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1. The IV International Symposium on Fungal Stress and the XIII International Fungal Biology Conference.

Author: Alder-Rangel A, Bailão AM, Herrera-Estrella A, Rangel AEA, Gácser A, Gasch AP, Campos CBL, Peters C, Camelim F, Verde F, Gadd GM, Braus G, Eisermann I, Quinn J, Latgé JP, Aguirre J, Bennett JW, Heitman J, Nosanchuk JD, Partida-Martínez LP, Bassilana M, Acheampong MA, Riquelme M, Feldbrügge M, Keller NP, Keyhani NO, Gunde-Cimerman N, Nascimento R, Arkowitz RA, Mouriño-Pérez RR, Naz SA, Avery SV, Basso TO, Terpitz U, Lin X, and Rangel DEN
Subjects: Brazil, France, Spain, Mexico, Biology
Abstract: For the first time, the International Symposium on Fungal Stress was joined by the XIII International Fungal Biology Conference. The International Symposium on Fungal Stress (ISFUS), always held in Brazil, is now in its fourth edition, as an event of recognized quality in the international community of mycological research. The event held in São José dos Campos, SP, Brazil, in September 2022, featured 33 renowned speakers from 12 countries, including: Austria, Brazil, France, Germany, Ghana, Hungary, México, Pakistan, Spain, Slovenia, USA, and UK. In addition to the scientific contribution of the event in bringing together national and international researchers and their work in a strategic area, it helps maintain and strengthen international cooperation for scientific development in Brazil., Competing Interests: Declaration of competing interest The manuscript has been prepared in accordance with the formatting guidelines for Fungal Biology. The work is not under consideration for publication in any form elsewhere. The manuscript does not infringe any personal or other copyright or property rights and has been approved for publication by all authors. All authors declare that they have no conflicting interests., (Copyright © 2023 British Mycological Society. Published by Elsevier Ltd. All rights reserved.)
Published: 2023
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2. Ottoline Leyser.

Author: Leyser O
Subjects: Botany, England, History, 21st Century, Biology, Genetics
Published: 2012
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3. The Rust Fungus Melampsora larici-populina Expresses a Conserved Genetic Program and Distinct Sets of Secreted Protein Genes During Infection of Its Two Host Plants, Larch and Poplar

Author: Sébastien Duplessis, Arnaud Hecker, Jérémy Pétrowski, Stéphane Hacquard, Clemence Marchal, Cécile Lorrain, Pascal Frey, Benjamin Petre, Christine Delaruelle, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), Agence Nationale de la Recherche, Lab of Excellence ARBRE (Advanced Research on the Biology of FoRest Ecosystem) ANR-11-LABX-0002-01, Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: 0106 biological sciences, 0301 basic medicine, Pharmacogenomic Variants, rouille du peuplier, Physiology, [SDV]Life Sciences [q-bio], Rust (fungus), Larix, populus, champignon pathogène, 01 natural sciences, Host Specificity, COLONIZATION, Fungal Proteins, 03 medical and health sciences, mélèze, larch, Gene Expression Regulation, Fungal, CANDIDATE EFFECTORS, Heteroecious, Gene family, fungal pathogen, Gene, Plant Diseases, 030304 developmental biology, Genetics, 0303 health sciences, biology, Host (biology), Basidiomycota, food and beverages, General Medicine, Melampsora, biology.organism_classification, EVOLUTION, TRANSCRIPTOME ANALYSIS, Sexual reproduction, melampsora larici populina, 030104 developmental biology, BIOTROPHY, PATTERNS, Larch, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: SummaryMechanims required for broad spectrum or specific host colonization of plant parasites are poorly understood. As a perfect illustration, heteroecious rust fungi require two alternate host plants to complete their life cycle. Melampsora larici-populina infects two taxonomically unrelated plants, larch on which sexual reproduction is achieved and poplar on which clonal multiplication occurs leading to severe epidemics in plantations. High-depth RNA sequencing was applied to three key developmental stages of M. larici-populina infection on larch: basidia, pycnia and aecia. Comparative transcriptomics of infection on poplar and larch hosts was performed using available expression data. Secreted protein was the only significantly over-represented category among differentially expressed M. larici-populina genes in basidia, pycnia and aecia compared together, highlighting their probable involvement in the infection process. Comparison of fungal transcriptomes in larch and poplar revealed a majority of rust genes commonly expressed on the two hosts and a fraction exhibiting a host-specific expression. More particularly, gene families encoding small secreted proteins presented striking expression profiles that highlight probable candidate effectors specialized on each host. Our results bring valuable new information about the biological cycle of rust fungi and identify genes that may contribute to host specificity.
Published: 2018

4. Lipo‐chitooligosaccharides promote lateral root formation and modify auxin homeostasis in Brachypodium distachyon

Author: Fabienne Maillet, Benoit Lefebvre, Luis Buendia, Devin O'Connor, Sandra Bensmihen, Quitterie van de-Kerkhove, Saïda Danoun, Clare Gough, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory Cambridge University (SLCU), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), INRA/SPE project 'LCAux', French 'Ministere de l'Enseignement Superieur et de la Recherche', ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), and ANR-16-CE20-0025,WHEATSYM,ROLES DES SIGNAUX MICROBIENS LCO/CO ET DE LEURS RECEPTEURS DE PLANTES DANS DES INTERACTIONS BENEFIQUES ENTRE MONOCOTYLEDONES ET MICROORGANISMES DU SOL(2016)
Subjects: 0106 biological sciences, 0301 basic medicine, Indoles, hormone homeostasis, Physiology, Oligosaccharides, lateral root primordia, Chitin, Endogeny, Plant Science, root architecture, indole-3-butyric acid (IBA), Models, Biological, Plant Roots, 01 natural sciences, Fluorescence, 03 medical and health sciences, lipochitooligosaccharide (LCO), Auxin, Nod factors, Homeostasis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, heterocyclic compounds, Gene, Lateral root formation, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Chitosan, Indoleacetic Acids, biology, Auxin homeostasis, Chemistry, fungi, food and beverages, biology.organism_classification, Lipids, Medicago truncatula, Cell biology, auxin dosage, 030104 developmental biology, Brachypodium, Brachypodium distachyon, symbiotic signal, Signal Transduction, 010606 plant biology & botany
Abstract: International audience; . Lipo-chitooligosaccharides (LCOs) are microbial symbiotic signals that also influence root growth. In Medicago truncatula, LCOs stimulate lateral root formation (LRF) synergistically with auxin. However, the molecular mechanisms of this phenomenon and whether it is restricted to legume plants are not known. . We have addressed the capacity of the model monocot Brachypodium distachyon (Brachypodium) to respond to LCOs and auxin for LRF. For this, we used a combination of root phenotyping assays, live-imaging and auxin quantification, and analysed the regulation of auxin homeostasis genes. We show that LCOs and a low dose of the auxin precursor indole-3-butyric acid (IBA) stimulated LRF in Brachypodium, while a combination of LCOs and IBA led to different regulations. Both LCO and IBA treatments locally increased endogenous indole-3-acetic acid (IAA) content, whereas the combination of LCO and IBA locally increased the endogenous concentration of a conjugated form of IAA (IAA-Ala). LCOs, IBA and the combination differentially controlled expression of auxin homeostasis genes. . These results demonstrate that LCOs are active on Brachypodium roots and stimulate LRF probably through regulation of auxin homeostasis. The interaction between LCO and auxin treatments observed in Brachypodium on root architecture opens interesting avenues regarding their possible combined effects during the arbuscular mycorrhizal symbiosis.
Published: 2018

5. The FERONIA receptor kinase maintains cell-wall integrity during salt stress through Ca2+ signaling

Author: Ming-Che Liu, Alexis Peaucelle, Heather N. Cartwright, Qiaohong Duan, José R. Dinneny, Ina Schmitz-Thom, Wei Feng, Leonie Steinhorst, Jörg Kudla, Daniel Kita, Robert Yvon, Vinh Doan, Jacob Maman, Alice Y. Cheung, Hen-Ming Wu, Department of Plant Biology, Carnegie Institution for Science [Washington], University of Massachusetts System (UMASS), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Institut für biologie und biotechnologie der pflanzen, Westfälische Wilhelms-Universität Münster (WWU), Department of Biology, Stanford University, Sainsbury Laboratory, Cambridge University, National Science Foundation (NSF) Plant Genome Research Program [IOS 1238202], NIH NIGMS [R01 GM123259-01], Carnegie Institution for Science Endowment, NSF [IOS-1146941, IOS-1147165, IOS-1645854], German Research Foundation [Ku 931/14-1], Howard Hughes Medical Institute, Simons Foundation, and Dinneny, José R.
Subjects: 0106 biological sciences, 0301 basic medicine, Mutant, Arabidopsis, chemistry.chemical_element, Calcium, 01 natural sciences, Salt Stress, General Biochemistry, Genetics and Molecular Biology, Article, Cell wall, 03 medical and health sciences, Cell Wall, Extracellular, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Calcium Signaling, Receptor, Plant Physiological Phenomena, Vegetal Biology, biology, Arabidopsis Proteins, Kinase, Endoplasmic reticulum, Phosphotransferases, biology.organism_classification, Cell biology, Corrosion, 030104 developmental biology, chemistry, Pectins, General Agricultural and Biological Sciences, Biologie végétale, 010606 plant biology & botany
Abstract: SUMMARY Cells maintain integrity despite changes in their mechanical properties elicited during growth and environmental stress. How cells sense their physical state and compensate for cell-wall damage is poorly understood, particularly in plants. Here we report that FERONIA (FER), a plasma-membrane-localized receptor kinase from Arabidopsis, is necessary for the recovery of root growth after exposure to high salinity, a widespread soil stress. The extracellular domain of FER displays tandem regions of homology with malectin, an animal protein known to bind diglucose in vitro and important for protein quality control in the endoplasmic reticulum. The presence of malectin-like domains in FER and related receptor kinases has led to widespread speculation that they interact with cell-wall polysaccharides and can potentially serve a wall-sensing function. Results reported here show that salinity causes softening of the cell wall and that FER is necessary to sense these defects. When this function is disrupted in the fer mutant, root cells explode dramatically during growth recovery. Similar defects are observed in the mur1 mutant, which disrupts pectin cross-linking. Furthermore, fer cell-wall integrity defects can be rescued by treatment with calcium and borate, which also facilitate pectin cross-linking. Sensing of these salinity-induced wall defects might therefore be a direct consequence of physical interaction between the extracellular domain of FER and pectin. FER-dependent signaling elicits cell-specific calcium transients that maintain cell-wall integrity during salt stress. These results reveal a novel extracellular toxicity of salinity, and identify FER as a sensor of damage to the pectin-associated wall., In Brief For plant cells, growth requires maintenance of cell-wall integrity. Feng et al. show that salinity weakens the cell wall, which triggers FER-mediated calcium signaling to prevent root cells from bursting during growth under salt stress. The extracellular domain of FER physically interacts with pectin, indicating a potential sensing mechanism.
Published: 2018

6. The ash dieback invasion of Europe was founded by two genetically divergent individuals

Author: Adam Vivian-Smith, Kentaro Yoshida, Halvor Solheim, Christine Fosker, Ari M. Hietala, Bernardo J. Clavijo, David Swarbreck, Gemy Kaithakottil, Lawrence Percival-Alwyn, Mark McMullan, Philip Jennings, James K. M. Brown, Diane G. O. Saunders, Matthew D. Clark, Walter Verweij, Louisa Williamson, Jonathan M. Wright, Lorelei Bilham, J. Allan Downie, Elizabeth S. Orton, Renaud Ioos, Dan MacLean, Maryam Rafiqi, Mark Blaxter, Georgios Koutsovoulos, Gonzalo Garcia Accinelli, Tsuyoshi Hosoya, Ben J. Ward, Anne Edwards, Neil Hall, Claude Husson, McMullan, Mark, Earlham Institute [Norwich], Kew Botanical Garden, John Innes Centre [Norwich], Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, The Sainsbury Laboratory, Department of Agrobioscience - Graduate School of Agricultural Science, Kobe University, National Museum of Nature and Science, Fera Science Limited, Laboratoire de la Santé des Végétaux, Unité de Mycologie (LSV Nancy), Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Norwegian Institute of Bioeconomy Research (NIBIO), Edinburgh Genomics, The Natural History Museum [London] (NHM), Biotechnology and Biological Sciences Research Council (BBSRC) BB/L024055/1, CyVerse UK of the Earlham Institute National Capability in e-Infrastructure, BBSRC BBS/E/J/000CA523, Department of Environment Food and Rural Affairs (Defra) BBS/E/J/000CA523, Economic and Social Research Council, Forestry Commission, Natural Environment Research Council (NERC), Scottish Government under Tree Health and Plant Biosecurity Initiative BB/L01291X/1, French National Research Agency (ANR) of the Investissements d'Avenir programme ANR-11-LABX-0002-01, BBSRC National Capability in Genomics grant BB/J010375/1, BBSRC Institute Strategic Programme Grant for Bioinformatics BB/ J004669/1, The Sainsbury Laboratory [Norwich] (TSL), Konan University [Kobe, Japan], Unité de Mycologie, and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: 0301 basic medicine, safety, Population genetics, [SDV]Life Sciences [q-bio], DIVERSITY, sécurité, Introgression, Biology, Fraxinus, Article, cinder, 03 medical and health sciences, Ascomycota, DNA POLYMORPHISM, medicine, PATHOGEN HYMENOSCYPHUS PSEUDOALBIDUS, REVEALS INSIGHTS, POPULATION-STRUCTURE, cendre, Ecology, Evolution, Behavior and Systematics, Plant Diseases, FUNGAL, Genetic diversity, GENOME EVOLUTION, PLANT-PATHOGENS, Ecology, Host (biology), Haplotype, Hymenoscyphus fraxineus, Ecological genetics, biology.organism_classification, frêne, medicine.drug_formulation_ingredient, FRAXINUS-EXCELSIOR, RESISTANCE, haploïde, 030104 developmental biology, Haplotypes, 13. Climate action, Evolutionary biology, Genome, Fungal, europe
Abstract: Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H. fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.
Published: 2018

7. SUPERMAN prevents class B gene expression and promotes stem cell termination in the fourth whorl of Arabidopsis thaliana flowers

Author: Thomas Jack, Pradeep Das, Elliot M. Meyerowitz, Nathanaël Prunet, Weibing Yang, Department of Biological Sciences, Dartmouth College, Division of Biology and Biological Engineering, Howard Hughes Medical Institute, California Institute of Technology (CALTECH), Sainsbury Laboratory, University of Cambridge, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), National Science Foundation [IOS-0926347], National Institutes of Health [R01 GM104244], Gordon and Betty Moore Foundation [GBMF3406], Prunet, Nathanaël, Meyerowitz, Elliot M., Dartmouth College [Hanover], Howard Hughes Medical Institute (HHMI), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)
Subjects: 0301 basic medicine, Gynoecium, [SDV]Life Sciences [q-bio], microscopie confocale, Mutant, Stamen, Biology, confocal microscopy, verticille, 03 medical and health sciences, SUPERMAN, stem cells, boundary formation, flower development, cellule souche, Arabidopsis thaliana, Superman, Gene, Whorl (botany), Genetics, floral organ identity, Multidisciplinary, développement de la fleur, arabidopsis thaliana, fungi, food and beverages, Biological Sciences, formation de bourgeon, organe floral, biology.organism_classification, stem cell, body regions, identité génique, 030104 developmental biology, Stem cell
Abstract: Significance The Arabidopsis thaliana flower is a complex structure that consists of discrete floral organs (sepals, petals, stamens, and carpels) that are separated by regions lacking organ growth called boundaries. The SUPERMAN ( SUP ) gene functions to define the boundary between the male organs (stamens) and female organs (carpels) in the flower. Previous work on boundary formation in plants has focused on growth repression, rather than on identity separation. Using live confocal imaging, we demonstrate that SUP functions by keeping the male and female developmental programs spatially and temporally separate, which is critical for the fertility of the flower. In addition, we show a second role of SUP in the timely termination of floral stem cells.
Published: 2017

8. Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal

Author: Pau Formosa-Jordan, Adrienne H. K. Roeder, José Teles, Heather M Meyer, Yassin Refahi, Gwyneth C. Ingram, Henrik Jönsson, Rita San-Bento, James C. W. Locke, Graduate Field of Genetics, Genomics and Development, Cornell University, Weill Institute for Cell and Molecular Biology, Sainsbury Laboratry, University of Cambridge, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory, University of Cambridge [UK] (CAM), Computational Biology and Biological Physics, Lund University, Department of Applied Mathematics and Theoretical Physics, Queen's University [Belfast] (QUB), Microsoft Research, Department of Biochemistry, Hôpital Lapeyronie, Section of Plant Biology, School of Integrated Plant Science, National Science Foundation, 10S-1553030 10S-1256733, Gatsby Charitable Foundation GAT3272/GLC GAT3395/PR4, Vetenskapsradet VR2013:4632, Herchel Smith Foundation, Cornell University [New York], Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Sainsbury Laboratory Cambridge University (SLCU), The Sainsbury Laboratory [Norwich] (TSL), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Lund University [Lund]
Subjects: 0301 basic medicine, Cell type, QH301-705.5, Science, [SDV]Life Sciences [q-bio], Cell fate determination, Biology, General Biochemistry, Genetics and Molecular Biology, endoreduplication, modelling, 03 medical and health sciences, sepal, pattern formation, Live cell imaging, Arabidopsis, transcription factors, Botany, Endoreduplication, giant cell, Biology (General), Transcription factor, cell fate specification, ATML1, modélisation, General Immunology and Microbiology, cellule epidermique, fluctuation, General Neuroscience, arabidopsis thaliana, General Medicine, Cell cycle, biology.organism_classification, Cell biology, 030104 developmental biology, Giant cell, Medicine, facteur de transcription
Abstract: Multicellular development produces patterns of specialized cell types. Yet, it is often unclear how individual cells within a field of identical cells initiate the patterning process. Using live imaging, quantitative image analyses and modeling, we show that during Arabidopsis thaliana sepal development, fluctuations in the concentration of the transcription factor ATML1 pattern a field of identical epidermal cells to differentiate into giant cells interspersed between smaller cells. We find that ATML1 is expressed in all epidermal cells. However, its level fluctuates in each of these cells. If ATML1 levels surpass a threshold during the G2 phase of the cell cycle, the cell will likely enter a state of endoreduplication and become giant. Otherwise, the cell divides. Our results demonstrate a fluctuation-driven patterning mechanism for how cell fate decisions can be initiated through a random yet tightly regulated process.
Published: 2017

