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1. A simple and efficient process for the synthesis of 2D carbon nitrides and related materials

Author: Huc, Vincent, Silva, Cora, Vallet, Maxime, Saint-Martin, Romuald, Leroy, Jocelyne, Semion, Clément, Dragoe, Diana, Brisset, François, Blin, Thomas, Guillot, Regis, Gillet, Cynthia, Université Paris-Saclay, ONERA, CNRS, Laboratoire d'étude des microstructures (LEM), ONERA-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mécanique Paris-Saclay (LMPS), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-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), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), CentraleSupélec, Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN UMR 3685), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: [CHIM.MATE]Chemical Sciences/Material chemistry
Abstract: This manuscript describes a new process for the synthesis of very high quality 2D Covalent Organic Frameworks (COFs), such a C2N and CN carbon nitrides. The structure/quality of these materials is demonstrated by extensive cross-characterisations at different scales. The availability of such very large, high quality layers of these materials opens interesting perspectives, for example in photochemistry and electronics (intrinsic transport properties, high gap substrate for graphene, etc...). We thus consider that this work could be of interest to a broad readership, considering that this topic is among the current hottest ones.
Published: 2023

2. Limiting etioplast gene‐expression induces apical hook twisting during skoto‐morphogenesis of Arabidopsis seedlings

Author: Salek Ahmed Sajib, Björn Grübler, Cylia Oukacine, Etienne Delannoy, Florence Courtois, Caroline Mauve, Claire Lurin, Bertrand Gakière, Thomas Pfannschmidt, Livia Merendino, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Université Paris Cité (UPCité), Light Photosynthesis & Metabolism (Photosynthesis), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Grenoble Alpes (UGA), Leibniz Universität Hannover=Leibniz University Hannover, PEPS CNRS, PF323-5-2 Deutsche Forschungsgemeinschaft, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010)
Subjects: Arabidopsis thaliana, spectinomycin, ROS, skoto-morphogenesis, Cell Biology, Plant Science, rifampicin, gene-expression, mitochondria, AOX1A, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, plastids, apical hook bending
Abstract: International audience; When covered by a layer of soil, seedling development follows a dark-specific program (skoto-morphogenesis) consisting of small, non-green cotyledons, a long hypocotyl and an apical hook to protect meristematic cells. We recently highlighted the role played by mitochondria in the high energy-consuming reprogramming of Arabidopsis skoto-morphogenesis. Here, the role played by plastids, another energy supplying organelle, in skoto-morphogenesis is investigated. This study was conducted in dark conditions to exclude light signals so as to better focus on those produced by plastids. It was found that limitation of plastid gene-expression (PGE) induced an exaggerated apical hook bending. Inhibition of PGE was obtained at the level of transcription and translation using the antibiotics rifampicin and spectinomycin, respectively, as well as plastid RPOTp RNA polymerase mutants. Rifampicin-treated seedlings also showed expression induction of marker nuclear genes for mitochondrial stress, perturbation of the mitochondrial metabolism, increase of ROS levels and an augmented capacity of oxygen consumption by mitochondrial alternative oxidases (AOX). AOX enzymes act to prevent over-reduction of the mitochondrial electron transport chain. Previously, we reported that AOX1A, the main AOX isoform, was a key component in the developmental response to mitochondrial respiration deficiency. In this work, we suggest the involvement of AOX1A in the response to PGE dysfunction and propose the importance of signalling between plastids and mitochondria. Finally, it was found that seedling architecture reprogramming in response to rifampicin was independent of canonical organelle retrograde pathways and the ethylene signaling pathway.
Published: 2023
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3. The transcriptional co-regulators NBCL1 and NBCL2 redundantly coordinate aerial organ development and root nodule identity in legumes

