Author: "Françoise Jardinaud" - Searchworks@Jio Institute Digital Library Search Results

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1. Comparative transcriptomics reveals a highly polymorphic Xanthomonas HrpG virulence regulon

Author: Thomas Quiroz Monnens, Brice Roux, Sébastien Cunnac, Erika Charbit, Sébastien Carrère, Emmanuelle Lauber, Marie-Françoise Jardinaud, Armelle Darrasse, Matthieu Arlat, Boris Szurek, Olivier Pruvost, Marie-Agnès Jacques, Lionel Gagnevin, Ralf Koebnik, Laurent D. Noël, and Alice Boulanger
Subjects: Xanthomonas, HrpG, Type III secretion system, Regulon diversity, Transcriptome sequencing, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. Results In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. Conclusions The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS.
Published: 2024
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2. The association between Dioscorea sansibarensis and Orrella dioscoreae as a model for hereditary leaf symbiosis.

Author: Tessa Acar, Sandra Moreau, Marie-Françoise Jardinaud, Gabriella Houdinet, Felicia Maviane-Macia, Frédéric De Meyer, Bart Hoste, Olivier Leroux, Olivier Coen, Aurélie Le Ru, Nemo Peeters, and Aurelien Carlier
Subjects: Medicine, Science
Abstract: Hereditary, or vertically-transmitted, symbioses affect a large number of animal species and some plants. The precise mechanisms underlying transmission of functions of these associations are often difficult to describe, due to the difficulty in separating the symbiotic partners. This is especially the case for plant-bacteria hereditary symbioses, which lack experimentally tractable model systems. Here, we demonstrate the potential of the leaf symbiosis between the wild yam Dioscorea sansibarensis and the bacterium Orrella dioscoreae (O. dioscoreae) as a model system for hereditary symbiosis. O. dioscoreae is easy to grow and genetically manipulate, which is unusual for hereditary symbionts. These properties allowed us to design an effective antimicrobial treatment to rid plants of bacteria and generate whole aposymbiotic plants, which can later be re-inoculated with bacterial cultures. Aposymbiotic plants did not differ morphologically from symbiotic plants and the leaf forerunner tip containing the symbiotic glands formed normally even in the absence of bacteria, but microscopic differences between symbiotic and aposymbiotic glands highlight the influence of bacteria on the development of trichomes and secretion of mucilage. This is to our knowledge the first leaf symbiosis where both host and symbiont can be grown separately and where the symbiont can be genetically altered and reintroduced to the host.
Published: 2024
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3. Wild Helianthus species: A reservoir of resistance genes for sustainable pyramidal resistance to broomrape in sunflower

Author: Mireille Chabaud, Marie-Christine Auriac, Marie-Claude Boniface, Sabine Delgrange, Tifaine Folletti, Marie-Françoise Jardinaud, Alexandra Legendre, Begoña Pérez-Vich, Jean-Bernard Pouvreau, Leonardo Velasco, Philippe Delavault, and Stéphane Muños
Subjects: Helianthus, Orobanche cumana, sunflower, genetic resistance, phenotyping, cytology, Plant culture, SB1-1110
Abstract: Orobanche cumana Wall., sunflower broomrape, is one of the major pests for the sunflower crop. Breeding for resistant varieties in sunflower has been the most efficient method to control this parasitic weed. However, more virulent broomrape populations continuously emerge by overcoming genetic resistance. It is thus essential to identify new broomrape resistances acting at various stages of the interaction and combine them to improve resistance durability. In this study, 71 wild sunflowers and wild relatives accessions from 16 Helianthus species were screened in pots for their resistance to broomrape at the late emergence stage. From this initial screen, 18 accessions from 9 species showing resistance, were phenotyped at early stages of the interaction: the induction of broomrape seed germination by sunflower root exudates, the attachment to the host root and the development of tubercles in rhizotron assays. We showed that wild Helianthus accessions are an important source of resistance to the most virulent broomrape races, affecting various stages of the interaction: the inability to induce broomrape seed germination, the development of incompatible attachments or necrotic tubercles, and the arrest of emerged structure growth. Cytological studies of incompatible attachments showed that several cellular mechanisms were shared among resistant Helianthus species.
Published: 2022
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4. Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the broad host range pathogenRalstonia pseudosolanacearum

Author: Rekha Gopalan-Nair, Françoise Jardinaud, Ludovic Legrand, Céline Lopez-Roques, Olivier Bouchez, Stéphane Genin, and Alice Guidot
Abstract: The impact of host diversity on the genotypic and phenotypic evolution of broad-spectrum pathogens is a remaining issue. Here, we used populations of the plant pathogenRalstonia pseudosolanacearumthat were experimentally evolved on five types of host plants, either belonging to different botanical families or differing in their susceptibility or resistance to the pathogen. We investigated whether changes in transcriptomic profiles dissociated from genetic changes could occur during the process of host adaptation, and whether transcriptomic reprogramming was dependent on host type. Genomic and transcriptomic variations were established for 31 evolved clones that showed a better fitness in their experimental host than the ancestral clone. Few genomic polymorphisms were detected in these clones, but significant transcriptomic variations were observed, with a high number of differentially expressed genes (DEGs). In a very clear way, a group of genes belonging to the network of regulation of the bacterial virulence such asefpR, efpHorhrpB, among others, were deregulated in several independent evolutionary lineages and appeared to play a key role in the transcriptomic rewiring observed in evolved clones. A double hierarchical clustering based on the 400 top DEGs for each clone revealed two major patterns of gene deregulation that depend on host genotype, but not on host susceptibility or resistance to the pathogen. This work therefore highlights the existence of two major evolutionary paths that result in a significant reorganization of gene expression during adaptive evolution and underscore clusters of co-regulated genes associated to bacterial adaptation on different host lines.
Published: 2023

5. Arabidopsis hydathodes are sites of intense auxin metabolism and nutrient scavenging

Author: Jean-Marc Routaboul, Caroline Bellenot, Gilles Clément, Sylvie Citerne, Céline Remblière, Magali Charvin, Lars Franke, Serge Chiarenza, Damien Vasselon, Marie-Françoise Jardinaud, Sébastien Carrère, Laurent Nussaume, Patrick Laufs, Nathalie Leonhardt, Lionel Navarro, Martin Schattat, Laurent D. Noël, 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), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Martin-Luther-University Halle-Wittenberg, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Martin-Luther-Universität Halle Wittenberg (MLU)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: Hydathodes are small organs located on the leaf margins of all vascular plants. They release excess xylem sap through guttation when stomata are closed or when the humidity level is high. Many promoter analyses have suggested other hydathode functions in metabolite transport and auxin metabolism, but experimental demonstration is still lacking. Here, we compared the transcriptomic and metabolomic features of mature Arabidopsis hydathodes to the leaf blade. 1460 differentially-expressed genes were identified revealing that genes related to auxin metabolism, transport, stress, DNA, plant cell wall, RNA or wax were on average more expressed in hydathodes. On the other hand, genes involved in glucosinolate metabolism, sulfation pathway, metal handling or photosynthesis were downregulated in hydathodes. In hydathodes, there are an increased expression of auxin transcriptional regulators and biosynthetic genes, a lower expression of auxin transport genes and a differential expression of genes related to its vacuolar storage that is consistent with increased contents of free and conjugated auxin. We also found that ca. 78% of the total content of 52 xylem sap metabolites were removed from guttation fluid at the hydathode level. Using reverse genetics, we showed that the capture of nitrate and phosphate in the guttation fluid relies on theNRT2.1andPHT1;4transporters, respectively. Thus, hydathodes absorb a significant part of xylem sap nutrients, limiting the loss of valuable chemicals during guttation. Our transcriptomic and metabolomic analyses reveal an organ with its own transcriptomic and physiological identity and highlight hydathode biological processes that may impact the whole plant.One sentence summaryTranscriptome and physiological analysis of mature and healthy hydathodes of Arabidopsis demonstrates that those organs are sites of intense auxin metabolism and nutrient scavenging
Published: 2022

6. NIN-like protein transcription factors regulate leghemoglobin genes in legume nodules

Author: Qiujiu Li, Kirankumar S. Mysore, Ping Xu, Suyu Jiang, Jiangqi Wen, Yiting Ruan, Ertao Wang, Yann Pecrix, Pascal Gamas, Carmen Sánchez-Cañizares, Marie-Françoise Jardinaud, Meijun Zhu, Jinpeng Gao, Fuyu Li, Phillip S. Poole, Jeremy D. Murray, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Fixation de l'azote, 0106 biological sciences, Root nodule, [SDV]Life Sciences [q-bio], nodosité racinaire, Biology, Plant Root Nodulation, 01 natural sciences, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Symbiosis, Gene Expression Regulation, Plant, Nitrogen Fixation, Medicago truncatula, Légumineuse, Promoter Regions, Genetic, Leghemoglobin, Gene, Transcription factor, ComputingMilieux_MISCELLANEOUS, Legume, Plant Proteins, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Léghémoglobine, food and beverages, Fabaceae, Facteur de transcription, Cell biology, Oxygen, Nitrogen fixation, Root Nodules, Plant, Transcription, Transcription Factors, 010606 plant biology & botany
Abstract: Leghemoglobins enable the endosymbiotic fixation of molecular nitrogen (N2) in legume nodules by channeling O2 for bacterial respiration while maintaining a micro-oxic environment to protect O2-sensitive nitrogenase. We found that the NIN-like protein (NLP) transcription factors NLP2 and NIN directly activate the expression of leghemoglobins through a promoter motif, resembling a “double” version of the nitrate-responsive elements (NREs) targeted by other NLPs, that has conserved orientation and position across legumes. CRISPR knockout of the NRE-like element resulted in strongly decreased expression of the associated leghemoglobin. Our findings indicate that the origins of the NLP-leghemoglobin module for O2 buffering in nodules can be traced to an ancient pairing of NLPs with nonsymbiotic hemoglobins that function in hypoxia.
Published: 2021