9. Morphological plant modeling: Unleashing geometric and topologic potential within the plant sciences

Author: Joseph H. Williams, Daniel H. Chitwood, Lilan Hong, Mao Li, Anjali S. Iyer-Pascuzzi, Erin E. Sparks, Thomas J. DeWitt, Cynthia C. Chang, Edgar P. Spalding, Dorjsuren Battogtokh, Jonathan P. Lynch, Samuel Leiboff, Diego Hernán Díaz Martínez, R. J. Cody Markelz, Eetu Puttonen, John B. Reese, Laura L. Klein, Alexis Maizel, Malia A. Gehan, Mathilde Balduzzi, Washington Mio, Christopher N. Topp, Ciera C. Martinez, Alexander Bucksch, Christophe Pradal, Julin N. Maloof, Alexander G. Fletcher, Viktoiriya Coneva, Laura Miller, Hendrik Poorter, Siobhan A. Braybrook, Wojtek Palubicki, Acheampong Atta-Boateng, Rubén Rellán-Álvarez, Akomian Fortuné Azihou, Charles A. Price, Brad M. Binder, Aly Baumgartner, University of Georgia [USA], Yale University [New Haven], Laboratory of Applied Ecology, University of Abomey-Calavi, University of Abomey Calavi (UAC), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Virginia Tech [Blacksburg], Baylor University, The University of Tennessee [Knoxville], Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), University of Washington-Bothell, Donald Danforth Plant Science Center, Department of Wildlife & Fisheries Sciences, Department of Plant Pathology & Microbiology, Texas A&M University [College Station], School of Mathematics and Statistics [Sheffield] (SoMaS), University of Sheffield [Sheffield], Florida State University [Tallahassee] (FSU), Cornell University [New York], Department of Botany and Plant Pathology, Purdue University [West Lafayette], Saint Louis University, Pennsylvania State University (Penn State), Penn State System, Center for Organismal Studies, Universität Heidelberg [Heidelberg], University of California Davis - Department of Plant Biology, University of California, Department of Molecular & Cell Biology [Berkeley], University of California [Berkeley], University of California-University of California, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Forschungszentrum Juelich, National Institute for Mathematical and Biological Synthesis, Finnish Geospatial Research Institute (FGI), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), University of Wisconsin-Madison, Duke University [Durham], Université d’Abomey-Calavi = University of Abomey Calavi (UAC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universität Heidelberg [Heidelberg] = Heidelberg University, University of California (UC), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Forschungszentrum Jülich GmbH, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Sainsbury Laboratory Cambridge, and Cornell University
Subjects: 0106 biological sciences, topology, Population, Biology, Topology, 01 natural sciences, 03 medical and health sciences, White paper, Botany, morphology, education, 030304 developmental biology, 2. Zero hunger, Plant biology, 0303 health sciences, education.field_of_study, mathematics, modeling, Vegetation, 15. Life on land, Natural resource, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Outreach, plant science, 13. Climate action, Plant morphology, 010606 plant biology & botany
Abstract: Plant morphology is inherently mathematical in that morphology describes plant form and architecture with geometrical and topological descriptors. The geometries and topologies of leaves, flowers, roots, shoots and their spatial arrangements have fascinated plant biologists and mathematicians alike. Beyond providing aesthetic inspiration, quantifying plant morphology has become pressing in an era of climate change and a growing human population. Modifying plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems with fewer natural resources. In this white paper, we begin with an overview of the mathematical models applied to quantify patterning in plants. We then explore fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leafs in air streams. We end with a discussion concerning the incorporation of plant morphology into educational programs. This strategy focuses on synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. This white paper arose from bringing mathematicians and biologists together at the National Institute for Mathematical and Biological Synthesis (NIMBioS) workshop titled “Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences” held at the University of Tennessee, Knoxville in September, 2015. Never has the need to quantify plant morphology been more imperative. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
Published: 2016

10. A pigeonpea gene confers resistance to Asian soybean rust in soybean

Author: Gustavo Tristão, Geeta Iyer, Karen Bacot, Burkhard Steuernagel, Brande B. H. Wulff, Sérgio Hermínio Brommonschenkel, Sônia Regina Nogueira, Gregory J. Rairdan, H. Peter van Esse, Gilda Rauscher, Jamile Camargos de Oliveira, Jong-Min Baek, Lisa Panichelli, Doug R. Cook, Bernardo do V A Melo, Eric R. Ward, Gustavo Augusto Guimarães, Dan MacLean, Shipra Mittal, Girma M. Tabor, Gusui Wu, Cintia G. Kawashima, Ebony Johnson, Costas Bouyioukos, Jonathan D. G. Jones, Karen E Broglie, Cintia G Kawashima, The Sainsbury Laboratory, Norwich, U.K., Gustavo Augusto Guimarães, Dep. de Fitopatologia, Universidade Federal de Viçosa, SONIA REGINA NOGUEIRA, CPAF-Acre, Dan MacLean, The Sainsbury Laboratory, Norwich, U.K., Doug R. Cook, Department of Plant Pathology, University of California Davis, Davis, California, USA., Burkhard Steuernagel, The John Innes Centre, Norwich, U.K., Jongmin Baek, Department of Plant Pathology, University of California Davis, Davis, California, USA., Costas Bouyioukos, The John Innes Centre, Norwich, U.K., Bernardo do V. A. Melo, Dep. de Fitopatologia, Universidade Federal de Viçosa, Gustavo Tristão, Dep. de Fitopatologia, Universidade Federal de Viçosa, Jamile Camargos de Oliveira, Dep. de Fitopatologia, Universidade Federal de Viçosa, Gilda Rauscher, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Shipra Mittal, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Lisa Panichelli, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Karen Bacot, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Ebony Johnson, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Geeta Iyer, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Girma Tabor, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Brande B H Wulff, The John Innes Centre, Norwich, U.K., Eric Ward, The John Innes Centre, Norwich, U.K., Gregory J Rairdan, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Karen E Broglie, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Gusui Wu, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., H Peter van Esse, The Sainsbury Laboratory, Norwich, U.K., Jonathan D G Jones, The Sainsbury Laboratory, Norwich, U.K., and Sérgio H Brommonschenkel, Dep. de Fitopatologia, Universidade Federal de Viçosa.
Subjects: Fitomejoramiento, 0106 biological sciences, 0301 basic medicine, Glycine max, Soja, Genótipo, Guandu, 01 natural sciences, Applied Microbiology and Biotechnology, Plant breeding, Molecular clonación, Cajanus, Molecular cloning, Doença de planta, Plant diseases and disorders, Cultivar, Roya de la soja, Legume, biology, Pigeon peas, food and beverages, Guandul, Fungicide, Phakopsora pachyrhizi, Molecular Medicine, Soybean rust, Biotechnology, Beans, Enfermedades y desórdenes de las plantas, Melhoramento genético vegetal, Variedade resistente, Biomedical Engineering, Bioengineering, Fungus, Plant disease resistance, Ferrugem asiática, Crop, 03 medical and health sciences, Clonagem, Semillas de soja, Frijoles, Fungo, Asian soybean, fungi, Fungi, Leguminosa com grão, biology.organism_classification, Pigeonpea gene, 030104 developmental biology, Agronomy, Phakpsora pachyrhizi, Soybeans, Feijão, Cajanus cajan, 010606 plant biology & botany
Abstract: Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.
Published: 2016

11. The Poplar Rust-Induced Secreted Protein (RISP) Inhibits the Growth of the Leaf Rust Pathogen Melampsora larici-populina and Triggers Cell Culture Alkalinisation

Author: Benjamin ePetre, Arnaud eHECKER, Hugo eGermain, Pascale eTsan, Jan eSklenar, Gervais ePelletier, Armand eSéguin, Sébastien eDuplessis, Nicolas eRouhier, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), Université du Québec à Trois-Rivières (UQTR), Cristallographie, Résonance Magnétique et Modélisations (CRM2), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Canadian Forest Service, Laurentian Forestry Centre, Natural Resources Canada (NRCan), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Sainsbury Laboratory, John Innes Centre [Norwich], Groupement de Recherche en Biologie Végétale & Centre de Recherche sur les Interactions Bassins Versants-Ecosystèmes Aquatiques, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), The Sainsbury Laboratory [Norwich] (TSL), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Laurentian Forestry Centre, ANR (ANR-11-LABX-0002-01), Region Lorraine, INRA, Gatsby Charitable Foundation, European Research Council, Biotechnology and Biological Sciences Research Council (BBSRC), and European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012)
Subjects: 0106 biological sciences, 0301 basic medicine, Populus trichocarpa, propriété antifongique, [SDV]Life Sciences [q-bio], Rust (fungus), Nicotiana benthamiana, Plant Science, champignon pathogène, Biology, lcsh:Plant culture, 01 natural sciences, Microbiology, 03 medical and health sciences, protéine sécrétée, obligate biotroph, Extracellular, lcsh:SB1-1110, Pathogen, ComputingMilieux_MISCELLANEOUS, Original Research, arbre, peptide elicitor, fungi, antifungal activity, plant immunity, rust fungus, food and beverages, Melampsora, biology.organism_classification, Apoplast, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, melampsora larici populina, Cell culture, 010606 plant biology & botany
Abstract: International audience; Plant cells secrete a wide range of proteins in extracellular spaces in response to pathogen attack. The poplar rust-induced secreted protein (RISP) is a small cationic protein of unknown function that was identified as the most induced gene in poplar leaves during immune responses to the leaf rust pathogen Melampsora larici-populina, an obligate biotrophic parasite. Here, we combined in planta and in vitro molecular biology approaches to tackle the function of RISP. Using a RISP-mCherry fusion transiently expressed in Nicotiana benthamiana leaves, we demonstrated that RISP is secreted into the apoplast. A recombinant RISP specifically binds to M. larici-populina urediniospores and inhibits their germination. It also arrests the growth of the fungus in vitro and on poplar leaves. Interestingly, RISP also triggers poplar cell culture alkalinisation and is cleaved at the C-terminus by a plant-encoded mechanism. Altogether our results indicate that RISP is an antifungal protein that has the ability to trigger cellular responses.
Published: 2016

12. Regulation of Meristem Morphogenesis by Cell Wall Synthases in Arabidopsis

Author: Monika S. Doblin, Christoph Schuster, Varodom Charoensawan, Cherie T. Beahan, Antony Bacic, Weibing Yang, Raymond Wightman, Elliot M. Meyerowitz, Alexis Peaucelle, Sainsbury Laboratory, University of Cambridge, ARC Centre of Excellence in Plant Cell Walls, University of Adelaide-University of Queensland [Brisbane]-School of BioSciences [Melbourne], Faculty of Science [Melbourne], University of Melbourne-University of Melbourne-Faculty of Science [Melbourne], University of Melbourne-University of Melbourne, Department of Biochemistry, Faculty of Science, Mahidol University [Bangkok]-Ramathibodi Hospital, Integrative Computational BioScience Center, Mahidol University [Bangkok], Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology (CALTECH), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), University of Queensland [Brisbane]-School of BioSciences [Melbourne], University of Melbourne-University of Melbourne-University of Adelaide, European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Yang, Weibing [0000-0002-2379-5729], Schuster, Christoph [0000-0002-1948-2367], Wightman, Raymond [0000-0003-1295-4875], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, XYLAN, [SDV]Life Sciences [q-bio], education, Meristem, Morphogenesis, Arabidopsis, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Cell wall, 03 medical and health sciences, PECTIN, Cell Wall, Gene Expression Regulation, Plant, BIOSYNTHETIC HOMOGALACTURONAN GALACTURONOSYLTRANSFERASE, Gene expression, Botany, MUTANTS REVEALS, Primordium, RNA, Messenger, health care economics and organizations, GENE-EXPRESSION, Regulation of gene expression, Agricultural and Biological Sciences(all), THALIANA, Biochemistry, Genetics and Molecular Biology(all), Arabidopsis Proteins, Sequence Analysis, RNA, Glycosyltransferases, food and beverages, Meristem maintenance, biology.organism_classification, Cell biology, 030104 developmental biology, CELLULOSE, GROWTH, ARABINOGALACTAN, SHOOT APICAL MERISTEM, General Agricultural and Biological Sciences
Abstract: The cell walls of the shoot apical meristem (SAM), containing the stem cell niche that gives rise to the above-ground tissues, are crucially involved in regulating differentiation. It is currently unknown how these walls are built and refined or their role, if any, in influencing meristem developmental dynamics. We have combined polysaccharide linkage analysis, immuno-labelling and transcriptome profiling of the SAM to provide a spatio-temporal plan of the walls of this dynamic structure. We find that meristematic cells express only a core subset of 152 genes encoding cell wall glycosyltransferases (GTs). Systemic localization of all these GT mRNAs by in situ hybridization reveals members with either enrichment in or specificity to apical subdomains such as emerging flower primordia, and a large class with high expression in dividing cells. The highly localized and coordinated expression of GTs in the SAM suggests distinct wall properties of meristematic cells, and specific differences between newly forming walls and their mature descendants. Functional analysis demonstrates that a subset of CSLD genes is essential for proper meristem maintenance, confirming the key role of walls in developmental pathways.
Published: 2016

13. Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies

Author: Jan Sklenar, Sophien Kamoun, Cécile Lorrain, Joe Win, Ksenia V. Krasileva, Sébastien Duplessis, Diane G. O. Saunders, Benjamin Petre, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), ANR (ANR-12-LABXARBRE-01, ANR-2010-JCJC-1709-01), European Project: 267196, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), The Sainsbury Laboratory [Norwich] (TSL), Gijzen, Mark, The Sainsbury Laboratory, John Innes Centre [Norwich], and The Genome Analysis Centre (TGAC)
Subjects: Cell Membranes, Nicotiana benthamiana, Plant Science, Pathogenesis, champignon phytopathogène, Pathology and Laboratory Medicine, Biochemistry, Tandem Mass Spectrometry, Protein Interaction Mapping, Aetiology, lcsh:Science, Liquid, Fungal protein, Microscopy, Confocal, Vegetal Biology, Effector, Plant Biochemistry, Microbiology and Parasitology, food and beverages, Plants, Microbiologie et Parasitologie, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Cellular Structures and Organelles, Infection, Cell Physiology, Imaging Techniques, In silico, Virulence, 03 medical and health sciences, Open Reading Frames, Botany, Genetics, Computer Simulation, RNA, Messenger, Grasses, Plant Diseases, lcsh:R, fungi, Organisms, Biology and Life Sciences, Plant, Plant Pathology, 030104 developmental biology, lcsh:Q, Biologie végétale, Cereal Crops, 0301 basic medicine, Leaves, [SDV]Life Sciences [q-bio], Messenger, lcsh:Medicine, Cell Fusion, Gene Expression Regulation, Plant, Medicine and Health Sciences, 2.1 Biological and endogenous factors, plante modèle, Pathogen, Triticum, 2. Zero hunger, Microscopy, Chromatography, Multidisciplinary, biology, Plant Anatomy, pipeline, Agriculture, Infectious Diseases, In Vivo Imaging, protéine, Confocal, Wheat, Host-Pathogen Interactions, Research Article, General Science & Technology, Green Fluorescent Proteins, Plant Pathogens, Crops, Research and Analysis Methods, Fungal Proteins, nicotiana benthamiana, Tobacco, effecteur moléculaire, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Enhancer, Basidiomycota, Gene Expression Profiling, Membrane Proteins, Cell Biology, biology.organism_classification, Plant Leaves, Gene Expression Regulation, puccinia striiformis f sp tritici, RNA, Heterologous expression, Chromatography, Liquid, Crop Science
Abstract: International audience; Rust fungal pathogens of wheat (Triticum spp.) affect crop yields worldwide. The molecular mechanisms underlying the virulence of these pathogens remain elusive, due to the limited availability of suitable molecular genetic research tools. Notably, the inability to perform high-throughput analyses of candidate virulence proteins (also known as effectors) impairs progress. We previously established a pipeline for the fast-forward screens of rust fungal candidate effectors in the model plant Nicotiana benthamiana. This pipeline involves selecting candidate effectors in silico and performing cell biology and protein-protein interaction assays in planta to gain insight into the putative functions of candidate effectors. In this study, we used this pipeline to identify and characterize sixteen candidate effectors from the wheat yellow rust fungal pathogen Puccinia striiformis f sp tritici. Nine candidate effectors targeted a specific plant subcellular compartment or protein complex, providing valuable information on their putative functions in plant cells. One candidate effector, PST02549, accumulated in processing bodies (P-bodies), protein complexes involved in mRNA decapping, degradation, and storage. PST02549 also associates with the P-body-resident ENHANCER OF mRNA DECAPPING PROTEIN 4 (EDC4) from N. benthamiana and wheat. We propose that P-bodies are a novel plant cell compartment targeted by pathogen effectors.
Published: 2016

