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1. Root membrane ubiquitinome under short-term osmotic stress

Author

Nathalie Berger, Vincent Demolombe, Sonia Hem, Valérie Rofidal, Laura Steinmann, Gabriel Krouk, Amandine Crabos, Philippe Nacry, Lionel Verdoucq, Véronique Santoni, Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Proteomics, 0106 biological sciences, Proteome, [SDV]Life Sciences [q-bio], Arabidopsis, aquaporin, mass spectrometry, osmotic stress, ubiquitination, Plant Roots, 01 natural sciences, Catalysis, Inorganic Chemistry, 03 medical and health sciences, Osmotic Pressure, ddc:570, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, 030304 developmental biology, 0303 health sciences, Ubiquitin, Lysine, Organic Chemistry, Membrane Proteins, General Medicine, Ubiquitinated Proteins, Computer Science Applications, Protein Processing, Post-Translational, 010606 plant biology & botany
Abstract

Osmotic stress can be detrimental to plants, whose survival relies heavily on proteomic plasticity. Protein ubiquitination is a central post-translational modification in osmotic mediated stress. Plants use the ubiquitin (Ub) proteasome system to modulate protein content, and a role for Ub in mediating endocytosis and trafficking plant plasma membrane proteins has recently emerged. In this study, we used the K-ε-GG antibody enrichment method integrated with high-resolution mass spectrometry to compile a list of 719 ubiquitinated lysine (K-Ub) residues from 450 Arabidopsis root membrane proteins (58% of which are transmembrane proteins), thereby adding to the database of ubiquitinated substrates in plants. Although no Ub motifs could be identified, the presence of acidic residues close to K-Ub was revealed. Our ubiquitinome analysis pointed to a broad role of ubiquitination in the internalization and sorting of cargo proteins. Moreover, the simultaneous proteome and ubiquitinome quantification showed that ubiquitination is mostly not involved in membrane protein degradation in response to short osmotic treatment, but putatively in protein internalization as described for the aquaporin PIP2;1. Our in silico analysis of ubiquitinated proteins shows that two E2 Ub ligases, UBC32 and UBC34, putatively target membrane proteins under osmotic stress. Finally, we revealed a positive role for UBC32 and UBC34 in primary root growth under osmotic stress.

Published
2021

2. A Global Proteomic Approach Sheds New Light on Potential Iron-Sulfur Client Proteins of the Chloroplastic Maturation Factor NFU3

Author

Vincent Demolombe, Florence Vignols, Véronique Santoni, Christian Dubos, Frédéric Gaymard, Nicolas Rouhier, Nathalie Berger, Brigitte Touraine, Maël Taupin-Broggini, Valérie Rofidal, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Arbres-Microorganismes (IAM), and Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Iron-Sulfur Proteins, 0106 biological sciences, 0301 basic medicine, quantitative proteomic, Chloroplasts, Proteome, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Iron–sulfur cluster, chemistry.chemical_element, NFU2, NFU3, NFU1, 01 natural sciences, Article, Catalysis, Inorganic Chemistry, lcsh:Chemistry, 03 medical and health sciences, chemistry.chemical_compound, iron-sulfur cluster, chloroplast, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Plastids, Physical and Theoretical Chemistry, Molecular Biology, lcsh:QH301-705.5, Spectroscopy, biology, Arabidopsis Proteins, Chemistry, Organic Chemistry, General Medicine, biology.organism_classification, maturation factor, Sulfur, Protein subcellular localization prediction, Computer Science Applications, Cell biology, Chloroplast, Cytosol, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, 010606 plant biology & botany
Abstract

International audience; Iron-sulfur (Fe-S) proteins play critical functions in plants. Most Fe-S proteins are synthetized in the cytosol as apo-proteins and the subsequent Fe-S cluster incorporation relies on specific protein assembly machineries. They are notably formed by a scaffold complex, which serves for the de novo Fe-S cluster synthesis, and by transfer proteins that insure cluster delivery to apo-targets. However, scarce information is available about the maturation pathways of most plastidial Fe-S proteins and their specificities towards transfer proteins of the associated SUF machinery. To gain more insights into these steps, the expression and protein localization of the NFU1, NFU2, and NFU3 transfer proteins were analyzed in various Arabidopsis thaliana organs and tissues showing quite similar expression patterns. In addition, quantitative proteomic analysis of an nfu3 loss-of-function mutant allowed to propose novel potential client proteins for NFU3 and to show that the protein accumulation profiles and thus metabolic adjustments differ substantially from those established in the nfu2 mutant. By clarifying the respective roles of the three plastidial NFU paralogs, these data allow better delineating the maturation process of plastidial Fe-S proteins.

