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110 results on '"MESH: Plants"'

1. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides

Author

Lucelia Cabral, Gabriela F. Persinoti, Douglas A. A. Paixão, Marcele P. Martins, Mariana A. B. Morais, Mariana Chinaglia, Mariane N. Domingues, Mauricio L. Sforca, Renan A. S. Pirolla, Wesley C. Generoso, Clelton A. Santos, Lucas F. Maciel, Nicolas Terrapon, Vincent Lombard, Bernard Henrissat, Mario T. Murakami, Architecture et fonction des macromolécules biologiques (AFMB), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Dietary Fiber, DIETARY FIBER, MESH: Carbohydrate Metabolism, [SDV]Life Sciences [q-bio], DIVERSITY, MESH: Plants, General Physics and Astronomy, MESH: Rodentia, Crystallography, X-Ray, Lignin, MESH: Animals, MESH: Phylogeny, Phylogeny, Multidisciplinary, MESH: Symbiosis, Plants, Multidisciplinary Sciences, Science & Technology - Other Topics, GASTROINTESTINAL-TRACT, Carbohydrate Metabolism, Xylans, Glycoside Hydrolases, Science, GENOMES, Rodentia, General Biochemistry, Genetics and Molecular Biology, MESH: Gastrointestinal Microbiome, Polysaccharides, MESH: Glycoside Hydrolases, STRUCTURE REFINEMENT, Animals, BIOSYNTHESIS, CELL, Symbiosis, Science & Technology, SEQUENCES, Bacteria, Bacteroidetes, General Chemistry, MESH: Crystallography, X-Ray, MESH: Lignin, MESH: Bacteroidetes, Gastrointestinal Microbiome, MESH: Bacteria, MESH: Xylans, MESH: Polysaccharides, BETA-GLUCANS, MESH: Dietary Fiber, XYLANASE-Z
Abstract

The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy. ispartof: NATURE COMMUNICATIONS vol:13 issue:1 ispartof: location:England status: published

Published
2022

2. The Andes through time: evolution and distribution of Andean floras

Author

Pérez-Escobar, Oscar Alejandro, Zizka, Alexander, Bermúdez, Mauricio A., Meseguer, Andrea S., Condamine, Fabien L., Hoorn, Carina, Hooghiemstra, Henry, Pu, Yuanshu, Bogarín, Diego, Boschman, Lydian M., Pennington, R. Toby, Antonelli, Alexandre, Chomicki, Guillaume, non-UU output of UU-AW members, Royal Botanic Gardens [Kew], Philipps Universität Marburg = Philipps University of Marburg, German Centre for Integrative Biodiversity Research (iDiv), Universidad Pedagógica y Tecnológica de Colombia (UPTC), Real Jardín Botánico de Madrid (RJB), Spanish National Research Council (CSIC), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), Universidad de Costa Rica (UCR), Naturalis Biodiversity Center [Leiden], Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of Exeter, University of Oxford, University of Gothenburg (GU), University of Sheffield [Sheffield], ANR-17-CE31-0009,GAARAnti,Pont terrestre 'GAARlandia' vs voies de dispersion à travers les Petites Antilles–Couplage entre dynamique de la subduction et processus de l'évolution des espèces dans le domaine des Caraïbes.(2017), Ecosystem and Landscape Dynamics (IBED, FNWI), and non-UU output of UU-AW members

Subjects
geology, [SDE.MCG]Environmental Sciences/Global Changes, MESH: Plants, Andes, Plant Science, Forests, MESH: Biodiversity, Eastern cordillera, Plant diversification, MESH: Ecosystem, vascular plants, Continental-scale, Climate-change, MESH: Phylogeny, biogeography, Ecosystem, Phylogeny, Adaptive radiation, Surface uplift, Northern andes, Biodiversity, plant diversity, Late miocene rise, MESH: Forests, Plants, Bolivian altiplano, Rapid diversification
Abstract

The Andes are the world's most biodiverse mountain chain, encompassing a complex array of ecosystems from tropical rainforests to alpine habitats. We provide a synthesis of Andean vascular plant diversity by estimating a list of all species with publicly available records, which we integrate with a phylogenetic dataset of 14 501 Neotropical plant species in 194 clades. We find that (i) the Andean flora comprises at least 28 691 georeferenced species documented to date, (ii) Northern Andean mid-elevation cloud forests are the most species-rich Andean ecosystems, (iii) the Andes are a key source and sink of Neotropical plant diversity, and (iv) the Andes, Amazonia, and other Neotropical biomes have had a considerable amount of biotic interchange through time., Trends in Plant Science, 27 (4), ISSN:1360-1385, ISSN:1878-4372

Published
2022

3. 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

4. Overview of the Structure–Function Relationships of Mannose-Specific Lectins from Plants, Algae and Fungi

Author

Pierre Rougé, Els J.M. Van Damme, Yves Bourne, Annick Barre, Pharmacochimie et Biologie pour le Développement (PHARMA-DEV), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University (UGENT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Universiteit Gent = Ghent University [Belgium] (UGENT), Surfaces Cellulaires et Signalisation chez les Végétaux (SCSV), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratory of Biochemistry and Glycobiology, Chent University, and Institut de pharmacologie et de biologie structurale (IPBS)

Subjects
Models, Molecular, 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Protein Conformation, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, MESH: Plants, AMINO-ACID-SEQUENCE, Oligosaccharides, Mannose, plant, Review, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, ENVELOPE GLYCOPROTEIN GP120, lcsh:Chemistry, GLYCAN-SPECIFIC LECTIN, chemistry.chemical_compound, MESH: Protein Conformation, MESH: Structure-Activity Relationship, PINELLIA-TERNATA AGGLUTININ, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, CANAVALIA-BRASILIENSIS LECTIN, use as tools, lcsh:QH301-705.5, Peptide sequence, Spectroscopy, CARBOHYDRATE-BINDING, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Structure function, General Medicine, Plants, Envelope glycoprotein GP120, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Computer Science Applications, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], JACALIN-RELATED, Biochemistry, mannose-binding specificity, MESH: Mannose, HUMAN-IMMUNODEFICIENCY-VIRUS, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, LECTINS, MESH: Models, Molecular, Protein Binding, MESH: Fungi, Glycan, Catalysis, Inorganic Chemistry, Structure-Activity Relationship, 03 medical and health sciences, Algae, MESH: Mannose-Binding Lectins, MESH: Protein Binding, structure, Physical and Theoretical Chemistry, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], AGENTS, ANTI-HIV ACTIVITY, Molecular Biology, function, Binding Sites, 030102 biochemistry & molecular biology, Organic Chemistry, Biology and Life Sciences, Lectin, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Mannose-Binding Lectins, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, MESH: Binding Sites, MANNOSE/GLUCOSE-SPECIFIC LECTIN, biology.protein, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, lectin, fungi, MESH: Oligosaccharides, Function (biology)
Abstract

International audience; To date, a number of mannose-binding lectins have been isolated and characterized from plants and fungi. These proteins are composed of different structural scaffold structures which harbor a single or multiple carbohydrate-binding sites involved in the specific recognition of mannose-containing glycans. Generally, the mannose-binding site consists of a small, central, carbohydrate-binding pocket responsible for the "broad sugar-binding specificity" toward a single mannose molecule, surrounded by a more extended binding area responsible for the specific recognition of larger mannose-containing N-glycan chains. Accordingly, the mannose-binding specificity of the so-called mannose-binding lectins towards complex mannose-containing N-glycans depends largely on the topography of their mannose-binding site(s). This structure⁻function relationship introduces a high degree of specificity in the apparently homogeneous group of mannose-binding lectins, with respect to the specific recognition of high-mannose and complex N-glycans. Because of the high specificity towards mannose these lectins are valuable tools for deciphering and characterizing the complex mannose-containing glycans that decorate both normal and transformed cells, e.g., the altered high-mannose N-glycans that often occur at the surface of various cancer cells.

Published
2019

5. The equivocal mean age of parents in a cohort

Author

François Bienvenu, Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Probabilités, Statistiques et Modélisations (LPSM (UMR_8001)), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)

Subjects
Male, Age structure, Offspring, [SDV]Life Sciences [q-bio], media_common.quotation_subject, MESH: Plants, Crump-Mode-Jagers processes, MESH: Reproduction, 01 natural sciences, Paternal Age, 010104 statistics & probability, cohort generation time, Animals, MESH: Animals, 0101 mathematics, Ecology, Evolution, Behavior and Systematics, media_common, Models, Statistical, Life span, Reproduction, 010102 general mathematics, Mean age, Plants, MESH: Male, mean age at reproduction, Cohort, MESH: Paternal Age, MESH: Maternal Age, Female, age-structured population, Psychology, MESH: Female, MESH: Models, Statistical, Maternal Age, mean age of mothers, Demography
Abstract

The mean age at childbirth is an important notion in demography, ecology and evolution, where it is used as a measure of generation time. A standard way to quantify it is to compute the mean age of the parents of the offspring produced by a cohort. The resulting measure, which can be computed from life-tables or projection matrices thanks to classic formulas, is thought to represent the mean age at which a typical parent produces offspring. In this note, I introduce a new measure of the mean age at reproduction of a typical parent. After giving a rigorous interpretation of the formulas used to estimate the mean age of parents of offspring of a cohort, I derive corresponding expressions for the mean age at reproduction and show that it can be very different from the mean age of parents of offspring of a cohort - both under simple hypotheses and in real-world applications. The mean age of parents of offspring of a cohort also systematically overestimates the mean age at reproduction, and can even be greater than the expected lifespan conditional on reproduction. Altogether, these results show that the familiar notion of "mean age of parents in a cohort" is in fact ambiguous, and that we may need to reevaluate whether we have been measuring it correctly.

Published
2018
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6. Positively Selected Effector Genes and Their Contribution to Virulence in the Smut Fungus Sporisorium reilianum

Author

Julien Y. Dutheil, Gabriel Schweizer, Karin Münch, Gertrud Mannhaupt, Regine Kahmann, Jan Schirawski, Max Planck Institute for Terrestrial Microbiology, Max-Planck-Gesellschaft, Department of Evolutionary Biology and Environmental Studies, Universität Zürich [Zürich] = University of Zurich (UZH), Helmholtz Zentrum München = German Research Center for Environmental Health, Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Evolutionary Biology, Helmholtz-Zentrum München (HZM), Rheinisch-Westfälische Technische Hochschule Aachen (RWTH), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)

Subjects
0106 biological sciences, 0301 basic medicine, Ustilago, MESH: Selection, Genetic, MESH: Plants, comparative genomics, smut fungi, 01 natural sciences, Genome, MESH: Plant Diseases, Ustilaginales, MESH: Phylogeny, Phylogeny, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Genetics, 0303 health sciences, Ustilago hordei, Effector, MESH: Genomics, Basidiomycota, Genomics, Plants, Multigene Family, Corrigendum, Research Article, effector evolution, Virulence Factors, Genes, Fungal, Virulence, Biology, 03 medical and health sciences, positive selection, Positive Selection, Effector Evolution, Smut Fungi, Comparative Genomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ddc:570, Gene family, Selection, Genetic, Gene, Ecology, Evolution, Behavior and Systematics, Plant Diseases, MESH: Virulence Factors, 030304 developmental biology, Comparative genomics, 030306 microbiology, Host (biology), MESH: Ustilaginales, biology.organism_classification, virulence, MESH: Basidiomycota, 030104 developmental biology, Smut, MESH: Multigene Family, MESH: Genes, Fungal, 010606 plant biology & botany
Abstract

Genome biology and evolution : GBE 10(2), 629-645 (2018). doi:10.1093/gbe/evy023, Published by Oxford Univ. Press, Oxford

Published
2018

7. Targeting of host organelles by pathogenic bacteria: a sophisticated subversion strategy

Author

Pedro Escoll, Carmen Buchrieser, Monica Rolando, Sonia Mondino, Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), The authors thank S. Gordon for critical reading of the manuscript. Work in the C.B. laboratory is financed by the Institut Pasteur, the Institut Carnot Pasteur Maladies Infectieuses, the French Region Ile de France (through the DIM Malinf programme) and the Infect-ERA project EUGENPATH (grant ANR-13-IFEC-0003-02). S.M. is financed by the French Agence Nationale de la Recherche (grant ANR-10-LABX- 62-IBEID). P.E. is funded by the Fondation pour la Recherche Médicale (grant DEQ20120323697)., ANR-13-IFEC-0003,EUGENPATH,Eukaryotic genes in vacuolar pathogens and symbionts - Implications for virulence, metabolism and ecology(2013), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, MESH: Plants, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, medicine.disease_cause, MESH: Eukaryotic Cells, Models, Biological, Microbiology, Bacterial genetics, 03 medical and health sciences, symbols.namesake, Bacterial secretion, Organelle, medicine, Animals, Humans, MESH: Animals, Organelles, MESH: Humans, Bacteria, General Immunology and Microbiology, biology, Host (biology), Endoplasmic reticulum, MESH: Host-Pathogen Interactions, MESH: Models, Biological, Bacterial pathogenesis, Pathogenic bacteria, Plants, Golgi apparatus, biology.organism_classification, Bacterial host response, Cell biology, MESH: Bacteria, Eukaryotic Cells, 030104 developmental biology, Infectious Diseases, Host-Pathogen Interactions, symbols, Pathogens, MESH: Organelles
Abstract

International audience; Many bacterial pathogens have evolved the ability to subvert and exploit host functions in order to enter and replicate in eukaryotic cells. For example, bacteria have developed specific mechanisms to target eukaryotic organelles such as the nucleus, the mitochondria, the endoplasmic reticulum and the Golgi apparatus. In this Review, we highlight the most recent advances in our understanding of the mechanisms that bacterial pathogens use to target these organelles. We also discuss how these strategies allow bacteria to manipulate host functions and to ultimately enable bacterial infection.