14. A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis

Author: Christophe Godin, Teva Vernoux, Etienne Farcot, Géraldine Brunoud, Yassin Refahi, Alain Jean-Marie, Minna Pulkkinen, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory, University of Cambridge [UK] (CAM), University of Nottingham, UK (UON), Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire d'Etudes des Ressources Forêt-Bois (LERFoB), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Sainsbury Laboratory Cambridge University (SLCU), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Models for the performance analysis and the control of networks (MAESTRO), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), AgroParisTech, Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), HFSP grant RGP0054-2013 BioSensors (Human Frontier Science Program) to TV and CG, Inria Project Lab Morphogenetics and ANR-funded Institute of Computational Biology (IBC) to CG, Jan Traas’s ERC Morphodynamics & INRA CJS to YR, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Sainsbury Laboratory Cambridge, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: 0301 basic medicine, noise, croissance végétale, Stochastic modelling, QH301-705.5, permutations, Science, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Biology, Plant Development, Model system, multi-scale modeling, Biology, Models, Biological, modèle de croissance, General Biochemistry, Genetics and Molecular Biology, modèle stochastique, 03 medical and health sciences, phyllotaxis, Gene Expression Regulation, Plant, emergence, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biology (General), phyllotaxie, General Immunology and Microbiology, Ecology, General Neuroscience, Locality, General Medicine, Phyllotaxis, Biological noise, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Multicellular organism, Shoot apex, Plant development, 030104 developmental biology, Developmental Biology and Stem Cells, A. thaliana, inhibitory fields, Medicine, organogénèse, Biological system, Plant Shoots, Research Article
Abstract: Exploration of developmental mechanisms classically relies on analysis of pattern regularities. Whether disorders induced by biological noise may carry information on building principles of developmental systems is an important debated question. Here, we addressed theoretically this question using phyllotaxis, the geometric arrangement of plant aerial organs, as a model system. Phyllotaxis arises from reiterative organogenesis driven by lateral inhibitions at the shoot apex. Motivated by recurrent observations of disorders in phyllotaxis patterns, we revisited in depth the classical deterministic view of phyllotaxis. We developed a stochastic model of primordia initiation at the shoot apex, integrating locality and stochasticity in the patterning system. This stochastic model recapitulates phyllotactic patterns, both regular and irregular, and makes quantitative predictions on the nature of disorders arising from noise. We further show that disorders in phyllotaxis instruct us on the parameters governing phyllotaxis dynamics, thus that disorders can reveal biological watermarks of developmental systems. DOI: http://dx.doi.org/10.7554/eLife.14093.001, eLife digest Plants grow throughout their lifetime, forming new flowers and leaves at the tips of their stems through a patterning process called phyllotaxis, which occurs in spirals for a vast number of plant species. The classical view suggests that the positioning of each new leaf or flower bud at the tip of a growing stem is based on a small set of principles. This includes the idea that buds produce inhibitory signals that prevent other buds from forming too close to each other. When computational models of phyllotaxis follow these ‘deterministic’ principles, they are able to recreate the spiral pattern the buds form on a growing stem. In real plants, however, the spiral pattern is not always perfect. The observed disturbances in the pattern are believed to reflect the presence of random fluctuations – regarded as noise – in phyllotaxis. Here, using numerical simulations, Refahi et al. noticed that the patterns of inhibitory signals in a shoot tip pre-determine the locations of several competing sites where buds could form in a robust manner. However, random fluctuations in the way cells perceive these inhibitory signals could greatly disturb the timing of organ formation and affect phyllotaxis patterns. Building on this, Refahi et al. created a new computational model of bud patterning that takes into account some randomness in how cells perceive the inhibitory signals released by existing buds. The model can accurately recreate the classical spiral patterns of buds and also produces occasional disrupted patterns that are similar to those seen in real plants. Unexpectedly, Refahi et al. show that these ‘errors’ reveal key information about how the signals that control phyllotaxis might work. These findings open up new avenues of research into the role of noise in phyllotaxis. The model can be used to predict how altering the activities of genes or varying plant growth conditions might disturb this patterning process. Furthermore, the work highlights how the structure of disturbances in a biological system can shed new light on how the system works. DOI: http://dx.doi.org/10.7554/eLife.14093.002
Published: 2016

15. Analyses of pig genomes provide insight to porcine demography and evolution

Author: Ronan Kapetanovic, Patrice Dehais, Zhi-Qiang Du, Loretta Auvil, Ricardo H. Ramirez-Gonzalez, Kyung-Tai Lee, Patrick Chardon, Hiroyuki Kanamori, Gary A. Rohrer, Jianguo Zhang, Celine Chen, Simon D. M. White, Guojie Zhang, Jian Wang, Hyeonju Ahn, Ole Madsen, Miguel Pérez-Enciso, Richard Clark, Bruce R. Southey, Yasuhiro Takeuchi, Bronwen Aken, Bo Thomsen, Frank Panitz, Katie E. Fowler, Peter F. Stadler, Jennifer Harrow, Takeya Morozumi, Ryan Cheng, Christian Bendixen, Laurent A. F. Frantz, Yogesh Paudel, Sara Botti, Kellye Eversole, Jaebum Kim, Jian Ma, Matthew Jones, Jan Gorodkin, Zhi-Liang Hu, John C. Schwartz, Suneel Kumar Onteru, Tae-Hun Kim, Fioravante De Sapio, Nizar Drou, Stephen M. J. Searle, Wan Sheng Liu, Yingrui Li, Yao Lu, Thomas Faraut, Richard P. M. A. Crooijmans, Joan K. Lunney, Göran O. Sperber, Bert Dibbits, Denis Milan, Richard M. Leggett, Boris Capitanu, Xun Xu, Bertrand Servin, Megan Bystrom, Carol Scott, Kyle M. Schachtschneider, Bouabid Badaoui, Harris A. Lewin, Mirte Bosse, Sang-Haeng Choi, Yongming Sang, Jane Rogers, Patric Jern, Kerstin Howe, Sean Humphray, Henrik Hornshøj, Martien A. M. Groenen, Jerzy Jurka, James M. Reecy, Frank Blecha, Darren K. Griffin, Susan Fairley, Jonas Blomberg, Claire Rogel-Gaillard, Eung-Woo Park, Jonathan V. Sweedler, Hong-Seog Park, Stuart McLaren, Denise Carvalho-Silva, Christopher K. Tuggle, Géraldine Pascal, Rashmi Wali, Mario Caccamo, Katherine M. Mann, Lawrence B. Schook, C M Clee, James G. R. Gilbert, Christian Anthon, Merete Fredholm, Chankyu Park, Harry D. Dawson, Craig W. Beattie, Elisabetta Giuffra, Zhan Bujie, Kyu-Won Kim, Toby Hunt, Jae-Hwan Kim, Daniel Berman, Shuhong Zhao, Hakim Tafer, Jin-Tae Jeon, Sandra L. Rodriguez-Zas, Hendrik-Jan Megens, Linda Scobie, Jie Zhang, Alan Archibald, Joshua G. Schraiber, Jitendra Narayan, Alexander Hayward, Lucy Matthews, Lauretta A. Rund, Jane E. Loveland, Peixiang Ni, Denis M. Larkin, Song-Jung Oh, Dinh Truong Nguyen, Kyooyeol Lee, Lars Bolund, João Fadista, William Chow, Jun Wang, Hirohide Uenishi, Shengting Li, Eric Fritz, Heebal Kim, Geoffrey J. Faulkner, Martine Yerle, Michael P. Murtaugh, Max F. Rothschild, Carol Churcher, Greger Larson, Anna Anselmo, Laboratoire de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), The Genome Analysis Centre (TGAC), Parco Tecnologico Padano, CERSA, Department of Clinical Genetics, Odense University Hospital, The Wellcome Trust Sanger Institute [Cambridge], Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), Faculty of Life Sciences, Division of Genetics and Bioinformatics, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory [Hong Kong], The University of Hong Kong (HKU), Beijing Genomics Institute [Shenzhen] (BGI), Department of Biochemistry, University of Nijmegen, The Netherlands, University of Nijmegen, Molecular Carcinogenesis [Sutton], Institute of cancer research, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT), Canadian Light Source Inc., University of Saskatchewan [Saskatoon] (U of S), Department of Mechanical Engineering, University of Auckland, University of Auckland [Auckland], ANR-07-GANI-0001,DELISUS,An integrated study of the haplotypic variability at the whole genome level on animals finely phenotyped from French porcine populations(2007), European Project: LSHB-CT-2006-037377, European Project: 249894,EC:FP7:ERC,ERC-2009-AdG,SELSWEEP(2010), European Project: 38710,SABRE, European Project: 222664,EC:FP7:KBBE,FP7-KBBE-2007-2A,QUANTOMICS(2009), European Commission, European Research Council, Biotechnology and Biological Sciences Research Council (UK), Wellcome Trust, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université de Tours, Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: pig, Evolution, receptor, Molecular Sequence Data, Population Dynamics, Sus scrofa, sus-scrofa, Locus (genetics), Genomics, Biology, Animal Breeding and Genomics, Genome, Article, genomic, taste, 03 medical and health sciences, Phylogenetics, evolution, Genetics, Animals, animal, Fokkerij en Genomica, Domestication, gene, Gene, Phylogeny, Demography, 030304 developmental biology, 0303 health sciences, locus, variants, Multidisciplinary, Phylogenetic tree, [SDV.BA]Life Sciences [q-bio]/Animal biology, 0402 animal and dairy science, 04 agricultural and veterinary sciences, sequence, 040201 dairy & animal science, Models, Animal, WIAS, genetic, Selective sweep, complex
Abstract: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model., The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 249894 (SelSweep)
Published: 2012

16. MASCP Gator: An Aggregation Portal for the Visualization of Arabidopsis Proteomics Data

Author: Ian Castleden, Stefanie Wienkoop, Matthias Hirsch-Hoffmann, Hirofumi Nakagami, Klaas J. van Wijk, Sandra K. Tanz, Christophe Bruley, Norbert Rolland, Joshua L. Heazlewood, Sacha Baginsky, Steven P. Briggs, Wilhelm Gruissem, A. Harvey Millar, R R Schmidt, Katja Baerenfaller, Alexandra M. E. Jones, Hiren J. Joshi, Waltraud X. Schulze, Volker Egelhofer, Tetsuro Toyoda, Wolfram Weckwerth, Qi Sun, Joint BioEnergy Institute, Department of Biology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Department of plant Biology, Cornell University, Molecular Systems Biology, universite de Vienne, Laboratoire d'Etude de la Dynamique des Proteomes, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Université Grenoble Alpes (UGA), Laboratoire de physiologie cellulaire végétale (LPCV), 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), RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, The Sainsbury Laboratory, Sainsbury Laboratory, Division of Biology, University of California [San Diego] (UC San Diego), University of California-University of California, Centre of Excellence for Computational Systems Biology, The University of Western Australia (UWA), Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, Cornell University [New York], Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), 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), The Sainsbury Laboratory [Norwich] (TSL), University of California (UC)-University of California (UC), U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231], AGRON-OMICS [LSHG-CT-2006-037704], Australian Research Council, Australian Research Council Centre of Excellence in Plant Energy Biology, Ministry of Education, Culture, Sports, Science and Technology [21770059], Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and 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)
Subjects: 0106 biological sciences, Bioinformatics, Physiology, Research areas, Arabidopsis, plant, Plant Science, Proteomics, 01 natural sciences, World Wide Web, User-Computer Interface, 03 medical and health sciences, proteomics, Resource (project management), online resources, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Phosphorylation, Databases, Protein, database, 030304 developmental biology, Internet, 0303 health sciences, biology, Arabidopsis Proteins, business.industry, data mining, Hyperlink, biology.organism_classification, Visualization, Identification (information), information networks, aggregator, The Internet, business, Protein Kinases, 010606 plant biology & botany
Abstract: Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (H.J.J., J.L.H.); Department of Biology, Eidgenossisch Technische Hochschule Zurich, CH-8092 Zurich, Switzerland (M. H.-H., K. B., W. G.); Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S. B.); Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (R. S., W. X. S.); Department of Plant Biology, Cornell University, Ithaca, New York 14853 (Q. S., K.J.v.W.); Molecular Systems Biology, University of Vienna, 1090 Vienna, Austria (V. E., S. W., W. W.); Institut National de la Sante et de la Recherche Medicale, Laboratoire d'Etude de la Dynamique des Proteomes, U880, F-38000 Grenoble, France (C. B.); Commissariat a l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38000 Grenoble, France (C.B., N.R.); Universite Joseph Fourier, F-38000 Grenoble, France (C. B., N.R.); CNRS, Laboratoire de Physiologie Cellulaire Vegetale, UMR5168, F-38000 Grenoble, France (N.R.); INRA, UMR1200, F-38000 Grenoble, France (N.R.); RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Tsurumi-ku, Yokohama 230-0045, Japan (T.T., H.N.); The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (A.M.J.); Division of Biology, University of California San Diego, La Jolla, California 92093 (S.P.B.); and Centre of Excellence for Computational Systems Biology (I.C.) and Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (I.C., S.K.T., A.H.M.), University of Western Australia, Crawley 6009, Western Australia, Australia
Published: 2010

17. Plants, fungi and oomycetes: a 400-million year affair that shapes the biosphere

Author: Sophien Kamoun, Paul Kenrick, Francis Martin, Christine Strullu-Derrien, Marc-André Selosse, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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), Department of Earth Sciences [NHM London] (DES-NHM), The Natural History Museum [London] (NHM), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Norwich Research Park, The Sainsbury Laboratory [Norwich] (TSL), Laboratoire d'Excellence ARBRE, ANR-11-LABX-0002-01 Laboratoire d'Excellence BCDiv., European Project: 298735, Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Physiology, DIVERSITY, EFFECTOR, Plant Science, Biology, co-evolution, RHYNIE CHERT, 01 natural sciences, 10(th) New Phytologist Workshop, 03 medical and health sciences, ATMOSPHERIC OXYGEN, Mycorrhizal fungi, Botany, Oomycota, LAND PLANTS, terrestrialization, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 0303 health sciences, GENOME EVOLUTION, Atmospheric oxygen, Ecology, plants, Biosphere, biogeochemical cycles, LINEAGE, POTATO FAMINE PATHOGEN, Eumycota, plant-fungal interactions, MYCORRHIZAL FUNGI, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, CARBON-CYCLE, 010606 plant biology & botany, Rhynie chert
Abstract: absent
Published: 2015

18. A snapshot of molecular plant-microbe interaction research

Author: Artemis Giannakopoulou, Clément Pellegrin, Rainer Boni, Sebastian Wittulsky, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), Molecular Plant Biology and Phytopathology Department, Institute of Plant Biology, University of Zurich, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: Physiology, Ecology, diagnosis, plant-pathogen interaction, receptor, [SDV]Life Sciences [q-bio], Arms race, Plant microbe, Environmental ethics, Translational research, Plant Science, Biology, symbiosis, mycorrhizal fungi, resistance, effector, translational research, Mycorrhizal fungi, International congress, Snapshot (computer storage)
Abstract: Plants and microbes are in a continuous arms race to maintain their predominance within their particular niche. Understanding the complexity of these plant–microbe interactions is of utmost importance as it can provide new insights into the mechanisms mediating disease processes and in turn inspire new plant breeding strategies. The International Society for Molecular Plant–Microbe Interactions (IS-MPMI) invited scientists from around the world to share their findings during the XVI International Congress on Molecular Plant–Microbe Interactions, which was held on the beautiful island of Rhodes in Greece (Fig. 1). The congress was organized by the Agricultural University of Athens, the Hellenic Phytopathology Society, and the Hellenic Society of Phytiatry and provided over 1100 participants from 55 countries with the opportunity to present and discuss their current and future research. A great number of talks and posters were presented, however our aim within this report is to provide a snapshot of the discipline by focusing on just some of the exciting research and discussions which took place. The key topics discussed were virulence factors, epigenetic regulation, hormones, symbiosis factors, toxins, signaling pathways, microbe recognition, immunity, and pathogen diagnostics. Effector biology was also a recurrent theme in many plenary and concurrent sessions, indicating the importance of a topic that was also highlighted recently by a Virtual Special Issue in New Phytologist (see Kuhn & Panstruga, 2014). In addition to this, throughout the meeting next generation sequencing (NGS) techniques were described and shown to be shedding new light on long-standing issues in microbial ecology.
Published: 2015

19. The Control of Growth Symmetry Breaking in the Arabidopsis Hypocotyl

Author: Herman Höfte, Alexis Peaucelle, Raymond Wightman, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), and Sainsbury Laboratory
Subjects: media_common.quotation_subject, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, Microscopy, Atomic Force, Asymmetry, Microtubules, Models, Biological, General Biochemistry, Genetics and Molecular Biology, Cell wall, 03 medical and health sciences, 0302 clinical medicine, Cell Wall, Botany, Tip growth, Symmetry breaking, Anisotropy, media_common, 030304 developmental biology, 0303 health sciences, Esterification, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Isotropy, Hypocotyl, Biomechanical Phenomena, Anisotropic cell growth, Biophysics, Pectins, General Agricultural and Biological Sciences, Cortical microtubule, 030217 neurology & neurosurgery
Abstract: in press; Complex shapes in biology depend on the ability of cells to shift from isotropic to anisotropic growth during development. In plants, this growth symmetry breaking reflects changes in the extensibility of the cell walls. The textbook view is that the direction of turgor-driven cell expansion depends on the cortical microtubule (CMT)-mediated orientation of cellulose microfibrils [1, 2]. Here, we show that this view is incomplete at best. We used atomic force microscopy (AFM) to study changes in cell-wall mechanics associated with growth symmetry breaking within the hypocotyl epidermis. We show that, first, growth symmetry breaking is preceded by an asymmetric loosening of longitudinal, as compared to transverse, anticlinal walls, in the absence of a change in CMT orientation. Second, this wall loosening is triggered by the selective de-methylesterification of cell-wall pectin in longitudinal walls, and, third, the resultant mechanical asymmetry is required for the growth symmetry breaking. Indeed, preventing or promoting pectin de-methylesterification, respectively, increased or decreased the stiffness of all the cell walls, but in both cases reduced the growth anisotropy. Finally, we show that the subsequent CMT reorientation contributes to the consolidation of the growth axis but is not required for the growth symmetry breaking. We conclude that growth symmetry breaking is controlled at a cellular scale by bipolar pectin de-methylesterification, rather than by the cellulose-dependent mechanical anisotropy of the cell walls themselves. Such a cell asymmetry-driven mechanism is comparable to that underlying tip growth in plants [3] but also anisotropic cell growth in animal cells [4].
Published: 2015