Author: Shengbin Liu, Kévin Magne, Jing Zhou, Juliette Laude, Marion Dalmais, Christine Le Signor, Abdelhafid Bendahmane, Richard Thompson, Jean-Malo Couzigou, Pascal Ratet, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, 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), This work was supported by the Centre National de la RechercheScientifique (CNRS) and by a grant from the French National ResearchAgency (ANR-14-CE19-0003-01) to PR. This work has benefittedfrom the support of the French Laboratory of Excellence (Labex) SaclayPlant Sciences (ANR-10-LABX-0040-SPS, LabEx SPS and ANR-17-EUR-0007, EUR SPS-GSR) which is managed by the French NationalResearch Agency under the program ‘Investissements d’avenir’ (ANR-11-IDEX-0003-02). J-MC and JZ were supported by the FrenchLaboratory of Excellence (Labex) project ‘TULIP’ (ANR-10-LABX-41, ANR-11-IDEX-0002-02), ANR-14-CE19-0003,NOOT,Les gènes NOOT gardiens de l'dentité des nodosités symbiotiques et de l'abscission(2014), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011)
Subjects: NODULE-ROOT, Physiology, [SDV]Life Sciences [q-bio], Plant Science, organ identity, symbiosis, stipule, Medicago truncatula, inflorescence, COCHLEATA, development, boundaries, Pisum sativum, NOOT-BOP-COCH-LIKE
Abstract: International audience; Medicago truncatula NODULE ROOT1 (MtNOOT1) and Pisum sativum COCHLEATA1 (PsCOCH1) are orthologous genes belonging to the NOOT-BOP-COCH-LIKE (NBCL) gene family which encodes key transcriptional co-regulators of plant development. In Mtnoot1 and Pscoch1 mutants, the development of stipule, flower and symbiotic nodules is altered. MtNOOT2 and PsCOCH2 represent the single paralogs of MtNOOT1 and PsCOCH1, respectively. In M. truncatula, MtNOOT1 and MtNOOT2 are both required for the establishment and maintenance of the symbiotic nodule identity. In contrast to the NBCL1 genes, the role of NBCL2 genes in legume above-ground development is not known. To better understand the roles of NBCL genes in legumes, we used M. truncatula and P. sativum nbcl mutants from the literature, isolated a knockout mutant for the PsCOCH2 locus and generated Pscoch1coch2 double mutants in P. sativum. These new mutant lines enabled to compare the roles of MtNOOT2 and PsCOCH2 in both M. truncatula and P. sativum legume development. Our work shows that the single Mtnoot2 and Pscoch2 mutants develop wild-type stipules, flowers and symbiotic nodules. However, the number of flowers was increased and the pods and seeds were smaller in comparison to wild type. Furthermore, in comparison to the corresponding nbcl1 single mutants, both the M. truncatula and P. sativum nbcl double mutants show a drastic alteration in stipule, inflorescence, flower and nodule development. Remarkably, in both M. truncatula and P. sativum nbcl double mutants, stipules are transformed into a range of aberrant leaf-like structures.
Published: 2022
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4. Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading

Author: Louis-Valentin Méteignier, Cécile Lecampion, Florent Velay, Cécile Vriet, Laura Dimnet, Martin Rougée, Christian Breuer, Ludivine Soubigou-Taconnat, Keiko Sugimoto, Fredy Barneche, Christophe Laloi, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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), Luminy Génétique et Biophysique des Plantes (LGBP), 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)), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), 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-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Velux Stiftung (Switzerland)., L.D. was supported by the Commissariat à l’énergie atomique et aux énergies alternatives and Région Provence-Alpes-Côte d’Azur. F.V. is a recipient of a PhD fellowship from the French Ministry of Higher Education, Research and Innovation., Mass spectrometry analysis was performed at the IMM platform supported by a grant from the Groupement d’Intérêt Scientifique (GIS) Infrastrutures en Biologie Sante et Agronomie (IBiSA)., ANR-14-CE02-0010,SLOSAM,Signalisation du stress photooxydant dans les mécanismes d'acclimatation des plantes aux changements climatiques(2014), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-18-CE13-0004,ChromaLight,Functional links between nuclear architecture and epigenome reprogramming during plant adaptive responses to light(2018), ANR-17-CE12-0026,RiboStress,Interconnections génétiques, épigénétiques et protéiques au cours de la réorganisation fonctionnelle du nucléole et des réponses aux stress(2017), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-JCJC-1205,CHROS,CHromatine et ROS : Rôle du facteur de remodelage de la chromatine topoisomérase VI dans la réponse transcriptionnelle des plantes à l'oxygène singulet et autres formes actives de l'oxygène lors de conditions de stress abiotique.(2010), BARNECHE, Fredy, Appel à projets générique - Signalisation du stress photooxydant dans les mécanismes d'acclimatation des plantes aux changements climatiques - - SLOSAM2014 - ANR-14-CE02-0010 - Appel à projets générique - VALID, Memory in living systems: an integrated approach - - MEMOLIFE2010 - ANR-10-LABX-0054 - LABX - VALID, APPEL À PROJETS GÉNÉRIQUE 2018 - Functional links between nuclear architecture and epigenome reprogramming during plant adaptive responses to light - - ChromaLight2018 - ANR-18-CE13-0004 - AAPG2018 - VALID, Interconnections génétiques, épigénétiques et protéiques au cours de la réorganisation fonctionnelle du nucléole et des réponses aux stress - - RiboStress2017 - ANR-17-CE12-0026 - AAPG2017 - VALID, Saclay Plant Sciences - - SPS2010 - ANR-10-LABX-0040 - LABX - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Jeunes Chercheuses et Jeunes Chercheurs - CHromatine et ROS : Rôle du facteur de remodelage de la chromatine topoisomérase VI dans la réponse transcriptionnelle des plantes à l'oxygène singulet et autres formes actives de l'oxygène lors de conditions de stress abiotique. - - CHROS2010 - ANR-10-JCJC-1205 - JCJC - VALID, and Aix Marseille Université (AMU)
Subjects: Topoisomerase, Multidisciplinary, Arabidopsis Proteins, [SDV]Life Sciences [q-bio], Arabidopsis, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Methionine Adenosyltransferase, Chromatin, Heterochromatin spreading, Euchromatin, Histones, [SDV] Life Sciences [q-bio], Topoisomerase VI, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Epigenome, DNA Topoisomerases, Type II, Heterochromatin, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, Euchromatin islands, DNA Transposable Elements, Insulator
Abstract: The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically down-regulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some transposable element loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine synthase methionine adenosyl transferase 3 (MAT3), which is required for H3K9me2. A Topoisomerase VI defect affects MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a possible mechanistic explanation to the essential role of Topoisomerase VI in the delimitation of chromatin domains.
Published: 2022
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5. Silencing the conserved small nuclear ribonucleoprotein SmD1 target gene alters susceptibility to root-knot nematodes in plants

