Author: "Department of Plant Microbe Interactions" - Searchworks@Jio Institute Digital Library Search Results

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399 results on '"Department of Plant Microbe Interactions"'

1. Structural Basis for Signaling by Exclusive EDS1 Heteromeric Complexes with SAG101 or PAD4 in Plant Innate Immunity

Author: Jaqueline Bautor, Jane E. Parker, Steffen Rietz, Stephan Wagner, Karsten Niefind, Johannes Stuttmann, Raphael Guerois, Elena Brunstein, Department of Mathematical Sciences [Matieland, Stellenbosch Uni.] (DMS), Stellenbosch University, Université de la Méditerranée - Aix-Marseille 2, Max Planck Institute for Plant Breeding Research (MPIPZ), Institut de Biologie et de Technologies de Saclay (IBITECS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Plant-Microbe Interactions, University of Cologne, and Department of Plant Microbe Interactions
Subjects: Models, Molecular, Cancer Research, Protein Conformation, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Immunity, Crystallography, X-Ray, Microbiology, Conserved sequence, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Protein structure, Virology, Immunology and Microbiology(all), Hydrolase, Gene, Molecular Biology, Genetics, Innate immune system, biology, Arabidopsis Proteins, biology.organism_classification, Immunity, Innate, DNA-Binding Proteins, Parasitology, Protein Multimerization, Signal transduction, Carboxylic Ester Hydrolases, Signal Transduction
Abstract: SummaryBiotrophic plant pathogens encounter a postinfection basal resistance layer controlled by the lipase-like protein enhanced disease susceptibility 1 (EDS1) and its sequence-related interaction partners, senescence-associated gene 101 (SAG101) and phytoalexin deficient 4 (PAD4). Maintainance of separate EDS1 family member clades through angiosperm evolution suggests distinct functional attributes. We report the Arabidopsis EDS1-SAG101 heterodimer crystal structure with juxtaposed N-terminal α/β hydrolase and C-terminal α-helical EP domains aligned via a large conserved interface. Mutational analysis of the EDS1-SAG101 heterodimer and a derived EDS1-PAD4 structural model shows that EDS1 signals within mutually exclusive heterocomplexes. Although there is evolutionary conservation of α/β hydrolase topology in all three proteins, a noncatalytic resistance mechanism is indicated. Instead, the respective N-terminal domains appear to facilitate binding of the essential EP domains to create novel interaction surfaces on the heterodimer. Transitions between distinct functional EDS1 heterodimers might explain the central importance and versatility of this regulatory node in plant immunity.
Published: 2013
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2. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

Author: Jeffrey A. Rollins, Ken Shirasu, Jochen Kleemann, Emiel Ver Loren van Themaat, Narmada Shenoy, Hiroyuki Takahara, Christian Becker, Maria F. Torres, Zehua Chen, Noam Alkan, Martin B. Dickman, Michael Place, Pamela Gan, Christopher L. Schardl, Neil Moore, Michael R. Thon, Richard J. Howard, Christian Koch, Lucia Alvarado-Balderrama, Stefan G. Amyotte, Christopher Bauser, Robert H. Proctor, James A. Sweigard, Audrey D. Law, Bruce W. Birren, Jaeyoung Choi, Daniel G. Panaccione, Serenella A. Sukno, Itay Miyara, Lars M. Voll, Karl Nordström, Li-Jun Ma, Yasuyuki Kubo, Usha Rani Sikhakolli, Sarah Young, Mark A. Farman, Yong-Hwan Lee, Ester Alvarenga Santos Buiate, Ulla Neumann, Ulrike Damm, Mehdi Kabbage, H. Charlotte van der Does, Bernard Henrissat, Kurt Stüber, Dov Prusky, Marc-Henri Lebrun, Richard J. O'Connell, Shiguo Zhou, Richard Reinhardt, Stéphane Hacquard, Jonathan P. Duvick, Gabriel E. Rech, Frances Trail, Steve Rounsley, David C. Schwartz, Yoshitaka Takano, Paul Schulze-Lefert, Jo Anne Crouch, Ralph Panstruga, Barbara Kracher, David I. Heiman, Janine Altmüller, Jingze Zhang, Qiandong Zeng, Isa Will, Lynn Epstein, Lisa J. Vaillancourt, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Centro Hispano-Luso de Investigaciones Agrarias, Departamento de Microbiología y Genétic, Universidad de Salamanca, Department of Plant Pathology, University of Kentucky (UK), 1. Department of Plant Microbe Interactions, Fungal Biodiversity Centre, 3. Department of Plant Pathology, Kentucky State University, University of California (UC), 6. Department of Postharvest Science of Fresh Produce, Agricultural Research Organizati, Agricultural Research Organization, Cologne Center for Genomics, University of Cologne, Broad Institute [Cambridge], Harvard University-Massachusetts Institute of Technology (MIT), GATC Biotech AG [Konstanz], Center for Genomics, Seoul National University [Seoul] (SNU), Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, DuPont Agricultural Biotechnology, Pioneer Hi-Bred International, Plant Immunity Research Group, RIKEN Plant Science Center, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), 15. Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Borlaug Genomics and Bioinformatics Center, Texas, Texas A&M University System, Department of Biology, Division of Biochemistry, Friedrich-Alexander, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Laboratory of Plant Pathology, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University (KPU), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 6. Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Department of Computer Science, Central Microscopy, Department of Plant Developmental Biology, Division of Plant and Soil Sciences, West Virginia University, Institute for Biology I, Unit of Plant Molecular Cell Biology, Rheinisch-Westfälische Technische Hochschule, Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Agriculture Research Service, National Center for Agricultural Utilization Research, 2. Centro Hispano-Luso de Investigaciones Agrarias, Departamento de Microbiología y Genética, Max Planck-Genome-centre Cologne (MP-GC), Max-Planck-Gesellschaft, University of Florida [Gainesville] (UF), Department of Plant Biology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, 12. Pioneer Hi-Bred International, Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Department of Biology, Division of Biochemistry, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, University of Kentucky, University of California, Harvard University [Cambridge]-Massachusetts Institute of Technology (MIT), Kyoto Prefectural University, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Rheinisch-Westfälische Technische Hochschule Aachen (RWTH), University of Florida [Gainesville], Kyoto University [Kyoto], Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and Vaillancourt, Lisa J
Subjects: operative targe, [SDV]Life Sciences [q-bio], Arabidopsis, specificity, Models, Biological, Transcriptome, 03 medical and health sciences, host status, Gene Expression Regulation, Fungal, Genetics, Colletotrichum, Cluster Analysis, Secondary metabolism, Gene, Colletotrichum higginsianum, Phylogeny, 030304 developmental biology, Plant Diseases, Comparative genomics, 0303 health sciences, biology, 030306 microbiology, nonhost, Gene Expression Profiling, fungi, Colletotrichum orbiculare, Fungal genetics, Gene Expression Regulation, Developmental, food and beverages, Sequence Analysis, DNA, biology.organism_classification, basal resistance, Host-Pathogen Interactions, Mitosporic Fungi, Genome, Fungal, effectors
Abstract: Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
Published: 2012

3. Moonlighting Function of Phytochelatin Synthase1 in Extracellular Defense against Fungal Pathogens

Author: Melisa Lim, Mariola Piślewska-Bednarek, Rene Fuchs, Volker Lipka, Kian Hématy, Paweł Bednarek, Shauna Somerville, Clara Sánchez-Rodríguez, Candice Cherk, Erwin Grill, Paul Schulze-Lefert, Mónica Stein, Antonio Molina, Christine Klapprodt, Carnegie Institution for Science, Department of Plant Biology, Stanford University-Stanford University, Energy Biosciences Institute, University of California [Berkeley], University of California-University of California, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Institute of Bioorganic Chemistry, Polish Academy of Sciences (PAN), Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Schwann-Schleiden Research Center for Molecular Cell Biology, University Medical Center Göttingen (UMG), Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Lehrstuhl für Botanik, Technische Universtät München, and National Science Foundation (NSF) Carnegie Institution for Science Stanford University Max Planck SocietyFoundation CELLEX German Research Foundation (DFG)SPP1212GR 938LI 1317/2-1Spanish Ministry of Economy and Competitiveness (MINECO) BIO2015-64077-RBIO2012-32910Polish National Science Centre 2012/07/E/NZ2/04098
Subjects: 0106 biological sciences, Protein moonlighting, Physiology, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Science, 01 natural sciences, Catalysis, chemistry.chemical_compound, Arabidopsis-thaliana, Ascomycota, Gene Expression Regulation, Plant, Phytochelatins, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Research Articles, Heavy metal detoxification, Glucosinolate Metabolism, biology, Arabidopsis Proteins, Myrosinase, Binding Cassette Transporter, Nonhost Resistance, Tryptophan, Glutathione, Plants, Genetically Modified, biology.organism_classification, Mitochondria, Metabolic pathway, Biochemistry, chemistry, Gamma-glutamylcysteine, Phytochelatin, Pathogens, Tolerance, 010606 plant biology & botany
Abstract: Phytochelatin synthase (PCS) is a key component of heavy metal detoxification in plants. PCS catalyzes both the synthesis of the peptide phytochelatin from glutathione and the degradation of glutathione conjugates via peptidase activity. Here, we describe a role for PCS in disease resistance against plant pathogenic fungi. The pen4 mutant, which is allelic to cadmium insensitive1 (cad1/pcs1) mutants, was recovered from a screen for Arabidopsis mutants with reduced resistance to the nonadapted barley fungal pathogen Blumeria graminis f. sp. hordei. PCS1, which is found in the cytoplasm of cells of healthy plants, translocates upon pathogen attack and colocalizes with the PEN2 myrosinase on the surface of immobilized mitochondria. pcs1 and pen2 mutant plants exhibit similar metabolic defects in the accumulation of pathogen-inducible indole glucosinolate-derived compounds, suggesting that PEN2 and PCS1 act in the same metabolic pathway. The function of PCS1 in this pathway is independent of phytochelatin synthesis and deglycination of glutathione conjugates, as catalytic-site mutants of PCS1 are still functional in indole glucosinolate metabolism. In uncovering a peptidase-independent function for PCS1, we reveal this enzyme to be a moonlighting protein important for plant responses to both biotic and abiotic stresses.
Published: 2020

4. A dominant‐interfering camta3 mutation compromises primary transcriptional outputs mediated by both cell surface and intracellular immune receptors in Arabidopsis thaliana

Author: Takaki Maekawa, Akira Mine, Kenichi Tsuda, Florence Jacob, Paul Schulze-Lefert, Servane Blanvillain-Baufumé, Barbara Kracher, Carolin Seyfferth, Jane E. Parker, 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), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Deutsche Forschungsgemeinschaft [SFB 670], Bundesministerium fur Bildung und Forschung (BMBF) project 'BALANCE', Max Planck Society, French-German university grant, French Ministry of Research PhD fellowship, Schulze-Lefert, Paul, and Maekawa, Takaki
Subjects: 0301 basic medicine, nucleotide‐binding domain and LRR‐containing proteins (NLRs), immediate early genes, Arabidopsis thaliana, Transcription, Genetic, Physiology, Arabidopsis, Intracellular Space, Plant Science, Transcriptome, Transcription (biology), Gene Expression Regulation, Plant, Gene expression, Transcriptional regulation, Plant Immunity, effector-triggered immunity (ETI), Receptors, Immunologic, pattern‐triggered immunity (PTI), Disease Resistance, Genes, Dominant, cross‐tolerance, Vegetal Biology, biology, Full Paper, Pattern recognition receptor, Full Papers, Cell biology, Up-Regulation, Regulatory sequence, Receptors, Pattern Recognition, Signal Transduction, pattern-triggered immunity (PTI), NLR Proteins, calmodulin-binding transcription activator (CAMTA), cross-tolerance, nucleotide-binding domain and LRR-containing proteins (NLRs), transcriptional responses, Genes, Plant, 03 medical and health sciences, effector‐triggered immunity (ETI), Stress, Physiological, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Plant Diseases, calmodulin‐binding transcription activator (CAMTA), Arabidopsis Proteins, Research, fungi, biology.organism_classification, 030104 developmental biology, Mutation, Biologie végétale, Transcription Factors
Abstract: International audience; Pattern recognition receptors (PRRs) and nucleotide-binding domain and leucine-rich repeat (LRR)-containing proteins (NLRs) initiate pattern-triggered immunity (PTI) and effector- triggered immunity (ETI), respectively, each associated with the activation of an overlapping set of defence genes. The regulatory mechanism behind this convergence of PTI- and ETI-mediated defence gene induction remains elusive. We generated transgenic Arabidopsis plants that enable conditional NLR activation without pathogen infection to dissect NLR- and PRR-mediated transcriptional signals. A comparative analysis of over 40 transcriptome datasets linked calmodulin-binding transcription activators (CAMTAs) to the activation of overlapping defence genes in PTI and ETI. We used a dominant camta3 mutant (camta3-D) to assess CAMTA functions in the corresponding transcriptional regulation. Transcriptional regulation by NLRs, although highly similar to PTI responses, can be established independently of pathogen-associated molecular pattern (PAMP) perception, defence phytohormones and host cell death. Conditional expression of the N-terminal coiled-coil domain of the barley MLA (Mildew resistance locus A) NLR is sufficient to trigger similar transcriptional reprogramming as full-length NLRs. CAMTA-binding motifs are overrepresented in the 5' regulatory regions of the identified primary immune response genes, consistent with their altered expression and disease resistance responses in camta3-D plants. We propose that CAMTA-mediated transcriptional regulation defines an early convergence point in NLR-and PRR-mediated signalling.
Published: 2017

