Biokemi och molekylärbiologi
Abstract: International audience; PIRIN (PRN) is a member of the functionally diverse cupin protein superfamily. There are four members of the Arabidopsis thaliana PRN family, but the roles of these proteins are largely unknown. Here we describe a function of the Arabidopsis PIRIN2 (PRN2) that is related to susceptibility to the bacterial plant pathogen Ralstonia solanacearum. Two prn2 mutant alleles displayed decreased disease development and bacterial growth in response to R. solanacearum infection. We elucidated the underlying molecular mechanism by analyzing PRN2 interactions with the papain-like cysteine proteases (PLCPs) XCP2, RD21A, and RD21B, all of which bound to PRN2 in yeast two-hybrid assays and in Arabidopsis protoplast co-immunoprecipitation assays. We show that XCP2 is stabilized by PRN2 through inhibition of its autolysis on the basis of PLCP activity profiling assays and enzymatic assays with recombinant protein. The stabilization of XCP2 by PRN2 was also confirmed in planta. Like prn2 mutants, an xcp2 single knockout mutant and xcp2 prn2 double knockout mutant displayed decreased susceptibility to R.solanacearum, suggesting that stabilization of XCP2 by PRN2 underlies susceptibility to R.solanacearum in Arabidopsis.
Published: 2014

36. Nod factor recognition in Medicago truncatula

Author: Bono, Jean-Jacques, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and FJ de Bruijn
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Published: 2014

37. Rapport d'étape chantier entrepôt et annuaire institutionnels pour les données de la recherche

Author: Windpouire Esther Dzale Yeumo, Lydie Soler, Sophie Aubin, Christine Boizot-Szantai, Patrice Buche, Sebastien Carrere, Stephane Dervaux, Juliette Dibie, Guinet, Nicolas N., F Hocquette, Jean-François J., Gilles Lasalle, Fabrice Legeai, Michel Passouant, Christian Pichot, Cyril Pommier, Direction de la Valorisation / Information Scientifique et Technique, Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Alimentation et sciences sociales (ALISS), Ingénierie des Agro-polymères et Technologies Émergentes (UMR IATE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), 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), Inconnu, 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, Ecologie des Forêts Méditerranéennes (URFM), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, 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)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), 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)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, 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 VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: données de la recherche, partage, chantier entrepôt et annuaire, open science, open data, service, entrepôt de données, [SDV]Life Sciences [q-bio], [SHS]Humanities and Social Sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDE]Environmental Sciences, gestion des données de la recherche, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [MATH]Mathematics [math]
Published: 2014

