Author: "Centre for Plant Sciences [Leeds]" - Searchworks@Jio Institute Digital Library Search Results

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29 results on '"Centre for Plant Sciences [Leeds]"'

1. Plasma Membrane-Associated Receptor-like Kinases Relocalize to Plasmodesmata in Response to Osmotic Stress 1[OPEN]

Author: Grison, Magali, Kirk, Philip, Brault, Marie, Wu, Xu Na, Schulze, Waltraud, Benitez-Alfonso, Yoselin, Immel, Françoise, BAYER, Emmanuelle, Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Laboratoire de Bioénergie Membranaire (LBM), Laboratoire de Bioénergie Membranaire, and University of Hohenheim
Subjects: [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract: International audience; Plasmodesmata act as key elements in intercellular communication, coordinating processes related to plant growth, development, and responses to environmental stresses. While many of the developmental, biotic, and abiotic signals are primarily perceived at the plasma membrane (PM) by receptor proteins, plasmodesmata also cluster receptor-like activities; whether these two pathways interact is currently unknown. Here, we show that specific PM-located Leu-rich-repeat receptor-like-kinases, Qi an Sh ou kinase (QSK1) and inflorescence meristem kinase2, which under optimal growth conditions are absent from plasmodesmata, rapidly relocate and cluster to the pores in response to osmotic stress. This process is remarkably fast, is not a general feature of PM-associated proteins, and is independent of sterol and sphingolipid membrane composition. Focusing on QSK1, previously reported to be involved in stress responses, we show that relocalization in response to mannitol depends on QSK1 phosphorylation. Loss-of-function mutation in QSK1 results in delayed lateral root (LR) development, and the mutant is affected in the root response to mannitol stress. Callose-mediated plasmodesmata regulation is known to regulate LR development. We found that callose levels are reduced in the qsk1 mutant background with a root phenotype resembling ectopic expression of PdBG1, an enzyme that degrades callose at the pores. Both the LR and callose phenotypes can be complemented by expression of wild-type and phosphomimic QSK1 variants, but not by phosphodead QSK1 mutant, which fails to relocalize at plasmodesmata. Together, the data indicate that reorganization of receptor-like-kinases to plasmodesmata is important for the regulation of callose and LR development as part of the plant response to osmotic stress.
Published: 2019
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2. Dynamics of cell wall assembly during early embryogenesis in the brown algaFucus

Author: J. Paul Knox, Murielle Jam, Marie-Anne Le Moigne, Thomas A. Torode, Susan E. Marcus, Delphine Duffieux, Amandine Siméon, Cécile Hervé, Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Végétaux marins et biomolécules, 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)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Fucus serratus, medicine.drug_class, Enzyme-Linked Immunosorbent Assay, Germination, sulfated fucan, zygote, Plant Science, Q1, brown algae, Monoclonal antibody, 01 natural sciences, Epitope, Cell wall, Epitopes, 03 medical and health sciences, Cell Wall, Botany, Cell polarity, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, QD, SB, ComputingMilieux_MISCELLANEOUS, Arabinogalactan protein, biology, Chemistry, QK, Alginate, Antibodies, Monoclonal, biology.organism_classification, Cell biology, arabinogalactan-protein, 030104 developmental biology, Rhizoid, monoclonal antibody, Fucus, Seeds, Research Paper, 010606 plant biology & botany
Abstract: Highlight New monoclonal antibodies to brown algal cell wall polymers allow tracing of in situ dynamics of alginates and sulfated fucans in Fucus zygotes and in the context of growth disruption, Zygotes from Fucus species have been used extensively to study cell polarization and rhizoid outgrowth, and in this model system cell wall deposition aligns with the establishment of polarity. Monoclonal antibodies are essential tools for the in situ analysis of cell wall glycans, and here we report the characteristics of six monoclonal antibodies to alginates (BAM6–BAM11). The use of these, in conjunction with monoclonal antibodies to brown algal sulfated fucans, has enabled the study of the developmental dynamics of the Fucus zygote cell walls. Young zygotes are spherical and all alginate epitopes are deposited uniformly following cellulose deposition. At germination, sulfated fucans are secreted in the growing rhizoid wall. The redistribution of cell wall epitopes was investigated during treatments that cause reorientation of the growth axis (change in light direction) or disrupt rhizoid development (arabinogalactan-protein-reactive Yariv reagent). Alginate modeling was drastically impaired in the latter, and both treatments cause a redistribution of highly sulfated fucan epitopes. The dynamics of cell wall glycans in this system have been visualized in situ for the first time, leading to an enhanced understanding of the early developmental mechanisms of Fucus species. These sets of monoclonal antibodies significantly extend the available molecular tools for brown algal cell wall studies.
Published: 2016
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3. Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development

Author: Gaudioso-Pedraza, R, Beck, M, Frances, L, Kirk, P, Ripodas, C, Niebel, A, Oldroyd, GED, Benitez-Alfonso, Y, de Carvalho-Niebel, F, Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory Cambridge University (SLCU), Leeds University : 110 French Laboratoire d'Excellence (Labex) TULIP post-doctoral grant 'Young Scientists for the Future', AgreenSkills fellowship : 2013609398, BBSRC DTP : BB/M011151/1, Royal Society, EPSRC : EF/M027740/1, Leverhulme Trust : RPG-2016-136, ANR COME-IN grant : ANR-14-CE35-0007-01, TULIP grant : ANR-10-LABX-41, and European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014)
Subjects: [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The formation of nitrogen-fixing nodules in legumes involves the initiation of synchronized programs in the root epidermis and cortex to allow rhizobial infection and nodule development. In this study, we provide evidence that symplastic communication, regulated by callose turnover at plasmodesmata (PD), is important for coordinating nodule development and infection in Medicago truncatula. Here, we show that rhizobia promote a reduction in callose levels in inner tissues where nodules initiate. This downregulation coincides with the localized expression of M. truncatula beta-1,3-glucanase 2 (MtBG2), encoding a novel PD-associated callose-degrading enzyme. Spatiotemporal analyses revealed that MtBG2 expression expands from dividing nodule initials to rhizobia-colonized cortical and epidermal tissues. As shown by the transport of fluorescent molecules in vivo, symplastic-connected domains are created in rhizobia-colonized tissues and enhanced in roots constitutively expressing MtBG2. MtBG2-overexpressing roots additionally displayed reduced levels of PD-associated callose. Together, these findings suggest an active role for MtBG2 in callose degradation and in the formation of symplastic domains during sequential nodule developmental stages. Interfering with symplastic connectivity led to drastic nodulation phenotypes. Roots ectopically expressing beta-1,3-glucanases (including MtBG2) exhibited increased nodule number, and those expressing MtBG2 RNAi constructs or a hyperactive callose synthase (under symbiotic promoters) showed defective nodulation phenotypes. Obstructing symplastic connectivity appears to block a signaling pathway required for the expression of NODULE INCEPTION (NIN) and its target NUCLEAR FACTOR-YA1 (NF-YA1) in the cortex. We conclude that symplastic intercellular communication is proactively enhanced by rhizobia, and this is necessary for appropriate coordination of bacterial infection and nodule development.
Published: 2018
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4. Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures

Author: Radwa H. Abou-Saleh, Yrjö Helariutta, Candelas Paniagua, Tatiana Budtova, Martin Fuller, Matthieu Bourdon, Shunsuke Miyashima, Sam Amsbury, Simon D. Connell, Michael E. Ries, Yoselin Benitez-Alfonso, Mercedes C. Hernandez-Gomez, Amsbury, Sam [0000-0002-2767-9768], Helariutta, Ykä [0000-0002-7287-8459], Connell, Simon D [0000-0003-2500-5724], Ries, Michael E [0000-0002-8050-3200], Benitez-Alfonso, Yoselin [0000-0001-9779-0413], Apollo - University of Cambridge Repository, Biologie du Fruit, Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Centre de Mise en Forme des Matériaux (CEMEF), Centre National de la Recherche Scientifique (CNRS)-PSL Research University (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, MINES ParisTech - École nationale supérieure des mines de Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Science, Proton Magnetic Resonance Spectroscopy, Arabidopsis, General Physics and Astronomy, Ionic Liquids, macromolecular substances, engineering.material, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Viscoelasticity, Article, Hydrogel, Polyethylene Glycol Dimethacrylate, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, [SPI]Engineering Sciences [physics], Spectroscopy, Fourier Transform Infrared, Cellulose, lcsh:Science, Glucans, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Multidisciplinary, Estradiol, Chemistry, Viscosity, Callose, technology, industry, and agriculture, Temperature, Hydrogen Bonding, General Chemistry, Polymer, Elasticity, 030104 developmental biology, Chemical engineering, Ionic liquid, Self-healing hydrogels, engineering, Nanoparticles, lcsh:Q, Biopolymer, 010606 plant biology & botany
Abstract: The properties of (1,3)-β-glucans (i.e., callose) remain largely unknown despite their importance in plant development and defence. Here we use mixtures of (1,3)-β-glucan and cellulose, in ionic liquid solution and hydrogels, as proxies to understand the physico-mechanical properties of callose. We show that after callose addition the stiffness of cellulose hydrogels is reduced at a greater extent than predicted from the ideal mixing rule (i.e., the weighted average of the individual components’ properties). In contrast, yield behaviour after the elastic limit is more ductile in cellulose-callose hydrogels compared with sudden failure in 100% cellulose hydrogels. The viscoelastic behaviour and the diffusion of the ions in mixed ionic liquid solutions strongly indicate interactions between the polymers. Fourier-transform infrared analysis suggests that these interactions impact cellulose organisation in hydrogels and cell walls. We conclude that polymer interactions alter the properties of callose-cellulose mixtures beyond what it is expected by ideal mixing., Despite their importance in plant development and defence the properties of (1,3)-β-glucan remain largely unknown. Here, the authors find that addition of (1,3)-β-glucans increases the flexibility of cellulose and its resilience to high strain, an effect originating in molecular level interactions.
Published: 2018
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5. Monoclonal Antibodies Directed to Fucoidan Preparations from Brown Algae

Author: J. Paul Knox, Susan E. Marcus, Thierry Tonon, Murielle Jam, Thomas A. Torode, Richard S. Blackburn, Cécile Hervé, Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), 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), University of Leeds, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Sustainable Materials Research Group
Subjects: Male, Salinity, medicine.drug_class, lcsh:Medicine, Monoclonal antibody, Phaeophyta, Q1, Epitope, Cell wall, chemistry.chemical_compound, Cell Wall, Polysaccharides, medicine, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Rats, Wistar, lcsh:Science, Multidisciplinary, biology, Fucoidan, Ectocarpus siliculosus, lcsh:R, Antibodies, Monoclonal, R735, Ectocarpus, biology.organism_classification, Chromatography, Ion Exchange, R1, Rats, Brown algae, Epitope mapping, Biochemistry, chemistry, lcsh:Q, Epitope Mapping, Research Article
Abstract: International audience; Cell walls of the brown algae contain a diverse range of polysaccharides with useful bioactivities. The precise structures of the sulfated fucan/fucoidan group of polysaccharides and their roles in generating cell wall architectures and cell properties are not known in detail. Four rat monoclonal antibodies, BAM1 to BAM4, directed to sulfated fucan preparations, have been generated and used to dissect the heterogeneity of brown algal cell wall polysaccharides. BAM1 and BAM4, respectively, bind to a non-sulfated epitope and a sulfated epitope present in the sulfated fucan preparations. BAM2 and BAM3 identified additional distinct epitopes present in the fucoidan preparations. All four epitopes, not yet fully characterised, occur widely within the major brown algal taxonomic groups and show divergent distribution patterns in tissues. The analysis of cell wall extractions and fluorescence imaging reveal differences in the occurrence of the BAM1 to BAM4 epitopes in various tissues of Fucus vesiculosus. In Ectocarpus subulatus, a species closely related to the brown algal model Ectocarpus siliculosus, the BAM4 sulfated epitope was modulated in relation to salinity levels. This new set of monoclonal antibodies will be useful for the dissection of the highly complex and yet poorly resolved sulfated polysaccharides in the brown algae in relation to their ecological and economic significance.
Published: 2015
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6. Analyzing lateral root development: how to move forward

Author: A. Glyn Bengough, Ulrich Schurr, Renze Heidstra, Sacha J. Mooney, Hidehiro Fukaki, Philip N. Benfey, Benjamin Péret, Jonathan P. Lynch, John P. Hammond, Lionel X. Dupuy, Ilda Casimiro, Marta Joan Laskowski, Marc Lepetit, Tom Beeckman, Ive De Smet, Phillipe Nacry, Laurent Laplaze, Xavier Draye, Hanma Zhang, Philip J. White, Frank Hochholdinger, Malcolm J. Bennett, Martin R. Broadley, Boris Parizot, Division of Plant and Crop Sciences (DPCS), School of Biosciences-University of Nottingham, UK (UON), The James Hutton Institute, Laboratoire Commun de Microbiologie (LCM), Department of Plant Systems Biology, State University of Ghent, Universidad de Extremadura (UEX), Molecular Genetic, Utrecht University [Utrecht]-Faculty of Science-Department of Biology, Biology Department, Oberlin College, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institute of Crop Science and Resource Conservation (INRES), Rheinische Friedrich-Wilhelms-Universität Bonn, Earth and Life Institute [Louvain-La-Neuve] (ELI), Université Catholique de Louvain (UCL), Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-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 Biology, Kobe University, Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), Division of Agricultural and Environmental Sciences, Department of Horticulture, Pennsylvania State University (Penn State), Penn State System-Penn State System, 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), Institute of Bio- and Geosciences-2: Plant Sciences, Forschungszentrum Jülich GmbH, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University [Durham], Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universidad de Extremadura - University of Extremadura (UEX), Institute of Crop Science and Resource Conservation [Bonn] (INRES), Université Catholique de Louvain = Catholic University of Louvain (UCL), Plant Environmental Physiology and Stress Signaling (PEPSS), 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)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Nottingham, UK (UON)-School of Biosciences, 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), 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), 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), Division of Plant and Crop Sciences ( DPCS ), School of Biosciences-Loughborough-University of Nottingham, UK ( UON ), James Hutton Institute ( JHI ), Invergowrie, Laboratoire Commun de Microbiologie ( LCM ), Universidad de Extremadura, Facultad de Ciencias, Laboratoire des symbioses tropicales et méditerranéennes ( LSTM ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université Montpellier 1 ( UM1 ) -Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institute of Crop Science and Resource Conservation ( INRES ), Bonn Universität [Bonn], Earth and Life Institute [Louvain-La-Neuve], Université Catholique de Louvain ( UCL ), Laboratoire de Biologie du Développement des Plantes ( LBDP ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Centre for Plant Integrative Biology [Nothingham] ( CPIB ), University of Nottingham, UK ( UON ), School of Biosciences-University of Nottingham, UK ( UON ), PennState University [Pennsylvania] ( PSU ), Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Forschungszentrum Jülich, IBG-2: Plant Sciences, Diversité, adaptation, développement des plantes ( DIADE ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), and Duke university [Durham]
Subjects: 0106 biological sciences, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, Root (linguistics), Process (engineering), growth, MESH : Plant Roots, Plant Developmental Biology, MESH: Plant Roots, plant, Plant Science, Agricultural engineering, system architecture, Biology, Plant Roots, 01 natural sciences, ray computed-tomography, 03 medical and health sciences, traits, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nutrient-uptake, phosphorus, MESH: Models, Theoretical, 030304 developmental biology, 2. Zero hunger, Abiotic component, 0303 health sciences, Vegetal Biology, MESH : Models, Theoretical, Ecology, business.industry, Lateral root, green-revolution, Biology and Life Sciences, Cell Biology, Models, Theoretical, 15. Life on land, Variety (cybernetics), arabidopsis, Agriculture, Sustainability, Commentary, Systems architecture, business, auxin, Biologie végétale, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; International audience; Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.
Published: 2012
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7. Monoclonal Antibodies, Carbohydrate-Binding Modules, and the Detection of Polysaccharides in Plant Cell Walls