20. Effector proteins of rust fungi

Author: S. Duplessis, Benjamin Petre, David L. Joly, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory, Université de Moncton, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and Sainsbury Laboratory Cambridge
Subjects: MESH: Epitopes, [SDV]Life Sciences [q-bio], Rust (fungus), Virulence, Genomics, Plant Science, Biology, lcsh:Plant culture, Pucciniales, Mini Review Article, transcriptomics, MESH: Electrophoresis, Paper, Botany, MESH: Antibodies, Bacterial, genomics, MESH: Glycolipids, MESH: Species Specificity, lcsh:SB1-1110, MESH: Polysaccharides, Bacterial, MESH: Salmonella, Genetics, Obligate, Effector, Host (biology), MESH: Hexosamines, MESH: Molecular Weight, effectoromics, MESH: Chromatography, Gas, MESH: Hemagglutination, food and beverages, MESH: Salmonella typhimurium, biology.organism_classification, MESH: Fatty Acids, carbohydrates (lipids), rust fungi, MESH: Chromatography, Thin Layer, Pucciniaceae, lipids (amino acids, peptides, and proteins), Function (biology), MESH: Immunodiffusion
Abstract: International audience; It has been assumed in the past that the lipid moieties of endotoxic lipopolysaccharides are quite similar if not identical. This has been tested in the reported work here, where the chemical composition and biological activities of the glycolipids of two heptoseless Re mutants, Salmonella minnesota R595 and Salmonella typhimurium SL1102, have been studied and compared. The two glycolipids, extracted with chloroform-methanol (4:1), showed identical thin-layer chromatographic patterns. The molar ratios for hexosamine, fatty acids, phosphorus, 2-keto-3-deoxyoctonate, total amines, and total nitrogen of the purified glycolipids were in the same range, but small differences could be established. Both glycolipids contained the same major fatty acids, i.e., lauric, myristic, palmitic, and 3-hydroxymyristic acids, in similar but not identical ratios. On paper electrophoresis, the acid hydrolysates of the two glycolipids showed analogous components. In the determination of molecular weight, whereas S. minnesota R595 glycolipid did not show concentration dependence, the molecular weight measured for S. typhimurium SL1102 increased with its concentration. The molecular weight of the fully endotoxic R595 glycolipid has been found to be 17,000 +/- 1,500. Both glycolipids showed similar activities in the Shwartzman skin reaction, Limulus-lysate clotting assay, mouse lethality, and enhancement of nonspecific resistance, but the R595 preparation appeared to be more active on a weight basis in some parameters than SL1102. Using passive hemagglutination, we observed cross-reactivity between the glycolipids. In the gel-diffusion test, they revealed clear identity. The antiserum against S. minnesota R595 neutralized the Shwartzman skin reactivity not only of R595 but also of SL1102 glycolipid. These results confirm that there are identical immunodeterminant group(s) in the two glycolipids. On the other hand, chemical analytical data for two glycolipids showed only similarities, indicating that although both glycolipids are of comparable chemical nature, differences between them exist.
Published: 2014

21. Subcellular and supracellular mechanical stress prescribes cytoskeleton behavior in Arabidopsis cotyledon pavement cells

Author: Henrik Jönsson, Elliot M. Meyerowitz, Pawel Krupinski, Olivier Hamant, Pascale Milani, Alexandre Berquand, Raymond Wightman, Arun Sampathkumar, Arezki Boudaoud, Division of Biology and Biological Engineering, Howard Hughes Medical Institute (HHMI), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Lund University [Lund], Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Bruker Nano GmbH, Bruker AXS, Partenaires INRAE, Sainsbury Lab, Norwich Research Park, California Institute of Technology (CALTECH), Howard Hughes Medical Institute, Gordon and Betty Moore Foundation [GBMF3406], Gatsby Charitable Foundation, US Department of Energy [DE-FG02-88ER13873], Agence Nationale de la Recherche [ANR-10-BLAN-1516], European Research Council [307387], Swedish Research Council, Crafoord Foundation, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), The Sainsbury Laboratory [Norwich] (TSL), Wightman, Raymond [0000-0003-1295-4875], Jonsson, Henrik [0000-0003-2340-588X], and Apollo - University of Cambridge Repository
Subjects: computational modeling, Time Factors, [SDV]Life Sciences [q-bio], Cell, Turgor pressure, GROWTH ANISOTROPY, Arabidopsis, Plant Biology, Microscopy, Atomic Force, Mechanotransduction, Cellular, Microtubules, Biology (General), Cytoskeleton, Feedback, Physiological, Pavement cells, Microscopy, Video, ORGANOGENESIS, CORTICAL MICROTUBULES, General Neuroscience, cytoskeleton, General Medicine, POSITIONAL INFORMATION, medicine.anatomical_structure, Medicine, biomechanic, SHOOT APICAL MERISTEM, Cotyledon, CELLULOSE SYNTHASE, Research Article, microtubule, QH301-705.5, Science, FUNCTIONAL ASSOCIATION, KATANIN, Biology, Models, Biological, General Biochemistry, Genetics and Molecular Biology, biomechanics, FORCE, Stress (mechanics), Cell wall, Microtubule, Botany, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Computer Simulation, Cell Shape, General Immunology and Microbiology, ORIENTATION, Cell Biology, Plant cell, Biophysics, cell wall, Stress, Mechanical
Abstract: Although it is a central question in biology, how cell shape controls intracellular dynamics largely remains an open question. Here, we show that the shape of Arabidopsis pavement cells creates a stress pattern that controls microtubule orientation, which then guides cell wall reinforcement. Live-imaging, combined with modeling of cell mechanics, shows that microtubules align along the maximal tensile stress direction within the cells, and atomic force microscopy demonstrates that this leads to reinforcement of the cell wall parallel to the microtubules. This feedback loop is regulated: cell-shape derived stresses could be overridden by imposed tissue level stresses, showing how competition between subcellular and supracellular cues control microtubule behavior. Furthermore, at the microtubule level, we identified an amplification mechanism in which mechanical stress promotes the microtubule response to stress by increasing severing activity. These multiscale feedbacks likely contribute to the robustness of microtubule behavior in plant epidermis. DOI: http://dx.doi.org/10.7554/eLife.01967.001, eLife digest The surfaces of plants are covered in epithelial cells that come in many different shapes, suggesting that individual cells must have some control over their own shape. An unusually shaped epithelial cell is the pavement cell, which looks like a jigsaw puzzle piece and is found in the leaves of many flowering plants. Relatively little was known about the exact contribution of mechanical properties of the wall to this shape. Furthermore, although it was known that parts of pavement cells are rich in microtubules—tubes of protein that act as a scaffold inside the cell— the possibility that shape impacts the behavior of microtubules was not fully addressed. Now, using a combination of computer modelling and experiments, Sampathkumar et al. reveal that the shape of the pavement cells relies in part on the response of the microtubules to stress. In an individual cell, microtubules align along the direction of the largest stress, with a protein severing those microtubules that are not aligned in this direction. As the stress inside a cell is determined in part by the cell’s shape, this sets up a feedback loop: the stress resulting from the cell shape aligns the microtubules that reinforce the cell wall, thus maintaining the shape of the cell. An external stress applied to the epithelium can override this internal stress. Because all of the plant cells are under turgor pressure from the inside, pressure from the outside, like squeezing a balloon, changes the stress pattern, causing the realignment of the microtubules so as to resist the new stress. This shows that the microtubules respond to local stresses within a cell, and are continually responsive to stress changes. DOI: http://dx.doi.org/10.7554/eLife.01967.002
Published: 2014

22. EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics

Author: Eric Kemen, Jonathan D. G. Jones, Ghanasyam Rallapalli, Kee Hoon Sohn, Cécile Segonzac, Graham J Etherington, Dan MacLean, Alexandre Robert-Seilaniantz, The Sainsbury Laboratory (TSL), Max Planck Institute for Plant Breeding Research (MPIPZ), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institute of Agriculture and Environment, Gatsby Charitable foundation, Dorothy Hodgkin Postgraduate award, The Sainsbury Laboratory [Norwich] (TSL), Jones, Jonathan D. G., AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: DNA, Complementary, [SDV]Life Sciences [q-bio], Tag-seq, Arabidopsis, Down-Regulation, RNA-Seq, Biology, EXPRSS, DNA sequencing, 03 medical and health sciences, Complementary DNA, Next generation sequencing, Genetics, High throughput expression profiling, Genomic library, RNA, Messenger, 3' Untranslated Regions, RNA-seq, Gene Library, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, 0303 health sciences, Sequence Analysis, RNA, Three prime untranslated region, Gene Expression Profiling, Methodology Article, 030302 biochemistry & molecular biology, Computational Biology, High-Throughput Nucleotide Sequencing, Up-Regulation, Gene expression profiling, Restriction enzyme, DNA microarray, Biotechnology
Abstract: Background Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and requires 10–20 times more reads than a typical Tag-seq. Most existing Tag-seq methods either have biases or not high throughput due to use of restriction enzymes or enzymatic manipulation of 5’ ends of mRNA or use of RNA ligations. Results We have developed EXpression Profiling through Randomly Sheared cDNA tag Sequencing (EXPRSS) that employs acoustic waves to randomly shear cDNA and generate sequence tags at a relatively defined position (~150-200 bp) from the 3′ end of each mRNA. Implementation of the method was verified through comparative analysis of expression data generated from EXPRSS, NlaIII-DGE and Affymetrix microarray and through qPCR quantification of selected genes. EXPRSS is a strand specific and restriction enzyme independent tag sequencing method that does not require cDNA length-based data transformations. EXPRSS is highly reproducible, is high-throughput and it also reveals alternative polyadenylation and polyadenylated antisense transcripts. It is cost-effective using barcoded multiplexing, avoids the biases of existing SAGE and derivative methods and can reveal polyadenylation position from paired-end sequencing. Conclusions EXPRSS Tag-seq provides sensitive and reliable gene expression data and enables high-throughput expression profiling with relatively simple downstream analysis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-341) contains supplementary material, which is available to authorized users.
Published: 2014

23. Natural variation in seed very long chain fatty acid content is controlled by a new isoform of KCS18 in [i]Arabidopsis thaliana[/i]

Author: Olivier Loudet, Sylvain Raffaele, Marine Froissard, Alain Lécureuil, Sophie Jasinski, Martine Miquel, Philippe Guerche, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, The Sainsbury Laboratory (TSL), 'Genetique et Amelioration des Plantes' department of INRA, 'Biologie Vegetale' department of INRA, and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: 0106 biological sciences, Candidate gene, Heredity, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, lcsh:Medicine, Plant Science, Plant Genetics, Biochemistry, 01 natural sciences, chemistry.chemical_compound, Plant Genomics, Protein Isoforms, lcsh:Science, 2. Zero hunger, Genetics, chemistry.chemical_classification, 0303 health sciences, education.field_of_study, Multidisciplinary, biology, Fatty Acids, Chromosome Mapping, food and beverages, Plants, Lipids, Phenotypes, Phenotype, Seeds, Fatty acid elongation, Research Article, Arabidopsis Thaliana, Genotypes, Quantitative Trait Loci, Very long chain fatty acid, Population, Quantitative trait locus, Chromosomes, Plant, 03 medical and health sciences, Model Organisms, Plant and Algal Models, 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase, Point Mutation, education, Biology, Crosses, Genetic, Genetic Association Studies, 030304 developmental biology, Quantitative Traits, Complex Traits, Arabidopsis Proteins, lcsh:R, Fatty acid, Lipid Metabolism, biology.organism_classification, Protein Structure, Tertiary, Amino Acid Substitution, chemistry, lcsh:Q, Oils, 010606 plant biology & botany
Abstract: Oil from oleaginous seeds is mainly composed of triacylglycerols. Very long chain fatty acids (VLCFAs) are major constituents of triacylglycerols in many seed oils and represent valuable feedstock for industrial purposes. To identify genetic factors governing natural variability in VLCFA biosynthesis, a quantitative trait loci (QTL) analysis using a recombinant inbred line population derived from a cross between accessions Bay-0 and Shahdara was performed in Arabidopsis thaliana. Two fatty acid chain length ratio (CLR) QTL were identified, with one major locus, CLR. 2, accounting for 77% of the observed phenotypic variation. A fine mapping and candidate gene approach showed that a key enzyme of the fatty acid elongation pathway, the beta-ketoacyl-CoA synthase 18 (KCS18), was responsible for the CLR. 2 QTL detected between Bay-0 and Shahdara. Association genetics and heterologous expression in yeast cells identified a single point mutation associated with an alteration of KCS18 activity, uncovering the molecular bases for the modulation of VLCFA content in these two natural populations of Arabidopsis. Identification of this kcs18 mutant with altered activity opens new perspectives for the modulation of oil composition in crop plants. Citation: Jasinski S, Lecureuil A, Miquel M, Loudet O, Raffaele S, et al. (2012) Natural Variation in Seed Very Long Chain Fatty Acid Content Is Controlled by a New Isoform of KCS18 in Arabidopsis thaliana. PLoS ONE 7(11): e49261. doi:10.1371/journal.pone.0049261
Published: 2012

24. Genome evolution in filamentous plant pathogens: why bigger can be better

Author: Sophien Kamoun, Sylvain Raffaele, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory, John Innes Centre [Norwich], Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: 0106 biological sciences, Genome evolution, Virulence Factors, Virulence, Bacterial genome size, Biology, 01 natural sciences, Microbiology, Genome, Evolution, Molecular, 03 medical and health sciences, plante pathogène, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genome size, Gene, 030304 developmental biology, Plant Diseases, 2. Zero hunger, Genetics, 0303 health sciences, General Immunology and Microbiology, Host (biology), Fungi, Infectious Diseases, Host-Pathogen Interactions, évolution du génome, Genome, Fungal, 010606 plant biology & botany
Abstract: Many species of fungi and oomycetes are plant pathogens of great economic importance. Over the past 7 years, the genomes of more than 30 of these filamentous plant pathogens have been sequenced, revealing remarkable diversity in genome size and architecture. Whereas the genomes of many parasites and bacterial symbionts have been reduced over time, the genomes of several lineages of filamentous plant pathogens have been shaped by repeat-driven expansions. In these lineages, the genes encoding proteins involved in host interactions are frequently polymorphic and reside within repeat-rich regions of the genome. Here, we review the properties of these adaptable genome regions and the mechanisms underlying their plasticity, and we illustrate cases in which genome plasticity has contributed to the emergence of new virulence traits. We also discuss how genome expansions may have had an impact on the co-evolutionary conflict between these filamentous plant pathogens and their hosts.
Published: 2012

25. A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula

Author: Kira Gysel, Feng Feng, Simona Radutoiu, Zoltan Bozsoki, Giles E. D. Oldroyd, Kasper R. Andersen, Mikkel B. Thygesen, Sébastien Fort, Jongho Sun, Guru V. Radhakrishnan, Aleksander Gavrin, Jens Stougaard, Tak Lee, Feng, Feng [0000-0003-1382-305X], Radhakrishnan, Guru V [0000-0003-0381-8804], Lee, Tak [0000-0001-7008-7605], Fort, Sébastien [0000-0002-6133-9900], Gavrin, Aleksander [0000-0003-0179-8491], Gysel, Kira [0000-0003-4245-9998], Thygesen, Mikkel B [0000-0002-0158-2802], Andersen, Kasper Røjkjær [0000-0002-4415-8067], Stougaard, Jens [0000-0002-9312-2685], Oldroyd, Giles ED [0000-0002-5245-6355], Apollo - University of Cambridge Repository, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Aarhus University [Aarhus], Centre de Recherches sur les Macromolécules Végétales (CERMAV ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), University of Copenhagen = Københavns Universitet (KU), and Oldroyd, Giles E D [0000-0002-5245-6355]
Subjects: 0106 biological sciences, 0301 basic medicine, Lipopolysaccharides, General Physics and Astronomy, Oligosaccharides, Chitin, 01 natural sciences, Plant Roots, Cell Wall, Gene Expression Regulation, Plant, Mycorrhizae, Plant symbiosis, Plant Immunity, Arbuscular mycorrhiza, lcsh:Science, Plant Proteins, Regulation of gene expression, Multidisciplinary, biology, Cell Death, Kinase, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Medicago truncatula, Cell biology, 3. Good health, Signalling, Signal Transduction, Science, Protein Serine-Threonine Kinases, Article, General Biochemistry, Genetics and Molecular Biology, Cell wall, 03 medical and health sciences, Symbiosis, Tobacco, Pattern recognition receptors in plants, Chitosan, fungi, General Chemistry, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Plant Leaves, 030104 developmental biology, lcsh:Q, Function (biology), [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, 010606 plant biology & botany
Abstract: Plants associate with beneficial arbuscular mycorrhizal fungi facilitating nutrient acquisition. Arbuscular mycorrhizal fungi produce chitooligosaccharides (COs) and lipo-chitooligosaccharides (LCOs), that promote symbiosis signalling with resultant oscillations in nuclear-associated calcium. The activation of symbiosis signalling must be balanced with activation of immunity signalling, which in fungal interactions is promoted by COs resulting from the chitinaceous fungal cell wall. Here we demonstrate that COs ranging from CO4-CO8 can induce symbiosis signalling in Medicago truncatula. CO perception is a function of the receptor-like kinases MtCERK1 and LYR4, that activate both immunity and symbiosis signalling. A combination of LCOs and COs act synergistically to enhance symbiosis signalling and suppress immunity signalling and receptors involved in both CO and LCO perception are necessary for mycorrhizal establishment. We conclude that LCOs, when present in a mix with COs, drive a symbiotic outcome and this mix of signals is essential for arbuscular mycorrhizal establishment., Polysaccharide molecules chitooligosaccharides (COs) and peptidoglycan not only activate plant immunity but also trigger plant symbiosis signalling. Here the authors show that a combination of COs and lipochitooligosaccharides (LCOs) act synergistically to suppress immunity and promote symbiosis to facilitate beneficial fungal associations.
Published: 2019