38. The receptor kinase impaires oomycète susceptibility1 attenuates abscisic acid responses in Arabidopsis

Author: Elsa Ribes, Sophie Hok, Jutta Ludwig-Müller, Corina Weis, Harald Keller, Ralph Hückelhoven, Yves Marco, Elodie Naessens, Mathilde Clément, Valérie Allasia, Erwin Grill, Alexandra Ammon, Ruth Eichmann, Agnès Attard, Emilie Andrio, Nicolas Ris, Franck Panabières, Xavier Barlet, Lars M. Voll, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Université de Nice Sophia-Antipolis (UNSA), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Technische Universität Dresden = Dresden University of Technology (TU Dresden), Institut National de la Recherche Agronomique (INRA)-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)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Physiology, STOMATAL APERTURE, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, 01 natural sciences, chemistry.chemical_compound, Gene Expression Regulation, Plant, Arabidopsis thaliana, TRANSCRIPTION FACTOR, Abscisic acid, 2. Zero hunger, Oomycete, Peronospora, 0303 health sciences, biology, food and beverages, Articles, Plants, Genetically Modified, Cell biology, Oomycetes, Host-Pathogen Interactions, [SDE]Environmental Sciences, Plant hormone, Signal transduction, PLANT-DEFENSE, POWDERY MILDEW FUNGUS, Signal Transduction, endocrine system, PATTERN-TRIGGERED IMMUNITY, SIGNAL-TRANSDUCTION, Germination, NECROTROPHIC PATHOGENS, macromolecular substances, BINDING PROTEIN, UBIQUITIN-LIGASE, SYRINGAE PV. TOMATO, 03 medical and health sciences, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Diseases, 030304 developmental biology, Hyaloperonospora arabidopsidis, Arabidopsis Proteins, organic chemicals, fungi, biology.organism_classification, chemistry, Mutation, Downy mildew, Protein Kinases, Abscisic Acid, 010606 plant biology & botany
Abstract: In plants, membrane-bound receptor kinases are essential for developmental processes, immune responses to pathogens and the establishment of symbiosis. We previously identified the Arabidopsis (Arabidopsis thaliana) receptor kinase IMPAIRED OOMYCETE SUSCEPTIBILITY1 (IOS1) as required for successful infection with the downy mildew pathogen Hyaloperonospora arabidopsidis. We report here that IOS1 is also required for full susceptibility of Arabidopsis to unrelated (hemi)biotrophic filamentous oomycete and fungal pathogens. Impaired susceptibility in the absence of IOS1 appeared to be independent of plant defense mechanism. Instead, we found that ios1-1 plants were hypersensitive to the plant hormone abscisic acid (ABA), displaying enhanced ABA-mediated inhibition of seed germination, root elongation, and stomatal opening. These findings suggest that IOS1 negatively regulates ABA signaling in Arabidopsis. The expression of ABA-sensitive COLD REGULATED and RESISTANCE TO DESICCATION genes was diminished in Arabidopsis during infection. This effect on ABA signaling was alleviated in the ios1-1 mutant background. Accordingly, ABA-insensitive and ABA-hypersensitive mutants were more susceptible and resistant to oomycete infection, respectively, showing that the intensity of ABA signaling affects the outcome of downy mildew disease. Taken together, our findings suggest that filamentous (hemi)biotrophs attenuate ABA signaling in Arabidopsis during the infection process and that IOS1 participates in this pathogen-mediated reprogramming of the host.
Published: 2014

39. Two-dimensional data binning for the analysis of genome architecture in filamentous plant pathogens and other eukaryotes

Author: Saunders, Diane G O, Win, Joe, Kamoun, Sophien, Raffaele, Sylvain, The Sainsbury Laboratory [Norwich] (TSL), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Genome, Virulence Factors, [SDV]Life Sciences [q-bio], Statistics as Topic, Fungi, Eukaryota, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, DNA, Intergenic, Plants
Abstract: International audience; Genome architecture often reflects an organism's lifestyle and can therefore provide insights into gene function, regulation, and adaptation. In several lineages of plant pathogenic fungi and oomycetes, characteristic repeat-rich and gene-sparse regions harbor pathogenicity-related genes such as effectors. In these pathogens, analysis of genome architecture has assisted the mining for novel candidate effector genes and investigations into patterns of gene regulation and evolution at the whole genome level. Here we describe a two-dimensional data binning method in R with a heatmap-style graphical output to facilitate analysis and visualization of whole genome architecture. The method is flexible, combining whole genome architecture heatmaps with scatter plots of the genomic environment of selected gene sets. This enables analysis of specific values associated with genes such as gene expression and sequence polymorphisms, according to genome architecture. This method enables the investigation of whole genome architecture and reveals local properties of genomic neighborhoods in a clear and concise manner.
Published: 2014

40. Appearance of membrane compromised, viable but not culturable and culturable rhizobial cells as a consequence of desiccation

Author: Vriezen, Jan A. C., De Bruijn, Frans Johannes, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Published: 2014

