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393 results on '"Laboratoire de Recherche en Sciences Végétales (LRSV)"'

1. Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition

Author: Houssein Zhour, Fabrice Bray, Israa Dandache, Guillaume Marti, Stéphanie Flament, Amélie Perez, Maëlle Lis, Llorenç Cabrera-Bosquet, Thibaut Perez, Cécile Fizames, Ezekiel Baudoin, Ikram Madani, Loubna El Zein, Anne-Aliénor Véry, Christian Rolando, Hervé Sentenac, Ali Chokr, Jean-Benoît Peltier, Bray, Fabrice, Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Faculty of Sciences [Lebanese University] | Faculté des Sciences [Université Libanaise], Lebanese University [Beirut] (LU), Miniaturisation pour la Synthèse, l’Analyse et la Protéomique - UAR 3290 (MSAP), Université de Lille-Centre National de la Recherche Scientifique (CNRS), MetaToul Agromix, MetaboHUB-MetaToul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: plant–microbiome communication, Organic Chemistry, diazotroph, durum wheat, PGPR, bacterial exudate, metabolomics, proteomics, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Catalysis, Computer Science Applications, Inorganic Chemistry, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.
Published: 2022

2. Transition to ripening in tomato requires hormone-controlled genetic reprogramming initiated in gel tissue

Author: Ximena, Chirinos, Shiyu, Ying, Maria Aurineide, Rodrigues, Elie, Maza, Anis, Djari, Guojian, Hu, Mingchun, Liu, Eduardo, Purgatto, Sylvie, Fournier, Farid, Regad, Mondher, Bouzayen, Julien, Pirrello, Génomique et Biotechnologie des Fruits, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Sichuan University [Chengdu] (SCU), Universidade de São Paulo = University of São Paulo (USP), MetaToul Agromix, MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and European Project: 679796,H2020,H2020-SFS-2015-2,TomGEM(2016)
Subjects: [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract: International audience; Ripening is the last stage of the developmental program in fleshy fruits. During this phase, fruits become edible and acquire their unique sensory qualities and post-harvest potential. Although our knowledge of the mechanisms that regulate fruit ripening has improved considerably over the past decades, the processes that trigger the transition to ripening remain poorly deciphered. While transcriptomic profiling of tomato (Solanum lycopersicum L.) fruit ripening to date has mainly focused on the changes occurring in pericarp tissues between the Mature Green and Breaker stages, our study addresses the changes between the Early Mature Green and Late Mature Green stages in the gel and pericarp separately. The data showed that the shift from an inability to initiate ripening to the capacity to undergo full ripening requires extensive transcriptomic reprogramming that takes place first in the locular tissues before extending to the pericarp. Genome-wide transcriptomic profiling revealed the wide diversity of transcription factor (TF) families engaged in the global reprogramming of gene expression and identified those specifically regulated at the Mature Green stage in the gel but not in the pericarp, thereby providing potential targets toward deciphering the initial factors and events that trigger the transition to ripening. The study also uncovered an extensive reformed homeostasis for most plant hormones, highlighting the multihormonal control of ripening initiation. Our data unveil the antagonistic roles of ethylene and auxin during the onset of ripening and show that auxin treatment delays fruit ripening via impairing the expression of genes required for System-2 autocatalytic ethylene production that is essential for climacteric ripening. This study unveils the detailed features of the transcriptomic reprogramming associated with the transition to ripening of tomato fruit and shows that the first changes occur in the locular gel before extending to pericarp and that a reformed auxin homeostasis is essential for the ripening to proceed.
Published: 2022

3. Comparative Transcriptomics Suggests Early Modifications by Vintec® in Grapevine Trunk of Hormonal Signaling and Secondary Metabolism Biosynthesis in Response to Phaeomoniella chlamydospora and Phaeoacremonium minimum

Author: Ana Romeo-Oliván, Justine Chervin, Coralie Breton, Thierry Lagravère, Jean Daydé, Bernard Dumas, Alban Jacques, Physiologie, Pathologie et Génétique Végétales (PPGV), Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), 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, MetaToul Agromix, MetaboHUB-MetaToul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Interactions Microbiennes dans la Rhizosphère et les Racines, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, and Benson-Rumiz, Alicia
Subjects: Microbiology (medical), Phaeomoniella chlamydospora, Phaeoacremonium minimum, esca, Trichoderma atroviride SC1, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, biocontrol, grapevine trunk diseases, Microbiology
Abstract: Given their well-known antifungal abilities, species of the genus Trichoderma are of significant interest in modern agriculture. Recent studies have shown that Trichoderma species can induce plant resistance against different phytopathogens. To further extend this line of investigation, we investigate herein the transcriptomic response of grapevine trunk to Vintec®, which is a Trichoderma atroviride SC1-based commercial formulation for biological control of grapevine trunk diseases and which reduces wood colonization. The aim of the study is to understand whether the biocontrol agent Vintec® modifies the trunk response to Phaeoacremonium minimum and Phaeomoniella chlamydospora, which are two esca-associated fungal pathogens. An analysis of transcriptional regulation identifies clusters of co-regulated genes whose transcriptomic reprogramming in response to infection depends on the absence or presence of Vintec®. On one hand, the results show that Vintec® differentially modulates the expression of putative genes involved in hormonal signaling, especially those involved in auxin signaling. On the other hand, most significant gene expression modifications occur among secondary-metabolism-related genes, especially regarding phenylpropanoid metabolism and stilbene biosynthesis. Taken together, these results suggest that the biocontrol agent Vintec® induces wood responses that counteract disease development.
Published: 2022

4. Ethylene Signaling Causing Tolerance of Arabidopsis thaliana Roots to Low pH Stress is Linked to Class III Peroxidase Activity

Author: Christophe Dunand, Victor Alexandre Vitorello, Christian Chervin, Elisabeth Jamet, Lázaro Eustáquio Pereira Peres, Jonathas Pereira Graças, Joni Esrom Lima, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement - INRAE (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Universidade Federal de Minas Gerais - UFMG (BRAZIL), Universidade de São Paulo - USP (BRAZIL), Laboratoire de Recherche en Sciences Végétales - LRSV (Castanet-Tolosan, France), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), Federal University of Minas Gerais (UFMG), Dynamique et Evolution des Parois cellulaires végétales, 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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centro de Energia Nuclear na Agricultura (CENA ), University of São Paulo (USP), Génomique et Biotechnologie des Fruits (GBF), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Programa de Doutorado-Sanduíche no Exterior - Brazilian CAPES (Grant # 88881.135425/2016-01)
Subjects: Cell death, 0106 biological sciences, 0301 basic medicine, Programmed cell death, Ethylene, Arabidopsis thaliana, Ethylene signaling, Biochimie, Biologie Moléculaire, Plant Science, Stress, 01 natural sciences, Cell wall, Soil, 03 medical and health sciences, chemistry.chemical_compound, Ethylène, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Peroxidase, chemistry.chemical_classification, biology, pH, Acidity, PEROXIDASE, Class III peroxidase, Plant physiology, biology.organism_classification, Roots, Cell wall stiffening, Salicylhydroxamic acid, 030104 developmental biology, Enzyme, Root, chemistry, biology.protein, Biophysics, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; One irreversible consequence of acidic pH for roots is cell death. Growing evidence suggests the role of hormones and cell wall-related enzymes in response to acidic pH that could possibly avoid cell mortality. Here, we have investigated the role of ethylene and class III peroxidases (CIII Prxs) activity on sensitivity to further low pH treatment. Seedlings of Arabidopsis thaliana were pretreated with ethylene, at various concentrations for various times, and then exposed to low pH. In contrast to non-treated roots, roots pretreated with ethylene for 3 h became tolerant to subsequent low pH, with negligible cell mortality in meristematic (MZ), transition (TZ), and early elongation (EZ) zones. This effect of ethylene was time dependent since it was achieved only when seedlings were pre-incubated with ethylene for at least 3 h. This tolerance induced by ethylene was not observed in the gain-of-function mutation etr1-1 (insensitive to ethylene 1–1). Besides, it was prevented by salicylhydroxamic acid (SHAM) which is an inhibitor of CIII Prxs activity. In late EZ, the decrease in cell expansion due to low pH was dependent on both ethylene signaling and a SHAM-sensitive process. The responses mediated by ethylene signaling might involve CIII Prxs-dependent cell wall modifications, leading to tolerance to low pH and arrest in cell expansion during stress.
Published: 2020

5. Cannabinoids vs. whole metabolome: Relevance of cannabinomics in analyzing Cannabis varieties

Author: Maxime Bonhomme, Pedro Vásquez-Ocmín, Sylvie Fournier, Alexandre Maciuk, Stéphane Bertani, Guillaume Marti, Fabienne Mathis, Pharmacochimie et Biologie pour le Développement (PHARMA-DEV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut de Recherche pour le Développement (IRD), Biomolécules : Conception, Isolement, Synthèse (BioCIS), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY), HEMP-it ADN, Fédération Nationale des Producteurs de Chanvre (FNPC), Metatoul - Agromix, 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), MetaToul Agromix, MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Bertani, Stéphane, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Chemotypes, Computational biology, Cannabis sativa, 01 natural sciences, Biochemistry, Cannabinomics, Analytical Chemistry, 03 medical and health sciences, [CHIM] Chemical Sciences, Metabolome, Environmental Chemistry, [CHIM]Chemical Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Statistical analysis, Genotyping, [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Spectroscopy, 030304 developmental biology, Cannabis, 0303 health sciences, Chemotype, biology, Cannabinoids, Chemistry, 010401 analytical chemistry, biology.organism_classification, MESH: Cannabis, 0104 chemical sciences, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, MESH: Cannabinoids, Identification (biology), MESH: Metabolome, Phytocannabinoids
Abstract: International audience; Cannabis sativa has a long history of domestication both for its bioactive compounds and its fibers. This has produced hundreds of varieties, usually characterized in the literature by chemotypes, with Δ9-THC and CBD content as the main markers. However, chemotyping could also be done based on minor compounds (phytocannabinoids and others). In this work, a workflow, which we propose to name cannabinomics, combines mass spectrometry of the whole metabolome and statistical analysis to help differentiate C. sativa varieties and deciphering their characteristic markers. By applying this cannabinomics approach to the data obtained from 20 varieties of C. sativa (classically classified as chemotype I, II, or III), we compared the results with those obtained by a targeted quantification of 11 phytocannabinoids. Cannabinomics can be considered as a complementary tool for phenotyping and genotyping, allowing the identification of minor compounds playing a key role as markers of differentiation.
Published: 2021

6. Fourier Transform InfraRed spectroscopy contribution to disentangle nanomaterial (DWCNT, TiO 2 ) impacts on tomato plants

Author: Mohammad Wazne, Mansi Bakshi, Valentin Costa, Camille Larue, Clarisse Liné, Juan Reyes-Herrera, Hiram Castillo-Michel, Elisabeth Jamet, David Roujol, Emmanuel Flahaut, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), 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), Centre interuniversitaire de recherche et d'ingenierie des matériaux (CIRIMAT), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), ID21 Beamline, European Synchrotron Radiation Facility (ESRF), Banaras Hindu University [Varanasi] (BHU), Dynamique et Evolution des Parois cellulaires végétales, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Toulouse Tech InterLab funding (SPECPLANP), Région Occitanie, Université Fédérale de Toulouse, Banaras Hindu University - BHU (INDIA), Centre National de la Recherche Scientifique - CNRS (FRANCE), European Synchrotron Radiation Facility - ESRF (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Laboratoire de Recherche en Sciences Végétales - LRSV (Castanet-Tolosan, France), 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)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Matériaux, Materials Science (miscellaneous), plant, Carbon nanotube, 010501 environmental sciences, 01 natural sciences, Nanomaterials, law.invention, soil, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, law, Screening method, Fourier transform infrared spectroscopy, carbon nanotube, Chemical composition, 030304 developmental biology, 0105 earth and related environmental sciences, General Environmental Science, 0303 health sciences, Plant physiology, toxicity, Xyloglucan, chemistry, FTIR, 13. Climate action, Environmental chemistry, [SDE]Environmental Sciences, cell wall
Abstract: International audience; Carbon nanotubes (CNTs) and titanium dioxide nanoparticles (TiO2-NPs) are among the most used nanomaterials (NMs). However, their impacts especially on the terrestrial ecosystems and on plants are still controversial. Apart from obvious physico-chemical differences, a possible explanation of these contrasting results could be the wide range of methods used to evaluate the toxicity at different levels of plant physiology. Fourier Transformed InfraRed (FTIR) spectroscopy is a sensitive and widely informative technique that probes the chemical composition of plants. In this study, we investigated the impacts of CNTs and TiO2-NPs (100 and 500 mg.kg-1) on tomato plants after 5, 10, 15 and 20 days of exposure in soil. Using morphological parameters, no toxicity was found except after 15 days of exposure (-57% in height and-62% in foliar area for plants exposed to 100 mg.kg-1 TiO2-NPs, but no impact after CNT exposure) while FTIR revealed effects of the two NMs starting after 5 days of exposure and being maximum after 15 days. After spectral data treatment optimization, FTIR results suggested modifications in leaf cell wall components of plants subjected to both NMs. Microarray polymer profiling confirmed changes in xyloglucan and homogalacturonan levels for plants exposed to TiO2-NPs. In summary, FTIR was an effective screening method to evaluate the impacts of NMs on tomato plants and to identify their implications on the plant cell walls.
Published: 2021

7. Phenolic profile of a Parma violet unveiled by chemical and fluorescence imaging

Author: Alain Jauneau, Valérie Bonzon-Ponnet, Claude Lafitte, Cécile Pouzet, Marie-Thérèse Esquerré-Tugayé, Justine Chervin, Moustafa Khatib, 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Metatoul - Agromix, MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Groupe Berdoues Parfums et Cosmétiques, Regional Council Occitanie (Project CLE 13053062), Municipal greenhouses of Toulouse, National Program for the Emergency Reception of Scientifics in Exile (PAUSE), 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-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Laboratoire de Recherche en Sciences Végétales (LRSV), MetaToul Agromix, MetaboHUB-MetaToul, and Benson-Rumiz, Alicia
Subjects: 0106 biological sciences, Fluorescence-lifetime imaging microscopy, chemical quantification, Plant Science, Biology, autofluorescence, confocal microscopy, 01 natural sciences, phenolic profile, law.invention, Cell wall, 03 medical and health sciences, Confocal microscopy, law, Studies, Fluorescence microscope, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 0303 health sciences, AcademicSubjects/SCI01210, fungi, food and beverages, Fluorescence, Anthocyanidins, Autofluorescence, Biochemistry, Parma violet, Aobpla/1031, Petal, Viola alba subsp. dehnhardtii, 010606 plant biology & botany
Abstract: The ability of phenolic compounds to autofluoresce upon illumination by UV or blue light was exploited to explore the nature and distribution of these metabolites within the flower petals, leaves and roots of the violet, Viola alba subsp. dehnhardtii. This was achieved through a dual complementary approach that combined fluorescence microscopy imaging of living intact tissues and chemical extraction of pulverized material. The blue to red fluorescence displayed by living tissues upon illumination was indicative of their richness in phenolic compounds. Phenolic acids were found in all tissues, while flavonoids characterized the aerial part of the plant, anthocyanidins being restricted to the petals. The chemical quantification of phenolics in plant extracts confirmed their tissue-specific distribution and abundance. A key finding was that the spectral signatures obtained through confocal microscopy of endogenous fluorophores in living tissues and their counterpart extracts share the same fluorescence patterns, pointing out the potential of fluorescence imaging of intact organs for a proper estimation of their phenolic content. In addition, this study highlighted a few distinct morphology cell types, in particular foliar-glandular-like structures, and jagged petal cell walls. Altogether, these data provide a comprehensive histochemical localization of phenolics in living tissues of a violet. Converting fluorescence imaging into a chemical imprint indicated that one can rely on fluorescence microscopy of intact living tissues as a rapid, non-destructive means to follow their phenolic imprint under various environmental conditions., The Parma violet Viola alba subsp. dehnhardtii distinguishes from other violets by the presence of double chasmogame flowers harbouring up to 40 petals. The phenolic imprint of its different plant parts was characterized by a dual approach that combines fluorescence imaging of living tissues and chemical analysis. The knowledge gained from this study indicated that one can rely on fluorescence microscopy as a rapid, non-destructive means to follow the phenolic pattern of a given organ or tissue. It also highlighted a few distinct morphology cell types, most notably foliar-glandular-like structures, and jagged petal cell walls.
Published: 2021