7. Symbiotic Nodule Development and Efficiency in the Medicago truncatula Mtefd-1 Mutant is Highly Dependent on Sinorhizobium Strains

Author: Marie-Françoise Jardinaud, Sebastien Carrere, Benjamin Gourion, and Pascal Gamas
Subjects: Physiology, Cell Biology, Plant Science, General Medicine
Abstract: Symbiotic nitrogen fixation (SNF) can play a key role in agroecosystems to reduce the negative impact of nitrogen fertilizers. Its efficiency is strongly affected by the combination of bacterial and plant genotypes, but the mechanisms responsible for the differences in the efficiency of rhizobium strains are not well documented. In Medicago truncatula, SNF has been mostly studied using model systems, such as M. truncatula A17 in interaction with Sinorhizobium meliloti Sm2011. Here we analyzed both the wild-type (wt) A17 and the Mtefd-1 mutant in interaction with five S. meliloti and two Sinorhizobium medicae strains. ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes a transcription factor, which contributes to the control of nodule number and differentiation in M. truncatula. We found that, in contrast to Sm2011, four strains induce functional (Fix+) nodules in Mtefd-1, although less efficient for SNF than in wt A17. In contrast, the Mtefd-1 hypernodulation phenotype is not strain-dependent. We compared the plant nodule transcriptomes in response to SmBL225C, a highly efficient strain with A17, versus Sm2011, in wt and Mtefd-1 backgrounds. This revealed faster nodule development with SmBL225C and early nodule senescence with Sm2011. These RNA sequencing analyses allowed us to identify candidate plant factors that could drive the differential nodule phenotype. In conclusion, this work shows the value of having a set of rhizobium strains to fully evaluate the biological importance of a plant symbiotic gene.
Published: 2022

8. A dual legume-rhizobium transcriptome of symbiotic nodule senescence reveals coordinated plant and bacterial responses

Author: Laurent Sauviac, Antoine Rémy, Emeline Huault, Mélanie Dalmasso, Théophile Kazmierczak, Marie‐Françoise Jardinaud, Ludovic Legrand, Corentin Moreau, Bryan Ruiz, Anne‐Claire Cazalé, Sophie Valière, Benjamin Gourion, Laurence Dupont, Véronique Gruber, Eric Boncompagni, Eliane Meilhoc, Pierre Frendo, Florian Frugier, Claude Bruand, Frugier, Florian, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universite Paris-Saclay, French National Research Agency (ANR), European Commission, Labex SPS, Labex TULIP, EUR SPS, Labex Signalife, EUR TULIP GS, IDEX UCA JEDI, 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), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), 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)-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), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: S4o, root nodule, senescence, Physiology, [SDV]Life Sciences [q-bio], NAC transcription factor, RNA sequencing, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV] Life Sciences [q-bio], cytokinin, Gene Expression Regulation, Plant, RNA, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Nitrogen Fixation, Medicago truncatula, cytokinin, NAC transcription factor, nitrogen fixation, RNA sequencing, root nodule, S4o, senescence, symbiosis, Root Nodules, Plant, Symbiosis, Transcriptome, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Plant Proteins, Rhizobium
Abstract: International audience; Senescence determines plant organ lifespan depending on aging and environmental cues. During the endosymbiotic interaction with rhizobia, legume plants develop a specific organ, the root nodule, which houses nitrogen (N)-fixing bacteria. Unlike earlier processes of the legume-rhizobium interaction (nodule formation, N fixation), mechanisms controlling nodule senescence remain poorly understood. To identify nodule senescence-associated genes, we performed a dual plant-bacteria RNA sequencing approach on Medicago truncatula-Sinorhizobium meliloti nodules having initiated senescence either naturally (aging) or following an environmental trigger (nitrate treatment or salt stress). The resulting data allowed the identification of hundreds of plant and bacterial genes differentially regulated during nodule senescence, thus providing an unprecedented comprehensive resource of new candidate genes associated with this process. Remarkably, several plant and bacterial genes related to the cell cycle and stress responses were regulated in senescent nodules, including the rhizobial RpoE2-dependent general stress response. Analysis of selected core nodule senescence plant genes allowed showing that MtNAC969 and MtS40, both homologous to leaf senescence-associated genes, negatively regulate the transition between N fixation and senescence. In contrast, overexpression of a gene involved in the biosynthesis of cytokinins, well-known negative regulators of leaf senescence, may promote the transition from N fixation to senescence in nodules.
Published: 2022

9. MtNF-YA1, a central transcriptional regulator of symbiotic nodule development, is also a determinant of Medicago truncatula susceptibility towards a root pathogen.

Author: Thomas Rey, Philippe Laporte, Maxime Bonhomme, Marie Françoise Jardinaud, Stéphanie Huguet, Sandrine Balzergue, Bernard Dumas, Andreas Niebel, and Christophe Jacquet
Subjects: Medicago truncatula, Plant Roots, Aphanomyces euteiches, symbiosis and immunity, NF-Y transcription factor, Plant culture, SB1-1110
Abstract: Plant NF-Y transcription factors control a wide array of biological functions enabling appropriate reproductive and developmental processes as well as adaptation to various abiotic and biotic environments. In Medicago truncatula, MtNF-YA1 was previously identified as a key determinant for nodule development and establishment of rhizobial symbiosis. Here we highlight a new role for this protein in compatibility to Aphanomyces euteiches, a root pathogenic oomycete. The Mtnf-ya1-1 mutant plants showed better survival rate, reduced symptoms, and increased development of their root apparatus as compared to their wild type background A17. MtNF-YA-1 was specifically up-regulated by A. euteiches in F83005.5, a highly susceptible natural accession of M. truncatula while transcript level remained stable in A17, which is partially resistant. The role of MtNF-YA1 in F83005.5 susceptibility was further documented by reducing MtNF-YA1 expression either by overexpression of the miR169q, a microRNA targeting MtNF-YA1, or by RNAi approaches leading to a strong enhancement in the resistance of this susceptible line. Comparative analysis of the transcriptome of wild type and Mtnf-ya1-1 led to the identification of 1509 differentially expressed genes. Among those, almost 36 defence-related genes were constitutively expressed in Mtnf-ya1-1, while 20 genes linked to hormonal pathways were repressed. In summary, we revealed an unexpected dual role for this symbiotic transcription factor as a key player in the compatibility mechanisms to a pathogen.
Published: 2016
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10. MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development

Author: Marie-Françoise Jardinaud, Justine Fromentin, Marie-Christine Auriac, Sandra Moreau, Yann Pecrix, Ludivine Taconnat, Ludovic Cottret, Grégoire Aubert, Sandrine Balzergue, Judith Burstin, Sébastien Carrere, Pascal Gamas, 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), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale du GEVES, Institut National de la Recherche Agronomique (INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), INRAE (CJS fellowship for J.F., SPE grant 'EFFOR'), ANR-09-GENM-0026,GENOPEA,Génomique comparative du cycle de l'azote entre M. truncatula et le pois : étude des potentialités de transfert des connaissances entre espèces modèles et cultivées(2009), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and 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
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Nitrogen, CNRS, Physiology, food and beverages, Plant Science, Ethylenes, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Gene Expression Regulation, Plant, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicago truncatula, Genetics, Root Nodules, Plant, Symbiosis, LIPME, Research Articles, Université de Toulouse, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Plant Proteins, Transcription Factors, INRAE
Abstract: Rhizobium–legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed with the MtEFD promoter complemented Mtefd-1 hypernodulation but not the nodule differentiation phenotype. Unexpectedly, a nonlegume homolog of MtEFD, AtERF003 in Arabidopsis (Arabidopsis thaliana), could efficiently complement both phenotypes of Mtefd-1, in contrast to the MtEFD paralog MtEFD2 expressed in the root and nodule meristematic zone. A domain swap experiment showed that MtEFD2 differs from MtEFD by its C-terminal fraction outside the DNA binding domain. Furthermore, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) mutagenesis of MtEFD2 led to a reduction in the number of nodules formed in Mtefd-1, with downregulation of a set of genes, including notably NUCLEAR FACTOR-YA1 (MtNF-YA1) and MtNF-YB16, which are essential for nodule meristem establishment. We, therefore, conclude that nitrogen-fixing symbiosis recruited two proteins originally expressed in roots, MtEFD and MtEFD2, with distinct functions and neofunctionalization processes for each of them.
Published: 2022

11. Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection

Author: Julien S. Luneau, Maël Baudin, Thomas Quiroz Monnens, Sébastien Carrère, Olivier Bouchez, Marie‐Françoise Jardinaud, Carine Gris, Jonas François, Jayashree Ray, Babil Torralba, Matthieu Arlat, Jennifer D. Lewis, Emmanuelle Lauber, Adam M. Deutschbauer, Laurent D. Noël, Alice Boulanger, 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), United States Department of Agriculture (USDA), University of California [Berkeley] (UC Berkeley), University of California (UC), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), 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)-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), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), USDA ARS Grants : 2030-21000-046-00D, 2030-21000-05000D, NSF Directorate for Biological Sciences Grant IOS1557661, ANR-18-EURE-0019,TULIP-GSR,The Toulouse-Perpignan(2018), and European Project
Subjects: Xanthomonas, Physiology, Plant Biology & Botany, Plant Science, Brassica, xylem, Xanthomonas campestris, Bacterial Proteins, Xylem, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, 2.2 Factors relating to the physical environment, RB-TnSeq, Aetiology, Plant Diseases, Agricultural and Veterinary Sciences, Virulence, Prevention, Biological Sciences, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, fitness, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Infectious Diseases, Emerging Infectious Diseases, hydathodes, Zero Hunger, Brassica oleracea, Infection
Abstract: International audience; Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization, especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) to perform a genome-wide screen and identify key bacterial fitness determinants of the vascular pathogen Xanthomonas campestris pv campestris (Xcc) during infection of the cauliflower host plant (Brassica oleracea). This high-throughput analysis was conducted in hydathodes, the natural entry site of Xcc, in xylem sap and in synthetic media. Xcc did not face a strong bottleneck during hydathode infection. In total, 181 genes important for fitness were identified in plant-associated environments with functional enrichment in genes involved in metabolism but only few genes previously known to be involved in virulence. The biological relevance of 12 genes was independently confirmed by phenotyping single mutants. Notably, we show that XC_3388, a protein with no known function (DUF1631), plays a key role in the adaptation and virulence of Xcc possibly through c-di-GMP-mediated regulation. This study revealed yet unsuspected social behaviors adopted by Xcc individuals when confined inside hydathodes at early infection stages.
Published: 2022

12. Genome-wide identification of fitness determinants in theXanthomonas campestrisbacterial pathogen during early stages of plant infection

Author: Julien S. Luneau, Maël Baudin, Thomas Quiroz-Monnens, Sébastien Carrère, Olivier Bouchez, Marie-Françoise Jardinaud, Carine Gris, Jonas François, Jayashree Ray, Babil Torralba, Matthieu Arlat, Jennifer D. Lewis, Adam M. Deutschbauer, Emmanuelle Lauber, Laurent D. Noël, and Alice Boulanger
Abstract: Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) to perform a genome-wide screen and identify key bacterial fitness determinants of the vascular pathogenXanthomonas campestrispv.campestris(Xcc) during infection of the cauliflower host plant (Brassica oleracea). This high-throughput analysis was conducted in hydathodes, the natural entry site ofXcc, in xylem sap and in synthetic media.Xccdid not face a strong bottleneck during hydathode infection. 183 genes important for fitness were identified in plant-associated environments with functional enrichment in genes involved in metabolism when only few genes known to be involved in virulence were found to be affected. The biological relevance of 13 genes was independently confirmed by phenotyping single mutants. Notably, we show that the XC_3388, a protein with no known function (DUF1631), plays a key role in the adaptation and virulence ofXccpossibly through c-di-GMP-mediated regulation. This study thus revealed yet unsuspected social behaviors adopted byXccindividuals when confined inside hydathodes at early infection stages.
Published: 2022

13. Characterization of the Interaction Between the Bacterial Wilt Pathogen Ralstonia solanacearum and the Model Legume Plant Medicago truncatula

Author: Fabienne Vailleau, Elodie Sartorel, Marie-Françoise Jardinaud, Fabien Chardon, Stéphane Genin, Thierry Huguet, Laurent Gentzbittel, and Michel Petitprez
Subjects: QTL, Microbiology, QR1-502, Botany, QK1-989
Abstract: The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt and attacks more than 200 plant species, including some legumes and the model legume plant Medicago truncatula. We have demonstrated that M. truncatula accessions Jemalong A17 and F83005.5 are susceptible to R. solanacearum and, by screening 28 R. solana-cearum strains on the two M. truncatula lines, differential interactions were identified. R. solanacearum GMI1000 infected Jemalong A17 line, and disease symptoms were dependent upon functional hrp genes. An in vitro root inoculation method was employed to demonstrate that R. solanacearum colonized M. truncatula via the xylem and intercellular spaces. R. solanacearum multiplication was restricted by a factor greater than 1 × 105 in the resistant line F83005.5 compared with susceptible Jemalong A17. Genetic analysis of recombinant inbred lines from a cross between Jemalong A17 and F83005.5 revealed the presence of major quantitative trait loci for bacterial wilt resistance located on chromosome 5. The results indicate that the root pathosystem for M. truncatula will provide useful traits for molecular analyses of disease and resistance in this model plant species.
Published: 2007
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14. Autoregulation dependent and independent mechanisms are responsible for the systemic control of nodule formation by the plant N demand

Author: Marc Tauzin, Dany Severac, Ilana Lambert, Stefano Colella, Marjorie Pervent, Alicia Karouani, Martha Nigg, Marie-Françoise Jardinaud, Marie-Laure Martin-Magniette, Marc Lepetit, 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)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut 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), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Colella, Stefano
Subjects: 2. Zero hunger, 0106 biological sciences, 0303 health sciences, biology, [SDV]Life Sciences [q-bio], Mutant, food and beverages, Organogenesis, biology.organism_classification, 01 natural sciences, Medicago truncatula, Rhizobia, Cell biology, [SDV] Life Sciences [q-bio], Transcriptome, 03 medical and health sciences, Rhizobium, Autoregulation, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: In legumes interacting with rhizobia the formation of symbiotic organs responsible for the acquisition of atmospheric nitrogen is depending of the plant nitrogen (N) demand. We discriminated between local and systemic impact of nitrogen on nodule formation using Medicago truncatula plants cultivated in split-root systems. We obtained evidence of the control of nodule formation by whole plant systemic N-satisfaction signaling but obtained little evidence of a local control by mineral nitrogen. We characterized the impact of systemic N signaling on the root transcriptome reprogramming associated to nodule formation. We identified, large genes clusters displaying common expression profiles in response to systemic N signaling enriched in particular fonctions required during these biological processes. We found evidence of a strong effect of SUNN in the control by systemic N signaling of many genes involved in the early interaction with rhizobium as well as organogenesis supporting a role of autoregulation pathway in systemic N signaling. However, we also found evidence that major SUNN independent systemic N signaling controls were maintained in the mutant. This study shed light on the unexpected high complexity of the control of nodule formation by systemic N signaling, that probably involves multiple pathways.
Published: 2021

15. Systemic control of nodule formation by plant nitrogen demand requires autoregulation-dependent and independent mechanisms

Author: Marie-Laure Martin-Magniette, Martha Nigg, Marc Lepetit, Stefano Colella, Marjorie Pervent, Marie-Françoise Jardinaud, Alicia Karouani, Dany Severac, Marc Tauzin, Ilana Lambert, 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)-Université de Montpellier (UM)-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), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), ANR-16-CE20-0009,PSYCHE,Réponses systémiques des plantes aux changements environnementaux(2016), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, Physiology, Nitrogen, Mutant, Plant Science, 01 natural sciences, Plant Root Nodulation, Rhizobia, Transcriptome, 03 medical and health sciences, Nitrogen Fixation, Medicago truncatula, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Homeostasis, Symbiosis, Gene, 030304 developmental biology, Plant Proteins, systemic signalling, 2. Zero hunger, 0303 health sciences, biology, nodule formation, fungi, food and beverages, biology.organism_classification, Phenotype, Legume, Cell biology, Nitrogen fixation, Root Nodules, Plant, Reprogramming, 010606 plant biology & botany, Rhizobium
Abstract: In legumes interacting with rhizobia, the formation of symbiotic organs involved in the acquisition of atmospheric nitrogen gas (N2) is dependent on the plant nitrogen (N) demand. We used Medicago truncatula plants cultivated in split-root systems to discriminate between responses to local and systemic N signaling. We evidenced a strong control of nodule formation by systemic N signaling but obtained no clear evidence of a local control by mineral nitrogen. Systemic signaling of the plant N demand controls numerous transcripts involved in root transcriptome reprogramming associated with early rhizobia interaction and nodule formation. SUPER NUMERIC NODULES (SUNN) has an important role in this control, but we found that major systemic N signaling responses remained active in the sunn mutant. Genes involved in the activation of nitrogen fixation are regulated by systemic N signaling in the mutant, explaining why its hypernodulation phenotype is not associated with higher nitrogen fixation of the whole plant. We show that the control of transcriptome reprogramming of nodule formation by systemic N signaling requires other pathway(s) that parallel the SUNN/CLE (CLAVATA3/EMBRYO SURROUNDING REGION-LIKE PEPTIDES) pathway.
Published: 2021

16. Medicago-Sinorhizobium-Ralstonia Co-infection Reveals Legume Nodules as Pathogen Confined Infection Sites Developing Weak Defenses

