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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. Morphology and anatomy of root nodules of Retama monosperma (L.)Boiss

Author: Delphine Capela, Ton Timmers, Nawel Selami, Meriem Kaid-Harche, Marie-Christine Auriac, Olivier Catrice, Laboratoire des Productions, Valorisations Végétales et Microbiennes, Université des sciences et de la Technologie d'Oran Mohamed Boudiaf [Oran] (USTO MB), 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), and French Laboratory of Excellence project 'TULIP' [ANR-10-LABX-41, ANR-11-IDEX-0002-02]
Subjects: 0106 biological sciences, Root nodule, [SDV]Life Sciences [q-bio], Soil Science, Retama, Plant Science, 01 natural sciences, Bradyrhizobium, Rhizobia, 03 medical and health sciences, Botany, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 14. Life underwater, 030304 developmental biology, 0303 health sciences, biology, Retama monosperma, Nodule (medicine), Anatomy, 15. Life on land, biology.organism_classification, Nitrogen fixation, Ultrastructure, medicine.symptom, 010606 plant biology & botany
Abstract: In spite of the importance of Retama species for dune stabilization and re-vegetation and the contribution to the bio-fertilization of semi-arid and arid ecosystems, the symbiotic interaction of Retama species with rhizobia remains largely unstudied. In this paper, we aim to provide the first detailed study on nodule morphology and anatomy of Retama monosperma. We collected nodules from coastal areas nearby Oran (Algeria) and studied in detail their anatomy and ultrastructure by light and electron microscopy. First, we confirmed the likely identity of the microsymbiont as B. retamae and found that nodules of R. monosperma belong to the genistoid type of indeterminate nodules. Infection threads, typical for most nodules of legumes, are absent in nodules of R. monosperma and bacterial spread is associated with plant cell division. The nitrogen fixation zone is homogenous with only invaded cells and a network of non-invaded cells found in many nodules, is absent. Moreover, endoreduplication does not take place in bacteroids in nodules of R. monosperma. The features observed in this study are compared to the morphology and anatomy of nodules of other legumes and the possible consequences for nodule functioning and the mode of infection during the establishment of the interaction are discussed.
Published: 2014

7. 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

8. 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

9. 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

10. Pathogenomics of the Ralstonia solanacearum Species Complex

Author: Stéphane Genin, Timothy P. Denny, 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), Dept Plant Pathol, and University of Georgia [USA]
Subjects: Species complex, Genetic Speciation, TRANSCRIPTIONAL REGULATOR, [SDV]Life Sciences [q-bio], Genomics, Plant Science, beta-proteobacteria, GLOBAL VIRULENCE REGULATOR, Genome, regulatory network, PSEUDOMONAS-SOLANACEARUM, Microbiology, 03 medical and health sciences, FRENCH-WEST-INDIES, Pathogenomics, Phylogenetics, host specificity, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulatory Networks, EFFECTOR PROTEINS, III SECRETION SYSTEM, Phylogeny, Plant Diseases, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Genetic diversity, Ralstonia solanacearum, Phylogenetic tree, biology, 030306 microbiology, BACTERIAL WILT, Genetic Variation, GENOME SEQUENCE, food and beverages, Sequence Analysis, DNA, biology.organism_classification, Biological Evolution, virulence, Genes, Bacterial, PATHOGENICITY GENES, HOST-RANGE, Genome, Bacterial, type III effector
Abstract: Ralstonia solanacearum is a major phytopathogen that attacks many crops and other plants over a broad geographical range. The extensive genetic diversity of strains responsible for the various bacterial wilt diseases has in recent years led to the concept of an R. solanacearum species complex. Genome sequencing of more than 10 strains representative of the main phylogenetic groups has broadened our knowledge of the evolution and speciation of this pathogen and led to the identification of novel virulence-associated functions. Comparative genomic analyses are now opening the way for refined functional studies. The many molecular determinants involved in pathogenicity and host-range specificity are described, and we also summarize current understanding of their roles in pathogenesis and how their expression is tightly controlled by an intricate virulence regulatory network.
Published: 2012