41. The plant pathogen Xanthomonas campestris pv. campestris exploits N-acetylglucosamine during infection

Author: Alice Boulanger, Stevie Jamet, Martine Lautier, Claudine Zischek, Sébastien Carrère, Matthieu Arlat, Pauline Rival, Emmanuelle Lauber, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: [SDV]Life Sciences [q-bio], Brassica, Peptidoglycan, Xanthomonas campestris, Microbiology, Acetylglucosamine, Xanthomonas campestris pv. campestris, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Cell Wall, Xylem, Virology, N-Acetylglucosamine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Glycoside hydrolase, Promoter Regions, Genetic, 030304 developmental biology, Plant Diseases, Plant Proteins, 2. Zero hunger, 0303 health sciences, biology, 030306 microbiology, fungi, Computational Biology, Membrane Transport Proteins, food and beverages, biology.organism_classification, QR1-502, carbohydrates (lipids), Phenotype, chemistry, Biochemistry, Mutation, Bacterial outer membrane, Bacteria, Research Article, Plasmids
Abstract: N-Acetylglucosamine (GlcNAc), the main component of chitin and a major constituent of bacterial peptidoglycan, is present only in trace amounts in plants, in contrast to the huge amount of various sugars that compose the polysaccharides of the plant cell wall. Thus, GlcNAc has not previously been considered a substrate exploited by phytopathogenic bacteria during plant infection. Xanthomonas campestris pv. campestris, the causal agent of black rot disease of Brassica plants, expresses a carbohydrate utilization system devoted to GlcNAc exploitation. In addition to genes involved in GlcNAc catabolism, this system codes for four TonB-dependent outer membrane transporters (TBDTs) and eight glycoside hydrolases. Expression of all these genes is under the control of GlcNAc. In vitro experiments showed that X. campestris pv. campestris exploits chitooligosaccharides, and there is indirect evidence that during the early stationary phase, X. campestris pv. campestris recycles bacterium-derived peptidoglycan/muropeptides. Results obtained also suggest that during plant infection and during growth in cabbage xylem sap, X. campestris pv. campestris encounters and metabolizes plant-derived GlcNAc-containing molecules. Specific TBDTs seem to be preferentially involved in the consumption of all these plant-, fungus- and bacterium-derived GlcNAc-containing molecules. This is the first evidence of GlcNAc consumption during infection by a phytopathogenic bacterium. Interestingly, N-glycans from plant N-glycosylated proteins are proposed to be substrates for glycoside hydrolases belonging to the X. campestris pv. campestris GlcNAc exploitation system. This observation extends the range of sources of GlcNAc metabolized by phytopathogenic bacteria during their life cycle., IMPORTANCE Despite the central role of N-acetylglucosamine (GlcNAc) in nature, there is no evidence that phytopathogenic bacteria metabolize this compound during plant infection. Results obtained here suggest that Xanthomonas campestris pv. campestris, the causal agent of black rot disease on Brassica, encounters and metabolizes GlcNAc in planta and in vitro. Active and specific outer membrane transporters belonging to the TonB-dependent transporters family are proposed to import GlcNAc-containing complex molecules from the host, from the bacterium, and/or from the environment, and bacterial glycoside hydrolases induced by GlcNAc participate in their degradation. Our results extend the range of sources of GlcNAc metabolized by this phytopathogenic bacterium during its life cycle to include chitooligosaccharides that could originate from fungi or insects present in the plant environment, muropeptides leached during peptidoglycan recycling and bacterial lysis, and N-glycans from plant N-glycosylated proteins present in the plant cell wall as well as in xylem sap.
Published: 2014