5. The ACER pollen and charcoal database: a global resource to document vegetation and fire response to abrupt climate changes during the last glacial period

Author: M. F. Sánchez Goñi, S. Desprat, A.-L. Daniau, F. C. Bassinot, J. M. Polanco-Martínez, S. P. Harrison, J. R. M. Allen, R. S. Anderson, H. Behling, R. Bonnefille, F. Burjachs, J. S. Carrión, R. Cheddadi, J. S. Clark, N. Combourieu-Nebout, Colin. J. Courtney Mustaphi, G. H. Debusk, L. M. Dupont, J. M. Finch, W. J. Fletcher, M. Giardini, C. González, W. D. Gosling, L. D. Grigg, E. C. Grimm, R. Hayashi, K. Helmens, L. E. Heusser, T. Hill, G. Hope, B. Huntley, Y. Igarashi, T. Irino, B. Jacobs, G. Jiménez-Moreno, S. Kawai, A. P. Kershaw, F. Kumon, I. T. Lawson, M.-P. Ledru, A.-M. Lézine, P. M. Liew, D. Magri, R. Marchant, V. Margari, F. E. Mayle, G. M. McKenzie, P. Moss, S. Müller, U. C. Müller, F. Naughton, R. M. Newnham, T. Oba, R. Pérez-Obiol, R. Pini, C. Ravazzi, K. H. Roucoux, S. M. Rucina, L. Scott, H. Takahara, P. C. Tzedakis, D. H. Urrego, B. van Geel, B. G. Valencia, M. J. Vandergoes, A. Vincens, C. L. Whitlock, D. A. Willard, M. Yamamoto, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Paléocéanographie (PALEOCEAN), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), University of Westminster [London] (UOW), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Catalan Institute of Human Palaeoecology and Social Evolution, Universitat Rovira i Virgili, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, University of York [York, UK], Department of Geosciences [Bremen], University of Bremen, Dipartimento di biologia ambientale, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Faculty of Geosciences, Kobe University, Hitotsubashi University, Hokkaido University [Sapporo, Japan], Departamento de Estratigrafia y paleontologia, Université de grenade, Universidade de Sao Paulo, Departamento Geologia Sedimentar e Ambiental (IRD/CNPQ), Universidade de São Paulo (USP), Biogéochimie-Traceurs-Paléoclimat (BTP), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Freie Universität Berlin, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, CNR-IDPA, Dipartimento di Scienze dell'Ambiente e del Territorio, Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Department of Earth Sciences [Nairobi], National Museums of Kenya, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Basque Government postdoctoral fellowship POS_2015_1_0006 ERC QUEST-DESIRE (UK and France) INQUA International Focus Group ACER INTIMATE-COST, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), VU University Amsterdam, Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Department of Geosciences, Università degli Studi di Roma 'La Sapienza' [Rome], Hokkaido University, Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Goethe-Universität Frankfurt am Main-Senckenberg Gesellschaft für Naturforschung, Ecosystem and Landscape Dynamics (IBED, FNWI), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Universidade de São Paulo = University of São Paulo (USP), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Vrije Universiteit Amsterdam [Amsterdam] (VU), University of St Andrews. School of Geography & Sustainable Development, and University of St Andrews. Bell-Edwards Geographic Data Institute
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, QH301 Biology, Biome, millennial scale variability, Greenland ice core, Late Pleistocene, North-Atlantic, Dansgaard-Oeschger, time scales, New-Zealand, record, age, Europe, medicine.disease_cause, computer.software_genre, 01 natural sciences, Millennial-scale variability, SDG 13 - Climate Action, Glacial period, database, lcsh:Environmental sciences, lcsh:GE1-350, GE, last glacial period, Database, 05 social sciences, lcsh:QE1-996.5, Vegetation, Late pleistocene, climate change, Climatology, pollen, Record, Radiometric dating, Dansgaard-oeschger, charcoal, GE Environmental Sciences, 010506 paleontology, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Climate change, 010603 evolutionary biology, QH301, Age, Pollen, environmental response, medicine, 0501 psychology and cognitive sciences, 050102 behavioral science & comparative psychology, 0105 earth and related environmental sciences, DAS, 15. Life on land, Time scales, lcsh:Geology, 13. Climate action, General Earth and Planetary Sciences, Environmental science, Quaternary, computer, Chronology
Abstract: The members of the ACER project wish to thank the QUEST-DESIRE (UK and France) bilateral project, the INQUA International Focus Group ACER and the INTIMATE-COST action for funding a suite of workshops to compile the ACER pollen and charcoal database and the workshop on ACER chronology that allow setting the basis for harmonizing the chronologies. Josué M. Polanco-Martinez was funded by a Basque Government postdoctoral fellowship (POS_2015_1_0006) and Sandy P. Harrison by the ERC Advanced Grant GC2.0: unlocking the past for a clearer future. Quaternary records provide an opportunity to examine the nature of the vegetation and fire responses to rapid past climate changes comparable in velocity and magnitude to those expected in the 21st-century. The best documented examples of rapid climate change in the past are the warming events associated with the Dansgaard–Oeschger (D–O) cycles during the last glacial period, which were sufficiently large to have had a potential feedback through changes in albedo and greenhouse gas emissions on climate. Previous reconstructions of vegetation and fire changes during the D–O cycles used independently constructed age models, making it difficult to compare the changes between different sites and regions. Here, we present the ACER (Abrupt Climate Changes and Environmental Responses) global database, which includes 93 pollen records from the last glacial period (73–15 ka) with a temporal resolution better than 1000 years, 32 of which also provide charcoal records. A harmonized and consistent chronology based on radiometric dating (14C, 234U∕230Th, optically stimulated luminescence (OSL), 40Ar∕39Ar-dated tephra layers) has been constructed for 86 of these records, although in some cases additional information was derived using common control points based on event stratigraphy. The ACER database compiles metadata including geospatial and dating information, pollen and charcoal counts, and pollen percentages of the characteristic biomes and is archived in Microsoft AccessTM at https://doi.org/10.1594/PANGAEA.870867 Publisher PDF
Published: 2017

6. Antagonistic actions of FPA and IBM2 regulate transcript processing from genes containing heterochromatin

Author: Cécile Brousse, Isabelle Gy, Nicolas Bouché, Yassir Idir, Astrid Agorio, Jane E. Parker, Aurélie Deremetz, Clémentine Le Roux, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Agence Nationale de la Recherche (ANR Project) [11-JSV7-0013], Max-Planck Society, H2020-Marie Sklodowska-Curie Actions Individual Fellowship [705631-CHERI], and LabEx Saclay Plant Sciences-SPS [10-LABX-0040-SPS]
Subjects: 0106 biological sciences, Physiology, Heterochromatin, [SDV]Life Sciences [q-bio], Plant Science, Polyadenylation, 01 natural sciences, Epigenesis, Genetic, Histone methylation, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, RNA, Messenger, Epigenetics, Gene, Regulation of gene expression, biology, Articles, Cell biology, Distal Myopathies, Histone, DNA methylation, biology.protein, Demethylase, 010606 plant biology & botany
Abstract: International audience; Repressive epigenetic marks, such as DNA and histone methylation, are sometimes located within introns. In Arabidopsis (Arabidopsis thaliana), INCREASE IN BONSAI METHYLATION2 (IBM2), an RNA-binding protein containing a bromo-adjacent homology domain, is required to process functional transcript isoforms of genes carrying intronic heterochromatin. In a genetic screen for suppressors of the ibm2 mutation, we identified FPA, an RNA-binding protein that promotes use of proximal polyadenylation sites in genes targeted by IBM2, including IBM1 encoding an essential H3K9 histone demethylase and the disease resistance gene RECOGNITION OF PERONOSPORA PARASITICA7. Both IBM2 and FPA are involved in the processing of their common mRNA targets: Transcription of IBM2 target genes is restored when FPA is mutated in ibm2 and impaired in transgenic plants overexpressing FPA. By contrast, transposons targeted by IBM2 and localized outside introns are not under this antagonistic control. The DNA methylation patterns of some genes and transposons are modified in fpa plants, including the large intron of IBM1, but these changes are rather limited and reversed when the mutant is complemented, indicating that FPA has a restricted role in mediating silencing. These data reveal a complex regulation by IBM2 and FPA pathways in processing mRNAs of genes bearing heterochromatic marks.
Published: 2019

7. Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Author: Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D. Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z. DeMaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Fernando Meyer, Monika Balvoit, Lars Hestbjerg Hansen, Søren J. Sørensen, Burton K. H. Chia, Bertrand Denis, Jeff L. Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J. Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W. Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z. Silva, Daniel A. Cuevas, Robert A. Edwards, Surya Saha, Vitor C. Piro, Bernhard Y. Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos C. Kyrpides, Tanja Woyke, Julia A. Vorholt, Paul Schulze-Lefert, Edward M. Rubin, Aaron E. Darling, Thomas Rattei, Alice C. McHardy, Center for Biotechnology (CeBiTec), Universität Bielefeld = Bielefeld University, Technische Fakultät, Universität Bielefeld, Algorithmische Bioinformatik [Düsseldorf], Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Computational Biology of Infection Research [Braunschweig], Helmholtz Centre for Infection Research (HZI), Braunschweig Integrated Centre of Systems Biology [Braunschweig] (BRICS), Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig]-Helmholtz Centre for Infection Research (HZI), Department of Mathematics [Corvallis, Oregon], Oregon State University (OSU), Department of Computer Science and Engineering [Univ California San Diego] (CSE - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Department of Pediatrics [Univ California San Diego] (UC San Diego), School of Medicine [Univ California San Diego] (UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), Max Planck Institute for Informatics [Saarbrücken], Faculty of Biology [Essen], Universität Duisburg-Essen = University of Duisburg-Essen [Essen], German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ)-Universität zu Köln = University of Cologne, Department of Environmental Science [Roskilde] (ENVS), Aarhus University [Aarhus], Section of Microbiology [Copenhagen], Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Department of Science and Environment [Roskilde], Roskilde University, DOE Joint Genome Institute [Walnut Creek], Pittsburgh Supercomputing Center (PSC), Center for Algorithmic Biotechnology [Saint Petersburg], Institute of Translational Biomedicine [Saint-Petersburg], Saint Petersburg University (SPBU)-Saint Petersburg University (SPBU), Centre of Excellence for Plant and Microbial Sciences (CEPAMS), John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC)-Chinese Academy of Agricultural Sciences (CAAS), Department of Microbiology and Ecosystem Science [Vienna], University of Vienna [Vienna], iThree Institute, University of Technology Sydney (UTS), Bioinformatics and Sequence Analysis (BONSAI), Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Computational and Systems Biology [Singapore], Genome Institute of Singapore (GIS), Department of Microbiology and Infection [Coventry], Warwick Medical School, University of Warwick [Coventry]-University of Warwick [Coventry], Intel Corporation [Hillsboro], Intel Corporation [USA], Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Department of Molecular Infection Biology [Braunschweig], Joint BioEnergy Institute [Emeryville], Graduate Institute of Biomedical Informatics [Taipei], Taipei Medical University, Biological Systems and Engineering [LBNL Berkeley], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Max planck Institute for Biology of Ageing [Cologne], Energy Engineering and Geomicrobiology [Calgary], University of Calgary, Institute of Microbiology and Genetics [Göttingen], Georg-August-University = Georg-August-Universität Göttingen, University Medical Center Göttingen (UMG), Institute of Population Health Sciences [Taiwan], National Health Research Institutes [Taiwan] (NHRI), San Diego State University (SDSU), Boyce Thompson Institute [Ithaca], Robert Koch Institute [Berlin] (RKI), Ministry of Education [Brazil], Center for Bioinformatics and Computational Biology [Maryland] (CBCB), University of Maryland [College Park], University of Maryland System-University of Maryland System, School of Biology [Newcastle upon Tyne], Newcastle University [Newcastle], Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), biological sciences department [Jeddah], King Abdulaziz University, Institute of Microbiology [Zurich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Computer Science and Engineering [San Diego] (CSE-UCSD), University of California-University of California, Department of Pediatrics [san Diego], UC San Diego School of Medicine, Universität Duisburg-Essen [Essen], Universität zu Köln-Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), John Innes Centre [Norwich]-Chinese Academy of Agricultural Sciences (CAAS), Centre National de la Recherche Scientifique (CNRS)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Georg-August-University [Göttingen], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)
Subjects: 0303 health sciences, Biological data, business.industry, Benchmarking, Biology, Data science, Genome, 03 medical and health sciences, 0302 clinical medicine, Software, Metagenomics, Profiling (information science), Critical assessment, Taxonomic rank, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.
Published: 2017