Author: Joffrey Mejias, Yongpan Chen, Jérémie Bazin, Nhat-My Truong, Karine Mulet, Yara Noureddine, Stéphanie Jaubert-Possamai, Sarah Ranty-Roby, Salomé Soulé, Pierre Abad, Martin D Crespi, Bruno Favery, Michaël Quentin, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), China Agricultural University (CAU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRAESyngenta Targetome project, by the French-Japanese bilateralcollaboration program PHC SAKURA 2016 #35891VD and 2019 #43006VJ, and by the French-Chinese bilateral collaboration program PHC XU GUANGQI 2020 #45478PF. J.M. held a doctoral fellowship from the French Ministe`re de l’Enseignement Superieur, de la Recherche et de l’Innovation (MENRT grant). N.M.T. was supported by a USTH fellowship, as part of the 911-USTH program of the Ministry of Education and Training of The Socialist Republic of Vietnam.Y.C. obtained scholarships from the China Scholarship, ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), ANR-21-CE20-0002,MASH,Modulation de l'épissage alternatif des ARNm de l'hôte par les nématodes à galles(2021), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: Crops, Agricultural, Physiology, [SDV]Life Sciences [q-bio], fungi, Arabidopsis, food and beverages, SmD1, Plant Science, Ribonucleoproteins, Small Nuclear, Plant Roots, Host-Parasite Interactions, Plant Breeding, Solanum lycopersicum, Genetics, Animals, a susceptibility gene to nematodes, Tylenchoidea, Research Articles, Plant Diseases
Abstract: Root-knot nematodes (RKNs) are among the most damaging pests of agricultural crops. Meloidogyne is an extremely polyphagous genus of nematodes that can infect thousands of plant species. A few genes for resistance (R-genes) to RKN suitable for use in crop breeding have been identified, but virulent strains and species of RKN have emerged that render these R-genes ineffective. Secretion of RKN effectors targeting plant functions mediates the reprogramming of root cells into specialized feeding cells, the giant cells, essential for RKN development and reproduction. Conserved targets among plant species define the more relevant strategies for controlling nematode infection. The EFFECTOR18 (EFF18) protein from M. incognita interacts with the spliceosomal small nuclear ribonucleoprotein D1 (SmD1) in Arabidopsis (Arabidopsis thaliana), disrupting its function in alternative splicing regulation and modulating the giant cell transcriptome. We show here that EFF18 is a conserved RKN-specific effector that targets this conserved spliceosomal SmD1 protein in Solanaceae. This interaction modulates alternative splicing events produced by tomato (Solanum lycopersicum) in response to M. incognita infection. The alteration of SmD1 expression by virus-induced gene silencing in Solanaceae affects giant cell formation and nematode development. Thus, our work defines a promising conserved SmD1 target gene to develop broad resistance for the control of Meloidogyne spp. in plants.
Published: 2022
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6. MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development