42. Multiple recent horizontal transfers of a large genomic region in cheese making fungi

Author: Anne-Laure Abraham, Anne Goarin, Jeanne Ropars, Maurizio Ceppi, Fabienne Malagnac, Jérôme Gouzy, Aaron Bensimon, Emmanuel Conseiller, Sandrine Lacoste, Erika Sallet, Yves Brygoo, Kevin Cheeseman, Philippe Silar, Tatiana Giraud, Robert Debuchy, Pierre Renault, Joëlle Dupont, Antoine Branca, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), 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), Laboratoire Interdisciplinaire des Energies de Demain (LIED (UMR_8236)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Univ. Paris-Sud, Université Paris-Saclay, AgroParisTech, Institut National de la Recherche Agronomique (INRA), ANR: FoodMicrobiome,ANR-08-ALIA-007-02, ANR-12-PDOC-0030,FROMA-GEN,Adaptation génomique chez les champignons du fromage (Penicillium)(2012), European Project: 309403,EC:FP7:ERC,ERC-2012-StG_20111109,GENOMEFUN(2013), Ecologie Systématique et Evolution (ESE), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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), Université Paris Diderot, Sorbonne Paris Cité, Paris, France, Université Paris Diderot - Paris 7 (UPD7), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Aigrefoin, ANR-08-ALIA-0007,FOOD-MICROBIOMES,Outils innovants pour favoriser, en toute sécurité, l'utilisation des microorganismes naturels dans l'alimentation(2008), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Giraud, Tatiana, Alimentation et industries alimentaires - Outils innovants pour favoriser, en toute sécurité, l'utilisation des microorganismes naturels dans l'alimentation - - FOOD-MICROBIOMES2008 - ANR-08-ALIA-0007 - ALIA - VALID, Retour Post-Doctorant - Adaptation génomique chez les champignons du fromage (Penicillium) - - FROMA-GEN2012 - ANR-12-PDOC-0030 - PDOC - VALID, and Genomics of adaptive divergence in Fungi - GENOMEFUN - - EC:FP7:ERC2013-03-01 - 2018-02-28 - 309403 - VALID
Subjects: Gene Transfer, Horizontal, Genomic Islands, media_common.quotation_subject, Microorganism, Applied Microbiology, [SDV]Life Sciences [q-bio], Molecular Sequence Data, General Physics and Astronomy, Biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, Competition (biology), genomic, cheese, domestication, Saccharomyces, Genomic island, Genetics, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Base sequence, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, DNA, Fungal, Gene, Molecular Biology, media_common, adaptive divergence, Multidisciplinary, region, Base Sequence, food, Fungal genetics, Penicillium, General Chemistry, biology.organism_classification, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, fungi, Food environment
Abstract: Horizontal gene transfers (HGT), i.e., the transmission of genetic material between species not directly attributable to meiotic gene exchange, have long been acknowledged as a major driver of prokaryotic evolution and is increasingly recognized as an important source of adaptation in eukaryotes. In fungi in particular, many convincing examples of HGT have been reported to confer selective advantages on the recipient fungal host, either promoting fungal pathogenicity on plants or increasing their toxicity by the acquisition of secondary metabolic clusters, resulting in adaptation to new niches and in some cases eventually even in speciation. These horizontal gene transfers involve single genes, complete metabolic pathways or even entire chromosomes. A recent study has uncovered multiple recent horizontal transfers of a 575 kb genomic island in cheese Penicillium fungi, representing ca. 2% of the Penicillium roqueforti’s genome, that may confer selective advantage in the competing cheese environment where bacteria and fungi occur. Novel phylogenomic methods are being developed, revealing massive HGT among fungi. Altogether, these recent studies indicate that HGT is a crucial mechanism of rapid adaptation, even among eukaryotes.
Published: 2014