8. Metabolomic characterization of 5 native Peruvian chili peppers (Capsicum spp.) as a tool for species discrimination

Author: Fabio Espichán, Rosario Rojas, Fredy Quispe, Guillaume Cabanac, Guillaume Marti, Universidad Peruana Cayetano Heredia (UPCH), Instituto Nacional de Innovación Agraria (INIA), Recherche d’Information et Synthèse d’Information (IRIT-IRIS), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Metatoul - Agromix, MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and FONDECYT-CONCYTEC under contract 134-2015-FONDECYT
Subjects: Metabolomic, General Medicine, OPLS-DA, Analytical Chemistry, SUS-plot, Fruit, [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], Peru, Vegetables, Metabolomics, [INFO.INFO-DL]Computer Science [cs]/Digital Libraries [cs.DL], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Capsicum, Biomarkers, Peruvian native chili peppers, Food Science
Abstract: International audience; Many species of chili peppers have overlapping morphological characters and delimitation by visual descriptors in many cases fails to differentiate one species from another. In Peru, there are 413 accessions of native chili pepper and 296 accessions of rocotos conserved in the Germplasm Collections of the National Institute of Agrarian Innovation (INIA), of which five accessions (three species from three locations) were selected for the present metabolomic study. The Discrimination of the three species of native chili peppers and identification of biomarkers was performed using untargeted metabolomic approach based on profiling by UHPLC-HRMS and multivariate data analysis. The samples of fresh chili peppers (whole fruit) from Chincha area were used to construct an OPLS-DA model. To validate the biomarkers (identified 15 biomarkers, mainly flavonoids), an external validation set of the OPLS-DA model was constructed using Chiclayo and Huaral collection datasets. Consequently, the OPLS-DA based on Chincha samples model has a high predictive capacity demonstrating that the biomarkers have a high probability of continuity in any culture space, being successful in discriminating the species by untargeted metabolomics.
Published: 2022

9. Laboratory test to assess sensitivity of bio-based earth materials to fungal growth

Author: Camille Magniont, Christine Roques, Jean-Emmanuel Aubert, Christophe Roux, Alexandra Bertron, Aurélie Laborel-Préneron, Kouka Amed Jérémy Ouedraogo, Matthieu Labat, Alexis Simons, Laboratoire Matériaux et Durabilité des constructions (LMDC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Laboratoire de Génie Chimique (LGC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Interactions Microbiennes dans la Rhizosphère et les Racines, Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Matériaux, Procédés et Technologie des Composites, Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Laboratoire Matériaux et Durabilité des constructions [Toulouse] ( LMDC ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ), Laboratoire de génie chimique ( LGC ), Institut National Polytechnique [Toulouse] ( INP ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Recherche en Sciences Végétales ( LRSV ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Laboratoire de génie chimique [ancien site de Basso-Cambo] (LGC), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, 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), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Fungal growth, Environmental Engineering, Geography, Planning and Development, [ SPI.MAT ] Engineering Sciences [physics]/Materials, 0211 other engineering and technologies, Earth materials, Building material, 02 engineering and technology, 010501 environmental sciences, engineering.material, Bacterial growth, medicine.disease_cause, Plant aggregate, 01 natural sciences, [SPI.MAT]Engineering Sciences [physics]/Materials, [ SPI.GCIV.CD ] Engineering Sciences [physics]/Civil Engineering/Construction durable, Mold, 021105 building & construction, medicine, Génie chimique, Relative humidity, Food science, Génie des procédés, 0105 earth and related environmental sciences, Civil and Structural Engineering, [SPI.GCIV.CD]Engineering Sciences [physics]/Civil Engineering/Construction durable, Inoculation, Chemistry, Indoor environment, Building and Construction, Straw, engineering, Aspergillus brasiliensis, Unfired earth
Abstract: International audience; The effect of molds present in buildings on the health of the occupants is a major issue hence, when a building material is developed, its sensitivity to microbial growth should be assessed. However, few studies have investigated fungal growth on bio-based building materials with the resources available in a laboratory specializing in materials. The objective of this paper is thus to propose a simple and efficient experimental method useful for construction materials laboratories, adapted from methods proposed in the literature. For this purpose, fungal growth was investigated under different environmental conditions on earth-based material with or without the addition of straw or hemp shiv. Samples were inoculated with a strain of Aspergillus brasiliensis and were incubated for 12 weeks at 76, 84 or 93% RH, and 30 °C or 20 °C. Reproducible results showed that earth-based materials were more sensitive to fungi when they were enriched in plant aggregates. Fungal development was observed on earth material containing plant aggregates after 4 weeks of exposure at 93% RH and 30 °C, whereas it was observed after 8 weeks on raw earth material under the same conditions. Additionally, the possibility of quantifying fungal development with increased sensitivity by using image analysis is proposed. Due to the growth of fungal species other than A. brasiliensis, a natural inoculation approach is recommended. One of the conclusions is that liquid water is more favorable to mold growth than relative humidity alone. The addition of liquid water is thus recommended to accelerate the test.
Published: 2018

10. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Author: Zhang, Runxuan, Calixto, Cristiane P.G., Marquez, Yamile, Venhuizen, Peter, Tzioutziou, Nikoleta A., Guo, Wenbin, Spensley, Mark, Entizne, Juan Carlos, Lewandowska, Dominika, ten Have, Sara, Frei dit Frey, Nicolas, Hirt, Heribert, James, Allan B., Nimmo, Hugh G., Barta, Andrea, Kalyna, Maria, Brown, John W.S., Informatics and Computational Sciences, The James Hutton Institute, Plant Sciences Division, College of Life Sciences, University of Dundee, Max Perutz Labs, University of Vienna [Vienna], The Donnelly Centre, University of Toronto, Cell and Molecular Sciences, Centre for Gene Regulation and Expression, School of Life Sciences Dundee, 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), Université Fédérale Toulouse Midi-Pyrénées, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université d'Evry Val d'Essonne, Institute of MoleculCell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Department of Applied Genetics and Cell Biology, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Biotechnology and Biological Sciences Research Council (BBSRC) [BB/K013661/1, BB/K006568/1, BB/K006835/1], Scottish Government Rural and Environment Science and Analytical Services division (RESAS), Austrian Science Fund (FWF) [P26333, DK W1207], LABEX Saclay Plant Sciences, BBSRC EASTBIO PhD studentships, European Alternative Splicing Network of Excellence (EURASNET) [LSHG-CT-2005-518238], James Hutton Institute, Max F. Perutz Laboratories, Laboratoire de Recherche en Sciences Végétales ( LRSV ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Université Paul Sabatier - Toulouse 3 ( UPS ), Institut des Sciences des Plantes de Paris-Saclay ( IPS2 ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), University of Natural Resources and Life Sciences, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Evolution des Interactions Plantes-Microorganismes, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, RNA, Untranslated, Transcription, Genetic, [ SDV ] Life Sciences [q-bio], Sequence Analysis, RNA, [SDV]Life Sciences [q-bio], Arabidopsis, Sequence analysis, Genetic Variation, Reproducibility of Results, Genes, Insect, Data Resources and Analyses, Reference Values, Transcriptome, Alternative splicing
Abstract: Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.
Published: 2017

11. The EXTENSIN enigma

Author: Steven Moussu, Gwyneth Ingram, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Université de Lausanne = University of Lausanne (UNIL), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV]Life Sciences [q-bio], Cell Biology, Molecular Biology, Applied Microbiology and Biotechnology, Microbiology
Abstract: International audience
Published: 2023

12. Protocols for Studying Protein Stability in an Arabidopsis Protoplast Transient Expression System

Author: Planchais, Séverine, Camborde, Laurent, Jupin, Isabelle, Université Sorbonne Paris Cité (USPC), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Adaptation des plantes à des contraintes environnementales (APCE), Sorbonne Université (SU), Interactions Microbiennes dans la Rhizosphère et les Racines, 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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité ( USPC ), Institut Jacques Monod ( IJM ), Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Adaptation des Plantes aux Contraintes Environnementales, Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut d'écologie et des sciences de l'environnement de Paris ( IEES ), Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ) -CNRS, Laboratoire de Recherche en Sciences Végétales ( LRSV ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Arabidopsis Proteins, Protein Stability, Protoplasts, fungi, Arabidopsis, Proteins, food and beverages, Transient expression, Transfection, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Gene Expression Regulation, Plant, UPR assay, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Immunoprecipitation, Pulse-chase, Molecular Biology
Abstract: International audience; Protein stability influences many aspects of biology, and measuring their stability in vivo can provide important insights into biological systems.This chapter describes in details two methods to assess the stability of a specific protein based on its transient expression in Arabidopsis protoplasts. First, a pulse-chase assay based on radioactive metabolic labeling of cellular proteins, followed by immunoprecipitation of the protein of interest. The decrease in radioactive signal is monitored over time and can be used to determine the protein's half-life.Alternatively, we also present a nonradioactive assay based on the use of reporter proteins, whose ratio can be quantified. This assay can be used to determine the relative stability of a protein of interest under specific conditions.
Published: 2016

13. Obituary: Dominique Job (1947-2022)

Author: Jamet, Elisabeth, Esquerré-Tugayé, Marie-Thérèse, Gallardo-Guerrero, Karine, Rolland, Norbert, Zivy, Michel, Blein-Nicolas, Mélisande, Vincent, Delphine, Gontero, Brigitte, Rajjou, Loïc, Université de Toulouse (UT), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Grenoble Alpes - Faculté d'Économie de Grenoble (UGA UFR FEG), Université Grenoble Alpes (UGA), Université Paris-Saclay, INRAE, AgroParisTech, UMR MoSAR (INRAE), Agriculture Victoria Research, La Trobe University, Australia, Service de gynécologie-obstétrique [Hôpital Nord - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital Nord [CHU - APHM], Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, Orsay, France (IGPS), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Université Paris Saclay, INRAE, CNRS, AgroParisTech, PAPPSO, Centre National de la Recherche Scientifique (CNRS), Centre for AgriBioscience, Bundoora, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Jean-Pierre Bourgin (IJPB), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Obituary and bibliography, Proteomics, French Academy of Agriculture, [SDV]Life Sciences [q-bio], obituary and bibliography, Dominique Job, Plant physiologist, Plant Science
Abstract: International audience
Published: 2023

14. Carotenoid accumulation during tomato fruit ripening is modulated by the auxin-ethylene balance

Author: Su, Liyan, Diretto, Gianfranco, Purgatto, Eduardo, Danoun, Saïda, Zouine, Mohamed, Li, Zhengguo, Roustan, Jean-Paul, Bouzayen, Mondher, Giuliano, Giovanni, Chervin, Christian, Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Xi'an University of Arts and Science (CHINA), Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Universidade de São Paulo (USP), 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), Chongqing University (CHINA), French Laboratory of Excellence project 'TULIP' [ANR-10-LABEX-41, ANR-11-IDEX-0002-02], Italian Ministry of Research, CSC PhD grant, European Commission Project TRADITOM - Traditional tomato varieties and cultural practices: a case for agricultural diversification with impact on food security and health of European population (634561), European Project: 613513,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,DISCO(2013), Centre National de la Recherche Scientifique - CNRS (FRANCE), Italian National Agency for New Technologies, Energy and Environment - ENEA (ITALY), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Universidade de São Paulo - USP (BRAZIL), Laboratoire de Recherche en Sciences Végétales - LRSV (Castanet-Tolosan, France), Universidade de São Paulo, Génomique et Biotechnologie des Fruits ( GBF ), Institut National Polytechnique [Toulouse] ( INP ) -Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Supérieure Agronomique de Toulouse, Italian National Agency for New Technologies, Energy and Sustainable Economic Development ( ENEA ), Universidade de São Paulo ( USP ), Laboratoire de Recherche en Sciences Végétales ( LRSV ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Chervin, Christian, Institut National Polytechnique de Toulouse - INPT (FRANCE), Université Toulouse III - Paul Sabatier - UPS (FRANCE), Génomique et Biotechnologie des Fruits - GBF (Castanet-Tolosan, France), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Agenzia Nazionale per le nuove Tecnologie, l’energia e lo sviluppo economico sostenibile = Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Universidade de São Paulo = University of São Paulo (USP), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), and European Project: 634561,H2020,H2020-SFS-2014-2,TRADITOM(2015)
Subjects: Chlorophyll, Plant Science, Plants genetics, Tomato, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Ethylene, Abscisic acid, Lycopene, Solanum lycopersicum, Gene Expression Regulation, Plant, Auxin, Carotenoids, Rin, Ripening, Génétique des plantes, Gene Regulatory Networks, heterocyclic compounds, RNA, Messenger, Plant Proteins, Indoleacetic Acids, Pigmentation, fungi, food and beverages, Ethylenes, Biosynthetic Pathways, Fruit, [ SDV.GEN.GPL ] Life Sciences [q-bio]/Genetics/Plants genetics, Carboxylic Ester Hydrolases, Research Article
Abstract: Background Tomato fruit ripening is controlled by ethylene and is characterized by a shift in color from green to red, a strong accumulation of lycopene, and a decrease in β-xanthophylls and chlorophylls. The role of other hormones, such as auxin, has been less studied. Auxin is retarding the fruit ripening. In tomato, there is no study of the carotenoid content and related transcript after treatment with auxin. Results We followed the effects of application of various hormone-like substances to “Mature-Green” fruits. Application of an ethylene precursor (ACC) or of an auxin antagonist (PCIB) to tomato fruits accelerated the color shift, the accumulation of lycopene, α-, β-, and δ-carotenes and the disappearance of β-xanthophylls and chlorophyll b. By contrast, application of auxin (IAA) delayed the color shift, the lycopene accumulation and the decrease of chlorophyll a. Combined application of IAA + ACC led to an intermediate phenotype. The levels of transcripts coding for carotenoid biosynthesis enzymes, for the ripening regulator Rin, for chlorophyllase, and the levels of ethylene and abscisic acid (ABA) were monitored in the treated fruits. Correlation network analyses suggest that ABA, may also be a key regulator of several responses to auxin and ethylene treatments. Conclusions The results suggest that IAA retards tomato ripening by affecting a set of (i) key regulators, such as Rin, ethylene and ABA, and (ii) key effectors, such as genes for lycopene and β-xanthophyll biosynthesis and for chlorophyll degradation. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0495-4) contains supplementary material, which is available to authorized users.
Published: 2015