8. Toward a better understanding of the plant microbiota

Author: Victoria Potdevin, Marie Chevallier, Ruben Garrido Oter, Anne Siegel, Stéphane Hacquard, Damien Eveillard, Philippe Vandenkoornhuyse, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), GDR Génomique Environnementale, Chevallier, Marie, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Combinatoire et Bioinformatique (COMBI), and Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique)
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: National audience; Every macroorganisms are associated with microorganisms forming the host-microbiota. Host-organisms are highly dependent on these symbioses for their survival and fitness. Theories about holobionts suggest that the microbiome is faster to adapt than the host, further emphasizing the need to focus on this cornerstone of ecosystems studies. A major concern is to improve the knowledge to explain the complexity of the microbiota communities as well as the mechanisms underlying the general ecosystem functionalities. To better understand the Arabidopsis thaliana microbiota, we developed, in the framework of the systems-based theory, a network modelling approach. Multi-omics data were used to improve our understanding of the microorganism coexistence within the microbiota. Functional annotation, metabolic network modeling and biological pathway completion inform on potential interaction mechanisms at the metabolic scale. The hypothesis according to which microbial communities gather preferentially in order to optimize functional complementarity can explain the metabolic richness and diversity of the microbiome observed in the plant holo-biont.
Published: 2017

9. Nonsense-Mediated mRNA Decay Modulates Immune Receptor Levels to Regulate Plant Antibacterial Defense

Author: Arunkumar Srinivasan, Bettina Dekrout, Claudia Jonak, Nina Riehs, Svetlana Akimcheva, Karel Riha, Branislav Kusenda, Jane E. Parker, José M. Jiménez-Gómez, Jaqueline Bautor, Jiradet Gloggnitzer, Hansjörg Stampfl, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Plant-Microbe Interactions, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, CEITEC, Masaryk University, Austrian Academy of Sciences, Austrian Science Fund ( P19256-B03), Max-Planck Society, Deutsche Forschungsgemeinschaft (SFB 680), and Masaryk University [Brno] (MUNI)
Subjects: Cancer Research, binding, disease resistance, growth, [SDV]Life Sciences [q-bio], Nonsense-mediated decay, Pseudomonas syringae, Immune receptor, Biology, Microbiology, Immune system, Virology, Arabidopsis, Immunology and Microbiology(all), Gene expression, RNA, Messenger, Receptors, Immunologic, Gene, Molecular Biology, Plant Diseases, Genetics, Innate immune system, Arabidopsis Proteins, upf1, biology.organism_classification, encoding genes, gene-expression, inhibition, Nonsense Mediated mRNA Decay, arabidopsis, Codon, Nonsense, Host-Pathogen Interactions, human-cells, Parasitology, nmd, Signal transduction, Carrier Proteins, RNA Helicases
Abstract: SummaryNonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs. NMD impairment in Arabidopsis is linked to constitutive immune response activation and enhanced antibacterial resistance, but the underlying mechanisms are unknown. Here we show that NMD contributes to innate immunity in Arabidopsis by controlling the turnover of numerous TIR domain-containing, nucleotide-binding, leucine-rich repeat (TNL) immune receptor-encoding mRNAs. Autoimmunity resulting from NMD impairment depends on TNL signaling pathway components and can be triggered through deregulation of a single TNL gene, RPS6. Bacterial infection of plants causes host-programmed inhibition of NMD, leading to stabilization of NMD-regulated TNL transcripts. Conversely, constitutive NMD activity prevents TNL stabilization and impairs plant defense, demonstrating that host-regulated NMD contributes to disease resistance. Thus, NMD shapes plant innate immunity by controlling the threshold for activation of TNL resistance pathways.
Published: 2014
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10. The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

Author: Roi Ben-David, Timothy Paape, Jaroslav Doležel, Hadi Quesneville, Pietro Spanu, Paul Schulze-Lefert, Joelle Amselem, Thomas Wicker, Jan P. Buchmann, Rémy Bruggmann, Emiel Ver Loren van Themaat, Kentaro Shimizu, Francis Parlange, Simone Oberhaensli, Beat Keller, Margarita Shatalina, Stefan Roffler, Hana Šimková, Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), University of Helsinki, Agricultural Research Organization, Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Life Sciences, Imperial College London, Universität Bern- University of Bern [Bern], Partenaires INRAE, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Institute of Evolutionary Biology and Environmental Studies, University of Zurich, and Keller, Beat
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Plant genetics, Adaptation, Biological, 580 Plants (Botany), 01 natural sciences, Genome, 10126 Department of Plant and Microbial Biology, wheat, Gene Order, fungal pathogen, Triticum, 2. Zero hunger, Genetics, 0303 health sciences, Mildew, biology, food and beverages, Genomics, Biological Evolution, Host-Pathogen Interactions, 590 Animals (Zoology), Genome, Fungal, Powdery mildew, biotroph, Genes, Fungal, Molecular Sequence Data, Blumeria graminis, Evolution, Molecular, 03 medical and health sciences, 10127 Institute of Evolutionary Biology and Environmental Studies, 1311 Genetics, Ascomycota, evolution, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, genome, 030304 developmental biology, Plant Diseases, Blumeria graminis forma specialis tritici, Whole genome sequencing, Genetic diversity, Polymorphism, Genetic, Obligate, Computational Biology, biology.organism_classification, 570 Life sciences, powdery mildew, U7 Systems Biology / Functional Genomics, 010606 plant biology & botany
Abstract: International audience; Wheat powdery mildew, Blumeria graminis forma specialis tritici, is a devastating fungal pathogen with a poorly understood evolutionary history. Here we report the draft genome sequence of wheat powdery mildew, the resequencing of three additional isolates from different geographic regions and comparative analyses with the barley powdery mildew genome. Our comparative genomic analyses identified 602 candidate effector genes, with many showing evidence of positive selection. We characterize patterns of genetic diversity and suggest that mildew genomes are mosaics of ancient haplogroups that existed before wheat domestication. The patterns of diversity in modern isolates suggest that there was no pronounced loss of genetic diversity upon formation of the new host bread wheat 10,000 years ago. We conclude that the ready adaptation of B. graminis f.sp. tritici to the new host species was based on a diverse haplotype pool that provided great genetic potential for pathogen variation.
Published: 2013
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11. Erratum: Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

Author: Stéphane Hacquard, Barbara Kracher, Kei Hiruma, Philipp C. Münch, Ruben Garrido-Oter, Michael R. Thon, Aaron Weimann, Ulrike Damm, Jean-Félix Dallery, Matthieu Hainaut, Bernard Henrissat, Olivier Lespinet, Soledad Sacristán, Emiel Ver Loren van Themaat, Eric Kemen, Alice C. McHardy, Paul Schulze-Lefert, Richard J. O’Connell, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), German Centre for Infection Research (DZIF), Partner Site Hamburg, Computational Biology of Infection Research [Braunschweig], Helmholtz Centre for Infection Research (HZI), Max Von Pettenkofer Institute (MVP), Ludwig-Maximilians-Universität München (LMU), Cluster of Excellence on Plant Sciences (CEPLAS), Department of Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf [Düsseldorf], Centro Hispano-Luso de Investigaciones Agrarias, Departamento de Microbiología y Genétic, Universidad de Salamanca, Fungal Biodiversity Centre, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Recherche en Imagerie : Méthodes d'imagerie des Échanges transcapillaires (LRI - EA4062), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), BioInformatique Moléculaire (BIM), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centro de Biotechnologia y Genomica de Plantas (UPM-INIA) and ETSI Agronomos, Universidad Politécnica de Madrid (UPM), German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) 15K18645, ANR-12-CHEX-0008,FUNAPP,Nouveaux rôles des appressoria de champignons pathogènes dans leurs interactions avec les plantes: détection des signaux de la plante et transfert d'effecteurs protéiques et de métabolites secondaires fongiques dans les cellules hôtes(2012), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Max Planck Institute for Plant Breeding Research ( MPIPZ ), German Centre for Infection Research ( DZIF ), Helmholtz Centre for Infection Research ( HZI ), Max von Pettenkofer-Institute, University of Munich, Cluster of Excellence on Plant Sciences ( CEPLAS ), BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes ( BIOGER-CPP ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), Laboratoire de Recherche en Imagerie : Méthodes d'imagerie des Échanges transcapillaires ( LRI - EA4062 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), BioInformatique Moléculaire ( BIM ), Département Biologie des Génomes ( DBG ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), and Universidad Politécnica de Madrid ( UPM )
Subjects: 0106 biological sciences, Science, [SDV]Life Sciences [q-bio], Arabidopsis, General Physics and Astronomy, Chitin, Plant Roots, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Phosphates, 03 medical and health sciences, Colletotrichum, Endophytes, Symbiosis, 030304 developmental biology, 0303 health sciences, Multidisciplinary, [ SDV ] Life Sciences [q-bio], fungi, General Chemistry, Starvation, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Erratum, Genome, Fungal, 010606 plant biology & botany
Abstract: The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or nutrient starvation. Here, we compare the genomes of a beneficial root endophyte, Colletotrichum tofieldiae and its pathogenic relative C. incanum, and examine the transcriptomes of both fungi and their plant host Arabidopsis during phosphate starvation. Although the two species diverged only 8.8 million years ago and have similar gene arsenals, we identify genomic signatures indicative of an evolutionary transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of chitin-binding and secondary metabolism-related proteins, and limited activation of pathogenicity-related genes in planta. We show that beneficial responses are prioritized in C. tofieldiae-colonized roots under phosphate-deficient conditions, whereas defense responses are activated under phosphate-sufficient conditions. These immune responses are retained in phosphate-starved roots colonized by pathogenic C. incanum, illustrating the ability of plants to maximize survival in response to conflicting stresses., Colletotrichum tofieldiae is a beneficial root endophyte, whereas the closely related C. incanum is pathogenic. Here the authors compare the genomes and transcriptomes during host plant interaction and demonstrate that the host plant can respond differently to the beneficial endophyte according to phosphate status.
Published: 2016

12. Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

Author: Soledad Sacristán, Stéphane Hacquard, Michael R. Thon, Kei Hiruma, Ulrike Damm, Paul Schulze-Lefert, Jean-Félix Dallery, Barbara Kracher, Olivier Lespinet, Bernard Henrissat, Philipp C. Münch, Matthieu Hainaut, Richard J. O'Connell, Ruben Garrido-Oter, Alice C. McHardy, Emiel Ver Loren van Themaat, Eric Kemen, Aaron Weimann, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Max Von Pettenkofer Institute (MVP), Ludwig-Maximilians-Universität München (LMU), German Center for Infection Research - Partner Site Bonn-Cologne (DZIF), Computational Biology of Infection Research [Braunschweig], Helmholtz Centre for Infection Research (HZI), Cluster of Excellence on Plant Sciences (CEPLAS), Department of Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf [Düsseldorf], Centro Hispano-Luso de Investigaciones Agrarias, Departamento de Microbiología y Genétic, Universidad de Salamanca, Fungal Biodiversity Centre, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, King Abdulazziz University, Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), BioInformatique Moléculaire (BIM), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centro de Biotechnologia y Genomica de Plantas (UPM-INIA) and ETSI Agronomos, Universidad Politécnica de Madrid (UPM), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Max Planck Society, Agence Nationale de la Recherche [ANR-12-CHEX-0008-01], 'Cluster of Excellence on Plant Sciences' program - Deutsche Forschungsgemeinschaft, German Center for Infection Research, DZIF, Japan Society for the Promotion of Science, European Project: 323094,EC:FP7:ERC,ERC-2012-ADG_20120314,ROOTMICROBIOTA(2013), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Hacquard, Stéphane, Kracher, Barbara, and BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56, 38106 Braunschweig, Germany.
Subjects: roots, 0301 basic medicine, Colletotrichum tofieldiae, Arabidopsis thaliana, plant innate immunity, Science, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Endophyte, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Symbiosis, Arabidopsis, Colletotrichum incanum, endophyte, genome, transcriptome, differential gene expression, symbiosis, Colonization, Gene, 2. Zero hunger, Genetics, Multidisciplinary, biology, Effector, Host (biology), fungi, food and beverages, General Chemistry, 15. Life on land, biology.organism_classification, 030104 developmental biology, Colletotrichum
Abstract: The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or nutrient starvation. Here, we compare the genomes of a beneficial root endophyte, Colletotrichum tofieldiae and its pathogenic relative C. incanum, and examine the transcriptomes of both fungi and their plant host Arabidopsis during phosphate starvation. Although the two species diverged only 8.8 million years ago and have similar gene arsenals, we identify genomic signatures indicative of an evolutionary transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of chitin-binding and secondary metabolism-related proteins, and limited activation of pathogenicity-related genes in planta. We show that beneficial responses are prioritized in C. tofieldiae-colonized roots under phosphate-deficient conditions, whereas defense responses are activated under phosphate-sufficient conditions. These immune responses are retained in phosphate-starved roots colonized by pathogenic C. incanum, illustrating the ability of plants to maximize survival in response to conflicting stresses.
Published: 2016

13. Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

Author: Hacquard, Stéphane, Hiruma, Kei, Kracher, Barbara, Gerlach, Nina, Sacristan, Soledad, Nakano, Ryohei Thomas, Thon, Michael R, Bucher, Marcel, O'Connell, Richard, Schulze-Lefert, Paul, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, University of Cologne, Universidad Politécnica de Madrid (UPM), Universidad de Salamanca, BIOlogie et GEstion des Risques en agriculture (BIOGER), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: Colletotrichum, comparative genomics, comparative transcriptomics, fungal endophyte, phosphate starvation response, plant immunity, [SDV]Life Sciences [q-bio], food and beverages
Abstract: National audience; Although most characterized species of the fungal genus Colletotrichum are destructive pathogens, we found recently that C. tofieldiae (Ct) is an endemic endophyte in natural A. thaliana populations in Central Spain. Colonization by Ct initiates in roots, but can also spread systemically into shoots. Ct transfers the macronutrient phosphorus to shoots, promotes plant growth and increases fertility only under phosphorus-deficient conditions, a nutrient status that might have facilitated the transition from pathogenic to beneficial lifestyles. Comparative genome and transcriptome analyses between Ct and its closely related pathogenic species C. incanum (Ci) identified genomic signatures reflecting this recent transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of secondary metabolism-related proteins, and limited activation of pathogenicity-related genes in planta. Analysis of the Arabidopsis transcriptome during root colonization by Ct revealed that beneficial responses are prioritized under phosphorus-deficient conditions whereas defense responses, involving ethylene and glucosinolate pathways, were activated under phosphorus-sufficient conditions. These data, together with the analysis of Arabidopsis mutants that are impaired in indole glucosinolate metabolism and the phosphate starvation response (PSR), provide evidence for a specific coordination between the PSR, the plant immune system and invasive fungal growth during beneficial interaction with Ct. Importantly, Arabidopsis immune responses were retained in phosphate-starved roots colonized by pathogenic Ci, illustrating the extraordinary ability of plants to maximize survival in response to conflicting stresses.
Published: 2016

14. Colletotrichum higginsianum extracellular LysM proteins play dual roles in appressorial function and suppression of chitin-triggered plant immunity

Author: Takahara, Hiroyuki, Hacquard, Stephane, KOMBRINK , Anja, Hiruma, Kei, Robin, Guillaume, HALDER , Vivek, HUGHES , Bleddyn, Shinya, Tomonori, NEUMANN, Ulla, O'Connell, Richard, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Nara Institute of Science and Technology, Graduate School of Biological Sciences, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Swiss Federal Institute of Technology, Department of Life Sciences, School of Agriculture, Meiji University [Tokyo], Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Meiji University
Subjects: virulence, effector, [SDV]Life Sciences [q-bio], LysM, [SDE]Environmental Sciences, appressoria, Arabidopsis, Colletotrichum, biotrophy, chitin, ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2016

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

Author: Tina Romeis, Sandra Franz, Anne-Claire Cazalé, Britta Ehlert, Joachim Kurth, Anja Liese, Free University of Berlin (FU), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), DFG : FOR964, and German Ministry of Education and Science BMBF
Subjects: Osmosis, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Science, ABIOTIC / ENVIRONMENTAL STRESS, CDPK, Stress, Physiological, Arabidopsis thaliana, Kinase activity, EF-HAND, Molecular Biology, CALCIUM SIGNALING / TRANSPORT, biology, Arabidopsis Proteins, Abiotic stress, EF hand, Kinase, Effector, ARABIDOPSIS THALIANA, biology.organism_classification, Protein Structure, Tertiary, Biochemistry, Calcium, Protein Kinases
Abstract: Calcium-dependent protein kinases (CDPKs) comprise a family of plant serine/threonine protein kinases in which the calcium sensing domain and the kinase effector domain are combined within one molecule. So far, a biological function in abiotic stress signaling has only been reported for few CDPK isoforms, whereas the underlying biochemical mechanism for these CDPKs is still mainly unknown. Here, we show that CPK21 from Arabidopsis thaliana is biochemically activated in vivo in response to hyperosmotic stress. Loss-of-function seedlings of cpk21 are more tolerant to hyperosmotic stress and mutant plants show increased stress responses with respect to marker gene expression and metabolite accumulation. In transgenic Arabidopsis complementation lines in the cpk21 mutant background, in which either CPK21 wild-type, or a full-length enzyme variant carrying an amino-acid substitution were stably expressed, stress responsitivity was restored by CPK21 but not with the kinase inactive variant. The biochemical characterization of in planta synthesized and purified CPK21 protein revealed that within the calcium-binding domain, N-terminal EF1- and EF2-motifs compared to C-terminal EF3- and EF4-motifs differ in their contribution to calcium-regulated kinase activity, suggesting a crucial role for the N-terminal EF-hand pair. Our data provide evidence for CPK21 contributing in abiotic stress signaling and suggest that the N-terminal EF-hand pair is a calcium-sensing determinant controlling specificity of CPK21 function.
Published: 2011

16. A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity

Author: Hiroaki Adachi, Hirofumi Yoshioka, Marie Levaillant, Jane E. Parker, Binbin Zhou, Laurent Deslandes, Clémentine Le Roux, Alain Jauneau, Dominique Tremousaygue, Alexandra Kraut, Sylvain Raffaele, Gaëlle Huet, Yohann Couté, Laurent Camborde, Richard Berthomé, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Plateforme Imagerie [Castanet-Tolosan] (IFR 3450 - Pôle de Biotechnologie Végétale), Institut Fédératif de Recherche, Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Etude de la dynamique des protéomes (EDyP), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Defense in Plant-Pathogen Interactions [Nagoya, Japan], Nagoya University-Graduate School of Bioagricultural Sciences [Nagoya, Japan], L.D. and G.H. were supported by a research grant from the Agence Nationale pour la Recherche (ANR, ANR-10-JCJC-1706). C.L.R. was funded by fellowships from INRA Contrat Jeune Scientifique and the Max Planck Society. This work was supported by the French Laboratory of Excellence project ‘‘TULIP’’ (ANR-10-LABX-41, ANR-11-IDEX-0002-02). A.K. and Y.C. were supported by the CNRS, INSERM, CEA, and ANR (Investissement d’Avenir Infrastructures, ProFi project ANR-10-INBS-08-01). H.Y. is supported by Grant-in-Aid from Japan Society of the Promotion of Science (26292023). S.R. is supported by a Starting Grant of the European Research Council (ERC-StG 336808 project VariWhim). J.E.P. is supported by the Max-Planck Society, DFG SFB grant 670, and the Cluster of Excellence on Plant Sciences (CEPLAS)., ANR-10-JCJC-1706,PERCEPtome,Identification des cibles de l'effecteur de type III PopP2, impliquées dans un complexe de perception R/Avr(2010), ANR-11-IDEX-0002-02/10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2011), ANR-10-INBS-08-01/10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), European Project: 336808,EC:FP7:ERC,ERC-2013-StG,VARIWHIM(2013), Couté, Yohann, Jeunes Chercheuses et Jeunes Chercheurs - Identification des cibles de l'effecteur de type III PopP2, impliquées dans un complexe de perception R/Avr - - PERCEPtome2010 - ANR-10-JCJC-1706 - JCJC - VALID, Initiative d'excellence - Université Fédérale de Toulouse - - UNITI2011 - ANR-11-IDEX-0002 - IDEX - VALID, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, Understanding White Mold disease quantitative resistance using natural variation - VARIWHIM - - EC:FP7:ERC2013-11-01 - 2018-10-31 - 336808 - VALID, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Interactions Microbiennes dans la Rhizosphère et les Racines, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Etude de la dynamique des protéomes (EDyP ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, 0106 biological sciences, [SDV]Life Sciences [q-bio], Arabidopsis, Virulence, Biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chemistry.chemical_compound, Acetyltransferases, Gene expression, Gene, Transcription factor, Plant Proteins, 030304 developmental biology, Genetics, Regulation of gene expression, 0303 health sciences, Arabidopsis Proteins, Effector, Biochemistry, Genetics and Molecular Biology(all), DNA, WRKY protein domain, Cell biology, [SDV] Life Sciences [q-bio], chemistry, Ralstonia solanacearum, Transcription Factors, 010606 plant biology & botany
Abstract: Comment in Treasure your exceptions: unusual domains in immune receptors reveal host virulence targets. [Cell. 2015]; International audience; Microbial pathogens infect host cells by delivering virulence factors (effectors) that interfere with defenses. In plants, intracellular nucleotide-binding/leucine-rich repeat receptors (NLRs) detect specific effector interference and trigger immunity by an unknown mechanism. The Arabidopsis-interacting NLR pair, RRS1-R with RPS4, confers resistance to different pathogens, including Ralstonia solanacearum bacteria expressing the acetyltransferase effector PopP2. We show that PopP2 directly acetylates a key lysine within an additional C-terminal WRKY transcription factor domain of RRS1-R that binds DNA. This disrupts RRS1-R DNA association and activates RPS4-dependent immunity. PopP2 uses the same lysine acetylation strategy to target multiple defense-promoting WRKY transcription factors, causing loss of WRKY-DNA binding and transactivating functions needed for defense gene expression and disease resistance. Thus, RRS1-R integrates an effector target with an NLR complex at the DNA to switch a potent bacterial virulence activity into defense gene activation.
Published: 2015

17. Colletotrichum orbiculare FAM1 Encodes a Novel Woronin Body-Associated Pex22 Peroxin Required for Appressorium-Mediated Plant Infection

Author: Richard J. O'Connell, Ken Harata, Ulla Neumann, Guillaume Robin, Naoki Fujihara, Yasuyuki Kubo, Laboratory of Plant Pathology, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University (KPU), Central Microscopy, Max Planck Institute for Plant Breeding Research (MPIPZ), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Plant Microbe Interactions, and ANR Chaire d'Excellence (grant number ANR-12-CHEX-0008-01)
Subjects: Receptor recycling, Saccharomyces cerevisiae Proteins, Virulence Factors, [SDV]Life Sciences [q-bio], Peroxin, Saccharomyces cerevisiae, Biology, Microbiology, Fungal Proteins, Woronin body, Virology, Peroxisomes, Colletotrichum, pathogenicity, peroxisome, Microscopy, Immunoelectron, Peroxisomal targeting signal, Plant Diseases, Organelles, Microscopy, Confocal, Organelle Biogenesis, peroxin, Peroxisomal matrix, fungi, Genetic Complementation Test, Colletotrichum orbiculare, Membrane Proteins, Peroxisome, biology.organism_classification, QR1-502, Cell biology, Cucurbitaceae, Membrane protein, Biochemistry, Gene Deletion, Research Article
Abstract: The cucumber anthracnose fungus Colletotrichum orbiculare forms specialized cells called appressoria for host penetration. We identified a gene, FAM1, encoding a novel peroxin protein that is essential for peroxisome biogenesis and that associates with Woronin bodies (WBs), dense-core vesicles found only in filamentous ascomycete fungi which function to maintain cellular integrity. The fam1 disrupted mutants were unable to grow on medium containing oleic acids as the sole carbon source and were nonpathogenic, being defective in both appressorium melanization and host penetration. Fluorescent proteins carrying peroxisomal targeting signals (PTSs) were not imported into the peroxisomes of fam1 mutants, suggesting that FAM1 is a novel peroxisomal biogenesis gene (peroxin). FAM1 did not show significant homology to any Saccharomyces cerevisiae peroxins but resembled conserved filamentous ascomycete-specific Pex22-like proteins which contain a predicted Pex4-binding site and are potentially involved in recycling PTS receptors from peroxisomes to the cytosol. C. orbiculare FAM1 complemented the peroxisomal matrix protein import defect of the S. cerevisiae pex22 mutant. Confocal microscopy of Fam1-GFP (green fluorescent protein) fusion proteins and immunoelectron microscopy with anti-Fam1 antibodies showed that Fam1 localized to nascent WBs budding from peroxisomes and mature WBs. Association of Fam1 with WBs was confirmed by colocalization with WB matrix protein CoHex1 (C. orbiculare Hex1) and WB membrane protein CoWsc (C. orbiculare Wsc) and by subcellular fractionation and Western blotting with antibodies to Fam1 and CoHex1. In WB-deficient cohex1 mutants, Fam1 was redirected to the peroxisome membrane. Our results show that Fam1 is a WB-associated peroxin required for pathogenesis and raise the possibility that localized receptor recycling occurs in WBs., IMPORTANCE Colletotrichum orbiculare is a fungus causing damaging disease on Cucurbitaceae plants. In this paper, we characterize a novel peroxisome biogenesis gene from this pathogen called FAM1. Although no genes with significant homology are present in Saccharomyces cerevisiae, FAM1 contains a predicted Pex4-binding site typical of Pex22 proteins, which function in the recycling of PTS receptors from peroxisomes to the cytosol. We show that FAM1 complements the defect in peroxisomal matrix protein import of S. cerevisiae pex22 mutants and that fam1 mutants are completely defective in peroxisome function, fatty acid metabolism, and pathogenicity. Remarkably, we found that this novel peroxin is specifically localized on the bounding membrane of Woronin bodies, which are small peroxisome-derived organelles unique to filamentous ascomycete fungi that function in septal pore plugging. Our finding suggests that these fungi have coopted the Woronin body for localized receptor recycling during matrix protein import.
Published: 2015