Author: Susan E. Marcus, Cécile Hervé, J. Paul Knox, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, and University of Leeds
Subjects: 0106 biological sciences, medicine.drug_class, [SDV]Life Sciences [q-bio], Polysaccharide, Monoclonal antibody, 01 natural sciences, Epitope, Cell wall, 03 medical and health sciences, medicine, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, fungi, food and beverages, Carbohydrate, 3. Good health, Biochemistry, chemistry, Monoclonal, biology.protein, Antibody, Molecular probe, 010606 plant biology & botany
Abstract: Plant cell walls are diverse composites of complex polysaccharides. Molecular probes such as monoclonal antibodies (MABs) and carbohydrate-binding modules (CBMs) are important tools to detect and dissect cell wall structures in plant materials. We provide an account of methods that can be used to detect cell wall polysaccharide structures (epitopes) in plant materials and also describe treatments that can provide information on the masking of sets of polysaccharides that may prevent detection. These masking -phenomena may indicate potential interactions between sets of cell wall polysaccharides, and methods to uncover them are an important aspect of cell wall immunocytochemistry.
Published: 2011
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8. The auxin signalling network translates dynamic input into robust patterning at the shoot apex

Author: Christophe Godin, Valérie Morin, Hilde Van den Daele, Géraldine Brunoud, Jonathan Legrand, Coralie Cellier, Malcolm J. Bennett, Yann Guédon, Stefan Kepinski, Lieven De Veylder, Soizic Guyomarc'h, Etienne Farcot, Rachil Koumproglou, Antoine Larrieu, Marina Oliva, Jan Traas, Mark Estelle, Lynne Armitage, Teva Vernoux, Geraint Parry, Pradeep Das, Franck Picard, John H. Doonan, Darren M. Wells, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Plant Biotechnology and Genetics [Ghent], Universiteit Gent = Ghent University (UGENT), Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Statistique en grande dimension pour la génomique, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Division of Biology [La Jolla], University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Department of Cell and Developmental Biology [Norwich], John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC)-Biotechnology and Biological Sciences Research Council (BBSRC)-Institute of Department of cell and Developmental Biology, Human Frontier Science Program Organization [CDA 0047/2007 HFSPO], Agence National de la Recherche [AuxFate ANR-07-JCJC-0115], Agence Nationale de la Recherche [NeMo ANR-08-BLAN-0304-01], EU [MRTN-CT2004-005336-SYSTEM], Biotechnology and Biological Research Council [BB/F007418/1, BB/F013981/1], Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universiteit Gent = Ghent University [Belgium] (UGENT), University of California-University of California, John Innes Centre [Norwich]-Institute of Department of cell and Developmental Biology, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Department of Plant Systems Biology, State University of Ghent, Ghent University [Belgium] (UGENT), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: 0106 biological sciences, ODE, auxin, biosensor, live imaging, signalling, Arabidopsis, F62 - Physiologie végétale - Croissance et développement, Organogenesis, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Auxin, Botany, Arabidopsis thaliana, heterocyclic compounds, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, General Immunology and Microbiology, biology, U10 - Informatique, mathématiques et statistiques, Applied Mathematics, fungi, food and beverages, Phyllotaxis, Meristem, biology.organism_classification, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Auxine, Cell biology, Signalling, Computational Theory and Mathematics, chemistry, Plant hormone, General Agricultural and Biological Sciences, Développement biologique, 010606 plant biology & botany, Information Systems
Abstract: International audience; The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting transcriptional activators and repressors, the auxin response factors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the shoot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive expression map and full interactome uncovered an unexpectedly simple distribution and structure of this pathway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predictions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunction with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex.
Published: 2011
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9. Functional analysis of folate polyglutamylation and its essential role in plant metabolism and development

Author: Mehrshahi, Payam, Gonzalez-Jorge, Sabrina, Akhtar, Tariq A, Ward, Jane L, Santoyo-Castelazo, Anahi, Marcus, Susan E, Lara-Núñez, Aurora, Ravanel, Stéphane, Hawkins, Nathaniel D, Beale, Michael H, Barrett, David A, Knox, J Paul, Gregory, Jesse F, Hanson, Andrew D, Bennett, Malcolm J, Dellapenna, Dean, Department of Biochemistry and Molecular Biology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, School of Biosciences, University of Nottingham, UK (UON), Horticultural Sciences Department, University of Florida [Gainesville] (UF), The National Centre for Plant and Microbial Metabolomics, School of Pharmacy, Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Food Science and Human Nutrition Department, 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), University of Florida [Gainesville], 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: folylpolyglutamate synthetase, Sucrose, one carbon metabolism, photorespiration, Arabidopsis thaliana, Arabidopsis, plant, MESH: Arabidopsis Proteins, folate, MESH: Phenotype, MESH: Folic Acid, Pantothenic Acid, coenzyme, Folic Acid, MESH: Pantothenic Acid, homeostasis, MESH: Arabidopsis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Peptide Synthases, gene, Arabidopsis Proteins, dual targeting, MESH: Sucrose, vitamin, polyglutamate, MESH: Peptide Synthases, Isoenzymes, enzyme, Phenotype, MESH: Seeds, MESH: Homeostasis, Multigene Family, Seeds, MESH: Isoenzymes, Pectins, MESH: Multigene Family, metabolism, MESH: Pectins
Abstract: International audience; Cellular folates function as co-enzymes in one-carbon metabolism and are predominantly decorated with a polyglutamate tail that enhances co-enzyme affinity, subcellular compartmentation and stability. Polyglutamylation is catalysed by folylpolyglutamate synthetases (FPGSs) that are specified by three genes in Arabidopsis, FPGS1, 2 and 3, which reportedly encode plastidic, mitochondrial and cytosolic isoforms, respectively. A mutational approach was used to probe the functional importance of folate polyglutamylation in one-carbon metabolism and development. Biochemical analysis of single FPGS loss-of-function mutants established that folate polyglutamylation is essential for organellar and whole-plant folate homeostasis. However, polyglutamylated folates were still detectable, albeit at lower levels, in organelles isolated from the corresponding isozyme knockout lines, e.g. in plastids and mitochondria of the fpgs1 (plastidial) and fpgs2 (mitochondrial) mutants. This result is surprising given the purported single-compartment targeting of each FPGS isozyme. These results indicate redundancy in compartmentalised FPGS activity, which in turn explains the lack of anticipated phenotypic defects for the single FPGS mutants. In agreement with this hypothesis, fpgs1 fpgs2 double mutants were embryo-lethal, fpgs2 fpgs3 mutants exhibited seedling lethality, and fpgs1 fpgs3 mutants were dwarfed with reduced fertility. These phenotypic, metabolic and genetic observations are consistent with targeting of one or more FPGS isozymes to multiple organelles. These data confirm the importance of polyglutamylation in folate compartmentation, folate homeostasis and folate-dependent metabolic processes, including photorespiration, methionine and pantothenate biosynthesis.
Published: 2010
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10. Pectic homogalacturonan masks abundant sets of xyloglucan epitopes in plant cell walls