15. Ants mediate community composition of root‐associated fungi in an ant‐plant mutualism

Author: Céline Leroy, Arthur QuyManh Maes, Eliane Louisanna, Jean‐François Carrias, Régis Céréghino, Bruno Corbara, Nathalie Séjalon‐Delmas, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), 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), Interactions Microbiennes dans la Rhizosphère et les Racines, Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: ITS metabarcoding, fungi, food and beverages, fungal functional guilds, biochemical phenomena, metabolism, and nutrition, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Camponotus femoratus, Symbiotrophic fungi, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Neoponera goeldii, Carton nest, Aechmea mertensii, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, Ant garden
Abstract: International audience; Cross-kingdom interactions with plants were frequently related to microbial pathogens and herbivores. Yet, mutualistic interactions that involve multiple partners can confer cross-kingdom functional benefits, which have been understudied. Ant gardens (AGs) are recognized as one of the most sophisticated of all symbioses between ants and flowering plants, forming good models to study cross-kingdom interactions. The aim of this study was to examine whether ant-plant interactions can influence the community composition of root-associated fungi. We assessed whether two AG ant species, Camponotus femoratus and Neoponera goeldii, confer different physico-chemical properties to their nests, and affect root fungal community composition and fungal functional guilds in the bromeliad Aechmea mertensii. The diversity and community composition of root-associated fungi depended on ant species identity. The two ants had a contrasting influence on the structure and chemistry of the nest, and on the floristic diversity of the AGs. Multiple drivers may therefore determine the root-associated fungal communities. As the outcome of the ant-bromeliad interaction depends on the ant species, and because the plants are also involved in interactions with root-associated symbionts, this study provided evidence that ecologically relevant symbioses can be mediated by cross-kingdom interactions.
Published: 2022

16. Mixotrophy in aquatic plants, an overlooked ability

Author: Antoine Firmin, Marc-André Selosse, Christophe Dunand, Arnaud Elger, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), 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), 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)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Gdańsk (UG), Dynamique et Evolution des Parois cellulaires végétales, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, Heterotroph, Plant Science, Biology, 01 natural sciences, Carbon Cycle, 03 medical and health sciences, mixotrophy, Aquatic plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Organic matter, 14. Life underwater, Autotroph, Ecosystem, 030304 developmental biology, chemistry.chemical_classification, heterotrophy, Autotrophic Processes, 0303 health sciences, Ecology, 010604 marine biology & hydrobiology, Aquatic ecosystem, Plants, 15. Life on land, dissolved organic carbon, Carbon, 6. Clean water, aquatic plant, chemistry, Mixotroph
Abstract: International audience; Aquatic plants are crucial for the proper functioning of aquatic environments. So far, mixotrophy, widespread in aquatic microbial communities and in certain terrestrial plants, has been studied rarely in aquatic plants other than carnivorous ones. New evidence, particularly in Lemna and other close genera, suggests that mixotrophy is much more widespread than previously thought. Three processes could be involved, namely biotrophic associations, capture of prey (e.g., in carnivorous plants), and absorbotrophy (uptake of dissolved organic carbon). The latter process seems to be the most probable hypothesis in regard to the physiology of aquatic plants, but further research at both organism and cellular levels is needed to understand and clarify the processes involved and their importance. This opinion opens a new window of opportunity in aquatic ecology, with possible unsuspected applications in water management.
Published: 2022

17. A fungal conserved gene from the basidiomycete Hebeloma cylindrosporum is essential for efficient ectomycorrhiza formation

Author: Jeanne Doré, Roland Marmeisse, Jean-Philippe Combier, Gilles Gay, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Peptides et petits ARN, Université Toulouse III - Paul Sabatier (UT3), 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), French Ministry of National Education, Office of Science of the U.S. Department of Energy DE-AC02-05CH11231, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire de Recherche en Sciences Végétales ( LRSV ), and Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Physiology, [ SDV.TOX ] Life Sciences [q-bio]/Toxicology, Mutant, Fungus, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Plant Roots, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Fungal Proteins, Insertional mutagenesis, Gene Expression Regulation, Fungal, Mycorrhizae, Botany, Hebeloma, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Mycorrhiza, Symbiosis, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Gene, Phylogeny, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Hartig net, Mycelium, biology, fungi, General Medicine, Pinus, biology.organism_classification, Ectomycorrhiza, Mutagenesis, Insertional, Open reading frame, Phenotype, Biochemistry, Multigene Family, [SDV.TOX]Life Sciences [q-bio]/Toxicology, Microscopy, Electron, Scanning, RNA Interference, Agronomy and Crop Science
Abstract: We used Agrobacterium-mediated insertional mutagenesis to identify genes in the ectomycorrhizal fungus Hebeloma cylindrosporum that are essential for efficient mycorrhiza formation. One of the mutants presented a dramatically reduced ability to form ectomycorrhizas when grown in the presence of Pinus pinaster. It failed to form mycorrhizas in the presence of glucose at 0.5 g liter–1, a condition favorable for mycorrhiza formation by the wild-type strain. However, it formed few mycorrhizas when glucose was replaced by fructose or when glucose concentration was increased to 1 g liter–1. Scanning electron microscopy examination of these mycorrhizas revealed that this mutant was unable to differentiate true fungal sheath and Hartig net. Molecular analyses showed that the single-copy disrupting T-DNA was integrated 6,884 bp downstream from the start codon, of an open reading frame potentially encoding a 3,096-amino-acid-long protein. This gene, which we named HcMycE1, has orthologs in numerous fungi as well as different other eukaryotic microorganisms. RNAi inactivation of HcMycE1 in the wild-type strain also led to a mycorrhizal defect, demonstrating that the nonmycorrhizal phenotype of the mutant was due to mutagenic T-DNA integration in HcMycE1. In the wild-type strain colonizing P. pinaster roots, HcMycE1 was transiently upregulated before symbiotic structure differentiation. Together with the inability of the mutant to differentiate these structures, this suggests that HcMycE1 plays a crucial role upstream of the fungal sheath and Hartig net differentiation. This study provides the first characterization of a fungal mutant altered in mycorrhizal ability.
Published: 2014

18. Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes

Author: Huang, Baowen, Hu, Guojian, Wang, Keke, Frasse, Pierre, Maza, Elie, Djari, Anis, Deng, Wei, Pirrello, Julien, Burlat, Vincent, Pons, Clara, Granell, Antonio, Li, Zhengguo, van der Rest, Benoît, Bouzayen, Mondher, Génomique et Biotechnologie des Fruits (GBF), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Génomique et Biotechnologie des Fruits, Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Chongqing University [Chongqing], Dynamique et Evolution des Parois cellulaires végétales, Universitat Politècnica de València (UPV), European Project: 679796,H2020,H2020-SFS-2015-2,TomGEM(2016), European Project: 101000716,HARNESSTOM, École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Agricultural genetics, Gene Expression Profiling, Science, fungi, Genetic Variation, food and beverages, MADS Domain Proteins, Molecular engineering in plants, Article, Plant breeding, Phenotype, Solanum lycopersicum, Cell Wall, Gene Expression Regulation, Plant, Fruit, Mutation, Plant development, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cell Proliferation, Plant Proteins
Abstract: [EN] All-flesh tomato cultivars are devoid of locular gel and exhibit enhanced firmness and improved postharvest storage. Here, we show that SlMBP3 is a master regulator of locular tissue in tomato fruit and that a deletion at the gene locus underpins the All-flesh trait. Intriguingly, All-flesh varieties lack the deleterious phenotypes reported previously for SlMBP3 under-expressing lines and which preclude any potential commercial use. We resolve the causal factor for this phenotypic divergence through the discovery of a natural mutation at the SlAGL11 locus, a close homolog of SlMBP3. Misexpressing SlMBP3 impairs locular gel formation through massive transcriptomic reprogramming at initial phases of fruit development. SlMBP3 influences locule gel formation by controlling cell cycle and cell expansion genes, indicating that important components of fruit softening are determined at early pre-ripening stages. Our findings define potential breeding targets for improved texture in tomato and possibly other fleshy fruits. The all-flesh type of tomato fruits is caused by mutation of the MBP3 gene, however, knocking down MBP3 in certain genotypes also affect plant and fruit development. Here, the authors show that a natural mutation of AGL11, a close homolog of MBP3, is responsible for the phenotypic divergence., The authors are grateful to L. Lemonnier and D. Saint-Martin for transformation and cultivation of tomato plants and GeT-PlaGe core facility (INRAe Toulouse) for ChIP deep sequencing. The authors also want to thank Dr. Christian Chevalier (INRAE et Univsersite de Bordeaux) for helping in analyzing genes related to cell cycle, cell division, and endoreduplication in tomato. This research was supported by the EU H2020 TomGEM 679796 and HARNESSTOM 101000716 projects.
Published: 2021

19. Comparative phylotranscriptomics reveals a 110 million years-old symbiotic program

Author: Cyril Libourel, Jean Keller, Lukas Brichet, Anne-Claire Cazalé, Sébastien Carrère, Tatiana Vernié, Jean-Malo Couzigou, Caroline Callot, Isabelle Dufau, Stéphane Cauet, William Marande, Tabatha Bulach, Amandine Suin, Catherine Masson-Boivin, Philippe Remigi, Pierre-Marc Delaux, Delphine Capela, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French National Research Institute for Agriculture, Food and Environment (INRAE, Plant Health and Environment Division), Fédération de Recherche Agrobiosciences, Interactions et Biodiversité, project Engineering Nitrogen Symbiosis for Africa (ENSA) currently funded through a grant to the University of Cambridge by the Bill & Melinda Gates Foundation (OPP1172165) and the UK Foreign, Commonwealth and Development Office as Engineering Nitrogen Symbiosis for Africa (OPP1172165)., European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 101001675 - ORIGINS), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-18-EURE-0019,TULIP-GSR,The Toulouse-Perpignan(2018), and European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: SummarySymbiotic interactions have structured past and present ecosystems and shaped the evolution of life. As any trait, the symbiotic state observed in extant species builds on ancestral and conserved features, and lineage-specific innovations. From these mixed origins, defining the ancestral state of symbiotic associations is challenging although it is instrumental for understanding how symbiotic abilities emerge from non-symbiotic states. Here we aimed at reconstructing the intermediate steps leading to the root-nodule nitrogen-fixing symbiosis (RNS) observed in some extant flowering plants. For this, we compared the transcriptomic responses of nine host plants in response to symbiotic bacteria. We included the mimosoid legume Mimosa pudica for which we assembled a chromosome-level genome and generated the transcriptomic response to experimentally evolved bacterial symbionts. With this dataset, we reconstructed the ancestral RNS transcriptome, composed of most already described symbiotic genes together with hundreds of novel candidates. We found that the response to the chemical signals produced by the symbiont, nodule organogenesis and nitrogen-fixation are predominantly linked to ancestral responses, although these traits have diversified in the different nitrogen-fixing lineages. We detected a clear signature of recent and convergent evolution for the ability to release intracellular symbiosomes in two legume lineages, exemplified by the expression of different classes of small proteins in each group, potentially leading to the convergent gain of symbiotic evolutionary stability. Our findings demonstrate that most of the novelties for RNS were mostly in place in the most recent common ancestor of the RNS-forming species that lived on Earth 110 million years ago.Graphical abstractA little graphical/nice phylogeny with nodes of interestHighlightsWe sequenced a high-quality genome of the Mimosoideae Mimosa pudicaThe nitrogen-fixing root-nodule symbiosis relies on an ancestral transcriptomic responseAll symbiotic traits involve genes of the ancestral symbiotic programSymbiont perception, nodule organogenesis and nitrogen-fixation are essentially ancestral processesConvergent evolution of intracellular accommodation of symbionts additionally involves lineage-specific genes
Published: 2022

20. MS2Snoop: un package R pour automatiser l'extraction et le nettoyage des spectres MS/MS en métabolomique

Author: Wagner, Kevin, Pavot, Lain, Giacomoni, Franck, Marti, Guillaume, Guitton, Yann, Debrauwer, Laurent, Jamin, Emilien L., Martin, Jean-François, Metatoul AXIOM (E20 ), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ToxAlim (ToxAlim), Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), MetaToul Agromix, Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'étude des Résidus et Contaminants dans les Aliments (LABERCA), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Metabolomics, Lipidomics and Steroidomics Analysis (MELISA), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Grand-Ouest, MetaboHUB-MetaboHUB, and ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011)
Subjects: XCMS, W4M, [SDV]Life Sciences [q-bio], MS/MS, Metabolomics, [CHIM]Chemical Sciences, [PHYS.PHYS.PHYS-DATA-AN]Physics [physics]/Physics [physics]/Data Analysis, Statistics and Probability [physics.data-an]
Abstract: International audience; Introduction Omics approaches including metabolomics generate huge datasets requiring powerful processing tools. In the field of non-targeted mass spectrometry metabolomics, HRMS data mining has been the subject of much work, with the development of powerful interactive tools, including Workflow4Metabolomics (W4M). One of the main bottlenecks of current workflows lies in the complexity of the interpretation of results, in particular a lack of reliable MS/MS spectra reference databases to be used for confident identification (level 1 and 2 according to the metabolomics standard initiative). Creating reliable and well curated DB remains a laborious and challenging task, but necessary to ensure the quality of the reference spectra. In this work, we present a tool inspired by manual curation allowing the export of MS/MS data from targeted and data dependent (DDA) fragmentation methods to laboratory spectral databases, named “MS2Snoop”. Method Already integrated in W4M pipelines, MS2Snoop works with R and uses as starting point the peak list extracted from LC-MS and MS/MS analyses with XCMS 3.0 using W4M. Then, lists of precursors and fragment ions are processed with MSPurity using W4M, to assign fragmentation spectra to XCMS features, and to filter data on the purity of precursor ions. From these data, MS2Snoop has been developed to allow: • Retrieval of precursor and fragment ions data (m/z, RT, scan-by-scan intensities). • Matching of precursor ions with a list of expected compounds. • Establishing relationships between a precursor and its potential fragment ions via grouping, to obtain a raw spectrum. • Selecting a reference ion in the spectrum (precursor ion if still present, otherwise the most abundant ion). • Determining correlation between the reference ion and the other ions of the fragmentation spectrum using all scans. • Constructing a curated spectrum by eliminating ions with a correlation value lower than a threshold defined by the user. Results MS2Snoop was assessed on targeted MSMS analyses for about 30 compounds (pesticides and some of their metabolites) by performing the steps presented above. To validate these spectra, a manual curation was performed on the same data to compare the m/z and relative abundances of raw and MS2snoop treated spectra. The majority of the automatically extracted spectra using MS2Snoop showed similar results as spectra curated by an expert (fragment ions list, relative abundances), showing that MS2Snoop deconvolution process was efficient to provide automatically cleaned MS/MS spectra without interfering ions on all tested compounds. Conclusion MS2Snoop already allows extracting and cleaning MS/MS datasets using common data processing steps for metabolomics studies as a starting point, and then combined with inputs of a list of expected compounds and MS/MS raw data deconvoluted by MSPurity. Developed and validated with targeted MS/MS spectra, MS2Snoop is compatible with DDA spectra in the limit of the number of MS/MS scans acquired. This package will allow high throughput extraction of MS/MS spectra in order to feed the PeakForest project. Preliminary results obtained with MS2Snoop allowed considering it as a valuable tool for confident annotation of metabolites on chromatographic methods coupled to non-targeted mass spectrometry. A beta version is already publicly available on W4M.
Published: 2022

21. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

Author: Marco Pagni, Claude Murat, Aikaterini Symeonidi, Diederik van Tuinen, Christophe Roux, Mathilde Malbreil, Steve Ndikumana, Nicolas Corradi, Yair Shachar-Hill, Igor V. Grigoriev, Bernard Henrissat, Franziska Krajinski, Nicolas Frei dit Frey, Francis Martin, Gerald A. Tuskan, Alan Kuo, Stefan A. Rensing, Annegret Kohler, Natalia Requena, Raffaella Balestrini, Uta Paszkowski, Pawel Rosikiewicz, Nina Duensing, Peter J. Lammers, Philippe Charron, Mohamed Hijri, Raman Koul, Vivienne Gianinazzi-Pearson, Harris Shapiro, Hélène San Clemente, Joshua R. Herr, Emilie Tisserant, Denis Petitpierre, Guillaume Bécard, Rohan Riley, Frédéric G. Masclaux, Katsuharu Saito, Yoshihiro Handa, Masayoshi Kawaguchi, Emmanuelle Morin, Luz B. Gilbert, Ian R. Sanders, Paola Bonfante, J. Peter W. Young, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), DOE Joint Genome Institute [Walnut Creek], Centre for Biological Signaling Studies [Freiburg] (BIOSS), University of Freiburg [Freiburg], Philipps Universität Marburg = Philipps University of Marburg, Istituto per la Protezione delle Piante, National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Ottawa [Ottawa], Max Planck Society, Evolution des Interactions Plantes-Microorganismes, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), 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, National Institute for Basic Biology [Okazaki], Institut de la Recherche en Biologie Végétale Departement de sciences biologiques, New Mexico State University, Université de Lausanne = University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Karlsruhe Institute of Technology (KIT), Shinshu University [Nagano], Interactions Microbiennes dans la Rhizosphère et les Racines, University of Cambridge [UK] (CAM), Michigan State University [East Lansing], Michigan State University System, Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, University of York [York, UK], Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH), European Commission [EcoFINDERS FP7-264465], French National Research Agency through the Clusters of Excellence ARBRE (Advanced Research on the Biology of Tree and Forest Ecosystems) [ANR-11-LABX-0002-01], French National Research Agency through TULIP (Toward a Unified Theory of Biotic Interactions: Role of Environmental Perturbations) [ANR-10-LABX-41], US Department of Energy's Oak Ridge National Laboratory Scientific Focus Area for Genomics Foundational Sciences, Conseil Regional Midi-Pyrenees, Natural Sciences and Engineering Research Council of Canada, German Federal Ministry of Education and Research, Swiss National Science Foundation, Italian Regional Project Converging Technologies-BIOBIT, Ministry of Education, Culture, Sports, Science, and Technology of Japan, Programme for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry, Office of Science of the US Department of Energy [DE-AC02-05CH11231], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Philipps Universität Marburg, Consiglio Nazionale delle Ricerche [Roma] (CNR), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Lausanne (UNIL), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), University of Copenhagen = Københavns Universitet (KU), Université de Lausanne ( UNIL ), Laboratoire de Recherche en Sciences Végétales ( LRSV ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Consiglio Nazionale delle Ricerche [Roma] ( CNR ), University of Cambridge [UK] ( CAM ), Oak Ridge National Laboratory [Oak Ridge] ( ORNL ), UI-Battelle, Centre for Biological Signaling Studies [Freiburg] ( BIOSS ), Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), University of Copenhagen ( KU ), Philipps-Universität Marburg, Equipe de droit public de Lyon, Université Jean Moulin - Lyon III, Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Max Planck Society (GERMANY), 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, Université de Montréal, Swiss Institute of Bioinformatics - Lausanne ( SIB ), Swiss Institute of Bioinformatics, Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation ( CEISAM ), Université de Nantes ( UN ) -Centre National de la Recherche Scientifique ( CNRS ), Karlsruhe Institute of Technology ( KIT ), University of Ottawa [Ottawa] (uOttawa), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Philipps Universität Marbug, Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Swiss Institute of Bioinformatics - Lausanne (SIB), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - Faculté des Sciences et des Techniques, and Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Rhizophagus irregularis, mutualism, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Fungus, 01 natural sciences, Genome, carbohydrate-active enzymes, effector, fungal evolution, glomales, Glomeromycota, Evolution, Molecular, 03 medical and health sciences, Symbiosis, Mycorrhizae, Botany, Gene, 030304 developmental biology, Genomic organization, Mucoromycotina, 0303 health sciences, Multidisciplinary, biology, [ SDV ] Life Sciences [q-bio], Base Sequence, fungi, Sequence Analysis, DNA, 15. Life on land, Plants, Biological Sciences, biology.organism_classification, Evolutionary biology, Genome, Fungal, 010606 plant biology & botany
Abstract: International audience; The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.
Published: 2013

22. The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont

Author: Julie Poulain, Erika Lindquist, Natalia Requena, Raman Koul, Yair Shachar-Hill, Gerald A. Tuskan, C. da Silva, Vivienne Gianinazzi-Pearson, Francis Martin, Valentina Fiorilli, Harris Shapiro, Christophe Roux, Stefan A. Rensing, Helge Küster, Raffaella Balestrini, Annegret Kohler, Maria J. Harrison, Uta Paszkowski, Karim Benabdellah, Mohamed Hijri, Guillaume Bécard, A. Waschke, Daniel Croll, P. Dozolme-Seddas, Ian R. Sanders, Damien Formey, Philipp Franken, Concepción Azcón-Aguilar, Emmanuelle Morin, Nicole Helber, D. van Tuinen, Luisa Lanfranco, Paola Bonfante, J. P. W. Young, Alexandre Colard, Y. Liu, Emilie Tisserant, Nuria Ferrol, S. K. Gomez, Mathilde Malbreil, Peter J. Lammers, Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Unité de recherche Mycologie et Sécurité des Aliments ( MSA ), Institut National de la Recherche Agronomique ( INRA ), Dipartimento di Biologia Vegetale, University of Turin, Departamento de Microbiologia del Suelo y Sistemas Simbioticos Estacion Experimental del Zaidin, Spanish National Research Council ( CSIC ), Department of Ecology and Evolution, Université de Lausanne ( UNIL ), Plant Pathology, Swiss Federal Institute of Technology in Zürich ( ETH Zürich ), IG Génoscope, Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Boyce Thompson Institute [Ithaca], Department of Chemistry and Biochemistry, New Mexico State University, Estacion Experimental del Zaidin, Instituto per la Protezione delle Plante del CNR, Laboratoire de Recherche en Sciences Végétales ( LRSV ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Leibniz-Institute of Vegetable and Ornamental Crops, Department of Plant Nutrition, Karlsruhe Institute of Technology ( KIT ), Institut de la Recherche en Biologie Végétale Departement de sciences biologiques, Université de Montréal, Joint Genome Institute ( JGI ), 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, Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Leibniz Institute of Vegetale and Ornamental Crops, Departamento de Microbiologia del Suelo y Sistemas Simbioticos, Institut für Pflanzengenetik, Gottfried Wilhelm Leibniz Universität Hannover, Departement de Biologie Moléculaire Végétale, Centre for Biological Signalling Studie Freiburg Initiative for Systems Biology and Faculty of Biology, Albert Ludwigs University, Department of Plant Biology, Michigan State University ( MSU ), Biosciences, Oak Ridge National Laboratory, Department of Biology, University of York [York, UK], Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Unité de recherche Mycologie et Sécurité des Aliments (MSA), Institut National de la Recherche Agronomique (INRA), Spanish National Research Council (CSIC), Université de Lausanne (UNIL), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Karlsruhe Institute of Technology (KIT), Joint Genome Institute (JGI), 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, Leibniz Universität Hannover [Hannover] (LUH), Michigan State University [East Lansing], Michigan State University System-Michigan State University System, BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Freiburg [Freiburg], Università degli studi di Torino = University of Turin (UNITO), Université de Lausanne = University of Lausanne (UNIL), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Leibniz Universität Hannover=Leibniz University Hannover
Subjects: 0106 biological sciences, Rhizophagus irregularis, Physiology, [SDV]Life Sciences [q-bio], Genes, Fungal, Colony Count, Microbial, mycorrhiza, Plant Science, 01 natural sciences, Polymorphism, Single Nucleotide, glomeromycota, glomus, meiosis and recombination genes, small secreted proteins, symbiosis, transcript profiling, Glomeromycota, Fungal Proteins, 03 medical and health sciences, Gene Expression Regulation, Fungal, Mycorrhizae, Botany, RNA, Messenger, Mycorrhiza, Mycelium, Glomus, 030304 developmental biology, Gene Library, 2. Zero hunger, Genetics, 0303 health sciences, biology, Obligate, Base Sequence, [ SDV ] Life Sciences [q-bio], arbuscular mycorrhiza, fungi, Fungal genetics, 15. Life on land, Plants, biology.organism_classification, Protein Structure, Tertiary, Up-Regulation, Arbuscular mycorrhiza, Meiosis, Transcriptome, 010606 plant biology & botany
Abstract: • The arbuscular mycorrhizal symbiosis is arguably the most ecologically important eukaryotic symbiosis, yet it is poorly understood at the molecular level. To provide novel insights into the molecular basis of symbiosis-associated traits, we report the first genome-wide analysis of the transcriptome from Glomus intraradices DAOM 197198. • We generated a set of 25,906 nonredundant virtual transcripts (NRVTs) transcribed in germinated spores, extraradical mycelium and symbiotic roots using Sanger and 454 sequencing. NRVTs were used to construct an oligoarray for investigating gene expression. • We identified transcripts coding for the meiotic recombination machinery, as well as meiosis-specific proteins, suggesting that the lack of a known sexual cycle in G. intraradices is not a result of major deletions of genes essential for sexual reproduction and meiosis. Induced expression of genes encoding membrane transporters and small secreted proteins in intraradical mycelium, together with the lack of expression of hydrolytic enzymes acting on plant cell wall polysaccharides, are all features of G. intraradices that are shared with ectomycorrhizal symbionts and obligate biotrophic pathogens. • Our results illuminate the genetic basis of symbiosis-related traits of the most ancient lineage of plant biotrophs, advancing future research on these agriculturally and ecologically important symbionts.
Published: 2012

23. Pathogenicity of animal and plant parasitic Aphanomyces spp and their economic impact on aquaculture and agriculture

Author: Thomas Becking, David Street-Jones, Andrei Kiselev, Elodie Gaulin, Frédéric Grandjean, Valentina Rossi, Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Swedish University of Agricultural Sciences (SLU), Maribohilleshög Research AB (DLF Beet Seed R&D), DLF Beet Seed, University of Aberdeen, Interactions Microbiennes dans la Rhizosphère et les Racines, Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Office Français de la Bio-diversitée (AFB) No 150656, European Project: 766048,MSCA-ITN-2017,PROTECTA, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), and European Union’s Horizon 2020 Research and Innovationprogramme No 766048
Subjects: Crayfish plague, Root rot, Zoology, Aphanomyces, Biology, Microbiology, 03 medical and health sciences, Aquaculture, Epizootic ulcerative syndrome, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Colonization, 14. Life underwater, 030304 developmental biology, 0303 health sciences, business.industry, Host (biology), [SDV.BA]Life Sciences [q-bio]/Animal biology, Pea, food and beverages, 04 agricultural and veterinary sciences, biology.organism_classification, Crayfish, Fish, Sugarbeet, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Sugar beet, business
Abstract: International audience; Parasitic Aphanomyces species are a global threat to agri- and aquaculture, causing multimillion USD damage every year. Via the global trade, Aphanomyces has spread across all continents with exception of South America and Antarctica, and has become a major problem in pea, sugar beet, fish and crayfish production. The widespread A. euteiches and A. cochlioides induce root rot diseases in leguminous species and sugar beet respectively. The fish pathogen A. invadans is the causative agent of Epizootic Ulcerative Syndrome in various fish species whilst A. astaci infects crayfishes causing crayfish plague. Aphanomyces have developed an efficient transmission and infection mechanism which allows a rapid colonization and disruption of the host's infected tissues. This review presents an overview on the current research on Aphanomyces genus. We summarise the latest research efforts on four pathogenic Aphanomyces species, shedding light on the biology of these microorganisms, the pathogenicity factors of these parasites, the diseases which they cause, their distribution and finally the strategies to control the diseases.
Published: 2022

24. Recent advances in mass spectrometry–based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions

Author: Jean-Philippe Combier, Serge Plaza, Bertrand Fabre, 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: Proteomics, 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Computational biology, 010402 general chemistry, Mass spectrometry, 01 natural sciences, Biochemistry, Enrichment methods, Mass Spectrometry, Workflow, 0104 chemical sciences, Analytical Chemistry, Open Reading Frames, 03 medical and health sciences, Open reading frame, 030104 developmental biology, [CHIM]Chemical Sciences, Ribosome profiling, Peptides, ComputingMilieux_MISCELLANEOUS
Abstract: Short open reading frame (sORF)-encoded polypeptides (SEPs) have recently emerged as key regulators of major cellular processes. Computational methods for the annotation of sORFs combined with transcriptomics and ribosome profiling approaches predicted the existence of tens of thousands of SEPs across the kingdom of life. Although, we still lack unambiguous evidence for most of them. The method of choice to validate the expression of SEPs is mass spectrometry (MS)-based peptidomics. Peptides are less abundant than proteins, which tends to hinder their detection. Therefore, optimization and enrichment methods are necessary to validate the existence of SEPs. In this article, we discuss the challenges for the detection of SEPs by MS and recent developments of biochemical approaches applied to the study of these peptides. We detail the advances made in the different key steps of a typical peptidomics workflow and highlight possible alternatives that have not been explored yet.
Published: 2021

25. The Phosphate Starvation Response System: Its Role in the Regulation of Plant–Microbe Interactions

Author: Pierre-Marc Delaux, Mariel C Isidra-Arellano, Oswaldo Valdés-López, Universidad Nacional Autónoma de México (UNAM), Evolution des Interactions Plantes-Microorganismes, 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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), IN201320/Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica, A1-S-9454/Consejo Nacional de Ciencia y Tecnologia, and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Plant Science, 01 natural sciences, MESH: Plants / microbiology, chemistry.chemical_compound, Mycorrhizae, MESH: Transcription Factors / physiology, PHR1, Soil Microbiology, 2. Zero hunger, Abiotic component, Plant immune system, MESH: Plants / metabolism, food and beverages, MESH: Arabidopsis Proteins / metabolism, General Medicine, Plants, Plant host Pi status, Cell biology, Plant-associated microbiota, AM fungi, Starvation response, MESH: Mycorrhizae / metabolism, MESH: Arabidopsis Proteins / physiology, Context (language use), Biology, Phosphates, MESH: Phosphates / metabolism, 03 medical and health sciences, Immune system, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, MESH: Mycorrhizae / physiology, Transcription factor, MESH: Transcription Factors / metabolism, Arabidopsis Proteins, Host (biology), fungi, Root microbiome, Cell Biology, MESH: Symbiosis* / physiology, 15. Life on land, Phosphate, MESH: Phosphates / deficiency, 030104 developmental biology, MESH: Soil Microbiology, chemistry, Transcription Factors, 010606 plant biology & botany
Abstract: Phosphate (Pi) deficiency is a major factor limiting plant productivity worldwide. Land plants have evolved different strategies to cope with Pi deficiency. For instance, plants activate the so-called Pi starvation response (PSR) system, which is regulated by the transcription factor Phosphate Starvation Response1 (PHR1), to adjust plant growth and metabolic activity accordingly. Additionally, land plants can also establish mutualistic associations with soil microbes able to solubilize Pi from plant-inaccessible soil complexes and to transfer it to the host plant. A growing body of evidence indicates that PHR1 and the PSR system not only regulate the plant responses to Pi deficiency in an abiotic context, but they are also crucial for plants to properly interact with beneficial soil microbes able to provide them with soluble Pi. Recent evidence indicates that PHR1 and the PSR system contribute to shaping the plant-associated microbiota through the modulation of the plant immune system. The PSR and immune system outputs are tightly integrated by PHR1. Here, we review how plant host Pi status influences the establishment of the mutualistic association with soil microbes. We also highlight the role of PHR1 and the PSR system in shaping both the root microbiome and plant responses to Pi deficiency.
Published: 2021