18. Reprogramming of plant cells by filamentous plant-colonizing microbes

Author: Frédéric Brunner, Natalia Requena, Richard J. O'Connell, Patrick Schaefer, Gunther Doehlemann, Jane E. Parker, Max Planck Institute for Terrestrial Microbiology, Max-Planck-Gesellschaft, University of Cologne, Karlsruhe Institute of Technology (KIT), University of Warwick, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: Physiology, mutualism, [SDV]Life Sciences [q-bio], Metabolic reprogramming, Plant Immunity, Plant Science, Biology, biotrophy, Symbiosis, Plant Cells, pathogenicity, Plant Diseases, 2. Zero hunger, Genetics, Mutualism (biology), Innate immune system, Ecology, Effector, fungi, Fungi, Plants, Plant cell, microbe-associated molecular pattern (MAMP), effector, Oomycetes, Host-Pathogen Interactions, Reprogramming
Abstract: International audience; Although phylogenetically unrelated, filamentous oomycetes and fungi establish similar structures to colonize plants and they represent economically the most important microbial threat to crop production. In mutualistic interactions established by root-colonizing fungi, clear differences to pathogens can be seen, but there is mounting evidence that their infection strategies and molecular interactions have certain common features. To infect the host, fungi and oomycetes employ similar strategies to circumvent plant innate immunity. This process involves the suppression of basal defence responses which are triggered by the perception of conserved molecular patterns. To establish biotrophy, effector proteins are secreted from mutualistic and pathogenic microbes to the host tissue, where they play central roles in the modulation of host immunity and metabolic reprogramming of colonized host tissues. This review article discusses key effector mechanisms of filamentous pathogens and mutualists, how they modulate their host targets and the fundamental differences or parallels between these different interactions. The orchestration of effector actions during plant infection and the importance of their localization within host tissues are also discussed. Featured paper: See also the Editorial by Hetherington
Published: 2014

19. The powdery mildew resistance protein RPW8.2 is carried on VAMP721/722 vesicles to the extrahaustorial membrane ofhaustorial complexes

Author: Paul Schulze-Lefert, Hyeran Kim, Ulla Neumann, Tomohiro Uemura, Richard J. O'Connell, Makoto Maekawa-Yoshikawa, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, The University of Tokyo (UTokyo), Central Microscopy, German Research Foundation (DFG) SPP1212, National Research Foundation of Korea 2010-220-C00039, and Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) 25840100
Subjects: 0106 biological sciences, Recombinant Fusion Proteins, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Biology, 01 natural sciences, Exocytosis, R-SNARE Proteins, 03 medical and health sciences, Powdery mildew, Ascomycota, Genes, Reporter, Haustorium, Genetics, Syntaxin, Secretion, Extrahaustorial membrane, Disease Resistance, Plant Diseases, 030304 developmental biology, 0303 health sciences, Arabidopsis Proteins, Qa-SNARE Proteins, Cell Membrane, food and beverages, Cell Biology, Plants, Genetically Modified, Entry into host, Cell biology, Transport protein, Resistance protein, Protein Transport, Host-Pathogen Interactions, Haustoria, 010606 plant biology & botany
Abstract: International audience; Plants employ multiple cell-autonomous defense mechanisms to impede pathogenesis of microbial intruders. Previously we identified an exocytosis defense mechanism in Arabidopsis against pathogenic powdery mildew fungi. This pre-invasive defense mechanism depends on the formation of ternary protein complexes consisting of the plasma membrane-localized PEN1 syntaxin, the adaptor protein SNAP33 and closely sequence-related vesicle-resident VAMP721 or VAMP722 proteins. The Arabidopsis thaliana resistance to powdery mildew 8.2 protein (RPW8.2) confers disease resistance against powdery mildews upon fungal entry into host cells and is specifically targeted to the extrahaustorial membrane (EHM), which envelops the haustorial complex of the fungus. However, the secretory machinery involved in trafficking RPW8.2 to the EHM is unknown. Here we report that RPW8.2 is transiently located on VAMP721/722 vesicles, and later incorporated into the EHM of mature haustoria. Resistance activity of RPW8.2 against the powdery mildew Golovinomyces orontii is greatly diminished in the absence of VAMP721 but only slightly so in the absence of VAMP722. Consistent with this result, trafficking of RPW8.2 to the EHM is delayed in the absence of VAMP721. These findings implicate VAMP721/722 vesicles as key components of the secretory machinery for carrying RPW8.2 to the plant-fungal interface. Quantitative fluorescence recovery after photobleaching suggests that vesicle-mediated trafficking of RPW8.2-yellow fluorescent protein (YFP) to the EHM occurs transiently during early haustorial development and that lateral diffusion of RPW8.2-YFP within the EHM exceeds vesicle-mediated replenishment of RPW8.2-YFP in mature haustoria. Our findings imply the engagement of VAMP721/722 in a bifurcated trafficking pathway for pre-invasive defense at the cell periphery and post-invasive defense at the EHM.
Published: 2014

20. Evolution and conservation of plant NLR functions

Author: Jacob, Florence, Vernaldi, Saskia, Maekawa, Takaki, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), 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), German Research Foundation in the Collaborative Research Centre [SFB670], Franco-German University, and University of Evry
Subjects: resistance protein, effector-triggered immunity, NB-LRR, [SDV]Life Sciences [q-bio], Immunology, fungi, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Review Article, innate immunity, NLR
Abstract: International audience; In plants and animals, nucleotide-binding domain and leucine-rich repeats (NLR)-containing proteins play pivotal roles in innate immunity. Despite their similar biological functions and protein architecture, comparative genome-wide analyses of NLRs and genes encoding NLR-like proteins suggest that plant and animal NLRs have independently arisen in evolution. Furthermore, the demonstration of interfamily transfer of plant NLR functions from their original species to phylogenetically distant species implies evolutionary conservation of the underlying immune principle across plant taxonomy. In this review we discuss plant NLR evolution and summarize recent insights into plant NLR-signaling mechanisms, which might constitute evolutionarily conserved NLR-mediated immune mechanisms.
Published: 2013

21. Pollen databases and their application

Author: Grimm, Eric Christopher, Bradshaw, Richard H.W., Giesecke, Thomas, Lézine, Anne-Marie, Takahara, Hikaru, Williams, John W., University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Department of Palynology and Climate Dynamics, Georg-August-University = Georg-August-Universität Göttingen-Georg-August-University = Georg-August-Universität Göttingen, Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Scott A. Elias, Georg-August-University [Göttingen]-Georg-August-University [Göttingen], Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)
Subjects: European Pollen Database, African Pollen Database, Pollen, Pollen Database for Siberia and the Russian Far East, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Cyberinfrastructure, North American Pollen Database, Global Pollen Database, Latin American Pollen Database, Palynology, Relational databases
Abstract: International audience; The Global Pollen Database is a public domain, relational database designed for Quaternary fossil-pollen data and modern pollen surface-samples. The database is the result of collaboration among a number of regional database cooperatives, including the European Pollen Database, the North American Pollen Database, the Latin American Pollen Database, the African Pollen Database, and the Pollen Database for Siberia and the Russian Far East. Some smaller database cooperatives have also contributed to it. The database cooperatives have set standards for data quality control and for taxonomic nomenclature and synonymy. The database is a secure archive of palynological data, and it is an essential cyberinfrastructure for paleoenvironmental research. The database facilitates integration, synthesis, and understanding, and it promotes information sharing and collaboration among scientists with different interests and from different countries. Applications range in scale from local studies to global-scale biome mapping and paleoclimatic reconstructions.
Published: 2013

22. Life-style transitions in hemibiotrophic Colletotrichum fungi uncovered by comparative genome and transcriptome analyses

Author: O'Connell, Richard, Thon, Michael, Hacquard, Stéphane, Kleemann, Jochen, Amyotte, Stefan, Lebrun, Marc-Henri, Ver Loren van Themaat, Emiel, Ma, Li-Jun, Vaillancourt, Lisa, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Universidad de Salamanca, Department of Plant Pathology, University of Kentucky, BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and University of Massachusetts System (UMASS)
Subjects: Colletotrichum, champignon, Arabidopsis, C. graminicola, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2012

23. Arabidopsis EDS1 connects pathogen effector recognition to cell compartment-specific immune responses

Author: Lennart Wirthmueller, Cécile Pouzet, Katharina Heidrich, Laurent Deslandes, Céline Tasset, Jane E. Parker, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), 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), Plateforme Imagerie TRI, Pôle de Biotechnologie Végétale, Partenaires INRAE, Max-Planck Society, IMPRS, Deutsche Forschungsgemeinschaft : SFB 670, and Laboratoire d'Excellence (LABEX) TULIP : ANR-10-LABX-41
Subjects: Programmed cell death, Cytoplasm, Transcription, Genetic, Recombinant Fusion Proteins, Cell, Arabidopsis, Pseudomonas syringae, Apoptosis, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Bacterial Proteins, Tobacco, medicine, Receptor, Plant Diseases, Plant Proteins, Cell Nucleus, Multidisciplinary, biology, Effector, Arabidopsis Proteins, fungi, biology.organism_classification, Plants, Genetically Modified, Immunity, Innate, Cell biology, DNA-Binding Proteins, Plant Leaves, medicine.anatomical_structure, Effector-triggered immunity, Intracellular
Abstract: Pathogen effectors are intercepted by plant intracellular nucleotide binding-leucine-rich repeat (NB-LRR) receptors. However, processes linking receptor activation to downstream defenses remain obscure. Nucleo-cytoplasmic basal resistance regulator EDS1 (ENHANCED DISEASE SUSCEPTIBILITY1) is indispensible for immunity mediated by TIR (Toll-interleukin-1 receptor)-NB-LRR receptors. We show that Arabidopsis EDS1 molecularly connects TIR-NB-LRR disease resistance protein RPS4 recognition of bacterial effector AvrRps4 to defense pathways. RPS4-EDS1 and AvrRps4-EDS1 complexes are detected inside nuclei of living tobacco cells after transient coexpression and in Arabidopsis soluble leaf extracts after resistance activation. Forced AvrRps4 localization to the host cytoplasm or nucleus reveals cell compartment-specific RPS4-EDS1 defense branches. Although nuclear processes restrict bacterial growth, programmed cell death and transcriptional resistance reinforcement require nucleo-cytoplasmic coordination. Thus, EDS1 behaves as an effector target and activated TIR-NB-LRR signal transducer for defenses across cell compartments.
Published: 2011

24. LEAFY target genes reveal floral regulatory logic, cis motifs, and a link to biotic stimulus response

Author: Miin-Feng Wu, Ayako Yamaguchi, François Parcy, Cara M. Winter, Nobutoshi Yamaguchi, Doris Wagner, Yi Sang, Hongzhe Li, Marie Monniaux, Maxwell A. Reback, Servane Blanvillain-Baufumé, Jane E. Parker, Shane T. Jensen, Ryan S. Austin, Department of Biology, University of Pennsylvania, University of Pennsylvania [Philadelphia], Centre for the Analysis of Genome Evolution and Function, University of Toronto, Department of Plant-Microbe Interactions, Max-Planck-Institut, Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Statistics, Department of Biostatistics, NSF [IOS 0849298], NIH [T32HG000046, T32-HD007516], Agri-Food Canada, JSPS, University of Pennsylvania, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Arabidopsis thaliana, Gene regulatory network, Arabidopsis, plant, chromatin immunoprecipitation, MESH: Arabidopsis Proteins, Biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Gene Expression Regulation, Plant, MESH: Gene Expression Regulation, Developmental, MESH: Arabidopsis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene Regulatory Networks, MESH: Gene Expression Regulation, Plant, Molecular Biology, Leafy, Psychological repression, Gene, Transcription factor, transcription factor, 030304 developmental biology, MESH: Gene Regulatory Networks, Genetics, 0303 health sciences, Arabidopsis Proteins, fungi, MESH: Genes, Homeobox, Genes, Homeobox, food and beverages, Gene Expression Regulation, Developmental, Cell Biology, MESH: Transcription Factors, biology.organism_classification, flower, LEAFY, regulatory mechanisms, MESH: Genome-Wide Association Study, gene expression, Homeotic gene, Flower formation, 010606 plant biology & botany, Developmental Biology, tiling array hybridization, Genome-Wide Association Study, Transcription Factors
Abstract: International audience; The transition from vegetative growth to flower formation is critical for the survival of flowering plants. The plant-specific transcription factor LEAFY (LFY) has central, evolutionarily conserved roles in this process, both in the formation of the first flower and later in floral patterning. We performed genome-wide binding and expression studies to elucidate the molecular mechanisms by which LFY executes these roles. Our study reveals that LFY directs an elaborate regulatory network in control of floral homeotic gene expression. LFY also controls the expression of genes that regulate the response to external stimuli in Arabidopsis. Thus, our findings support a key role for LFY in the coordination of reproductive stage development and disease response programs in plants that may ensure optimal allocation of plant resources for reproductive fitness. Finally, motif analyses reveal a possible mechanism for stage-specific LFY recruitment and suggest a role for LFY in overcoming polycomb repression.
Published: 2010