Author: Pascal Ratet, Fabienne Vailleau, Fathi Berrabah, Jeoffrey George, Benjamin Gourion, Marine Milhes, Claire Benezech, Gaofei Jiang, Marie-Françoise Jardinaud, Alexandre Le Scornet, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génome et Transcriptome - Plateforme Génomique, Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR), Labex TULIP : ANR-10-LABX-41, ANR-11-IDEX-000202, ANR-17-CE20-0013, ANR-10-LABX-0040-SPS, ANR-11-IDEX-000302, Labex SPS : ANR-10-LABX-41, ANR-11-IDEX-000202, ANR-17-CE20-0013, ANR-10-LABX-0040-SPS, ANR-11-IDEX-000302, Departement Sante des Plantes et Environnement of the INRA, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-17-CE20-0013,TrolesInfidels,Compromis dans les symbioses rhizobium-légumineuse, influence de l'immunité et des défenses sur la symbiose et vice versa(2017), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC)-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)-Université Toulouse III - Paul Sabatier (UT3), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, Root nodule, cost of mutualism, [SDV]Life Sciences [q-bio], legumes, Sinorhizobium, rhizobia, symbiotic organ, General Biochemistry, Genetics and Molecular Biology, Microbiology, Rhizobia, 03 medical and health sciences, 0302 clinical medicine, Symbiosis, Medicago truncatula, medicine, Plant Immunity, Plant Diseases, Ralstonia solanacearum, Medicago, biology, food and beverages, Nodule (medicine), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, plant pathogen, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, nitrogen fixation, defense responses, medicine.symptom, General Agricultural and Biological Sciences, Root Nodules, Plant, 030217 neurology & neurosurgery, Sinorhizobium meliloti
Abstract: Summary Legumes have the capacity to develop root nodules hosting nitrogen-fixing bacteria, called rhizobia. For the plant, the benefit of the symbiosis is important in nitrogen-deprived conditions, but it requires hosting and feeding massive numbers of rhizobia. Recent studies suggest that innate immunity is reduced or suppressed within nodules [ 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 ]; this likely maintains viable rhizobial populations. To evaluate the potential consequences and risks associated with an altered immuni`ty in the symbiotic organ, we developed a tripartite system with the model legume Medicago truncatula [ 11 , 12 ], its nodulating symbiont of the genus Sinorhizobium (syn. Ensifer) [ 13 , 14 ], and the pathogenic soil-borne bacterium Ralstonia solanacearum [ 15 , 16 , 17 , 18 ]. We show that nodules are frequent infection sites where pathogen multiplication is comparable to that in the root tips and independent of nodule ability to fix nitrogen. Transcriptomic analyses indicate that, despite the presence of the hosted rhizobia, nodules are able to develop weak defense reactions against pathogenic R. solanacearum. Nodule defense response displays specificity compared to that activated in roots. In agreement with nodule innate immunity, optimal R. solanacearum growth requires pathogen virulence factors. Finally, our data indicate that the high susceptibility of nodules is counterbalanced by the existence of a diffusion barrier preventing pathogen spreading from nodules to the rest of the plant.
Published: 2020

17. Laser Capture Micro-Dissection Coupled to RNA Sequencing: A Powerful Approach Applied to the Model Legume Medicago truncatula in Interaction with Sinorhizobium meliloti

Author: Brice, Roux, Nathalie, Rodde, Sandra, Moreau, Marie-Françoise, Jardinaud, and Pascal, Gamas
Subjects: Paraffin Embedding, Tissue Fixation, RNA, Plant, RNA, Ribosomal, Sequence Analysis, RNA, Medicago truncatula, Laser Capture Microdissection, Models, Biological, Sinorhizobium meliloti
Abstract: Understanding the development of multicellular organisms requires the identification of regulators, notably transcription factors, and specific transcript populations associated with tissue differentiation. Laser capture microdissection (LCM) is one of the techniques that enable the analysis of distinct tissues or cells within an organ. Coupling this technique with RNA sequencing (RNAseq) makes it extremely powerful to obtain a genome-wide and dynamic view of gene expression. Moreover, RNA sequencing allows two or potentially more interacting organisms to be analyzed simultaneously. In this chapter, a LCM-RNAseq protocol optimized for root and symbiotic root nodule analysis is presented, using the model legume Medicago truncatula (in interaction with Sinorhizobium meliloti in the nodule samples). This includes the description of procedures for plant material fixation, embedding, and micro-dissection; it is followed by a presentation of techniques for RNA extraction and amplification, adapted for the simultaneous analysis of plant and bacterial cells in interaction or, more generally, polyadenylated and non-polyadenylated RNAs. Finally, step-by-step statistical analyses of RNAseq data are described. Those are critical for quality assessment of the whole procedure and for the identification of differentially expressed genes.
Published: 2018

18. Laser Capture Micro-Dissection Coupled to RNA Sequencing: A Powerful Approach Applied to the Model Legume Medicago truncatula in Interaction with Sinorhizobium meliloti

Author: Nathalie Rodde, Sandra Moreau, Brice Roux, Pascal Gamas, Marie-Françoise Jardinaud, Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Nobutoshi Yamaguchi, ANR-08-GENM-0015,SYMbiMICS,Dissection moléculaire de l'interaction symbiotique rhizobium-légumineuse : une approche combinée de micro-dissection laser et de séquençage massif d?ESTs(2008), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, Sinorhizobium meliloti, biology, Polyadenylation, [SDV]Life Sciences [q-bio], RNA, Computational biology, biology.organism_classification, 01 natural sciences, Medicago truncatula, 03 medical and health sciences, 030104 developmental biology, Gene expression, RNA extraction, Transcription factor, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany, Laser capture microdissection
Abstract: Understanding the development of multicellular organisms requires the identification of regulators, notably transcription factors, and specific transcript populations associated with tissue differentiation. Laser capture microdissection (LCM) is one of the techniques that enable the analysis of distinct tissues or cells within an organ. Coupling this technique with RNA sequencing (RNAseq) makes it extremely powerful to obtain a genome-wide and dynamic view of gene expression. Moreover, RNA sequencing allows two or potentially more interacting organisms to be analyzed simultaneously. In this chapter, a LCM-RNAseq protocol optimized for root and symbiotic root nodule analysis is presented, using the model legume Medicago truncatula (in interaction with Sinorhizobium meliloti in the nodule samples). This includes the description of procedures for plant material fixation, embedding, and micro-dissection; it is followed by a presentation of techniques for RNA extraction and amplification, adapted for the simultaneous analysis of plant and bacterial cells in interaction or, more generally, polyadenylated and non-polyadenylated RNAs. Finally, step-by-step statistical analyses of RNAseq data are described. Those are critical for quality assessment of the whole procedure and for the identification of differentially expressed genes.
Published: 2018

19. Whole-genome landscape of Medicago truncatula symbiotic genes

Author: David Latrasse, Christine Lelandais-Brière, William Marande, Hélène Bergès, Frédéric Debellé, Stéphane Muños, Julia Buitink, Sébastien Carrère, Andreas Niebel, Mohamed Zouine, Pascal Gamas, Jonathan Kreplak, Moussa Benhamed, Olivier Bouchez, Sandra Moreau, Marie-Françoise Jardinaud, Stéphane Cauet, Thomas Blein, Jérôme Gouzy, Carine Satgé, Erika Sallet, Yann Pecrix, Céline Lopez-Roques, Margot Zahm, Baptiste Mayjonade, Aurélie Bérard, Florian Frugier, S. Evan Staton, Martin Crespi, Abdelhafid Bendahmane, Céline Chantry-Darmon, Magali Perez, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of British Columbia, 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, ANR grants EPISYM (grant no. ANR-15-CE20-0002), NODCCAAT (no. ANR-15-CE20-0012), REGULEG (no. ANR-15-CE20-0001), the ‘Laboratoire d’Excellence (LABEX)’ TULIP (no. ANR-10-LABX-41), the LABEX Saclay Plant Sciences (SPS, no. ANR-10-LABX-40) and the European Research Council (no. ERC-SEXYPARTH), and we made use of data previously generated in the ANR SYMbiMICS (ANR-08-GENO-106) and the INRA SPE EPINOD projects. The sequencing platform was supported by France Génomique National infrastructure (grant no. ANR-10-INBS-09) and by the GET-PACBIO programme (Programme opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020)., Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université 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), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, 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, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), 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 Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-15-CE20-0002,EPISYM,Régulations épigénétiques dans le développement de nodules symbiotiques racinaires chez les légumineuses(2015), ANR-15-CE20-0012,NODCCAAT,Comprendre le mode d'action du facteur de transcription NF-YA1 spécifique de l'intearction symbiotique rhizobium-légumineuses chez Medicago truncatula(2015), ANR-15-CE20-0001,REGULEG,Identification des régulateurs participant à la plasticité d'adaptation des graines de légumineuses aux changements environnementaux(2015), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0044,CEMAM,Center of Excellence in Multifunctional Architectured Materials(2010), ANR-08-GENM-0015,SYMbiMICS,Dissection moléculaire de l'interaction symbiotique rhizobium-légumineuse : une approche combinée de micro-dissection laser et de séquençage massif d?ESTs(2008), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université Bourgogne Franche-Comté [COMUE] (UBFC)-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, 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), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, AgroParisTech-Institut National de la Recherche Agronomique (INRA), 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), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-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)-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), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Laboratoire des Interactions Plantes Micro organismes, Université Fédérale Toulouse Midi-Pyrénées, Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), UR Etude du Polymorphisme des Génomes végétaux, Centre National de Génotypage (CNG), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Transposable element, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], RNA, Untranslated, [SDV]Life Sciences [q-bio], Symbiose, Sequence assembly, Genomics, Plant Science, Computational biology, 01 natural sciences, Genome, DNA sequencing, Epigenesis, Genetic, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Genome-wide analysis of gene expression, Gene Expression Regulation, Plant, Medicago truncatula, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, Gene, ComputingMilieux_MISCELLANEOUS, Plant Proteins, Rhizobial symbiosis, Whole genome sequencing, Symbiote, Génome, biology, phytogénétique, DNA Methylation, biology.organism_classification, 030104 developmental biology, RNA, Plant, Multigene Family, Next-generation sequencing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Root Nodules, Plant, Genome, Plant, 010606 plant biology & botany
Abstract: This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PSQE00000000.; Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.
Published: 2018

20. The Decoy Substrate of a Pathogen Effector and a Pseudokinase Specify Pathogen-Induced Modified-Self Recognition and Immunity in Plants