26. In Depth Exploration of the Alternative Proteome of Drosophila melanogaster

Author: Fabre, Bertrand, Choteau, Sebastien A, Duboé, Carine, Pichereaux, Carole, Montigny, Audrey, Korona, Dagmara, Deery, Michael, Camus, Mylène, Brun, Christine, Burlet-Schiltz, Odile, Russell, Steve, Combier, Jean-Philippe, Lilley, Kathryn S, Plaza, Serge, Peptides et petits ARN, 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de pharmacologie et de biologie structurale (IPBS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Cambridge [UK] (CAM), Centre National de la Recherche Scientifique (CNRS), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), ANR-16-CE12-0018,biomiPEPs,Vers une compréhension globale des miPEPs(2016), Brun, C., Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, Vers une compréhension globale des miPEPs - - biomiPEPs2016 - ANR-16-CE12-0018 - AAPG2016 - VALID, Pichereaux, Carole [0000-0002-7559-5358], Apollo - University of Cambridge Repository, Deery, Michael [0000-0001-6895-9814], Russell, Steve [0000-0003-0546-3031], Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cell and Developmental Biology, short open reading frame–encoded polypeptide, microprotein, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], alternative proteins, peptidomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], mass spectrometry
Abstract: Recent studies have shown that hundreds of small proteins were occulted when protein coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocystronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome wide exploration of the alternative proteome is still limited to a few species. In the present article we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster. Subcellular localization, protein domains and short linear motifs were predicted for 235 of the alternative proteins identified and point towards specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed fourteen alternative proteins with developmentally regulated expression patterns and ten induced upon heat shock treatment of embryos, demonstrating stage or stress specific production of alternative proteins.
Published: 2022

27. An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase <scp>MtLYR3</scp>

Author: Younes Bouchiba, Jérémy Esque, Ludovic Cottret, Maude Maréchaux, Mégane Gaston, Virginie Gasciolli, Jean Keller, Nico Nouwen, Djamel Gully, Jean‐François Arrighi, Clare Gough, Benoit Lefebvre, Sophie Barbe, Jean‐Jacques Bono, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), ANR-16-CE20-0025,WHEATSYM,ROLES DES SIGNAUX MICROBIENS LCO/CO ET DE LEURS RECEPTEURS DE PLANTES DANS DES INTERACTIONS BENEFIQUES ENTRE MONOCOTYLEDONES ET MICROORGANISMES DU SOL(2016), ANR-14-CE18-0008,NICE CROPS,Bio-stimulateurs chitiniques naturels pour une agriculture durable(2014), ANR-20-CE20-0017,DUALITY,Récepteurs et contrôle de l'état redox à l'interface symbiose et immunité(2020), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-18-EURE-0019,TULIP-GSR,The Toulouse-Perpignan(2018)
Subjects: Chitosan, lysin motif receptor-like receptor, Oligosaccharides, lipo-chitooligosaccharide, Chitin, Lupinus angustifolius, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Biochemistry, biosis, Molecular Docking Simulation, free energy landscape, plant endosym, receptor ligand binding, docking, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], Medicago truncatula, Aeschynomene spp, Tyrosine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, steered molecular dynamics, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, Molecular Biology
Abstract: International audience; N-acetylglucosamine containing compounds acting as pathogenic or symbiotic signals are perceived by plant-specific Lysin Motif Receptor-Like Kinases (LysM-RLKs). The molecular mechanisms of this perception are not fully understood, notably those of lipo-chitooligosaccharides (LCOs) produced during root endosymbioses with nitrogen-fixing bacteria or arbuscular mycorrhizal fungi. In Medicago truncatula, we previously identified the LysM-RLK LYR3 (MtLYR3) as a specific LCO-binding protein. We also showed that the absence of LCO binding to LYR3 of the non-mycorrhizal Lupinus angustifolius, (LanLYR3), was related to LysM3, which differs from that of MtLYR3 by several amino acids and, particularly, by a critical tyrosine residue absent in LanLYR3. Here, we aimed to define the LCO binding site of MtLYR3 by using molecular modelling and simulation approaches, combined with site-directed mutagenesis and LCO binding experiments. 3D models of MtLYR3 and LanLYR3 ectodomains were built, and homology modelling and molecular dynamics (MD) simulations were performed. Molecular docking and MD simulation on the LysM3 identified potential key residues for LCO binding. We highlighted by steered MD simulations that in addition to the critical tyrosine, two other residues were important for LCO binding in MtLYR3. Substitution of these residues in LanLYR3-LysM3 by those of MtLYR3-LysM3 allowed the recovery of high-affinity LCO binding in experimental radioligand-binding assays. An analysis of selective constraints revealed that the critical tyrosine has experienced positive selection pressure and is absent in some LYR3 proteins. These findings now pave the way to uncover the functional significance of this specific evolutionary pattern.
Published: 2022

28. Ontogenetic changes in root traits and root-associated fungal community composition in an heteroblastic epiphytic bromeliad

Author: Leroy, Céline, Maes, Arthur QuyManh, Louisanna, Eliane, Séjalon-Delmas, Nathalie, Erktan, Amandine, Schimann, Heidy, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Interactions Microbiennes dans la Rhizosphère et les Racines, Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Georg-August-University = Georg-August-Universität Göttingen, Pioneer Company through ANRT support., and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: Bromeliaceae, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, ITS metabarcoding, Ontogeny, Fungal functional guilds, Heteroblasty, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Root trait gradients, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Bromeliaceae, Fungal functional guilds, heteroblasty, ITS metabarcoding, ontogeny, root trait gradients, Ecology, Evolution, Behavior and Systematics
Abstract: csv file and appendix of manuscript entitled "Ontogenetic changes in root traits and root-associated fungal community composition in an heteroblastic epiphytic bromeliad" by Leroy C., Maes AQ, Louisanna, Séjalon-Delmas N, Erktan A, Schimann H and accepted for publication in Oikos (10.1111/oik.09213) Abstract: Heteroblastic variations among leaf traits is a well‐known process, especially in bromeliad species that show abrupt changes, but little effort was directed to test whether comparable ontogenetic variation occurs among root traits and their fungal partners. Usually considered for their mechanical role, roots of bromeliads may also play a role in resource use that we expect to differ between ontogenetic stages, namely nutrient pulse-supplied atmospherics (young stage) and continuously-supplied tanks (later stage). On a selection of adventitious roots of the heteroblastic epiphyte Lutheria splendens, we explored (i) ontogenetic variations in morphological and anatomical root traits, namely the number of adventitious roots and tips, total root length, average root diameter, root tissue density, specific root length, and root tissue areas, and (ii) ontogenetic changes in the composition of the root-associated fungal communities using ITS1 region-based high-throughput sequencing. Plant size, taken as an indicator of gradual ontogenetic variations, and plant stage had significant effects on root traits, unless for root tissue density. The number of adventitious roots and tips, the total root length, average root diameter, and all root tissue areas (i.e., velamen, outer cortex, inner cortex, vascular cylinder) increased gradually with ontogeny while the specific root length decreased abruptly. The root-associated fungal communities varied with plant stage. The tank stage showed higher proportion of mycorrhizal fungi and a lower abundance of dark septate endophyte as compared to atmospheric stage. Overall, we demonstrated significant ontogenetic variations of root traits and fungal partners in bromeliad species that suggest important changes in the strategy for resource use as plants mature. We invite future root trait studies to better account for ontogenetic variations.
Published: 2022
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29. De l’incidentalomeà la découverte secondaire

Author: Cedric Gesbert, Cécile Torregrosa, Marie-France Mamzer, Laboratoire Ethique Politique et Santé (EA 4569), Université Paris Descartes - Paris 5 (UPD5), Laboratoire de Recherche en Sciences Végétales (LRSV), 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: 0301 basic medicine, Modern medicine, [SDV]Life Sciences [q-bio], Incidentaloma, Incidental Discovery, Health technology, General Medicine, General Biochemistry, Genetics and Molecular Biology, Term (time), 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, 030220 oncology & carcinogenesis, Phenomenon, Psychology, Cognitive psychology, Medical literature
Abstract: Le termeincidentalome, créé en 1982, s’est, depuis, diffusé dans la littérature médicale. Il ne semble cependant pas exister de définition précise pour décrire ce qu’est un incidentalome. Dans les usages initiaux, l’incidentalome désignait une masse détectée à l’occasion d’un examen d’imagerie prescrit à visée diagnostique sans qu’un lien ne soit déterminé avec le motif de réalisation de l’examen. La qualification d’« incidentalome » de cette masse n’apportait aucune précision sur sa nature, celle-ci pouvant être située dans de nombreuses zones anatomiques, être sécrétante ou non, être bénigne ou maligne… Aujourd’hui, le terme d’incidentalomeporte une dimension beaucoup plus large, semblant recouvrir la notion de découverte fortuite, qu’elle soit radiologique, biologique ou génétique. Cet usage évolutif du terme démontre son caractère heuristique. Il est le signe d’une modification de la médecine moderne qui hésite entre une clinique des patients et une clinique des données. Les découvertes fortuites sont un phénomène connu et anticipé par les radiologues. Ces découvertes ne sont donc plus fortuites, ni même inattendues, mais bien secondaires à l’usage de la technologie en santé.
Published: 2020

30. DELLA family duplication events lead to different selective constraints in angiosperms

Author: Francisco Cabello-Hurtado, Cyril Libourel, Abdelkader Aïnouche, Pauline Delcros, Jean Keller, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), 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), Thesis Grant, Ministère de l'Enseignement Supérieur et de la Recherche, Ecological Genomics of Polyploidy, International Associated Laboratory, OPP1172165, Bill and Melinda Gates Foundation, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Subfamily, Lineage (evolution), MESH: Selection, Genetic, Plant Science, MESH: Gibberellins / metabolism, Biology, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, Evolutionary history, Magnoliopsida, 03 medical and health sciences, Phylogenetics, Molecular evolution, MESH: Transcription Factors / genetics, Gene Duplication, MESH: Evolution, Molecular, Gene duplication, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Selection, Genetic, MESH: Phylogeny, Eudicots, Clade, MESH: Magnoliopsida / genetics, Phylogeny, MESH: Gene Duplication, Plant Proteins, MESH: Magnoliopsida / classification, Fabaceae, Subclade, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Gibberellins, MESH: Plant Proteins / genetics, 030104 developmental biology, Evolutionary biology, Multigene Family, Insect Science, MESH: Multigene Family, Animal Science and Zoology, DELLA, Transcription Factors
Abstract: International audience; Gibberellic acid (GA) is a major plant hormone involved in several biological processes from the flowering to the symbiosis with microorganisms. Thus, the GA regulation is crucial for plant biology. This regulation occurs via the DELLA proteins that belong to the GRAS transcription factor family. DELLA proteins are characterised by a DELLA N-terminal and a GRAS C-terminal domains. It is well known that DELLA activity appears after the bryophytes divergence and then evolved in the vascular plant lineages. Here we present the phylogeny of DELLA across 75 species belonging to various lineages from algae, liverworts and angiosperms. Our study confirmed two main duplication events, the first occurring before the angiosperms divergence and the other specific to the eudicots lineage. Comparative analysis of DELLA subclades in angiosperms revealed the loss in Poaceae and strong alteration in other species of the DELLA functional domain in the DELLA2 clade. In addition, molecular evolution analysis suggests that each of the clades (named DELLA1.1, DELLA1.2 and DELLA2) evolved differently but copies of each subclade are under strong purifying selection. This also suggests that, although the DELLA functional domain is altered in DELLA2, DELLA2 orthologs are still functional and operate in a different way compared to DELLA1 copies. In angiosperms, additional duplication events occurred and led to duplicate copies in species, genus or family such as in the Fabaceae subfamily Papilionoideae. This duplication led to the formation of additional paralogs in the DELLA1.2 subclade (DELLA1.2.1 and DELLA1.2.2). Interestingly, both copies appeared to be under relaxing selection revealing different evolutionary fate of the DELLA duplicated copies.
Published: 2020

31. Lipo-chitooligosaccharides as regulatory signals of fungal growth and development

Author: Candice L. Swift, Arthur QuyManh Maes, Nancy P. Keller, Cristobal Carrera Carriel, Kevin Garcia, Guillaume Bécard, Joanna Tannous, Quanita J. Choudhury, Jean-Michel Ané, Michelle A. O’Malley, Junko Maeda, Jin Woo Bok, Michelle Keller-Pearson, Tomás Allen Rush, Patricia Jargeat, Virginie Puech-Pagès, Sylvain Cottaz, Michael R. Sussman, Fabienne Maillet, Jeniel E. Nett, Adeline Bascaules, Jessy Labbé, Kevin R. Cope, Alexandra Haouy, Bailey Kleven, Véréna Poinsot, Chad J. Johnson, Sébastien Fort, Corinne Lefort, Devanshi Khokhani, Fort, Sébastien, University of Wisconsin-Madison, Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Evolution des Interactions Plantes-Microorganismes, 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)-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)-MetaboHUB-MetaToul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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), Interactions moléculaires et réactivité chimique et photochimique (IMRCP), Institut de Chimie de Toulouse (ICT-FR 2599), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), South Dakota State University (SDSTATE), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), The University of Tennessee [Knoxville], University of Georgia [USA], University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Fédérale Toulouse Midi-Pyrénées, Interactions Microbiennes dans la Rhizosphère et les Racines, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-MetaToul-MetaboHUB, 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-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), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of California [Santa Barbara] (UCSB), University of California, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), MetaToul Agromix, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Fluides, Energie, Réacteurs, Matériaux et Transferts (FERMAT), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), BIBAC - Chimie analytique et interactions biomolécules - matière molle biomimétique (BIBAC), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT), and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)
Subjects: 0301 basic medicine, Hypha, Science, General Physics and Astronomy, Oligosaccharides, Chitin, 02 engineering and technology, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Microbiology, Microbial ecology, 03 medical and health sciences, Fungal biology, Pseudohyphal growth, Symbiosis, Ascomycota, Mycorrhizae, Spore germination, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Cellular microbiology, Fungal ecology, lcsh:Science, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Chitosan, Multidisciplinary, Ecology, Phylum, Basidiomycota, Fatty Acids, fungi, Fungi, General Chemistry, Spores, Fungal, 021001 nanoscience & nanotechnology, biology.organism_classification, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Spore, 030104 developmental biology, lcsh:Q, 0210 nano-technology, Bacteria, Rhizobium, Signal Transduction
Abstract: Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by rhizobial bacteria that trigger the nodulation process in legumes, and by some fungi that also establish symbiotic relationships with plants, notably the arbuscular and ecto mycorrhizal fungi. Here, we show that many other fungi also produce LCOs. We tested 59 species representing most fungal phyla, and found that 53 species produce LCOs that can be detected by functional assays and/or by mass spectroscopy. LCO treatment affects spore germination, branching of hyphae, pseudohyphal growth, and transcription in non-symbiotic fungi from the Ascomycete and Basidiomycete phyla. Our findings suggest that LCO production is common among fungi, and LCOs may function as signals regulating fungal growth and development., Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by certain bacteria and fungi that establish symbiotic relationships with plants. Here, the authors show that LCOs are produced also by many other, non-symbiotic fungi, and regulate fungal growth and development.
Published: 2020