11. 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

12. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

Author: Claude Scarpelli, Thomas Schiex, Ghislaine Magdelenat, Michael K. Udvardi, Baifang Qin, Xinbin Dai, Jeff J. Doyle, Patrick X. Zhao, Hélène Bergès, Vagner A. Benedito, Arvind K. Bharti, Chrystel Gibelin, Dong-Hoon Jeong, Stéphane De Mita, Stephane Rombauts, Mingyi Wang, Nathalie Choisne, Simone L. Macmil, Patrick Wincker, Senjuti Sinharoy, Sylvie Samain, Christopher D. Town, Susan R. Singer, Heidrun Gundlach, Anne Berger, Jane Rogers, Kathrin Klee, Sarah Sims, Nevin D. Young, Stéphanie Fouteau, Claire Riddle, Iryna Sanders, John Gish, Limei Yang, René Geurts, Gregory D. May, Shiguo Zhou, Shweta Deshpande, David C. Schwartz, Anika Jöcker, Christine Nicholson, Ton Bisseling, Klaus F. X. Mayer, Antoine Zuber, Roxanne Denny, Chunting Lang, Carolien Franken, Douglas R. Cook, Ruihua Shi, Frédéric Debellé, Valérie Barbe, Giles E. D. Oldroyd, Foo Cheung, Lucy Matthews, Blake C. Meyers, Jeremy D. Murray, Dong-Jin Kim, Joann Mudge, Agnès Viollet, Heiko Schoof, Graham B. Wiley, Benjamin D. Rosen, Jean Dénarié, Florent Prion, Keqin Wang, Arnaud Bellec, Béatrice Segurens, Jeong Hwan Mun, Ernest F. Retzel, Sean Humphray, Andrew Farmer, D. Janine Sherrier, Lieven Sterck, Richard A. Dixon, Steven B. Cannon, Steve Kenton, Philippe Bardou, Alvaro J. González, Haibao Tang, Julie Poulain, Arnaud Couloux, Majesta O'Bleness, Pamela J. Green, Manuel Spannagl, Shelby L. Bidwell, Jixian Zhai, Asis Hallab, Anne Marie Dudez, Michael Bechner, Marina Naoumkina, James D. White, Francis Quetier, Marijke Hartog, Erin L. Monaghan, Charles Paule, Chunmei Qu, Andrew J. Severin, Céline Noirot, Fu Ying, Shaoping Lin, Ziyun Yao, Vivek Krishnakumar, Steven A. Goldstein, Axin Hua, Erika Sallet, Bing Bing Wang, Peng Zhou, Hongshing Lai, Yanbo Xing, Nicolas Samson, Jamison McCorrison, Doug White, Yi Jing, Olivier Saurat, Liping Zhou, Kevin A. T. Silverstein, Jean Weissenbach, Bruce A. Roe, Sebastian Proost, Yves Van de Peer, Xiaohong Wang, Jens Warfsmann, Jérôme Gouzy, Fares Z. Najar, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, 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), Department of Disease and Stress Biology, John Innes Centre [Norwich], Laboratory of Molecular Biology, Department of Plant Science, Wageningen University and Research [Wageningen] (WUR), Corn Insects and Crop Genetics Research Unit, USDA-ARS : Agricultural Research Service, Department of Agronomy, Purdue University [West Lafayette], Plant Biology Division, The Samuel Roberts Noble Foundation, West Virginia University, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Centre National de la Recherche Scientifique (CNRS), Rheinische Friedrich-Wilhelms-Universität Bonn, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department plant pathology, Pennsylvania State University (Penn State), Penn State System-Penn State System, University of Delaware [Newark], J. Craig Venter Institute [La Jolla, USA] (JCVI), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, National center for genome resources (NCGR), BBSRC John Innes Centre, Partenaires INRAE, Bayer Cropscience, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), College of Science [Swansea], Swansea University, University of Oklahoma (OU), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Max Planck Institute for Plant Breeding Research (MPIPZ), Wageningen University and Research Centre (WUR), Wellcome Trust, International Institute of Tropical Agriculture, Department of Plant Pathology, University of Kentucky, Rural Development Administration, Unité de Biométrie et Intelligence Artificielle (UBIA), Carleton College, Funding support to N.D.Y., C. D. T. and B. A. R. from The Noble Foundation and NSF-PGRP 0321460, 0604966, to N.D.Y., J.M. and G. D. M. from NSF-PGRP 0820005, to C. D. T. from NSF-PGRP 0821966, to F. D., G.E.D.O., R. G., K. F. X. M., T. B., J. Denarie, F. Q. and J. R. from FP6 EU project GLIP/Grain Legumes FOOD-CT-2004-506223, to G.E.D.O. and J.R. from BBSRC BBS/B/11524, to F. D. and F. Q. from ANR project SEQMEDIC 2006-01122, to R. G. from the Dutch Science Organization VIDI 864.06.007, ERA-PG FP-06.038A, to Y.V.d.P. from the Belgian Federal Science Policy Office IUAP P6/25, Fund for Scientific Research Flanders, Institute for the Promotion of Innovation by Science and Technology in Flanders and Ghent University (MRP N2N), to D. R. C. from NSF IOS-0531408, IOS-0605251, to D.J.S., B. C. M. and P.J.G. from USDA CSREES 2006-03567, and to J. Gouzy from 'Laboratoire d'Excellence' (LABEX) TULIP (ANR-10-LABX-41). We also acknowledge technical support from the University of Minnesota Supercomputer Institute and thank Y.W. Nam for a BamHI BAC library used by Genoscope, S. Park and M. Accerbi for RNA isolation, T. Paape for statistical consulting, and M. Harrison for supplying myc infected and control root tissues used to make small RNA libraries.
Subjects: 0106 biological sciences, multidisciplinary science, 01 natural sciences, Genome, genomic, flavonoid biosynthesis, Vitis, genes, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Medicago, biology, truncatula, food and beverages, Biological Evolution, Medicago truncatula, plant science, duplications, Rhizobium, Laboratory of Molecular Biology, Genome, Plant, signal-transduction, science and technology, Lotus japonicus, Molecular Sequence Data, Genomics, Synteny, tetraploidy, Article, 03 medical and health sciences, Nitrogen Fixation, Botany, evolution, expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Laboratorium voor Moleculaire Biologie, Medicago sativa, Symbiosis, 030304 developmental biology, fungi, Fabaceae, sequence, biology.organism_classification, arabidopsis, leguminosae, Soybeans, genetic, EPS, 010606 plant biology & botany
Abstract: Chantier qualité GA; International audience; Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.
Published: 2011

13. Nuclear Dynamics during Plant Innate Immunity

Author: Susana Rivas, 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), French Agence Nationale de la Recherche (grant no. ANR JC08_324792), and Laboratoire d’Excellence (LABEX) entitled TULIP (grant no. ANR–10–LABX–41)
Subjects: Pathogen detection, Nuclear Envelope, Physiology, Somatic cell, [SDV]Life Sciences [q-bio], Plant Science, Biology, Nuclear dynamics, Gene Expression Regulation, Plant, Immunity, Plant Cells, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Updates - Focus Issue, Plant Proteins, Cell Nucleus, Innate immune system, fungi, Nuclear Proteins, food and beverages, Plants, Acquired immune system, Immunity, Innate, Cell biology, Host-Pathogen Interactions, Immunology, bacteria, Transcription Factors
Abstract: Plants are sessile organisms living in an environment rich in microbes that are potentially able to cause disease. As a result, plant survival depends on the ability to couple rapid pathogen detection to an efficient defense response. In contrast to the somatic adaptive immune system of mammals
Published: 2011

14. 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

15. 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

16. 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

17. 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

18. Calcium-Dependent Protein Kinase CPK21 Functions in Abiotic Stress Response in Arabidopsis thaliana

Author: Tina Romeis, Sandra Franz, Anne-Claire Cazalé, Britta Ehlert, Joachim Kurth, Anja Liese, Free University of Berlin (FU), 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), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), DFG : FOR964, and German Ministry of Education and Science BMBF
Subjects: Osmosis, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Science, ABIOTIC / ENVIRONMENTAL STRESS, CDPK, Stress, Physiological, Arabidopsis thaliana, Kinase activity, EF-HAND, Molecular Biology, CALCIUM SIGNALING / TRANSPORT, biology, Arabidopsis Proteins, Abiotic stress, EF hand, Kinase, Effector, ARABIDOPSIS THALIANA, biology.organism_classification, Protein Structure, Tertiary, Biochemistry, Calcium, Protein Kinases
Abstract: Calcium-dependent protein kinases (CDPKs) comprise a family of plant serine/threonine protein kinases in which the calcium sensing domain and the kinase effector domain are combined within one molecule. So far, a biological function in abiotic stress signaling has only been reported for few CDPK isoforms, whereas the underlying biochemical mechanism for these CDPKs is still mainly unknown. Here, we show that CPK21 from Arabidopsis thaliana is biochemically activated in vivo in response to hyperosmotic stress. Loss-of-function seedlings of cpk21 are more tolerant to hyperosmotic stress and mutant plants show increased stress responses with respect to marker gene expression and metabolite accumulation. In transgenic Arabidopsis complementation lines in the cpk21 mutant background, in which either CPK21 wild-type, or a full-length enzyme variant carrying an amino-acid substitution were stably expressed, stress responsitivity was restored by CPK21 but not with the kinase inactive variant. The biochemical characterization of in planta synthesized and purified CPK21 protein revealed that within the calcium-binding domain, N-terminal EF1- and EF2-motifs compared to C-terminal EF3- and EF4-motifs differ in their contribution to calcium-regulated kinase activity, suggesting a crucial role for the N-terminal EF-hand pair. Our data provide evidence for CPK21 contributing in abiotic stress signaling and suggest that the N-terminal EF-hand pair is a calcium-sensing determinant controlling specificity of CPK21 function.
Published: 2011