43. RNA-Seq profile of flavescence dorée phytoplasma in grapevine

Author: Sébastien Carrère, Massimo Delledonne, Luciana Galetto, Cristina Marzachì, F. Veratti, Simona Abbà, Xavier Foissac, Sabrina Palmano, Patricia Carle, Istituto per la Protezione delle Piante (IPP), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Dipartimento di Biotecnologie, University of Verona (UNIVR), Biologie du fruit et pathologie (BFP), and Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Phytoplasma, Hypothetical proteins, Sequence assembly, RNA-Seq, Computational biology, Real-Time Polymerase Chain Reaction, Bioinformatics, Genome, Transcriptome, mollicute phytopathogène, Flavescence doree phytoplasma, Flavescence dorée phytoplasma, Bacterial Proteins, santé des plantes, Genetics, Vitis, Gene, pathologie végétale, Plant Diseases, 2. Zero hunger, bactérie phytopathogène, biology, Sequence Analysis, RNA, Group II intron, Molecular Sequence Annotation, qRT-PCR, Vitis vinifera, biology.organism_classification, Plant Leaves, RNA, Bacterial, Flavescence dorée, DNA microarray, vigne, Genome, Bacterial, Research Article, Biotechnology, Autre (Sciences du Vivant)
Abstract: The phytoplasma-borne disease flavescence dorée is still a threat to European viticulture, despite mandatory control measures and prophylaxis against the leafhopper vector. Given the economic importance of grapevine, it is essential to find alternative strategies to contain the spread, in order to possibly reduce the current use of harmful insecticides. Further studies of the pathogen, the vector and the mechanisms of phytoplasma-host interactions could improve our understanding of the disease. In this work, RNA-Seq technology followed by three de novo assembly strategies was used to provide the first comprehensive transcriptomics landscape of flavescence dorée phytoplasma (FD) infecting field-grown Vitis vinifera leaves., With an average of 8300 FD-mapped reads per library, we assembled 347 sequences, corresponding to 215 annotated genes, and identified 10 previously unannotated genes, 15 polycistronic transcripts and three genes supposedly localized in the gaps of the FD92 draft genome. Furthermore, we improved the annotation of 44 genes with the addition of 5'/3' untranslated regions. Functional classification revealed that the most expressed genes were either related to translation and protein biosynthesis or hypothetical proteins with unknown function. Some of these hypothetical proteins were predicted to be secreted, so they could be bacterial effectors with a potential role in modulating the interaction with the host plant. Interestingly, qRT-PCR validation of the RNA-Seq expression values confirmed that a group II intron represented the FD genomic region with the highest expression during grapevine infection. This mobile element may contribute to the genomic plasticity that is necessary for the phytoplasma to increase its fitness and endorse host-adaptive strategies., The RNA-Seq technology was successfully applied for the first time to analyse the FD global transcriptome profile during grapevine infection. Our results provided new insights into the transcriptional organization and gene structure of FD. This may represent the starting point for the application of high-throughput sequencing technologies to study differential expression in FD and in other phytoplasmas with an unprecedented resolution.
Published: 2014

44. Bridging physiological and evolutionary time-scales in a gene regulatory network

Author: Sandrine Arribat, Loren H. Rieseberg, Matthieu Vignes, Vân Anh Huynh-Thu, Nicolas B. Langlade, Didier Varès, Patrick Vincourt, David Rengel, Sandrine Balzergue, Pierre Geurts, Gwenaëlle Marchand, Nolan C. Kane, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Liège, Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Indiana University [Bloomington], Indiana University System-Indiana University System, Florida Museum of Natural History, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), OLEOSOL (F.U.I.), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Physiology, abscisic acid (ABA), Systems biology, [SDV]Life Sciences [q-bio], Gene regulatory network, Plant Science, drought, Biology, CLC-A chloride channel protein, Gene Expression Regulation, Plant, Helianthus annuus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulatory Networks, [INFO]Computer Science [cs], [MATH]Mathematics [math], Gene, Plant Proteins, Genetic diversity, Nitrates, Models, Genetic, Ecology, food and beverages, 15. Life on land, Biological Evolution, Phenotype, NITRATE TRANSPORTER 1.1 (NRT1.1), Droughts, network inference, Nitrate transport, Evolutionary biology, Helianthus, genetic differentiation, Adaptation, Transcriptome, Algorithms, Abscisic Acid
Abstract: International audience; Gene regulatory networks (GRNs) govern phenotypic adaptations and reflect the trade-offs between physiological responses and evolutionary adaptation that act at different time-scales. To identify patterns of molecular function and genetic diversity in GRNs, we studied the drought response of the common sunflower, Helianthus annuus, and how the underlying GRN is related to its evolution. We examined the responses of 32 423 expressed sequences to drought and to abscisic acid (ABA) and selected 145 co-expressed transcripts. We characterized their regulatory relationships in nine kinetic studies based on different hormones. From this, we inferred a GRN by meta-analyses of a Gaussian graphical model and a random forest algorithm and studied the genetic differentiation among populations (FST ) at nodes. We identified two main hubs in the network that transport nitrate in guard cells. This suggests that nitrate transport is a critical aspect of the sunflower physiological response to drought. We observed that differentiation of the network genes in elite sunflower cultivars is correlated with their position and connectivity. This systems biology approach combined molecular data at different time-scales and identified important physiological processes. At the evolutionary level, we propose that network topology could influence responses to human selection and possibly adaptation to dry environments.
Published: 2014