Published
2020
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3. Identification of client iron-sulfur proteins of the chloroplastic NFU2 transfer protein in Arabidopsis thaliana

Author

Brigitte Touraine, Nicolas Rouhier, Nathalie Berger, Florence Vignols, Valérie Rofidal, Véronique Santoni, Krzysztof Zienkiewicz, Mélanie Roland, Christian Dubos, Jonathan Przybyla-Toscano, Ivo Feussner, Jérémy Couturier, Frédéric Gaymard, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Albrecht von Haller Institute for Plant Sciences Department of Plant Biochemistry, Georg-August-University [Göttingen], ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), and ANR-15-IDEX-0004,LUE,Isite LUE(2015)

Subjects
Iron-Sulfur Proteins, Proteomics, 0106 biological sciences, Scaffold protein, quantitative proteomics, Chloroplasts, Physiology, [SDV]Life Sciences [q-bio], Quantitative proteomics, protein-protein interactions, Arabidopsis, Iron–sulfur cluster, NFU2, Plant Science, 01 natural sciences, Protein–protein interaction, 03 medical and health sciences, chemistry.chemical_compound, Bimolecular fluorescence complementation, iron-sulfur cluster, chloroplast, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 0303 health sciences, biology, Arabidopsis Proteins, biology.organism_classification, Chloroplast, chemistry, Biochemistry, 010606 plant biology & botany
Abstract

Iron–sulfur (Fe-S) proteins have critical functions in plastids, notably participating in photosynthetic electron transfer, sulfur and nitrogen assimilation, chlorophyll metabolism, and vitamin or amino acid biosynthesis. Their maturation relies on the so-called SUF (sulfur mobilization) assembly machinery. Fe-S clusters are synthesized de novo on a scaffold protein complex and then delivered to client proteins via several transfer proteins. However, the maturation pathways of most client proteins and their specificities for transfer proteins are mostly unknown. In order to decipher the proteins interacting with the Fe-S cluster transfer protein NFU2, one of the three plastidial representatives found in Arabidopsis thaliana, we performed a quantitative proteomic analysis of shoots, roots, and seedlings of nfu2 plants, combined with NFU2 co-immunoprecipitation and binary yeast two-hybrid experiments. We identified 14 new targets, among which nine were validated in planta using a binary bimolecular fluorescence complementation assay. These analyses also revealed a possible role for NFU2 in the plant response to desiccation. Altogether, this study better delineates the maturation pathways of many chloroplast Fe-S proteins, considerably extending the number of NFU2 clients. It also helps to clarify the respective roles of the three NFU paralogs NFU1, NFU2, and NFU3.

Published
2020
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4. Targeted Proteomics Allows Quantification of Ethylene Receptors and Reveals SlETR3 Accumulation in Never-Ripe Tomatoes

Author

G. Eric Schaller, Nathalie Berger, Yi Chen, Christian Chervin, Samina N. Shakeel, Beenish J. Azhar, Vincent Demolombe, Sonia Hem, Véronique Santoni, Brad M. Binder, Julie Gil, Joanna Nosarzewska, Valérie Rofidal, Mondher Bouzayen, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Montpellier SupAgro (FRANCE), Dartmouth College (USA), Quaid-i-Azam University (Pakistan), Université de Montpellier (FRANCE), University of Tennessee - UT (USA), Génomique et Biotechnologie des Fruits (GBF), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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), Dept Biochem, University of Nairobi (UoN), Dept Biol Sci, Univ London Imperial Coll Sci Technol & Med, Department of Biochemistry, Cellular, and Molecular Biology, The University of Tennessee [Knoxville], CSC, INRA, National Science Foundation (IOS-1456487), (MCB-1517032), International Research Support Initiative Program of Higher Education Commission of Pakistan, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), 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), UMR 0990 GBF Génomique et Biotechnologie des Fruits, Institut National de la Recherche Agronomique (INRA), Dept Biochem Cellular & Mol Biol, and University of Tennessee