26. Chaperone-like protein DAY plays critical roles in photomorphogenesis

Author: Sung Hee Lee, Hee-Kyung Ahn, Tak Lee, Insuk Lee, Hyun Sook Pai, Ilyeong Choi, Dong Hye Seo, Ji Woo Kim, Ho Seok Lee, Huikyong Cho, Jae Hee Kim, Julian Bünting, Young Eun Jeon, Youssef Belkhadir, D. Lee, Tae Wuk Kim, Jung Min Lee, Man Ho Oh, Ahn, Hee-Kyung [0000-0002-8884-0156], Lee, Tak [0000-0001-7008-7605], Lee, Du-Hwa [0000-0003-4106-7730], Lee, Insuk [0000-0003-3146-6180], Belkhadir, Youssef [0000-0001-7149-7139], Pai, Hyun-Sook [0000-0003-1345-5840], Apollo - University of Cambridge Repository, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Yonsei University Seoul, Korea, University of East Anglia [Norwich] (UEA), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), College of Life Sciences and Biotechnology, Korea University, Chungnam National University (CNU), Hanyang University, Vienna Biocenter - VBC [Austria], and Yonsei University
Subjects: 0106 biological sciences, 0301 basic medicine, Chlorophyll, Chloroplasts, Light, [SDV]Life Sciences [q-bio], Arabidopsis, General Physics and Astronomy, 631/449/2653/1359, 01 natural sciences, chemistry.chemical_compound, 38/1, Gene Expression Regulation, Plant, Morphogenesis, Brassinosteroid, RNA-Seq, 14/19, 13/89, Multidisciplinary, biology, Chemistry, article, Plant morphogenesis, Plant physiology, food and beverages, Plants, Genetically Modified, Recombinant Proteins, Cell biology, Chloroplast, Transmembrane domain, Gene Knockdown Techniques, Photomorphogenesis, 38/39, Microtubule-Associated Proteins, Signal Transduction, Science, 38/90, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Brassinosteroids, Etiolation, Light responses, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Endomembrane system, 14/35, 631/449/2686, Arabidopsis Proteins, fungi, Membrane Proteins, General Chemistry, HSP40 Heat-Shock Proteins, 030104 developmental biology, Seedlings, Chaperone (protein), Mutation, 14/63, biology.protein, Protein Kinases, Biogenesis, 010606 plant biology & botany
Abstract: Photomorphogenesis, light-mediated development, is an essential feature of all terrestrial plants. While chloroplast development and brassinosteroid (BR) signaling are known players in photomorphogenesis, proteins that regulate both pathways have yet to be identified. Here we report that DE-ETIOLATION IN THE DARK AND YELLOWING IN THE LIGHT (DAY), a membrane protein containing DnaJ-like domain, plays a dual-role in photomorphogenesis by stabilizing the BR receptor, BRI1, as well as a key enzyme in chlorophyll biosynthesis, POR. DAY localizes to both the endomembrane and chloroplasts via its first transmembrane domain and chloroplast transit peptide, respectively, and interacts with BRI1 and POR in their respective subcellular compartments. Using genetic analysis, we show that DAY acts independently on BR signaling and chlorophyll biogenesis. Collectively, this work uncovers DAY as a factor that simultaneously regulates BR signaling and chloroplast development, revealing a key regulator of photomorphogenesis that acts across cell compartments., Chloroplast development and brassinosteroid (BR) signaling both regulate plant photomorphogenesis. Here the authors show that DAY, a DnaJ-like domain-containing membrane protein, regulates both processes by binding and stabilizing both BRI1, the BR receptor, and POR, a key enzyme in chlorophyll biosynthesis.
Published: 2021
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27. What is quantitative plant biology?

Author: Autran, Daphné, Bassel, George W., Chae, Eunyoung, Ezer, Daphne, Ferjani, Ali, Fleck, Christian, Hamant, Olivier, Hartmann, Félix P., Jiao, Yuling, Johnston, Iain G., Kwiatkowska, Dorota, Lim, Boon L., Mahönen, Ari Pekka, Morris, Richard J., Mulder, Bela M., Nakayama, Naomi, Sozzani, Ross, Strader, Lucia C., Ten Tusscher, Kirsten, Ueda, Minako, Wolf, Sebastian, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Birmingham [Birmingham], National University of Singapore (NUS), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Tokyo Gakugei University, University of Freiburg [Freiburg], Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), University of Chinese Academy of Sciences [Beijing] (UCAS), University of Bergen (UiB), Silesian University in Opava, The University of Hong Kong (HKU), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, John Innes Centre [Norwich], FOM Institute for Atomic and Molecular Physics (AMOLF), Imperial College London, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Utrecht University [Utrecht], Tohoku University [Sendai], Universität Heidelberg [Heidelberg], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Biotechnology and Biological Sciences Research Council (BBSRC), and Universität Heidelberg [Heidelberg] = Heidelberg University
Subjects: 0106 biological sciences, 0301 basic medicine, Computer science, biology, Ecology (disciplines), Rehabilitation, biomathematics, Physical Therapy, Sports Therapy and Rehabilitation, General Medicine, Plant, Plant biology, 01 natural sciences, Data science, Field (computer science), 03 medical and health sciences, 030104 developmental biology, Robustness (computer science), Citizen science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Noise (video), quantitative plant biology, Topology (chemistry), 010606 plant biology & botany, Interdisciplinarity
Abstract: Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.
Published: 2021

28. Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process

Author: Jan Sklenar, Yasin F. Dagdas, Silke Robatzek, Sophien Kamoun, Joe Win, Rosa Lozano-Durán, Jack H. Vossen, Benjamin Petre, Mauricio P Contreras, Alexandra M. E. Jones, Ahmed Abd-El-Haliem, Sebastian Schornack, Frank L.H. Menke, Roger Castells-Graells, Tolga O. Bozkurt, Martin H. Schattat, The Sainsbury Laboratory [Norwich] (TSL), and Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Plant Biology, Nicotiana benthamiana, Plant Science, 0601 Biochemistry and Cell Biology, 01 natural sciences, Interactome, 2.1 Biological and endogenous factors, Protein Interaction Maps, Aetiology, Pathogen, Plant Proteins, 0303 health sciences, Effector, food and beverages, Cell biology, Infectious Diseases, Host-Pathogen Interactions, Phytophthora infestans, Infection, SNARE Proteins, Endosome, Immunoprecipitation, Large-Scale Biology Articles, Plant Biology & Botany, 0607 Plant Biology, Endosomes, Biology, 03 medical and health sciences, Tobacco, Genetics, Life Science, Transport Vesicles, SB, 030304 developmental biology, Plant Diseases, 0604 Genetics, Host (biology), Cell Membrane, fungi, QK, Proteins, Cell Biology, biology.organism_classification, QR, Plant Breeding, 030104 developmental biology, Biochemistry and Cell Biology, Function (biology), 010606 plant biology & botany
Abstract: Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by co-immunoprecipitation (co-IP) and liquid chromatography tandem mass spectrometry (LC-MS/MS). This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and co-localize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. We anticipate that the interactome dataset we generated will serve as a useful community resource for functional studies of P. infestans effectors and of effector-targeted host processes.
Published: 2021

29. The molecular signatures of compatible and incompatible pollination in Arabidopsis

Author: Frédérique Rozier, Jonathan Legrand, Martine Da Rocha, Jérémy Just, Thierry Gaude, Antoine Larrieu, Isabelle Fobis-Loisy, Lucie Riglet, Chie Kodera, Fobis-Loisy, Isabelle [0000-0003-4522-2515], Apollo - University of Cambridge Repository, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Ecole normale supérieure de Lyon (Ens Lyon), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Nice Sophia Antipolis (1965 - 2019) (UNS), University of Leeds, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), and ANR-14-CE11-0021,Invader,Réponse des épidermes végétaux aux intrusions cellulaires(2014)
Subjects: 0106 biological sciences, incompatible pollination, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Pollination, Pollen-stigma interaction, [SDV]Life Sciences [q-bio], Arabidopsis, Single-nucleotide polymorphism, QH426-470, medicine.disease_cause, 01 natural sciences, Transcriptome, 03 medical and health sciences, Pollen, medicine, Genetics, Arabidopsis thaliana, Gene, 030304 developmental biology, 0303 health sciences, PTI pathway, biology, Compatible / incompatible pollination, food and beverages, Compatible, RNA sequencing, biology.organism_classification, Male-female transcriptome, DNA microarray, TP248.13-248.65, Research Article, 010606 plant biology & botany, Biotechnology, SNPs
Abstract: Background Fertilization in flowering plants depends on the early contact and acceptance of pollen grains by the receptive papilla cells of the stigma. Deciphering the specific transcriptomic response of both pollen and stigmatic cells during their interaction constitutes an important challenge to better our understanding of this cell recognition event. Results Here we describe a transcriptomic analysis based on single nucleotide polymorphisms (SNPs) present in two Arabidopsis thaliana accessions, one used as female and the other as male. This strategy allowed us to distinguish 80% of transcripts according to their parental origins. We also developed a tool which predicts male/female specific expression for genes without SNP. We report an unanticipated transcriptional activity triggered in stigma upon incompatible pollination and show that following compatible interaction, components of the pattern-triggered immunity (PTI) pathway are induced on the female side. Conclusions Our work unveils the molecular signatures of compatible and incompatible pollinations both at the male and female side. We provide invaluable resource and tools to identify potential new molecular players involved in pollen-stigma interaction.
Published: 2021
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30. A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

Author: Laetitia Vachez, Elliot M. Meyerowitz, Jan Traas, Argyris Zardilis, Yassin Refahi, Gael Michelin, Pradeep Das, Henrik Jönsson, Christophe Godin, Emmanuel Faure, Nathanaël Prunet, Feng Zhao, Jonathan Legrand, Bruno Leggio, Raymond Wightman, Grégoire Malandain, Anne Evodie Risson, Alessia Armezzani, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Cambridge [UK] (CAM), Fractionnement des AgroRessources et Environnement (FARE), Université de Reims Champagne-Ardenne (URCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Morphologie et Images (MORPHEME), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Image & Interaction (ICAR), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Caltech Department of Astronomy [Pasadena], California Institute of Technology (CALTECH), University of California [Los Angeles] (UCLA), University of California (UC), Sainsbury Laboratory Cambridge University (SLCU), Simulation et Analyse de la morphogenèse in siliCo (MOSAIC), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Lund University [Lund], ERC grant morphogenetics17-CAPS-0006-01Gene2Shape ERACAPS via BBSRCBB/S004645/1Gene2Shape ERACAPS via the U.S. National Science Foundation Division of Integrative Organismal Systems, the US part of the Genes2Shape ERACAPS grantIOS1826567, ANR-19-CE43-0010,BIOMOD,Analyse Multiéchelle et Modélisation Spatio-temporelle de la Déconstruction de la Biomasse Lignocellulosique(2019), Zardilis, Argyris [0000-0003-4582-9421], Wightman, Raymond [0000-0003-1295-4875], Jonsson, Henrik [0000-0003-2340-588X], Apollo - University of Cambridge Repository, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), University of California, Ministère de la Défense, Gouvernement - France, and Université Côte d'Azur (UCA)
Subjects: 0106 biological sciences, Gene regulatory network, Morphogenesis, Regulator, Arabidopsis, morphogenesis, Computational biology, Flowers, Genes, Plant, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Gene Expression Regulation, Plant, flower development, Cell Lineage, Gene Regulatory Networks, Transcription factor, Molecular Biology, Gene, Leafy, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, Regulator gene, Body Patterning, Regulation of gene expression, 0303 health sciences, biology, Arabidopsis Proteins, Gene Expression Regulation, Developmental, Cell Biology, molecular network, biology.organism_classification, Multicellular organism, Mutation, gene expression, 030217 neurology & neurosurgery, 010606 plant biology & botany, Developmental Biology
Abstract: The link between gene regulation and morphogenesis of multicellular organisms is a fundamental problem in biology. We address this question in the floral meristem of Arabidopsis, which generates new tissues and organs through complex changes in growth patterns. Starting from high-resolution time-lapse images, we generated a comprehensive 4-D atlas of early flower development including cell lineage, cellular growth rates and the expression patterns of 28 regulatory genes. This information was introduced in MorphoNet, a web-based open-access platform. The application of mechanistic computational models indicated that the molecular network based on the literature only explained a minority of the expression patterns. This was substantially improved by adding single regulatory hypotheses for individual genes. We next used the integrated information to correlate growth with the combinatorial expression of multiple genes. This led us to propose a set of hypotheses for the action of individual genes in morphogenesis, not visible by simply correlating gene expression and growth. This identified the central transcription factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated, multiscale view of flower development, this atlas should represent a fundamental step towards mechanistic multiscale-scale models of flower development.
Published: 2021

31. Diversity and distribution of pathotypes of the soybean rust fungus Phakopsora pachyrhizi in east africa

Author: Matthieu H. A. J. Joosten, H. M. Murithi, Rafael Moreira Soares, H. Peter van Esse, George Mahuku, lnternational Institute of Tropical Agriculture, Dar es Salaam, Tanzania, RAFAEL MOREIRA SOARES, CNPSO, The Sainsbury Laboratory, Norwich Research Park, Norwich, UK, and Laboratory of Phytopathology, Wageningen University and Research, Wageningen, Netherlands.
Subjects: 0106 biological sciences, 0301 basic medicine, Veterinary medicine, virulence diversity, Soja, Virulence, Plant Science, Fungus, Horticulture, 01 natural sciences, Rust, 03 medical and health sciences, soybean rust, Genotype, Genetics, Cultivar, Phakopsora pachyrhizi, biology, Host (biology), fungi, Vírus, food and beverages, pathotype, biology.organism_classification, Laboratorium voor Phytopathologie, Rpp gene, 030104 developmental biology, Laboratory of Phytopathology, EPS, Soybean rust, Ferrugem, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: Phakopsora pachyrhizi is a biotrophic fungus that causes rust on soybean, leading to devastating yield losses. Development of resistant cultivars for deployment in different geographic regions requires a comprehensive understanding of the prevalent P. pachyrhizi pathotypes. To determine the pathotypes existing in four East African countries, 65 isolates were tested on 11 soybean host differentials. In addition, the virulence spectrum of isolates collected from the same region over multiple years was compared. The majority of the isolates (54%) belonged to pathotype 1000, which was found in all countries. The pathotypes with the most complex virulence spectrum, which comprised isolates from Kenya and Malawi, were virulent on four differentials. All pathotypes were virulent on soybean genotypes carrying the Rpp1 resistance gene to P. pachyrhizi, but they were avirulent on cultivars carrying the Rpp1b, Rpp2, or Rpp3 gene, as well as on cultivar No6-12-1 that carries Rpp2, Rpp4, and Rpp5. Two of the pathotypes were virulent on cultivar UG 5 that carries Rpp1 and Rpp3 and on Hyuuga that carries Rpp3 and Rpp5. The isolates collected from different countries differed in their virulence spectrum across the years. Shannon's index (H) and Simpson's index (S) of diversity indicated that the isolates from Malawi were more diverse (H = 1.55, S = 0.90) while those from Uganda had lower diversity (H = 0.78, S = 0.46). The Rpp genes that were found to provide resistance to all pathotypes of P. pachyrhizi can be employed for soybean breeding aimed at durable rust resistance.
Published: 2020

32. Unravelling Chemical Composition of Agave Spines: News from Agave fourcroydes Lem

Author: John Z. Tang, José A. Guerrero-Analco, Laura Trejo, Luis F. Maceda-López, Adrien Gauthier, Lorena Rodríguez-López, Juan L. Monribot-Villanueva, Matthieu Bourdon, Dalia C. Morán-Velázquez, Parastoo Azadi, Francisco Vilaplana, Fulgencio Alatorre-Cobos, José L. Villalpando-Aguilar, Itzel López-Rosas, Monribot-Villanueva, Juan L [0000-0003-2394-0524], Bourdon, Matthieu [0000-0001-7243-5642], Tang, John Z [0000-0002-1907-9260], López-Rosas, Itzel [0000-0003-3864-260X], Maceda-López, Luis F [0000-0001-8304-4348], Gauthier, Adrien [0000-0002-1351-353X], Trejo, Laura [0000-0002-7136-6566], Vilaplana, Francisco [0000-0003-3572-7798], Guerrero-Analco, José A [0000-0003-0998-757X], Apollo - University of Cambridge Repository, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), University of Georgia [USA], Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Tecnológico Nacional de México (TecNM), Agro-écologie, Hydrogéochimie, Milieux et Ressources (AGHYLE), UniLaSalle, and Royal Institute of Technology [Stockholm] (KTH )
Subjects: 0106 biological sciences, musculoskeletal diseases, food.ingredient, Pectin, lignin, Plant Science, fibers, 01 natural sciences, 7. Clean energy, Article, 03 medical and health sciences, chemistry.chemical_compound, food, tannins, Botany, Agave fourcroydes, Lignin, Hemicellulose, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Cellulose, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Ecology, biology, Chemistry, secondary metabolites, fungi, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Agave, biology.organism_classification, musculoskeletal system, cellulose, Proanthocyanidin, QK1-989, Condensed tannin, 010606 plant biology & botany
Abstract: Spines are key plant modifications developed to deal against herbivores, however, its physical structure and chemical composition have been little explored in plant species. Here, we took advantage of high-throughput chromatography to characterize chemical composition of Agave fourcroydes Lem. spines, a species traditionally used for fiber extraction. Analyses of structural carbohydrate showed that spines have lower cellulose content than leaf fibers (52 and 72%, respectively) but contain more than 2-fold the hemicellulose and 1.5-fold pectin. Xylose and galacturonic acid were enriched in spines compared to fibers. The total lignin content in spines was 1.5-fold higher than those found in fibers, with elevated levels of syringyl (S) and guaiacyl (G) subunits but similar S/G ratios within tissues. Metabolomic profiling based on accurate mass spectrometry revealed the presence of phenolic compounds including quercetin, kaempferol, (+)-catechin, and (&minus, )-epicatechin in A. fourcroydes spines, which were also detected in situ in spines tissues and could be implicated in the color of these plants&rsquo, structures. Abundance of (+)-catechins could also explain proanthocyanidins found in spines. Agave spines may become a plant model to obtain more insights about cellulose and lignin interactions and condensed tannin deposition, which is valuable knowledge for the bioenergy industry and development of naturally dyed fibers, respectively.
Published: 2020