Author: Yves Verhertbruggen, William G.T. Willats, Cécile Hervé, José Juan Ordaz-Ortiz, Susan E. Marcus, J. Paul Knox, Henriette L. Pedersen, Vladimír Farkaš, Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, University of Leeds, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of Chemistry, and University of Copenhagen = Københavns Universitet (KU)
Subjects: Nasturtium, 0106 biological sciences, Glycan, Cellular differentiation, [SDV]Life Sciences [q-bio], Fluorescent Antibody Technique, Enzyme-Linked Immunosorbent Assay, Plant Science, Biology, 01 natural sciences, Epitope, Cell wall, Epitopes, 03 medical and health sciences, chemistry.chemical_compound, Cell Wall, lcsh:Botany, Tobacco, Tamarindus, Animals, Hemicellulose, Glucans, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Polysaccharide-Lyases, 030304 developmental biology, 0303 health sciences, Plant Stems, Cell growth, Peas, Antibodies, Monoclonal, Rats, lcsh:QK1-989, Xyloglucan, Solubility, chemistry, Biochemistry, Seeds, biology.protein, Pectins, Xylans, Cotyledon, Secondary cell wall, Research Article, 010606 plant biology & botany
Abstract: Background Molecular probes are required to detect cell wall polymers in-situ to aid understanding of their cell biology and several studies have shown that cell wall epitopes have restricted occurrences across sections of plant organs indicating that cell wall structure is highly developmentally regulated. Xyloglucan is the major hemicellulose or cross-linking glycan of the primary cell walls of dicotyledons although little is known of its occurrence or functions in relation to cell development and cell wall microstructure. Results Using a neoglycoprotein approach, in which a XXXG heptasaccharide of tamarind seed xyloglucan was coupled to BSA to produce an immunogen, we have generated a rat monoclonal antibody (designated LM15) to the XXXG structural motif of xyloglucans. The specificity of LM15 has been confirmed by the analysis of LM15 binding using glycan microarrays and oligosaccharide hapten inhibition of binding studies. The use of LM15 for the analysis of xyloglucan in the cell walls of tamarind and nasturtium seeds, in which xyloglucan occurs as a storage polysaccharide, indicated that the LM15 xyloglucan epitope occurs throughout the thickened cell walls of the tamarind seed and in the outer regions, adjacent to middle lamellae, of the thickened cell walls of the nasturtium seed. Immunofluorescence analysis of LM15 binding to sections of tobacco and pea stem internodes indicated that the xyloglucan epitope was restricted to a few cell types in these organs. Enzymatic removal of pectic homogalacturonan from equivalent sections resulted in the abundant detection of distinct patterns of the LM15 xyloglucan epitope across these organs and a diversity of occurrences in relation to the cell wall microstructure of a range of cell types. Conclusion These observations support ideas that xyloglucan is associated with pectin in plant cell walls. They also indicate that documented patterns of cell wall epitopes in relation to cell development and cell differentiation may need to be re-considered in relation to the potential masking of cell wall epitopes by other cell wall components.
Published: 2008
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11. Trafficking routes to the plant vacuole: connecting alternative and classical pathways.

Author: Di Sansebastiano GP, Barozzi F, Piro G, Denecke J, and de Marcos Lousa C
Subjects: Protein Transport, Plant Proteins metabolism, Plants metabolism, Secretory Pathway, Vacuoles metabolism
Abstract: Due to the numerous roles plant vacuoles play in cell homeostasis, detoxification, and protein storage, the trafficking pathways to this organelle have been extensively studied. Recent evidence, however, suggests that our vision of transport to the vacuole is not as simple as previously imagined. Alternative routes have been identified and are being characterized. Intricate interconnections between routes seem to occur in various cases, complicating the interpretation of data. In this review, we aim to summarize the published evidence and link the emerging data with previous findings. We discuss the current state of information on alternative and classical trafficking routes to the plant vacuole., (© The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
Published: 2017
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12. DNA methylation systems and targets in plants.

Author: Meyer P
Subjects: DNA Methylation physiology, DNA, Plant genetics, Epigenesis, Genetic genetics, Heterochromatin genetics, RNA, Small Interfering genetics, DNA Methylation genetics, Plants genetics
Abstract: Plants contain three distinct DNA methyltransferase types that are responsible for the establishment and maintenance of cytosine methylation patterns at heterochromatic and euchromatic target regions. RNA transcripts play an important role in recruiting DNA methylation systems to specific loci, where methylation patterns are controlled by distinct epigenetic pathways that often work co-operatively and in competition with demethylation functions. DNA methylation patterns are faithfully propagated by maintenance systems that involve re-enforcing feedback effects between DNA methylation and histone marks. Our detailed knowledge about the composition of DNA methylation patterns is contrasted by a poorer understanding of the variability of DNA methylation and its contribution to gene regulation, genome evolution and adaptation to environmental changes., (Copyright © 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.)
Published: 2011
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13. An experimental method to facilitate the identification of hybrid sporophytes in the moss Physcomitrella patens using fluorescent tagged lines.

Author: Perroud PF, Cove DJ, Quatrano RS, and McDaniel SF
Subjects: Crosses, Genetic, Green Fluorescent Proteins analysis, Green Fluorescent Proteins genetics, Luminescent Proteins genetics, Plants, Genetically Modified metabolism, Transgenes, Bryopsida genetics, Genetic Engineering methods, Hybridization, Genetic, Luminescent Proteins analysis
Abstract: • The sequencing of the Physcomitrella patens genome, combined with the high frequency of gene targeting in this species, makes it ideal for reverse genetic studies. For forward genetic studies, experimental crosses and genetic analysis of progeny are essential. • Since P. patens is monoicous, producing both male and female gametes on the same gametophore, and undergoing self-fertilization at a high frequency, the identification of crossed sporophytes is difficult. Usually spores from many sporophytes from a mixed culture must be tested for the production of recombinant progeny. • Here, we describe the use of transgenic lines that express a fluorescent transgene constitutively, to provide a direct visual screen for hybrid sporophytes. • We show that segregations in crosses obtained with this technique are as expected, and demonstrate its utility for the study of the rate of outcrossing between three isolates of P. patens., (© 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.)
Published: 2011
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14. Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region.

Author: Zubko E, Kunova A, and Meyer P
Subjects: Arabidopsis metabolism, Codon chemistry, Codon genetics, Codon metabolism, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Genotype, Oligonucleotide Array Sequence Analysis, Plants, Genetically Modified, Poly A genetics, Poly A metabolism, RNA Processing, Post-Transcriptional genetics, RNA, Antisense chemistry, RNA, Antisense genetics, RNA, Double-Stranded metabolism, RNA, Messenger chemistry, RNA, Messenger genetics, Transcription, Genetic, Arabidopsis genetics, Polyadenylation genetics, RNA, Antisense metabolism, RNA, Messenger metabolism, Regulatory Sequences, Ribonucleic Acid physiology
Abstract: The Arabidopsis genome contains a large number of gene pairs that encode sense and antisense transcripts with overlapping 3' regions, indicative for a potential role of natural antisense transcription in regulating sense gene expression or transcript processing. When we mapped poly(A) transcripts of three plant gene pairs with long overlapping antisense transcripts, we identified an unusual transcript composition for two of the three gene pairs. Both genes pairs encoded a class of long sense transcripts and a class of short sense transcripts that terminate within the same polyadenylation region as the antisense transcripts encoded by the opposite strand. We find that the presence of the short sense transcript was not dependent on the expression of an antisense transcript. This argues against the assumption that the common termination region for sense and antisense poly(A) transcripts is the result of antisense-specific regulation. We speculate that for some genes evolution may have especially favoured alternative polyadenylation events that shorten transcript length for gene pairs with overlapping sense/antisense transcription, if this reduces the likelihood for dsRNA formation and transcript degradation.
Published: 2011
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15. The Arabidopsis peroxisomal ABC transporter, comatose, complements the Saccharomyces cerevisiae pxa1 pxa2Delta mutant for metabolism of long-chain fatty acids and exhibits fatty acyl-CoA-stimulated ATPase activity.