19. Phospholipases in action during plant defense signaling

Author: Susana Rivas, Joanne Canonne, Solène Froidure-Nicolas, 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), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cell signaling, RELATION PLANTE MICROORGANISME, Plant Science, Phospholipase, Biology, Models, Biological, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, chemistry.chemical_compound, Plant immunity, Extracellular, Plant defense against herbivory, ATTAQUE PATHOGENE, AMELIORATION DES PLANTES, Phosphatidic acid, Plants, Mini-Review, Plant cell, Cell biology, chemistry, Phospholipases, Second messenger system, PLA, lipid signaling, PLC, PLD, Signal transduction, PA, Signal Transduction
Abstract: International audience; Eukaryotic organisms rely on intricate signaling networks to connect recognition of microbes with the activation of efficient defense reactions. Accumulating evidence indicates that phospholipids are more than mere structural components of biological membranes. Indeed, phospholipid-based signal transduction is widely used in plant cells to relay perception of extracellular signals. Upon perception of the invading microbe, several phospholipid hydrolyzing enzymes are activated that contribute to the establishment of an appropriate defense response. Activation of phospholipases is at the origin of the production of important defense signaling molecules, such as oxylipins and jasmonates, as well as the potent second messenger phosphatidic acid (PA), which has been shown to modulate the activity of a variety of proteins involved in defense signaling. Here, we provide an overview of recent reports describing the different plant phospholipase pathways that are activated during the establishment of plant defense reactions in response to pathogen attack.
Published: 2011

20. EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes

Author: Jérôme Gouzy, Erika Sallet, Thomas Schiex, 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), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), and ANR
Subjects: 0106 biological sciences, Statistics and Probability, Computer science, [SDV]Life Sciences [q-bio], Computational biology, Vertebrate and Genome Annotation Project, Bioinformatics, 01 natural sciences, Biochemistry, Genome, Automation, 03 medical and health sciences, Annotation, Sense (molecular biology), [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Coding region, [INFO]Computer Science [cs], [MATH]Mathematics [math], Molecular Biology, Gene, 030304 developmental biology, 0303 health sciences, Tiling array, Bacteria, Sequence Analysis, RNA, Molecular Sequence Annotation, Genomics, Pipeline (software), Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Transcription Initiation Site, Genome, Bacterial, Software, 010606 plant biology & botany
Abstract: Summary: It is now easy and increasingly usual to produce oriented RNA-Seq data as a prokaryotic genome is being sequenced. However, this information is usually just used for expression quantification. EuGene-PP is a fully automated pipeline for structural annotation of prokaryotic genomes integrating protein similarities, statistical information and any oriented expression information (RNA-Seq or tiling arrays) through a variety of file formats to produce a qualitatively enriched annotation including coding regions but also (possibly antisense) non-coding genes and transcription start sites. Availability and implementation: EuGene-PP is an open-source software based on EuGene-P integrating a Galaxy configuration. EuGene-PP can be downloaded at eugene.toulouse.inra.fr. Contact: erika.sallet@toulouse.inra.fr Supplementary information: Supplementary data are available at Bioinformatics online.
Published: 2014

21. 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

22. Expression of the Arabidopsis transcription factor AtMYB30 is post-transcriptionally regulated

Author: Solène Froidure, Dominique Roby, Susana Rivas, 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), and Centre National de la Recherche Scientifique (Bourse Docteur-Ingenieur)
Subjects: Transcription, Genetic, Physiology, RNA SILENCING, Arabidopsis, AtMYB30, Pseudomonas syringae, Plant Science, Gene Expression Regulation, Plant, RNA interference, Transcription (biology), Gene expression, POST-TRANSCRIPTIONAL REGULATION, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, TRANSCRIPTION FACTOR, Transcription factor, Post-transcriptional regulation, RELATION HOTE-PARASITE, Regulation of gene expression, Models, Genetic, biology, Arabidopsis Proteins, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Gene Expression Regulation, Developmental, Plants, Genetically Modified, biology.organism_classification, Molecular biology, RNA silencing, Seedlings, Host-Pathogen Interactions, RNA Interference, Transcription Factors
Abstract: The Arabidopsis transcription factor AtMYB30 was previously identified as a positive regulator of plant hypersensitive cell death and defence responses to inoculation with bacterial pathogens. In this study, we attempted to generate Arabidopsis transgenic lines that overexpress AtMYB30 under the control of the constitutive 35S promoter. However, no transgenic lines overexpressing AtMYB30 could be obtained, suggesting the existence of a molecular mechanism that negatively regulates AtMYB30 expression in planta. Our results suggest that RNA silencing directly mediates downregulation of AtMYB30 expression, both in young seedlings and in adult plants. In contrast, an indirect RNA silencing mechanism is responsible for the induction of AtMYB30 expression after bacterial inoculation, possibly via the degradation of a yet unknown negative regulator of its expression. These results underline the importance of RNA silencing in the regulation of the activity of transcription factors both during plant development and in response to microbes.
Published: 2010

23. Molecular traits controlling host range and adaptation to plants in Ralstonia solanacearum

Author: Stéphane Genin, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physiology, Plant Science, Biology, Microbiology, Type three secretion system, RALSTONIA SOLANACEARUM, 03 medical and health sciences, Bacterial Proteins, SOLANACEAE, INFECTION, PSEUDOMONAS SOLANACEARUM, PLANT RESISTANCE, Pathogen, Gene, Plant Diseases, 030304 developmental biology, Genetics, Mutualism (biology), 0303 health sciences, Ralstonia solanacearum, 030306 microbiology, Host (biology), Effector, SYMBIOSIS, BACTERIAL WILT, Gene Expression Regulation, Bacterial, BIOLOGIE MOLECULAIRE, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Genes, Bacterial, Host-Pathogen Interactions, Host adaptation, PATHOGENICITY, Transcription Factors
Abstract: Summary Ralstonia solanacearum is regarded as one of the world’s most important bacterial plant pathogens because of its aggressiveness, large host range, broad geographical distribution and long persistence in soil and water environments. This root pathogen is an attractive model to investigate the question of host adaptation as it exhibits a remarkably broad host range, being able to infect numerous plant species belonging to different botanical families. Several effector proteins transiting through the type III secretion system have been shown to restrict or extend specifically the host range of the bacterium. Recent investigations on the mechanisms that coordinate changes in gene expression during the passage between saprophytism and life within host tissues have allowed the identification of other molecular determinants implicated in the adaptation of R. solanacearum to its hosts and pathogenesis. Among these determinants are genes involved in chemotaxis, secondary metabolic pathways and the detoxification of various antimicrobial compounds, and genes directing the biosynthesis of phytohormones or adherence factors. The regulation of many of these genes is coordinated by the master pathogenicity regulator HrpG. These hrpG-dependent genes control major steps during the interaction with plant cells, and probably determine the ecological behaviour of the microorganism, being required for the establishment of pathogenesis or mutualism.
Published: 2010