45. High-Quality Draft Genome Sequence of Xanthomonas alfalfae subsp. alfalfae Strain CFBP 3836

Author: Stéphanie Bolot, Armelle Darrasse, Martial Briand, Ralf Koebnik, Marie-Agnès Jacques, Mathieu Arlat, Sébastien Carrère, Tristan Boureau, Laurent D. Noël, Perrine Portier, Lionel Gagnevin, E. Charbit, 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), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)
Subjects: Comparative genomics, Whole genome sequencing, Genetics, 0303 health sciences, 030306 microbiology, [SDV]Life Sciences [q-bio], Strain (biology), fungi, food and beverages, biochemical phenomena, metabolism, and nutrition, Biology, biology.organism_classification, Medicago truncatula, 03 medical and health sciences, Xanthomonas alfalfae, [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Prokaryotes, Medicago sativa, Molecular Biology, Pathogen, H20 - Maladies des plantes, 030304 developmental biology
Abstract: We report the high-quality draft genome sequence of Xanthomonas alfalfae subsp. alfalfae strain CFBP 3836, the causal agent of bacterial leaf and stem spot in lucerne ( Medicago sativa ). Comparative genomics will help to decipher the mechanisms provoking disease and triggering the defense responses of this pathogen of the model legume Medicago truncatula .
Published: 2013

46. Ligand specificity of a high-affinity binding site for lipo-chitooligosaccharidic Nod factors in Medicago cell suspension cultures

Author: Julie V. Cullimore, Andreas Niebel, Jean-Jacques Bono, Raoul Ranjeva, Natacha Mantegazza, Sophie Drouillard, Frederic Gressent, Hugues Driguez, Eric Samain, Roberto A. Geremia, Hervé Canut, Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, nodule, Stereochemistry, [SDV]Life Sciences [q-bio], Biology, ligand, 01 natural sciences, Nod factor, site de liaison, 03 medical and health sciences, chemistry.chemical_compound, rhizobium meliloti, Glucosamine, développement de la plante, oligosaccharide, nodulation, Binding site, Sugar, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, Medicago, flore du sol, medicago varia, food and beverages, Fatty acid, Biological Sciences, Ligand (biochemistry), biology.organism_classification, Reducing sugar, Biochemistry, chemistry, récepteur, 010606 plant biology & botany
Abstract: Rhizobial lipo-chitooligosaccharides (LCOs) are signaling molecules involved in host-range recognition for the establishment of the symbiosis with leguminous plants. The major LCO of Rhizobium meliloti , the symbiont of Medicago plants contains four or five N -acetylglucosamines, O-acetylated and N-acylated with a C16:2 fatty acid on the terminal nonreducing sugar and O-sulfated on the reducing sugar. In this paper, the ligand specificity of a high-affinity binding site (Nod factor binding site 2 or NFBS2), enriched in a plasma membrane-enriched fraction of Medicago cell suspension cultures, is reported. By using chemically synthesized LCOs, the role of structural elements, important for symbiotic activities, as recognition motifs for NFBS2 was determined. The results show that the substitutions on the nonreducing sugar of the LCOs (the O -acetate group, the fatty acid, and the hydroxyl group on the C 4 of the sugar) are determinants for high-affinity binding to NFBS2. In contrast, the sulfate group, which is necessary for all biological activities on Medicago , is not discriminated by NFBS2. However, the reducing sugar of the LCO seems to interact with NFBS2, because ligand binding is affected by the reduction of the free anomeric carbon and depends on the number of N -acetyl glucosamine residues. These results suggest that the recognition of the LCOs by NFBS2 is mediated by structural elements in both the lipid and oligosaccharidic moities, but not by the sulfate group.
Published: 1999