Subjects
0106 biological sciences, 0301 basic medicine, Proteomics, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Ethylene, receptor, Quantitative proteomics, hormone, Biotechnologies, Plant Science, Biology, lcsh:Plant culture, tomato, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, ethylene, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Food and Nutrition, lcsh:SB1-1110, Receptor, Original Research, 2. Zero hunger, Messenger RNA, Vegetal Biology, Wild type, food and beverages, Ripening, 030104 developmental biology, chemistry, Membrane protein, Biochemistry, signaling, Alimentation et Nutrition, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Biologie végétale, 010606 plant biology & botany
Abstract

Ethylene regulates fruit ripening and several plant functions (germination, plant growth, plant-microbe interactions). Protein quantification of ethylene receptors (ETRs) is essential to study their functions, but is impaired by low resolution tools such as antibodies that are mostly nonspecific, or the lack of sensitivity of shotgun proteomic approaches. We developed a targeted proteomic method, to quantify low-abundance proteins such as ETRs, and coupled this to mRNAs analyses, in two tomato lines: Wild Type (WT) and Never-Ripe (NR) which is insensitive to ethylene because of a gain-of-function mutation in ETR3. We obtained mRNA and protein abundance profiles for each ETR over the fruit development period. Despite a limiting number of replicates, we propose Pearson correlations between mRNA and protein profiles as interesting indicators to discriminate the two genotypes: such correlations are mostly positive in the WT and are affected by the NR mutation. The influence of putative post-transcriptional and post-translational changes are discussed. In NR fruits, the observed accumulation of the mutated ETR3 protein between ripening stages (Mature Green and Breaker + 8 days) may be a cause of NR tomatoes to stay orange. The label-free quantitative proteomics analysis of membrane proteins, concomitant to Parallel Reaction Monitoring analysis, may be a resource to study changes over tomato fruit development. These results could lead to studies about ETR subfunctions and interconnections over fruit development. Variations of RNA-protein correlations may open new fields of research in ETR regulation. Finally, similar approaches may be developed to study ETRs in whole plant development and plant-microorganism interactions.

Published
2019
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5. MYB118 Represses Endosperm Maturation in Seeds of Arabidopsis

Author

Chloé Marchive, Véronique Brunaud, Guillaume Barthole, Ludivine Soubigou-Taconnat, Sébastien Baud, Bertrand Dubreucq, Loïc Lepiniec, Nathalie Berger, Alexandra To, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, Plant Science, 01 natural sciences, Endosperm, DOMAIN, Gene Expression Regulation, Plant, Arabidopsis thaliana, Research Articles, GENE-EXPRESSION, chemistry.chemical_classification, 0303 health sciences, biology, TRANSCRIPTIONAL REGULATION, digestive, oral, and skin physiology, Gene Expression Regulation, Developmental, food and beverages, Embryo, ABSCISIC-ACID, OIL, Cell biology, embryonic structures, Protein Binding, Transcriptional Activation, animal structures, DNA-BINDING, Molecular Sequence Data, Morphogenesis, Genes, Plant, 03 medical and health sciences, Botany, Storage protein, PLANTS, DEVELOPMENTAL REGULATION, 030304 developmental biology, EMBRYO DEVELOPMENT, Base Sequence, THALIANA, Arabidopsis Proteins, fungi, Embryogenesis, Cell Biology, biology.organism_classification, chemistry, Mutation, Transcription Factors, 010606 plant biology & botany
Abstract