Author: Martine Lautier, Feng Feng, Xiaojuan Zhang, Lin Li, Nannan Li, Matthieu Chabannes, Endrick Guy, Laurent D. Noël, Marie-Françoise Jardinaud, She Chen, Chaozu He, Guoxun Wang, Matthieu Arlat, Brice Roux, Jianmin Zhou, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences [Changchun Branch] (CAS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), National Institute of Biological Sciences, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, École nationale supérieure agronomique de Toulouse [ENSAT], Hainan University, and ANR JCJC XOPaque
Subjects: Kinase, Cancer Research, [SDV]Life Sciences [q-bio], Arabidopsis, Pseudomonas syringae, Xanthomonas campestris, Immunologie, Plant Proteins, Effector, Mécanisme de défense cellulaire, Cell biology, Host-Pathogen Interactions, Decoy, Génétique moléculaire, Plante hôte, Virulence Factors, Pouvoir pathogène, Virulence, Biology, Microbiology, Immune system, Immunity, Immunology and Microbiology(all), Virology, Effecteur moléculaire, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Plant Diseases, H20 - Maladies des plantes, Génie génétique, fungi, Résistance aux maladies, biology.organism_classification, Parasitology, Plante de culture, Protein Processing, Post-Translational
Abstract: International audience; In plants, host response to pathogenic microbes is driven both by microbial perception and detection of modified-self. The Xanthomonas campestris effector protein AvrAC/XopAC uridylylates the Arabidopsis BIK1 kinase to dampen basal resistance and thereby promotes bacterial virulence. Here we show that PBL2, a paralog of BIK1, is similarly uridylylated by AvrAC. However, in contrast to BIK1, PBL2 uridylylation is specifically required for host recognition of AvrAC to trigger immunity, but not AvrAC virulence. PBL2 thus acts as a decoy and enables AvrAC detection. AvrAC recognition also requires the RKS1 pseudokinase of the ZRK family and the NOD-like receptor ZAR1, which is known to recognize the Pseudomonas syringae effector HopZ1a. ZAR1 forms a stable complex with RKS1, which specifically recruits PBL2 when the latter is uridylylated by AvrAC, triggering ZAR1-mediated immunity. The results illustrate how decoy substrates and pseudokinases can specify and expand the capacity of the plant immune system.
Published: 2015

21. Combined genetic and transcriptomic analysis reveals three major signalling pathways activated by Myc‐ <scp>LCO</scp> s in Medicago truncatula

Author: Pascal Gamas, David Rengel, Sébastien Carrère, Céline Camps, Sandra Bensmihen, Christine Hervé, Frédéric Debellé, Clare Gough, Marie-Françoise Jardinaud, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), École nationale supérieure agronomique de Toulouse [ENSAT], French Agence Nationale de la Recherche [MycSignalling ANR-09-BLAN-0241, SYMbiMICS ANR-08-GENO-106], and 'Laboratoire d'Excellence' (LABEX) [ANR-10-LABX-41, ANR-11-IDEX-0002-02]
Subjects: 0106 biological sciences, Genotype, Physiology, [SDV]Life Sciences [q-bio], Mutant, Oligosaccharides, Chitin, Plant Science, Genes, Plant, Plant Roots, 01 natural sciences, Genome, Transcriptome, 03 medical and health sciences, Gene Expression Regulation, Plant, Transcription (biology), Mycorrhizae, Medicago truncatula, Botany, Gene expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, Gene, Transcription factor, Plant Proteins, 030304 developmental biology, 2. Zero hunger, Genetics, Chitosan, 0303 health sciences, biology, Sequence Analysis, RNA, Fungi, Fungal Polysaccharides, biology.organism_classification, Mutation, Signal Transduction, Transcription Factors, 010606 plant biology & botany
Abstract: International audience; Myc-LCOs are newly identified symbiotic signals produced by arbuscular mycorrhizal (AM) fungi. Like rhizobial Nod factors, they are lipo-chitooligosaccharides that activate the common symbiotic signalling pathway (CSSP) in plants. To increase our limited understanding of the roles of Myc-LCOs we aimed to analyse Myc-LCO-induced transcriptional changes and their genetic control. Whole genome RNA sequencing (RNA-seq) was performed on roots of Medicago truncatula wild-type plants, and dmi3 and nsp1 symbiotic mutants affected in nodulation and mycorrhizal signalling. Plants were treated separately with the two major types of Myc-LCOs, sulphated and nonsulphated. Generalized linear model analysis identified 2201 differentially expressed genes and classified them according to genotype and/or treatment effects. Three genetic pathways for Myc-LCO-regulation of transcriptomic reprogramming were highlighted: DMI3- and NSP1-dependent; DMI3-dependent and NSP1-independent; and DMI3- and NSP1-independent. Comprehensive analysis revealed overlaps with previous AM studies, and highlighted certain functions, especially signalling components and transcription factors. These data provide new insights into mycorrhizal signalling mechanisms, supporting a role for NSP1, and specialisation for NSP1-dependent and -independent pathways downstream of DMI3. Our data also indicate significant Myc-LCO-activated signalling upstream of DMI3 and/or parallel to the CSSP and some constitutive activity of the CSSP.
Published: 2015

22. Cytokinins in Symbiotic Nodulation: When, Where, What For?

Author: Pascal Gamas, Mathias Brault, Florian Frugier, Marie-Françoise Jardinaud, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), 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 Paris Diderot - Paris 7 (UPD7), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Ecole d'Ingénieurs de Purpan (INP - PURPAN), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), École nationale supérieure agronomique de Toulouse (ENSAT), Agence Nationale de la Recherche (ANR), Université Fédérale Toulouse Midi-Pyrénées, Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École nationale supérieure agronomique de Toulouse [ENSAT], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), 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), Université Paris Sud (Paris 11), Ecole Nationale Supérieure Agronomique de Toulouse, Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Toulouse, 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 ), Université Paris Diderot (Paris 7), Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique ( INRA ), and Ecole d'Ingénieurs de Purpan ( INPT - EI Purpan )
Subjects: 0106 biological sciences, 0301 basic medicine, Cytokinins, Organogenesis, [SDV.CAN]Life Sciences [q-bio]/Cancer, Plant Science, Root hair, Biology, Plant Root Nodulation, Plant Roots, 01 natural sciences, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 03 medical and health sciences, chemistry.chemical_compound, cytokinin, Symbiosis, Nitrogen Fixation, Botany, nodulation, cytokinine, food and beverages, Fabaceae, biology.organism_classification, Cell biology, 030104 developmental biology, chemistry, Cytokinin, Nitrogen fixation, Rhizobium, 010606 plant biology & botany
Abstract: Substantial progress has been made in the understanding of early stages of the symbiotic interaction between legume plants and rhizobium bacteria. Those include the specific recognition of symbiotic partners, the initiation of bacterial infection in root hair cells, and the inception of a specific organ in the root cortex, the nodule. Increasingly complex regulatory networks have been uncovered in which cytokinin (CK) phytohormones play essential roles in different aspects of early symbiotic stages. Intriguingly, these roles can be either positive or negative, cell autonomous or non-cell autonomous, and vary, depending on time, root tissues, and possibly legume species. Recent developments on CK symbiotic functions and interconnections with other signaling pathways during nodule initiation are the focus of this review.
Published: 2017

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

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

24. Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula

Author: Carine Satgé, Marie-Françoise Jardinaud, Karine Gallardo, Marie-Christine Auriac, Ludovic Cottret, Erika Sallet, Céline Noirot, Sandra Moreau, Pascal Gamas, Gaëlle Lefort, Céline Remblière, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), and INRA SPE EPINOD project, ANR EPISYM project, Laboratoire d’Excellence (LABEX) TULIP (ANR-10- LABX-41)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Bisulfite sequencing, Plant Science, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, Medicago truncatula, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], Epigenetics, [MATH]Mathematics [math], Symbiosis, Gene, Plant Proteins, Genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, DNA Methylation, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, DNA demethylation, DNA methylation, [SDE]Environmental Sciences, biology.protein, Demethylase, Root Nodules, Plant, Reprogramming, 010606 plant biology & botany, Rhizobium
Abstract: The legume–Rhizobium symbiosis leads to the formation of a new organ, the root nodule, involving coordinated and massive induction of specific genes. Several genes controlling DNA methylation are spatially regulated within the Medicago truncatula nodule, notably the demethylase gene, DEMETER (DME), which is mostly expressed in the differentiation zone. Here, we show that MtDME is essential for nodule development and regulates the expression of 1,425 genes, some of which are critical for plant and bacterial cell differentiation. Bisulphite sequencing coupled to genomic capture enabled the identification of 474 regions that are differentially methylated during nodule development, including nodule-specific cysteine-rich peptide genes. Decreasing DME expression by RNA interference led to hypermethylation and concomitant downregulation of 400 genes, most of them associated with nodule differentiation. Massive reprogramming of gene expression through DNA demethylation is a new epigenetic mechanism controlling a key stage of indeterminate nodule organogenesis during symbiotic interactions. The legume–Rhizobium symbiosis allows nitrogen fixation. Development of nodules is a finely regulated developmental process that involves a DNA demethylase called DEMETER, linking epigenetic regulation and symbiosis.
Published: 2016

25. A laser dissection-RNAseq analysis highlights the activation of cytokinin pathways by nod factors in the Medicago truncatula root epidermis