Published
2015

8. Minimum Information about a Biosynthetic Gene cluster

Author

Patrick Caffrey, Renzo Kottmann, Eriko Takano, Sean Doyle, Axel A. Brakhage, Matthew Cummings, Juan Pablo Gomez-Escribano, Yvonne Mast, Ryan F. Seipke, Rob Lavigne, Markus Nett, Hans-Wilhelm Nützmann, Jan Claesen, David H. Sherman, Daniel Petras, Pablo Cruz-Morales, Carl J. Balibar, Anne Osbourn, Oscar P. Kuipers, Leonilde M. Moreira, Xinyu Liu, Marcia S. Osburne, Bohdan Ostash, David P. Fewer, Changsheng Zhang, Pelin Yilmaz, Mohamed S. Donia, Anja Greule, Hyun Uk Kim, Nicholas J. Tobias, Frank Oliver Glöckner, Christoph Geiger, Chia Y. Lee, William H. Gerwick, Philipp Wiemann, Bertolt Gust, Susan E. Jensen, Wilfred A. van der Donk, Jan Kormanec, Ben Shen, Christopher M. Thomas, Jason Micklefield, Srikanth Duddela, R. Cameron Coates, René De Mot, Anthony S. Haines, Neha Garg, Guohui Pan, Roderich D. Süssmuth, Hyung Jin Kwon, Jonathan D. Walton, Lena Gerwick, Jörn Piel, Monika Ehling-Schulz, Zhenhua Tian, Jonathan L. Klassen, Xiaohui Yan, Emily A. Monroe, Yunchang Xie, Russell J. Cox, Keishi Ishida, Grace Yim, Stefano Donadio, Nadine Ziemert, Yuta Tsunematsu, Matthew L. Hillwig, Miroslav Petricek, Sylvie Lautru, Tilmann Weber, Andrew W. Truman, Rainer Breitling, Peter Kötter, Nikos C. Kyrpides, Stephanie Düsterhus, Christian Hertweck, Hideaki Oikawa, Sean F. Brady, Christopher T. Walsh, Adam C. Jones, Marcus A. Moore, Bradley S. Moore, Barrie Wilkinson, Simone M. Mantovani, Nathan A. Moss, Elizabeth E. Wyckoff, Emily P. Balskus, Kapil Tahlan, Fengan Yu, Monica Höfte, Jos M. Raaijmakers, Taifo Mahmud, Yit-Heng Chooi, Yi Tang, Andreas Bechthold, Douglas A. Mitchell, Joanne M. Willey, Helge B. Bode, John B. Biggins, Margherita Sosio, Yi-Qiang Cheng, Carmen Méndez, Leonard Kaysser, Joleen Masschelein, Daniel Krug, Federico Rosconi, Marnix H. Medema, Kaarina Sivonen, Tomohisa Kuzuyama, Mikko Metsä-Ketelä, Esther K. Schmitt, Carsten Kegler, Andriy Luzhetskyy, Gilles P. van Wezel, Bai Linquan, Kai Blin, Jens Nielsen, Bertrand Aigle, Amrita Pati, Harald Gross, Muriel Viaud, Pieter C. Dorrestein, Carla S. Jones, Michael A. Fischbach, Shelley M. Payne, Zhe Rui, Gerard D. Wright, Wen Liu, Alexey V. Melnik, Barry Scott, Brett A. Neilan, Nancy P. Keller, Rainer Borriss, Katrin Jungmann, Michalis Hadjithomas, Evi Stegmann, Daniel J. Edwards, F. Jerry Reen, Alexander Kristian Apel, Wolfgang Wohlleben, Michael J. Smanski, Leonard Katz, Fergal O'Gara, Eric J. N. Helfrich, Sergey B. Zotchev, Olivier Ploux, Arnold J. M. Driessen, Rolf Müller, Jean-Luc Pernodet, K. D. Entian, José A. Salas, Irene de Bruijn, Francisco Barona-Gómez, Jianhua Ju, Jon Clardy, Molecular Microbiology, Molecular Genetics, Jacobs University [Bremen], Microbial genomics and bioinformatics research group, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Max-Planck-Gesellschaft, Atmospheric Chemistry Observations and Modeling Laboratory (ACOML), National Center for Atmospheric Research [Boulder] (NCAR), Department of Food and Environmental Sciences, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Collaborative Mass Spectrometry Innovation Center, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Heilongjiang Institute of Science and Technology, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Merck Stiftungsprofessur fûr Molekulare Biotechnologie Fachbereich Biowissenscharten, Goethe-University Frankfurt am Main, Department of Opto-Mechatronics Engineering and Cogno-Mechatronics Engineering, Pusan National University, University of Liverpool, College of Computer Science and Technology [Zhejiang] (Zhejiang University), University of Florida [Gainesville] (UF), School of Management, University of Science and Technology of China [Hefei] (USTC), State Key Laboratory of Nuclear Physics and Technology (SKL-NPT), Peking University [Beijing], Massachusetts Institute of Technology (MIT), Memorial Sloane Kettering Cancer Center [New York], South China Sea Institute of Oceanology, Chinese Academy of Sciences [Beijing] (CAS), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut für Biologie [Berlin] (IFB), Humboldt University Of Berlin, School of Biomolecular and Biomedical Science and Centre for Synthesis and Chemical Biology, University College Dublin [Dublin] (UCD), Parallélisme, Réseaux, Systèmes, Modélisation (PRISM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], Grenoble Institut des Neurosciences (GIN), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pixyl Medical [Grenoble], Integrated Optical MicroSystems (IOMS), University of Twente-MESA+ Institute for Nanotechnology, 7Lehrstuhl für Mikrobielle Ökologie, Department für Grundlagen der Biowissenschaften, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Service Néphrologie Pédiatrique, CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Advanced Resources and Risk Technology, Laboratory of Phytopathology (K.C., H.S., B.A., M.H.), Universiteit Gent = Ghent University (UGENT), Trifork Aarhus C, Aalborg University [Denmark] (AAU), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Groupe d'Etude de la Matière Condensée (GEMAC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen [Groningen], DOE Joint Genome Institute [Walnut Creek], Microbiologie Moléculaire des Actinomycètes (ACTINO), Département Microbiologie (Dpt Microbio), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Gene Technology, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Joint Center for Structural Genomics (JCSG), Stanford University, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches et d'Applications Pédagogiques en Langues (CRAPEL), Université Nancy 2, Space Sciences Laboratory [Berkeley] (SSL), University of California [Berkeley] (UC Berkeley), Polytechnic Institute of Leiria, NMR Laboratory, Université de Mons, Université de Mons (UMons), School of Biomedical Science, Curtin University [Perth], Planning and Transport Research Centre (PATREC)-Planning and Transport Research Centre (PATREC), BIOMERIT Research Centre, School of Microbiology, University College Cork (UCC), Department of Engineering Science, University of Oxford, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire Charles Friedel, Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Phytopathology, Wageningen University and Research [Wageningen] (WUR), Department of Microbial Ecology, Netherlands Institute of Ecology, Department of Animal Production, Universidad de Córdoba = University of Córdoba [Córdoba], IMV Technologies, Gulliver (UMR 7083), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Institut für Chemie, Technical University of Berlin / Technische Universität Berlin (TU), Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Centre de Recherche Paul Pascal (CRPP), Université de Bordeaux (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), DEPARTMENT OF CHEMISTRY, Durham University, Molekulare Ökologie, Joint Attosecond Science Laboratory, University of Ottawa and National Research Council, Department of Mechanical and Aerospace Engineering [Univ California Davis] (MAE - UC Davis), University of California [Davis] (UC Davis), University of Helsinki, University of California-University of California, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Humboldt-Universität zu Berlin, University of Twente [Netherlands]-MESA+ Institute for Nanotechnology, Technische Universität München [München] (TUM), Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Biosystems, KU Leuven, Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of California [Berkeley], NMR and Molecular Imaging Laboratory [Mons], University of Mons [Belgium] (UMONS), University of Oxford [Oxford], Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC), Universidad de Córdoba [Cordoba], Technische Universität Berlin (TU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Mechanical and Aerospace Engineering [Davis], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), University of Florida [Gainesville], Institut für Biologie, Humboldt Universität zu Berlin, Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Ghent University [Belgium] (UGENT), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Stanford University [Stanford], Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), NMR and Molecular Imaging Laboratory, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), Gulliver, ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS), Technische Universität Berlin (TUB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Max Planck Society (GERMANY), Max Planck Society (GERMANY)-Max Planck Society (GERMANY), Laboratoire Leprince-Ringuet ( LLR ), Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -École polytechnique ( X ) -Centre National de la Recherche Scientifique ( CNRS ), Atmospheric Chemistry Observations and Modeling Laboratory ( ACOML ), National Center for Atmospheric Research [Boulder] ( NCAR ), University of California [San Diego] ( UC San Diego ), Eidgenössische Technische Hochschule [Zürich] ( ETH Zürich ), University of Science and Technology of China [Hefei] ( USTC ), State Key Laboratory of Nuclear Physics and Technology ( SKL-NPT ), Massachusetts Institute of Technology ( MIT ), Memorial Sloan Kettering Cancer Center ( MSKCC ), Shanghai Ocean University, Dynamique des Génomes et Adaptation Microbienne ( DynAMic ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), University College Dublin [Dublin] ( UCD ), Parallélisme, Réseaux, Systèmes, Modélisation ( PRISM ), Université de Versailles Saint-Quentin-en-Yvelines ( UVSQ ) -Centre National de la Recherche Scientifique ( CNRS ), Grenoble Institut des Neurosciences ( GIN ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Grenoble-Université Joseph Fourier - Grenoble 1 ( UJF ), Integrated Optical MicroSystems ( IOMS ), Technische Universität München [München] ( TUM ), Ghent University [Belgium] ( UGENT ), Aalborg University [Denmark] ( AAU ), Centers for Disease Control and Prevention [Atlanta] ( CDC ), Groupe d'Etude de la Matière Condensée ( GEMAC ), Groningen Biomolecular Sciences and Biotechnology Institute ( GBB ), Microbiologie Moléculaire des Actinomycètes ( ACTINO ), Département Microbiologie ( Dpt Microbio ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Joint Center for Structural Genomics ( JCSG ), Centre européen de recherche et d'enseignement de géosciences de l'environnement ( CEREGE ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Collège de France ( CdF ) -Institut National de la Recherche Agronomique ( INRA ) -Institut national des sciences de l'Univers ( INSU - CNRS ), Centre de Recherches et d'Applications Pédagogiques en Langues ( CRAPEL ), Space Sciences Laboratory [Berkeley] ( SSL ), Université de Mons ( UMons ), Planning and Transport Research Centre ( PATREC ) -Planning and Transport Research Centre ( PATREC ), University College Cork ( UCC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL ( ENSCP ) -Centre National de la Recherche Scientifique ( CNRS ), Wageningen University and Research Centre [Wageningen] ( WUR ), ESPCI ParisTech, Technische Universität Berlin ( TUB ), Lipides - Nutrition - Cancer (U866) ( LNC ), Université de Bourgogne ( UB ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon ( ENSBANA ), Centre de recherche Paul Pascal, CNRS, Université de Bordeaux ( UPR8641 ), Centre de Recherche Paul Pascal, CNRS, Université de Bordeaux, University Durham, University of California [Davis] ( UC Davis ), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), [GIN] Grenoble Institut des Neurosciences (GIN), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), and Saarland University, Building A4.1, 66123 Saarbruecken, Germany.

Subjects
MESH : Protein Biosynthesis, protein synthesis, Operon, MESH : Polysaccharides, International Cooperation, MESH: Plants, plant, Review, MESH: Terpenes, gene cluster, polyketide, data base, genetic database, Gene cluster, acyltransferase, Databases, Genetic, MESH : Metagenome, MESH : Genetic Markers, genetics, terpene, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), ComputingMilieux_MISCELLANEOUS, MESH : Peptides, MESH: Peptides, biology, fungus, nonribosomal peptide synthesis, Plants, bacterium, peptide, priority journal, MESH: Protein Biosynthesis, Multigene Family, MESH : Terpenes, MESH: Computational Biology, Genetic Markers, MESH: Terminology as Topic, Bioinformatics, MESH : Multigene Family, biological activity, Article, metagenome, Alkaloids, Manchester Institute of Biotechnology, Terminology as Topic, Bioinformatica, MESH : Bacteria, Peptide Biosynthesis, MESH : Databases, Genetic, Molecular Biology, MESH : Fungi, MESH: Polyketides, standardization, secondary metabolism, [ SDV ] Life Sciences [q-bio], Bacteria, ta1182, Computational Biology, MESH : Terminology as Topic, operon, Laboratorium voor Phytopathologie, MESH: International Cooperation, gene function, Metagenomics, polysaccharide, Laboratory of Phytopathology, chemical structure, Metagenome, MESH: Multigene Family, EPS, biosynthesis, Peptides, MESH : Computational Biology, MESH : International Cooperation, [SDV]Life Sciences [q-bio], MESH: Genetic Markers, information, MESH : Alkaloids, Synthetic biology, MESH: Peptide Biosynthesis, Nucleic Acid-Independent, database, MESH: Databases, Genetic, Genetics, MESH : Polyketides, MESH : Peptide Biosynthesis, Nucleic Acid-Independent, ddc:540, standards, Peptide Biosynthesis, Nucleic Acid-Independent, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, nomenclature, genetic marker, alkaloid derivative, MESH: Fungi, Biology, MESH : Plants, peptide derivative, Polyketide, MESH: Alkaloids, Polysaccharides, ddc:570, Life Science, 14. Life underwater, Secondary metabolism, enzyme specificity, Gene, nonhuman, Terpenes, Fungi, nucleotide sequence, Cell Biology, MESH: Metagenome, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, alkaloid, MESH: Bacteria, MESH: Polysaccharides, 13. Climate action, Polyketides, Protein Biosynthesis, synthetic biology, metabolism
Abstract

M.H.M. was supported by a Rubicon fellowship of the Netherlands Organization for Scientific Research (NWO;Rubicon 825.13.001). The work of R.K. was supported by the European Union’s Seventh Framework Programme(Joint Call OCEAN.2011–2: Marine microbial diversity—new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no.287589 (Micro B3). M.C. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC)studentship (BB/J014478/1). The GSC is supported by funding from the Natural Environment Research Council(UK), the National Institute for Energy Ethics and Society(NIEeS; UK), the Gordon and Betty Moore Foundation,the National Science Foundation (NSF; US) and the US Department of Energy. The Manchester Synthetic Biology Research Centre, SYNBIOCHEM, is supported by BBSRC/Engineering and Physical Sciences Research Council(EPSRC) grant BB/M017702/1, Medema, M.H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J.B., Blin, K., De Bruijn, I., Chooi, Y.H., Claesen, J., Coates, R.C., Cruz-Morales, P., Duddela, S., Düsterhus, S., Edwards, D.J., Fewer, D.P., Garg, N., Geiger, C., Gomez-Escribano, J.P., Greule, A., Hadjithomas, M., Haines, A.S., Helfrich, E.J.N., Hillwig, M.L., Ishida, K., Jones, A.C., Jones, C.S., Jungmann, K., Kegler, C., Kim, H.U., Kötter, P., Krug, D., Masschelein, J., Melnik, A.V., Mantovani, S.M., Monroe, E.A., Moore, M., Moss, N., Nützmann, H.-W., Pan, G., Pati, A., Petras, D., Reen, F.J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N.J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A.K., Balibar, C.J., Balskus, E.P., Barona-Gómez, F., Bechthold, A., Bode, H.B., Borriss, R., Brady, S.F., Brakhage, A.A., Caffrey, P., Cheng, Y.Q., Clardy, J., Cox, R.J., De Mot, R., Donadio, S., Donia, M.S., Van Der Donk, W.A., Dorrestein, P.C., Doyle, S., Driessen, A.J.M., Ehling-Schulz, M., Entian, K.-D., Fischbach, M.A., Gerwick, L., Gerwick, W.H., Gross, H., Gust, B., Hertweck, C., Höfte, M., Jensen, S.E., Ju, J., Katz, L., Kaysser, L., Klassen, J.L., Keller, N.P., Kormanec, J., Kuipers, O.P., Kuzuyama, T., Kyrpides, N.C., Kwon, H.-J., Lautru, S., Lavigne, R., Lee, C.Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Méndez, C., Metsä-Ketelä, M., Micklefield, J., Mitchell, D.A., Moore, B.S., Moreira, L.M., Müller, R., Neilan, B.A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M.S., Ostash, B., Payne, S.M., Pernodet, J.-L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J.M., Salas, J.A., Schmitt, E.K., Scott, B., Seipke, R.F., Shen, B., Sherman, D.H., Sivonen, K., Smanski, M.J., Sosio, M., Stegmann, E., Süssmuth, R.D., Tahlan, K., Thomas, C.M., Tang, Y., Truman, A.W., Viaud, M., Walton, J.D., Walsh, C.T., Weber, T., Van Wezel, G.P., Wilkinson, B., Willey, J.M., Wohlleben, W., Wright, G.D., Ziemert, N., Zhang, C., Zotchev, S.B., Breitling, R., Takano, E., Glöckner, F.O.