In the exalbuminous species Arabidopsis thaliana, seed maturation is accompanied by the deposition of oil and storage proteins and the reduction of the endosperm to one cell layer. Here, we consider reserve partitioning between embryo and endosperm compartments. The pattern of deposition, final amount, and composition of these reserves differ between the two compartments, with the embryo representing the principal storage tissue in mature seeds. Complex regulatory mechanisms are known to prevent activation of maturation-related programs during embryo morphogenesis and, later, during vegetative growth. Here, we describe a regulator that represses the expression of maturation-related genes during maturation within the endosperm. MYB118 is transcriptionally induced in the maturing endosperm, and seeds of myb118 mutants exhibit an endosperm-specific derepression of maturation-related genes associated with a partial relocation of storage compounds from the embryo to the endosperm. Moreover, MYB118 activates endosperm-induced genes through the recognition of TAACGG elements. These results demonstrate that the differential partitioning of reserves between the embryo and endosperm in exalbuminous Arabidopsis seeds does not only result from developmental programs that establish the embryo as the preponderant tissue within seeds. This differential partitioning is also regulated by MYB118, which regulates the biosynthesis of reserves at the spatial level during maturation.

Published
2014
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6. Deciphering the molecular mechanisms underpinning the transcriptional control of gene expression by L-AFL proteins in Arabidopsis seed

Author

Johanne Thévenin, Roberto Solano, Marta Godoy, Loïc Lepiniec, Bertrand Dubreucq, Emmanuel Thévenon, François Parcy, Alexandra To, Delphine Effroy-Cuzzi, Sébastien Baud, Sandrine Blanchet, Manon Payre, Zsolt Kelemen, Nathalie Berger, José Manuel Franco-Zorrilla, Céline Boulard, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-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 Plant Molecular Genetics, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), ERA-CAPS ABCEEDS, ANR-07-BLAN-0211,BLANC,Cracking the code of transcriptional regulation: the key to the past and future evolution of plants(2007), ANR-10-BLAN-1238,CERES,Contrôle de l'expression des gènes du REseau de régulation AFL et développement de la graine(2010), ANR-11-IDEX-02/10-LABX-0040,SPS,Saclay Plant Sciences(2011), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), ANR-07-BLAN-0211,Plant-TFcode,Cracking the code of transcriptional regulation: the key to the past and future evolution of plants(2007), ANR-10-BLAN-1238,CERES,Contrôle de l'expression des gènes du REseau de régulation 'AFL' et développement de la graine(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Centro Nacional de Biotecnología [Madrid] (CNB-CSIC)

Subjects
0106 biological sciences, 0301 basic medicine, LEAFY COTYLEDON2, Arabidopsis thaliana, Physiology, ABI3, Oleosin, Plant Science, Physcomitrella patens, 01 natural sciences, 03 medical and health sciences, Arabidopsis, Seed maturation, Genetics, Transcriptional regulation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, B3 domain, Gene, Transcription factor, Moss, Regulation of gene expression, Transcriptional Regulation, DNA binding sites, biology, LEC2, FUSCA3, AFLs, Protein, Plant, FUS3, biology.organism_classification, Cell biology, ABSCISIC ACID INSENSITIVE3, DNA binding site, 030104 developmental biology, Gene expression, OLEI promoter, 010606 plant biology & botany
Abstract

International audience; In Arabidopsis (Arabidopsis thaliana), transcriptional control of seed maturation involves three related regulators with a B3domain, namely LEAFY COTYLEDON2 (LEC2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (ABI3/FUS3/LEC2[AFLs]). Although genetic analyses have demonstrated partially overlapping functions of these regulators, the underlyingmolecular mechanisms remained elusive. The results presented here confirmed that the three proteins bind RY DNA elements(with a 59-CATG-39 core sequence) but with different specificities for flanking nucleotides. In planta as in the moss Physcomitrellapatens protoplasts, the presence of RY-like (RYL) elements is necessary but not sufficient for the regulation of the OLEOSIN1 (OLE1)promoter by the B3AFLs. G box-like domains, located in the vicinity of the RYL elements, also are required for proper activation ofthe promoter, suggesting that several proteins are involved. Consistentwith this idea, LEC2 andABI3 showed synergistic effects onthe activation of the OLE1 promoter. What is more, LEC1 (a homolog of the NF-YB subunit of the CCAAT-binding complex)further enhanced the activation of this target promoter in the presence of LEC2 and ABI3. Finally, recombinant LEC1 and LEC2proteins produced in Arabidopsis protoplasts could form a ternary complex with NF-YC2 in vitro, providing a molecular explanationfor their functional interactions. Taken together, these results allow us to propose a molecularmodel for the transcriptional regulationof seed genes by the L-AFL proteins, based on the formation of regulatory multiprotein complexes between NF-YBs, which carry aspecific aspartate-55 residue, and B3 transcription factors.