Author: Nyathi Y, De Marcos Lousa C, van Roermund CW, Wanders RJ, Johnson B, Baldwin SA, Theodoulou FL, and Baker A
Subjects: Adenosine Triphosphatases, Amino Acid Motifs, Arabidopsis genetics, Arabidopsis Proteins, Genetic Complementation Test, Oxidation-Reduction, Substrate Specificity, ATP-Binding Cassette Transporters, Arabidopsis enzymology, Fatty Acids metabolism, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins
Abstract: The Arabidopsis ABC transporter Comatose (CTS; AtABCD1) is required for uptake into the peroxisome of a wide range of substrates for β-oxidation, but it is uncertain whether CTS itself is the transporter or if the transported substrates are free acids or CoA esters. To establish a system for its biochemical analysis, CTS was expressed in Saccharomyces cerevisiae. The plant protein was correctly targeted to yeast peroxisomes, was assembled into the membrane with its nucleotide binding domains in the cytosol, and exhibited basal ATPase activity that was sensitive to aluminum fluoride and abrogated by mutation of a conserved Walker A motif lysine residue. The yeast pxa1 pxa2Δ mutant lacks the homologous peroxisomal ABC transporter and is unable to grow on oleic acid. Consistent with its exhibiting a function in yeast akin to that in the plant, CTS rescued the oleate growth phenotype of the pxa1 pxa2Δ mutant, and restored β-oxidation of fatty acids with a range of chain lengths and varying degrees of desaturation. When expressed in yeast peroxisomal membranes, the basal ATPase activity of CTS could be stimulated by fatty acyl-CoAs but not by fatty acids. The implications of these findings for the function and substrate specificity of CTS are discussed.
Published: 2010
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16. Plant-pathogen interactions: a view from the evolutionary basement.

Author: Cuming AC
Subjects: Genes, Plant, Plant Proteins genetics, Plant Proteins metabolism, Plants genetics, Reactive Oxygen Species metabolism, Biological Evolution, Host-Pathogen Interactions, Plants microbiology
Published: 2009
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17. The evolution of the abscisic acid-response in land plants: comparative analysis of group 1 LEA gene expression in moss and cereals.

Author: Kamisugi Y and Cuming AC
Subjects: Amino Acid Sequence, Base Sequence, Bryopsida metabolism, Hordeum metabolism, Molecular Sequence Data, Osmotic Pressure, Plant Proteins chemistry, Plant Proteins metabolism, Promoter Regions, Genetic genetics, RNA, Plant genetics, RNA, Plant metabolism, Response Elements genetics, Sequence Alignment, Sequence Homology, Nucleic Acid, Transcription, Genetic drug effects, Triticum, Abscisic Acid pharmacology, Biological Evolution, Bryopsida genetics, Gene Expression Regulation, Plant drug effects, Hordeum genetics, Plant Proteins genetics
Abstract: The moss Physcomitrella patens possesses a single copy of a Group 1 LEA gene, designated PpLEA-1. Sequence analysis of the PpLEA-1 gene reveals the gene to contain a single intron in a position conserved in all members of the Group 1 LEA gene family, but also to contain a premature termination codon within the first exon. Nevertheless, a PpLEA-1 transcript accumulates in moss tissues in response both to the imposition of osmotic stress, and to the plant growth regulator abscisic acid (ABA). This response appears to be mediated at the transcriptional level, and observation of the pattern of gene expression, reported by histochemical staining of plants expressing a PpLea-1::GUS transgene suggests that the promoter responds preferentially to ABA in protonemal filaments, whereas osmotic stress induces gene expression primarily in the gametophores. Quantitative analysis of promoter activity by transient expression in Physcomitrella protoplasts shows the PpLEA-1 promoter to be highly active in response to ABA and osmotic stress. ABA-mediated transgene expression from the PpLea-1 promoter occurs at a level similar to that driven by the highly active promoter of the wheat Group 1 LEA gene, E(m). Site-directed mutagenesis of the PpLEA-1 promoter indicates that ABA-inducibility is mediated via an ACGT-core motif similar to that seen in the ABA response elements of higher plant LEA genes. However, whereas the wheat E(m )promoter is active in moss tissues, the moss promoter is not reciprocally active in cereal cells: no activity, ABA-inducible or otherwise was detected in barley aleurone protoplasts transfected with the PpLEA-1::GUS construct. We propose that ABA activation of gene expression in moss cells represents an ancestral state, with only minimal requirements for promoter recognition, whereas cereal cells require the interaction of additional factors with ABA-responsive promoters.
Published: 2005
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18. Formation of wheat ( Triticum aestivum L.) embryogenic callus involves peroxide-generating germin-like oxalate oxidase.

Author: Caliskan M, Turet M, and Cuming AC
Subjects: Germination, Glycoproteins metabolism, Indoleacetic Acids pharmacology, Peroxides metabolism, Plant Proteins, Seeds ultrastructure, Triticum metabolism, Oxidoreductases metabolism, Seeds metabolism, Triticum embryology
Abstract: In wheat ( Triticum aestivum L.), embryogenic callus formation comprises suppression of precocious germination by the zygotic embryo and the initiation of dedifferentiated cellular proliferation within it. Embryogenic calli are induced by treating immature embryos with 2,4-dichlorophenoxyacetic acid (2,4-D). Upon withdrawal from 2,4-D, somatic embryos develop from the periphery of the callus. Prior to visible callus formation, there is a striking induction of "germin-like" oxalate oxidase ("gl-OXO": EC 1.2.3.4) gene expression. Accumulation of gl-OXO mRNA is rapidly stimulated upon auxin treatment, with a consequent development of apoplastic enzyme activity producing H(2)O(2) within the cell wall. Within the dedifferentiated calli, gl-OXO enzyme activity becomes widespread over the surface of embryogenic calli. Differentiation of somatic embryos is initiated in regions of densely cytoplasmic, meristematic cells that are marked by highly localised expression of gl-OXO activity within these embryogenic cell masses. We suggest that this localised generation of H(2)O(2) by gl-OXO promotes peroxidative cross-linking of cell wall components, thereby preventing cellular expansion and maintaining these cell masses in an embryogenically competent condition.
Published: 2004
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19. An abscisic acid-sensitive checkpoint in lateral root development of Arabidopsis.