32. Tracking the evolutionary history of the Allium ampeloprasum L. complex (section Allium) provides evidence of the contribution of North African diploids to the formation of allopolyploid horticultural groups

Author: Malika Ourari, Rachid Amirouche, Nabila Amirouche, Abdelkader Aïnouche, Thinhinan Khedim, Jean Keller, Malika L. Aïnouche, Université des Sciences et de la Technologie Houari Boumediene [Alger] (USTHB), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université Abderrahmane Mira [Béjaïa], 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), international Project CMEP-Tassili Hubert Curien, 'Polyploidy, Genome Evolution and Biodiversity' [08 MDU 724], Laboratory of Biology and Physiology of Organisms, University of Sciences and Technology Houari Boumediene (USTHB, Algiers, Algeria), UMR-CNRS 6553 Ecobio, University of Rennes 1 (France), CNEPRU project [F00220100043], USTHB-internship grants, Université des Sciences et de la Technologie Houari Boumediene = University of Sciences and Technology Houari Boumediene [Alger] (USTHB), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Molecular phylogeny, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, 03 medical and health sciences, Intergenic region, Allium ampeloprasum, Botany, Genetics, Wild genetic resources, Domestication, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, biology, Allium ampeloprasum complex, Diploids, food and beverages, Polyploids, Polyploid complex, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 15. Life on land, biology.organism_classification, 030104 developmental biology, Algeria, Molecular phylogenetics, Allium, Gene pool, Ploidy, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; The economically important Allium ampeloprasum L. represents a polyploid complex, comprising hexa- and octoploid Great Headed Garlic horticultural cultivars (6x-8x GHG) and several traditional varieties of the tetraploid (4x) leeks (Leek, Bulbous leek, Kurrat and Pearl onion). Its wild representatives were indicated as rare in the Mediterranean region. This study aims to explore the diversity and origin of polyploidy in this complex, including its wild relatives A. baeticum Bossier and A. guttatum Steven with particular focus on the poorly investigated North-African region. Natural populations were sampled in Algeria in various bioclimatic conditions, then subjected to karyological and molecular phylogenetic analyses based on nuclear rDNA ITS region and chloroplast trnL-trnF and trnD-trnT intergenic spacers. Comparative analyses included available Genbank accession sequences representing old-world relatives. Chromosome count surveys revealed an unexpected higher occurrence of diploid (2n = 16) than tetraploid (2n = 32) cytotypes. The phylogenetic analyses first allowed positioning the Algerian material within the A. ampeloprasum complex. Interestingly, all the Algerian diploid and tetraploid populations from A. ampeloprasum and A. baeticum form a distinct monophyletic group. The results provide novel and robust evidence demonstrating that the North African diploid A. ampeloprasum genetic pool widely contributed as a source of progenitors not only for the A. ampeloprasum and A. baeticum Algerian tetraploids, but also in the formation of the GHG and Leek cultivated allopolyploids. Therefore, the North African populations emerge as an important reservoir of new wild genetic resources of great interest for tracing the origin of crop domestication and for breeding programs of cultivated varieties.
Published: 2020

33. An oomycete effector targets a plant RNA helicase involved in root development and defense

Author: Camborde, Laurent, Kiselev, Andrei, Pel, Michiel J. C., Le Ru, Aurélie, Jauneau, Alain, Pouzet, Cécile, Dumas, Bernard, Gaulin, Elodie, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Plateforme TRI FR-AIB, Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Réseau Imagerie-Genotoul ( TRI-Genotoul), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), and European Project: 766048,MSCA-ITN-2017,PROTECTA
Subjects: MtRH10, fungi, food and beverages, Aphanomyces, Plant Roots, Gene Expression Regulation, Plant, RNA, Plant, Medicago truncatula, Medicago, oomycete, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nucleolar stress, plant development, RNA Helicases, Plant Proteins, effectors
Abstract: International audience; Oomycete plant pathogens secrete effector proteins to promote disease. The damaging soilborne legume pathogen Aphanomyces euteiches harbors a specific repertoire of Small Secreted Protein effectors (AeSSPs), but their biological functions remain unknown. Here we characterize AeSSP1256. The function of AeSSP1256 is investigated by physiological and molecular characterization of Medicago truncatula roots expressing the effector. A potential protein target of AeSSP1256 is identified by yeast-two hybrid, co-immunoprecipitation, and fluorescent resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM) assays, as well as promoter studies and mutant characterization. AeSSP1256 impairs M. truncatula root development and promotes pathogen infection. The effector is localized to the nucleoli rim, triggers nucleoli enlargement and downregulates expression of M. truncatula ribosome-related genes. AeSSP1256 interacts with a functional nucleocytoplasmic plant RNA helicase (MtRH10). AeSSP1256 relocates MtRH10 to the perinucleolar space and hinders its binding to plant RNA. MtRH10 is associated with ribosome-related genes, root development and defense. This work reveals that an oomycete effector targets a plant RNA helicase, possibly to trigger nucleolar stress and thereby promote pathogen infection.
Published: 2022

34. FOLFIRI plus BEvacizumab or aFLIbercept after FOLFOX-bevacizumab Failure for COlorectal Cancer (BEFLICO): An AGEO Multicenter Study

Author: Torregrosa, Cécile, Pernot, Simon, Vaflard, Pauline, Perret, Audrey, Tournigand, Christophe, Randrian, Violaine, Doat, Solene, Neuzillet, Cindy, Moulin, Valérie, Stouvenot, Morgane, Roth, Gael, Darbas, Tiffany, Auberger, Benjamin, Godet, Tiphaine, Jaffrelot, Marion, Lambert, Aurélien, Dubreuil, Olivier, Gluszak, Cassandre, Bernard-Tessier, Alice, Turpin, Anthony, Palmieri, Lola-Jade, Bouche, Olivier, Goujon, Gael, Lecomte, Thierry, Sefrioui, David, Locher, Christophe, Grados, Lucien, Gignoux, Pauline, Trager, Stéphanie, Nassif, Elise, Saint, Angélique, Hammel, Pascal, Lecaille, Cédric, Bureau, Mathilde, Perrier, Marine, Botsen, Damien, Bourgeois, Vincent, Taieb, Julien, Auclin, Edouard, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Bergonié [Bordeaux], UNICANCER, Institut Curie [Paris], Ethologie animale et humaine (EthoS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre hospitalier universitaire de Poitiers (CHU Poitiers), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Groupe hospitalier de La Rochelle, Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Centre Hospitalier Universitaire [Grenoble] (CHU), Université Grenoble Alpes (UGA), CHU Limoges, Hopital de Bohars - CHRU Brest (CHU - BREST ), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Institut de Cancérologie de Lorraine - Alexis Vautrin [Nancy] (UNICANCER/ICL), Commissariat à l'énergie atomique et aux énergies alternatives - Laboratoire d'Electronique et de Technologie de l'Information (CEA-LETI), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Cancérologie de l'Ouest [Angers/Nantes] (UNICANCER/ICO), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Cancer Heterogeneity, Plasticity and Resistance to Therapies - UMR 9020 - U 1277 (CANTHER), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université - Faculté de Médecine (SU FM), Sorbonne Université (SU), Université de Reims Champagne-Ardenne (URCA), Centre Hospitalier Universitaire de Reims (CHU Reims), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Nutrition, croissance et cancer (U 1069) (N2C), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Groupe innovation et ciblage cellulaire (GICC), EA 7501 [2018-...] (GICC EA 7501), Université de Tours (UT), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Communications Cellulaires et Différenciation (CCD), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier de Meaux, Périnatalité et Risques Toxiques - UMR INERIS_I 1 (PERITOX), Institut National de l'Environnement Industriel et des Risques (INERIS)-Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Hôpital Louis Domergue [CHU de la Martinique], CHU de la Martinique [Fort de France], Clinique de l'Estrée, Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Centre de Lutte contre le Cancer Antoine Lacassagne [Nice] (UNICANCER/CAL), UNICANCER-Université Côte d'Azur (UCA), Hôpital Paul Brousse, Polyclinique Bordeaux Nord Aquitaine (PBNA), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Saint-Antoine [AP-HP], Institut Jean Godinot [Reims], Centre Hospitalier Boulogne-sur-mer, Cancer Research and Personalized Medicine - CARPEM [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Necker - Enfants Malades [AP-HP], Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Service d'Hépato-Gastro-Entérologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Polyclinique Bordeaux Nord Aquitaine, Laboratoire de Virologie [CHU Saint-Antoine], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), and École pratique des hautes études (EPHE)
Subjects: Male, Proto-Oncogene Proteins B-raf, Recombinant Fusion Proteins, Leucovorin, Middle Aged, Bevacizumab, Receptors, Vascular Endothelial Growth Factor, Antineoplastic Combined Chemotherapy Protocols, Humans, Camptothecin, Female, Fluorouracil, Colorectal Neoplasms, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; After failure of first line FOLFOX-bevacizumab for metastatic colorectal cancer (mCRC), adding either bevacizumab or aflibercept to second-line FOLFIRI increases survival compared to FOLFIRI alone. In this French retrospective multicentre cohort, we included patients with a mCRC treated with either FOLFIRI-aflibercept or FOLFIRI-bevacizumab. The primary endpoint was overall survival (OS), and secondary endpoints were progression-free survival (PFS), disease control rate (DCR: CR\,+\,PR\,+\,SD) and safety. We included 681 patients from 36 centers, 326 and 355 in the aflibercept and bevacizumab groups, respectively. Median age was 64.2\,years and 45.2% of patients were men. Most patients had RAS-mutated tumors (80.8%) and synchronous metastases (85.7%). After a median follow up of 31.2~months, median OS was 13.0~months (95% CI: 11.3-14.7) and 10.4~months (95% CI: 8.8-11.4) in the bevacizumab and aflibercept groups, respectively (P\
Published: 2022

35. Ecological succession and fine sediment accretion influence local patch dynamics of a pioneer riparian species ( Typha minima Hoppe)

Author: Caroline Le Bouteiller, Yoan Paillet, André Evette, Margot Trinquier, Renaud Jaunatre, Nadège Popoff, Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Erosion torrentielle neige et avalanches (UR ETGR (ETNA)), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, and Symbhi (Syndicat Mixte des Bassins Hydrauliques de l'Isere)
Subjects: 010504 meteorology & atmospheric sciences, wandering river, Ecological succession, Aquatic Science, 010502 geochemistry & geophysics, 01 natural sciences, hydrogeomorphology, Typha minima, 0105 earth and related environmental sciences, Riparian zone, Abiotic component, Hydrology, geography, geography.geographical_feature_category, biology, Hydrogeomorphology, abiotic factors, Sediment, 15. Life on land, biology.organism_classification, clonal plant, Patch dynamics, [SDE]Environmental Sciences, Riparian vegetation, Geology, Accretion (coastal management)
Abstract: International audience; Changes in environmental variables induced by ecological succession and hydrogeomorphological processes affects riparian vegetation dynamics along rivers. The biotic and abiotic factors driving local patch dynamics of riparian species is little known for early successional stages. To fill this gap, we examined local patch dynamics and frequency of occurrence of a protected riparian pioneer species (Typha minima Hoppe) and related it to several biotic and abiotic variables along the Isere River (France) from 2016 to 2019. We monitored biotic and abiotic factors related to ecological succession and sediment accretion. We implemented Linear Mixed and Generalized Mixed Models to analyze how environmental factors affected patch boundary dynamics of T. minima. Finally, we built a Structural Equation Model to describe potential relationships between T. minima frequency, height above mean water level, vegetation cover and composition. We found that a thick layer of silt and sand deposits as well as a moderate herbaceous and low shrub cover layer characterized T. minima patch progression close to the mean water level. Typha minima stands did not seem to expand on coarser substrates with lower herbaceous cover. Its maintenance was associated with large silt and sand deposits and high cover of herbaceous plants and shrubs well above the mean water level. The variables characterizing patch regression were not clearly identified. Finally, the interaction between bar height, vegetation cover and succession stage did not explain variations in T. minima frequency. Our results provide knowledge about the environmental variables associated with T. minima patch dynamics, which are useful for future conservation and restoration projects. Habitat rejuvenation through restoration of natural river flow regimes could sustain local T. minima transplantation and large population turnover essential to the conservation of this species.
Published: 2021

36. The Jo-In protein welding system is a relevant tool to create CBM-containing plant cell wall degrading enzymes

Author: Guy Lippens, Pierre Roblin, Cedric Montanier, Thomas Enjalbert, Immacolata Venditto, Michael J. O’Donohue, Louise Badruna, Vincent Burlat, Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dynamique et Evolution des Parois cellulaires végétales, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Laboratoire de Génie Chimique (LGC), Newcastle University [Newcastle], Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Protein domain, Carbohydrates, CBM family 3, Bioengineering, Computational biology, Welding, CBM family 2, Protein Engineering, law.invention, Substrate Specificity, 03 medical and health sciences, 0302 clinical medicine, law, Cell Wall, Catalytic Domain, Plant Cells, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, 030304 developmental biology, chemistry.chemical_classification, Flexibility (engineering), 0303 health sciences, beta-xylanase, Endo-1,4-beta Xylanases, Substrate (chemistry), General Medicine, Ligand (biochemistry), Spatial proximity, Enzyme, chemistry, Bio Molecular Welding, Xylanase, 030217 neurology & neurosurgery, Function (biology), Biotechnology
Abstract: International audience; Irrespective of their biological origin, most proteins are composed of several elementary domains connected by linkers. These domains are either functionally independent units, or part of larger multidomain structures whose functions are defined by their spatial proximity. Carbohydrate-degrading enzymes provide examples of a range of multidomain structures, in which catalytic protein domains are frequently appended to one or more non-catalytic carbohydrate-binding modules which specifically bind to carbohydrate motifs. While the carbohydrate-binding specificity of these modules is clear, their function is not fully elucidated. Herein, an original approach to tackle the study of carbohydrate-binding modules using the Jo-In biomolecular welding protein pair is presented. To provide a proof of concept, recombinant xylanases appended to two different carbohydrate-binding modules have been created and produced. The data reveal the biochemical properties of four xylanase variants and provide the basis for correlating enzyme activity to structural properties and to the nature of the substrate and the ligand specificity of the appended carbohydrate-binding module. It reveals that specific spatial arrangements favour activity on soluble polymeric substrates and that activity on such substrates does not predict the behaviour of multimodular enzymes on insoluble plant cell wall samples. The results highlight that the Jo-In protein welding system is extremely useful to design multimodular enzyme systems, especially to create rigid conformations that decrease the risk of intermodular interference. Further work on Jo-In will target the introduction of varying degrees of flexibility, providing the means to study this property and the way it may influence multimodular enzyme functions.
Published: 2021

