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1. Nonselective Chemical Inhibition of Sec7 Domain-Containing ARF GTPase Exchange Factors

Author

Steven De Munck, Riet De Rycke, Bram Denoo, Sacco C. de Vries, Jan Hullaert, Wim Annaert, Isha Sharma, Kaija Goodman, Wim Dejonghe, Johan M. Winne, Marisa S. Otegui, François Peurois, Wim Nerinckx, Andrzej Drozdzecki, Annemieke Madder, Jacqueline Cherfils, Marine Bretou, Qing Lu, Sara Martins, Sjef Boeren, Grégory Vert, Kamila Kalinowska, Veronique Storme, Long Nguyen, Dominique Audenaert, Erika Isono, Kiril Mishev, Savvas N. Savvides, Eugenia Russinova, Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, Flanders Institute for Biotechnology, Ghent University Hospital, Laboratory of Biochemistry, Wageningen University and Research [Wageningen] (WUR), Immunité et cancer (U932), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry, Physiology and Microbiology, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Plant Biotechnology and Bioinformatics, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ghent University, Compound Screening Facility, VIB, Signalisation Cellulaire et Ubiquitination chez les plantes (UBINET), Département Biologie Cellulaire (BioCell), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Organic and Biomimetic Chemistry Research Group, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Laboratory of Membrane Trafficking and VIB11, Center for Human Genetics, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Polymer Research Group, State Univ Ghent, Department of Systems Biology, Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Ghent University [Belgium] (UGENT), Laboratoire de dynamique membranaire et maladies neurologiques (UMR 8192), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), VIB Inflammation Research Center, Laboratoire d'enzymologie et biochimie structurales (LEBS), Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Curie [Paris]-Université Paris Descartes - Paris 5 (UPD5), Universiteit Gent [Ghent], Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Université Polytechnique Hauts-de-France (UPHF)-Institut supérieur de l'électronique et du numérique (ISEN), Wageningen University and Research Centre [Wageningen] (WUR), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris Descartes - Paris 5 (UPD5)-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, ADP ribosylation factor, Endosome, [SDV]Life Sciences [q-bio], Arabidopsis, Biochemie, Endosomes, Plant Science, arabidopsis-thaliana, Biology, receptor kinase bri1, Endocytosis, Biochemistry, UBINET, Piperazines, 03 medical and health sciences, symbols.namesake, chemistry.chemical_compound, golgi network/early endosome, BIOCELL, Guanine Nucleotide Exchange Factors, Life Science, Endomembrane system, endomembrane trafficking, Research Articles, brefeldin-a, Brefeldin A, protein complexes, Arabidopsis Proteins, plasma-membrane, plant-cells, Cell Biology, Golgi apparatus, Plants, Genetically Modified, Transport protein, Cell biology, wide analysis, Protein Transport, small molecules, 030104 developmental biology, chemistry, Vacuoles, symbols, Phthalazines, Guanine nucleotide exchange factor, Protein Kinases
Abstract

International audience; Small GTP-binding proteins from the ADP-ribosylation factor (ARF) family are important regulators of vesicle formation and cellular trafficking in all eukaryotes. ARF activation is accomplished by a protein family of guanine nucleotide exchange factors (GEFs) that contain a conserved catalytic Sec7 domain. Here, we identified and characterized Secdin, a small-molecule inhibitor of Arabidopsis thaliana ARF-GEFs. Secdin application caused aberrant retention of plasma membrane (PM) proteins in late endosomal compartments, enhanced vacuolar degradation, impaired protein recycling, and delayed secretion and endocytosis. Combined treatments with Secdin and the known ARF-GEF inhibitor Brefeldin A (BFA) prevented the BFA-induced PM stabilization of the ARF-GEF GNOM, impaired its translocation from the Golgi to the trans-Golgi network/early endosomes, and led to the formation of hybrid endomembrane compartments reminiscent of those in ARF-GEF-deficient mutants. Drug affinity-responsive target stability assays revealed that Secdin, unlike BFA, targeted all examined Arabidopsis ARF-GEFs, but that the interaction was probably not mediated by the Sec7 domain because Secdin did not interfere with the Sec7 domain-mediated ARF activation. These results show that Secdin and BFA affect their protein targets through distinct mechanisms, in turn showing the usefulness of Secdin in studies in which ARF-GEF-dependent endomembrane transport cannot be manipulated with BFA.