Author: Nathalie Rodde, Marie-Françoise Jardinaud, Anna Kisiala, Jérôme Gouzy, Erika Sallet, Mathias Brault, Sandra Moreau, Olivier Catrice, R. J. Neil Emery, Stéphane Boivin, Agnes Lepage, Florian Frugier, Pascal Gamas, Brice Roux, Ludovic Cottret, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), 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), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Department of Biology, University of Technology and Life Sciences in Bydgoszcz, Trent University, ANR-06-GANI-0008,IMMOPIG,Etude de la réponse immunitaire des porcs français de race Large White et analyse conjointe du transcriptome des leucocytes du sang périphérique(2006), ANR-10-LABX-0032,LaSIPS,LABORATORY FOR SYSTEMS AND ENGINEERING OF PARIS SACLAY(2010), and ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011)
Subjects: 0106 biological sciences, 0301 basic medicine, Regulation of gene expression, Genetics, Epidermis (botany), Physiology, RNA, Plant Science, Biology, biology.organism_classification, 01 natural sciences, Medicago truncatula, Cell biology, Transcriptome, 03 medical and health sciences, 030104 developmental biology, Gene expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Signal transduction, Gene, 010606 plant biology & botany
Abstract: International audience; Nod factors (NFs) are lipochitooligosaccharidic signal molecules produced by rhizobia, which play a key role in the rhizobium-legume symbiotic interaction. In this study, we analyzed the gene expression reprogramming induced by purified NF (4 and 24 h of treatment) in the root epidermis of the model legume Medicago truncatula. Tissue-specific transcriptome analysis was achieved by laser-capture microdissection coupled to high-depth RNA sequencing. The expression of 17,191 genes was detected in the epidermis, among which 1,070 were found to be regulated by NF addition, including previously characterized NF-induced marker genes. Many genes exhibited strong levels of transcriptional activation, sometimes only transiently at 4 h, indicating highly dynamic regulation. Expression reprogramming affected a variety of cellular processes, including perception, signaling, regulation of gene expression, as well as cell wall, cytoskeleton, transport, metabolism, and defense, with numerous NF-induced genes never identified before. Strikingly, early epidermal activation of cytokinin (CK) pathways was indicated, based on the induction of CK metabolic and signaling genes, including the CRE1 receptor essential to promote nodulation. These transcriptional activations were independently validated using promoter:β-glucuronidase fusions with the MtCRE1 CK receptor gene and a CK response reporter (TWO COMPONENT SIGNALING SENSOR NEW). A CK pretreatment reduced the NF induction of the EARLY NODULIN11 (ENOD11) symbiotic marker, while a CK-degrading enzyme (CYTOKININ OXIDASE/DEHYDROGENASE3) ectopically expressed in the root epidermis led to increased NF induction of ENOD11 and nodulation. Therefore, CK may play both positive and negative roles in M. truncatula nodulation.
Published: 2016

26. Additional file 5: of Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome

Author: Roux, Brice, Bolot, Stéphanie, Endrick Guy, Denancé, Nicolas, Lautier, Martine, Marie-Françoise Jardinaud, Saux, Marion Fischer-Le, Portier, Perrine, Marie-Agnès Jacques, Gagnevin, Lionel, Pruvost, Olivier, Lauber, Emmanuelle, Arlat, Matthieu, Carrère, Sébastien, Koebnik, Ralf, and Noël, Laurent
Subjects: body regions, nervous system, fungi
Abstract: Oligonucleotides used in this study. (PDF 865 kb)
Published: 2015
Full Text: View/download PDF

27. Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome

Author: Matthieu Arlat, Marion Fischer-Le Saux, Brice Roux, Olivier Pruvost, Martine Lautier, Marie-Agnès Jacques, Laurent D. Noël, Marie-Françoise Jardinaud, Perrine Portier, Ralf Koebnik, Lionel Gagnevin, Endrick Guy, Sébastien Carrère, Emmanuelle Lauber, Nicolas Denancé, Stéphanie Bolot, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS), ANR Xanthomix, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées, UNIVERSITE TOULOUSE, Ecole Nationale Supérieure Agronomique de Toulouse, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Xanthomonas campestris, 01 natural sciences, Type three secretion system, Maladie des plantes, Séquence d'ADN, ORFeome, Genetics, 0303 health sciences, biology, Effector, food and beverages, RNA sequencing, Genomics, Transcription d'ADN, Protéine bactérienne, Pathovar, Research Article, Biotechnology, Virulence, Regulon, Microbiology, génomique, Open Reading Frames, 03 medical and health sciences, Bacterial Proteins, Xanthomonas, Type III secretion, Xanthomonas outer protein, Transcriptome, 030304 developmental biology, H20 - Maladies des plantes, Bactérie pathogène, Génome, Transcription génique, Gene Expression Profiling, fungi, Molecular Sequence Annotation, biology.organism_classification, 010606 plant biology & botany, Sécrétion
Abstract: The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani)., In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins., This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.
Published: 2015

28. Additional file 2: of Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome

Author: Roux, Brice, Bolot, Stéphanie, Endrick Guy, Denancé, Nicolas, Lautier, Martine, Marie-Françoise Jardinaud, Saux, Marion Fischer-Le, Portier, Perrine, Marie-Agnès Jacques, Gagnevin, Lionel, Pruvost, Olivier, Lauber, Emmanuelle, Arlat, Matthieu, Carrère, Sébastien, Koebnik, Ralf, and Noël, Laurent
Abstract: Scatter plots of the normalized expression levels of the 141 hrpG -regulated genes of strain CFBP 5828R of X. campestris pv. raphani by RNA sequencing (Table 4 , Fig. 4a ). (PDF 635 kb)
Published: 2015
Full Text: View/download PDF

29. Mass cloning of differential and nondifferential transcript-derived fragments from cDNA-AFLP experiments in sunflower

Author: Cecilia Tamborindeguy, Thierry Liboz, Cécile Ben, Françoise Jardinaud, and Laurent Gentzbittel
Subjects: Genetics, Cdna aflp, Gene expression, food and beverages, Amplified fragment length polymorphism, Embryo, Plant Science, Pcr method, Biology, Proteomics, Molecular Biology, Sunflower
Abstract: We have developed a 1-step procedure for cloning multiple bands obtained through cDNA-amplified fragment length polymorphism (AFLP) experiments. This protocol enables us to clone differential and nondifferential transcript-derived fragments (TDFs) in the same experiment. It consists of a mass cloning of cDNA-AFLP amplification products, identification of clones of interest with electrophoresis, and characterization through sequencing. The entire experiment can be performed in 1 wk because of the reduced time and effort needed for cloning, and it can be applied to any PCR method that produces complex band patterns. This method, tested on a comparison of gene expression between globular and heart embryo stages in sunflower embryogenesis, enabled us to clone 10 differential TDFs in the same experiment.
Published: 2004

30. [Untitled]

Author: Gilbert Alibert, Jean Kallerhoff, Tarek Hewezi, and Françoise Jardinaud
Subjects: Basal shoot, Regeneration (biology), fungi, Shoot, Botany, Helianthus annuus, food and beverages, Organogenesis, Horticulture, Meristem, Biology, Somaclonal variation, Explant culture
Abstract: A new approach for shoot regeneration from split embryonic axes of Helianthus annuus var. RHA266, a poor responding genotype to in vitro culture, has been developed. The regeneration procedure is based on successive excision of the apical and axillary shoots originating from pre-existing meristems. This elimination process stimulates adventitious shoot bud formation in 80% of treated explants. Although newly induced buds were observed on hormone-free medium, higher rate of induction and bud development were obtained on medium containing 0.1 mg l−1 BA. All regenerated plants were phenotypically similar to seed-derived RHA 266 plants with no observed somaclonal variation, as assessed by AFLP analysis. The efficient shoot regeneration from newly formed meristematic cells should offer opportunities to genetically engineer economically important sunflower genotypes that have proven till now, to be recalcitrant towards other regeneration systems.
Published: 2003

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

Author: Benjamin Billault-Penneteau, Andreas Niebel, Marion R. Cerri, Tom Laloum, Maël Baudin, Pascal Gamas, Agnes Lepage, Lisa Frances, Federico Ariel, Marie-Françoise Jardinaud, Fernanda de Carvalho-Niebel, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), École nationale supérieure agronomique de Toulouse [ENSAT], French Ministry of Education and Research, INRA CJS (Contrat Jeune Scientifique) contract, European Molecular Biology Organization (EMBO), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-09-BLAN-0033,HAPIHUB(2009), ANR-08-GENM-0015,SYMbiMICS,Dissection moléculaire de l'interaction symbiotique rhizobium-légumineuse : une approche combinée de micro-dissection laser et de séquençage massif d?ESTs(2008), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Faculty of Biology, Adam Mickiewicz University in Poznań (UAM), Ludwig Maximilians University of Munich, UPR2355 Institut des sciences du végétal, and Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], CAAT box, Gene Expression, Plant Science, Plant Roots, Rhizobia, Nod factor, Transactivation, Gene Expression Regulation, Plant, Genes, Reporter, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Tobacco, Botany, Medicago truncatula, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nuclear factor Y, Symbiosis, Transcription factor, Gene, transcription factor, Plant Proteins, Nod factor signaling, biology, Endosymbiosis, Sequence Analysis, RNA, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Cell biology, legume-rhizobium symbiosis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, CCAAT-Binding Factor, RNA, Plant, CCAAT box-binding factor, Root Nodules, Plant, Microdissection, Signal Transduction, Sinorhizobium meliloti, Transcription Factors
Abstract: International audience; During endosymbiotic interactions between legume plants and nitrogen-fixing rhizobia, successful root infection by bacteria and nodule organogenesis requires the perception and transduction of bacterial lipo-chitooligosaccharidic signal called Nod factor (NF). NF perception in legume roots leads to the activation of an early signaling pathway and of a set of symbiotic genes which is controlled by specific early transcription factors (TFs) including CYCLOPS/IPD3, NSP1, NSP2, ERN1 and NIN. In this study, we bring convincing evidence that the Medicago truncatula CCAAT-box-binding NF-YA1 TF, previously associated with later stages of rhizobial infection and nodule meristem formation is, together with its closest homolog NF-YA2, also an essential positive regulator of the NF-signaling pathway. Here we show that NF-YA1 and NF-YA2 are both expressed in epidermal cells responding to NFs and their knock-down by reverse genetic approaches severely affects the NF-induced expression of symbiotic genes and rhizobial infection. Further over-expression, transactivation and ChIP-PCR approaches indicate that NF-YA1 and NF-YA2 function, at least in part, via the direct activation of ERN1. We thus propose a model in which NF-YA1 and NF-YA2 appear as early symbiotic regulators acting downstream of DMI3 and NIN and possibly within the same regulatory complexes as NSP1/2 to directly activate the expression of ERN1.
Published: 2014