24. The Response to Nitric Oxide of the Nitrogen-Fixing Symbiont Sinorhizobium meliloti

Author: Claude Bruand, Agnès Skapski, Eliane Meilhoc, Yvan Cam, 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), Agence Nationale de Is Recherche, and BLAN07-2_184783
Subjects: Physiology, Mutant, Biology, Nitric Oxide, Microbiology, Transcriptome, 03 medical and health sciences, Bacterial Proteins, Symbiosis, Nitrogen Fixation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, RELATION HOTE-PARASITE, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Sinorhizobium meliloti, INTERACTION PLANTE-PATHOGENE, 030306 microbiology, food and beverages, Gene Expression Regulation, Bacterial, General Medicine, biology.organism_classification, Medicago truncatula, Cell biology, Nitrogen fixation, MEDICAGO TRUNCATULA, Agronomy and Crop Science
Abstract: Nitric oxide (NO) is crucial in animal– and plant–pathogen interactions, during which it participates in host defense response and resistance. Indications for the presence of NO during the symbiotic interaction between the model legume Medicago truncatula and its symbiont Sinorhizobium meliloti have been reported but the role of NO in symbiosis is far from being elucidated. Our objective was to understand the role or roles played by NO in symbiosis. As a first step toward this goal, we analyzed the bacterial response to NO in culture, using a transcriptomic approach. We identified approximately 100 bacterial genes whose expression is upregulated in the presence of NO. Surprisingly, most of these genes are regulated by the two-component system FixLJ, known to control the majority of rhizobial genes expressed in planta in mature nodules, or the NO-dedicated regulator NnrR. Among the genes responding to NO is hmp, encoding a putative flavohemoglobin. We report that an hmp mutant displays a higher sensitivity toward NO in culture and leads to a reduced nitrogen fixation efficiency in planta. Because flavohemoglobins are known to detoxify NO in numerous bacterial species, this result is the first indication of the importance of the bacterial NO response in symbiosis.
Published: 2010

25. A Point Mutation in the Polymerase of Potato virus Y Confers Virulence Toward the Pvr4 Resistance of Pepper and a High Competitiveness Cost in Susceptible Cultivar

Author: Benoît Moury, Bérenger Janzac, Josselin Montarry, Olivier Navaud, Alain Palloix, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Génétique et Amélioration des Fruits et Légumes (GAFL), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Nonsynonymous substitution, Physiology, Molecular Sequence Data, DURABILITY, Virulence, Plant disease resistance, 01 natural sciences, PVY, Virus, Viral Proteins, 03 medical and health sciences, Plant virus, Point Mutation, DISEASE RESISTANCE, Genetic Predisposition to Disease, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Plant Diseases, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, biology, PEPPER, Potyvirus, DNA-Directed RNA Polymerases, General Medicine, POTYVIRUS, biology.organism_classification, Virology, Reverse genetics, NIb PROTEIN, Potato virus Y, POTATO VIRUS Y, Capsicum, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: To understand why the Pvr4 resistance of pepper against Potyvirus spp. remained durable in field conditions while virulent Potato virus Y (PVY) variants could be selected in the laboratory, we studied the molecular mechanisms which generated these variants and the consequences on viral fitness. Using a reverse genetics approach with an infectious cDNA clone of PVY, we found that the region coding for the NIb protein (RNA-dependent RNA polymerase) of PVY was the avirulence factor corresponding to Pvr4 and that a single nonsynonymous nucleotide substitution in that region, an adenosine to guanosine substitution at position 8,424 of the PVY genome (A8424G), was sufficient for virulence. This substitution imposed a high competitiveness cost to the virus against an avirulent PVY variant in plants devoid of Pvr4. In addition, during serial passages in susceptible pepper plants, the only observed possibility of the virulent mutant to increase its fitness was through the G8424A reversion, strengthening the high durability potential of the Pvr4 resistance. This is in accordance with the fact that the NIb protein is one of the most constrained proteins expressed by the PVY genome and, more generally, by Potyvirus spp., and with a previously developed model predicting the durability of virus resistances as a function of the evolutionary constraint applied on corresponding avirulence factors.
Published: 2010

26. 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

27. 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

28. 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

29. 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

30. In Vivo Interference with AtTCP20 Function Induces Severe Plant Growth Alterations and Deregulates the Expression of Many Genes Important for Development

Author: Patrick Dabos, Marie Christine Auriac, Alain Jauneau, Claude Bardet, Dominique Tremousaygue, Christine Hervé, Agnès Ramboer, Fabrice Lacout, 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), and Centre National de la Recherche Scientifique (CNRS)
Subjects: Transcription, Genetic, Physiology, Recombinant Fusion Proteins, Cellular differentiation, Molecular Sequence Data, Arabidopsis, Repressor, Plant Science, Biology, Genes, Plant, Plant Roots, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Gene Expression Regulation, Plant, Proliferating Cell Nuclear Antigen, Gene expression, Genetics, AtTCP20, Promoter Regions, Genetic, Transcription factor, Gene, Oligonucleotide Array Sequence Analysis, MORPHOGENESE, Base Sequence, Arabidopsis Proteins, Reverse Transcriptase Polymerase Chain Reaction, Reproducibility of Results, ARABIDOPSIS THALIANA, food and beverages, Herpes Simplex Virus Protein Vmw65, Promoter, Fusion protein, Repressor Proteins, Gene expression profiling, Protein Transport, Phenotype, Research Article, Transcription Factors
Abstract: AtTCP20 is a transcription factor belonging to the Arabidopsis (Arabidopsis thaliana) TCP-P subfamily, characterized by its capacity to bind to site II motifs (TGGGCY). Our aim was to understand the role of AtTCP20 in plant development. The expression pattern of a translational fusion of PromTCP20:CDS20∷GUS∷GFP suggested a function for AtTCP20 in several plant organs and stages of development. The role of AtTCP20 was challenged in planta by inducing expression of AtTCP20 proteins fused with either a transcriptional activator domain (VP16) or a repressor domain (EAR). Expression of both modified proteins led to severe developmental phenotypes. In-depth analysis suggested that AtTCP20 may participate in the regulation of cell expansion, cell division, and cell differentiation. Gene expression profiling in roots and hypocotyls revealed that 252 genes were down-regulated in both organs after induction of the AtTCP20∷EAR repressor gene. Site II motifs (TGGGCY) were underrepresented in their promoters. Conversely, GG(A/T)CCC sequences related to binding sites identified for TCP proteins in rice (Oryza sativa) were overrepresented, and a TCP20 fusion protein was shown to bind to these sequences in vitro. Gene ontology indicated that many targeted genes were involved in cell wall biogenesis and modification during expansion and also encoded numerous transcription factors controlling plant development. Our results are consistent with the previous proposal that AtTCP20 is involved in cell division and growth coordination. Moreover, they further suggest that AtTCP20 also contributes to cell expansion control and indicate a different involvement of this protein in plant morphogenesis depending on the organ and the developmental stage.
Published: 2008