Published
2016
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7. Arabidopsis glucosidase I mutants reveal a critical role of N-glycan trimming in seed development

Author

Véronique Gomord, Michel Caboche, Corinne Audran, Bertrand Dubreucq, Murielle Boisson, Loïc Faye, Patrice Lerouge, Nathalie Berger, Fabienne Granier, Loïc Lepiniec, Biologie des Semences (LBS), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Laboratoire de biologie cellulaire et moléculaire, and Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, N-GLYCAN, Glycosylation, Mutant, Arabidopsis, 01 natural sciences, chemistry.chemical_compound, GCS1-1, N-linked glycosylation, Gene Expression Regulation, Plant, Cloning, Molecular, DIFFERENTIATION CELLULAIRE, GCS1-2, chemistry.chemical_classification, 0303 health sciences, Genes, Essential, biology, Histocytochemistry, General Neuroscience, Cell Differentiation, Phenotype, Biochemistry, Seeds, Intracellular, DNA, Bacterial, Glycan, Immunoblotting, Molecular Sequence Data, GLYCOSILATION, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, ALPHA-GLUCOSIDASE I, Polysaccharides, Storage protein, Amino Acid Sequence, RNA, Messenger, Molecular Biology, Alleles, 030304 developmental biology, Sequence Homology, Amino Acid, General Immunology and Microbiology, Gene Expression Profiling, Genetic Complementation Test, alpha-Glucosidases, biology.organism_classification, carbohydrates (lipids), Microscopy, Electron, chemistry, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Mutation, biology.protein, Glycoprotein, 010606 plant biology & botany
Abstract

Glycoproteins with asparagine-linked (N-linked) glycans occur in all eukaryotic cells. The function of their glycan moieties is one of the central problems in contemporary cell biology. N-glycosylation may modify physicochemical and biological protein properties such as conformation, degradation, intracellular sorting or secretion. We have isolated and characterized two allelic Arabidopsis mutants, gcs1-1 and gcs1-2, which produce abnormal shrunken seeds, blocked at the heart stage of development. The mutant seeds accumulate a low level of storage proteins, have no typical protein bodies, display abnormal cell enlargement and show occasional cell wall disruptions. The mutated gene has been cloned by T-DNA tagging. It codes for a protein homologous to animal and yeast alpha-glucosidase I, an enzyme that controls the first committed step for N-glycan trimming. Biochemical analyses have confirmed that trimming of the alpha1,2- linked glucosyl residue constitutive of the N-glycan precursor is blocked in this mutant. These results demonstrate the importance of N-glycan trimming for the accumulation of seed storage proteins, the formation of protein bodies, cell differentiation and embryo development.

Published
2001
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8. Regulation of flavonoid biosynthesis involves an unexpected complex transcriptional regulation of TT8 expression, in Arabidopsis

Author

Nathalie Berger, Zsolt Kelemen, Antoine Baudry, Wenjia Xu, Christian Dubos, Fabien Salsac, Jean-Marc Routaboul, Erwana Harscoët, Loïc Lepiniec, Przemyslaw Bidzinski, José Le Gourrierec, Damaris Grain, Aurélie Scagnelli, Adeline Berger, Vincent Jauvion, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), 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 EU [Food CT-2004-513960]