32. The CCAAT box-binding transcription factor NF-YA1 controls rhizobial infection

Author: Sandra Moreau, Douglas R. Cook, Agnes Lepage, Marie-Françoise Jardinaud, Olivier Catrice, Pascal Gamas, Andreas Niebel, Philippe Laporte, Joëlle Fournier, Estíbaliz Larrainzar, Jeong-Hwan Mun, Universidad Pública de Navarra. Departamento de Ciencias del Medio Natural, Nafarroako Unibertsitate Publikoa. Natura Ingurunearen Zientziak Saila, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), National Academy of Agricultural Science, Myongji University, and University of California
Subjects: 0106 biological sciences, Physiology, [SDV]Life Sciences [q-bio], Mutant, symbiosis, Plant Biology, Plant Science, infection thread, 01 natural sciences, rhizobium, Gene Expression Regulation, Plant, 2.1 Biological and endogenous factors, Aetiology, Plant Proteins, 2. Zero hunger, 0303 health sciences, Sinorhizobium meliloti, biology, Nodule development, food and beverages, Phenotype, Medicago truncatula, Cell biology, Infection thread, CCAAT box-binding factor, Root Nodules, Root Nodules, Plant, Infection, Research Paper, Rhizobium, Crop and Pasture Production, Plant Biology & Botany, nodule development, NF-YA, Rhizobia, 03 medical and health sciences, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, Transcription factor, 030304 developmental biology, Base Sequence, Genetic Complementation Test, Wild type, Plant, Meristem, biology.organism_classification, infection, Gene Expression Regulation, Mutation, 010606 plant biology & botany, Transcription Factors
Abstract: Symbiosis between legume plants and soil rhizobia culminates in the formation of a novel root organ, the 'nodule', containing bacteria differentiated as facultative nitrogen-fixing organelles. MtNF-YA1 is a Medicago truncatula CCAAT box-binding transcription factor (TF), formerly called HAP2-1, highly expressed in mature nodules and required for nodule meristem function and persistence. Here a role for MtNF-YA1 during early nodule development is demonstrated. Detailed expression analysis based on RNA sequencing, quantitiative real-time PCR (qRT-PCR), as well as promoter–β-glucuronidase (GUS) fusions reveal that MtNF-YA1 is first induced at the onset of symbiotic development during preparation for, and initiation and progression of, symbiotic infection. Moreover, using a new knock-out mutant, Mtnf-ya1-1, it is shown that MtNF-YA1 controls infection thread (IT) progression from initial root infection through colonization of nodule tissues. Extensive confocal and electronic microscopic observations suggest that the bulbous and erratic IT growth phenotypes observed in Mtnf-ya1-1 could be a consequence of the fact that walls of ITs in this mutant are thinner and less coherent than in the wild type. It is proposed that MtNF-YA1 controls rhizobial infection progression by regulating the formation and the wall of ITs. This work was funded by the ANR-09-BLAN-0033-01 HAPIHUB project, including a post-doctoral grant to PL. This work is part of the 'Laboratoire d'Excellence' (LABEX) entitled TULIP (ANR-10-LABX-41). The Mtnf-ya1-1 mutant was identified by a TILLING approach within a A17 Jemalong EMS-mutagenized population, in the frame of the FP6-GLIP (Grain Legume Integrated Project) project. EL is a recipient of the Marie Curie International Outgoing Fellowships for Career Development within the 7th European Union Framework Program (FP7-PEOPLE-2009). This work was carried out with the support of the 'Cooperative Research Program for Agricultural Science & Technology Development (Project no. PJ906910)', Rural Development Administration, Republic of Korea, to JHM and DRC.
Published: 2014

33. An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing

Author: Ludovic Cottret, Sébastien Carrère, Pascal Gamas, Fernanda de Carvalho-Niebel, Jérôme Gouzy, Laurent Sauviac, Sandra Moreau, Claude Bruand, Frédéric Debellé, Ton Timmers, Delphine Capela, Marie-Françoise Jardinaud, Erika Sallet, Nathalie Rodde, Brice Roux, Emmanuel Courcelle, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, ANR [ANR-08-GENO-106], French Laboratory of Excellence project 'TULIP' [ANR-10-LABX-41, ANR-11-IDEX-0002-02], Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), École nationale supérieure agronomique de Toulouse [ENSAT], the FR AIB microscopy platform (Toulouse), ANR-08-GENM-0015,SYMbiMICS,Dissection moléculaire de l'interaction symbiotique rhizobium-légumineuse : une approche combinée de micro-dissection laser et de séquençage massif d?ESTs(2008), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)
Subjects: regulators, Root nodule, [SDV]Life Sciences [q-bio], Meristem, Gene Expression, Plant Science, Computational biology, Bacterial genome size, Laser Capture Microdissection, Plant Roots, nitrogen-fixing symbiosis, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Nitrogen Fixation, Gene expression, Botany, Medicago truncatula, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, Gene, Laser capture microdissection, 2. Zero hunger, Sinorhizobium meliloti, biology, Sequence Analysis, RNA, Gene Expression Profiling, fungi, food and beverages, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 15. Life on land, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genes, Bacterial, Root Nodules, Plant, transcriptome, model legume
Abstract: International audience; Rhizobium-induced root nodules are specialized organs for symbiotic nitrogen fixation. Indeterminate-type nodules are formed from an apical meristem and exhibit a spatial zonation which corresponds to successive developmental stages. To get a dynamic and integrated view of plant and bacterial gene expression associated with nodule development, we used a sensitive and comprehensive approach based upon oriented high-depth RNA sequencing coupled to laser microdissection of nodule regions. This study, focused on the association between the model legume Medicago truncatula and its symbiont Sinorhizobium meliloti, led to the production of 942million sequencing read pairs that were unambiguously mapped on plant and bacterial genomes. Bioinformatic and statistical analyses enabled in-depth comparison, at a whole-genome level, of gene expression in specific nodule zones. Previously characterized symbiotic genes displayed the expected spatial pattern of expression, thus validating the robustness of our approach. We illustrate the use of this resource by examining gene expression associated with three essential elements of nodule development, namely meristem activity, cell differentiation and selected signaling processes related to bacterial Nod factors and redox status. We found that transcription factor genes essential for the control of the root apical meristem were also expressed in the nodule meristem, while the plant mRNAs most enriched in nodules compared with roots were mostly associated with zones comprising both plant and bacterial partners. The data, accessible on a dedicated website, represent a rich resource for microbiologists and plant biologists to address a variety of questions of both fundamental and applied interest.
Published: 2013

34. MtQRRS1, an R-locus required for Medicago truncatula quantitative resistance to Ralstonia solanacearum

Author: Cécile Ben, Laurent Gentzbittel, Hélène Bergès, Fabienne Vailleau, Arnaud Bellec, Frédéric Debellé, Thierry Huguet, Philippe Anson, Marie-Françoise Jardinaud, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Candidate gene, Physiology, [SDV]Life Sciences [q-bio], root pathogen, Plant Science, CORE COLLECTION, 01 natural sciences, PSEUDOMONAS-SOLANACEARUM, Gene Expression Regulation, Plant, Cluster Analysis, Inbreeding, mapping, Disease Resistance, Genetics, 0303 health sciences, Ralstonia solanacearum, biology, Bacterial wilt, LRR GENES, food and beverages, Physical Chromosome Mapping, Medicago truncatula, Hypocotyl, Phenotype, quantitative resistance, Genotype, Molecular Sequence Data, Quantitative Trait Loci, Locus (genetics), Quantitative trait locus, Polymorphism, Single Nucleotide, Chromosomes, Plant, quantitative trait locus (QTL), 03 medical and health sciences, APHRESISTANCE, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Crosses, Genetic, Genetic Association Studies, 030304 developmental biology, Plant Diseases, Bacterial artificial chromosome, APHANOMYCES-EUTEICHES, Gene Expression Profiling, BACTERIAL WILT, Reproducibility of Results, Molecular Sequence Annotation, biology.organism_classification, TRAIT LOCI, MODEL LEGUME, TOMATO, 010606 plant biology & botany
Abstract: International audience; Ralstonia solanacearum is a major soilborne pathogen that attacks > 200 plant species, including major crops. To characterize MtQRRS1, a major quantitative trait locus (QTL) for resistance towards this bacterium in the model legume Medicago truncatula, genetic and functional approaches were combined. QTL analyses together with disease scoring of heterogeneous inbred families were used to define the locus. The candidate region was studied by physical mapping using a bacterial artificial chromosome (BAC) library of the resistant line, and sequencing. In planta bacterial growth measurements, grafting experiments and gene expression analysis were performed to investigate the mechanisms by which this locus confers resistance to R. solanacearum. The MtQRRS1 locus was localized to the same position in two recombinant inbred line populations and was narrowed down to a 64 kb region. Comparison of parental line sequences revealed 15 candidate genes with sequence polymorphisms, but no evidence of differential gene expression upon infection. A role for the hypocotyl in resistance establishment was shown. These data indicate that the quantitative resistance to bacterial wilt conferred by MtQRRS1, which contains a cluster of seven R genes, is shared by different accessions and may act through intralocus interactions to promote resistance.
Published: 2013