31. A gene expression atlas of the model legumeMedicago truncatula

Author: Ji He, Andreas Niebel, Jeremy D. Murray, Tancred Frickey, Georg F. Weiller, Jerome Verdier, Hélène Zuber, Yuhong Tang, Sandra Moreau, Ivone Torres-Jerez, Maren Wandrey, Thomas Ott, Patrick X. Zhao, Stacy N. Allen, Andry Andriankaja, Michael K. Udvardi, Vagner A. Benedito, Klementina Kakar, Xinbin Dai, The Samuel Roberts Noble Foundation, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, 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, 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), Research School of Biological Sciences, and Australian National University (ANU)
Subjects: 0106 biological sciences, SEED, Gene Expression, Genomics, Plant Science, Plant Roots, 01 natural sciences, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, DEVELOPMENT, 03 medical and health sciences, Species Specificity, Nitrogen Fixation, Databases, Genetic, Botany, Genetics, Cluster Analysis, RNA, Messenger, TRANSCRIPTOME, Symbiosis, Gene, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, Regulator gene, 2. Zero hunger, 0303 health sciences, Medicago, biology, Gene Expression Profiling, Cell Biology, biology.organism_classification, Medicago truncatula, Plant Leaves, Gene expression profiling, Evolutionary biology, Root Nodules, Plant, MEDICAGO TRUNCATULA, Transcription Factor Gene, Functional genomics, NODULE, Sinorhizobium meliloti, 010606 plant biology & botany
Abstract: International audience; Legumes played central roles in the development of agriculture and civilization, and today account for approximately one-third of the world's primary crop production. Unfortunately, most cultivated legumes are poor model systems for genomic research. Therefore, Medicago truncatula, which has a relatively small diploid genome, has been adopted as a model species for legume genomics. To enhance its value as a model, we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, with special emphasis on nodule and seed development. The atlas reveals massive differences in gene expression between organs that are accompanied by changes in the expression of key regulatory genes, such as transcription factor genes, which presumably orchestrate genetic reprogramming during development and differentiation. Interestingly, many legume-specific genes are preferentially expressed in nitrogen-fixing nodules, indicating that evolution endowed them with special roles in this unique and important organ. Comparative transcriptome analysis of Medicago versus Arabidopsis revealed significant divergence in developmental expression profiles of orthologous genes, which indicates that phylogenetic analysis alone is insufficient to predict the function of orthologs in different species. The data presented here represent an unparalleled resource for legume functional genomics, which will accelerate discoveries in legume biology.
Published: 2008

32. 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

33. Cultivation-Independent Characterization of Methylobacterium Populations in the Plant Phyllosphere by Automated Ribosomal Intergenic Spacer Analysis

Author: Lisa Frances, Franck Cantet, Julia A. Vorholt, Claudia Knief, 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), and Institute of Microbiology
Subjects: Sequence analysis, Ribosomal Intergenic Spacer analysis, Molecular Sequence Data, DNA, Ribosomal, Plant Roots, Applied Microbiology and Biotechnology, Microbial Ecology, 23S ribosomal RNA, RNA, Ribosomal, 16S, DNA, Ribosomal Spacer, Botany, Soil Microbiology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, biology, Genes, rRNA, Sequence Analysis, DNA, Ribosomal RNA, biology.organism_classification, 16S ribosomal RNA, RNA, Ribosomal, 23S, Methylobacterium, bacteria, Phyllosphere, Soil microbiology, Food Science, Biotechnology
Abstract: Bacteria of the genus Methylobacterium are widespread in the environment, but their ecological role in ecosystems, such as the plant phyllosphere, is not very well understood. To gain better insight into the distribution of different Methylobacterium species in diverse ecosystems, a rapid and specific cultivation-independent method for detection of these organisms and analysis of their community structure is needed. Therefore, 16S rRNA gene-targeted primers specific for this genus were designed and evaluated. These primers were used in PCR in combination with a reverse primer that binds to the tRNA Ala gene, which is located upstream of the 23S rRNA gene in the 16S-23S intergenic spacer (IGS). PCR products that were of different lengths were obtained due to the length heterogeneity of the IGS of different Methylobacterium species. This length variation allowed generation of fingerprints of Methylobacterium communities in environmental samples by automated ribosomal intergenic spacer analysis. The Methylobacterium communities on leaves of different plant species in a natural field were compared using this method. The new method allows rapid comparisons of Methylobacterium communities and is thus a useful tool to study Methylobacterium communities in different ecosystems.
Published: 2008

34. 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

35. 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

36. Functional mapping in pea, as an aid to the candidate gene selection and for investigating synteny with the model legume Medicago truncatula

Author: A. Petit, Julie Morin, Marie-Christine Quillet, Judith Burstin, Isabelle Lejeune-Hénaut, Françoise Jacquin, Thierry Huguet, Grégoire Aubert, Catherine Rameau, K. Loridon, 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, Domaine Brunehaut, Institut National de la Recherche Agronomique (INRA), Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), Institut National de la Recherche Agronomique (INRA)-Université de Lille, Sciences et Technologies, Unité de recherche Génétique et amélioration des plantes (GAP), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genetic Markers, 0106 biological sciences, Candidate gene, DNA, Plant, Genotype, Positional cloning, Genetic Linkage, Transposon tagging, Single-nucleotide polymorphism, Flowers, QTLS, CARTOGRAPHIE GENETIQUE, Genes, Plant, Models, Biological, Polymorphism, Single Nucleotide, Synteny, 01 natural sciences, Chromosomes, Plant, 03 medical and health sciences, Gene mapping, Databases, Genetic, Medicago truncatula, Genetics, Selection, Genetic, GENETIQUE VEGETALE, Gene, Polymorphism, Single-Stranded Conformational, 030304 developmental biology, 2. Zero hunger, QUANTITATIVE TRAIT LOCI, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, biology, Peas, Chromosome Mapping, food and beverages, General Medicine, biology.organism_classification, Agronomy and Crop Science, Microsatellite Repeats, 010606 plant biology & botany, Biotechnology
Abstract: Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; The identification of the molecular polymorphisms giving rise to phenotypic trait variability—both quantitative and qualitative—is a major goal of the present agronomic research. Various approaches such as positional cloning or transposon tagging, as well as the candidate gene strategy have been used to discover the genes underlying this variation in plants. The construction of functional maps, i.e. composed of genes of known function, is an important component of the candidate gene approach. In the present paper we report the development of 63 single nucleotide polymorphism markers and 15 single-stranded conformation polymorphism markers for genes encoding enzymes mainly involved in primary metabolism, and their genetic mapping on a composite map using two pea recombinant inbred line populations. The complete genetic map covers 1,458 cM and comprises 363 loci, including a total of 111 gene-anchored markers: 77 gene-anchored markers described in this study, 7 microsatellites located in gene sequences, 16 flowering time genes, the Tri gene, 5 morphological markers, and 5 other genes. The mean spacing between adjacent markers is 4 cM and 90% of the markers are closer than 10 cM to their neighbours. We also report the genetic mapping of 21 of these genes in Medicago truncatula and add 41 new links between the pea and M. truncatula maps. We discuss the use of this new composite functional map for future candidate gene approaches in pea.
Published: 2006