Subjects
0106 biological sciences, MESH: Mutation, Molecular model, Transcription, Genetic, Arabidopsis thaliana, Physiology, Regulator, Arabidopsis, Plant Science, MESH: Arabidopsis Proteins, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Biosynthesis, Gene Expression Regulation, Plant, transcription factors, MESH: Basic Helix-Loop-Helix Transcription Factors, MESH: Promoter Regions, Genetic, Transcriptional regulation, Basic Helix-Loop-Helix Transcription Factors, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Arabidopsis, MESH: Gene Expression Regulation, Plant, Promoter Regions, Genetic, Transcription factor, 030304 developmental biology, Genetics, Flavonoids, 0303 health sciences, biology, Arabidopsis Proteins, MESH: Transcription, Genetic, transparent testa, food and beverages, MESH: Transcription Factors, TT8, MESH: Multiprotein Complexes, biology.organism_classification, anthocyanins, Cell biology, Flavonoid biosynthesis, chemistry, Multiprotein Complexes, Mutation, proanthocyanidins, MESH: Flavonoids, 010606 plant biology & botany
Abstract

International audience; TT8/bHLH042 is a key regulator of anthocyanins and proanthocyanidins (PAs) biosynthesis in Arabidopsis thaliana. TT8 transcriptional activity has been studied extensively, and relies on its ability to form, with several R2R3-MYB and TTG1 (WD-Repeat protein), different MYB-bHLH-WDR (MBW) protein complexes. By contrast, little is known on how TT8 expression is itself regulated. Transcriptional regulation of TT8 expression was studied using molecular, genetic and biochemical approaches. Functional dissection of the TT8 promoter revealed its modular structure. Two modules were found to specifically drive TT8 promoter activity in PA- and anthocyanin-accumulating cells, by differentially integrating the signals issued from different regulators, in a spatio-temporal manner. Interestingly, this regulation involves at least six different MBW complexes, and an unpredicted positive feedback regulatory loop between TT8 and TTG2. Moreover, the results suggest that some putative new regulators remain to be discovered. Finally, specific cis-regulatory elements through which TT8 expression is regulated were identified and characterized. Together, these results provide a molecular model consistent with the specific and highly regulated expression of TT8. They shed new light into the transcriptional regulation of flavonoid biosynthesis and provide new clues and tools for further investigation in Arabidopsis and other plant species.

Published
2013
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9. Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE,a cis-element that regulates Trimethylation of Histone H3 at Lysine-27

Author

François Roudier, Christian Dubos, Loïc Lepiniec, Bertrand Dubreucq, Nathalie Berger, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, and Lepiniec, Loïc

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Molecular Sequence Data, Arabidopsis, Plant Science, macromolecular substances, cotyledon, Regulatory Sequences, Ribonucleic Acid, 01 natural sciences, Histones, 03 medical and health sciences, Histone H3, régulation, Gene Expression Regulation, Plant, Transcriptional regulation, Promoter Regions, Genetic, Leafy, Research Articles, 030304 developmental biology, Regulation of gene expression, Genetics, 0303 health sciences, Base Sequence, biology, Arabidopsis Proteins, Lysine, food and beverages, Promoter, Cell Biology, biology.organism_classification, histone h3, Regulatory sequence, Seeds, biology.protein, PRC2, Transcription Factors, 010606 plant biology & botany
Abstract

LEAFY COTYLEDON2 (LEC2) is a master regulator of seed development in Arabidopsis thaliana. In vegetative organs, LEC2 expression is negatively regulated by Polycomb Repressive Complex2 (PRC2) that catalyzes histone H3 Lys 27 trimethylation (H3K27me3) and plays a crucial role in developmental phase transitions. To characterize the cis-regulatory elements involved in the transcriptional regulation of LEC2, molecular dissections and functional analyses of the promoter region were performed in vitro, both in yeast and in planta. Two cis-activating elements and a cis-repressing element (RLE) that is required for H3K27me3 marking were characterized. Remarkably, insertion of the RLE cis-element into pF3H, an unrelated promoter, is sufficient for repressing its transcriptional activity in different tissues. Besides improving our understanding of LEC2 regulation, this study provides important new insights into the mechanisms underlying H3K27me3 deposition and PRC2 recruitment at a specific locus in plants.

Published
2011
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