25. SGT1 contributes to coronatine signaling and Pseudomonas syringae pv. tomato disease symptom development in tomato and Arabidopsis

Author: Jane E. Parker, Kirankumar S. Mysore, Srinivasa Rao Uppalapati, Keri Wang, Choong-Min Ryu, Takako Ishiga, Yasuhiro Ishiga, Laurent D. Noël, Plant Biology Division, The Samuel Roberts Noble Foundation, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Samuel Roberts Noble Foundation, Oklahoma Center for Advancement of Science and Technology : PSB09-021, Deutsche Forschungsgemeinschaft : SFB 635, and Alexander von Humboldt postdoctoral fellowship
Subjects: 0106 biological sciences, SGT1, Physiology, chlorosis, Arabidopsis, Nicotiana benthamiana, Plant Science, 01 natural sciences, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, reverse genetics, VIGS, Solanum lycopersicum, Pseudomonas, Botany, Pseudomonas syringae, Gene silencing, cardiovascular diseases, Gene Silencing, Amino Acids, 030304 developmental biology, Plant Diseases, Plant Proteins, 0303 health sciences, Chlorosis, biology, Arabidopsis Proteins, Jasmonic acid, fungi, Intracellular Signaling Peptides and Proteins, food and beverages, Coronatine, biology.organism_classification, Reverse genetics, respiratory tract diseases, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, chemistry, bacterial speck disease, Indenes, Glucosyltransferases, coronatine, Carrier Proteins, 010606 plant biology & botany, Signal Transduction
Abstract: International audience; Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) causes an economically important bacterial speck disease on tomato and produces symptoms with necrotic lesions surrounded by chlorosis. The chlorosis is mainly attributed to a jasmonic acid (JA)-isoleucine analogue, coronatine (COR), produced by Pst DC3000. However, the molecular processes underlying lesion development and COR-induced chlorosis are poorly understood. In this study, we took advantage of a chlorotic phenotype elicited by COR on Nicotiana benthamiana leaves and virus-induced gene silencing (VIGS) as a rapid reverse genetic screening tool and identified a role for SGT1 suppressor of G2 allele of skp1) in COR-induced chlorosis. Silencing of SGT1 in tomato resulted in reduction of disease-associated symptoms (cell death and chlorosis), suggesting a molecular connection between CORinduced chlorosis and cell death. In Arabidopsis, AtSGT1b but not AtSGT1a was required for COR responses, including root growth inhibition and Pst DC3000 symptom (water soaked lesion) development. Notably, overexpression of AtSGT1b did not alter Pst DC3000 symptoms or sensitivity to COR. Taken together, our results demonstrate that SGT1 ⁄ SGT1b is required for CORinduced chlorosis and subsequent necrotic disease development in tomato and Arabidopsis. SGT1 is therefore a component of the COR⁄ JA-mediated signal transduction pathway.
Published: 2010

26. A locus conferring resistance to Colletotrichum higginsianum is shared by four geographically distinct Arabidopsis accessions

Author: Birker, Doris, Heidrich, Katharina, Takahara, Hiroyuki, Narusaka, Mari, Deslandes, Laurent, Narusaka, Yoshihiro, Reymond, Matthieu, Parker, Jane, O'Connell, Richard, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Research Institute for Biological Sciences, Partenaires INRAE, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Department of Plant Breeding and Genetics, Max-Planck Society, and Deutsche Forschungsgemeinschaft : SPP-1212 SFB 670
Subjects: [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, PSEUDOMONAS SYRINGAE, R GENE, COLLELOTRICHUM HIGGINSIANUM, PENETRATION RESISTANCE, PLANT IMMUNE SIGNALING, RESISTANCE, RECESSIVE RESISTANCE, RELATION HOTE-PARASITE
Abstract: International audience; Colletotrichum higginsianum is a hemibiotrophic fungal pathogen that causes anthracnose disease on Arabidopsis and other crucifer hosts. By exploiting natural variation in Arabidopsis we identified a resistance locus that is shared by four geographically distinct accessions (Ws-0, Kondara, Gifu-2 and Can-0). A combination of quantitative trait loci (QTL) and Mendelian mapping positioned this locus within the major recognition gene complex MRC-J on chromosome 5 containing the Toll-interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat (TIR-NB-LRR) genes RPS4 and RRS1 that confer dual resistance to C. higginsianum in Ws-0 (Narusaka et al., 2009). We find that the resistance shared by these diverse Arabidopsis accessions is expressed at an early stage of fungal invasion, at the level of appressorial penetration and establishment of intracellular biotrophic hyphae, and that this determines disease progression. Resistance is not associated with host hypersensitive cell death, an oxidative burst or callose deposition in epidermal cells but requires the defense regulator EDS1, highlighting new functions of TIR-NB-LRR genes and EDS1 in limiting early establishment of fungal biotrophy. While the Arabidopsis accession Ler-0 is fully susceptible to C. higginsianum infection, Col-0 displays intermediate resistance that also maps to MRC-J. By analysis of null mutants of RPS4 and RRS1 in Col-0 we show that these genes, individually, do not contribute strongly to C. higginsianum resistance but are both required for resistance to Pseudomonas syringae bacteria expressing the Type III effector, AvrRps4. We conclude that distinct allelic forms of RPS4 and RRS1 probably cooperate to confer resistance to different pathogens.
Published: 2009

27. Identification of grapevine MLO gene candidates involved in susceptibility to powdery mildew

Author: Angela Feechan, Ian B. Dry, Ralph Panstruga, Angelica M. Jermakow, Laurent Torregrosa, Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), and Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: 0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, family, MLO, Genomics, Plant Science, Erysiphe necator, 01 natural sciences, Genome, 03 medical and health sciences, Arabidopsis, Complementary DNA, Botany, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nonhost resistance, expression analysis, domain proteins, Gene, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, 0303 health sciences, biology, Host (biology), fungi, vitis-vinifera, fungus, food and beverages, barley, biology.organism_classification, cell-death, grapevine, defense, arabidopsis, powdery mildew, Agronomy and Crop Science, Powdery mildew, 010606 plant biology & botany
Abstract: International audience; The European cultivated grapevine, Vitis vinifera L., is a host for the powdery mildew pathogen Erisyphe necator, which is the most economically important fungal disease of viticulture. MLO proteins mediate powdery mildew susceptibility in the model plant species Arabidopsis and the crop plants barley and tomato. Seven VvMLO cDNA sequences were isolated from grapevine and were subsequently identified as part of a 17 member VvMLO gene family within the V. vinifera genome. Phylogenetic analysis of the 17 VvMLO genes in the grape genome indicated that the proteins they encode fall into six distinct clades. The expression of representative VvMLOs from each clade were analysed in a range of grape tissues, as well as in response to a range of biotic and abiotic factors. The VvMLOs investigated have unique, but overlapping tissue expression patterns. Expression analysis of VvMLO genes following E. necator infection identified four upregulated VvMLOs which are orthologous to the Arabidopsis AtMLO2, AtMLO6 and AtMLO12 and tomato SlMLO1 genes required for powdery mildew susceptibility. This suggests a degree of functional redundancy between the proteins encoded by these genes in terms of susceptibility to powdery mildew, and, as such, represent potential targets for modi. cation to generate powdery mildew resistant grapevines.
Published: 2008

28. Conserved ERAD-like quality control of a plant polytopic membrane protein

Author: Bodo Ortmann, Marco Miklis, Ralph Panstruga, Paul Schulze-Lefert, Alessandra Devoto, Judith Müller, Pietro Piffanelli, Candace E. Elliott, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research (MPIPZ), Polymorphismes d'intérêt agronomique (UMR PIA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), BBSRC John Innes Centre, and Partenaires INRAE
Subjects: 0106 biological sciences, Proteasome Endopeptidase Complex, Saccharomyces cerevisiae Proteins, Saccharomyces cerevisiae, Plant Science, macromolecular substances, Endoplasmic-reticulum-associated protein degradation, Protein degradation, Endoplasmic Reticulum, 01 natural sciences, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, BIOLOGIE DU DEVELOPPEMENT, Conserved Sequence, Phylogeny, Research Articles, Mitogen-Activated Protein Kinase 6, Plant Proteins, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, Ubiquitin, Endoplasmic reticulum, Membrane Proteins, food and beverages, Hordeum, Cell Biology, biology.organism_classification, Yeast, AAA proteins, Protein Transport, Amino Acid Substitution, Membrane protein, Biochemistry, Mutation, MUTANT MLO, Hordeum vulgare, 010606 plant biology & botany
Abstract: International audience; The endoplasmic reticulum (ER) of eukaryotic cells serves as a checkpoint tightly monitoring protein integrity and channeling malformed proteins into different rescue and degradation routes. The degradation of several ER lumenal and membrane-localized proteins is mediated by ER-associated protein degradation (ERAD) in yeast (Saccharomyces cerevisiae) and mammalian cells. To date, evidence for the existence of ERAD-like mechanisms in plants is indirect and based on heterologous or artificial substrate proteins. Here, we show that an allelic series of single amino acid substitution mutants of the plant-specific barley (Hordeum vulgare) seven-transmembrane domain mildew resistance o (MLO) protein generates substrates for a postinsertional quality control process in plant, yeast, and human cells, suggesting conservation of the underlying mechanism across kingdoms. Specific stabilization of mutant MLO proteins in yeast strains carrying defined defects in protein quality control demonstrates that MLO degradation is mediated by HRD pathway-dependent ERAD. In plants, individual aberrant MLO proteins exhibit markedly reduced half-lives, are polyubiquitinated, and can be stabilized through inhibition of proteasome activity. This and a dependence on homologs of the AAA ATPase CDC48/p97 to eliminate the aberrant variants strongly suggest that MLO proteins are endogenous substrates of an ERAD-related plant quality control mechanism
Published: 2005

29. From synthetic communities to synthetic ecosystems: exploring causalities in plant-microbe-environment interactions.

Author: Chesneau G, Herpell J, Garrido-Oter R, and Hacquard S
Abstract: The plant microbiota research field has rapidly shifted from efforts aimed at gaining a descriptive understanding of microbiota composition to a focus on acquiring mechanistic insights into microbiota functions and assembly rules. This evolution was driven by our ability to establish comprehensive collections of plant-associated microbes and to reconstruct meaningful microbial synthetic communities (SynComs). We argue that this powerful deconstruction-reconstruction strategy can be used to reconstitute increasingly complex synthetic ecosystems (SynEcos) and mechanistically understand high-level biological organization. The transitioning from simple to more advanced, fully tractable and programmable gnotobiotic SynEcos is ongoing and aims at rationally simplifying natural ecosystems by engineering them. Such reconstitution ecology approaches represent an untapped strategy for bridging the gap between ecology and functional biology and for unraveling plant-microbiota-environment mechanisms that modulate ecosystem health, assembly, and functioning., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)
Published: 2024
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30. The chemical language of plant-microbe-microbe associations: an introduction to a Virtual Issue.

Author: Hacquard S and Martin FM
Subjects: Plants microbiology
Published: 2024
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31. Taming of the microbial beasts: Plant immunity tethers potentially pathogenic microbiota members.

Author: Entila F and Tsuda K
Abstract: Plants are in intimate association with taxonomically structured microbial communities called the plant microbiota. There is growing evidence that the plant microbiota contributes to the holistic performance and general health of plants, especially under unfavorable situations. Despite the attached benefits, surprisingly, the plant microbiota in nature also includes potentially pathogenic strains, signifying that the plant hosts have tight control over these microbes. Despite the conceivable role of plant immunity in regulating its microbiota, we lack a complete understanding of its role in governing the assembly, maintenance, and function of the plant microbiota. Here, we highlight the recent progress on the mechanistic relevance of host immunity in orchestrating plant-microbiota dialogues and discuss the pluses and perils of these microbial assemblies., (© 2024 Wiley Periodicals LLC.)
Published: 2024
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32. Soybean breeders can count on nodules.

Author: Shen D and Bisseling T
Abstract: Soybean, the most important legume crop, plays a crucial role in food security and sustainable agriculture. Recently, Zhong et al. demonstrated that a moderate increase in nodule number in soybean improves field yield and protein content. Their findings propose a potential strategy to enhance yield performance in other legume crops., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
Published: 2024
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33. The imprint of microbe-induced plant resistance in plant-associated insects.