37. 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

38. Breeding for resistances to Ralstonia solanacearum

Author: GaÃ«lle Huet, 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), Agence Nationale pour la Recherche [ANR-10-JCIC-1706], and Laboratoire d'Excellence (LABEX) 'TULIP' [ANR-10-LABX-41, ANR-11-IDEX-0002-02]
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], mécanisme de résistance, Resistance, Plant Immunity, Virulence, Plant Science, Breeding, lcsh:Plant culture, 01 natural sciences, Ralstonia solanacearum, control, resistance, breeding, effector, Type three secretion system, Crop, Mini Review Article, 03 medical and health sciences, Control, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Pathogen, 030304 developmental biology, 2. Zero hunger, virulence bactérienne, bactérie phytopathogène, 0303 health sciences, biology, Effector, business.industry, résistance quantitative, Bacterial wilt, fungi, food and beverages, système de sécrétion de type iii, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Biotechnology, facteur de virulence, pseudomonas solanacearum, effecteur type III, business, 010606 plant biology & botany
Abstract: International audience; Ralstonia solanacearum is one of the most devastating bacterial plant pathogens due to its large host range, worldwide geographic distribution and persistence in fields.This soilborne pathogen is the causal agent of bacterial wilt and it can infect major agricultural crops thereby reducing significantly their yield. To favor infection, the bacterium delivers, through the type three secretion system, effectors that manipulate plant immunity. In this review, the relative efficiency of control strategies and existing resistances to R. solanacearum will be presented. Then, the genetic and molecular insights gained from the study of bacterial wilt in model plants will be described. Finally, I will explore how the knowledge gathered from unraveling avirulence and virulence mechanisms of R. solanacearum effectors could help to develop more durable resistances in crop plants toward this destructive pathogen.
Published: 2014

39. 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

40. Probing the Hydrophobic Cavity of Lipid Transfer Protein from Nicotiana tabacum through Xenon-Based NMR Spectroscopy

Author: Patrick Berthault, Lionel Dubois, Céline Landon, Françoise Vovelle, J. Gaspard Huber, Hervé Desvaux, Pedro Da Silva, Michel Ponchet, Département de Recherche sur l'Etat Condensé, les Atomes et les Molécules (DRECAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 'Interactions Plantes-Microorganismes et Santé Végétale' (U.M.R. - I.P.M.S.V.), Institut National de la Recherche Agronomique (INRA), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: Models, Molecular, inorganic chemicals, Xenon, [SDV]Life Sciences [q-bio], Analytical chemistry, chemistry.chemical_element, 010402 general chemistry, 01 natural sciences, Biochemistry, Catalysis, Colloid and Surface Chemistry, Chemical affinity, Tobacco, Isotopes of xenon, Molecule, Computer Simulation, cardiovascular diseases, Nuclear Magnetic Resonance, Biomolecular, Plant Proteins, integumentary system, 010405 organic chemistry, Chemical shift, Noble gas, General Chemistry, Nuclear magnetic resonance spectroscopy, Antigens, Plant, Binding constant, 0104 chemical sciences, Solutions, Kinetics, Crystallography, chemistry, Thermodynamics, Carrier Proteins, Hydrophobic and Hydrophilic Interactions, circulatory and respiratory physiology
Abstract: The hydrophobic cavity of Lipid Transfer Protein 1 from Nicotiana tabacum is investigated in detail by NMR using xenon as a spy. The analysis of the (129)Xe chemical shifts and self-relaxation times gives evidence of protein-xenon interaction. Thermodynamics of the binding is characterized through the study of aliphatic (1)H and (13)C chemical shift variation as a function of xenon pressure. The binding constant is evaluated to 75.5 +/- 1.0 M(-1) at 293 K. The location of xenon inside the cavity is deduced from SPINOE experiments. The noble gas appears to occupy four sites, and xenon self-relaxation experiments indicate that it quickly jumps between different sites. The chemical shifts of amide protons and nitrogens also depend on the xenon concentration, either specifically or nonspecifically for atoms at the external surface of the protein. Yet, contrary to aliphatic atoms, they do not correspond to short-range interactions as confirmed by magnetization transfer experiments between laser-polarized xenon and protons in H(2)O. These (15)N chemical shift variations, used in combination with (15)N transverse self-relaxation rates to determine the lower limit of the binding rate, consequently reveal subtle changes in the structure of the protein upon binding.
Published: 2004

41. Distribution and Sequence Analysis of a Family of Type III-Dependent Effectors Correlate with the Phylogeny of Ralstonia solanacearum Strains

Author: Muriel Lavie, Christian Boucher, Benjamin Seunes, Philippe Prior, 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), Unité de Pathologie Végétale (PV), and Institut National de la Recherche Agronomique (INRA)
Subjects: Phytopathology and phytopharmacy, Physiology, Sequence analysis, Virologie, Genome, plante ornementale, Evolution, Molecular, 03 medical and health sciences, pcr, Phylogenetics, Gene Duplication, Virology, génome bactérien, phylogénie, petunia, évolution, intéraction génotype environnement, Insertion sequence, Gene, Alleles, Phylogeny, 030304 developmental biology, bactérie phytopathogène, Genetics, Whole genome sequencing, 0303 health sciences, Ralstonia solanacearum, biology, 030306 microbiology, Genetic Variation, General Medicine, séquence nucléotidique, biology.organism_classification, Phytopathologie et phytopharmacie, Pathogenicity island, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, arabidopsis, Genes, Bacterial, Multigene Family, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, interaction plante bactérie, Sequence Analysis, Agronomy and Crop Science
Abstract: International audience; In Ralstonia solanacearum, we previously have reported on the characterization of popP1 and popP2 genes. These genes encode type III-dependent pathogenicity effectors related to the large family of AvrRxv/YopJ cysteine prote-ases that are shared among pathogens of plants and animals. In this study, we identify a third gene, named popP3, that is inactivated in the genome sequence of strain GMI1000 by insertion of a copy of the insertion sequence ISRso13. The three popP genes are localized on two large chromosomal pathogenicity islands, with popP1 and popP2 being present on the same island. Phylogenic analysis demonstrated that the PopP2 and PopP3 proteins are clearly distinct from other effectors of this family previously characterized in plant and animal pathogens. Analysis of the distribution and allelic variations of the three genes in 30 strains representative of the biodiversity of R. solanacearum established that popP genes are distributed widely among strains from two of the three phyla previously defined on the basis of the structure of the core genome. Sequencing of the popP genes from the different strains revealed limited allelic variations at the three loci but did not show evidence of recombination between the popP genes. Limited allelic variation together with occurrence of insertion sequences within or in the close vicinity of popP genes and the presence of gene duplications in these pathogenicity islands suggest that genomic rearrangements might be a major evolutionary driving force controlling evolution of the genes encoded in these regions. The implications of these observations in terms of bacterial evolution, gene acquisition, and horizontal gene transfers are discussed.
Published: 2004