Published
2015

9. A communal catalogue reveals Earth’s multiscale microbial diversity

Author

Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, Zhao, Hongxia, University of California [San Diego] (UC San Diego), University of California, University of Southern Mississippi (USM), NOAA Atlantic Oceanographic and Meteorological Laboratory (AOML), National Oceanic and Atmospheric Administration (NOAA), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), University of California [San Francisco] (UCSF), Indiana University [Bloomington], Indiana University System, IBM Almaden Research Center [San Jose], IBM, Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], University of California-University of California, Massachusetts Institute of Technology (MIT), Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Harvard University [Cambridge], The Pathogen and Microbiome Institute, Northern Arizona University [Flagstaff], Pacific Northwest National Laboratory (PNNL), Argonne National Laboratory [Lemont] (ANL), University of Illinois [Chicago] (UIC), University of Illinois System, University of Colorado [Boulder], University of Southern California (USC), University of Chicago, Michigan State University [East Lansing], Michigan State University System, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Tieleman lab, Biological Sciences, Department of Food and Nutrition, Arctic Microbial Ecology, Thompson, Luke R., Sanders, Jon G., Mcdonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, Mckenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Agosto Rivera, Jose L., Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jiří, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, Jolynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chri, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Ander, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lanede Graaf, Kelly, Laroche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., Maccormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., Mcdonald, James E., Mcguire, Krista L., Mcmahon, Katherine D., Mcminds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Luca, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Mile, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguinorlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Taş, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., Van Der Lelie, Daniel, Van Treuren, William, Van Zwieten, Luka, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia

Subjects
MARINE BACTERIAL, 0301 basic medicine, Earth, Planet, Gene Dosage, Biodiversity, MESH: Plants, Geographic Mapping, OPERON COPY NUMBER, MESH: Gene Dosage, purl.org/becyt/ford/1 [https], RNA, Ribosomal, 16S, EARTH MICROBIOME PROJECT, MESH: Animals, MESH: Geographic Mapping, MESH: Earth, Planet, GENE-EXPRESSION, media_common, GLOBAL PATTERNS, Multidisciplinary, Ecology, Microbiota, Bacteriologie, GUT MICROBIOTA, 1184 Genetics, developmental biology, physiology, ARCHAEAL, Bacteriology, Host Pathogen Interaction & Diagnostics, Plants, MESH: RNA, Ribosomal, 16S, Food Quality and Design, MESH: Archaea, CIENCIAS NATURALES Y EXACTAS, MESH: Ecology, Rare biosphere, Otras Ciencias Biológicas, Ecology (disciplines), media_common.quotation_subject, CONSISTENT, 030106 microbiology, Context (language use), [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Article, MESH: Biodiversity, Ciencias Biológicas, 03 medical and health sciences, Microbial ecology, Animals, Humans, Life Science, MESH: Microbiota, Microbiome, purl.org/becyt/ford/1.6 [https], VLAG, Host Pathogen Interaction & Diagnostics, BACTERIAL DIVERSITY, MESH: Humans, SEQUENCES, Bacteria, Bacteriology, NESTEDNESS, 15. Life on land, RARE BIOSPHERE, Archaea, Data science, Host Pathogen Interactie & Diagnostiek, EVOLUTION, ONTOLOGY, AMPLICON SEQUENCING, MESH: Bacteria, 030104 developmental biology, Earth Microbiome Project, Bacteriologie, Host Pathogen Interactie & Diagnostiek, NESTEDNESS ANALYSIS, COMMUNITIES, MICROBIAL DIVERSITY, Diversity (politics)
Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity. Fil: Thompson, Luke R.. University of California at San Diego; Estados Unidos. University of Southern Mississippi; Estados Unidos. National Oceanic and Atmospheric Administration; Estados Unidos Fil: Sanders, Jon G.. University of California at San Diego; Estados Unidos Fil: McDonald, Daniel. University of California at San Diego; Estados Unidos Fil: Amir, Amnon. University of California at San Diego; Estados Unidos Fil: Ladau, Joshua. University of California San Francisco; Estados Unidos Fil: Locey, Kenneth J.. Indiana University; Estados Unidos Fil: Prill, Robert J.. IBM Almaden Research Center; Estados Unidos Fil: Tripathi, Anupriya. University of California at San Diego; Estados Unidos Fil: Gibbons, Sean M.. Massachusetts Institute of Technology; Estados Unidos Fil: Ackermann, Gail. University of California San Diego; Estados Unidos Fil: Navas Molina, Jose A.. University of California at San Diego; Estados Unidos Fil: Janssen, Stefan. University of California at San Diego; Estados Unidos Fil: Kopylova, Evguenia. University of California at San Diego; Estados Unidos Fil: Vázquez Baeza, Yoshiki. University of California at San Diego; Estados Unidos Fil: González, Antonio. University of California at San Diego; Estados Unidos Fil: Morton, James T.. University of California at San Diego; Estados Unidos Fil: Mirarab, Siavash. University of California at San Diego; Estados Unidos Fil: Xu, Zhenjiang Zech. University of California at San Diego; Estados Unidos Fil: Jiang, Lingjing. University of California at San Diego; Estados Unidos Fil: Haroon, Mohamed F.. Harvard University; Estados Unidos Fil: Kanbar, Jad. University of California at San Diego; Estados Unidos Fil: Zhu, Qiyun. University of California at San Diego; Estados Unidos Fil: Song, Se Jin. University of California at San Diego; Estados Unidos Fil: Kosciolek, Tomasz. University of California at San Diego; Estados Unidos Fil: Bokulich, Nicholas A.. Northern Arizona University; Estados Unidos Fil: Lefler, Joshua. University of California at San Diego; Estados Unidos Fil: Brislawn, Colin J.. Earth and Biological Sciences Directorate; Estados Unidos Fil: Humphrey, Gregory. University of California at San Diego; Estados Unidos Fil: Owens, Sarah M.. Argonne National Laboratory; Estados Unidos Fil: Hampton Marcell, Jarrad. Argonne National Laboratory; Estados Unidos. University of Illinois at Chicago; Estados Unidos Fil: Berg Lyons, Donna. University of Colorado; Estados Unidos Fil: McKenzie, Valerie. University of Colorado; Estados Unidos Fil: Fierer, Noah. University of Colorado; Estados Unidos Fil: Fuhrman, Jed A.. University of Colorado; Estados Unidos Fil: Clauset, Aaron. University of Colorado; Estados Unidos Fil: Stevens, Rick L.. Argonne National Laboratory; Estados Unidos. University of Chicago; Estados Unidos Fil: Shade, Ashley. Michigan State University; Estados Unidos Fil: Pollard, Katherine S.. The Gladstone Institutes; Estados Unidos. University of California San Francisco; Estados Unidos Fil: Goodwin, Kelly D.. National Oceanic and Atmospheric Administration; Estados Unidos Fil: Jansson, Janet K.. Earth and Biological Sciences Directorate; Estados Unidos Fil: Gilbert, Jack A.. Argonne National Laboratory; Estados Unidos. University of Chicago; Estados Unidos Fil: Knight, Rob. University of California San Diego; Estados Unidos Fil: Dionisi, Hebe Monica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Lozada, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Mac Cormack, Walter Patricio. Universidad de Buenos Aires; Argentina. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina

Published
2017

10. Precision targeting by phosphoinositides: how PIs direct endomembrane trafficking in plants Sort title: PIPs and vesicular trafficking in plants

Author

Noack, Lise, Jaillais, Yvon, 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), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), ERC under FP 3363360-APPL, ENS Lyon, 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
autophagy, MESH: Protein Transport, vacuole, MESH: Plants, tip growth, MESH: Organelle Biogenesis, PIP, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, pollen tube, MESH: Vacuoles, phosphoinositide, cell polarity, exocyst, MESH: Endosomes, phosphatidylinositol 3-phosphate, MESH: Phosphatidylinositols, endocytosis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, PtdIns, exocytosis, auxin, actin, root hair
Abstract

International audience; Each phosphoinositide (PI, also known as phosphatidylinositol phosphate, polyphosphoinositide, PtdInsP or PIP) species is partitioned in the endomembrane system and thereby contributes to the identity of membrane compartments. However, membranes are in constant flux within this system, which raises the questions of how the spatiotemporal pattern of phosphoinositides is established and maintained within the cell. Here we review the general mechanisms by which phosphoinositides and membrane trafficking feedbacks on each other to regulate cellular patterning. We then use the specific examples of polarized trafficking, endosomal sorting and vacuolar biogenesis to illustrate these general concepts.

Published
2017

11. Molecular mechanisms of gravity perception and signal transduction in plants

Author

Igor D. Volotovsky, Elizabeth Kordyum, S. V. Kretynin, Yaroslav S. Kolesnikov, V. S. Kravets, Eric Ruelland, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine (NASU), Institute of Biophysics and Cell Engineering, NASB, Minsk, National Academy of Sciences of Belarus (NASB), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), and Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) )

Subjects
0106 biological sciences, 0301 basic medicine, MESH: Signal Transduction, MESH: Gravity Sensing, Gravity, MESH: Plants, Plant Development, Plant Science, Signalling, Stimulus (physiology), Biology, 01 natural sciences, 03 medical and health sciences, MESH: Cytoskeleton, Amyloplast, MESH: Plant Development, Phospholipase, Gravity Sensing, Phosphorylation, Cytoskeleton, Plant Proteins, MESH: Phosphorylation, MESH: Plant Proteins, Cell Biology, General Medicine, Membrane transport, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cell biology, 030104 developmental biology, MESH: Protein Processing, Post-Translational, Proteome, Calcium, Signal transduction, Protein Processing, Post-Translational, Biogenesis, 010606 plant biology & botany, Signal Transduction
Abstract

International audience; Gravity is one of the environmental cues that direct plant growth and development. Recent investigations of different gravity signalling pathways have added complexity to how we think gravity is perceived. Particular cells within specific organs or tissues perceive gravity stimulus. Many downstream signalling events transmit the perceived information into subcellular, biochemical, and genomic responses. They are rapid, non-genomic, regulatory, and cell-specific. The chain of events may pass by signalling lipids, the cytoskeleton, intracellular calcium levels, protein phosphorylation-dependent pathways, proteome changes, membrane transport, vacuolar biogenesis mechanisms, or nuclear events. These events culminate in changes in gene expression and auxin lateral redistribution in gravity response sites. The possible integration of these signalling events with amyloplast movements or with other perception mechanisms is discussed. Further investigation is needed to understand how plants coordinate mechanisms and signals to sense this important physical factor.

Published
2016

12. Forecasting changes in population genetic structure of Alpine plants in response to global warming

Author

Jay, Flora, Manel, Stéphanie, Alvarez, Nadir, Durand, Eric Y, Thuiller, Wilfried, Holderegger, Rolf, Taberlet, Pierre, François, Olivier, Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire d'Entomologie Evolutive, Université de Neuchâtel (UNINE), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour le Développement (IRD [France-Sud]), and Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])

Subjects
MESH: Forecasting, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Genotype, Models, Genetic, Altitude, Population Dynamics, Temperature, MESH: Plants, MESH: Genetics, Population, MESH: Global Warming, Plants, MESH: Population Dynamics, MESH: Altitude, Adaptation, Physiological, Global Warming, MESH: Adaptation, Physiological, MESH: Temperature, MESH: Genotype, Genetics, Population, MESH: Models, Genetic, Forecasting
Abstract

International audience; Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways because of adaptation to their environment. Here, we introduced ancestry distribution models, that is, statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic admixture instead of species occurrence data. Using multi-locus genotypes and extensive geographic coverage of distribution data across the European Alps, we applied this approach to 20 alpine plant species considering a global increase in temperature from 0.25 to 4 °C. We forecasted the magnitudes of displacement of contact zones between plant populations potentially adapted to warmer environments and other populations. While a global trend of movement in a north-east direction was predicted, the magnitude of displacement was species-specific. For a temperature increase of 2 °C, contact zones were predicted to move by 92 km on average (minimum of 5 km, maximum of 212 km) and by 188 km for an increase of 4 °C (minimum of 11 km, maximum of 393 km). Intra-specific turnover-measuring the extent of change in global population genetic structure-was generally found to be moderate for 2 °C of temperature warming. For 4 °C of warming, however, the models indicated substantial intra-specific turnover for ten species. These results illustrate that, in spite of unavoidable simplifications, ancestry distribution models open new perspectives to forecast population genetic changes within species and complement more traditional distribution-based approaches.

Published
2012
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13. Occurrence and toxicity of antimicrobial triclosan and by-products in the environment

Author

Olivier Thomas, Barbara Le Bot, Benoit Roig, Virginie Dupont, Gilles Bedoux, Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'étude et de recherche en environnement et santé (LERES), École des Hautes Études en Santé Publique [EHESP] (EHESP), Domaines Océaniques (LDO), Centre National de la Recherche Scientifique (CNRS)-Institut d'écologie et environnement-Observatoire des Sciences de l'Univers-Université de Brest (UBO)-Institut national des sciences de l'Univers (INSU - CNRS), Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), Université de Bretagne Sud (UBS)-Institut Brestois du Numérique et des Mathématiques (IBNM), and Université de Brest (UBO)-Université de Brest (UBO)-Université de Brest (UBO)

Subjects
Aquatic Organisms, Geologic Sediments, Health, Toxicology and Mutagenesis, MESH: Plants, 010501 environmental sciences, MESH: Triclosan, MESH: Risk Assessment, 01 natural sciences, chemistry.chemical_compound, MESH: Animals, MESH: Vertebrates, Antibacterial agent, 0303 health sciences, Chemistry, General Medicine, Plants, Antimicrobial, Pollution, 6. Clean water, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Water Pollutants, Chemical, Environmental chemistry, Vertebrates, [SDE]Environmental Sciences, Toxicity, Sewage treatment, MESH: Aquatic Organisms, MESH: Environmental Monitoring, Environmental Monitoring, Environment, Risk Assessment, Microbiology, 03 medical and health sciences, MESH: Anti-Infective Agents, Local, MESH: Invertebrates, Animals, Humans, Environmental Chemistry, Ecotoxicology, Effluent, 030304 developmental biology, 0105 earth and related environmental sciences, EC50, MESH: Humans, Bacteria, fungi, MESH: Geologic Sediments, Invertebrates, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Triclosan, MESH: Bacteria, 13. Climate action, Anti-Infective Agents, Local, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Water Pollutants, Chemical
Abstract

International audience; INTRODUCTION AND AIMS: A review was undertaken on the occurrence, toxicity, and degradation of triclosan (TCS; 5-chloro-2,4-dichlorophenoxy)phenol) in the environment. TCS is a synthetic, broad-spectrum antibacterial agent incorporated in a wide variety of household and personal care products such as hand soap, toothpaste, and deodorants but also in textile fibers used in a range of other consumer products (e.g., toys, undergarments and cutting boards among other things). OCCURRENCE: Because of its partial elimination in sewage treatment plants, most reports describe TCS as one of the most commonly encountered substances in solid and water environmental compartments. It has been detected in a microgram per liter or microgram per kilogram level in sewage treatment plants (influents, effluents, and sludges), natural waters (rivers, lakes, and estuarine waters), and sediments as well as in drinking water. TOXICITY: Moreover, due to its high hydrophobicity, TCS can accumulate in fatty tissues and has been found in fish and human samples (urine, breast milk, and serum). TCS is known to be biodegradable, photo-unstable, and reactive towards chlorine and ozone. DISCUSSION: As a consequence, it can be transformed into potentially more toxic and persistent compounds, such as chlorinated phenols and biphenyl ethers after chlorination, methyl triclosan after biological methylation, and chlorinated dibenzodioxins after photooxidation. The toxicity of TCS toward aquatic organisms like fish, crustaceans, and algae has been demonstrated with EC50 values near TCS environmental concentrations. It has even been shown to produce cytotoxic, genotoxic, and endocrine disruptor effects. CONCLUSION: Furthermore, the excessive use of TCS is suspected to increase the risk of emergence of TCS-resistant bacteria and the selection of resistant strains.

Published
2011

14. Plant noncoding RNA gene discovery by 'single-genome comparative genomics'

Author

Liang-Hu Qu, Chong-Jian Chen, Yue-Qin Chen, Hui Zhou, Daniel Gautheret, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Genome, Plant, 0106 biological sciences, Untranslated region, RNA, Untranslated, Bioinformatics, Molecular Sequence Data, MESH: Plants, MESH: Base Sequence, MESH: RNA, Plant, Biology, Genes, Plant, Polymerase Chain Reaction, MESH: Sequence Homology, Nucleic Acid, 01 natural sciences, Genome, MESH: RNA, Untranslated, 03 medical and health sciences, Sequence Homology, Nucleic Acid, Gene duplication, MESH: Genes, Plant, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Small nucleolar RNA, Molecular Biology, Gene, 030304 developmental biology, 2. Zero hunger, Comparative genomics, Genetics, Comparative Genomic Hybridization, 0303 health sciences, MESH: Molecular Sequence Data, Base Sequence, Computational Biology, MESH: Polymerase Chain Reaction, Plants, Non-coding RNA, MESH: Comparative Genomic Hybridization, MESH: Nucleic Acid Conformation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, RNA, Plant, Multigene Family, Nucleic Acid Conformation, MESH: Multigene Family, Genome, Plant, MESH: Computational Biology, 010606 plant biology & botany
Abstract

International audience; Plant genomes have undergone multiple rounds of duplications that contributed massively to the growth of gene families. The structure of resulting families has been studied in depth for protein-coding genes. However, little is known about the impact of duplications on noncoding RNA (ncRNA) genes. Here we perform a systematic analysis of duplicated regions in the rice genome in search of such ncRNA repeats. We observe that, just like their protein counterparts, most ncRNA genes have undergone multiple duplications that left visible sequence conservation footprints. The extent of ncRNA gene duplication in plants is such that these sequence footprints can be exploited for the discovery of novel ncRNA gene families on a large scale. We developed an SVM model that is able to retrieve likely ncRNA candidates among the 100,000+ repeat families in the rice genome, with a reasonably low false-positive discovery rate. Among the nearly 4000 ncRNA families predicted by this means, only 90 correspond to putative snoRNA or miRNA families. About half of the remaining families are classified as structured RNAs. New candidate ncRNAs are particularly enriched in UTR and intronic regions. Interestingly, 89% of the putative ncRNA families do not produce a detectable signal when their sequences are compared to another grass genome such as maize. Our results show that a large fraction of rice ncRNA genes are present in multiple copies and are species-specific or of recent origin. Intragenome comparison is a unique and potent source for the computational annotation of this major class of ncRNA.