37. NIN-Like Proteins; interesting Players in Rhizobia-Induced Nitrate Signaling Response during Interaction with Non-Legume Host Arabidopsis thaliana

Author: Jean Keller, Sebastian T. Schenk, Thomas Ott, Pierre-Marc Delaux, Elisabeth Lichtenberg, Casandra Hernández-Reyes, University of Freiburg [Freiburg], 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy grant CIBSS – EXC-2189 – Project ID 39093984, University of Cambridge by the Bill & Melinda Gates Foundation (OPP1172165), UK government's Department for International Development (DFID), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: Root nodule, Physiology, Arabidopsis, Root hair, Rhizobia, 03 medical and health sciences, Symbiosis, Non-legume host, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, NIN-like Proteins (NLPs), Nitrate-related signaling, biology, Lateral root, food and beverages, 04 agricultural and veterinary sciences, General Medicine, biology.organism_classification, Cell biology, Rhizobia-interaction, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Signal transduction, NLP-pathway, Agronomy and Crop Science
Abstract: Nitrogen is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. This is exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where nitrate availability inhibits this mutualistic interaction. Additionally, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively crosstalk with other physiological pathways. Nodule inception-like proteins (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription during legume–rhizobia interactions. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigated rhizobia-induced changes in the root system architecture of the non-legume host arabidopsis under different nitrate conditions. We demonstrate that rhizobium-induced lateral root growth and increased root hair length and density are regulated by a nitrate-related signaling pathway. Key players in this process are AtNLP4 and AtNLP5, because the corresponding mutants failed to respond to rhizobia. At the cellular level, AtNLP4 and AtNLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independently of AtNLP4. In summary, our data suggest that root morphological responses to rhizobia are coordinated by a newly considered nitrate-related NLP pathway that is evolutionarily linked to regulatory circuits described in legumes. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Published: 2021

38. Lipid Interactions Between Flaviviruses and Mosquito Vectors

Author: Vial, Thomas, Marti, Guillaume, Missé, Dorothée, Pompon, Julien, Duke-NUS Medical School [Singapore], Pharmacochimie et Biologie pour le Développement (PHARMA-DEV), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), MetaToul Agromix, MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and ANR-20-CE15-0006,VirSalivaEnhancer,Amplificateur de transmission d'origine flavivirale dans la salive de moustique(2020)
Subjects: flavivirus, Physiology, [SDV]Life Sciences [q-bio], Physiology (medical), viruses, parasitic diseases, transmission, virus diseases, lipids (amino acids, peptides, and proteins), mosquito, Review, metabolomics, phospholipids
Abstract: International audience; Mosquito-borne flaviviruses, such as dengue (DENV), Zika (ZIKV), yellow fever (YFV), West Nile (WNV), and Japanese encephalitis (JEV) viruses, threaten a large part of the human populations. In absence of therapeutics and effective vaccines against each flaviviruses, targeting viral metabolic requirements in mosquitoes may hold the key to new intervention strategies. Development of metabolomics in the last decade opened a new field of research: mosquito metabolomics. It is now clear that flaviviruses rely on mosquito lipids, especially phospholipids, for their cellular cycle and propagation. Here, we review the biosyntheses of, biochemical properties of and flaviviral interactions with mosquito phospholipids. Phospholipids are structural lipids with a polar headgroup and apolar acyl chains, enabling the formation of lipid bilayer that form plasma- and endomembranes. Phospholipids are mostly synthesized through the de novo pathway and remodeling cycle. Variations in headgroup and acyl chains influence phospholipid physicochemical properties and consequently the membrane behavior. Flaviviruses interact with cellular membranes at every step of their cellular cycle. Recent evidence demonstrates that flaviviruses reconfigure the phospholipidome in mosquitoes by regulating phospholipid syntheses to increase virus multiplication. Identifying the phospholipids involved and understanding how flaviviruses regulate these in mosquitoes is required to design new interventions.
Published: 2021

39. An Ancestral Function of Strigolactones as Symbiotic Rhizosphere Signals

Author: Junko Kyozuka, Aino Komatsu, Kaori Yoneyama, Masaki Shimamura, Kiyoshi Mashiguchi, Takahito Nomura, Pierre-Marc Delaux, Tomomi Nakagawa, Yoshikazu Tanaka, Hidemasa Suzuki, Cyril Libourel, Akiyoshi Yoda, Tomoaki Nishiyama, Xiaonan Xie, Kyoichi Kodama, Jean Keller, Shinjiro Yamaguchi, Hiromu Kameoka, Keiko Sakakibara, Kohki Akiyama, Yi Luo, Yohei Mizuno, Kenichi Uchida, Shota Shimazaki, Mélanie K. Rich, 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, Cell signaling, Mutant, Arabidopsis, General Physics and Astronomy, Plant Roots, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Lactones, 03 medical and health sciences, Symbiosis, Mycorrhizae, Gene expression, 030304 developmental biology, 0303 health sciences, Rhizosphere, Multidisciplinary, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, food and beverages, General Chemistry, biology.organism_classification, Cell biology, Plant hormone, Heterocyclic Compounds, 3-Ring, Function (biology), 010606 plant biology & botany
Abstract: In flowering plants, carotenoid-derived strigolactones (SLs) have dual functions as hormones that regulate growth and development, and as rhizosphere signaling molecules that induce symbiosis with arbuscular mycorrhizal (AM) fungi. Here, we report the identification of bryosymbiol (BSB), a previously unidentified SL from the bryophyte Marchantia paleacea. BSB is also found in vascular plants, indicating that it is ancestral in land plants. BSB synthesis is enhanced at AM symbiosis permissive conditions and BSB deficient mutants are impaired in AM symbiosis. In contrast, the absence of BSB synthesis has little effect on the growth and gene expression. We show that the introduction of the SL receptor of Arabidopsis renders M. paleacea cells BSB-responsive. These results suggest that BSB is not perceived by M. paleacea cells due to the lack of cognate SL receptors. We propose that SLs originated as AM symbiosis-inducing rhizosphere signaling molecules and were later recruited as plant hormone.
Published: 2021

40. 1-Aminocyclopropane-1-carboxylic acid stimulates tomato pollen tube growth independently of ethylene receptors

Author: Christian Chervin, Huguette Sallanon, Rasha Althiab-Almasaud, Caren Chang, Centre de Coopération Internationale en Recherche Agronomique - CIRAD (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut Méditerranéen d'Océanologie - MIO (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Université de La Réunion (FRANCE), University of Maryland (USA), Université d'Avignon et des Pays de Vaucluse (FRANCE), Université de Montpellier (FRANCE), Démarche intégrée pour l'obtention d'aliments de qualité - UMR QualiSud (Montpellier, France), 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Démarche intégrée pour l'obtention d'aliments de qualité (UMR QualiSud), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Maryland [College Park], University of Maryland System, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Institut Agro - Montpellier SupAgro
Subjects: 0106 biological sciences, Cell signaling, Ethylene, Physiology, Transgene, Mutant, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Amino Acids, Cyclic, Plant Science, Pollen Tube, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Solanum lycopersicum, Gene expression, Genetics, 1-Aminocyclopropane-1-carboxylic acid, Receptor, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, 0303 health sciences, biology, fungi, food and beverages, Cell Biology, General Medicine, Ethylenes, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Cell biology, Chimie organique, chemistry, Plant hormone, 010606 plant biology & botany
Abstract: International audience; The plant hormone ethylene plays vital roles in plant development, including pollen tube (PT) growth. Many studies have used the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), as a tool to trigger ethylene signaling. Several studies have suggested that ACC can act as a signal molecule independently of ethylene, inducing responses that are distinct from those induced by ethylene. In this study, we confirmed that ethylene receptor function is essential for promoting PT growth in tomato, but interestingly, we discovered that ACC itself can act as a signal that also promotes PT growth. Exogenous ACC stimulated PT growth even when ethylene perception was inhibited either chemically by treating with 1-methylcyclopropene (1-MCP) or genetically by using the ethyleneinsensitive Never Ripe (NR) mutant. Treatment with aminoethoxyvinylglycine, which reduces endogenous ACC levels, led to a reduction of PT growth, even in the NR mutants. Furthermore, GUS activity driven by an EIN3 Binding Site promoter (EBS:GUS transgene) was triggered by ACC in the presence of 1-MCP. Taken together, these results suggest that ACC signaling can bypass the ethylene receptor step to stimulate PT growth and EBS driven gene expression.
Published: 2021

41. Low pH-induced cell wall disturbances in Arabidopsis thaliana roots lead to a pattern-specific programmed cell death in the different root zones and arrested elongation in late elongation zone

Author: Victor Alexandre Vitorello, Jonathas Pereira Graças, Vincent Burlat, Mariana Belloti, Lázaro Eustáquio Pereira Peres, Joni Esrom Lima, Elisabeth Jamet, Federal University of Minas Gerais (UFMG), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Centro de Energia Nuclear na Agricultura (CENA ), University of São Paulo (USP), Dynamique et Evolution des Parois cellulaires végétales, and Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0106 biological sciences, 0303 health sciences, Programmed cell death, Acidic stress, Root zone, biology, Chemistry, Plant Science, 15. Life on land, biology.organism_classification, 01 natural sciences, Cell wall stiffness, Cell biology, Cell wall, 03 medical and health sciences, Cell wall integrity, Arabidopsis thaliana, Cell mortality, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Elongation, Agronomy and Crop Science, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Low pH stress (pH < 5.5) triggers sensitivity responses in roots such as cell death (CD) or arrest in elongation which are detrimental to the development of many plant species. The involvement of the cell wall (CW) with these sensitive responses and their spatiotemporal dynamics in the distinct root zones remains poorly understood. The spatio-temporal analysis of primary roots of Arabidopsis thaliana upon low pH (pH 4.6) revealed that the CD repeatedly started in cells of the transition zone (TZ). Then, CD dynamically moved downward to the meristematic zone (MZ) and upward to the early elongation zone (EZ). The dead cells exhibited coordinated in situ DNA fragmentation, highlighted by the deformity in the nuclei of dead cells and positive reaction for Terminal Deoxynucleotidyl Transferase-mediated dUTP Nick-End Labeling (TUNEL). This DNA fragmentation strongly suggests that the low pH-driven CD occurred through a programmed cell death (PCD) pathway. In addition, a decreased CW stiffness in TZ epidermal cells before the onset of CD suggests that low pH first triggers cell wall disturbances (CWDs) in these root cells. Disruption in CW integrity caused by incorrect cellulose deposition in cobra (cob-1) mutant enhanced CD in TZ and early EZ. Supporting this notion, an increase in calcium concentration upon low pH alleviated the CD in roots, probably due to its role in stabilization of the pectin crosslinking in CWs and likely counteracting the low pH-induced CWDs. Moreover, the CD was significantly decreased when roots were exposed to low pH under reduced CW tension, however, a sudden increase in turgor pressure and CW tension (hypoosmotic treatment) combined with low pH accelerated CD in TZ and early EZ. The CD was not observed in the wild type late EZ trichoblasts upon low pH but rather an orchestrated arrest in elongation. An increase in calcium concentration inhibited this elongation arrest upon low pH, suggesting that the onset of this response also required CWDs. Altogether, these results indicate that low pH-induced CWDs triggered sensitive responses within defined root zones. The low pH-activated PCD and an orchestrated elongation arrest occurring in different root zones suggest the occurrence of yet to be identified signaling cascades.
Published: 2021

42. The Same against Many: AtCML8, a Ca2+ Sensor Acting as a Positive Regulator of Defense Responses against Several Plant Pathogens

Author: Zhu, Xiaoyang, Mazard, Julie, Robe, Eugénie, Pignoly, Sarah, Aguilar, Marielle, San Clemente, Hélène, Lauber, Emmanuelle, Berthomé, Richard, Galaud, Jean-Philippe, South China Agricultural University (SCAU), 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), the CaPPTure project, the International Science and Technology Cooperation Major Project Cultivation Special Fund of SCAU (2019SCAUGH05), Pearl River Talent Program for Young Talent (grant no. 2017GC010321)., ANR-17-CE20-0017,CaPPTure,Interaction plante-pathogène: influence de la température et contribution de la signalisation calcium(2017), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-18-EURE-0019,TULIP-GSR,The Toulouse-Perpignan(2018)
Subjects: Arabidopsis thaliana, QH301-705.5, Ralstonia solanacearum, food and beverages, Xanthomonas campestris, calcium signaling, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Phytophtora capsica, Chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], calmodulin-like protein, Biology (General), plant immunity, QD1-999, multi-pathogens
Abstract: Calcium signals are crucial for the activation and coordination of signaling cascades leading to the establishment of plant defense mechanisms. Here, we studied the contribution of CML8, an Arabidopsis calmodulin-like protein in response to Ralstonia solanacearum and to pathogens with different lifestyles, such as Xanthomonas campestris pv. campestris and Phytophtora capsici. We used pathogenic infection assays, gene expression, RNA-seq approaches, and comparative analysis of public data on CML8 knockdown and overexpressing Arabidopsis lines to demonstrate that CML8 contributes to defense mechanisms against pathogenic bacteria and oomycetes. CML8 gene expression is finely regulated at the root level and manipulated during infection with Ralstonia, and CML8 overexpression confers better plant tolerance. To understand the processes controlled by CML8, genes differentially expressed at the root level in the first hours of infection have been identified. Overexpression of CML8 also confers better tolerance against Xanthomonas and Phytophtora, and most of the genes differentially expressed in response to Ralstonia are differentially expressed in these different pathosystems. Collectively, CML8 acts as a positive regulator against Ralstonia solanaceraum and against other vascular or root pathogens, suggesting that CML8 is a multifunctional protein that regulates common downstream processes involved in the defense response of plants to several pathogens.
Published: 2021
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43. Myxospermy Evolution in Brassicaceae

Author: Sébastien Viudes, Christophe Dunand, Vincent Burlat, 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Dynamique et Evolution des Parois cellulaires végétales, Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), ANR-18-CE20-0007,MicroWall,Les assemblages moléculaires de microdomaines pariétaux contrôlent la dynamique des parois végétales(2018), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011)
Subjects: mucilage secretory cells (MSCs), seed mucilage (SM), Arabidopsis thaliana MSC toolbox gene orthologs, QH301-705.5, seed mucilage (SM, evolution, food and beverages, Brassicaceae species, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, mucilage secretory cells (MSCs), Biology (General), cell wall microdomains, diversity
Abstract: The ability to extrude mucilage upon seed imbibition (myxospermy) occurs in several Angiosperm taxonomic groups, but its ancestral nature or evolutionary convergence origin remains misunderstood. We investigated seed mucilage evolution in the Brassicaceae family with comparison to the knowledge accumulated in Arabidopsis thaliana. The myxospermy occurrence was evaluated in 27 Brassicaceae species. Phenotyping included mucilage secretory cell morphology and topochemistry to highlight subtle myxospermy traits. In parallel, computational biology was driven on the one hundred genes constituting the so-called A. thaliana mucilage secretory cell toolbox to confront their sequence conservation to the observed phenotypes. Mucilage secretory cells show high morphology diversity, the three studied Arabidopsis species had a specific extrusion modality compared to the other studied Brassicaceae species. Orthologous genes from the A. thaliana mucilage secretory cell toolbox were mostly found in all studied species without correlation with the occurrence of myxospermy or even more sub-cellular traits. Seed mucilage may be an ancestral feature of the Brassicaceae family. It consists of highly diverse subtle traits, probably underlined by several genes not yet characterized in A. thaliana or by species-specific genes. Therefore, A. thaliana is probably not a sufficient reference for future myxospermy evo–devo studies.
Published: 2021