Author: De Smet I, Signora L, Beeckman T, Inzé D, Foyer CH, and Zhang H
Subjects: Arabidopsis drug effects, Indoleacetic Acids pharmacology, Meristem drug effects, Meristem growth & development, Mutation, Naphthaleneacetic Acids pharmacology, Plant Growth Regulators pharmacology, Plant Roots drug effects, Signal Transduction physiology, Abscisic Acid pharmacology, Arabidopsis growth & development, Plant Roots growth & development
Abstract: Lateral root (LR) formation displays considerable plasticity in response to developmental and environmental signals. The mechanism whereby plants incorporate diverse regulatory signals into the developmental programme of LRs remains to be elucidated. Current concepts of lateral root regulation focus on the role of auxin. In this study, we show that another plant hormone, abscisic acid (ABA), also plays a critical role in the regulation of this post-embryonic developmental event. In the presence of exogenous ABA, LR development is inhibited. This occurs at a specific developmental stage, i.e. immediately after the emergence of the LR primordium (LRP) from the parent root and prior to the activation of the LR meristem, and is reversible. Interestingly, this inhibition requires 10-fold less ABA than the inhibition of seed germination and is only slightly reduced in characterised abi mutants, suggesting that it may involve novel ABA signalling mechanisms. We also present several lines of evidence to support the conclusion that the ABA-induced lateral root inhibition is mediated by an auxin-independent pathway. First, the inhibition could not be rescued by either exogenous auxin application or elevated auxin synthesis. Secondly, a mutation in the ALF3 gene, which is believed to encode an important component in the auxin-dependent regulatory pathway for the post-emergence LR development, does not affect the sensitivity of LRs to ABA. Thirdly, ABA and the alf3-1 mutation do not act at the same developmental point. To summarise, these results demonstrate a novel ABA-sensitive, auxin-independent checkpoint for lateral root development in Arabidopsis at the post-emergence stage. In addition, we also present data indicating that regulation of this developmental checkpoint may require novel ABA signalling mechanisms and that ABA suppresses auxin response in the LRPs.
Published: 2003
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20. Secretory bulk flow of soluble proteins is efficient and COPII dependent.

Author: Phillipson BA, Pimpl P, daSilva LL, Crofts AJ, Taylor JP, Movafeghi A, Robinson DG, and Denecke J
Subjects: Calcium-Binding Proteins metabolism, Calreticulin, Escherichia coli, Fungal Proteins genetics, Fungal Proteins metabolism, Gene Expression, Guanine Nucleotide Exchange Factors, Ligands, Membrane Glycoproteins genetics, Membrane Glycoproteins metabolism, Models, Biological, Monomeric GTP-Binding Proteins genetics, Monomeric GTP-Binding Proteins metabolism, Mutation, Oligopeptides metabolism, Protein Sorting Signals, Protein Transport, Proteins genetics, Receptors, Peptide metabolism, Ribonucleoproteins metabolism, Solubility, Substrate Specificity, Temperature, Vesicular Transport Proteins, alpha-Amylases antagonists & inhibitors, alpha-Amylases genetics, alpha-Amylases metabolism, COP-Coated Vesicles metabolism, Endoplasmic Reticulum metabolism, Golgi Apparatus metabolism, Proteins metabolism, Saccharomyces cerevisiae Proteins, Nicotiana cytology, Nicotiana metabolism
Abstract: COPII-coated vesicles, first identified in yeast and later characterized in mammalian cells, mediate protein export from the endoplasmic reticulum (ER) to the Golgi apparatus within the secretory pathway. In these organisms, the mechanism of vesicle formation is well understood, but the process of soluble cargo sorting has yet to be resolved. In plants, functional complements of the COPII-dependent protein traffic machinery were identified almost a decade ago, but the selectivity of the ER export process has been subject to considerable debate. To study the selectivity of COPII-dependent protein traffic in plants, we have developed an in vivo assay in which COPII vesicle transport is disrupted at two distinct steps in the pathway. First, overexpression of the Sar1p-specific guanosine nucleotide exchange factor Sec12p was shown to result in the titration of the GTPase Sar1p, which is essential for COPII-coated vesicle formation. A second method to disrupt COPII transport at a later step in the pathway was based on coexpression of a dominant negative mutant of Sar1p (H74L), which is thought to interfere with the uncoating and subsequent membrane fusion of the vesicles because of the lack of GTPase activity. A quantitative assay to measure ER export under these conditions was achieved using the natural secretory protein barley alpha-amylase and a modified version carrying an ER retention motif. Most importantly, the manipulation of COPII transport in vivo using either of the two approaches allowed us to demonstrate that export of the ER resident protein calreticulin or the bulk flow marker phosphinothricin acetyl transferase is COPII dependent and occurs at a much higher rate than estimated previously. We also show that the instability of these proteins in post-ER compartments prevents the detection of the true rate of bulk flow using a standard secretion assay. The differences between the data on COPII transport obtained from these in vivo experiments and in vitro experiments conducted previously using yeast components are discussed.
Published: 2001
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21. A vacuolar sorting domain may also influence the way in which proteins leave the endoplasmic reticulum.

Author: Törmäkangas K, Hadlington JL, Pimpl P, Hillmer S, Brandizzi F, Teeri TH, and Denecke J
Subjects: Animals, Aspartic Acid Endopeptidases chemistry, Aspartic Acid Endopeptidases genetics, COP-Coated Vesicles metabolism, Cathepsins chemistry, Cathepsins genetics, Glycoproteins chemistry, Golgi Apparatus metabolism, Models, Biological, Plants, Genetically Modified, Protein Precursors chemistry, Protein Precursors metabolism, Protein Transport, Saposins, Sequence Deletion, Solubility, Nicotiana genetics, Aspartic Acid Endopeptidases metabolism, Cathepsins metabolism, Endoplasmic Reticulum metabolism, Protein Sorting Signals physiology, Nicotiana cytology, Nicotiana metabolism, Vacuoles metabolism
Abstract: Protein sorting to plant vacuoles is known to be dependent on a considerable variety of protein motifs recognized by a family of sorting receptors. This can involve either traffic from the endoplasmic reticulum (ER) through the Golgi apparatus or direct ER-to-vacuole transport. Barley aspartic protease (Phytepsin) was shown previously to reach the vacuole via trafficking through the Golgi apparatus. Here we show that Phytepsin normally exits the ER in a COPII-mediated manner, because the Phytepsin precursor accumulates in the ER upon specific inhibition of the formation of COPII vesicles in vivo. Phytepsin differs from its yeast and mammalian counterparts by the presence of a saposin-like plant-specific insert (PSI). Deletion of this domain comprising 104 amino acids causes efficient secretion of the truncated molecule (Phytepsin Delta PSI) without affecting the enzymatic activity of the enzyme. Interestingly, deletion of the PSI also changes the way in which Phytepsin exits the ER. Inhibition of COPII vesicle formation causes accumulation of the Phytepsin precursor in the ER but has no effect on the secretion of Phytepsin Delta PSI. This suggests either that vacuolar sorting commences at the ER export step and involves recruitment into COPII vesicles or that the PSI domain carries two signals, one for COPII-dependent export from the ER and one for vacuolar delivery from the Golgi. The relevance of these observations with respect to the bulk flow model of secretory protein synthesis is discussed.
Published: 2001
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22. Calmodulin as a versatile calcium signal transducer in plants.

Author: Snedden WA and Fromm H
Abstract: The complexity of Ca 2+ patterns observed in eukaryotic cells, including plants, has led to the hypothesis that specific patterns of Ca 2+ propagation, termed Ca 2+ signatures, encode information and relay it to downstream elements (effectors) for translation into appropriate cellular responses. Ca 2+ -binding proteins (sensors) play a key role in decoding Ca 2+ signatures and transducing signals by activating specific targets and pathways. Calmodulin is a Ca 2+ sensor known to modulate the activity of many mammalian proteins, whose targets in plants are now being actively characterized. Plants possess an interesting and rapidly growing list of calmodulin targets with a variety of cellular roles. Nevertheless, many targets appear to be unique to plants and remain uncharacterized, calling for a concerted effort to elucidate their functions. Moreover, the extended family of calmodulin-related proteins in plants consists of evolutionarily divergent members, mostly of unknown function, although some have recently been implicated in stress responses. It is hoped that advances in functional genomics, and the research tools it generates, will help to explain themultiplicity of calmodulin genes in plants, and to identify their downstream effectors. This review summarizes current knowledge of the Ca 2+ -calmodulin messenger system in plants and presents suggestions for future areas of research. Contents I. Introduction 36 II. CaM isoforms and CaM-like proteins 37 III. CaM-target proteins 42 IV. CaM and nuclear functions 46 V. Regulation of ion transport 49 VI. CaM and plant responses to environmental stimuli 52 VII. Conclusions and future studies 58 Acknowledgements 59 References 59.
Published: 2001
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23. Protease inhibitors and directed evolution: enhancing plant resistance to nematodes.