Published
2011

15. Actin dynamics in plant cells: a team effort from multiple proteins orchestrates this very fast-paced game

Author

Rajaa Boujemaa-Paterski, Laurent Blanchoin, Christopher J. Staiger, Jessica L. Henty, Parul Khurana, 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)-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), Department of Biological Sciences [Lafayette IN], Purdue University [West Lafayette], Department of Biological Sciences and Bindley Bioscience Center, 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), 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, review, MESH: Plants, Arp2/3 complex, macromolecular substances, Plant Science, MESH: Actins, Microfilament, 01 natural sciences, actin dynamics, 03 medical and health sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cytoskeleton, plant cell, Actin, Plant Proteins, 030304 developmental biology, 0303 health sciences, Total internal reflection fluorescence microscope, MESH: Plant Proteins, biology, Actin remodeling, cytoskeleton, in vitro, Plants, actin binding protein, Actin cytoskeleton, Plant cell, Actins, Cell biology, in vivo, Biophysics, biology.protein, 010606 plant biology & botany
Abstract

International audience; Gazing at a giant redwood tree in the Pacific Northwest, that has grown to enormous heights over centuries, does little to convince one that plants are built for speed and versatility. Even at the cellular level, a system of polymers-the cell skeleton or cytoskeleton-integrates signals and generates subcellular structures spanning scales of a few nanometers to hundreds of micrometers that coordinate cell growth. The term cytoskeleton itself connotes a stable structure. Clearly, this is not the case. Recent studies using advanced imaging modalities reveal the plant actin cytoskeleton to be a highly dynamic, ever changing assemblage of polymers. These insights along with growing evidence about the biochemical/biophysical properties of plant cytoskeletal polymers, especially those obtained by single filament imaging and reconstituted systems of purified proteins analyzed by total internal reflection fluorescence microscopy, allow the generation of a unique model for the dynamic turnover of actin filaments, termed stochastic dynamics. Here, we review several significant advances and highlight opportunities that will position plants at the vanguard of research on actin organization and turnover. A challenge for the future will be to apply the power of reverse-genetics in several model organisms to test the molecular details of this new model.

Published
2010

16. Cellular Remodeling During Plant Virus Infection

Author

Hélène Sanfaçon, Jean-François Laliberté, Institut Armand Frappier (INRS-IAF), Réseau International des Instituts Pasteur (RIIP)-Institut National de la Recherche Scientifique [Québec] (INRS), Pacific Agri-Food Research Center, and Agriculture and Agri-Food [Ottawa] (AAFC)

Subjects
viroplasm, viruses, MESH: Plants, Plant Science, Biology, Virus, Plant Viruses, MESH: Plant Diseases, RNA Virus Infections, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Viral entry, Viral structural protein, Viroplasm, membrane/organelle alteration, Viral shedding, Plant Diseases, MESH: Plant Viruses, MESH: RNA Virus Infections, viral replication complex, positive-sense RNA viruses, RNA, RNA virus, Plants, biology.organism_classification, Virology, Cell biology, Viral replication complex, vesicle trafficking, virus factories
Abstract

International audience; This review focuses on the extensive membrane and organelle rearrangements that have been observed in plant cells infected with RNA viruses. The modifications generally involve the formation of spherules, vesicles, and/or multivesicular bodies associated with various organelles such as the endoplasmic reticulum and peroxisomes. These virus-induced organelles house the viral RNA replication complex and are known as virus factories or viroplasms. Membrane and organelle alterations are attributed to the action of one or two viral proteins, which additionally act as a scaffold for the assembly of a large complex of proteins of both viral and host origin and viral RNA. Some virus factories have been shown to align with and traffic along microfilaments. In addition to viral RNA replication, the factories may be involved in other processes such as viral RNA translation and cell-to-cell virus transport. Confining the process of RNA replication to a specific location may also prevent the activation of certain host defense functions.

Published
2010

17. Lateral root emergence: a difficult birth

Author

Benjamin Péret, Antoine Larrieu, Malcolm J. Bennett, Centre for Plant Integrative Biology [Nothingham] (CPIB), and University of Nottingham, UK (UON)

Subjects
MESH: Signal Transduction, 0106 biological sciences, Physiology, MESH: Plants, Arabidopsis, MESH: Plant Roots, Plant Development, Plant Science, Plant Roots, 01 natural sciences, Cell wall, 03 medical and health sciences, Gene Expression Regulation, Plant, Auxin, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, MESH: Arabidopsis, MESH: Plant Development, Primordium, MESH: Gene Expression Regulation, Plant, Transcellular, Lateral root formation, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, fungi, Lateral root, Plants, biology.organism_classification, Cell biology, chemistry, Signal Transduction, 010606 plant biology & botany
Abstract

International audience; Lateral root initiation takes place deep within the parental root, requiring new primordia to break through the overlying tissues before they emerge into the soil. Lateral root emergence has been well described at the cellular level but, until recently, the molecular mechanisms involved were unclear. Scientists in the 19th and 20th centuries hypothesized that the cell wall of the overlying tissues was modified by enzymes released by cells within the primordium. Recent studies in the model plant Arabidopsis thaliana revealed the existence of a complex transcellular signalling network regulated by auxin that controls cell wall remodelling in cells overlying lateral root primordia. In the first part of this review, early observations on the cell biology of lateral root formation and emergence are summarized, and in the following two sections recent observations in Arabidopsis that led to the identification of the molecular mechanism regulating lateral root emergence are described.

Published
2009

18. New insights into ferritin synthesis and function highlight a link between iron homeostasis and oxidative stress in plants

Author

Jossia Boucherez, Nicolas Arnaud, Brigitte Touraine, Jean-François Briat, Frédéric Gaymard, Karl Ravet, Céline Duc, Françoise Cellier, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-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 National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
ferritins, Nuclear gene, Iron, MESH: Plants, MESH: Ferritins, Plant Science, seeds, Biology, 03 medical and health sciences, Arabidopsis, Gene expression, bacterioferritins, oxidative stress, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Cellular localization, 030304 developmental biology, 2. Zero hunger, MESH: Iron, 0303 health sciences, MESH: Oxidative Stress, ACL, fungi, 030302 biochemistry & molecular biology, food and beverages, Plant physiology, pathogens, Plants, biology.organism_classification, iron storage, Ferritin, Iron Homeostasis and Iron Acquisition in Plants, nutrition, Biochemistry, biology.protein, Function (biology)
Abstract

International audience; BACKGROUND: Iron is an essential element for both plant productivity and nutritional quality. Improving plant iron content was attempted through genetic engineering of plants overexpressing ferritins. However, both the roles of these proteins in plant physiology, and the mechanisms involved in the regulation of their expression are largely unknown. Although the structure of ferritins is highly conserved between plants and animals, their cellular localization differs. Furthermore, regulation of ferritin gene expression in response to iron excess occurs at the transcriptional level in plants, in contrast to animals which regulate ferritin expression at the translational level. SCOPE: In this review, an overview of our knowledge of bacterial and mammalian ferritin synthesis and functions is presented. Then the following will be reviewed: (a) the specific features of plant ferritins; (b) the regulation of their synthesis during development and in response to various environmental cues; and (c) their function in plant physiology, with special emphasis on the role that both bacterial and plant ferritins play during plant-bacteria interactions. Arabidopsis ferritins are encoded by a small nuclear gene family of four members which are differentially expressed. Recent results obtained by using this model plant enabled progress to be made in our understanding of the regulation of the synthesis and the in planta function of these various ferritins. CONCLUSIONS: Studies on plant ferritin functions and regulation of their synthesis revealed strong links between these proteins and protection against oxidative stress. In contrast, their putative iron-storage function to furnish iron during various development processes is unlikely to be essential. Ferritins, by buffering iron, exert a fine tuning of the quantity of metal required for metabolic purposes, and help plants to cope with adverse situations, the deleterious effects of which would be amplified if no system had evolved to take care of free reactive iron.

Published
2009

19. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Author

Robert Otillar, Olivier Panaud, Aaron Poliakov, Ian T. Paulsen, Eve Toulza, Steven Robbens, Heidrun Gundlach, Pedro M. Coutinho, E. Virginia Armbrust, Jill E. Gready, Klaus F. X. Mayer, Jasmyn Pangilinan, Kemin Zhou, Igor V. Grigoriev, Wenche Eikrem, Marie L. Cuvelier, Elif Demir, Ursula Goodenough, Jonathan H. Badger, Hervé Moreau, Susan Lucas, Peter von Dassow, Yves Van de Peer, Evelyne Derelle, Pierre Rouzé, Andrew E. Allen, Erika Lindquist, Uwe John, Elodie Foulon, Jeremy Schmutz, Fabrice Not, William Lanier, Meredith V. Everett, Alex N. Zelensky, Sarah M. McDonald, Benoît Piégu, Jane Grimwood, Tania Wyss, Chelle L. Gentemann, Aasf Salamov, Micaela S. Parker, Stephane Rombauts, Alexandra Z. Worden, Carolyn A. Napoli, Thomas Mock, Bernard Henrissat, Jae-Hyeok Lee, Inna Dubchak, Melinda P. Simmons, Andrea Aerts, Debashish Bhattacharya, Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, School of Oceanography [Seattle], University of Washington [Seattle], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Biology Institute, University of Arizona, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, Stanford University School of Medicine [Stanford], Stanford University [Stanford], and Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, MESH: Sequence Analysis, DNA, RNA, Untranslated, MESH: Oceans and Seas, MESH: Introns, MESH: Plants, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genome, 18S ribosomal RNA, Bathycoccus, MESH: Chlorophyta, MESH: RNA, Untranslated, Chlorophyta, MESH: Ecosystem, MESH: Genetic Variation, Photosynthesis, MESH: Phylogeny, Clade, Phylogeny, MESH: Photosynthesis, Plant evolution, 0303 health sciences, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], MESH: Transcription Factors, Plants, Adaptation, Physiological, Biological Evolution, MESH: Gene Expression Regulation, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Genes, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Meiosis, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], MESH: DNA Transposable Elements, Oceans and Seas, Molecular Sequence Data, MESH: Biological Evolution, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 14. Life underwater, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Ecosystem, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, Micromonas, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Repetitive Sequences, Nucleic Acid, MESH: Molecular Sequence Data, Genetic Variation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Sequence Analysis, DNA, biology.organism_classification, MESH: Adaptation, Physiological, Introns, MESH: Meiosis, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Gene Expression Regulation, Genes, Phytoplankton, DNA Transposable Elements, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Transcription Factors, MESH: Phytoplankton, 010606 plant biology & botany
Abstract

Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18 S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

Published
2009

20. Genomic imprinting in Singapore

Author

Benjamin Loppin, Rebecca J. Oakey, Centre de génétique et de physiologie moléculaire et cellulaire (CGPhiMC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Singapore, MESH: Plants, Review Article, Biology, Biochemistry, Germline, Genomic Imprinting, 03 medical and health sciences, MESH: Invertebrates, 0302 clinical medicine, X Chromosome Inactivation, Genetics, Animals, Humans, MESH: Animals, Imprinting (psychology), Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Singapore, 0303 health sciences, MESH: Humans, MESH: X Chromosome Inactivation, Dosage compensation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Congresses as Topic, Plants, MESH: Gene Expression Regulation, Invertebrates, MESH: Genomic Imprinting, Chromatin, Organization workshop, Gene Expression Regulation, Evolutionary biology, B-Lymphocyte-Induced Maturation Protein 1, Genomic imprinting, Reprogramming, MESH: Congresses as Topic, 030217 neurology & neurosurgery
Abstract

The EMBO Workshop on Genomic Imprinting took place between 21 and 24 September 2008, in Singapore, and was organized by F. Berger, M. Bartolomei and R. Feil. This painting, entitled ‘Back of Telok Ayer Street 2007’ and painted by C. Ek Kay, was the image included in the meeting poster. ![][1] See Glossary for abbreviations used in this article The organizers of the European Molecular Biology Organization Workshop on Genomic Imprinting chose a truly trans‐kingdom selection of speakers; there was a strong representation of those working in plants and mammals, with a sprinkling of those studying flies and worms. This organismal diversity was layered further with talks on topics ranging from germ cells, genomic imprinting and dosage compensation to genome‐wide screens, evolution and human disease. These areas dovetailed well, converging ideas from various species and unifying seemingly divergent fields. Here, we highlight a few of the topics from an excellent programme of riveting news and novel findings. One of the main themes threading through this workshop was that of commitment, reprogramming and pluripotency. A. Surani (Cambridge, UK) discussed the initiation of epigenetic reprogramming in the germline. The main focus was on BLIMP1, which is an important regulator of germ cells that has roles in diverse processes, including the initiation of the PGC‐specification programme and exit from the pluripotent state. In this plenary address, Surani drew from several studies that illustrate the induction of cells to exit the pluripotent state and initiate the PGC‐specific programme, including the role of STELLA —a mammalian maternal‐effect gene that probably has a role in chromosomal organization. The BLIMP1 protein sets up chromatin signatures and influences the epigenetic reprogramming associated with X‐chromosome reactivation (Chuva de Sousa et al , 2008) and imprinting, emphasizing the links among pluripotency, reprogramming and commitment that were reiterated in several other talks. W. … [1]: /embed/graphic-1.gif

Published
2009

21. Glutaredoxins and thioredoxins in plants

Author

Christophe Riondet, Florence Vignols, Jean-Philippe Reichheld, Yves Meyer, Wafi Siala, Talaat Bashandy, Laboratoire Génome et développement des plantes (LGDP), and Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH: Genome, Plant, MESH: Oxidation-Reduction, 0106 biological sciences, Thioredoxin reductase, Glutaredoxin, Mutant, Arabidopsis, MESH: Plants, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Proteomics, 01 natural sciences, Thioredoxins, MESH: Thioredoxins, Plant Proteins, 0303 health sciences, MESH: Plant Proteins, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], food and beverages, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Plants, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Phenotype, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Biochemistry, Thioredoxin, Oxidation-Reduction, Genome, Plant, MESH: Glutaredoxins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Redox, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, Glutaredoxins, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, biology.organism_classification, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Rice, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract

International audience; During the 70s and 80s two plant thioredoxin systems were identified. The chloroplastic system is composed of a ferredoxin-dependent thioredoxin, with two thioredoxin types (m and f) regulating the activity of enzymes implicated in photosynthetic carbon assimilation. In the cytosol of heterotrophic tissues, an NADP dependent thioredoxin reductase and a thioredoxin (h) were identified. The first plant glutaredoxin was only identified later, in 1994. Our view of plant thioredoxins and glutaredoxins was profoundly modified by the sequencing programs which revealed an unexpected number of genes encoding not only the previously identified disulfide reductases, but also numerous new types. At the same time it became clear that plant genomes encode chloroplastic, cytosolic and mitochondrial peroxiredoxins, suggesting a major role for redoxins in anti-oxidant defense. Efficient proteomics approaches were developed allowing the characterization of numerous thioredoxin target proteins. They are implicated in different aspects of plant life including development and adaptation to environmental changes and stresses. The most important challenge for the next years will probably be to identify in planta which redoxin reduces which target, a question which remains unsolved due to the low specificities of redoxins in vitro and the numerous redundancies which in most cases mask the phenotype of redoxin mutants.