42. Global Changes in Gene Expression in Sinorhizobium meliloti 1021 under Microoxic and Symbiotic Conditions

Author: Anne Francez-Charlot, Joëlle Fourment, Claude Bruand, Hélène Bergès, Frédéric Ampe, Anke Becker, Jacques Batut, Emmanuelle Lauber, Stefan Weidner, Elizaveta Krol, Silvia Rüberg, Alfred Pühler, Frans J. de Bruijn, Helge Küster, Daniel Kahn, Delphine Capela, Eliane Meilhoc, Carine Liebe, 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), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], root nodule, Rhizobiaceae, Root nodule, Proteome, Transcription, Genetic, Physiology, Adaptation, Biological, Protein Array Analysis, Microbiology, Transcriptome, 03 medical and health sciences, Nitrogen Fixation, Gene expression, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Symbiosis, Gene, Phylogeny, 030304 developmental biology, 0303 health sciences, Sinorhizobium meliloti, biology, 030306 microbiology, Gene Expression Profiling, food and beverages, macroarray, Gene Expression Regulation, Bacterial, General Medicine, GENETIQUE, BASE DE DONNEES, biology.organism_classification, Cell biology, Oxygen, Gene expression profiling, PHYSIOLOGIE, DNA microarray, Agronomy and Crop Science, CONDITION SYMBIOTIQUE
Abstract: Sinorhizobium meliloti is an α-proteobacterium that alternates between a free-living phase in bulk soil or in the rhizosphere of plants and a symbiotic phase within the host plant cells, where the bacteria ultimately differentiate into nitrogen-fixing organelle-like cells, called bacteroids. As a step toward understanding the physiology of S. meliloti in its free-living and symbiotic forms and the transition between the two, gene expression profiles were determined under two sets of biological conditions: growth under oxic versus microoxic conditions, and in free-living versus symbiotic state. Data acquisition was based on both macro- and microarrays. Transcriptome profiles highlighted a profound modification of gene expression during bacteroid differentiation, with 16% of genes being altered. The data are consistent with an overall slow down of bacteroid metabolism during adaptation to symbiotic life and acquisition of nitrogen fixation capability. A large number of genes of unknown function, including potential regulators, that may play a role in symbiosis were identified. Transcriptome profiling in response to oxygen limitation indicated that up to 5% of the genes were oxygen regulated. However, the microoxic and bacteroid transcriptomes only partially overlap, implying that oxygen contributes to a limited extent to the control of symbiotic gene expression.
Published: 2004

43. 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

44. 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

45. Shoot control of root development and nodulation is mediated by a receptor-like kinase

Author: Lene Krusell, Lene H. Madsen, Krzysztof Szczyglowski, Jens Stougaard, Takakazu Kaneko, Eloísa Pajuelo, Grégoire Aubert, Niels Sandal, Satoshi Tabata, Gérard Duc, Shusei Sato, Frans J. de Bruijn, Aratz Genua, 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, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Root nodule, Molecular Sequence Data, Lotus japonicus, Organogenesis, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Protein Serine-Threonine Kinases, Genes, Plant, Plant Roots, 01 natural sciences, Rhizobia, 03 medical and health sciences, Symbiosis, Nitrogen Fixation, Botany, Amino Acid Sequence, Cloning, Molecular, ComputingMilieux_MISCELLANEOUS, Alleles, 030304 developmental biology, Feedback, Physiological, 0303 health sciences, Multidisciplinary, biology, Gene Expression Profiling, Plant Root Nodulation, Peas, food and beverages, biology.organism_classification, Protein Structure, Tertiary, Cell biology, Mutation, Lotus, Nitrogen fixation, Rhizobium, Plant Shoots, CONTROLE DE MALADIES, 010606 plant biology & botany
Abstract: In legumes, root nodule organogenesis is activated in response to morphogenic lipochitin oligosaccharides that are synthesized by bacteria, commonly known as rhizobia. Successful symbiotic interaction results in the formation of highly specialized organs called root nodules, which provide a unique environment for symbiotic nitrogen fixation. In wild-type plants the number of nodules is regulated by a signalling mechanism integrating environmental and developmental cues to arrest most rhizobial infections within the susceptible zone of the root. Furthermore, a feedback mechanism controls the temporal and spatial susceptibility to infection of the root system. This mechanism is referred to as autoregulation of nodulation, as earlier nodulation events inhibit nodulation of younger root tissues. Lotus japonicus plants homozygous for a mutation in the hypernodulation aberrant root (har1) locus escape this regulation and form an excessive number of nodules. Here we report the molecular cloning and expression analysis of the HAR1 gene and the pea orthologue, Pisum sativum, SYM29. HAR1 encodes a putative serine/threonine receptor kinase, which is required for shoot-controlled regulation of root growth, nodule number, and for nitrate sensitivity of symbiotic development.
Published: 2002

46. High-Affinity Nod Factor Binding Site from Phaseolus vulgaris Cell Suspension Cultures

Author: Julie V. Cullimore, Hugues Driguez, Jean-Jacques Bono, Natacha Mantegazza, Raoul Ranjeva, Frederic Gressent, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Centre de Recherches sur les Macromolecules Vegetales, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Lipopolysaccharides, Rhizobiaceae, Physiology, [SDV]Life Sciences [q-bio], Microsomes/metabolism, Nod, Phaseolus/cytology/*metabolism, Microbiology, Rhizobia, Nod factor, Microsomes, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Support, Non-U.S. Gov't, Binding site, Cells, Cultured, Phaseolus, Sinorhizobium meliloti, Binding Sites, Medicago, biology, food and beverages, General Medicine, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Biochemistry, [SDE]Environmental Sciences, Agronomy and Crop Science
Abstract: 0894-0282 Journal Article; International audience; The lipo-chitooligosaccharidic Nod factors produced by rhizobia are key molecules in the establishment of symbiosis with legumes and probably are recognized by the host plant via specific receptors. Here, we report on the presence of a binding site in cell cultures of Phaseolus vulgaris displaying a high affinity for Nod factors from Rhizobium tropici (NodRt-V) (Me, S, C18:1), a symbiont of this legume. The binding site shares common properties with NFBS2, a Nod-factor binding site previously characterised in Medicago varia, in terms of affinity, preferential plasma-membrane location, and sensitivity to proteases and lysine reactive reagents. However, the bean site poorly recognizes the Nod factors produced by Sinorhizobium meliloti, the symbiont of Medicago. The study of selectivity toward the Nod factors reveals that the length and degree of unsaturation of the acyl chain and the length of the oligosaccharidic moiety are important determinants of high affinity binding to the bean site; whereas, the N-methyl and O-sulfuryl groups play a minor role. Thus, the common characteristics of P. vulgaris and M. varia Nod-factor binding sites suggest that they probably correspond to structurally related proteins, but their different selectivity suggests that they may be involved in a differential perception system for Nod factors in legumes.
Published: 2002