Published
2018
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2. Mapping of Plasma Membrane Proteins Interacting With Arabidopsis thaliana Flotillin 2

Author

Petra Junková, Michal Daněk, Daniela Kocourková, Jitka Brouzdová, Kristýna Kroumanová, Enric Zelazny, Martin Janda, Radovan Hynek, Jan Martinec, Olga Valentová, Czech Academy of Sciences [Prague] (CAS), Signalisation Cellulaire et Ubiquitination chez les plantes (UBINET), Département Biologie Cellulaire (BioCell), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Institute of Chemical Technology [Prague] (ICT), and University of Chemistry and Technology Prague (UCT Prague)

Subjects
0301 basic medicine, water transport, intracellular trafficking, ATPase, [SDV]Life Sciences [q-bio], plant–pathogen interaction, Aquaporin, Plant Science, protein–protein interactions, lcsh:Plant culture, UBINET, immunopurification, Protein–protein interaction, 03 medical and health sciences, Arabidopsis, BIOCELL, Arabidopsis thaliana, lcsh:SB1-1110, Original Research, mass spectrometry, Water transport, biology, split-ubiquitin yeast system, Chemistry, biology.organism_classification, Cell biology, 030104 developmental biology, Membrane protein, Arabidopsis flotillin 2, biology.protein, Intracellular
Abstract

Arabidopsis flotillin 2 (At5g25260) belongs to the group of plant flotillins, which are not well characterized. In contrast, metazoan flotillins are well known as plasma membrane proteins associated with membrane microdomains that act as a signaling hub. The similarity of plant and metazoan flotillins, whose functions most likely consist of affecting other proteins via protein-protein interactions, determines the necessity of detecting their interacting partners in plants. Nevertheless, identifying the proteins that form complexes on the plasma membrane is a challenging task due to their low abundance and hydrophobic character. Here we present an approach for mapping Arabidopsis thaliana flotillin 2 plasma membrane interactors, based on the immunoaffinity purification of crosslinked and enriched plasma membrane proteins with mass spectrometry detection. Using this approach, 61 proteins were enriched in the AtFlot-GFP plasma membrane fraction, and 19 of them were proposed to be flotillin 2 interaction partners. Among our proposed partners of Flot2, proteins playing a role in the plant response to various biotic and abiotic stresses were detected. Additionally, the use of the split-ubiquitin yeast system helped us to confirm that plasma-membrane ATPase 1, early-responsive to dehydration stress protein 4, syntaxin-71, harpin-induced protein-like 3, hypersensitive-induced response protein 2 and two aquaporin isoforms interact with flotillin 2 directly. Based on the results of our study and the reported properties of Flot2 interactors, we propose that Flot2 complexes may be involved in plant-pathogen interactions, water transport and intracellular trafficking.

Published
2018
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3. Internalization and vacuolar targeting of the brassinosteroid hormone receptor BRI1 are regulated by ubiquitination