Author: McPherson MJ and Harrison DJ
Subjects: Animals, Cystatins genetics, Cystatins metabolism, Cystatins pharmacology, Directed Molecular Evolution, Drug Resistance genetics, Genetic Engineering, Nematoda drug effects, Nematoda enzymology, Nematoda genetics, Peptide Library, Plants genetics, Plants metabolism, Plants, Genetically Modified, Protease Inhibitors pharmacology, Nematoda pathogenicity, Plants parasitology, Protease Inhibitors metabolism
Abstract: Plant nematodes are agricultural pests, the control of which relies on chemical nematicides and fumigants that are among the most toxic and environmentally damaging of all agrochemicals. New approaches to control, based on transgenic resistance, would provide important health and environmental benefits. In this chapter we consider briefly some targets for engineering nematode resistance and discuss the use of plant protease inhibitors as anti-feedants. This approach has provided plants that display good levels of resistance against a range of nematode species. To enhance this defence strategy further we are investigating the value of directed evolution to improve the characteristics of protease inhibitors. We describe the approaches of DNA shuffling and phage display that are being used to create and screen variant libraries in the search for inhibitors with improved features.
Published: 2001
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24. Stress induces peroxisome biogenesis genes.

Author: Lopez-Huertas E, Charlton WL, Johnson B, Graham IA, and Baker A
Subjects: ATPases Associated with Diverse Cellular Activities, Amino Acid Sequence, Arabidopsis genetics, Base Sequence, Glycoproteins chemistry, Hydrogen Peroxide pharmacology, Light, Luciferases genetics, Molecular Sequence Data, Peroxisomes drug effects, Peroxisomes radiation effects, Plant Proteins chemistry, Plant Proteins genetics, Plants, Genetically Modified, Promoter Regions, Genetic, Recombinant Fusion Proteins biosynthesis, Arabidopsis physiology, Gene Expression Regulation, Plant drug effects, Glycoproteins genetics, Membrane Proteins, Oxidative Stress, Peroxisomes genetics
Abstract: Peroxisomes are the cellular location of many antioxidants and are themselves significant producers of reactive oxygen species. In this report we demonstrate the induction of peroxisome biogenesis genes in both plant and animal cells by the universal stress signal molecule hydrogen peroxide. Using PEX1-LUC transgenic plants, rapid local and systemic induction of PEX1-luciferase could be demonstrated in vivo in response to physiological levels of hydrogen peroxide. PEX1-luciferase was also induced in response to wounding and to infection with an avirulent pathogen. We propose a model in which various stress situations that lead to the production of hydrogen peroxide can be ameliorated by elaboration of the peroxisome compartment to assist in restoration of the cellular redox balance.
Published: 2000
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25. Functional characterization of the EMCV IRES in plants.

Author: Urwin P, Yi L, Martin H, Atkinson H, and Gilmartin PM
Subjects: DNA, Recombinant, Gene Expression Regulation, Plant, Green Fluorescent Proteins, Luciferases genetics, Luciferases metabolism, Luminescent Proteins genetics, Luminescent Proteins metabolism, Microscopy, Fluorescence, Open Reading Frames genetics, Plants, Genetically Modified, Plants, Toxic, RNA, Messenger genetics, RNA, Messenger metabolism, Recombinant Fusion Proteins genetics, Recombinant Fusion Proteins metabolism, Nicotiana genetics, Transcription, Genetic, Encephalomyocarditis virus genetics, Plants genetics, Regulatory Sequences, Nucleic Acid genetics
Abstract: The translation of eukaryotic messenger RNA is typically dependent upon the presence of an m7GpppN cap structure at the 5' end of the transcript. However, several animal viruses, including the Picorna viruses, have been shown to exhibit cap-independent translation through the presence of an internal ribosome entry site or IRES. This IRES-mediated cap-independent internal translation initiation has been exploited to generate bicistronic transcripts that function in animal cells. Recently IRES elements have also been identified in a small number of vertebrate, insect and yeast cellular messenger RNAs although no such sequences have been identified in endogenous plant genes and there are no reports of animal virus derived IRES activity in plant cells. Here we have constructed a bicistronic gene containing both green fluorescent protein and luciferase open-reading frames separated by the encephalomyocarditis IRES element under the control of the CaMV 35S promoter. Northern analysis reveals expression of the bicistronic transcript and in vivo imaging of GFP and luciferase activities demonstrates the functional presence of both proteins. Western blot analysis confirms the independent translation of both reporter proteins. These data suggest that insertion of the encephalomyocarditis virus (EMCV) IRES element between two open-reading frames of a plant bicistronic transcript can mediate translation of the second open-reading frame. This activity is more apparent in the leaves, than in the roots, of transgenic seedlings carrying the bicistronic reporter gene construct.
Published: 2000
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26. Analysis of pectic epitopes recognised by hybridoma and phage display monoclonal antibodies using defined oligosaccharides, polysaccharides, and enzymatic degradation.

Author: Willats WG, Limberg G, Buchholt HC, van Alebeek GJ, Benen J, Christensen TM, Visser J, Voragen A, Mikkelsen JD, and Knox JP
Subjects: Combinatorial Chemistry Techniques, Enzyme-Linked Immunosorbent Assay methods, Hybridomas, Oligosaccharides immunology, Pectins analysis, Peptide Library, Polysaccharides immunology, Antibodies, Monoclonal, Epitopes analysis, Oligosaccharides analysis, Pectins chemistry, Pectins immunology, Polysaccharides analysis
Abstract: The structure of epitopes recognised by anti-pectin monoclonal antibodies (mAbs) has been investigated using a series of model lime-pectin samples with defined degrees and patterns of methyl esterification, a range of defined oligogalacturonides and enzymatic degradation of pectic polysaccharides. In immuno-dot-assays, the anti-homogalacturonan (HG) mAbs JIM5 and JIM7 both bound to samples with a wide range of degrees of methyl esterification in preference to fully de-esterified samples. In contrast, the anti-HG phage display mAb PAM1 bound most effectively to fully de-esterified pectin. In competitive inhibition ELISAs using fully methyl-esterified or fully de-esterified oligogalacturonides with 3-9 galacturonic acid residues, JIM5 bound weakly to a fully de-esterified nonagalacturonide but JIM7 did not bind to any of the oligogalacturonides tested. Therefore, optimal JIM5 and JIM7 binding occurs where specific but undefined methyl-esterification patterns are present on HG domains, although fully de-esterified HG samples contain sub-optimal JIM5 epitopes. The persistence of mAb binding to epitopes in pectic antigens, with 41% blockwise esterification (P41) and 43% random esterification (F43) subject to fragmentation by endo-polygalacturonase II (PG II) and endo-pectin lyase (PL), was also studied. Time course analysis of PG II digestion of P41 revealed that JIM5 epitopes were rapidly degraded, but a low level of PAM1 and JIM7 epitopes existed even after extensive digestion, indicating that some HG domains were more resistant to cleavage by PG II. The chromatographic separation of fragments produced by the complete digestion of P41 by pectin lyase indicated that a very restricted population of fragments contained the PAM1 epitope while a (1-->4)-beta-D-galactan epitope occurring on the side chains of pectic polysaccharides was recovered in a broad range of fractions.
Published: 2000
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27. Antibodies against pex14p block ATP-independent binding of matrix proteins to peroxisomes in vitro.