47. 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

48. Two CCAAT-box-binding transcription factors redundantly regulate early steps of the legume-rhizobia endosymbiosis

Author: Benjamin Billault-Penneteau, Andreas Niebel, Marion R. Cerri, Tom Laloum, Maël Baudin, Pascal Gamas, Agnes Lepage, Lisa Frances, Federico Ariel, Marie-Françoise Jardinaud, Fernanda de Carvalho-Niebel, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-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), École nationale supérieure agronomique de Toulouse [ENSAT], French Ministry of Education and Research, INRA CJS (Contrat Jeune Scientifique) contract, European Molecular Biology Organization (EMBO), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-09-BLAN-0033,HAPIHUB(2009), ANR-08-GENM-0015,SYMbiMICS,Dissection moléculaire de l'interaction symbiotique rhizobium-légumineuse : une approche combinée de micro-dissection laser et de séquençage massif d?ESTs(2008), 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), Faculty of Biology, Adam Mickiewicz University in Poznań (UAM), Ludwig Maximilians University of Munich, UPR2355 Institut des sciences du végétal, and Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], CAAT box, Gene Expression, Plant Science, Plant Roots, Rhizobia, Nod factor, Transactivation, Gene Expression Regulation, Plant, Genes, Reporter, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Tobacco, Botany, Medicago truncatula, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nuclear factor Y, Symbiosis, Transcription factor, Gene, transcription factor, Plant Proteins, Nod factor signaling, biology, Endosymbiosis, Sequence Analysis, RNA, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Cell biology, legume-rhizobium symbiosis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, CCAAT-Binding Factor, RNA, Plant, CCAAT box-binding factor, Root Nodules, Plant, Microdissection, Signal Transduction, Sinorhizobium meliloti, Transcription Factors
Abstract: International audience; During endosymbiotic interactions between legume plants and nitrogen-fixing rhizobia, successful root infection by bacteria and nodule organogenesis requires the perception and transduction of bacterial lipo-chitooligosaccharidic signal called Nod factor (NF). NF perception in legume roots leads to the activation of an early signaling pathway and of a set of symbiotic genes which is controlled by specific early transcription factors (TFs) including CYCLOPS/IPD3, NSP1, NSP2, ERN1 and NIN. In this study, we bring convincing evidence that the Medicago truncatula CCAAT-box-binding NF-YA1 TF, previously associated with later stages of rhizobial infection and nodule meristem formation is, together with its closest homolog NF-YA2, also an essential positive regulator of the NF-signaling pathway. Here we show that NF-YA1 and NF-YA2 are both expressed in epidermal cells responding to NFs and their knock-down by reverse genetic approaches severely affects the NF-induced expression of symbiotic genes and rhizobial infection. Further over-expression, transactivation and ChIP-PCR approaches indicate that NF-YA1 and NF-YA2 function, at least in part, via the direct activation of ERN1. We thus propose a model in which NF-YA1 and NF-YA2 appear as early symbiotic regulators acting downstream of DMI3 and NIN and possibly within the same regulatory complexes as NSP1/2 to directly activate the expression of ERN1.
Published: 2014

49. Shaping Bacterial Symbiosis With Legumes by Experimental Evolution

Author: Philippe Remigi, Marta Marchetti, Alain Jauneau, Catherine Masson-Boivin, Delphine Capela, Carine Gris, Jacques Batut, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 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), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Centre National de la Recherche Scientifique (CNRS)
Subjects: COMPARATIVE GENOMICS, Mimosa, Physiology, [SDV]Life Sciences [q-bio], Plant Root Nodulation, Plant Roots, Rhizobia, Symbiosis, Nitrogen Fixation, Botany, INFECTION, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Immunity, ADAPTATION, Gene, Experimental evolution, Ralstonia solanacearum, HOST SANCTIONS, biology, Cupriavidus taiwanensis, FIX NITROGEN, Cupriavidus, fungi, RHIZOBIA, food and beverages, General Medicine, RALSTONIA-SOLANACEARUM, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Leghemoglobin, Phenotype, Horizontal gene transfer, ARABIDOPSIS-THALIANA, Rhizobium, bacteria, REACTIVE OXYGEN, Directed Molecular Evolution, NITROGEN-FIXATION, Reactive Oxygen Species, Agronomy and Crop Science, Plasmids
Abstract: Nitrogen-fixing symbionts of legumes have appeared after the emergence of legumes on earth, approximately 70 to 130 million years ago. Since then, symbiotic proficiency has spread to distant genera of α- and β-proteobacteria, via horizontal transfer of essential symbiotic genes and subsequent recipient genome remodeling under plant selection pressure. To tentatively replay rhizobium evolution in laboratory conditions, we previously transferred the symbiotic plasmid of the Mimosa symbiont Cupriavidus taiwanensis in the plant pathogen Ralstonia solanacearum, and selected spontaneous nodulating variants of the chimeric Ralstonia sp. using Mimosa pudica as a trap. Here, we pursued the evolution experiment by submitting two of the rhizobial drafts to serial ex planta–in planta (M. pudica) passages that may mimic alternating of saprophytic and symbiotic lives of rhizobia. Phenotyping 16 cycle-evolved clones showed strong and parallel evolution of several symbiotic traits (i.e., nodulation competitiveness, intracellular infection, and bacteroid persistence). Simultaneously, plant defense reactions decreased within nodules, suggesting that the expression of symbiotic competence requires the capacity to limit plant immunity. Nitrogen fixation was not acquired in the frame of this evolutionarily short experiment, likely due to the still poor persistence of final clones within nodules compared with the reference rhizobium C. taiwanensis. Our results highlight the potential of experimental evolution in improving symbiotic proficiency and for the elucidation of relationship between symbiotic capacities and elicitation of immune responses.
Published: 2014

50. 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

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371 results on '"Unité mixte de recherche interactions plantes-microorganismes"'

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