Author: Martínez-Medina A, Biere A, and Pozo MJ
Subjects: Animals, Food Chain, Insecta physiology, Insecta microbiology, Herbivory, Plants microbiology, Plants immunology, Plant Defense Against Herbivory
Abstract: Beneficial microbes induce resistance in plants (MIR), imposing both lethal and sublethal effects on herbivorous insects. We argue that herbivores surviving MIR carry metabolic and immunological imprints of MIR with cascading effects across food webs. We propose that incorporating such cascading effects will strongly enhance the current MIR research framework., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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34. Plant Immunity Modulation in Arbuscular Mycorrhizal Symbiosis and Its Impact on Pathogens and Pests.

Author: Fiorilli V, Martínez-Medina A, Pozo MJ, and Lanfranco L
Subjects: Plants immunology, Plants microbiology, Plant Diseases microbiology, Plant Diseases immunology, Mycorrhizae physiology, Symbiosis, Plant Immunity
Abstract: Arbuscular mycorrhizal (AM) symbiosis is the oldest and most widespread mutualistic association on Earth and involves plants and soil fungi belonging to Glomeromycotina. A complex molecular, cellular, and genetic developmental program enables partner recognition, fungal accommodation in plant tissues, and activation of symbiotic functions such as transfer of phosphorus in exchange for carbohydrates and lipids. AM fungi, as ancient obligate biotrophs, have evolved strategies to circumvent plant defense responses to guarantee an intimate and long-lasting mutualism. They are among those root-associated microorganisms able to boost plants' ability to cope with biotic stresses leading to mycorrhiza-induced resistance (MIR), which can be effective across diverse hosts and against different attackers. Here, we examine the molecular mechanisms underlying the modulation of plant immunity during colonization by AM fungi and at the onset and display of MIR against belowground and aboveground pests and pathogens. Understanding the MIR efficiency spectrum and its regulation is of great importance to optimizing the biotechnological application of these beneficial microbes for sustainable crop protection.
Published: 2024
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35. Oligomerization-mediated autoinhibition and cofactor binding of a plant NLR.

Author: Ma S, An C, Lawson AW, Cao Y, Sun Y, Tan EYJ, Pan J, Jirschitzka J, Kümmel F, Mukhi N, Han Z, Feng S, Wu B, Schulze-Lefert P, and Chai J
Subjects: Binding Sites, Cell Death, Cryoelectron Microscopy, Models, Molecular, Mutation, Nicotiana cytology, Nicotiana immunology, Nicotiana metabolism, Plant Immunity, Protein Binding, Protein Domains, NLR Proteins antagonists & inhibitors, NLR Proteins chemistry, NLR Proteins genetics, NLR Proteins metabolism, NLR Proteins ultrastructure, Phytic Acid metabolism, Phytic Acid chemistry, Plant Proteins antagonists & inhibitors, Plant Proteins chemistry, Plant Proteins genetics, Plant Proteins metabolism, Plant Proteins ultrastructure, Protein Multimerization, Solanum lycopersicum cytology, Solanum lycopersicum genetics, Solanum lycopersicum immunology, Solanum lycopersicum metabolism
Abstract: Nucleotide-binding leucine-rich repeat (NLR) proteins play a pivotal role in plant immunity by recognizing pathogen effectors 1,2 . Maintaining a balanced immune response is crucial, as excessive NLR expression can lead to unintended autoimmunity 3,4 . Unlike most NLRs, the plant NLR required for cell death 2 (NRC2) belongs to a small NLR group characterized by constitutively high expression without self-activation 5 . The mechanisms underlying NRC2 autoinhibition and activation are not yet understood. Here we show that Solanum lycopersicum (tomato) NRC2 (SlNRC2) forms dimers and tetramers and higher-order oligomers at elevated concentrations. Cryo-electron microscopy shows an inactive conformation of SlNRC2 in these oligomers. Dimerization and oligomerization not only stabilize the inactive state but also sequester SlNRC2 from assembling into an active form. Mutations at the dimeric or interdimeric interfaces enhance pathogen-induced cell death and immunity in Nicotiana benthamiana. The cryo-electron microscopy structures unexpectedly show inositol hexakisphosphate (IP 6 ) or pentakisphosphate (IP 5 ) bound to the inner surface of the C-terminal leucine-rich repeat domain of SlNRC2, as confirmed by mass spectrometry. Mutations at the inositol phosphate-binding site impair inositol phosphate binding of SlNRC2 and pathogen-induced SlNRC2-mediated cell death in N. benthamiana. Our study indicates a negative regulatory mechanism of NLR activation and suggests inositol phosphates as cofactors of NRCs., (© 2024. The Author(s).)
Published: 2024
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36. The Arabidopsis SGN3/GSO1 receptor kinase integrates soil nitrogen status into shoot development.

Author: Shen D, Wippel K, Remmel S, Zhang Y, Kuertoes N, Neumann U, Kopriva S, and Andersen TG
Subjects: Soil chemistry, Gene Expression Regulation, Plant, Protein Kinases metabolism, Protein Kinases genetics, Cell Wall metabolism, Transcription Factors metabolism, Transcription Factors genetics, Arabidopsis metabolism, Arabidopsis growth & development, Arabidopsis genetics, Arabidopsis Proteins metabolism, Arabidopsis Proteins genetics, Nitrogen metabolism, Plant Shoots metabolism, Plant Shoots growth & development, Signal Transduction
Abstract: The Casparian strip is a barrier in the endodermal cell walls of plants that allows the selective uptake of nutrients and water. In the model plant Arabidopsis thaliana, its development and establishment are under the control of a receptor-ligand mechanism termed the Schengen pathway. This pathway facilitates barrier formation and activates downstream compensatory responses in case of dysfunction. However, due to a very tight functional association with the Casparian strip, other potential signaling functions of the Schengen pathway remain obscure. In this work, we created a MYB36-dependent synthetic positive feedback loop that drives Casparian strip formation independently of Schengen-induced signaling. We evaluated this by subjecting plants in which the Schengen pathway has been uncoupled from barrier formation, as well as a number of established barrier-mutant plants, to agar-based and soil conditions that mimic agricultural settings. Under the latter conditions, the Schengen pathway is necessary for the establishment of nitrogen-deficiency responses in shoots. These data highlight Schengen signaling as an essential hub for the adaptive integration of signaling from the rhizosphere to aboveground tissues., (© 2024. The Author(s).)
Published: 2024
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37. Physiochemical interaction between osmotic stress and a bacterial exometabolite promotes plant disease.

Author: Getzke F, Wang L, Chesneau G, Böhringer N, Mesny F, Denissen N, Wesseler H, Adisa PT, Marner M, Schulze-Lefert P, Schäberle TF, and Hacquard S
Subjects: Sodium Chloride pharmacology, Sodium Chloride metabolism, Soil Microbiology, Lipopeptides pharmacology, Lipopeptides metabolism, Arabidopsis microbiology, Arabidopsis metabolism, Arabidopsis genetics, Arabidopsis drug effects, Plant Diseases microbiology, Pseudomonas metabolism, Pseudomonas genetics, Plant Roots microbiology, Plant Roots metabolism, Osmotic Pressure
Abstract: Various microbes isolated from healthy plants are detrimental under laboratory conditions, indicating the existence of molecular mechanisms preventing disease in nature. Here, we demonstrated that application of sodium chloride (NaCl) in natural and gnotobiotic soil systems is sufficient to induce plant disease caused by an otherwise non-pathogenic root-derived Pseudomonas brassicacearum isolate (R401). Disease caused by combinatorial treatment of NaCl and R401 triggered extensive, root-specific transcriptional reprogramming that did not involve down-regulation of host innate immune genes, nor dampening of ROS-mediated immunity. Instead, we identified and structurally characterized the R401 lipopeptide brassicapeptin A as necessary and sufficient to promote disease on salt-treated plants. Brassicapeptin A production is salt-inducible, promotes root colonization and transitions R401 from being beneficial to being detrimental on salt-treated plants by disturbing host ion homeostasis, thereby bolstering susceptibility to osmolytes. We conclude that the interaction between a global change stressor and a single exometabolite from a member of the root microbiome promotes plant disease in complex soil systems., (© 2024. The Author(s).)
Published: 2024
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38. Author Correction: MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins.

Author: Oppermann J, Fischer P, Silapetere A, Liepe B, Rodriguez-Rozada S, Flores-Uribe J, Schiewer E, Keidel A, Vierock J, Kaufmann J, Broser M, Luck M, Bartl F, Hildebrandt P, Wiegert JS, Béjà O, Hegemann P, and Wietek J
Published: 2024
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39. Long-term and rapid evolution in powdery mildew fungi.

Author: Kusch S, Qian J, Loos A, Kümmel F, Spanu PD, and Panstruga R
Subjects: Host Specificity genetics, Genome, Fungal genetics, Biological Evolution, Evolution, Molecular, Plant Immunity genetics, Ascomycota genetics, Ascomycota pathogenicity, Plant Diseases microbiology, Plant Diseases genetics, DNA Transposable Elements genetics
Abstract: The powdery mildew fungi (Erysiphaceae) are globally distributed plant pathogens with a range of more than 10,000 plant hosts. In this review, we discuss the long- and short-term evolution of these obligate biotrophic fungi and outline their diversity with respect to morphology, lifestyle, and host range. We highlight their remarkable ability to rapidly overcome plant immunity, evolve fungicide resistance, and broaden their host range, for example, through adaptation and hybridization. Recent advances in genomics and proteomics, particularly in cereal powdery mildews (genus Blumeria), provided first insights into mechanisms of genomic adaptation in these fungi. Transposable elements play key roles in shaping their genomes, where even close relatives exhibit diversified patterns of recent and ongoing transposon activity. These transposons are ubiquitously distributed in the powdery mildew genomes, resulting in a highly adaptive genome architecture lacking obvious regions of conserved gene space. Transposons can also be neofunctionalized to encode novel virulence factors, particularly candidate secreted effector proteins, which may undermine the plant immune system. In cereals like barley and wheat, some of these effectors are recognized by plant immune receptors encoded by resistance genes with numerous allelic variants. These effectors determine incompatibility ("avirulence") and evolve rapidly through sequence diversification and copy number variation. Altogether, powdery mildew fungi possess plastic genomes that enable their fast evolutionary adaptation towards overcoming plant immunity, host barriers, and chemical stress such as fungicides, foreshadowing future outbreaks, host range shifts and expansions as well as potential pandemics by these pathogens., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)
Published: 2024
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40. Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly.

Author: Tao K, Jensen IT, Zhang S, Villa-Rodríguez E, Blahovska Z, Salomonsen CL, Martyn A, Björgvinsdóttir ÞN, Kelly S, Janss L, Glasius M, Waagepetersen R, and Radutoiu S
Subjects: Rhizosphere, Bacterial Proteins metabolism, Bacterial Proteins genetics, Soil Microbiology, Nitrogen Fixation, Plant Exudates metabolism, Lotus microbiology, Lotus metabolism, Symbiosis, Nitrogen metabolism, Plant Roots microbiology, Plant Roots metabolism, Signal Transduction, Microbiota physiology
Abstract: Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is unknown how the interaction between the legume host and rhizobia impacts the remaining microbiota and whether it depends on nitrogen nutrition. Here, we use plant and bacterial mutants to address the role of Nod factor signaling on Lotus japonicus root microbiota assembly. We find that Nod factors are produced by symbionts to activate Nod factor signaling in the host and that this modulates the root exudate profile and the assembly of a symbiotic root microbiota. Lotus plants with different symbiotic abilities, grown in unfertilized or nitrate-supplemented soils, display three nitrogen-dependent nutritional states: starved, symbiotic, or inorganic. We find that root and rhizosphere microbiomes associated with these states differ in composition and connectivity, demonstrating that symbiosis and inorganic nitrogen impact the legume root microbiota differently. Finally, we demonstrate that selected bacterial genera characterizing state-dependent microbiomes have a high level of accurate prediction., (© 2024. The Author(s).)
Published: 2024
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41. Bacillus cereus NJ01 induces SA- and ABA-mediated immunity against bacterial pathogens through the EDS1-WRKY18 module.