Author: Marie-Françoise Jardinaud, Justine Fromentin, Marie-Christine Auriac, Sandra Moreau, Yann Pecrix, Ludivine Taconnat, Ludovic Cottret, Grégoire Aubert, Sandrine Balzergue, Judith Burstin, Sébastien Carrere, Pascal Gamas, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale du GEVES, Institut National de la Recherche Agronomique (INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), INRAE (CJS fellowship for J.F., SPE grant 'EFFOR'), ANR-09-GENM-0026,GENOPEA,Génomique comparative du cycle de l'azote entre M. truncatula et le pois : étude des potentialités de transfert des connaissances entre espèces modèles et cultivées(2009), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Nitrogen, CNRS, Physiology, food and beverages, Plant Science, Ethylenes, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Gene Expression Regulation, Plant, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicago truncatula, Genetics, Root Nodules, Plant, Symbiosis, LIPME, Research Articles, Université de Toulouse, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Plant Proteins, Transcription Factors, INRAE
Abstract: Rhizobium–legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed with the MtEFD promoter complemented Mtefd-1 hypernodulation but not the nodule differentiation phenotype. Unexpectedly, a nonlegume homolog of MtEFD, AtERF003 in Arabidopsis (Arabidopsis thaliana), could efficiently complement both phenotypes of Mtefd-1, in contrast to the MtEFD paralog MtEFD2 expressed in the root and nodule meristematic zone. A domain swap experiment showed that MtEFD2 differs from MtEFD by its C-terminal fraction outside the DNA binding domain. Furthermore, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) mutagenesis of MtEFD2 led to a reduction in the number of nodules formed in Mtefd-1, with downregulation of a set of genes, including notably NUCLEAR FACTOR-YA1 (MtNF-YA1) and MtNF-YB16, which are essential for nodule meristem establishment. We, therefore, conclude that nitrogen-fixing symbiosis recruited two proteins originally expressed in roots, MtEFD and MtEFD2, with distinct functions and neofunctionalization processes for each of them.
Published: 2022
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7. Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa genotypes

Author: A. Monti, François Perreau, Etienne Delannoy, F. Zanetti, Massimiliano Corso, Loïc Lepiniec, Marie-Laure Martin-Magniette, S. Boutet, Grégory Mouille, L. Barreda, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), Department of Agricultural and Food Sciences, University of Bologna/Università di Bologna, 'Departement de Biologie et Amelioration des Plantes' (BAP) of INRAE (grant 'Appel a projets scientifiques BAP 2020'), IJPB's Plant Observatory technological platforms, IPS2's metabolomic platform, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Boutet, Stéphanie, Barreda, Léa, Perreau, Françoi, Totozafy, Jean‐Chrisologue, Mauve, Caroline, Gakière, Bertrand, Delannoy, Etienne, Martin‐Magniette, Marie‐Laure, Monti, Andrea, Lepiniec, Loïc, Zanetti, Federica, and Corso, Massimiliano
Subjects: Genotype, metabolic signature, Camelina sativa, Growing season, Plant Science, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Crop, Flavonols, Metabolomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], rassicaceae,Camelina sativa, metabolic signature, metabolite decorations, environmentalchanges, molecular networks, untargeted metabolomic, lipidomics, metabolite decorations, Genetics, Metabolome, molecular networks, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cultivar, chemistry.chemical_classification, biology, food and beverages, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Cell Biology, biology.organism_classification, Camelina, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, chemistry, Agronomy, environmental changes, Seeds, Brassicaceae, untargeted metabolomics and lipidomics
Abstract: SummaryDespite the essential role of Specialized Metabolites (SMs) in the interaction of plants with the environment, studying the ability of crop seeds to produce these protective compounds has been neglected. Furthermore, seeds produce a myriad of SMs providing an interesting model to investigate their diversity and plasticity. Camelina sativa gained a lot of interest in the past few years as rustic oil seed crop. A characterization of seed SM landscapes in six camelina genotypes grown in the field and harvested during five growing seasons has been undertaken in this work. This allowed a comprehensive annotation of seed SMs combining analyses that cluster SMs based on their chemical structures and co-accumulation patterns. These data showed broad effects of the environment on the stimulation of the seed-specialized metabolome. Among well annotated compounds, flavonols were identified as the metabolic class characterised by high plasticity, revealing significant variable accumulation according to the year and/or the genotype. Lastly, a deeper characterisation of primary metabolites and lipids in two selected genotypes has been performed. We showed that, in addition to flavonols, alkaloids and glucosinolates displayed a higher phenotypic plasticity with respect to most of the primary metabolites, including some sugars and major storage compounds such as fatty acids, proteins and most lipid classes (e.g. DAG, TAG), but similar plasticity compared to free aminoacids and carboxylic acids. This work highlighted major and unexplored effects of the environment on the seed specialized metabolome demonstrating that seeds exhibit a dynamic and plastic metabolism, with an impact on seed quality.Significance statementSeeds produce a myriad of Specialized Metabolites (SMs) with an essential role in the interaction of plants with the environment. We characterized SM landscapes, primary metabolites and lipid composition in the seeds of camelina genotypes grown in the open field in five consecutive growing seasons. Our results showed the predominant effect of the environment on the regulation of the seed - specialized metabolome, with a potential impact on seed quality of camelina that may also occur in other oilseed crops.
Published: 2022
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8. Prime Editing in the model plant Physcomitrium patens and its potential in the tetraploid potato