Published
2008

22. Allergenic pollen and pollen allergy in Europe

Author

Gennaro Liccardi, P. Van Cauwenberge, Sergio Bonini, Todor A. Popov, Isabella Annesi-Maesano, Heidrun Behrendt, Gennaro D'Amato, Lorenzo Cecchi, Carlos Nunes, Damato, G, Cecchi, L, Bonini, Sergio, Nunes, C, ANNESI MAESANO, I, Behrendt, H, Liccardi, G, Popov, T, VAN CAUWENBERGE, P., Epidémiologie des maladies infectieuses et modélisation (ESIM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Informatique de Paris-Nord (LIPN), Université Paris 13 (UP13)-Institut Galilée-Université Sorbonne Paris Cité (USPC)-Centre National de la Recherche Scientifique (CNRS), G D'Amato, L Cecchi, S Bonini, C Nunes, Annesi-Maesano I, H Behrendt, G Liccardi, T Popov, and P Van Cauwenberge

Subjects
Ragweed, MESH: Air Pollution, MESH: Allergens, MESH: Hypersensitivity, Climate, Immunology, MESH: Plants, Air pollution, Climate change, medicine.disease_cause, Air Pollution, Pollen, Hypersensitivity, otorhinolaryngologic diseases, medicine, Humans, Immunology and Allergy, MESH: Weather, Cypress, Weather, MESH: Humans, Pollen calendar, biology, business.industry, Ecology, food and beverages, Allergens, Plants, MESH: Climate, biology.organism_classification, Europe, Seasonal allergy, MESH: Pollen, Biological dispersal, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Europe, business
Abstract

International audience; The allergenic content of the atmosphere varies according to climate, geography and vegetation. Data on the presence and prevalence of allergenic airborne pollens, obtained from both aerobiological studies and allergological investigations, make it possible to design pollen calendars with the approximate flowering period of the plants in the sampling area. In this way, even though pollen production and dispersal from year to year depend on the patterns of preseason weather and on the conditions prevailing at the time of anthesis, it is usually possible to forecast the chances of encountering high atmospheric allergenic pollen concentrations in different areas. Aerobiological and allergological studies show that the pollen map of Europe is changing also as a result of cultural factors (for example, importation of plants such as birch and cypress for urban parklands), greater international travel (e.g. colonization by ragweed in France, northern Italy, Austria, Hungary etc.) and climate change. In this regard, the higher frequency of weather extremes, like thunderstorms, and increasing episodes of long range transport of allergenic pollen represent new challenges for researchers. Furthermore, in the last few years, experimental data on pollen and subpollen-particles structure, the pathogenetic role of pollen and the interaction between pollen and air pollutants, gave new insights into the mechanisms of respiratory allergic diseases.

Published
2007

23. Optimizing Polychlorinated Biphenyl Degradation by Flavonoid-Induced Cells of the Rhizobacterium Rhodococcus erythropolis U23A

Author

Nancy Johanna Pino Rodriguez, Thi Thanh My Pham, Michel Sylvestre, Mohamed Hijri, Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Institut de la Recherche en Biologie Végétale Departement de sciences biologiques, and This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) (grant RGPIN/39579-2012).

Subjects
MESH: Hydrogen-Ion Concentration, Metabolite, [SDV]Life Sciences [q-bio], Flavonoid, MESH: Plants, lcsh:Medicine, MESH: Plant Roots, Disaccharides, Plant Roots, Polymerase Chain Reaction, MESH: Biodegradation, Environmental, chemistry.chemical_compound, MESH: Disaccharides, [SDV.IDA]Life Sciences [q-bio]/Food engineering, MESH: Hexoses, Rhodococcus, heterocyclic compounds, lcsh:Science, MESH: Bacterial Proteins, MESH: Rhizobiaceae, chemistry.chemical_classification, Biphenyl, Growth medium, MESH: Gene Expression Regulation, Bacterial, Multidisciplinary, food and beverages, Hydrogen-Ion Concentration, Plants, Polychlorinated Biphenyls, Biodegradation, Environmental, Biochemistry, MESH: Environmental Pollutants, DNA Gyrase, MESH: Rhodococcus, Biological Assay, Environmental Pollutants, Mannitol, Flavanone, medicine.drug, Research Article, MESH: DNA Gyrase, MESH: Biological Assay, Dioxygenases, Bacterial Proteins, Rhizobiaceae, MESH: Dioxygenases, medicine, MESH: Chlorobenzoates, Hexoses, Flavonoids, organic chemicals, lcsh:R, fungi, MESH: Polymerase Chain Reaction, Gene Expression Regulation, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Culture Media, Chlorobenzoates, Metabolic pathway, MESH: Polychlorinated Biphenyls, Enzyme, chemistry, MESH: Culture Media, lcsh:Q, MESH: Flavonoids
Abstract

International audience; There is evidence that many plant secondary metabolites may act as signal molecules to trigger the bacterial ability to metabolize polychlorinated biphenyls (PCBs) during the rhizoremediation process. However, the bases for the PCB rhizoremediation process are still largely unknown. The rhizobacterium Rhodococcus erythropolis U23A is unable to use flavanone as a growth substrate. However, on the basis of an assay that monitors the amount of 4-chlorobenzoate produced from 4-chlorobiphenyl by cells grown co-metabolically on flavanone plus sodium acetate, this flavonoid was previously found to be a potential inducer of the U23A biphenyl catabolic pathway. In this work, and using the same assay, we identified ten other flavonoids that did not support growth, but that acted as inducers of the U23A biphenyl pathway, and we confirmed flavonoid induction of the biphenyl catabolic pathway using quantitative real-time polymerase chain reaction (RT-qPCR) on the bphA gene. We also examined the effect of the growth co-substrate on flavonoid induction. Sodium acetate was replaced by glucose, mannose, sucrose, or mannitol, which are sugars found in plant root exudates. The data showed that the level of induction of strain U23A biphenyl-degrading enzymes was significantly influenced by the nature and concentration of the flavonoid in the growth medium, as well as by the substrate used for growth. Sucrose allowed for an optimal induction response for most flavonoids. Some flavonoids, such as flavone and isoflavone, were better inducers of the biphenyl catabolic enzymes than biphenyl itself. We also found that all flavonoids tested in this work were metabolized by strain U23A during co-metabolic growth, but that the metabolite profiles, as well as the level of efficiency of degradation, differed for each flavonoid. To obtain insight into how flavonoids interact with strain U23A to promote polychlorinated biphenyl (PCB) degradation, we determined the concentration of flavanone at which optimal PCB-degrading performance of strain U23A was achieved. We showed that it corresponded to the concentration required to fully induce the biphenyl catabolic pathway of the strain. Together, our data demonstrate that optimal PCB degradation during the rhizoremediation process will require the adjustment of several parameters, including the presence of the appropriate flavonoids at the proper concentrations and the presence of proper growth substrates that positively influence the ability of flavonoids to induce the pathway.

Published
2015

24. Evolution of the Rho Family of Ras-Like GTPases in Eukaryotes

Author

Emmanuel Vignal, Philippe Fort, Sandrine Faure, Anthony Boureux, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherches de biochimie macromoléculaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-IFR122-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Université de Montpellier (UM)-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)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Philippe, Fort

Subjects
rho GTP-Binding Proteins, Subfamily, MESH: Plants, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], MESH: Amino Acid Sequence, CDC42, GTPase, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 0302 clinical medicine, Gene Duplication, MESH: Pseudogenes, MESH: Animals, MESH: Phylogeny, MESH: Vertebrates, Phylogeny, ComputingMilieux_MISCELLANEOUS, MESH: Evolution, Molecular, 0303 health sciences, MESH: Gene Duplication, [SDV.BDD.EO] Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, cytoskeleton, Plants, Cell biology, 030220 oncology & carcinogenesis, Vertebrates, Pseudogenes, MESH: Fungi, Pseudogene, Molecular Sequence Data, MESH: Sequence Alignment, [SDV.CAN]Life Sciences [q-bio]/Cancer, Chordate, RAC1, Biology, Article, Evolution, Molecular, 03 medical and health sciences, MESH: Invertebrates, [SDV.CAN] Life Sciences [q-bio]/Cancer, Rho, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, evolution, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Genetics, Animals, Humans, cell signaling, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, RhoBTB, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, MESH: Molecular Sequence Data, MESH: Humans, Alternative splicing, Fungi, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: rho GTP-Binding Proteins, biology.organism_classification, Invertebrates, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Sequence Alignment
Abstract

International audience; GTPases of the Rho family are molecular switches that play important roles in converting and amplifying external signals into cellular effects. Originally de onstrated to control the dynamics of the F-actin cytoskeleton, Rho GTPases have been implicated in many basic cellular processes that influence cell proliferation, differentiation, motility, adhesion, survival, or secretion. To elucidate the evolutionary history of the Rho family, we have analyzed over 20 species covering major eukaryotic clades from unicellular organisms to mammals, including platypus and opossum, and have reconstructed the ontogeny and the chronology of emergence of the different subfamilies. Our data establish that the 20 mammalian Rho members are structured into 8 subfamilies, among which Rac is the founder of the whole family. Rho, Cdc42, RhoUV, and RhoBTB subfamilies appeared before Coelomates and RhoJQ, Cdc42 isoforms, RhoDF, and Rnd emerged in chordates. In vertebrates, gene duplications and retrotranspositions increased the size of each chordate Rho subfamily, whereas RhoH, the last subfamily, arose probably by horizontal gene transfer. Rac1b, a Rac1 isoform generated by alternative splicing, emerged in amniotes, and RhoD, only in therians. Analysis of Rho mRNA expression patterns in mouse tissues shows that recent subfamilies have tissue-specific and low-level expression that supports their implication only in narrow time windows or in differentiated metabolic functions. These findings give a comprehensive view of the evolutionary canvas of the Rho family and provide guides for future structure and evolution studies of other components of Rho signaling pathways, in particular regulators of the RhoGEF family.

Published
2006

25. Spatio-temporal variability of faunal and floral assemblages in Mediterranean temporary wetlands

Author

Zeineb Ghrabi-Gammar, Ali Bouattour, Amina Daoud-Bouattour, Stéphanie Gascón, Serge Muller, Jordi Sala, Samia Ben Saad-Limam, Dani Boix, Maya Rouissi, Albert Ruhí, Imtinen Ben Haj Jilani, Faculté des Lettres, des Arts et des Humanités de la Manouba (FLAHM), Université de la Manouba [Tunisie] (UMA), Faculté des Sciences Mathématiques, Physiques et Naturelles de Tunis (FST), Université de Tunis El Manar (UTM), Faculté des Sciences de Bizerte [Université de Carthage], Université de Carthage - University of Carthage, Universitat de Girona, Universitat de Girona (UdG), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Institut supérieur des études préparatoires en biologie et géologie, Insititut National d'Agronomie de Tunisie, Financial support was provided by UR99/UR/02-04 Biogéographie, Climatologie Appliquée et Dynamique Erosive, FLAHM, Université de la Manouba, Tunisia, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)

Subjects
0106 biological sciences, Mediterranean climate, Aquatic Organisms, Fauna, [SDV]Life Sciences [q-bio], Biodiversity, Endangered species, MESH: Plants, Wetland, 01 natural sciences, Hydrophytes, MESH: Mediterranean Region, MESH: Animals, geography.geographical_feature_category, Mediterranean Region, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, Aquatic fauna, Faune aquatique, General Medicine, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 6. Clean water, Geography, Seasons, Biodiversité, General Agricultural and Biological Sciences, MESH: Tunisia, MESH: Aquatic Organisms, Tunisia, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, MESH: Biodiversity, MESH: Endangered Species, Northern Tunisia, Aquatic plant, MESH: Water, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 14. Life underwater, MESH: Wetlands, General Immunology and Microbiology, Dynamique saisonnière, 010604 marine biology & hydrobiology, Endangered Species, Water, 15. Life on land, Seasonal dynamics, 13. Climate action, Wetlands, Tunisie septentrionale, MESH: Seasons
Abstract

International audience; Six temporary wetlands in the region of Sejenane (Mogods, NW Tunisia) were studied in order to characterize the aquatic flora and fauna and to quantify their spatio-temporal variability. Samplings of aquatic fauna, phytosociological relevés, and measurements of the physicochemical parameters of water were taken during four different field visits carried out during the four seasons of the year (November 2009-July 2010). Despite the strong anthropic pressures on them, these temporary wetlands are home to rich and diversified biodiversity, including rare and endangered species. Spatial and temporal variations affect fauna and flora differently, as temporal variability influences the fauna rather more than the plants, which are relatively more dependent on spatial factors. These results demonstrate the interest of small water bodies for maintaining biodiversity at the regional level, and thus underscore the conservation issues of Mediterranean temporary wetlands that are declining on an ongoing basis currently.

Published
2014

26. Diversity of the exoproteome of Fusarium graminearum grown on plant cell wall

Author

Emmanuelle Leize-Wagner, Florence Goubet, Vincent Phalip, François Delalande, Didier Hatsch, Christine Carapito, Paul Dupree, Jean-Marc Jeltsch, Alain Van Dorsselaer, Klotz, Evelyne, Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Substances naturelles/chimie moléculaire, Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique (CNRS), and Institut Pluridisciplinaire Hubert Curien (IPHC)

Subjects
Polysaccharides/chemistry, Humulus lupulus, MESH: Plants, MESH: Cellulose 1,4-beta-Cellobiosidase, Proteomics, Cellulose 1, Plant Proteins/*chemistry/metabolism, Fusarium, Cell Wall, Gene Expression Regulation, Plant, Glucose/metabolism, Non-U.S. Gov't, Plant Proteins, chemistry.chemical_classification, MESH: Fusarium, 0303 health sciences, MESH: Plant Proteins, biology, food and beverages, General Medicine, Plants, 4-beta-Cellobiosidase/chemistry/metabolism, MESH: Glucose, Biochemistry, Fusarium/*chemistry/growth & development, Fungus, Research Support, Microbiology, Cell wall, 03 medical and health sciences, MESH: Cell Wall, Polysaccharides, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Cellulose 1,4-beta-Cellobiosidase, Genetics, Extracellular, Secretion, MESH: Gene Expression Regulation, Plant, 030304 developmental biology, Plants/*microbiology, 030306 microbiology, Cell Wall/chemistry/*metabolism, Plant, biology.organism_classification, MESH: Polysaccharides, Glucose, Enzyme, Gene Expression Regulation, chemistry
Abstract

0172-8083 (Print) Journal Article; The exoproteome of the fungus Fusarium graminearum grown on glucose and on hop (Humulus lupulus, L.) cell wall has been investigated. The culture medium was found to contain a higher quantity of proteins and the proteins are more diverse when the fungus is grown on cell wall. Using both 1D and 2D electrophoresis followed by mass spectrometry analysis and protein identification based on similarity searches, 84 unique proteins were identified in the cell wall-grown fungal exoproteome. Many are putatively implicated in carbohydrate metabolism, mainly in cell wall polysaccharide degradation. The predicted carbohydrate-active enzymes fell into 24 different enzymes classes, and up to eight different proteins within a same class are secreted. This indicates that fungal metabolism becomes oriented towards synthesis and secretion of a whole arsenal of enzymes able to digest almost the complete plant cell wall. Cellobiohydrolase is one of the only four proteins found both after growth on glucose and on plant cell wall and we propose that this enzyme could act as a sensor of the extracellular environment. Extensive knowledge of this very diverse F. graminearum exoproteome is an important step towards the full understanding of Fusarium/plants interactions.

Published
2005

27. A meta-analysis of arbuscular mycorrhizal effects on plants grown under salt stress

Author

Tongmin Sa, Sonia Boughattas, Sang-Hyon Oh, Murugesan Chandrasekaran, Shuijin Hu, Department of Environmental and Biological Chemistry, Chungbuk National University, Laboratoire d'Epidémiologie et d'Ecologie parasitaire, Institut Pasteur de Tunis, Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Department of Animal Sciences, North Carolina A&T State University, University of North Carolina System (UNC)-University of North Carolina System (UNC), and This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean Government (MEST) (No. 2012R1A2A1A01005294).