Author: Wang D, Wei L, Ma J, Wan Y, Huang K, Sun Y, Wen H, Chen Z, Li Z, Yu D, Cui H, Wu J, Wu Y, Kim ST, Zhao J, Parker JE, Tsuda K, Jiang C, and Wang Y
Subjects: Gene Expression Regulation, Plant, Transcription Factors metabolism, Transcription Factors genetics, Oryza microbiology, Oryza immunology, Oryza genetics, Disease Resistance genetics, Disease Resistance immunology, Plant Immunity, Bacillus cereus genetics, Abscisic Acid metabolism, Arabidopsis immunology, Arabidopsis microbiology, Arabidopsis genetics, Arabidopsis Proteins metabolism, Arabidopsis Proteins genetics, Plant Diseases microbiology, Plant Diseases immunology, DNA-Binding Proteins metabolism, DNA-Binding Proteins genetics, Salicylic Acid metabolism
Abstract: Emerging evidence suggests a beneficial role of rhizobacteria in ameliorating plant disease resistance in an environment-friendly way. In this study, we characterize a rhizobacterium, Bacillus cereus NJ01, that enhances bacterial pathogen resistance in rice and Arabidopsis. Transcriptome analyses show that root inoculation of NJ01 induces the expression of salicylic acid (SA)- and abscisic acid (ABA)-related genes in Arabidopsis leaves. Genetic evidence showed that EDS1, PAD4, and WRKY18 are required for B. cereus NJ01-induced bacterial resistance. An EDS1-PAD4 complex interacts with WRKY18 and enhances its DNA binding activity. WRKY18 directly binds to the W box in the promoter region of the SA biosynthesis gene ICS1 and ABA biosynthesis genes NCED3 and NCED5 and contributes to the NJ01-induced bacterial resistance. Taken together, our findings indicate a role of the EDS1/PAD4-WRKY18 complex in rhizobacteria-induced disease resistance., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
Published: 2024
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42. Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis.

Author: Loo EP, Durán P, Pang TY, Westhoff P, Deng C, Durán C, Lercher M, Garrido-Oter R, and Frommer WB
Subjects: Bacteria metabolism, Rhizosphere, Sugars metabolism, Plant Roots microbiology, Monosaccharide Transport Proteins metabolism, Arabidopsis microbiology, Microbiota, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism
Abstract: Plant roots are functionally heterogeneous in cellular architecture, transcriptome profile, metabolic state, and microbial immunity. We hypothesized that axial differentiation may also impact spatial colonization by root microbiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotron, to grow and then dissect Arabidopsis thaliana roots into three segments. We demonstrate that distinct endospheric and rhizosphere bacterial communities colonize the segments, supporting the hypothesis of microbiota differentiation along the axis. Root metabolite profiling of each segment reveals differential metabolite enrichment and specificity. Bioinformatic analyses and GUS histochemistry indicate microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root segments from sweet mutants shows altered spatial metabolic profiles and reorganization of endospheric root microbiota. This work reveals the interdependency between root metabolites and microbial colonization and the contribution of SWEETs to spatial diversity and stability of microbial ecosystem., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
Published: 2024
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43. Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota.

Author: Ordon J, Thouin J, Nakano RT, Ma KW, Zhang P, Huettel B, Garrido-Oter R, and Schulze-Lefert P
Subjects: Humans, Bacteria genetics, Genes, Bacterial, Symbiosis, Microbiota genetics, Arabidopsis genetics, Arabidopsis microbiology
Abstract: DNA-amplicon-based microbiota profiling can estimate species diversity and abundance but cannot resolve genetic differences within individuals of the same species. Here we report the development of modular bacterial tags (MoBacTags) encoding DNA barcodes that enable tracking of near-isogenic bacterial commensals in an array of complex microbiome communities. Chromosomally integrated DNA barcodes are then co-amplified with endogenous marker genes of the community by integrating corresponding primer binding sites into the barcode. We use this approach to assess the contributions of individual bacterial genes to Arabidopsis thaliana root microbiota establishment with synthetic communities that include MoBacTag-labelled strains of Pseudomonas capeferrum. Results show reduced root colonization for certain mutant strains with defects in gluconic-acid-mediated host immunosuppression, which would not be detected with traditional amplicon sequencing. Our work illustrates how MoBacTags can be applied to assess scaling of individual bacterial genetic determinants in the plant microbiota., (© 2024. The Author(s).)
Published: 2024
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44. From the archives: male-female communication, glue that keeps cells together, and a SUPERMAN for all flowering plants.

Author: Somssich M
Subjects: Transcription Factors, Flowers, Magnoliopsida, Arabidopsis Proteins
Abstract: Competing Interests: Conflict of interest statement. None declared.
Published: 2024
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45. Substrate-induced condensation activates plant TIR domain proteins.

Author: Song W, Liu L, Yu D, Bernardy H, Jirschitzka J, Huang S, Jia A, Jemielniak W, Acker J, Laessle H, Wang J, Shen Q, Chen W, Li P, Parker JE, Han Z, Schulze-Lefert P, and Chai J
Subjects: Arabidopsis Proteins chemistry, Arabidopsis Proteins genetics, Arabidopsis Proteins immunology, Arabidopsis Proteins metabolism, Cell Death, Mutation, NLR Proteins chemistry, NLR Proteins genetics, NLR Proteins immunology, NLR Proteins metabolism, Plant Diseases immunology, Plant Immunity genetics, Promoter Regions, Genetic, Receptors, Immunologic chemistry, Receptors, Immunologic genetics, Receptors, Immunologic immunology, Receptors, Immunologic metabolism, Signal Transduction, Toll-Like Receptors chemistry, Receptors, Interleukin-1 chemistry, Adenosine Triphosphate metabolism, Arabidopsis genetics, Arabidopsis immunology, Arabidopsis metabolism, NAD metabolism, Nicotiana genetics, Nicotiana immunology, Nicotiana metabolism, Plant Proteins chemistry, Plant Proteins genetics, Plant Proteins immunology, Plant Proteins metabolism, Protein Domains genetics, Phase Separation
Abstract: Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors with an N-terminal Toll/interleukin-1 receptor (TIR) domain mediate recognition of strain-specific pathogen effectors, typically via their C-terminal ligand-sensing domains 1 . Effector binding enables TIR-encoded enzymatic activities that are required for TIR-NLR (TNL)-mediated immunity 2,3 . Many truncated TNL proteins lack effector-sensing domains but retain similar enzymatic and immune activities 4,5 . The mechanism underlying the activation of these TIR domain proteins remain unclear. Here we show that binding of the TIR substrates NAD + and ATP induces phase separation of TIR domain proteins in vitro. A similar condensation occurs with a TIR domain protein expressed via its native promoter in response to pathogen inoculation in planta. The formation of TIR condensates is mediated by conserved self-association interfaces and a predicted intrinsically disordered loop region of TIRs. Mutations that disrupt TIR condensates impair the cell death activity of TIR domain proteins. Our data reveal phase separation as a mechanism for the activation of TIR domain proteins and provide insight into substrate-induced autonomous activation of TIR signalling to confer plant immunity., (© 2024. The Author(s).)
Published: 2024
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46. Arabidopsis PHYTOALEXIN DEFICIENT 4 promotes the maturation and nuclear accumulation of immune-related cysteine protease RD19.

Author: Zeng Y, Zheng Z, Hessler G, Zou K, Leng J, Bautor J, Stuttmann J, Xue L, Parker JE, and Cui H
Subjects: Carboxylic Ester Hydrolases chemistry, Phytoalexins, Plant Diseases microbiology, Plant Immunity genetics, Arabidopsis, Arabidopsis Proteins genetics, Arabidopsis Proteins chemistry, Cysteine Proteases genetics
Abstract: Arabidopsis PHYTOALEXIN DEFICIENT 4 (PAD4) has an essential role in pathogen resistance as a heterodimer with ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1). Here we investigated an additional PAD4 role in which it associates with and promotes the maturation of the immune-related cysteine protease RESPONSIVE TO DEHYDRATION 19 (RD19). We found that RD19 and its paralog RD19c promoted EDS1- and PAD4-mediated effector-triggered immunity to an avirulent Pseudomonas syringae strain, DC3000, expressing the effector AvrRps4 and basal immunity against the fungal pathogen Golovinomyces cichoracearum. Overexpression of RD19, but not RD19 protease-inactive catalytic mutants, in Arabidopsis transgenic lines caused EDS1- and PAD4-dependent autoimmunity and enhanced pathogen resistance. In these lines, RD19 maturation to a pro-form required its catalytic residues, suggesting that RD19 undergoes auto-processing. In transient assays, PAD4 interacted preferentially with the RD19 pro-protease and promoted its nuclear accumulation in leaf cells. Our results lead us to propose a model for PAD4-stimulated defense potentiation. PAD4 promotes maturation and nuclear accumulation of processed RD19, and RD19 then stimulates EDS1-PAD4 dimer activity to confer pathogen resistance. This study highlights potentially important additional PAD4 functions that eventually converge on canonical EDS1-PAD4 dimer signaling in plant immunity., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
Published: 2024
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47. Commensal lifestyle regulated by a negative feedback loop between Arabidopsis ROS and the bacterial T2SS.

Author: Entila F, Han X, Mine A, Schulze-Lefert P, and Tsuda K
Subjects: Reactive Oxygen Species metabolism, Feedback, NADPH Oxidases genetics, NADPH Oxidases metabolism, Bacteria metabolism, Gene Expression Regulation, Plant, Plant Immunity genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism
Abstract: Despite the plant health-promoting effects of plant microbiota, these assemblages also comprise potentially detrimental microbes. How plant immunity controls its microbiota to promote plant health under these conditions remains largely unknown. We find that commensal bacteria isolated from healthy Arabidopsis plants trigger diverse patterns of reactive oxygen species (ROS) production dependent on the immune receptors and completely on the NADPH oxidase RBOHD that selectively inhibited specific commensals, notably Xanthomonas L148. Through random mutagenesis, we find that L148 gspE, encoding a type II secretion system (T2SS) component, is required for the damaging effects of Xanthomonas L148 on rbohD mutant plants. In planta bacterial transcriptomics reveals that RBOHD suppresses most T2SS gene expression including gspE. L148 colonization protected plants against a bacterial pathogen, when gspE was inhibited by ROS or mutation. Thus, a negative feedback loop between Arabidopsis ROS and the bacterial T2SS tames a potentially detrimental leaf commensal and turns it into a microbe beneficial to the host., (© 2024. The Author(s).)
Published: 2024
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48. Plant NLR immunity activation and execution: a biochemical perspective.

Author: Locci F and Parker JE
Subjects: Animals, Cell Death, Cell Membrane, Nucleotides, Mammals, Calcium, Immunity, Innate
Abstract: Plants deploy cell-surface and intracellular receptors to detect pathogen attack and trigger innate immune responses. Inside host cells, families of nucleotide-binding/leucine-rich repeat (NLR) proteins serve as pathogen sensors or downstream mediators of immune defence outputs and cell death, which prevent disease. Established genetic underpinnings of NLR-mediated immunity revealed various strategies plants adopt to combat rapidly evolving microbial pathogens. The molecular mechanisms of NLR activation and signal transmission to components controlling immunity execution were less clear. Here, we review recent protein structural and biochemical insights to plant NLR sensor and signalling functions. When put together, the data show how different NLR families, whether sensors or signal transducers, converge on nucleotide-based second messengers and cellular calcium to confer immunity. Although pathogen-activated NLRs in plants engage plant-specific machineries to promote defence, comparisons with mammalian NLR immune receptor counterparts highlight some shared working principles for NLR immunity across kingdoms.
Published: 2024
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49. ER body-resident myrosinases and tryptophan specialized metabolism modulate root microbiota assembly.

Author: Basak AK, Piasecka A, Hucklenbroich J, Türksoy GM, Guan R, Zhang P, Getzke F, Garrido-Oter R, Hacquard S, Strzałka K, Bednarek P, Yamada K, and Nakano RT
Subjects: Glycoside Hydrolases, Bacteria, Soil chemistry, Soil Microbiology, Plant Roots microbiology, Rhizosphere, Tryptophan, Microbiota
Abstract: Endoplasmic reticulum (ER) bodies are ER-derived structures that contain a large amount of PYK10 myrosinase, which hydrolyzes tryptophan (Trp)-derived indole glucosinolates (IGs). Given the well-described role of IGs in root-microbe interactions, we hypothesized that ER bodies in roots are important for interaction with soil-borne microbes at the root-soil interface. We used mutants impaired in ER bodies (nai1), ER body-resident myrosinases (pyk10bglu21), IG biosynthesis (myb34/51/122), and Trp specialized metabolism (cyp79b2b3) to profile their root microbiota community in natural soil, evaluate the impact of axenically collected root exudates on soil or synthetic microbial communities, and test their response to fungal endophytes in a mono-association setup. Tested mutants exhibited altered bacterial and fungal communities in rhizoplane and endosphere, respectively. Natural soils and bacterial synthetic communities treated with mutant root exudates exhibited distinctive microbial profiles from those treated with wild-type (WT) exudates. Most tested endophytes severely restricted the growth of cyp79b2b3, a part of which also impaired the growth of pyk10bglu21. Our results suggest that root ER bodies and their resident myrosinases modulate the profile of root-secreted metabolites and thereby influence root-microbiota interactions., (© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation.)
Published: 2024
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50. Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota.

Author: Vannier N, Mesny F, Getzke F, Chesneau G, Dethier L, Ordon J, Thiergart T, and Hacquard S
Subjects: Bacteria, Plant Roots microbiology, Soil Microbiology, Microbiota genetics, Arabidopsis genetics, Arabidopsis microbiology
Abstract: The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains' abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots., (© 2023. The Author(s).)
Published: 2023
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