Author: Pierre-François Perroud, Anouchka Guyon-Debast, Florian Veillet, Marie-Paule Kermarrec, Laura Chauvin, Jean-Eric Chauvin, Jean-Luc Gallois, Fabien Nogué, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The work was supported by the French National Research Agency (ANR11-BTBR-0001-GENIUS). The IJPB benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS)., ANR-11-BTBR-0001,GENIUS,Ingénierie cellulaire : amélioration et innovation technologiques pour les plantes d'une agriculture(2011), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: Gene Editing, pegRNA, [SDV]Life Sciences [q-bio], Plant Science, General Medicine, Tetraploidy, Plant Breeding, Physcomitrium patens, [SDE]Environmental Sciences, Genetics, Prime Editing, CRISPR-Cas Systems, CRISPR-Cas9, Agronomy and Crop Science, Genome, Plant, Genome editing, Solanum tuberosum
Abstract: International audience; Since its discovery and first applications for genome editing in plants, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology has revolutionized plant research and precision crop breeding. Although the classical CRISPR-Cas9 system is a highly efficient tool for disruptive targeted mutagenesis, this system is mostly inefficient for the introduction of precise and predictable nucleotide substitutions. Recently, Prime Editing technology has been developed, allowing the simultaneous generation of nucleotide transitions and transversions but also short defined indels. In this study, we report on the successful use of Prime Editing in two plants of interest: the plant model Physcomitrium patens and the tetraploid and highly heterozygous potato (Solanum tuberosum). In both cases editing rates were lower than with other CRISPR-Cas9 based techniques, but we were able to successfully introduce nucleotide transversions into targeted genes, a unique feature of Prime Editing. Additionally, the analysis of potential off-target mutation sites in P. patens suggested very high targeting fidelity in this organism. The present work paves the way for the use Prime Editing in Physcomitrium patens and potato, however highlighting the limitations that need to be overcome for more efficient precision plant breeding.
Published: 2022
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9. Genotypic Variation of Nitrogen Use Efficiency and Amino Acid Metabolism in Barley