33. Does Gene Expression Noise Play a Functional Role in Plants?

Author: Sandra Cortijo, James C. W. Locke, Sainsbury Laboratory Cambridge University (SLCU), and University of Cambridge [UK] (CAM)
Subjects: 0106 biological sciences, 0301 basic medicine, MESH: Gene Expression, [SDV]Life Sciences [q-bio], Population, MESH: Plants, Gene Expression, Plant Science, Computational biology, Biology, risk spreading, 01 natural sciences, 03 medical and health sciences, Stress, Physiological, Gene expression, transcriptional noise, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, MESH: Stress, Physiological, education.field_of_study, stochasticity, single-cell RNA-seq, Mechanism (biology), fungi, time-lapse microscopy, food and beverages, Plants, medicine.disease, Phenotype, Noise, Multicellular organism, 030104 developmental biology, Function (biology), Transcriptional noise, 010606 plant biology & botany
Abstract: International audience; Gene expression in individual cells can be surprisingly noisy. In unicellular organisms this noise can be functional; for example, by allowing a subfraction of the population to prepare for environmental stress. The role of gene expression noise in multicellular organisms has, however, remained unclear. In this review, we discuss how new techniques are revealing an unexpected level of variability in gene expression between and within genetically identical plants. We describe recent progress as well as speculate on the function of transcriptional noise as a mechanism for generating functional phenotypic diversity in plants.
Published: 2020

34. Viburnum tinus Fruits Use Lipids to Produce Metallic Blue Structural Color

Author: Rox Middleton, Gianni Jacucci, Michael J. Donoghue, Maria Conejero, Miranda Sinnott-Armstrong, Beverley J. Glover, Yu Ogawa, Edwige Moyroud, Paula J. Rudall, Chrissie Prychid, Silvia Vignolini, Department of Biochemistry, University of Cambridge, Department of Ecology and Evolutionary Biology, Yale University, Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Department of Chemistry [Cambridge, UK], University of Cambridge [UK] (CAM), Sainsbury Laboratory Cambridge University (SLCU), Royal Botanic Garden , Kew, Department of Plant Sciences (Cambridge, UK), Jacucci, Gianni [0000-0002-9156-0876], Moyroud, Edwige [0000-0001-7908-3205], Glover, Beverley [0000-0002-6393-819X], Vignolini, Silvia [0000-0003-0664-1418], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, plant color, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, Color, Shrub, honest signaling, General Biochemistry, Genetics and Molecular Biology, Cell wall, Metal, Anthocyanins, 03 medical and health sciences, chemistry.chemical_compound, Pigment, Structure-Activity Relationship, 0302 clinical medicine, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, plant-animal interaction, [PHYS]Physics [physics], [PHYS.PHYS.PHYS-OPTICS]Physics [physics]/Physics [physics]/Optics [physics.optics], biology, cell walls, ved/biology, Pigmentation, Viburnum, biophotonics, food and beverages, Evergreen, structural color, biology.organism_classification, Lipid Metabolism, Lipids, fruit color, seed dispersal, 030104 developmental biology, chemistry, visual_art, Anthocyanin, Fruit, visual_art.visual_art_medium, Viburnum tinus, TEM tomography, plant lipids, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery, Structural coloration
Abstract: International audience; 16 Viburnum tinus is an evergreen shrub that is native to the Mediterranean region but cultivated 17 widely in Europe and around the world. It produces ripe metallic blue fruits throughout winter [1]. 18 Despite its limited fleshy pulp,[2] its high lipid content[3] makes it a valuable resource to the small 19 birds[4] that act as its seed-dispersers[5]. Here, we find that the metallic blue appearance of the 20 fruits is produced by globular lipid inclusions arranged in a disordered multilayer structure. This 21 structure is embedded in the cell walls of the epicarp and underlaid with a dark layer of anthocyanin 22 pigments. The presence of such large, organised lipid aggregates in plant cell walls represents a new 23 mechanism for structural colouration and may serve as an honest signal of nutritional content. 24 Results and Discussion 25 The colours of fleshy fruits are thought to serve primarily to attract animal dispersers, and 26 understanding the origins and diversity of fleshy fruit colours provides insight into the ecological 27 interactions between plants and their dispersers.[7] Viburnum tinus (Adoxaceae) is a shrub native to 28 the Mediterranean region that is now cultivated around the world.[8] It produces large numbers of 29 metallic blue fruits throughout the year. Although a variety of bird dispersers consume V. tinus 30 fruits,[2] these serve as an especially important food source for birds during winter, including the 31 Eurasian blackcap (Sylvia atricapilla)[9] and the European robin (Erithacus rubecola).[10] While the 32 remarkable blue metallic appearance of V. tinus fruits (Figure 1) is commonly known and previously 33 reported,[11] the mechanism by which such blue colour is produced has not been elucidated. In a 34 review of earlier literature,[12] the colour of V. tinus has been attributed to the presence of 35 anthocyanin pigments. 36
Published: 2020

35. A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis

Author: Philip A. Wigge, Antonio Daniel Barbosa, Mingjun Gao, Stephanie Hutin, Elodie Pierre, Feng Geng, Xuelei Lai, Dorothee Derwort, Catarina S. Silva, Sol-Bi Kim, Katja E. Jaeger, Sujeong Baek, Janet R. Kumita, Chloe Zubieta, Jaehoon Jung, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Dept of Biological Sciences, Sungkyunkwan University, StructDev (StructDev), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Leibniz-Institut für Gemüse- und Zierpflanzenbau, Institute of Biochemistry and Biology, University of Potsdam, Grant from the National Research Foundation of Korea (NRF), funded by the Korean government (grant 2019R1C1C1010507), Gatsby Charitable Foundation (grant GAT3273/GLB), Funding from the Leibniz Foundation, ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-19-CE20-0021,TEMPSENS,Mécanismes moléculaires de détection de la température chez les plantes(2019), European Project: PID 2236, European Project: 243140,EC:FP7:ERC,ERC-2009-StG,TEMPEST(2009), Kumita, Janet [0000-0002-3887-4964], Apollo - University of Cambridge Repository, and Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
Subjects: 0106 biological sciences, 0301 basic medicine, Scaffold protein, Models, Molecular, Hot Temperature, Acclimatization, Protein domain, Arabidopsis, Heterologous, Repressor, MESH: Acclimatization, MESH: Arabidopsis Proteins, MESH: Hot Temperature, 01 natural sciences, Phase Transition, Prion Proteins, Green fluorescent protein, 03 medical and health sciences, Protein Domains, MESH: Arabidopsis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Transcription factor, Multidisciplinary, biology, Chemistry, Arabidopsis Proteins, MESH: Peptides, Temperature, MESH: Transcription Factors, MESH: Prion Proteins, biology.organism_classification, MESH: Temperature, Cell biology, Repressor Proteins, 030104 developmental biology, 13. Climate action, MESH: Repressor Proteins, MESH: Protein Domains, MESH: Phase Transition, Peptides, Function (biology), MESH: Models, Molecular, 010606 plant biology & botany, Transcription Factors
Abstract: International audience; Temperature controls plant growth and development, and climate change has already altered the phenology of wild plants and crops1. However, the mechanisms by which plants sense temperature are not well understood. The evening complex is a major signalling hub and a core component of the plant circadian clock2,3. The evening complex acts as a temperature-responsive transcriptional repressor, providing rhythmicity and temperature responsiveness to growth through unknown mechanisms2,4-6. The evening complex consists of EARLY FLOWERING 3 (ELF3)4,7, a large scaffold protein and key component of temperature sensing; ELF4, a small α-helical protein; and LUX ARRYTHMO (LUX), a DNA-binding protein required to recruit the evening complex to transcriptional targets. ELF3 contains a polyglutamine (polyQ) repeat8-10, embedded within a predicted prion domain (PrD). Here we find that the length of the polyQ repeat correlates with thermal responsiveness. We show that ELF3 proteins in plants from hotter climates, with no detectable PrD, are active at high temperatures, and lack thermal responsiveness. The temperature sensitivity of ELF3 is also modulated by the levels of ELF4, indicating that ELF4 can stabilize the function of ELF3. In both Arabidopsis and a heterologous system, ELF3 fused with green fluorescent protein forms speckles within minutes in response to higher temperatures, in a PrD-dependent manner. A purified fragment encompassing the ELF3 PrD reversibly forms liquid droplets in response to increasing temperatures in vitro, indicating that these properties reflect a direct biophysical response conferred by the PrD. The ability of temperature to rapidly shift ELF3 between active and inactive states via phase transition represents a previously unknown thermosensory mechanism.
Published: 2020

36. Ligand-recognizing motifs in plant LysM receptors are major determinants of specificity

Author: Damiano Lironi, Simon Boje Hansen, Maria Vinther, Feng Feng, Giles E. D. Oldroyd, Zoltan Bozsoki, Christian Kofoed, Sébastien Fort, John T. Sullivan, Manoj Kamble, Ebbe Engholm, Knud J. Jensen, Noor de Jong, Kira Gysel, Clive W. Ronson, Christina Krönauer, Mikkel B. Thygesen, Mickaël Blaise, Simona Radutoiu, Kasper R. Andersen, Jens Stougaard, Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), and Aarhus University [Aarhus]
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Lotus japonicus, Protein domain, Amino Acid Motifs, Chitin, Nod, Biology, Ligands, 01 natural sciences, Nod factor, 03 medical and health sciences, chemistry.chemical_compound, Symbiosis, Protein Domains, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [CHIM]Chemical Sciences, Receptor, 030304 developmental biology, Plant Proteins, 0303 health sciences, Multidisciplinary, fungi, food and beverages, biology.organism_classification, Cell biology, chemistry, Lotus, Protein Kinases, Intracellular, 010606 plant biology & botany
Abstract: Switching perception of friend and foe Lysine motif receptors in plants perceive glycans that signal the presence of pathogenic or symbiotic nitrogen-fixing microbes. Bozsoki et al. now define the portions of these receptors that create the discriminatory binding pocket (see the Perspective by Bisseling and Geurts). The motifs were conserved in receptors that initiate immune responses, reflecting the invariable nature of the chitin fragments that they sense. Conversely, the motifs in receptors that respond to symbiotic signals were more varied, reflecting the greater diversity of the lipochitooligosaccharides (Nod factors) that they sense. With domain swapping, the authors switched the Nod factor specificity of receptors from two legume species and also enabled a chitin receptor that was otherwise dedicated to the detection of pathogenic microbes to instead recognize Nod factors. Science , this issue p. 663 ; see also p. 620
Published: 2020

37. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5′ and 3′ ends of its target genes

Author: Ruggieri, Valentino, Alexiou, Konstantinos, Morata, Jordi, Argyris, Jason, Pujol, Marta, Yano, Ryoichi, Nonaka, Satoko, Ezura, Hiroshi, Cigliano, Riccardo Aiese, Sanseverino, Walter, Puigdomenech, Pere, Casacuberta, Josep, Kirienko, Anna, Porozov, Yuri, Malkov, Nikita, Akhtemova, Gulnara, Le Signor, Christine, Thompson, Richard, Saffray, Christine, Dalmais, Marion, Tikhonovich, Igor, Dolgikh, Elena, Boucheham, Anouar, Sommard, Vivien, Zehraoui, Farida, Batouche, Mohamed, Israeli, David, Tahi, Fariza, Jacob, Pierre, Avni, Adi, Ligerot, Yasmine, De Saint Germain, Alexandre, Waldie, Tanya, Kadakia, Nikita, Pillot, Jean-Paul, Prigge, Michael, Aubert, Gregoire, Leyser, Ottoline, Estelle, Mark, Debellé, Frederic, Rameau, Catherine, GOUZY, Jerome, Badouin, Hélène, Lemainque, Arnaud, Vergne, Philippe, Moja, Sandrine, Choisne, Nathalie, Pont, Caroline, Carrere, Sebastien, Caissard, Jean-Claude, Couloux, Arnaud, Cottret, Ludovic, Aury, Jean-Marc, Szécsi, Judit, Madoui, Mohammed-Amin, Yang, Shu-Hua, Piola, Florence, Larrieu, Antoine, Perez, Magali, Labadie, Karine, Perrier, Lauriane, govetto, Benjamin, LABROUSSE, Yoan, Villand, Priscilla, Bardoux, Claudia, Boltz, Véronique, Lopez-Roques, Celine, Heitzler, Pascal, Vernoux, Teva, Quesneville, Hadi, Boualem, Adnane, Liu, Chang, Le Bris, Manuel, Salse, Jerome, Baudino, Sylvie, Wincker, Patrick, François, Léa, Verdenaud, Marion, Fu, Xiaopeng, Ruleman, Darcy, Dubois, Annick, Vandenbussche, Michiel, Raymond, Olivier, Just, Jérémy, Bendahmane, Mohammed, Giner, Ana, Pascual, Laura, Bourgeois, Michael, Gyetvai, Gabor, Rios, Pablo, Picó, Belén, Troadec, Christelle, Bendahmane, Abdel, Garcia-Mas, Jordi, MARTIN-HERNANDEZ, Ana Montserrat, Kim, Soonkap, Piquerez, Sophie, Ramirez-Prado, Juan, Mastorakis, Emmanouil, Veluchamy, Alaguraj, Latrasse, David, Manza-Mianza, Deborah, Brik-Chaouche, Rim, Huang, Ying, Rodriguez-Granados, Natalia, Concia, Lorenzo, Blein, Thomas, Citerne, Sylvie, Bendahmane, Abdelhafid, Bergounioux, Catherine, Crespi, Martin, Mahfouz, Magdy, Raynaud, Cécile, Hirt, Heribert, Ntoukakis, Vardis, BENHAMED, Moussa, Centre for Research in Agricultural Genomics (CRAG), IRTA, Center for Research in Agricultural Genomics, University of Tsukuba, Sequentia Biotech SL, LAboratoire PLasma et Conversion d'Energie (LAPLACE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut 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), All-Russia Research Institute for Agricultural Microbiology, University Salah Boubnider Constantine 3, Laboratoire d'Informatique de Paris-Nord (LIPN), Université Sorbonne Paris Cité (USPC)-Institut Galilée-Université Paris 13 (UP13)-Centre National de la Recherche Scientifique (CNRS), LIRE laboratory, Constantine, University of Constantine, GENETHON 3, Université Paris Saclay (COmUE), Tel Aviv University [Tel Aviv], Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Sainsbury Laboratory, University of Cambridge [UK] (CAM), University of California [San Diego] (UC San Diego), University of California, Laboratoire de chimie organique et organométallique (LCOO), Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), Division of Biology [La Jolla], University of California-University of California, UMR 0441 INRA / CNRS : Laboratoire de Biologie moléculaire des relations plantes-microorganismes, Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), Unité de Recherche Génomique Info (URGI), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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)-Université Paris-Saclay, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), GeT PlaGe, Genotoul, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University [Guangzhou] (SYSU), Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Huazhong Agricultural University, Division of Biology [Pasadena], California Institute of Technology (CALTECH), Unité de recherche Génétique et amélioration des fruits et légumes (GAFL), Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universitat Politecnica de Valencia (UPV), Institute of Agrifood Research and Technology (IRTA), Institut de Recerca i Tecnologia Agroalimentaries, King Abdullah University of Science and Technology (KAUST), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Economics and Management [Beijing] (BUAA), Beihang University, Institut de biotechnologie des plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Warwick [Coventry], AgroParisTech, and ANR-18-CE20-0015,EPICLIPSE,Dynamique des marques épigénétiques dans les cellules hôtes infectées et subversion de l'épigénome par le pathogène.(2018)
Subjects: 0106 biological sciences, Transcription, Genetic, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, Genes, Plant, 01 natural sciences, Histones, 03 medical and health sciences, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Homeostasis, Plant Immunity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Epigenetics, Promoter Regions, Genetic, QH426, ComputingMilieux_MISCELLANEOUS, Histone Acetyltransferases, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Arabidopsis Proteins, Lysine, Gene regulation, Chromatin and Epigenetics, Acetylation, Biotic stress, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cell biology, Chromatin, enzymes and coenzymes (carbohydrates), Histone, Acetyltransferase, Transcription Coactivator, biology.protein, 5' Untranslated Regions, Salicylic Acid, 010606 plant biology & botany
Abstract: The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.
Published: 2020

38. ChIP-seq and RNA-seq for complex and low-abundance tree buds reveal chromatin and expression co-dynamics during sweet cherry bud dormancy

Author: Elisabeth Dirlewanger, Philip A. Wigge, Sandra Cortijo, François Roudier, Bénédicte Wenden, Noémie Vimont, Fu Xiang Quah, David Guillaume-Schöpfer, Cortijo, Sandra [0000-0003-3291-6729], Apollo - University of Cambridge Repository, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Sainsbury Laboratory [Norwich] (TSL), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), and Quah, Fu Xiang [0000-0002-4616-5324]
Subjects: 0106 biological sciences, 0301 basic medicine, genetic processes, RNA-seq/RNA-sequencing, RNA-Seq, Horticulture, Biology, Prunus persica L batch, 01 natural sciences, 3105 Genetics, 3102 Bioinformatics and Computational Biology, 03 medical and health sciences, Prunus, chemistry.chemical_compound, Tree buds, Genetics, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, natural sciences, Prunus avium L, Molecular Biology, Transcription factor, Gene, 030304 developmental biology, 0303 health sciences, Human Genome, Forestry, biology.organism_classification, Cell biology, Chromatin, ChIP-seq/chromatin Immunoprecipitation-sequencing, 030104 developmental biology, chemistry, FOS: Biological sciences, Original Article, Epigenetics, Malus x domestica Borkh, RNA extraction, DNA, 31 Biological Sciences, 010606 plant biology & botany
Abstract: Funder: CIFRE, Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-BOX 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.
Published: 2020
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39. Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers

Author: Weibing Yang, Benoit Landrein, Elliot M. Meyerowitz, Qingkun Dong, Christoph Schuster, Nathanaël Prunet, Raymond Wightman, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Caltech Department of Astronomy [Pasadena], California Institute of Technology (CALTECH), University of California [Los Angeles] (UCLA), University of California, South China Agricultural University (SCAU), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gatsby Charitable Foundation GAT3395/DAAHoward Hughes Medical Institute Gatsby Charitable Foundation Graduate Student Oversea Study Program South China Agricultural University 2018LHPY011, University of California (UC), and École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: 0106 biological sciences, RNA localization, Physiology, Meristem, Arabidopsis, Plant Science, In situ hybridization, Flowers, Biology, 01 natural sciences, Breakthrough Technologies - Focus Issue, Gene Expression Regulation, Plant, Gene expression, Genetics, Transcriptional regulation, Gene, In Situ Hybridization, Fluorescence, RNA, Nuclear, Regulation of gene expression, Messenger RNA, Arabidopsis Proteins, RNA, Gene Expression Regulation, Developmental, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Plants, Genetically Modified, Cell biology, Plant Shoots, 010606 plant biology & botany
Abstract: International audience; In addition to transcriptional regulation, gene expression is further modulated through mRNA spatiotemporal distribution, by RNA movement between cells, and by RNA localization within cells. Here, we have adapted RNA fluorescence in situ hybridization (FISH) to explore RNA localization in Arabidopsis (Arabidopsis thaliana). We show that RNA FISH on sectioned material can be applied to investigate the tissue and subcellular localization of meristem and flower development genes, cell cycle transcripts, and plant long noncoding RNAs. We also developed double RNA FISH to dissect the coexpression of different mRNAs at the shoot apex and nuclear-cytoplasmic separation of cell cycle gene transcripts in dividing cells. By coupling RNA FISH with fluorescence immunocytochemistry, we further demonstrate that a gene's mRNA and protein may be simultaneously detected, for example revealing uniform distribution of PIN-FORMED1 (PIN1) mRNA and polar localization of PIN1 protein in the same cells. Therefore, our method enables the visualization of gene expression at both transcriptional and translational levels with subcellular spatial resolution, opening up the possibility of systematically tracking the dynamics of RNA molecules and their cognate proteins in plant cells.
Published: 2020

40. Co-expression Networks From Gene Expression Variability Between Genetically Identical Seedlings Can Reveal Novel Regulatory Relationships

Author: Sandra Cortijo, Marcel Bhattarai, James C. W. Locke, Sebastian E. Ahnert, Locke, James [0000-0003-0670-1943], Apollo - University of Cambridge Repository, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Cavendish Laboratory
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Population, Arabidopsis, Computational biology, Plant Science, Biology, lcsh:Plant culture, 01 natural sciences, Transcriptome, 03 medical and health sciences, Gene expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, co-expression analysis, lcsh:SB1-1110, education, Transcription factor, Gene, Original Research, 030304 developmental biology, 2. Zero hunger, Regulation of gene expression, 0303 health sciences, Developmental stage, education.field_of_study, variability, modules, fungi, seedlings, food and beverages, 15. Life on land, biology.organism_classification, Plant development, 030104 developmental biology, Expression (architecture), networks, gene expression, Function (biology), 010606 plant biology & botany
Abstract: Co-expression networks are a powerful tool to understand gene regulation. They have been used to identify new regulation and function of genes involved in plant development and their response to the environment. Up to now, co-expression networks have been inferred using transcriptomes generated on plants experiencing genetic or environmental perturbation, or from expression time series. We propose a new approach by showing that co-expression networks can be constructed in the absence of genetic and environmental perturbation, for plants at the same developmental stage. For this we used transcriptomes that were generated from genetically identical individual plants that were grown in the same conditions and for the same amount of time. Twelve time points were used to cover the 24h light/dark cycle. We used variability in gene expression between individual plants of the same time point to infer a co-expression network. We show that this network is biologically relevant and use it to suggest new gene functions and to identify new targets for the transcription factors GI, PIF4 and PRR5. Moreover, we find different co-regulation in this network based on changes in expression between individual plants, compared to the usual approach requiring environmental perturbation. Our work shows that gene co-expression networks can be identified using variability in gene expression between individual plants, without the need for genetic or environmental perturbations. It will allow further exploration of gene regulation in contexts with subtle differences between plants, which could be closer to what individual plants in a population might face in the wild.Author summaryPlant development and response to changes in the environment are strongly regulated at the level of gene expression. That is why understanding how gene expression is regulated is key, and transcriptome approaches have allowed the analysis of transcription for all genes of the genome. Extracting useful information from the high amount of data generated by transcriptomes is a challenge, and gene co-expression networks are a powerful tool to do this. The principle is to find genes that co-vary in expression in different conditions and to pair them together. Communities of genes that are more closely linked are then identified and this is the starting point to look for their implication in the same pathway. Co-expression networks have been used to identify new regulation and function of genes involved in plant development and their response to the environment. They were constructed using transcriptomes generated on plants experiencing genetic or environmental perturbation. We show that co-expression networks can in fact be constructed in the absence of genetic and environmental perturbation. Our work will allow further exploration of gene co-regulation in contexts with subtle differences between plants, which could be closer to what individual plants in a population might face in the wild.
Published: 2020

41. Current status of the multinational Arabidopsis community

Author: Parry, Geraint, Provart, Nicholas J., Brady, Siobhan M., Uzilday, Baris, Adams, K., Araújo, W., Aubourg, S., Baginsky, S., Bakker, E., Bärenfaller, K., Batley, J., Beale, M., Beilstein, M., Belkhadir, Y., Berardini, T., Bergelson, J., Blanco-Herrera, F., Brady, S., Braun, Hans-Peter, Briggs, S., Brownfield, L., Cardarelli, M., Castellanos-Uribe, M., Coruzzi, G., Dassanayake, M., Jaeger, G.D., Dilkes, B., Doherty, C., Ecker, J., Edger, P., Edwards, D., Kasmi, F.E., Eriksson, M., Exposito-Alonso, M., Falter-Braun, P., Fernie, A., Ferro, M., Fiehn, O., Friesner, J., Greenham, K., Guo, Y., Hamann, T., Hancock, A., Hauser, M.-T., Heazlewood, J., Ho, C.-H., Hõrak, H., Huala, E., Hwang, I., Iuchi, S., Jaiswal, P., Jakobson, L., Jiang, Y., Jiao, Y., Jones, A., Kadota, Y., Khurana, J., Kliebenstein, D., Knee, E., Kobayashi, M., Koch, M., Krouk, G., Larson, T., Last, R., Lepiniec, L., Li, S., Lurin, C., Lysak, M., Maere, S., Malinowski, R., Maumus, F., May, S., Mayer, K., Mendoza-Cozatl, D., Mendoza-Poudereux, I., Meyers, B., Micol, J.L., Millar, H., Mock, H.-P., Mukhtar, K., Mukhtar, S., Murcha, M., Nakagami, H., Nakamura, Y., Nicolov, L., Nikolau, B., Nowack, M., Nunes-Nesi, A., Palmgren, M., Parry, G., Patron, N., Peck, S., Pedmale, U., Perrot-Rechenmann, C., Pieruschka, R., Pío-Beltrán, J., Pires, J.C., Provart, N., Rajjou, L., Reiser, L., Reumann, S., Rhee, S., Rigas, S., Rolland, N., Romanowski, A., Santoni, V., Savaldi-Goldstein, S., Schmitz, R., Schulze, W., Seki, M., Shimizu, K.K., Slotkin, K., Small, I., Somers, D., Sozzani, R., Spillane, C., Srinivasan, R., Taylor, N., Tello-Ruiz, M.-K., Thelen, J., Tohge, T., Town, C., Toyoda, T., Uzilday, B., Peer, Y.V.D., Wijk, K., Gillhaussen, P.V., Walley, J., Ware, D., Weckwerth, W., Whitelegge, J., Wienkoop, S., Wright, C., Wrzaczek, M., Yamazaki, M., Yanovsky, M., Žárský, V., Zhong, X., Biological Systems Engineering, Organisms and Environment Research Division, Cardiff School of Biosciences, Cardiff University, University of Toronto, University of California [Davis] (UC Davis), University of California, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany, Department of Ecology and Evolution [Chicago], University of Chicago, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), University of Arizona, Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), University of California (UC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Flanders Institute for Biotechnology, National Center for Atmospheric Research [Boulder] (NCAR), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Université Grenoble Alpes (UGA), Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, Norwegian University of Science and Technology (NTNU), University of Melbourne, King Abdullah University of Science and Technology (KAUST), University of Chinese Academy of Sciences [Beijing] (UCAS), The Sainsbury Laboratory [Norwich] (TSL), IBM Research – Tokyo, University Medical Center Groningen [Groningen] (UMCG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Novel Agricultural Products, Department of Biology, University of York [York, UK], Biologie des Semences (LBS), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Sichuan University [Chengdu] (SCU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Nottingham, UK (UON), Institute of Bioinformatics and System Biology (IBIS), Helmholtz Zentrum München = German Research Center for Environmental Health, Saint Mary's University [Halifax], Max Planck Institute for Plant Breeding Research (MPIPZ), National Institute of Genetics (NIG), University of Copenhagen = Københavns Universitet (UCPH), Division of Biology [La Jolla], University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Earlham Institute [Norwich], Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, University of Missouri [Columbia] (Mizzou), University of Missouri System, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology, Carnegie Institution for Science, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Systems Biology, Institute of Physiology and Biotechnology of plants, RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), Department of Biology, Duke University, Genetics and Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland [Galway] (NUI Galway), Universidade Federal de São Paulo, RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Cold Spring Harbor Laboratory (CSHL), University of Vienna [Vienna], University of California [Los Angeles] (UCLA), Department of Plant Molecular Biology, Université de Lausanne = University of Lausanne (UNIL), UKRI-BBSRC grant BB/M004376/1, HHMI Faculty Scholar Fellowship, Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) 118Z137, UK Research & Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) BB/M004376/1, Sainsbury Lab, Norwich Research Park, Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Helmholtz-Zentrum München (HZM), University of Copenhagen = Københavns Universitet (KU), University of California-University of California, Carnegie Institution for Science [Washington], Université de Lausanne (UNIL), Ege Üniversitesi, Organismal and Evolutionary Biology Research Programme, Plant Biology, Viikki Plant Science Centre (ViPS), Receptor-Ligand Signaling Group, University of Zurich, Parry, Geraint, Provart, Nicholas J, and Brady, Siobhan M
Subjects: 0106 biological sciences, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], White Paper, Genetics and Molecular Biology (miscellaneous), Plant Science, Biochemistry, 01 natural sciences, Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik), Research community, Arabidopsis, 1110 Plant Science, 0303 health sciences, Ecology, biology, 1184 Genetics, developmental biology, physiology, ddc:580, Multinational corporation, MAP, 590 Animals (Zoology), Life Sciences & Biomedicine, Arabidopsis research community, Evolution, Steering committee, Multinational Arabidopsis Steering Committee, Library science, 1301 Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, Genetics and Molecular Biology (miscellaneous), Business and Economics, 10127 Institute of Evolutionary Biology and Environmental Studies, 03 medical and health sciences, Behavior and Systematics, Political science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MASC, roadmap, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Plant Sciences, Botany, 15. Life on land, 11831 Plant biology, biology.organism_classification, White Papers, collaboration, 1105 Ecology, Evolution, Behavior and Systematics, QK1-989, Arabidopsis Thaliana, Collaboration, Research Network, Roadmap, 570 Life sciences, 1182 Biochemistry, cell and molecular biology, 2303 Ecology, 010606 plant biology & botany
Abstract: The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plantArabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community., UKRI-BBSRC grant [BB/M004376/1]; HHMI Faculty Scholar Fellowship; Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [118Z137], UKRI-BBSRC grant, Grant/Award Number: BB/M004376/1; HHMI Faculty Scholar Fellowship; the Scientific and Technological Research Council of Turkey, Grant/Award Number: 118Z137
Published: 2020

42. The Evening Complex Establishes Repressive Chromatin Domains Via H2A.Z Deposition

Author: Nozomu Takahashi, Paloma Mas, Sandra Cortijo, Mathew S. Box, Varodom Charoensawan, Daphne Ezer, Kyounghee Lee, Pil Joon Seo, Jaehoon Jung, Philip A. Wigge, Meixuezi Tong, Katja E. Jaeger, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Sungkyunkwan University [Suwon] (SKKU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre for Research in Agricultural Genomics (CRAG), Institute of Agrifood Research and Technology (IRTA), Universitat Autònoma de Barcelona (UAB), Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Seoul National University [Seoul] (SNU), and Institut de biologie de l'ENS Paris (IBENS)
Subjects: 0106 biological sciences, Physiology, Circadian clock, Arabidopsis, Plant Science, 01 natural sciences, Histones, Evening Complex, Chromatin remodeling, 03 medical and health sciences, Circadian Clocks, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], circadian clock, Genetics, Nucleosome, Arabidopsis thaliana, Circadian rhythm, Research Articles, 030304 developmental biology, 0303 health sciences, biology, Chemistry, Arabidopsis Proteins, H2A.Z, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Chromatin, Cell biology, CLOCK, Repressor Proteins, Histone, SWR1, biology.protein, 010606 plant biology & botany, Transcription Factors
Abstract: The Evening Complex (EC) is a core component of the Arabidopsis (Arabidopsis thaliana) circadian clock, which represses target gene expression at the end of the day and integrates temperature information to coordinate environmental and endogenous signals. Here we show that the EC induces repressive chromatin structure to regulate the evening transcriptome. The EC component ELF3 directly interacts with a protein from the SWI2/SNF2-RELATED (SWR1) complex to control deposition of H2A.Z-nucleosomes at the EC target genes. SWR1 components display circadian oscillation in gene expression with a peak at dusk. In turn, SWR1 is required for the circadian clockwork, as defects in SWR1 activity alter morning-expressed genes. The EC-SWR1 complex binds to the loci of the core clock genes PSEUDO-RESPONSE REGULATOR7 (PRR7) and PRR9 and catalyzes deposition of nucleosomes containing the histone variant H2A.Z coincident with the repression of these genes at dusk. This provides a mechanism by which the circadian clock temporally establishes repressive chromatin domains to shape oscillatory gene expression around dusk.
Published: 2020

43. The Medicago truncatula GRAS protein RAD1 supports arbuscular mycorrhiza symbiosis and Phytophthora palmivora susceptibility

Author: Abhishek Chatterjee, Maxime Bonhomme, Weibing Yang, Aleksandr Gavrin, Thomas Rey, Olivier André, Christophe Jacquet, Justine Toulotte, Sebastian Schornack, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), European Project: 637537,H2020,ERC-2014-STG,ACHILLES-HEEL(2015), Gavrin, Aleksandr [0000-0003-0179-8491], Yang, Weibing [0000-0002-2379-5729], Schornack, Sebastian [0000-0002-7836-5881], and Apollo - University of Cambridge Repository
Subjects: Phytophthora, 0106 biological sciences, 0301 basic medicine, Root nodule, Hypha, genome-wide association mapping, Physiology, Phytophthora palmivora, Plant Science, 01 natural sciences, 03 medical and health sciences, Symbiosis, Gene Expression Regulation, Plant, Mycorrhizae, Medicago truncatula, Botany, oomycete, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MtSymSCL3, Arbuscular mycorrhiza, RAD1, Plant Diseases, Plant Proteins, Genetics, Oomycete, Endodeoxyribonucleases, biology, fungi, food and beverages, biology.organism_classification, Research Papers, symbiosis, host susceptibility, 030104 developmental biology, Host-Pathogen Interactions, Disease Susceptibility, Plant–Environment Interactions, root colonization, Genome-Wide Association Study, 010606 plant biology & botany
Abstract: Using a genome-wide association mapping approach, we identified a new role for the GRAS transcription factor RAD1 in supporting infection by an oomycete root pathogen. Previously, RAD1 was exclusively implicated in symbiosis signalling., The roots of most land plants are colonized by symbiotic arbuscular mycorrhiza (AM) fungi. To facilitate this symbiosis, plant genomes encode a set of genes required for microbial perception and accommodation. However, the extent to which infection by filamentous root pathogens also relies on some of these genes remains an open question. Here, we used genome-wide association mapping to identify genes contributing to colonization of Medicago truncatula roots by the pathogenic oomycete Phytophthora palmivora. Single-nucleotide polymorphism (SNP) markers most significantly associated with plant colonization response were identified upstream of RAD1, which encodes a GRAS transcription regulator first negatively implicated in root nodule symbiosis and recently identified as a positive regulator of AM symbiosis. RAD1 transcript levels are up-regulated both in response to AM fungus and, to a lower extent, in infected tissues by P. palmivora where its expression is restricted to root cortex cells proximal to pathogen hyphae. Reverse genetics showed that reduction of RAD1 transcript levels as well as a rad1 mutant are impaired in their full colonization by AM fungi as well as by P. palmivora. Thus, the importance of RAD1 extends beyond symbiotic interactions, suggesting a general involvement in M. truncatula microbe-induced root development and interactions with unrelated beneficial and detrimental filamentous microbes.
Published: 2017