Subjects
Soil salinity, MESH: Sodium Chloride, Perennial plant, MESH: Plant Shoots, [SDV]Life Sciences [q-bio], Salt stress, MESH: Plants, MESH: Plant Roots, Plant Science, Sodium Chloride, Biology, Plant Roots, Nutrient, MESH: Biomass, Mycorrhizae, Genetics, Biomass, Nutrient uptake, Arbuscular mycorrhiza, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Plant growth, 2. Zero hunger, MESH: Salt-Tolerance, fungi, food and beverages, Salt Tolerance, General Medicine, Plants, 15. Life on land, Herbaceous plant, biology.organism_classification, Salinity, Meta-analysis, Agronomy, Shoot, Antioxidant enzymes, MESH: Mycorrhizae, Plant Shoots, Woody plant
Abstract

International audience; Salt stress limits crop yield and sustainable agriculture in most arid and semiarid regions of the world. Arbuscular mycorrhizal fungi (AMF) are considered bio-ameliorators of soil salinity tolerance in plants. In evaluating AMF as significant predictors of mycorrhizal ecology, precise quantifiable changes in plant biomass and nutrient uptake under salt stress are crucial factors. Therefore, the objective of the present study was to analyze the magnitude of the effects of AMF inoculation on growth and nutrient uptake of plants under salt stress through meta-analyses. For this, data were compared in the context of mycorrhizal host plant species, plant family and functional group, herbaceous vs. woody plants, annual vs. perennial plants, and the level of salinity across 43 studies. Results indicate that, under saline conditions, AMF inoculation significantly increased total, shoot, and root biomass as well as phosphorous (P), nitrogen (N), and potassium (K) uptake. Activities of the antioxidant enzymes superoxide dismutase, catalase, peroxidase, and ascorbate peroxidase also increased significantly in mycorrhizal compared to nonmycorrhizal plants growing under salt stress. In addition, sodium (Na) uptake decreased significantly in mycorrhizal plants, while changes in proline accumulation were not significant. Across most subsets of the data analysis, identities of AMF (Glomus fasciculatum) and host plants (Acacia nilotica, herbs, woody and perennial) were found to be essential in understanding plant responses to salinity stress. For the analyzed dataset, it is concluded that under salt stress, mycorrhizal plants have extensive root traits and mycorrhizal morphological traits which help the uptake of more P and K, together with the enhanced production of antioxidant enzymes resulting in salt stress alleviation and increased plant biomass.

Published
2014

28. Editorial overview: Host–microbe interactions: viruses: Viral sensing and activation of immunity

Author

Maria-Carla Saleh, Virus et Interférence ARN - Viruses and RNA Interference, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), [SDV]Life Sciences [q-bio], MESH: Plants, Virus Physiological Phenomena, Biology, Microbiology, Article, MESH: Viruses, 03 medical and health sciences, Immunity, Animals, Humans, MESH: Animals, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, MESH: Humans, 030306 microbiology, Host (biology), MESH: Host-Pathogen Interactions, MESH: Virus Physiological Phenomena, Plants, Virology, Immunity, Innate, 3. Good health, Infectious Diseases, Host-Pathogen Interactions, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: Immunity, Innate, Introductory Journal Article
Abstract

International audience

Published
2014

29. Mitochondria: An organelle for life

Author

Laurence Maréchal-Drouard, Ivan Tarassov, Marie Sissler, and Centre National de la Recherche Scientifique (CNRS)

Subjects
Mitochondrial Diseases, MESH: Mitochondria, [SDV]Life Sciences [q-bio], 030231 tropical medicine, MESH: Plants, Mitochondrion, Biology, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Organelle, Animals, Humans, MESH: Animals, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, MESH: Humans, MESH: Mitochondrial Diseases, General Medicine, Plants, Cell biology, Mitochondria, Genome, Mitochondrial, Organelle biogenesis, MESH: Genome, Mitochondrial
Abstract

International audience

Published
2014

30. Fast and Efficient Estimation of Individual Ancestry Coefficients

Author

Théo Trouillon, Eric Frichot, Guillaume Bouchard, François Mathieu, Olivier François, Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Xerox Research Centre Europe [Meylan], Xerox Company, This work has been partially supported by the LabExPERSYVAL-Lab(ANR-11-LABX-0025-01), ANR-11-LABX-0025,PERSYVAL-lab,Systemes et Algorithmes Pervasifs au confluent des mondes physique et numérique(2011), Francois, Olivier, and Laboratoires d'excellence - Systemes et Algorithmes Pervasifs au confluent des mondes physique et numérique - - PERSYVAL-lab2011 - ANR-11-LABX-0025 - LABX - VALID

Subjects
Time Factors, Genotype, Genomic data, Population, Large population, MESH: Plants, MESH: Population Groups, Inference, MESH: Genetics, Population, MESH: Algorithms, Biology, Investigations, Bioinformatics, Non-negative matrix factorization, MESH: Genotype, MESH: Software, Software, Gene Frequency, Population Groups, Genetics, MESH: Gene Frequency, Humans, education, Genetic Association Studies, MESH: Genetic Association Studies, Estimation, education.field_of_study, Likelihood Functions, MESH: Humans, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Computer program, business.industry, MESH: Time Factors, Computational Biology, Plants, Genetics, Population, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], MESH: Likelihood Functions, business, Algorithm, Algorithms, MESH: Computational Biology
Abstract

Inference of individual ancestry coefficients, which is important for population genetic and association studies, is commonly performed using computer-intensive likelihood algorithms. With the availability of large population genomic data sets, fast versions of likelihood algorithms have attracted considerable attention. Reducing the computational burden of estimation algorithms remains, however, a major challenge. Here, we present a fast and efficient method for estimating individual ancestry coefficients based on sparse nonnegative matrix factorization algorithms. We implemented our method in the computer program sNMF and applied it to human and plant data sets. The performances of sNMF were then compared to the likelihood algorithm implemented in the computer program ADMIXTURE. Without loss of accuracy, sNMF computed estimates of ancestry coefficients with runtimes ∼10–30 times shorter than those of ADMIXTURE.

Published
2014

31. Plant phosphoinositide-dependent phospholipases C: Variations around a canonical theme

Author

Yaroslav S. Kolesnikov, Igor Pokotylo, Alain Zachowski, V. S. Kravets, Eric Ruelland, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine (NASU), Physiologie cellulaire et moléculaire des plantes (PCMP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), and Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Phosphoinositides, MESH: Plants, MESH: Catalytic Domain, 01 natural sciences, Biochemistry, chemistry.chemical_compound, Inositol-phosphate, Phosphoinositide Phospholipase C, Gene Expression Regulation, Plant, Catalytic Domain, Phosphatidic acid, MESH: Animals, Lipid signalling, Inositol phosphate, MESH: Phylogeny, Phylogeny, MESH: Organ Specificity, Plant Proteins, MESH: Lipid Metabolism, chemistry.chemical_classification, 0303 health sciences, MESH: Plant Proteins, General Medicine, Plants, Adaptation, Physiological, Pleckstrin homology domain, Organ Specificity, Biology, 03 medical and health sciences, Phospholipase C, MESH: Phosphoinositide Phospholipase C, Animals, Humans, Phosphatidylinositol, MESH: Gene Expression Regulation, Plant, 030304 developmental biology, Diacylglycerol kinase, MESH: Humans, Phospholipase D, Lipid signaling, Lipid Metabolism, MESH: Adaptation, Physiological, Inositol pentakisphosphate, chemistry, MESH: Protein Processing, Post-Translational, Protein Processing, Post-Translational, 010606 plant biology & botany
Abstract

International audience; Phosphoinositide-specific phospholipase C (PI-PLC) cleaves, in a Ca 2þ-dependent manner, phosphati-dylinositol-4,5-bisphosphate (PI-4,5-P 2) into diacylglycerol (DAG) and inositol triphosphate (IP 3). PI-PLCs are multidomain proteins that are structurally related to the PI-PLCzs, the simplest animal PI-PLCs. Like these animal counterparts, they are only composed of EF-hand, X/Y and C2 domains. However, plant PI-PLCs do not have a conventional EF-hand domain since they are often truncated, while some PI-PLCs have no EF-hand domain at all. Despite this simple structure, plant PI-PLCs are involved in many essential plant processes, either associated with development or in response to environmental stresses. The action of PI-PLCs relies on the mediators they produce. In plants, IP 3 does not seem to be the sole active soluble molecule. Inositol pentakisphosphate (IP 5) and inositol hexakisphosphate (IP 6) also transmit signals, thus highlighting the importance of coupling PI-PLC action with inositol-phosphate kinases and phosphatases. PI-PLCs also produce a lipid molecule, but plant PI-PLC pathways show a peculiarity in that the active lipid does not appear to be DAG but its phosphorylated form, phosphatidic acid (PA). Besides, PI-PLCs can also act by altering their substrate levels. Taken together, plant PI-PLCs show functional differences when compared to their animal counterparts. However, they act on similar general signalling pathways including calcium homeostasis and cell phosphoproteome. Several important questions remain unanswered. The cross-talk between the soluble and lipid mediators generated by plant PI-PLCs is not understood and how the coupling between PI-PLCs and inositol-kinases or DAG-kinases is carried out remains to be established.

Published
2014

32. The cytochrome b6f complex: structural studies and comparison with the bc1 complex

Author

Cécile Breyton, Max Planck Institute of Biophysics [Frankfurt am Main] (MPIBP), and Max-Planck-Gesellschaft

Subjects
MESH: Chlamydomonas reinhardtii, Cytochrome, Stereochemistry, MESH: Plants, Biophysics, Polyenes, Biology, Biochemistry, Electron Transport Complex III, chemistry.chemical_compound, MESH: Electron Transport Complex III, MESH: Polyenes, Stigmatellin, Animals, MESH: Cytochrome b Group, MESH: Animals, Cytochrome b6f complex, Cytochrome bc1 complex, MESH: Crystallization, Crystallography, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Electron crystallography, Cytochrome b, MESH: Crystallography, MESH: Cytochrome b6f Complex, Eukaryota, Membrane Proteins, Cell Biology, Plants, Cytochrome b Group, MESH: Eukaryota, Transmembrane domain, chemistry, Membrane protein, Coenzyme Q – cytochrome c reductase, biology.protein, Rieske protein, MESH: Membrane Proteins, Crystallization, Chlamydomonas reinhardtii
Abstract

Electron crystallography of the chloroplastic b6f complex allowed the calculation of projection maps of crystals negatively stained or embedded in glucose. This gives insights into the overall structure of the extra- and transmembrane domains of the complex. A comparison with the structure of the bc1 complex, the mitochondrial homologue of the b6f complex, suggests that the transmembrane domains of the two complexes are very similar, confirming the structural homology deduced from sequence analysis. On the other hand, the extramembrane organisation of the c-type cytochrome and of the Rieske protein seems quite different. Nevertheless, the same type of movement of the Rieske protein is observed in the b6f as in the bc1 complex upon the binding of the quinol analogue stigmatellin. Crystallographic data also suggest movements in the transmembrane domains of the b6f complex, which would be specific of the b6f complex. fl 2000 Elsevier Science B.V. All rights reserved.

Published
2000

33. Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species

Author

Matthew Hartfield, Sylvain Glémin, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226

Subjects
MESH: Selection, Genetic, MESH: Plants, MESH: Genetics, Population, Plant Development, adaptation, Self-Fertilization, Biology, mating system evolution, Investigations, dominance, MESH: Genetic Fitness, Effective selfing model, MESH: Inbreeding, MESH: Polymorphism, Genetic, Genetics, Inbreeding depression, selfing, MESH: Plant Development, Inbreeding, MESH: Models, Genetic, Selection, Genetic, MESH: Genetic Drift, Alleles, Recombination, Genetic, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Self-Fertilization, Polymorphism, Genetic, Models, Genetic, MESH: Alleles, Genetic Drift, Selfing, Plants, Background selection, background selection, Fixation (population genetics), Genetic hitchhiking, Genetics, Population, Evolutionary biology, Mutation–selection balance, MESH: Recombination, Genetic, Genetic Fitness, Neutral theory of molecular evolution
Abstract

Self-fertilization is generally seen to be disadvantageous in the long term. It increases genetic drift, which subsequently reduces polymorphism and the efficiency of selection, which also challenges adaptation. However, high selfing rates can increase the fixation probability of recessive beneficial mutations, but existing theory has generally not accounted for the effect of linked sites. Here, we analyze a model for the fixation probability of deleterious mutants that hitchhike with selective sweeps in diploid, partially selfing populations. Approximate analytical solutions show that, conditional on the sweep not being lost by drift, higher inbreeding rates increase the fixation probability of the deleterious allele, due to the resulting reduction in polymorphism and effective recombination. When extending the analysis to consider a distribution of deleterious alleles, as well as the average fitness increase after a sweep, we find that beneficial alleles generally need to be more recessive than the previously assumed dominance threshold (h < 1/2) for selfing to be beneficial from one-locus theory. Our results highlight that recombination aiding the efficiency of selection on multiple loci amplifies the fitness benefits of outcrossing over selfing, compared to results obtained from one-locus theory. This effect additionally increases the parameter range under which obligate outcrossing is beneficial over partial selfing.

Published
2013

34. Signals from chloroplasts and mitochondria for iron homeostasis regulation

Author

Khurram Bashir, Gianpiero Vigani, Graziano Zocchi, Jean-François Briat, Katrin Philippar, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia, Università degli studi di Milano [Milano], Center for Sustainable Resource Sciences, RIKEN Yokohama campus, Ludwig-Maximilians-University München (LMU), Department Biology I-Plant Biochemistry and Physiology, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-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 National de la Recherche Scientifique (CNRS), Università degli Studi di Milano [Milano] (UNIMI), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Plant Biochemistry and Physiology, Ludwig-Maximilians-Universität München (LMU), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, MESH: Signal Transduction, Cell signaling, Chloroplasts, MESH: Mitochondria, Iron, MESH: Plants, Cell Communication, Plant Science, Mitochondrion, Biology, Fe homeostasis, 01 natural sciences, Plant Physiological Phenomena, 03 medical and health sciences, Iron homeostasis, MESH: Cell Communication, Homeostasis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, 030304 developmental biology, 0303 health sciences, MESH: Iron, MESH: Chloroplasts, MESH: Plant Physiological Phenomena, Plants, Mitochondria, Cell biology, Chloroplast, Fe stress, Biochemistry, MESH: Homeostasis, Signal transduction, Signal Transduction, 010606 plant biology & botany
Abstract

International audience; Iron (Fe) is an essential element for human nutrition. Given that plants represent a major dietary source of Fe worldwide, it is crucial to understand plant Fe homeostasis fully. A major breakthrough in the understanding of Fe sensing and signaling was the identification of several transcription factor cascades regulating Fe homeostasis. However, the mechanisms of activation of these cascades still remain to be elucidated. In this opinion, we focus on the possible roles of mitochondria and chloroplasts as cellular Fe sensing and signaling sites, offering a new perspective on the integrated regulation of Fe homeostasis and its interplay with cellular metabolism.