Author: Lopez-Huertas E, Oh J, and Baker A
Subjects: Biological Transport, Carbonates metabolism, Fungal Proteins metabolism, Glyoxysomes immunology, Glyoxysomes metabolism, Helianthus, Humans, Intracellular Membranes metabolism, Membrane Proteins metabolism, Molecular Weight, Peroxisomal Targeting Signal 2 Receptor, Peroxisome-Targeting Signal 1 Receptor, Peroxisomes immunology, Receptors, Cytoplasmic and Nuclear metabolism, Adenosine Triphosphate metabolism, Antibodies immunology, Carrier Proteins, Extracellular Matrix Proteins metabolism, Fungal Proteins immunology, Membrane Proteins immunology, Peroxisomes metabolism, Repressor Proteins
Abstract: The membrane protein Pex14p is a key component of the protein import machinery of peroxisomes. Antibodies raised against human Pex14p recognise a 66 kDa protein in sunflower glyoxysomes (HaPex14p) and immunoprecipitate in vitro-translated Arabidopsis Pex14p (AtPex14p). These antibodies inhibit the ATP-independent binding to sunflower peroxisome membranes of peroxisome targeting signal type (PTS) 1- and PTS2-targeted matrix proteins, but not an integral membrane protein. These results suggest that Pex14p functions before the ATP-dependent step of peroxisome assembly.
Published: 1999
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28. Arabidopsis 22-kilodalton peroxisomal membrane protein. Nucleotide sequence analysis and biochemical characterization.

Author: Tugal HB, Pool M, and Baker A
Subjects: Amino Acid Sequence, Arabidopsis growth & development, DNA, Complementary genetics, DNA, Plant genetics, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genes, Plant, Molecular Sequence Data, Sequence Homology, Amino Acid, Arabidopsis chemistry, Arabidopsis genetics, Membrane Proteins chemistry, Membrane Proteins genetics, Microbodies chemistry, Plant Proteins chemistry, Plant Proteins genetics
Abstract: We sequenced and characterized PMP22 (22-kD peroxisomal membrane protein) from Arabidopsis, which shares 28% to 30% amino acid identity and 55% to 57% similarity to two related mammalian peroxisomal membrane proteins, PMP22 and Mpv17. Subcellular fractionation studies confirmed that the Arabidopsis PMP22 is a genuine peroxisomal membrane protein. Biochemical analyses established that the Arabidopsis PMP22 is an integral membrane protein that is completely embedded in the lipid bilayer. In vitro import assays demonstrated that the protein is inserted into the membrane posttranslationally in the absence of ATP, but that ATP stimulates the assembly into the native state. Arabidopsis PMP22 is expressed in all organs of the mature plant and in tissue-cultured cells. Expression of PMP22 is not associated with a specific peroxisome type, as it is detected in seeds and throughout postgerminative growth as cotyledon peroxisomes undergo conversion from glyoxysomes to leaf-type peroxisomes. Although PMP22 shows increased accumulation during the growth of young seedlings, its expression is not stimulated by light.
Published: 1999
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29. Characterization of intermediates in the process of plant peroxisomal protein import.

Author: Pool MR, López-Huertas E, and Baker A
Subjects: Adenosine Triphosphate, Alcohol Oxidoreductases genetics, Alcohol Oxidoreductases isolation & purification, Biological Transport, Endopeptidases, Recombinant Fusion Proteins genetics, Recombinant Fusion Proteins isolation & purification, Recombinant Fusion Proteins metabolism, Sodium Chloride, Staphylococcal Protein A genetics, Staphylococcal Protein A isolation & purification, Alcohol Oxidoreductases metabolism, Spinacia oleracea enzymology, Staphylococcal Protein A metabolism
Abstract: A hybrid protein in which the immunoglobulin G-binding domain of Staphylococcus aureus protein A replaced the N-terminal 43 amino acids of glycolate oxidase (a peroxisomal protein) was affinity purified after expression in Escherichia coli and used to study peroxisomal protein import in vitro. The fusion protein, which co-purifies with the bacterial chaperones dnaK and groEL, binds to glyoxysomes and is partially translocated in an ATP-dependent reaction which is independent of eukaryotic cytosol. Both binding and translocation are dependent upon the amount of glyoxysomes present. The partially translocated species has a transmembrane location and is extractable by salt, indicating that it is held in the membrane by ionic interactions. In the absence of ATP, the fusion protein binds to the surface of the glyoxysomes and competes the binding of authentic matrix proteins. The surface-bound protein can be chased to the transmembrane species upon the addition of ATP. These results indicate that the surface-bound form is a true translocation intermediate. The availability of this fusion protein in milligram quantities offers the possibility to use the intermediate formed in the absence of ATP and the transmembrane species to probe interactions with the peroxisome import machinery.
Published: 1998
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29 results on '"Centre for Plant Sciences [Leeds]"'

1. Plasma Membrane-Associated Receptor-like Kinases Relocalize to Plasmodesmata in Response to Osmotic Stress 1[OPEN]

2. Dynamics of cell wall assembly during early embryogenesis in the brown algaFucus

3. Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development

4. Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures

5. Monoclonal Antibodies Directed to Fucoidan Preparations from Brown Algae

6. Analyzing lateral root development: how to move forward

7. Monoclonal Antibodies, Carbohydrate-Binding Modules, and the Detection of Polysaccharides in Plant Cell Walls

8. The auxin signalling network translates dynamic input into robust patterning at the shoot apex

9. Functional analysis of folate polyglutamylation and its essential role in plant metabolism and development

10. Pectic homogalacturonan masks abundant sets of xyloglucan epitopes in plant cell walls

11. Trafficking routes to the plant vacuole: connecting alternative and classical pathways.

12. DNA methylation systems and targets in plants.

13. An experimental method to facilitate the identification of hybrid sporophytes in the moss Physcomitrella patens using fluorescent tagged lines.

14. Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region.

15. The Arabidopsis peroxisomal ABC transporter, comatose, complements the Saccharomyces cerevisiae pxa1 pxa2Delta mutant for metabolism of long-chain fatty acids and exhibits fatty acyl-CoA-stimulated ATPase activity.

16. Plant-pathogen interactions: a view from the evolutionary basement.

17. The evolution of the abscisic acid-response in land plants: comparative analysis of group 1 LEA gene expression in moss and cereals.

18. Formation of wheat ( Triticum aestivum L.) embryogenic callus involves peroxide-generating germin-like oxalate oxidase.

19. An abscisic acid-sensitive checkpoint in lateral root development of Arabidopsis.

20. Secretory bulk flow of soluble proteins is efficient and COPII dependent.

21. A vacuolar sorting domain may also influence the way in which proteins leave the endoplasmic reticulum.

22. Calmodulin as a versatile calcium signal transducer in plants.

23. Protease inhibitors and directed evolution: enhancing plant resistance to nematodes.

24. Stress induces peroxisome biogenesis genes.

25. Functional characterization of the EMCV IRES in plants.

26. Analysis of pectic epitopes recognised by hybridoma and phage display monoclonal antibodies using defined oligosaccharides, polysaccharides, and enzymatic degradation.

27. Antibodies against pex14p block ATP-independent binding of matrix proteins to peroxisomes in vitro.

28. Arabidopsis 22-kilodalton peroxisomal membrane protein. Nucleotide sequence analysis and biochemical characterization.

29. Characterization of intermediates in the process of plant peroxisomal protein import.

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29 results on '"Centre for Plant Sciences [Leeds]"'

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