Author: Bérengère Decouard, Marlène Bailly, Martine Rigault, Anne Marmagne, Mustapha Arkoun, Fabienne Soulay, José Caïus, Christine Paysant-Le Roux, Said Louahlia, Cédric Jacquard, Qassim Esmaeel, Fabien Chardon, Céline Masclaux-Daubresse, Alia Dellagi, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Timac - Agro International, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Sidi Mohamed Ben Abdellah - Fès [Université de Taza] (USMBA), Résistance Induite et Bioprotection des Plantes - EA 4707 (RIBP), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Centre National de la Recherche Scientifique (CNRS), ARIMNET 2 project entitled 'Exploring genotypic diversity to optimize barley grain and straw quality under marginal/stressful growth conditions,' BEST. IJPB benefits from the support of the LABEX Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: [SDV]Life Sciences [q-bio], natural variability, Plant culture, food and beverages, crop/stress physiology, barley, Plant Science, lysine (amino acids), NUE (nitrogen use efficiency), SB1-1110
Abstract: International audience; Owing to the large genetic diversity of barley and its resilience under harsh environments, this crop is of great value for agroecological transition and the need for reduction of nitrogen (N) fertilizers inputs. In the present work, we investigated the diversity of a North African barley genotype collection in terms of growth under limiting N (LN) or ample N (HN) supply and in terms of physiological traits including amino acid content in young seedlings. We identified a Moroccan variety, Laanaceur, accumulating five times more lysine in its leaves than the others under both N nutritional regimes. Physiological characterization of the barley collection showed the genetic diversity of barley adaptation strategies to LN and highlighted a genotype x environment interaction. In all genotypes, N limitation resulted in global biomass reduction, an increase in C concentration, and a higher resource allocation to the roots, indicating that this organ undergoes important adaptive metabolic activity. The most important diversity concerned leaf nitrogen use efficiency (LNUE), root nitrogen use efficiency (RNUE), root nitrogen uptake efficiency (RNUpE), and leaf nitrogen uptake efficiency (LNUpE). Using LNUE as a target trait reflecting barley capacity to deal with N limitation, this trait was positively correlated with plant nitrogen uptake efficiency (PNUpE) and RNUpE. Based on the LNUE trait, we determined three classes showing high, moderate, or low tolerance to N limitation. The transcriptomic approach showed that signaling, ionic transport, immunity, and stress response were the major functions affected by N supply. A candidate gene encoding the HvNRT2.10 transporter was commonly up-regulated under LN in the three barley genotypes investigated. Genes encoding key enzymes required for lysine biosynthesis in plants, dihydrodipicolinate synthase (DHPS) and the catabolic enzyme, the bifunctional Lys-ketoglutarate reductase/saccharopine dehydrogenase are up-regulated in Laanaceur and likely account for a hyperaccumulation of lysine in this genotype. Our work provides key physiological markers of North African barley response to low N availability in the early developmental stages.
Published: 2022
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10. HYPK promotes the activity of the Nα-acetyltransferase A complex to determine proteostasis of nonAc-X2/N-degron-containing proteins

Author: Pavlína Miklánková, Eric Linster, Jean-Baptiste Boyer, Jonas Weidenhausen, Johannes Mueller, Laura Armbruster, Karine Lapouge, Carolina De La Torre, Willy Bienvenut, Carsten Sticht, Matthias Mann, Thierry Meinnel, Irmgard Sinning, Carmela Giglione, Rüdiger Hell, Markus Wirtz, Heidelberg University, Centre for Organismal Studies [Heidelberg] (COS), 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), Maturation des proteines, destinée cellulaire et thérapeutique (PROMTI), Département Biologie des Génomes (DBG), 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), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, ANR-17-CAPS-0001,KatNat,Elucider les fonctions multifacettes des protéines acétyl transferase en réponse au stress et dans la régulation métabolique(2017), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: Multidisciplinary, Acetyltransferases/metabolism, N-Terminal Acetyltransferase A/genetics, N-Terminal Acetyltransferase E/genetics, Proteostasis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Acetylation, Arabidopsis/genetics
Abstract: In humans, the Huntingtin yeast partner K (HYPK) binds to the ribosome-associated N α -acetyltransferase A (NatA) complex that acetylates ~40% of the proteome in humans and Arabidopsis thaliana . However, the relevance of Hs HYPK for determining the human N-acetylome is unclear. Here, we identify the At HYPK protein as the first in vivo regulator of NatA activity in plants . At HYPK physically interacts with the ribosome-anchoring subunit of NatA and promotes N α -terminal acetylation of diverse NatA substrates. Loss-of- At HYPK mutants are remarkably resistant to drought stress and strongly resemble the phenotype of NatA-depleted plants. The ectopic expression of Hs HYPK rescues this phenotype. Combined transcriptomics, proteomics, and N-terminomics unravel that HYPK impairs plant metabolism and development, predominantly by regulating NatA activity. We demonstrate that HYPK is a critical regulator of global proteostasis by facilitating masking of the recently identified nonAc-X 2 /N-degron. This N-degron targets many nonacetylated NatA substrates for degradation by the ubiquitin-proteasome system.
Published: 2022
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11. Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models