Published
2013

35. Nomenclature for members of the two-component signaling pathway of plants

Author

G. Eric Schaller, Aaron M. Rashotte, Václav Motyka, Radomira Vankova, Mathias Brault, Alexander Heyl, Florian Frugier, Alena Kuderová, Klaus von Schwartzenberg, Ann-Cathrin Lindner, Laboratoire d'Electrophysiologie des Membranes (LEM) EA 3514, Université Paris Diderot - Paris 7 (UPD7), Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, MESH: Signal Transduction, MESH: Terminology as Topic, Histidine Kinase, Physiology, MESH: Plants, CLOCK Proteins, Plant Science, Genes, Plant, 01 natural sciences, 03 medical and health sciences, Terminology as Topic, Arabidopsis, Genetics, MESH: Genes, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Red light, Letter to the Editor, Nomenclature, MESH: Protein Kinases, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 030304 developmental biology, 0303 health sciences, biology, MESH: Plant Proteins, Component (thermodynamics), Plant physiology, Plants, biology.organism_classification, MESH: CLOCK Proteins, Cell biology, Signal transduction, Protein Kinases, Signal Transduction, 010606 plant biology & botany
Abstract

Plants make use of “two-component systems” ([TCS][1]s) for signal transduction, and these are involved in a number of vital cellular responses, such as responses to cytokinins, ethylene, red light, and osmosensing ([Schaller et al., 2011][2]). The [TCS][1] as found in plants incorporates three

Published
2013

36. Duplication and familial promiscuity within the proteasome lid and COP9 signalosome kin complexes

Author

Elah Pick, Giovanna Serino, Department of Biology and Biotechnology 'Charles Darwin', Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Department of Biology, Faculty of Sciences and Science Education, University of Haifa [Haifa], and This work was supported by a Institut Pasteur-Fondazione Cenci-Bolognetti grant 2009-2011 to G.S., by an Israel Science Foundation grant [EP355/10] to E.P., and by a Ministry of Science and Technology (M.O.S.T)-Ministry of Foreign Affairs (MAE), Israel-Italy grant [3-9022] to G.S. and E.P. References

Subjects
0106 biological sciences, Arabidopsis thaliana, Mutant, Arabidopsis, MESH: Plants, Plant Science, pci complexes cop9 signalosome proteasome lid eif3 arabidopsis thaliana saccharomyces cerevisiae, 01 natural sciences, COP9 signalosome, Ubiquitin, Gene duplication, MESH: Arabidopsis, MESH: Models, Genetic, arabidopsis thaliana, cop9 signalosome, eif3, elf3, gene duplication, pci complexes, proteasome lid, protein complexes, saccharomyces cerevisiae, ubiquitin ligase, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, Plant Proteins, Genetics, 0303 health sciences, MESH: Plant Proteins, Proteasome lid, MESH: Proteasome Endopeptidase Complex, MESH: Gene Duplication, General Medicine, Plants, PCI complexes, Proteasome Endopeptidase Complex, Ubiquitin-Protein Ligases, MESH: Peptide Hydrolases, Saccharomyces cerevisiae, Biology, Evolution, Molecular, 03 medical and health sciences, elF3, 030304 developmental biology, Models, Genetic, COP9 Signalosome Complex, fungi, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Multiprotein Complexes, biology.organism_classification, MESH: Ubiquitin-Protein Ligases, Proteasome, Multiprotein Complexes, biology.protein, Agronomy and Crop Science, Function (biology), Peptide Hydrolases, 010606 plant biology & botany
Abstract

Two paralogous complexes, the proteasome lid and the COP9 signalosome (CSN), have diverged from a common ancestor; yet fulfill distinctive roles within the ubiquitin-proteasome sphere. The CSN regulates the largest family of E3 ubiquitin ligases, called CRLs (Cullin-RING ubiquitin Ligases), while the lid is a subcomplex of the 26 S proteasome, a proteolytic machinery responsible for the degradation of ubiquitinated proteins. Remarkably, in many organisms, several subunits of both complexes are duplicated, a circumstance that can hypothetically increase the number of different complexes that can be formed. Duplication, however, is not the only complexity trait within the lid and the CSN, because many of their subunits are not fully committed only to one of the two complexes, but they are able to associate with both. Indeed, their corresponding mutants have features that can be due to the absence of more than one complex. This could be simply explained by the subunits being able to carry an identical function within more than one paralogdus complex or by the subunits having a certain level of promiscuity, i.e. being able to carry more than one function, depending on the complex they are associating with. Recent data show that both options are possible and, although their functional relevance still needs to be fully uncovered, evidence is accumulating, which indicates a promiscuous trading of paralogous subunits, and suggests that this may occur transiently, and/or in response to particular environmental conditions. (C) 2013 Elsevier Ireland Ltd. All rights reserved.

Published
2013

37. Plant science: the key to preventing slow cadmium poisoning

Author

Nathalie Verbruggen, Mark G. M. Aarts, Stephan Clemens, Sébastien Thomine, Leibniz-Institut fur Pflanzenbiochemie, Leibniz Association, Laboratory of Genetics, Wageningen University and Research [Wageningen] (WUR), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, and Université libre de Bruxelles (ULB)

Subjects
0106 biological sciences, heavy-metal atpase, MESH: Plant Shoots, MESH: Plants, MESH: Plant Roots, Plant Science, accumulating cd, 010501 environmental sciences, shoot cd translocation, Plant Roots, 01 natural sciences, MESH: Biodegradation, Environmental, Cadmium poisoning, Soil, Plant science, quantitative trait locus, Adverse health effect, Soil Pollutants, MESH: Genetic Variation, 2. Zero hunger, Cadmium, food and beverages, Plants, MESH: Cadmium Poisoning, Biodegradation, Environmental, Shoot, Margin of safety, Laboratory of Genetics, potato-tubers, Plant Shoots, MESH: Food, Crops, Agricultural, Cadmium Poisoning, durum-wheat, MESH: Biological Transport, grain cadmium, MESH: Cadmium, chemistry.chemical_element, Biology, Laboratorium voor Erfelijkheidsleer, MESH: Soil, medicine, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 0105 earth and related environmental sciences, MESH: Soil Pollutants, Oryza sativa, MESH: Humans, Plant roots, business.industry, Genetic Variation, Biological Transport, medicine.disease, MESH: Crops, Agricultural, Biotechnology, arabidopsis, wheat cultivars, chemistry, Food, rice oryza-sativa, EPS, business, 010606 plant biology & botany
Abstract

International audience; Practically all human populations are environmentally exposed to cadmium (Cd), mostly through plant-derived food. A growing body of epidemiological evidence suggests that there is no margin of safety between current Cd exposure levels and the threshold for adverse health effects and, hence, there is an urgent need to lower human Cd intake. Here we review recent studies on rice (Oryza sativa) and Cd-hyperaccumulating plants that have led to important insights into the processes controlling the passage of Cd from the soil to edible plant organs. The emerging molecular understanding of Cd uptake, root retention, root-to-shoot translocation and grain loading will enable the development of low Cd-accumulating crops.

Published
2013

38. Nitrate sensing and signaling in plants

Author

Eléonore Bouguyon, Philippe Nacry, Alain Gojon, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-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), and Université de Montpellier (UM)-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 National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, MESH: Signal Transduction, MESH: Indoleacetic Acids, Nitrogen, Anion Transport Proteins, Arabidopsis, MESH: Plants, Plant Development, MESH: Carrier Proteins, MESH: Arabidopsis Proteins, Development, 01 natural sciences, 03 medical and health sciences, Transduction (genetics), Gene expression, Botany, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Arabidopsis, MESH: Plant Development, Transcription factor, Plant Proteins, 030304 developmental biology, Nutrition, 0303 health sciences, Nitrates, Indoleacetic Acids, biology, MESH: Plant Proteins, Arabidopsis Proteins, Transporter, Cell Biology, MESH: Anion Transport Proteins, Plants, biology.organism_classification, Yeast, Hormones, Cell biology, MESH: Nitrates, Developmental plasticity, Signal transduction, Carrier Proteins, Signal Transduction, 010606 plant biology & botany, Developmental Biology
Abstract

International audience; Nitrate (NO(3)(-)) is a major nutrient for plants, taken up by their roots from the soil. Plants are able to sense NO(3)(-) in their environment, allowing them to quickly respond to the dramatic fluctuations of its availability. Significant advances have been made during the recent period concerning the molecular mechanisms of NO(3)(-) sensing and signaling in the model plant Arabidopsis thaliana. The striking action of NO(3)(-) as a signal regulating genome expression has been unraveled. Note worthily, NO(3)(-) sensing systems have been identified. These correspond to membrane transporters also ensuring the uptake of NO(3)(-) into root cells, thus generalizing the nutrient 'transceptor' (transporter/receptor) concept defined in yeast. Furthermore, components of the downstream transduction cascades, such as transcription factors or kinases, have also been isolated. A breakthrough arising from this improved knowledge is a better understanding of the integration of NO(3)(-) and hormone signaling pathways, that explains the extraordinary developmental plasticity of plants in response to NO(3)(-).

Published
2012

39. Identification of a new phospholipase D in Carica papaya latex

Author

Slim Abdelkafi, Nathalie Barouh, Benjamin Fouquet, Frédéric Carrière, Abdelkarim Abousalham, Pierre Villeneuve, Frantz Scheirlinckx, Imen Fendri, Hiroshi Y. Ogata, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Enzymologie interfaciale et de physiologie de la lipolyse (EIPL), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)

Subjects
Latex, Sequence analysis, F60 - Physiologie et biochimie végétale, Molecular Sequence Data, MESH: Plants, MESH: Amino Acid Sequence, Glycerophospholipids, Biology, Spectrométrie de masse, MESH: Base Sequence, F30 - Génétique et amélioration des plantes, MESH: Carica, 03 medical and health sciences, chemistry.chemical_compound, Complementary DNA, Phosphatidylcholine, Phospholipase D, Genetics, Amino Acid Sequence, Phospholipase, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH: Phylogeny, Phylogeny, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, MESH: Molecular Sequence Data, Base Sequence, Molecular mass, Carica, Carica papaya, 030302 biochemistry & molecular biology, MESH: Latex, General Medicine, Plants, biology.organism_classification, Amino acid, chemistry, Biochemistry, MESH: Phospholipase D, lipids (amino acids, peptides, and proteins)
Abstract

International audience; Phospholipase D (PLD) is a lipolytic enzyme involved in signal transduction, vesicle trafficking and membrane metabolism. It catalyzes the hydrolysis and transphosphatidylation of glycerophospholipids at the terminal phosphodiester bond. The presence of a PLD in the latex of Carica papaya (CpPLD1) was demonstrated by transphosphatidylation of phosphatidylcholine (PtdCho) in the presence of 2% ethanol. Although the protein could not be purified to homogeneity due to its presence in high molecular mass aggregates, a protein band was separated by SDS-PAGE after SDS/chloroform-methanol/TCA-acetone extraction of the latex insoluble fraction. This material was digested with trypsin and the amino acid sequences of the tryptic peptides were determined by micro-LC/ESI/MS/MS. These sequences were used to identify a partial cDNA (723 bp) from expressed sequence tags (ESTs) of C. papaya. Based upon EST sequences, a full-length gene was identified in the genome of C. papaya, with an open reading frame of 2424 bp encoding a protein of 808 amino acid residues, with a theoretical molecular mass of 92.05 kDa. From sequence analysis, CpPLD1 was identified as a PLD belonging to the plant phosphatidylcholine phosphatidohydrolase family.

Published
2012

40. When bacteria target the nucleus: the emerging family of nucleomodulins

Author

Hélène, Bierne, Pascale, Cossart, Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur, INRA, INSERM, French Ligue Nationale Contre le Cancer (LNCC) [RS10/75-76], European Research Council (ERC) [233348], La fondation des Mousquetaires, French National Research Agency (ANR) [EPILIS], ANR-11-BSV3-0003,EPILIS,Reprogrammation épigénétique par la bactérie pathogène Listeria monocytogenes(2011), European Project: 233348,EC:FP7:ERC,ERC-2008-AdG,MODELIST(2009), and Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
DNA, Bacterial, MESH: Cell Nucleus, Virulence Factors, [SDV]Life Sciences [q-bio], NF-KAPPA-B, MESH: Plants, Models, Biological, E3 UBIQUITIN LIGASES, CELL-CYCLE PROGRESSION, Bacterial Proteins, Animals, Humans, MESH: Animals, TRANSCRIPTION FACTOR, MESH: Bacterial Proteins, GENE-EXPRESSION, MESH: Virulence Factors, Cell Nucleus, MESH: Humans, Bacteria, RICKETTSIA-RICKETTSII, MESH: Host-Pathogen Interactions, MESH: Models, Biological, PARAMECIUM-CAUDATUM, Plants, MESH: DNA, Bacterial, CYTOLETHAL-DISTENDING TOXIN, MESH: Bacteria, EFFECTOR XOPD TARGETS, Host-Pathogen Interactions, ANAPLASMA-PHAGOCYTOPHILUM
Abstract

International audience; The nucleus, at the heart of the eukaryotic cell, hosts and protects the genetic material, governs gene expression and regulates the whole cell physiology, including cell division. A growing number of studies indicate that various animal and plant pathogenic bacteria can deliver factors to this central organelle to subvert host defences by directly interfering with transcription, chromatin-remodelling, RNA splicing or DNA replication and repair. Such bacterial molecules entering the nucleus, which we propose to term nucleomodulins, use diverse strategies to hijack nuclear processes by targeting host DNA or an array of nuclear proteins. In some cases, bacteria can even enter the nucleus. These bacterial nuclear attacks might have permanent genetic or long-term epigenetic effects on the host. Studying nucleomodulins and endonuclear bacteria can thus generate new insights into long-term impacts of infectious diseases and create novel tools for biotechnological applications and for deciphering the regulation of nuclear dynamics.

Published
2012

41. Ubiquitination of transporters at the forefront of plant nutrition

Author

Marie Barberon, Enric Zelazny, Catherine Curie, Grégory Vert, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-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 National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, MESH: Protein Transport, MESH: Ubiquitin, BOR1, Iron, MESH: Plants, plant nutrition, Plant Science, Vacuole, Biology, Endocytosis, Models, Biological, monoubiquitin, 01 natural sciences, MESH: Membrane Transport Proteins, Cell membrane, Degradation, 03 medical and health sciences, Ubiquitin, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Nutritional Physiological Phenomena, MESH: Nutritional Physiological Phenomena, 030304 developmental biology, 0303 health sciences, Membrane transport protein, Cell Membrane, Ubiquitination, MESH: Models, Biological, Membrane Transport Proteins, Transporter, Plants, transporter IRT1, Article Addendum, Cell biology, Transport protein, Protein Transport, arabidopsis, medicine.anatomical_structure, Biochemistry, Membrane protein, biology.protein, MESH: Ubiquitination, IRT1, 010606 plant biology & botany, MESH: Cell Membrane
Abstract

International audience; In plants, the tight regulation of plasma membrane transporters is essential to maintain nutrient homeostasis. The mechanisms controlling the abundance of transporters, and other integral plasma membrane proteins, now come to light. Ubiquitination appears as a major signal initiating cargo endocytosis and sorting into multivesicular bodies prior to degradation in the vacuole. We have indeed demonstrated that the root iron transporter IRT1 is subjected to ubiquitin-dependent trafficking in root epidermal cells. This control is crucial to keep IRT1 levels at the cell surface low and to cope with the toxicity associated with other readily available metal substrates of IRT1. Our work combined with recent report on the BOR1 boron transporter establishes ubiquitination as a conserved mechanism of plasma membrane protein trafficking in plants, and highlights its importance for plant nutrition.

Published
2011

42. MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

Author

Stéphane Bernillon, Daniel J. Jacob, Macha Nikolski, Laurent Gil, Dominique Rolin, Hélène Ferry-Dumazet, Annick Moing, Antoine de Daruvar, Catherine Deborde, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Biologie végétale intégrative (BVI), Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, and Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)

Subjects
0106 biological sciences, Magnetic Resonance Spectroscopy, Databases, Factual, Knowledge Bases, Metabolite, MESH: Plants, Plant Science, Bioinformatics, 01 natural sciences, nmr, imaginerie rmn du proton, User-Computer Interface, chemistry.chemical_compound, métabolite, lcsh:Botany, Statistical analysis, banque de données, MESH: Metabolomics, bioinformatique, Principal Component Analysis, 0303 health sciences, Vegetal Biology, Plants, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], lcsh:QK1-989, Identification (information), MESH: Internet, plante, métabolomique, profil métabolique, MESH: Knowledge Bases, Computational biology, Biology, Profile management, Database, physiologie végétale, 03 medical and health sciences, Annotation, Metabolomics, MESH: Analysis of Variance, métabolisme, MESH: User-Computer Interface, 030304 developmental biology, végétal, MESH: Principal Component Analysis, Analysis of Variance, Internet, MESH: Magnetic Resonance Spectroscopy, MESH: Databases, Factual, Visualization, Metadata, chemistry, Database Management Systems, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Biologie végétale, MESH: Database Management Systems, 010606 plant biology & botany
Abstract

Background Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments. Description MeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues. Conclusion MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php.