44. NIN Acts as a Network Hub Controlling a Growth Module Required for Rhizobial Infection

Author: Guru V. Radhakrishnan, Kirsty Jackson, Caitlin Bone, Fernanda de Carvalho-Niebel, Fran Robson, Suyu Jiang, Nicola Stacey, Giles E. D. Oldroyd, Jeremy D. Murray, Cheng-Wu Liu, Martin Trick, Dian Guan, Marion R. Cerri, Sonali Roy, Andreas Niebel, Christian Rogers, Andrew Breakspear, Department of Cell Biology, John Innes Centre, Norwich Research Park, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Chinese Academy of Sciences [Beijing] (CAS)-Shanghai Institutes for Biological Sciences-Institute of Plant Physiology and Ecology, Department of Cell and Developmental Biology, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), John Innes Centre [Norwich], Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Chinese Academy of Sciences [Changchun Branch] (CAS), Biotechnology and Biological Sciences Research Council (BBSRC) : BB/L010305/1, John Innes Foundation, ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-15-CE20-0012,NODCCAAT,Comprendre le mode d'action du facteur de transcription NF-YA1 spécifique de l'intearction symbiotique rhizobium-légumineuses chez Medicago truncatula(2015), and ANR-14-CE35-0007,COME-IN,Cell-specific reprogramming of legume roots for endosymbiotic infection(2014)
Subjects: 0106 biological sciences, Physiology, [SDV]Life Sciences [q-bio], Plant Science, Cyclopentanes, Root hair, 01 natural sciences, chemistry.chemical_compound, Gene Expression Regulation, Plant, Medicago truncatula, Genetics, Gene Regulatory Networks, Oxylipins, Gene, Transcription factor, ComputingMilieux_MISCELLANEOUS, Plant Proteins, Regulation of gene expression, biology, Jasmonic acid, Articles, biology.organism_classification, Gibberellins, Cell biology, Biosynthetic Pathways, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Regulon, chemistry, Pectate lyase, Rhizobium, 010606 plant biology & botany
Abstract: International audience; The symbiotic infection of root cells by nitrogen-fixing rhizobia during nodulation requires the transcription factor Nodule Inception (NIN). Our root hair transcriptomic study extends NIN's regulon to include Rhizobium Polar Growth and genes involved in cell wall modification, gibberellin biosynthesis, and a comprehensive group of nutrient (N, P, and S) uptake and assimilation genes, suggesting that NIN's recruitment to nodulation was based on its role as a growth module, a role shared with other NIN-Like Proteins. The expression of jasmonic acid genes in nin suggests the involvement of NIN in the resolution of growth versus defense outcomes. We find that the regulation of the growth module component Nodulation Pectate Lyase by NIN, and its function in rhizobial infection, are conserved in hologalegina legumes, highlighting its recruitment as a major event in the evolution of nodulation. We find that Nodulation Pectate Lyase is secreted to the infection chamber and the lumen of the infection thread. Gene network analysis using the transcription factor mutants for ERF Required for Nodulationl and Nuclear Factor-Y Subunit Al confirms hierarchical control of NIN over Nuclear Factor-Y Subunit Al and shows that ERF Required for Nodulationl acts independently to control infection. We conclude that while NIN shares functions with other NIN-Like Proteins, the conscription of key infection genes to NIN's control has made it a central regulatory hub for rhizobial infection.
Published: 2019

45. The grapevine (Vitis vinifera) LysM receptor kinases VvLYK1-1 and VvLYK1-2 mediate chitooligosaccharide-triggered immunity

Author: Justine Claverie, Freddy Boutrot, Lena Stransfeld, Daphnée Brulé, Lucie Trdá, Marie-Claire Héloir, Pablo Tornero, Laura J. Davies, Clizia Villano, Annick Chiltz, Benoît Darblade, Marielle Adrian, Cyril Zipfel, Benoît Poinssot, Ian B. Dry, University of Zurich, Dry, Ian B, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre National de la Recherche Scientifique (CNRS), University of Naples Federico II, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Elicityl SA, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Norwich Research Park, The Sainsbury Laboratory [Norwich] (TSL), ANR (PATRIC project) [ANR-13-KBBE-0001], Regional Council of Bourgogne Franche-Comte (PARI grant) [2016-9201AAO050S016 36, 2015-9201AAO048502578, 29000907], Regional Council of Bourgogne Franche-Comte (FEDER) [2015-9201AAO048502578, 29000907, BG0005888], INRA [2015-9201AAO048502578, 29000907], Gatsby Charitable Foundation, Biotechnology and Biological Sciences Research Council (BBSRC) [BB/G024936/1], Dry, Ian B., Poinssot, Benoît, Brule, Daphnee, Villano, Clizia, Davies, Laura J., Trda, Lucie, Claverie, Justine, Heloir, Marie-Claire, Chiltz, Annick, Adrian, Marielle, Darblade, Benoıt, Tornero, Pablo, Stransfeld, Lena, Boutrot, Freddy, Zipfel, Cyril, and Poinssot, Benoit
Subjects: 0106 biological sciences, 0301 basic medicine, pattern recognition receptor, [SDV]Life Sciences [q-bio], Resistance, Mutant, Arabidopsis, Oligosaccharides, Chitin, Immune responses, Plant Science, 580 Plants (Botany), Erysiphe necator, 01 natural sciences, immune response, chemistry.chemical_compound, 10126 Department of Plant and Microbial Biology, Gene expression, 1110 Plant Science, Plant Immunity, Vitis, pathogen-associated molecular pattern, Vitis vinifera, immune responses, resistance, Research Articles, Phylogeny, Plant Proteins, 2. Zero hunger, Pattern recognition receptor, Cell biology, Elicitor, [SDE]Environmental Sciences, 1305 Biotechnology, Research Article, Biotechnology, macromolecular substances, Pathogen-associated molecular pattern, Biology, pathogen‐associated molecular pattern, Protein Serine-Threonine Kinases, 03 medical and health sciences, Ascomycota, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 1102 Agronomy and Crop Science, 10211 Zurich-Basel Plant Science Center, Gene, Plant Diseases, Chitosan, Arabidopsis Proteins, fungi, 15. Life on land, biology.organism_classification, 030104 developmental biology, chemistry, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: [EN] Chitin, a major component of fungal cell walls, is a well-known pathogen-associated molecular pattern (PAMP) that triggers defense responses in several mammal and plant species. Here, we show that two chitooligosaccharides, chitin and chitosan, act as PAMPs in grapevine (Vitis vinifera) as they elicit immune signalling events, defense gene expression and resistance against fungal diseases. To identify their cognate receptors, the grapevine family of LysM receptor kinases (LysM-RKs) was annotated and their gene expression profiles were characterized. Phylogenetic analysis clearly distinguished three V. vinifera LysM-RKs (VvLYKs) located in the same clade as the Arabidopsis CHITIN ELICITOR RECEPTOR KINASE1 (AtCERK1), which mediates chitin-induced immune responses. The Arabidopsis mutant Atcerk1, impaired in chitin perception, was transformed with these three putative orthologous genes encoding VvLYK1-1, -2, or -3 to determine if they would complement the loss of AtCERK1 function. Our results provide evidence that VvLYK1-1 and VvLYK1-2, but not VvLYK1-3, functionally complement the Atcerk1 mutant by restoring chitooligosaccharide-induced MAPK activation and immune gene expression. Moreover, expression of VvLYK1-1 in Atcerk1 restored penetration resistance to the non-adapted grapevine powdery mildew (Erysiphe necator). On the whole, our results indicate that the grapevine VvLYK1-1 and VvLYK1-2 participate in chitin- and chitosan-triggered immunity and that VvLYK1-1 plays an important role in basal resistance against E. necator., This work has been financially supported by ANR (PATRIC project, grant ANR-13-KBBE-0001) (to BP), the Regional Council of Bourgogne Franche-Comte (PARI grant 2016-9201AAO050S016 36 and FEDER grant BG0005888) and INRA for the funding of Justine Claverie's PhD (grants 2015-9201AAO048502578 and 29000907), by the Gatsby Charitable Foundation (to CZ), and by the Biotechnology and Biological Sciences Research Council (BBSRC) grants BB/G024936/1 (ERA-PG PRR CROP (to CZ).
Published: 2019

46. Expression of the Arabidopsis thaliana immune receptor EFR in Medicago truncatula reduces infection by a root pathogenic bacterium, but not nitrogen‐fixing rhizobial symbiosis

Author: Arry Morel, J. Allan Downie, Nemo Peeters, Sebastian Pfeilmeier, Lena Stransfeld, Cyril Zipfel, Matthew Smoker, Jacob G. Malone, Sonali Roy, Jeoffrey George, University of Zurich, Zipfel, Cyril, The Sainsbury Laboratory [Norwich] (TSL), John Innes Centre [Norwich], Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Universität Zürich [Zürich] = University of Zurich (UZH), School of Biological Sciences, University of East Anglia [Norwich] (UEA), Norwich Research Park, BBSRC Institute Strategic Program Grant : BB/J004553/1, Gatsby Charitable Foundation, Laboratoire d'Excellence (LABEX) TULIP : ANR-10-LABX-41, and John Innes Foundation
Subjects: 0106 biological sciences, 0301 basic medicine, Root nodule, PAMPs, Arabidopsis, Plant Science, 580 Plants (Botany), 01 natural sciences, Plant Root Nodulation, Plant Roots, immunity, PRRs, symbiosis, disease resistance, biotechnology, 10126 Department of Plant and Microbial Biology, Gene Expression Regulation, Plant, 1110 Plant Science, Arabidopsis thaliana, Research Articles, Sinorhizobium meliloti, Vegetal Biology, biology, food and beverages, Plants, Genetically Modified, Medicago truncatula, Receptors, Pattern Recognition, 1305 Biotechnology, Rhizobium, Research Article, Plant disease resistance, Microbiology, Rhizobia, 03 medical and health sciences, Nitrogen Fixation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Immunity, 1102 Agronomy and Crop Science, 10211 Zurich-Basel Plant Science Center, Plant Diseases, Arabidopsis Proteins, fungi, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, 030104 developmental biology, Agronomy and Crop Science, Biologie végétale, 010606 plant biology & botany
Abstract: Interfamily transfer of plant pattern recognition receptors (PRRs) represents a promising biotechnological approach to engineer broad‐spectrum, and potentially durable, disease resistance in crops. It is however unclear whether new recognition specificities to given pathogen‐associated molecular patterns (PAMPs) affect the interaction of the recipient plant with beneficial microbes. To test this in a direct reductionist approach, we transferred the Brassicaceae‐specific PRR ELONGATION FACTOR‐THERMO UNSTABLE RECEPTOR (EFR), conferring recognition of the bacterial EF‐Tu protein, from Arabidopsis thaliana to the legume Medicago truncatula. Constitutive EFR expression led to EFR accumulation and activation of immune responses upon treatment with the EF‐Tu‐derived elf18 peptide in leaves and roots. The interaction of M. truncatula with the bacterial symbiont Sinorhizobium meliloti is characterized by the formation of root nodules that fix atmospheric nitrogen. Although nodule numbers were slightly reduced at an early stage of the infection in EFR‐Medicago when compared to control lines, nodulation was similar in all lines at later stages. Furthermore, nodule colonization by rhizobia, and nitrogen fixation were not compromised by EFR expression. Importantly, the M. truncatula lines expressing EFR were substantially more resistant to the root bacterial pathogen Ralstonia solanacearum. Our data suggest that the transfer of EFR to M. truncatula does not impede root nodule symbiosis, but has a positive impact on disease resistance against a bacterial pathogen. In addition, our results indicate that Rhizobium can either avoid PAMP recognition during the infection process, or is able to actively suppress immune signaling., Plant Biotechnology Journal, 17 (3), ISSN:1467-7644, ISSN:1467-7652
Published: 2019

47. Precision genetic engineering tools for next-generation plant breeding

Author: Fabien Nogué, Günther Hahne, Laurence Tomlinson, Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), The Sainsbury Laboratory [Norwich] (TSL), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Université Paris Saclay (COmUE)
Subjects: 0106 biological sciences, 0303 health sciences, Management science, [SDV]Life Sciences [q-bio], MEDLINE, Plant Science, General Medicine, Plants, Biology, 01 natural sciences, Plant Breeding, 03 medical and health sciences, Plant biochemistry, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Engineering tool, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Plant breeding, Genetic Engineering, Agronomy and Crop Science, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 010606 plant biology & botany, Introductory Journal Article
Abstract: International audience
Published: 2019

48. Primary wall cellulose synthase regulates shoot apical meristem mechanics and growth

Author: Staffan Persson, Geoffrey O. Wasteneys, Alexis Peaucelle, Arun Sampathkumar, Miki Fujita, Elliot M. Meyerowitz, Christoph Schuster, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Botany, University of British Columbia (UBC), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), School of Biosciences, University of Birmingham [Birmingham], Howard Hughes Medical Institute (HHMI), Division of Biology and Biological Engineering, Max-Planck-GesellschaftMax Planck Society, Gatsby Charitable Foundation fellowship [GAT3395/DAA], ARCFondation ARC pour la Recherche sur le CancerAustralian Research Council [FT160100218], and Natural Sciences and Engineering Research Council of CanadaNatural Sciences and Engineering Research Council of Canada [201406080]
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Turgor pressure, Meristem, Morphogenesis, Arabidopsis, Biology, Mechanics, 01 natural sciences, Microtubules, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Cell growth, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Cellulose, Molecular Biology, 030304 developmental biology, 0303 health sciences, Arabidopsis Proteins, food and beverages, Plant cell, chemistry, Glucosyltransferases, Developmental biology, 010606 plant biology & botany, Developmental Biology, Research Article
Abstract: International audience; How organisms attain their specific shapes and modify their growth patterns in response to environmental and chemical signals has been the subject of many investigations. Plant cells are at high turgor pressure and are surrounded by a rigid yet flexible cell wall, which is the primary determinant of plant growth and morphogenesis. Cellulose microfibrils, synthesized by plasma membrane-localized cellulose synthase complexes, are major tension-bearing components of the cell wall that mediate directional growth. Despite advances in understanding the genetic and biophysical regulation of morphogenesis, direct studies of cellulose biosynthesis and its impact on morphogenesis of different cell and tissue types are largely lacking. In this study, we took advantage of mutants of three primary cellulose synthase (CESA) genes that are involved in primary wall cellulose synthesis. Using field emission scanning electron microscopy, live cell imaging and biophysical measurements, we aimed to understand how the primary wall CESA complex acts during shoot apical meristem development. Our results indicate that cellulose biosynthesis impacts the mechanics and growth of the shoot apical meristem.
Published: 2019

49. Hydrodynamic Shape Changes Underpin Nuclear Rerouting in Branched Hyphae of an Oomycete Pathogen

Author: Liron Shenhav, Marie Le Naour--Vernet, Philipp Rink, Temur Yunusov, Edouard Evangelisti, Sebastian Schornack, The Sainsbury Laboratory [Norwich] (TSL), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Gatsby Charitable Foundation, GAT3395/GLD Royal Society of London, UF160413 ERASMUS program, Evangelisti, Edouard [0000-0002-7218-7850], Shenhav, Liron [0000-0003-1961-4187], Yunusov, Temur [0000-0001-9936-4354], Le Naour-Vernet, Marie [0000-0003-4923-8039], Rink, Philipp [0000-0003-0932-2658], Schornack, Sebastian [0000-0002-7836-5881], and Apollo - University of Cambridge Repository
Subjects: Phytophthora, Hypha, Movement, Hyphae, Microbiology, Host-Microbe Biology, oomycetes, Phytophthora palmivora, nucleus movement, centrosome, hydrodynamics, 03 medical and health sciences, Multinucleate, phytophthora palmivora, Microtubule, Virology, Pathogen, pathologie végétale, 030304 developmental biology, 2. Zero hunger, Oomycete, Cell Nucleus, 0303 health sciences, biology, 030306 microbiology, fungi, Microbiology and Parasitology, Computational Biology, biology.organism_classification, QR1-502, Microbiologie et Parasitologie, Cell biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Cytoplasm, Centrosome, Research Article
Abstract: Despite their fungal morphology, oomycetes constitute a distinct group of protists related to brown algae and diatoms. Many oomycetes are pathogens and cause diseases of plants, insects, mammals, and humans. Extensive efforts have been made to understand the molecular basis of oomycete infection, but durable protection against these pathogens is yet to be achieved. We use a plant-pathogenic oomycete to decipher a key physiological aspect of oomycete growth and infection. We show that oomycete nuclei travel actively and over long distances within hyphae and during infection. Such movements require microtubules anchored on the centrosome. Nuclei hydrodynamically adapt their shape to travel in or against the flow. In contrast, fungi lack a centrosome and have much less flexible nuclei. Our findings provide a basis for modeling of flexible nuclear shapes in branched hyphal networks and may help in finding hard-to-evade targets to develop specific antioomycete strategies and achieve durable crop disease protection., Multinucleate fungi and oomycetes are phylogenetically distant but structurally similar. To address whether they share similar nuclear dynamics, we carried out time-lapse imaging of fluorescently labeled Phytophthora palmivora nuclei. Nuclei underwent coordinated bidirectional movements during plant infection. Within hyphal networks growing in planta or in axenic culture, nuclei either are dragged passively with the cytoplasm or actively become rerouted toward nucleus-depleted hyphal sections and often display a very stretched shape. Benomyl-induced depolymerization of microtubules reduced active movements and the occurrence of stretched nuclei. A centrosome protein localized at the leading end of stretched nuclei, suggesting that, as in fungi, astral microtubule-guided movements contribute to nuclear distribution within oomycete hyphae. The remarkable hydrodynamic shape adaptations of Phytophthora nuclei contrast with those in fungi and likely enable them to migrate over longer distances. Therefore, our work summarizes mechanisms which enable a near-equal nuclear distribution in an oomycete. We provide a basis for computational modeling of hydrodynamic nuclear deformation within branched tubular networks.
Published: 2019

50. Widespread inter‐individual gene expression variability in Arabidopsis thaliana

Author: Sebastian E. Ahnert, James C. W. Locke, Zeynep Aydin, Sandra Cortijo, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The Sainsbury Laboratory [Norwich] (TSL), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Arabidopsis thaliana, Light, Photoperiod, transcriptional variability, Arabidopsis, Plant Biology, RNA-Seq, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, inter‐individual heterogeneity, Gene, 030304 developmental biology, Genetics, Regulation of gene expression, 0303 health sciences, General Immunology and Microbiology, Arabidopsis Proteins, Sequence Analysis, RNA, Applied Mathematics, noise in gene expression, Articles, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Phenotype, Chromatin, Circadian Rhythm, Multicellular organism, Computational Theory and Mathematics, Seedlings, Genome-Scale & Integrative Biology, RNA‐seq, General Agricultural and Biological Sciences, Transcriptome, Transcription, 030217 neurology & neurosurgery, Software, Information Systems, Transcription Factors
Abstract: International audience; A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered although it could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform, and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about inter-individual transcriptional variability in multicellular organisms. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24-h time course. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses, with different classes of genes variable between the day and night. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.
Published: 2019

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