Author: Guillem Rigaill, Arnaud Liehrmann, Toby Dylan Hocking, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University [Flagstaff], Northern Arizona University startup grant., ATIGE grant from Genopole., ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: FOS: Computer and information sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Computer science, computer.software_genre, Poisson distribution, 01 natural sciences, Biochemistry, Quantitative Biology - Quantitative Methods, Field (computer science), 010104 statistics & probability, Structural Biology, Statistics - Machine Learning, Segmentation, Biology (General), Quantitative Methods (q-bio.QM), 0303 health sciences, Noise (signal processing), Applied Mathematics, High-Throughput Nucleotide Sequencing, Computer Science Applications, Multiple changepoint detection, ChIP-seq, Likelihood inference, symbols, Chromatin Immunoprecipitation Sequencing, Data mining, Algorithms, Count data, Chromatin Immunoprecipitation, QH301-705.5, Computer applications to medicine. Medical informatics, R858-859.7, Machine Learning (stat.ML), Over-dispersion, 03 medical and health sciences, symbols.namesake, Overdispersion, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 0101 mathematics, Molecular Biology, 030304 developmental biology, Research, Histone modifications, Supervised learning, Sequence Analysis, DNA, Peak calling, FOS: Biological sciences, computer
Abstract: Motivation: Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq). This technique provides a direct survey of the DNA regions associated to these modifications. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed or adapted to analyze the massive amount of data it generates. Many of these algorithms were built around natural assumptions such as the Poisson one to model the noise in the count data. In this work we start from these natural assumptions and show that it is possible to improve upon them. Results: The results of our comparisons on seven reference datasets of histone modifications (H3K36me3 and H3K4me3) suggest that natural assumptions are not always realistic under application conditions. We show that the unconstrained multiple changepoint detection model, with alternative noise assumptions and a suitable setup, reduces the over-dispersion exhibited by count data and turns out to detect peaks more accurately than algorithms which rely on these natural assumptions., Comment: 20 pages, 8 figures; updated broken citations and references
Published: 2021
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12. Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin

Author: Arpòn, Javier, Sakai, Kaori, Gaudin, Valérie, Andrey, Philippe, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and European Project: 316965,EC:FP7:PEOPLE,FP7-PEOPLE-2012-ITN,EPITRAITS(2012)
Subjects: Nuclear organization, Image processing, Statistical methods, Heterochromatin, Science, Arabidopsis, Medicine, Cellular imaging, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Models, Biological, Article
Abstract: International audience; The spatial organization in the cell nucleus is tightly linked to genome functions such as gene regulation. Similarly, specific spatial arrangements of biological components such as macromolecular complexes, organelles and cells are involved in many biological functions. Spatial interactions among elementary components of biological systems define their relative positioning and are key determinants of spatial patterns. However, biological variability and the lack of appropriate spatial statistical methods and models limit our current ability to analyze these interactions. Here, we developed a framework to dissect spatial interactions and organization principles by combining unbiased statistical tests, multiple spatial descriptors and new spatial models. We used plant constitutive heterochromatin as a model system to demonstrate the potential of our framework. Our results challenge the common view of a peripheral organization of chromocenters, showing that chromocenters are arranged along both radial and lateral directions in the nuclear space and obey a multiscale organization with scale-dependent antagonistic effects. The proposed generic framework will be useful to identify determinants of spatial organizations and to question their interplay with biological functions.
Published: 2021
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13. Brachypodium distachyon UNICULME4 and LAXATUM-A are redundantly required for development

Author: Kevin Magne, Sylviane Daniel, Shengbin Liu, Richard Sibout, Pascal Ratet, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), TRANSFORM Division (INRAE), S. Liu was supported by a 4-year Chinese scholarship council PhD 38 scholarship (CSC grant n° 201608510056)., ANR-14-CE19-0003,NOOT,Les gènes NOOT gardiens de l'dentité des nodosités symbiotiques et de l'abscission(2014), ANR-14-CE19-0012,BRAVO,Ontogénie des tissus vasculaires chez les graminées(2014), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, TILLING, Genotype, Physiology, Plant Science, Genes, Plant, 01 natural sciences, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Abscission, Gene Expression Regulation, Plant, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Inflorescence, Gene, Conserved Sequence, Research Articles, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Oryza sativa, biology, Genetic Variation, food and beverages, biology.organism_classification, Reverse Genetics, Plant Leaves, Mutation, Seeds, [SDE]Environmental Sciences, Brachypodium, Brachypodium distachyon, Hordeum vulgare, 010606 plant biology & botany
Abstract: In cultivated grasses, tillering, leaf, and inflorescence architecture, as well as abscission ability, are major agronomical traits. In barley (Hordeum vulgare), maize (Zea mays), rice (Oryza sativa), and brachypodium (Brachypodium distachyon), NOOT-BOP-COCH-LIKE (NBCL) genes are essential regulators of vegetative and reproductive development. Grass species usually possess 2–4 NBCL copies and until now a single study in O. sativa showed that the disruption of all NBCL genes strongly altered O. sativa leaf development. To improve our understanding of the role of NBCL genes in grasses, we extended the study of the two NBCL paralogs BdUNICULME4 (CUL4) and BdLAXATUM-A (LAXA) in the nondomesticated grass B. distachyon. For this, we applied reversed genetics and generated original B. distachyon single and double nbcl mutants by clustered regularly interspaced short palindromic repeats – CRISPR associated protein 9 (CRISPR-Cas9) approaches and genetic crossing between nbcl targeting induced local lesions in genomes (TILLING) mutants. Through the study of original single laxa CRISPR–Cas9 null alleles, we validated functions previously proposed for LAXA in tillering, leaf patterning, inflorescence, and flower development and also unveiled roles for these genes in seed yield. Furthermore, the characterization of cul4laxa double mutants revealed essential functions for nbcl genes in B. distachyon development, especially in the regulation of tillering, stem cell elongation and secondary cell wall composition as well as for the transition toward the reproductive phase. Our results also highlight recurrent antagonist interactions between NBCLs occurring in multiple aspects of B. distachyon development.
Published: 2021
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14. $Sinorhizobium\ meliloti$ functions required for resistance to antimicrobial NCR peptides and bacteroid differentiation