47. A biomarker based on gene expression indicates plant water status in controlled and natural environments

Author: MARCHAND, Gwenaëlle, Mayjonade, Baptiste, Vares, Didier, Blanchet, Nicolas, Boniface, Marie-Claude, Maury, Pierre, Andrianasolo, Fety, Burger, Philippe, Debaeke, Philippe, Casadebaig, Pierre, Vincourt, Patrick, Langlade, Nicolas, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Centre Technique Interprofessionnel des Oléagineux Métropolitains (CETIOM)
Subjects: sunflower, indicator, [SDV]Life Sciences [q-bio], fungi, food and beverages, soil water content, drought, transcriptomic, Quantitative Biology - Quantitative Methods, leaf water potential, [SHS]Humanities and Social Sciences, FOS: Biological sciences, [SDE]Environmental Sciences, helianthus annuus L, soil water deficit, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ftsw, Quantitative Methods (q-bio.QM)
Abstract: Plant or soil water status are required in many scientific fields to understand plant responses to drought. Because the transcriptomic response to abiotic conditions, such as water deficit, reflects plant water status, genomic tools could be used to develop a new type of molecular biomarker. Using the sunflower (Helianthus annuus L.) as a model species to study the transcriptomic response to water deficit both in greenhouse and field conditions, we specifically identified three genes that showed an expression pattern highly correlated to plant water status as estimated by the pre-dawn leaf water potential, fraction of transpirable soil water, soil water content or fraction of total soil water in controlled conditions. We developed a generalized linear model to estimate these classical water status indicators from the expression levels of the three selected genes under controlled conditions. This estimation was independent of the four tested genotypes and the stage (pre- or post-flowering) of the plant. We further validated this gene expression biomarker under field conditions for four genotypes in three different trials, over a large range of water status, and we were able to correct their expression values for a large diurnal sampling period., Plant, Cell & Environment, 2013
Published: 2013

48. Genetic control of protein, oil and fatty acids content under partial drought stress and late sowing conditions in sunflower (Helianthus annuus)

Author: Parham Haddadi, Bahman Yazdi-Samadi, Nicolas Langlade, Mohammad Reza Naghavi, Monique Berger, Afshin Kalantari, Anne Calmon, Pierre Maury, Patrick Vincourt, Ahmad Sarrafi, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Tehran, ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), 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-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), and École nationale supérieure agronomique de Toulouse [ENSAT]
Subjects: analyse chromosomique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, acide gras, QUANTITATIVE TRAIT LOCUS, helianthus annuus, qtl, gène, food and beverages, CONTROLE GENETIQUE, Biotechnologies, SUNFLOWER, AMELIORATION DES PLANTES, SIMPLE SEQUENCE REPEATS, acide linoléique, environnement, tournesol, PROTEIN CONTENT, santé des plantes, OIL CONTENT, FATTY ACIDS, Sunflower, quantitative trait locus, simple sequence repeats, oil content, protein content, fatty acids, acide oléique
Abstract: The purpose of the present study was to map quantitative trait locus (QTLs) associated with percentage of seed protein, oil and fatty acids content under different conditions in a population of recombinant inbred lines (RILs) of sunflower. Three independent field experiments were conducted with well-, partial-irrigated and late-sowing conditions in randomized complete block design with three replications. High significant variation among genotypes is observed for the studied traits in all conditions. Several specific and non-specific QTLs for the aforementioned traits were detected. Under late-sowing condition, a specific QTL of palmitic acid content on linkage group 6 (PAC-LS.6) is located between ORS1233 and SSL66_1 markers. Common chromosomic regions are observed for percentage of seed oil and stearic acid content on linkage group 10 (PSO-PI.10 and SAC-WI.10) and 15 (PSO-PI.15 and SAC-LS.15). Overlapping occurs for QTLs of oleic and linoleic acids content on linkage groups 10, 11 and 16. Seven QTLs associated with palmitic, stearic, oleic and linoleic acids content are identified on linkage group 14. These common QTLs are linked to HPPD homologue, HuCL04260C001. Coincidence of the position for some detected QTLs and candidate genes involved in enzymatic and non-enzymatic antioxidants would be useful for the function of the respective genes in fatty acid stability.Key words: Sunflower, quantitative trait locus, simple sequence repeats, oil content, protein content, fatty acids.
Published: 2013

49. Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex

Author: Sébastien Carrère, Stéphane Genin, Nemo Peeters, Anne-Claire Cazalé, Laure Plener, Maria Anisimova, Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Department of Computer Science, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Ludwig Maximilians University of Munich, 'Laboratoire d'Excellence' (LABEX) entitled TULIP [ANR-10-LABX-41], Swiss National Science Foundation [31003A_127325], Peeters, Nemo, and Genin, Stéphane
Subjects: Species complex, Gene Transfer, Horizontal, [SDV]Life Sciences [q-bio], Genomics, Type III effector, Ralstonia solanacearum, Selection, Horizontal gene transfer, Host specificity, Evolution, Molecular, 03 medical and health sciences, Open Reading Frames, Bacterial Proteins, Phylogenetics, Terminology as Topic, Databases, Genetic, Gene Order, Genetics, sélection, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, spécificité de l'hôte, Selection, Genetic, Gene, Phylogeny, 030304 developmental biology, 2. Zero hunger, Recombination, Genetic, 0303 health sciences, Phylogenetic tree, biology, 030306 microbiology, Effector, food and beverages, Computational Biology, biology.organism_classification, effecteur type III, transfert horizontal de gènes, ralstonia, Biotechnology, Research Article
Abstract: International audience; Background: Ralstonia solanacearum is a soil-borne beta-proteobacterium that causes bacterial wilt disease in many food crops and is a major problem for agriculture in intertropical regions. R. solanacearum is a heterogeneous species, both phenotypically and genetically, and is considered as a species complex. Pathogenicity of R. solanacearum relies on the Type III secretion system that injects Type III effector (T3E) proteins into plant cells. T3E collectively perturb host cell processes and modulate plant immunity to enable bacterial infection. Results: We provide the catalogue of T3E in the R. solanacearum species complex, as well as candidates in newly sequenced strains. 94 T3E orthologous groups were defined on phylogenetic bases and ordered using a uniform nomenclature. This curated T3E catalog is available on a public website and a bioinformatic pipeline has been designed to rapidly predict T3E genes in newly sequenced strains. Systematical analyses were performed to detect lateral T3E gene transfer events and identify T3E genes under positive selection. Our analyses also pinpoint the RipF translocon proteins as major discriminating determinants among the phylogenetic lineages. Conclusions: Establishment of T3E repertoires in strains representatives of the R. solanacearum biodiversity allowed determining a set of 22 T3E present in all the strains but provided no clues on host specificity determinants. The definition of a standardized nomenclature and the optimization of predictive tools will pave the way to understanding how variation of these repertoires is correlated to the diversification of this species complex and how they contribute to the different strain pathotypes.
Published: 2013

50. ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

Author: Edward Y. Chen, Avi Ma'ayan, Christopher M. Tan, Yan Kou, Yujin E. Kim, Ihor R. Lemischka, Huilei Xu, Ruth Dannenfelser, Caroline Baroukh, Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai [New York] (MSSM), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Pluripotent Stem Cells, Systems biology, [SDV]Life Sciences [q-bio], Biology, Proteomics, computer.software_genre, General Biochemistry, Genetics and Molecular Biology, Deep sequencing, Transcriptome, 03 medical and health sciences, Mice, 0302 clinical medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animals, Humans, Cell Lineage, ComputingMilieux_MISCELLANEOUS, Embryonic Stem Cells, 030304 developmental biology, 0303 health sciences, Database, Publications, Phosphoproteomics, Embryonic stem cell, High-Throughput Screening Assays, Search Engine, Databases as Topic, 030220 oncology & carcinogenesis, [SDE]Environmental Sciences, Original Article, Stem cell, General Agricultural and Biological Sciences, computer, Chromatin immunoprecipitation, Biomarkers, Information Systems
Abstract: High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE
Published: 2013

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