Published
2011

43. Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937

Author

Xiangyang Shi, Sheng Yang He, Maria C. Holeva, Pablo Rodríguez-Palenzuela, Pritin Soni, Béatrice Py, Guy Condemine, Michael Rusch, Jeremy D. Glasner, Guy Plunkett, Derrick E. Fouts, Michael San Francisco, Frédérique Van Gijsegem, Vanessa Douet, Bradley D. Anderson, Magdalen Lindeberg, Sylvie Reverchon, Mee-Ngan Frances Yap, George F. Mayhew, Jihyun F. Kim, Steven R. Gill, Mathilde Carpentier, Frederick R. Blattner, Michael E. Hibbing, Shinji Tsuyumu, Sarah M. Flynn, Kenneth S. Bell, Shihui Yang, Nicole T. Perna, Frédéric Barras, Martine Boccara, Dominique Expert, Bryan S. Biehl, Elie Dassa, Lise Rauscher, Carlos Blanco, Noel T. Keen, Paul R. J. Birch, Thierry Franza, Ching Hong Yang, Masahiro Umehara, Ariane Toussaint, Jean Pierre Bohin, Bob Mau, Ian K. Toth, Nicole Hugouvieux-Cotte-Pattat, Amy O. Charkowski, Chromatine et Régulation de la Pathogénie bactérienne (CRP), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Trafic et signalisation membranaires chez les bactéries (MTSB), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Polytech'Paris-UPMC, Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Interactions cellulaires et moléculaires (ICM), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Plant Pathology, Scottish Crop Research Institute, Atelier de BioInformatique (ABI), Membranes bactériennes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, Functional Genomics Program, University of Science and Technology, USDA Cooperative State Research, Education and Extension Service (2001-52100-11316), Brébion, Alice, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-IFR140-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon, Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, MESH: Sequence Analysis, DNA, Molecular Sequence Data, MESH: Plants, MESH: Genome, Bacterial, Microbiology, 03 medical and health sciences, MESH: Enterobacteriaceae, MESH: Plant Diseases, Enterobacteriaceae, Molecular Biology, 030304 developmental biology, Sequence (medicine), Plant Diseases, Whole genome sequencing, 0303 health sciences, MESH: Molecular Sequence Data, biology, 030306 microbiology, Strain (biology), fungi, food and beverages, Sequence Analysis, DNA, Plants, SOFT ROT, BIOLOGIE MOLECULAIRE, biology.organism_classification, Pathogenicity, Dickeya dadantii, Soft rot disease, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genome Announcements, DICKEYA DADANTII, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bacteria, Genome, Bacterial
Abstract

International audience; Dickeya dadantii is a plant-pathogenic enterobacterium responsible for the soft rot disease of many plants of economic importance. We present here the sequence of strain 3937, a strain widely used as a model system for research on the molecular biology and pathogenicity of this group of bacteria.

Published
2011

44. Plant growth and architectural modelling and its applications. Preface

Author

Guo, Yan, Fourcaud, Thierry, Jaeger, Marc, Zhang, Xiaopeng, Li, Baoguo, Key Laboratory of Plant-Soil Interactions - College of Resources and Environmental Sciences (PSI), China Agricultural University (CAU), Eco-informatics (LIAMA), Institut National de la Recherche Agronomique (INRA)-Chinese Academy of Sciences [Changchun Branch] (CAS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institute of Automation - Chinese Academy of Sciences-Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Chinese Academy of Sciences [Changchun Branch] (CAS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institute of Automation - Chinese Academy of Sciences-Centre National de la Recherche Scientifique (CNRS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
FSPM, Root system, Plasticity, MESH: Models, Biological, MESH: Plants, MESH: Plant Roots, Source and sink, Plant morpholog, Functional-structural plant model, Computational plants, MESH: Computer Simulation, Architecture, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Photosynthesis, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MESH: Environment, ComputingMilieux_MISCELLANEOUS, Simulation
Abstract

ACL-11-25; International audience; Over the last decade, a growing number of scientists around the world have invested in research on plant growth and architectural modelling and applications (often abbreviated to plant modelling and applications, PMA). By combining physical and biological processes, spatially explicit models have shown their ability to help in understanding plant-environment interactions. This Special Issue on plant growth modelling presents new information within this topic, which are summarized in this preface. Research results for a variety of plant species growing in the field, in greenhouses and in natural environments are presented. Various models and simulation platforms are developed in this field of research, opening new features to a wider community of researchers and end users. New modelling technologies relating to the structure and function of plant shoots and root systems are explored from the cellular to the whole-plant and plant-community levels.

Published
2011

45. Exploring the mechanistic bases of heterosis from the perspective of macromolecular complexes

Author

Reiner A. Veitia, Daniel Vaiman, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique, Université Paris-Diderot, Association pour la Recherche sur le Cancer, Fondation pour la Recherche Médicale, Institut Universitaire de France, Institut Jacques Monod (IJM), Université Paris Diderot - Paris 7 (UPD7) - Centre National de la Recherche Scientifique (CNRS), Institut Cochin (UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Centre National de la Recherche Scientifique (CNRS), and Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Genotype, Heterosis, Macromolecular Substances, Gene Dosage, MESH: Plants, Context (language use), MESH: Breeding, Biology, Breeding, 01 natural sciences, Biochemistry, MESH: Gene Dosage, MESH: Genotype, 03 medical and health sciences, MESH: Hybrid Vigor, Genetic model, Genetics, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Hybrid Vigor, Animals, Allelic diversity, MESH: Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Models, Genetic, Molecular Biology, 030304 developmental biology, Hybrid, 0303 health sciences, Genetic diversity, Models, Genetic, Heterozygote advantage, MESH: Macromolecular Substances, Plants, Macromolecular Complexes, 010606 plant biology & botany, Biotechnology
Abstract

International audience; Heterosis is defined as greater biomass, fertility or other traits in heterozygotes, polyploids or hybrids compared to their genetically divergent (often homozygous) parents. Heterosis was noticed by various civilizations and scientifically reported by Darwin himself. Despite the importance of heterosis, its molecular bases are still enigmatic. Several genetic models have been proposed but fail to give mechanistic insights. Here we show how dominant negative interactions might give rise to heterotic responses. We also explore a biochemical model of gene dosage effects in macromolecular complexes in a similar context. With the help of heuristic examples and computer simulations we find that heterotic individuals display higher allelic diversity and smaller average multimer concentrations than nonheterotic ones. As intuitively expected, the existence of heterosis involving multimeric complexes arises when the inbred parents have on average smaller genetic values than the maximum possible. Despite its simplicity, the dosage model accounts for the puzzling phenomenon of "progressive heterosis" in which polyploids with increasing genetic diversity exhibit progressively greater heterosis.

Published
2011

46. The various lifestyles of the Burkholderia cepacia complex species: a tribute to adaptation

Author

Vial, Ludovic, Chapalain, Annelise, Groleau, Marie-Christine, Déziel, Eric, Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), and Work on Burkholderia in ED laboratory is supported by a Canadian Institutes of Health Research Operating Grant.

Subjects
MESH: Burkholderia cepacia complex, MESH: Humans, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Cystic Fibrosis, MESH: Burkholderia Infections, MESH: Cystic Fibrosis, Burkholderia cepacia complex, MESH: Adaptation, Biological, fungi, Adaptation, Biological, MESH: Plants, food and beverages, Burkholderia Infections, Plants, Granulomatous Disease, Chronic, MESH: Granulomatous Disease, Chronic, MESH: Soil Microbiology, Rhizosphere, Humans, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, MESH: Rhizosphere, Soil Microbiology
Abstract

International audience; The Burkholderia cepacia complex (Bcc) is composed of 17 closely related species. These bacteria are widely but heterogeneously distributed in the natural environment, such as soil, water and rhizosphere. Bcc strains are able to colonize various ecological niches by adopting versatile lifestyles, including saprophytism and (positive or deleterious) association with eukaryotic cells. Bcc strains have proven to be very efficient in biocontrol, plant growth promotion and bioremediation. However, they also are important opportunistic pathogens that can cause severe respiratory infections among individuals suffering from cystic fibrosis or chronic granulomatous disease. Therefore, considering that the distinction between plant beneficial and clinical strains is not obvious, biotechnological applications of Bcc strains are currently not allowed. This minireview provides an overview of the wide range of lifestyles that Bcc bacteria can adopt, leading to glimpses into their tremendous adaptation potential and highlighting remaining questions concerning potential implicated mechanisms.

Published
2011

47. Trained immunity: a memory for innate host defense

Author

Mihai G. Netea, Jessica Quintin, Jos W. M. van der Meer, and Radboud University Medical Center [Nijmegen]

Subjects
Intrinsic immunity, Cancer Research, [SDV]Life Sciences [q-bio], animal diseases, MESH: Plants, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Adaptive Immunity, Microbiology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Immune system, MESH: Invertebrates, Immunity, Virology, Immunology and Microbiology(all), medicine, Animals, MESH: Animals, Molecular Biology, MESH: Vertebrates, Innate immune system, Host (biology), [SDV.BA]Life Sciences [q-bio]/Animal biology, Innate lymphoid cell, Pathogenesis and modulation of inflammation Infection and autoimmunity [N4i 1], Plants, biochemical phenomena, metabolism, and nutrition, medicine.disease, Acquired immune system, Invertebrates, Immunity, Innate, Transplant rejection, Immunology, Vertebrates, MESH: Immunologic Memory, [SDV.IMM]Life Sciences [q-bio]/Immunology, bacteria, Parasitology, MESH: Immunity, Innate, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, Immunologic Memory, MESH: Adaptive Immunity
Abstract

Contains fulltext : 96477.pdf (Publisher’s version ) (Closed access) Immune responses in vertebrates are classically divided into innate and adaptive, with only the latter being able to build up immunological memory. However, although lacking adaptive immune responses, plants and invertebrates are protected against reinfection with pathogens, and invertebrates even display transplant rejection. In mammals, past "forgotten" studies demonstrate cross-protection between infections independently of T and B cells, and more recently memory properties for NK cells and macrophages, prototypical cells of innate immunity, have been described. We now posit that mammalian innate immunity also exhibits an immunological memory of past insults, for which we propose the term "trained immunity." Understanding trained immunity will revolutionize our view of host defense and immunological memory, and could lead to defining a new class of vaccines and immunotherapies.

Published
2011

48. A modern ionotropic glutamate receptor with a K(+) selectivity signature sequence

Author

Harald Janovjak, Ehud Y. Isacoff, Guillaume Sandoz, The Helen Wills Neuroscience Institute (HWNI), University of California [Berkeley], University of California-University of California, Institute of Science and Technology [Austria] (IST Austria), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Physical Biosciences Division [LBNL Berkeley], and Lawrence Berkeley National Laboratory [Berkeley] (LBNL)

Subjects
Amino Acid Motifs, Rotifera, MESH: Plants, General Physics and Astronomy, Gene Expression, Kainate receptor, MESH: Amino Acid Sequence, MESH: Recombinant Proteins, Xenopus laevis, MESH: Amino Acid Motifs, 0302 clinical medicine, 571 Physiology, Databases, Genetic, MESH: Animals, MESH: Phylogeny, Phylogeny, MESH: Databases, Genetic, 0303 health sciences, Multidisciplinary, MESH: Receptors, Ionotropic Glutamate, Metabotropic glutamate receptor 5, Metabotropic glutamate receptor 6, MESH: Glutamic Acid, Plants, Recombinant Proteins, Biochemistry, Metabotropic glutamate receptor 1, Ligand-gated ion channel, Ion Channel Gating, MESH: Gene Expression, Molecular Sequence Data, MESH: Sequence Alignment, Glutamic Acid, Biology, Receptors, Ionotropic Glutamate, Transfection, General Biochemistry, Genetics and Molecular Biology, MESH: Rotifera, MESH: Oocytes, 03 medical and health sciences, MESH: Xenopus laevis, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, RNA, Messenger, 030304 developmental biology, MESH: RNA, Messenger, MESH: Molecular Sequence Data, Bacteria, MESH: Transfection, General Chemistry, MESH: Ion Channel Gating, MESH: Bacteria, Metabotropic glutamate receptor, MESH: Potassium, Biophysics, Oocytes, Potassium, 570 Life sciences, biology, Ionotropic glutamate receptor, Sequence Alignment, 030217 neurology & neurosurgery, Ion channel linked receptors
Abstract

International audience; Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system and gates non-selective cation channels. The origins of glutamate receptors are not well understood as they differ structurally and functionally from simple bacterial ligand-gated ion channels. Here we report the discovery of an ionotropic glutamate receptor that combines the typical eukaryotic domain architecture with the 'TXVGYG' signature sequence of the selectivity filter found in K(+) channels. This receptor exhibits functional properties intermediate between bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the evolution of ionotropic glutamate receptors.

Published
2011

49. R type anion channel: a multifunctional channel seeking its molecular identity

Author

Jean Colcombet, Eugene Diatloff, Hélène Barbier-Brygoo, Rémi Peyronnet, Sébastien Thomine, Jean-Marie Frachisse, Lancaster Environment Centre, Lancaster University, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Division of Biological Sciences [San Diego], University of California [San Diego] (UC San Diego), University of California-University of California, Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, MESH: Plants, Calcium Channels, R-Type, Plant Science, Biology, MESH: Calcium Signaling, 01 natural sciences, Ion, 03 medical and health sciences, Gene Expression Regulation, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Calcium Signaling, MESH: Gene Expression Regulation, Plant, Ion channel, Plant Proteins, 030304 developmental biology, Calcium signaling, 0303 health sciences, MESH: Calcium Channels, R-Type, MESH: Plant Proteins, Mini-Review, Plants, Light-gated ion channel, MESH: Ion Channel Gating, Electrophysiology, Membrane, Biochemistry, Biophysics, Identity (object-oriented programming), Ion Channel Gating, 010606 plant biology & botany, Communication channel
Abstract

International audience; Plant genomes code for channels involved in the transport of cations, anions and uncharged molecules through membranes. Although the molecular identity of channels for cations and uncharged molecules has progressed rapidly in the recent years, the molecular identity of anion channels has lagged behind. Electrophysiological studies have identified S-type (slow) and R-type (rapid) anion channels. In this brief review, we summarize the proposed functions of the R-type anion channels which, like the S-type, were first characterized by electrophysiology over 20 years ago, but unlike the S-type, have still yet to be cloned. We show that the R-type channel can play multiple roles.

Published
2010

50. Genome-wide analysis of plant metal transporters, with an emphasis on poplar

Author

Malcolm M. Campbell, Barbara Montanini, Pierre Richaud, Aude Migeon, Damien Blaudez, Olivia Wilkins, Sébastien Thomine, Michel Chalot, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Biologie végétale et microbiologie environnementale - UMR7265 ( BVME ), Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Aix Marseille Université ( AMU ), Institut des sciences du végétal ( ISV ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Chrono-environnement ( LCE ), and Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC )

Subjects
0106 biological sciences, Populus trichocarpa, MESH: Genome, Plant, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, MESH : Populus, MESH : Saccharomyces cerevisiae, MESH: Plants, Chlamydomonas reinhardtii, MESH: Carrier Proteins, Saccharomyces cerevisiae, MESH : Plants, Physcomitrella patens, 01 natural sciences, Genome, Fungal Proteins, 03 medical and health sciences, Cellular and Molecular Neuroscience, Selaginella moellendorffii, Botany, Arabidopsis thaliana, Gene family, MESH : Fungal Proteins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Phylogeny, Molecular Biology, Gene, Phylogeny, 030304 developmental biology, Pharmacology, 0303 health sciences, MESH: Metals, biology, MESH : Metals, MESH : Phylogeny, food and beverages, Cell Biology, Plants, biology.organism_classification, MESH: Saccharomyces cerevisiae, MESH : Genome, Plant, MESH: Populus, Populus, Metals, Molecular Medicine, MESH: Fungal Proteins, MESH : Carrier Proteins, Carrier Proteins, Genome, Plant, 010606 plant biology & botany
Abstract

International audience; The specific transport of metal ions, mediated by membrane-localized metal transporters, is of fundamental importance in all eukaryotes. Genome-wide analysis of metal transporters was undertaken, making use of whole genome sequences of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, as well as of the yeast Saccharomyces cerevisiae. A repertoire of 430 metal transporters was found in total across eight photosynthetic plants, as well as in S. cerevisiae. Seventy-two full-length metal transporter genes were identified in the Populus genome alone, which is the largest number of metal transporters genes identified in any single species to date. Diversification of some transporter family gene clusters appears to have occurred in a lineage-specific manner. Expression analysis of Populus metal transporters indicates that some family members show tissue-specific transcript abundance. Taken together, the data provide a picture into the diversification of these important gene families.

Published
2010

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