Author

Anne Cayrel, Niko Geldner, Wolfgang H. Fischer, Esther M. N. Dohmann, Sara Martins, Béatrice Satiat-Jeunemaitre, Florence Pojer, Alexander W. Johnson, Joanne Chory, Yvon Jaillais, Grégory Vert, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Dynamique de la Compartimentation cellulaire dans les cellules de plantes supérieures (DYNBSJ), Département Biologie Cellulaire (BioCell), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Signalisation Cellulaire et Ubiquitination chez les plantes (UBINET), 'Infrastructures en Biologie Sante et Agronomie' (IBiSA), French National Research Agency under Investments for the Future programmes 'France-BioImaging infrastructure' [ANR-10-INSB-04-01], Saclay Plant Sciences initiative [ANR-10-LABX-0040-SPS], 'Conseil General de l'Essonne', Saclay Plant Sciences LabEx initiative - French government [ANR-10-LABX-0040-SPS], Agence Nationale de la Recherche [ANR-11-IDEX-0003-02, ANR-13-JSV2-0004-01], EMBO long-term fellowship, National Institutes of Health [5 R01 GM094428], Howard Hughes Medical Institute, Swiss National Science Foundation [31003A_120558], and Marie Curie Action [PCIG-GA-2012-334021]

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Endocytic cycle, Arabidopsis, General Physics and Astronomy, 01 natural sciences, UBINET, chemistry.chemical_compound, Ubiquitin, Gene Expression Regulation, Plant, Brassinosteroid, Phosphorylation, Internalization, Receptor, Polyubiquitin, media_common, 0303 health sciences, Microscopy, Multidisciplinary, biology, Atomic and molecular interactions with photons, Plants, Protein-Serine-Threonine Kinases, Plants, Genetically Modified, Cell biology, Transport protein, Protein Transport, Signal transduction, Signal Transduction, trans-Golgi Network, DYNBSJ, Endosome, media_common.quotation_subject, Genetically Modified, Endosomes, Protein Serine-Threonine Kinases, Article, General Biochemistry, Genetics and Molecular Biology, Fluorescence, 03 medical and health sciences, Arabidopsis/genetics, Arabidopsis/metabolism, Arabidopsis Proteins/genetics, Arabidopsis Proteins/metabolism, Brassinosteroids/metabolism, Cell Membrane/metabolism, Cell Membrane/ultrastructure, Endosomes/metabolism, Endosomes/ultrastructure, Lysine/metabolism, Microscopy, Fluorescence/methods, Polyubiquitin/genetics, Polyubiquitin/metabolism, Protein Kinases/genetics, Protein Kinases/metabolism, Protein-Serine-Threonine Kinases/genetics, Protein-Serine-Threonine Kinases/metabolism, Vacuoles/metabolism, Vacuoles/ultrastructure, trans-Golgi Network/metabolism, trans-Golgi Network/ultrastructure, Brassinosteroids, Author Correction, Protein Processing, 030304 developmental biology, Attosecond science, Arabidopsis Proteins, Lysine, fungi, Cell Membrane, Post-Translational, Ubiquitination, General Chemistry, Plant, chemistry, Gene Expression Regulation, Microscopy, Fluorescence, Mutation, Proteolysis, Vacuoles, biology.protein, High-harmonic generation, Protein Kinases, Protein Processing, Post-Translational, 010606 plant biology & botany
Abstract

Brassinosteroids (BRs) are plant steroid hormones that control many aspects of plant growth and development. BRs are perceived at the cell-surface by the plasma membrane-localized receptor complex composed of the receptor kinase BRI1 and its co-receptor BAK1. Here we show that BRI1 is post-translationally modified by K63 polyubiquitin chains in vivo. Artificially ubiquitinated BRI1 is recognized at the trans-Golgi Network/Early Endosomes (TGN/EE) and rapidly routed for vacuolar degradation. Mass spectrometry analyses identified residue K866 as an in vivo ubiquitination target in BRI1 involved in the negative regulation of BRI1. Model prediction revealed several redundant ubiquitination sites required for the endosomal sorting and vacuolar targeting of BRI1. Using total internal reflection fluorescence microscopy (TIRF), we also uncovered a role for BRI1 ubiquitination in promoting internalization from the cell-surface. Finally, we demonstrate that the control of BRI1 protein dynamics by ubiquitination is a fundamental control mechanism for BR responses in plants. Altogether, our results identify K63-linked polyubiquitin chain formation as a dual targeting signal for BRI1 internalization and sorting along the endocytic pathway, and highlight its role in hormonally controlled plant development.

Published
2014
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