35. NFP, a LysM protein controlling Nod factor perception, also intervenes in Medicago truncatula resistance to pathogens

Author: Maxime Bonhomme, Christophe Jacquet, Sandrine Balzergue, Jean-Jacques Bono, Arnaud Bottin, Stéphanie Huguet, Bernard Dumas, Thomas Rey, Clare Gough, Amaury Nars, Marie-Françoise Jardinaud, Julie V. Cullimore, 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), 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), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Interactions Microbiennes dans la Rhizosphère et les Racines, Region Midi-Pyrenees, CNRS [INEE 36], Universite Paul Sabatier, Ministere de l'Enseignement Superieur et de la Recherche, French Agence Nationale de la Recherche [ANR-08-BLAN-0208-01], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, Physiology, [SDV]Life Sciences [q-bio], Mutant, Plant Science, 01 natural sciences, Plant Roots, ARBUSCULAR MYCORRHIZAL FUNGI, Nod factor, Transcriptome, Aphanomyces euteiches, Gene Expression Regulation, Plant, CELL-WALL, DISEASE DEVELOPMENT, GENE-EXPRESSION, Disease Resistance, Plant Proteins, Genetics, Oomycete, 0303 health sciences, biology, food and beverages, legume, PLANT-MICROBE INTERACTIONS, Plants, Genetically Modified, Medicago truncatula, Host-Pathogen Interactions, RECEPTOR KINASE, plant immunity, Colletotrichum trifolii, Aphanomyces, Protein Serine-Threonine Kinases, 03 medical and health sciences, Botany, Colletotrichum, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Symbiosis, Gene, 030304 developmental biology, Plant Diseases, APHANOMYCES-EUTEICHES, Gene Expression Profiling, fungi, LysM protein, biology.organism_classification, RHIZOBIAL INFECTION, PLASMA-MEMBRANE, Mutation, INNATE IMMUNITY, 010606 plant biology & botany
Abstract: International audience; Plant LysM proteins control the perception of microbial-derived N-acetylglucosamine compounds for the establishment of symbiosis or activation of plant immunity. This raises questions about how plants, and notably legumes, can differentiate friends and foes using similar molecular actors and whether any receptors can intervene in both symbiosis and resistance. To study this question, nfp and lyk3 LysM-receptor like kinase mutants of Medicago truncatula that are affected in the early steps of nodulation, were analysed following inoculation with Aphanomyces euteiches, a root oomycete. The role of NFP in this interaction was further analysed by overexpression of NFP and by transcriptome analyses. nfp, but not lyk3, mutants were significantly more susceptible than wildtype plants to A.euteiches, whereas NFP overexpression increased resistance. Transcriptome analyses on A.euteiches inoculation showed that mutation in the NFP gene led to significant changes in the expression of c. 500 genes, notably involved in cell dynamic processes previously associated with resistance to pathogen penetration. nfp mutants also showed an increased susceptibility to the fungus Colletotrichum trifolii. These results demonstrate that NFP intervenes in M.truncatula immunity, suggesting an unsuspected role for NFP in the perception of pathogenic signals.
Published: 2012

36. Dissection of Bacterial Wilt on Medicago truncatula Revealed Two Type III Secretion System Effectors Acting on Root Infection Process and Disease Development[C][W][OA]

Author: Marie-José Tavella, Laurent Gentzbittel, Fabienne Vailleau, Stéphane Genin, Alain Jauneau, Marie-Françoise Jardinaud, and Marie Turner
Subjects: Physiology, Mutant, Colony Count, Microbial, Plant Science, Biology, Plant disease resistance, Lignin, Plant Roots, Fluorescence, Type three secretion system, Microbiology, Pathosystem, Bacterial Proteins, Cell Wall, Botany, Medicago truncatula, Genetics, Plant Diseases, Ralstonia solanacearum, Effector, Bacterial wilt, food and beverages, biology.organism_classification, Immunity, Innate, Focus Issue on Plant Interactions with Bacterial Pathogens, Host-Pathogen Interactions, Mutation
Abstract: Ralstonia solanacearum is the causal agent of the devastating bacterial wilt disease, which colonizes susceptible Medicago truncatula via the intact root tip. Infection involves four steps: appearance of root tip symptoms, root tip cortical cell invasion, vessel colonization, and foliar wilting. We examined this pathosystem by in vitro inoculation of intact roots of susceptible or resistant M. truncatula with the pathogenic strain GMI1000. The infection process was type III secretion system dependent and required two type III effectors, Gala7 and AvrA, which were shown to be involved at different stages of infection. Both effectors were involved in development of root tip symptoms, and Gala7 was the main determinant for bacterial invasion of cortical cells. Vessel invasion depended on the host genetic background and was never observed in the resistant line. The invasion of the root tip vasculature in the susceptible line caused foliar wilting. The avrA mutant showed reduced aggressiveness in all steps of the infection process, suggesting a global role in R. solanacearum pathogenicity. The roles of these two effectors in subsequent stages were studied using an assay that bypassed the penetration step; with this assay, the avrA mutant showed no effect compared with the GMI1000 strain, indicating that AvrA is important in early stages of infection. However, later disease symptoms were reduced in the gala7 mutant, indicating a key role in later stages of infection.
Published: 2009

37. Characterization of the Interaction Between the Bacterial Wilt Pathogen Ralstonia solanacearum and the Model Legume Plant Medicago truncatula

Author: Fabien Chardon, Fabienne Vailleau, Thierry Huguet, Michel Petitprez, Elodie Sartorel, Laurent Gentzbittel, Stéphane Genin, Marie-Françoise Jardinaud, Laboratoire Symbiose et Pathologie des Plantes (S2P), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Time Factors, Physiology, QTL, Quantitative Trait Loci, Biotechnologies, Quantitative trait locus, Plant Roots, 01 natural sciences, Genetic analysis, Chromosomes, Plant, 03 medical and health sciences, Pathosystem, Inbred strain, Xylem, Medicago truncatula, Botany, Crosses, Genetic, Plant Diseases, 030304 developmental biology, 0303 health sciences, Ralstonia solanacearum, Microscopy, Confocal, biology, Inoculation, Bacterial wilt, fungi, Chromosome Mapping, food and beverages, General Medicine, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Amélioration des plantes, Immunity, Innate, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt and attacks more than 200 plant species, including some legumes and the model legume plant Medicago truncatula. We have demonstrated that M. truncatula accessions Jemalong A17 and F83005.5 are susceptible to R. solanacearum and, by screening 28 R. solana-cearum strains on the two M. truncatula lines, differential interactions were identified. R. solanacearum GMI1000 infected Jemalong A17 line, and disease symptoms were dependent upon functional hrp genes. An in vitro root inoculation method was employed to demonstrate that R. solanacearum colonized M. truncatula via the xylem and intercellular spaces. R. solanacearum multiplication was restricted by a factor greater than 1 × 105 in the resistant line F83005.5 compared with susceptible Jemalong A17. Genetic analysis of recombinant inbred lines from a cross between Jemalong A17 and F83005.5 revealed the presence of major quantitative trait loci for bacterial wilt resistance located on chromosome 5. The results indicate that the root pathosystem for M. truncatula will provide useful traits for molecular analyses of disease and resistance in this model plant species.
Published: 2007

38. Optimisation of DNA transfer and transientβ-glucuronidase expression in electroporated maize (Zea mays L.) microspores

Author: André Souvré, Gilbert Alibert, Marie-Françoise Jardinaud, and Michel Beckert
Subjects: Genetics, Reporter gene, Genetically modified maize, Expression vector, Electroporation, Plant Science, General Medicine, Biology, biology.organism_classification, Cell biology, Microspore, Gene expression, Cauliflower mosaic virus, Agronomy and Crop Science, Gene
Abstract: The ability to deliver free DNA into microspores of a highly androgenic hybrid of maize was assessed by electroporation, using a square wave pulse discharge apparatus. The electroporation medium was chosen according to its ability to maintain a high level of regeneration. Nuclease activities were analyzed and were inhibited by the addition of 100 mM KNO3 and MgSO4 in the electroporation medium. Seven expression vectors withUid A as the reporter gene under the control of cauliflower mosaic virus 35S, Lat 52-7, Zmg 13, Emu, Ubiq-1, Al, or Actl promoters were tested in relation to the level of s-glucuronidase expression in maize microspores. The highest level of expression was obtained when theUid A gene was driven by the Actl promoter. Therefore, this vector was further used to define optimal conditions leading to highest levels of s-glucuronidase expression. The parameters determined in this study could provide an ideal starting point for the obtention of transgenic maize plants from electroporated microspores.
Published: 1994

39. A new approach for efficient regeneration of a recalcitrant genotype of sunflower (Helianthus annuus) by organogenesis induction on split embryonic axes.

Author: Tarek Hewezi, Françoise Jardinaud, Gilbert Alibert, and Jean Kallerhoff
Published: 2003
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