44. Automatic Prediction and Annotation: There Are Strong Biases for Multigenic Families

Author: Catherine Mathé, Christophe Dunand, Dynamique et Evolution des Parois cellulaires végétales, 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, 0303 health sciences, Opinion, mis-annotation, protein annotation, Gene prediction, food and beverages, Computational biology, Biology, QH426-470, 01 natural sciences, 03 medical and health sciences, Annotation, Protein Annotation, Genetics, gene family, Molecular Medicine, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, mis-prediction, gene prediction, Genetics (clinical), 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; In the last few decades, the explosion of genomic projects has produced huge sets of predicted genes and annotated sequences. The prediction of a gene structure can be defined as the capacity to determine the start and the stop of the gene as well as the positions of introns, if present. Despite the number of performant gene prediction programs combining ab initio and homology-based approaches (Mathe et al., 2002; Hoff and Stanke, 2015), the rate of mis-predicted genes is not negligible and can be due to several factors (Scalzitti et al., 2020). For example, unusually long introns, short exons or long genes can generate incomplete or partially predicted gene structure; short intergenic regions can lead to gene fusion; DNA sequencing errors (nucleotide deletions or insertions) introducing frameshifts can affect predictions; non-canonical splice sites, overlapping genes and genes located within introns are also a source of erroneous predictions. [...]
Published: 2021

45. A quick journey into the diversity of iron uptake strategies in photosynthetic organisms

Author: Amanda Martín-Barranco, Sébastien Thomine, Grégory Vert, Enric Zelazny, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Signalisation Cellulaire et Ubiquitination, 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)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), h2020 marie sklodowska-curie actions PCIG-GA-2012-334021, ANR-17-CE20-0008,MOBIFER,Dynamique de la sécrétion de coumarines dans le sol, un processus développé par les plantes pour améliorer la nutrition en fer(2017), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-18-CE20-0008,NUTRIR,Protéines HIR des microdomaines membranaires : contrôle de la machinerie d'acquisition du fer et nouvelles fonctions chez Arabidopsis(2018), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Iron, Arabidopsis, Cellular homeostasis, Plant Science, Cyanobacteria, Photosynthesis, 01 natural sciences, 03 medical and health sciences, Algae, Gene Expression Regulation, Plant, Botany, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, iron-acquisition complex, 030304 developmental biology, 0303 health sciences, Rhizosphere, Iron uptake, Iron uptake strategies, photosynthetic organisms, Oryza sativa, biology, food and beverages, Biological Transport, Oryza, Mini-Review, 15. Life on land, biology.organism_classification, Metabolic Networks and Pathways, 010606 plant biology & botany
Abstract: Early Access; International audience; Iron (Fe) is involved in multiple processes that contribute to the maintenance of the cellular homeostasis of all living beings. In photosynthetic organisms, Fe is notably required for photosynthesis. Although iron is generally abundant in the environment, it is frequently poorly bioavailable. This review focuses on the molecular strategies that photosynthetic organisms have evolved to optimize iron acquisition, using Arabidopsis thaliana, rice (Oryza sativa), and some unicellular algae as models. Non-graminaceous plants, including Arabidopsis, take up iron from the soil by an acidification-reduction-transport process (strategy I) requiring specific proteins that were recently shown to associate in a dedicated complex. On the other hand, graminaceous plants, such as rice, use the so-called strategy II to acquire iron, which relies on the uptake of Fe3+ chelated by phytosiderophores that are secreted by the plant into the rhizosphere. However, apart these main strategies, accessory mechanisms contribute to robust iron uptake in both Arabidopsis and rice. Unicellular algae combine reductive and non-reductive mechanisms for iron uptake and present important specificities compared to land plants. Since the majority of the molecular actors required for iron acquisition in algae are not conserved in land plants, questions arise about the evolution of the Fe uptake processes upon land colonization.
Published: 2021

46. 450 million years between the two DELLA-mediated green revolutions

Author: El Mahboubi, Karima, Delaux, Pierre-Marc, 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Evolution des Interactions Plantes-Microorganismes, and Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3)
Subjects: [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, food and beverages
Abstract: International audience; Plant hormone signaling pathways have diversified during plant evolution. A new study reveals conservation of DELLA functions in growth and environmental stress responses across land plants.
Published: 2021

47. Taxonomic, phylogenetic, and functional diversity of root‐associated fungi in bromeliads: effects of host identity, life forms, and nutritional modes

Author: Nathalie Séjalon-Delmas, Arthur QuyManh Maes, Céline Leroy, Heidy Schimann, Eliane Louisanna, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Interactions Microbiennes dans la Rhizosphère et les Racines, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: 0106 biological sciences, 0301 basic medicine, Bromeliaceae, Physiology, Biodiversity, Plant Science, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Plant Roots, 01 natural sciences, Plant use of endophytic fungi in defense, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Phylogenetics, Mycorrhizae, Endophytes, Fungal functional guilds, Nutritional modes, Phylogeny, Taxonomy, Life forms, biology, Phylogenetic tree, Ecology, Host (biology), ITS metabarcoding, Fungi, Plants, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, 030104 developmental biology, Taxonomy (biology), Epiphyte, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Mycobiome, 010606 plant biology & botany
Abstract: International audience; Bromeliads represent a major component of neotropical forests and encompass a considerable diversity of life forms and nutritional modes. Bromeliads explore highly stressful habitats and root-associated fungi may play a crucial role but their driving factors and variations in root-associated fungi remain largely unknown. ⦁We explored root-associated fungal communities in 17 bromeliad species and their variations linked to host identity, life forms, and nutritional modes by using ITS1 gene-based high-throughput sequencing and by characterising fungal functional guilds. ⦁We found a dual association of mycorrhizal and non-mycorrhizal fungi. The different species, life forms, and nutritional modes among bromeliad hosts had fungal communities that differ in their taxonomical and functional composition. Specifically, roots of epiphytic bromeliads had more endophytic fungi and dark septate endophytes and fewer mycorrhizal fungi than terrestrials and lithophytes. ⦁Our results contribute to a fundamental knowledge base on different fungal groups in previously undescribed Bromeliaceae. The diverse root-associated fungal communities in bromeliads may enhance plant fitness in both stressful and nutrient-poor environments and may give more flexibility to the plants to adapt to changing environmental conditions.
Published: 2021

48. Changes in the Cell Wall Proteome of Leaves in Response to High Temperature Stress in Brachypodium distachyon

Author: Urszula Jankowska, Alexander Betekhtin, Artur Pinski, Bozena Skupien-Rabian, Robert Hasterok, Elisabeth Jamet, University of Silesia in Katowice, Uniwersytet Jagielloński w Krakowie = Jagiellonian University (UJ), Dynamique et Evolution des Parois cellulaires végétales, 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, 0301 basic medicine, Proteomics, Hot Temperature, Proteome, medicine.medical_treatment, 01 natural sciences, high temperature stress, Cell Wall, Gene Expression Regulation, Plant, Glycoside hydrolase, glycoside hydrolase, Biology (General), Spectroscopy, Plant Proteins, chemistry.chemical_classification, Brachypodium distachyon, biology, General Medicine, Computer Science Applications, Chemistry, Biochemistry, leaves, Brachypodium, QH301-705.5, Polysaccharide, Catalysis, Article, Inorganic Chemistry, Cell wall, 03 medical and health sciences, Qualitative analysis, Stress, Physiological, cell wall proteomics, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Physical and Theoretical Chemistry, Molecular Biology, QD1-999, Protease, Organic Chemistry, biology.organism_classification, Temperature stress, Plant Leaves, 030104 developmental biology, chemistry, sense organs, 010606 plant biology & botany
Abstract: International audience; High temperature stress leads to complex changes to plant functionality, which affects, i.a., the cell wall structure and the cell wall protein composition. In this study, the qualitative and quantitative changes in the cell wall proteome of Brachypodium distachyon leaves in response to high (40 °C) temperature stress were characterised. Using a proteomic analysis, 1533 non-redundant proteins were identified from which 338 cell wall proteins were distinguished. At a high temperature, we identified 46 differentially abundant proteins, and of these, 4 were over-accumulated and 42 were under-accumulated. The most significant changes were observed in the proteins acting on the cell wall polysaccharides, specifically, 2 over- and 12 under-accumulated proteins. Based on the qualitative analysis, one cell wall protein was identified that was uniquely present at 40 °C but was absent in the control and 24 proteins that were present in the control but were absent at 40 °C. Overall, the changes in the cell wall proteome at 40 °C suggest a lower protease activity, lignification and an expansion of the cell wall. These results offer a new insight into the changes in the cell wall proteome in response to high temperature.
Published: 2021
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49. Formin-mediated bridging of cell wall, plasma membrane, and cytoskeleton in symbiotic infections of Medicago truncatula

Author: Clara Schmitz, Thomas Ott, Julian Knerr, Beatrice Lace, Chao Su, Cyril Libourel, Pierre-Marc Delaux, Franck Anicet Ditengou, Pengbo Liang, Jean Keller, Robert Grosse, Eija Schulze, University of Freiburg [Freiburg], 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), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: 0301 basic medicine, Root nodule, nodule, formin, [SDV]Life Sciences [q-bio], Formins, Biology, Root hair, Microtubules, Plant Roots, General Biochemistry, Genetics and Molecular Biology, Rhizobia, Nod factor, 03 medical and health sciences, rhizobium, 0302 clinical medicine, Cell Wall, Report, Plant Cells, Medicago truncatula, Cytoskeleton, Plant Proteins, Sinorhizobium meliloti, Cell Membrane, fungi, food and beverages, Plants, biology.organism_classification, root, Actins, symbiosis, infection, 3. Good health, Cell biology, 030104 developmental biology, biology.protein, General Agricultural and Biological Sciences, actin, 030217 neurology & neurosurgery
Abstract: Summary Legumes have maintained the ability to associate with rhizobia to sustain the nitrogen-fixing root nodule symbiosis (RNS). In Medicago truncatula, the Nod factor (NF)-dependent intracellular root colonization by Sinorhizobium meliloti initiates from young, growing root hairs. They form rhizobial traps by physically curling around the symbiont.1,2 Although alterations in root hair morphology like branching and swelling have been observed in other plants in response to drug treatments3 or genetic perturbations,4, 5, 6 full root hair curling represents a rather specific invention in legumes. The entrapment of the symbiont completes with its full enclosure in a structure called the “infection chamber” (IC),1,2,7,8 from which a tube-like membrane channel, the “infection thread” (IT), initiates.1,2,9 All steps of rhizobium-induced root hair alterations are aided by a tip-localized cytosolic calcium gradient,10,11 global actin re-arrangements, and dense subapical fine actin bundles that are required for the delivery of Golgi-derived vesicles to the root hair tip.7,12, 13, 14 Altered actin dynamics during early responses to NFs or rhizobia have mostly been shown in mutants that are affected in the actin-related SCAR/WAVE complex.15, 16, 17, 18 Here, we identified a polarly localized SYMBIOTIC FORMIN 1 (SYFO1) to be required for NF-dependent alterations in membrane organization and symbiotic root hair responses. We demonstrate that SYFO1 mediates a continuum between the plasma membrane and the cell wall that is required for the onset of rhizobial infections., Graphical abstract, Highlights • The SYMBIOTIC FORMIN 1 (SYFO1) specifically regulates symbiotic root hair curling • SYFO1 directly binds actin and polarizes in responding root hairs • SYFO1 induces membrane protrusions in cell-wall-devoid protoplasts • Cell wall association of SYFO1 is indispensable for its function in root hairs, Here, Liang et al. report that the formin SYFO1 specifically regulates polar actin alignments during symbiotic root hair responses in Medicago truncatula. Although SYFO1 is able to induce membrane protrusions in protoplasts, its endogenous function requires an association with the cell wall.
Published: 2021

50. Physiological and Biochemical Traits of Two Major Arabidopsis Accessions, Col-0 and Ws, Under Salinity

Author: Elisabeth Jamet, Catherine Rayon, Karine Pageau, Romain Roulard, Maïté Leschevin, Paulo Marcelo, Hélène San Clemente, Marwa Ismael, Solène Bassard, Anthony Quéro, Transfrontalière BioEcoAgro (Transfrontalière BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV), 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), Plateforme d’Ingénierie Cellulaire et Analyses des Protéines (ICAP) (ICAP), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Dynamique et Evolution des Parois cellulaires végétales, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)
Subjects: 0106 biological sciences, 0301 basic medicine, pigments, Plant Science, Biology, Protein degradation, 01 natural sciences, SB1-1110, 03 medical and health sciences, chemistry.chemical_compound, antioxidant enzymes, Arabidopsis, TMTs quantitative proteomics, Botany, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Raffinose, metabolites, salt stress, Plant culture, biology.organism_classification, Salinity, arabidopsis, 030104 developmental biology, Inflorescence, chemistry, Shoot, cell wall, Osmoprotectant, 010606 plant biology & botany
Abstract: Salinity affects plant growth and development as shown with the glycophyte model plant, Arabidopsis thaliana (Arabidopsis). Two Arabidopsis accessions, Wassilewskija (Ws) and Columbia (Col-0), are widely used to generate mutants available from various Arabidopsis seed resources. However, these two ecotypes are known to be salt-sensitive with different degrees of tolerance. In our study, 3-week-old Col-0 and Ws plants were treated with and without 150 mM NaCl for 48, 72, or 96 h, and several physiological and biochemical traits were characterized on shoots to identify any specific traits in their tolerance to salinity. Before salt treatment was carried out, a different phenotype was observed between Col-0 and Ws, whose main inflorescence stem became elongated in contrast to Col-0, which only displayed rosette leaves. Our results showed that Col-0 and Ws were both affected by salt stress with limited growth associated with a reduction in nutrient uptake, a degradation of photosynthetic pigments, an increase in protein degradation, as well as showing changes in carbohydrate metabolism and cell wall composition. These traits were often more pronounced in Col-0 and occurred usually earlier than in Ws. Tandem Mass Tags quantitative proteomics data correlated well with the physiological and biochemical results. The Col-0 response to salt stress was specifically characterized by a greater accumulation of osmoprotectants such as anthocyanin, galactinol, and raffinose; a lower reactive oxygen detoxification capacity; and a transient reduction in galacturonic acid content. Pectin degradation was associated with an overaccumulation of the wall-associated kinase 1, WAK1, which plays a role in cell wall integrity (CWI) upon salt stress exposure. Under control conditions, Ws produced more antioxidant enzymes than Col-0. Fewer specific changes occurred in Ws in response to salt stress apart from a higher number of different fascilin-like arabinogalactan proteins and a greater abundance of expansin-like proteins, which could participate in CWI. Altogether, these data indicate that Col-0 and Ws trigger similar mechanisms to cope with salt stress, and specific changes are more likely related to the developmental stage than to their respective genetic background.
Published: 2021

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