Author: Sándor Jenei, Peter Mergaert, Quentin Nicoud, Claire Boulogne, Quentin Barrière, Atilla Kereszt, Sara Dendene, Marie Lecroël, Romain Le Bars, Dmitrii Y. Travin, Nicolas Busset, Emanuele G. Biondi, Benoit Alunni, Eva Kondorosi, Mickael Bourge, Tatiana Timchenko, 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), Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia, Département Plateforme (PF 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), Institute of Plant Biology Biological Research Centre, Institute of Plant Biology, Biological Research Centre, Szeged, Hungary, ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-CE20-0011,SymbiontCellCyc,Rôle du cycle cellulaire bactérien dans la fixation symbiotique d'azote chez les Légumineuses(2017), ANR-16-CE20-0013,SymEffectors,Système de sécrétion de type 3 pour la symbiose fixatrice d'azote(2016), Institute for Integrative Biology of the Cell [Gif-sur-Yvette] (I2BC), and Centre National de la Recherche Scientifique (CNRS)
Subjects: Root nodule, Membrane permeability, [SDV]Life Sciences [q-bio], Antimicrobial peptides, Mutant, Microbiology, antimicrobial peptides, 03 medical and health sciences, Sigma factor, Virology, Drug Resistance, Bacterial, Medicago truncatula, Symbiosis, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Sinorhizobium meliloti, biology, 030306 microbiology, fungi, food and beverages, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, QR1-502, Cell biology, mechanisms of resistance, nitrogen fixation, bacteria, Cell envelope, Root Nodules, Plant, Bacteria, Research Article
Abstract: Legumes of the Medicago genus form symbiosis with the bacterium Sinorhizobium meliloti and develop root nodules housing large numbers of the intracellular symbionts. Members of the Nodule-specific Cysteine Rich peptide (NCRs) family induce the endosymbionts into a terminal differentiated state. Individual cationic NCRs are antimicrobial peptides that have the capacity to kill the symbiont but the nodule cell environment prevents killing. Moreover, the bacterial broad-specificity peptide uptake transporter BacA and exopolysaccharides contribute to protect the endosymbionts against the toxic activity of NCRs. Here, we show that other S. meliloti functions participate in the protection of the endosymbionts, including an additional broad-specificity peptide uptake transporter encoded by the yejABEF genes, lipopolysaccharide modifications mediated by lpsB and lpxXL as well as rpoH1, encoding a stress sigma factor. Mutants of these genes show in vitro a strain-specific increased sensitivity profile against a panel of NCRs and form nodules in which bacteroid differentiation is affected. The lpsB mutant nodule bacteria do not differentiate, the lpxXL and rpoH1 mutants form some seemingly fully differentiated bacteroids although most of the nodule bacteria are undifferentiated, while the yejABEF mutants form hypertrophied but nitrogen-fixing bacteroids. The nodule bacteria of all the mutants have a strongly enhanced membrane permeability, which is dependent on the transport of NCRs to the endosymbionts. Our results suggest that S. meliloti relies on a suite of functions including peptide transporters, the bacterial envelope structures and stress response regulators to resist the aggressive assault of NCR peptides in the nodule cells.ImportanceThe nitrogen fixing symbiosis of legumes with rhizobium bacteria has a predominant ecological role in the nitrogen cycle and has the potential to provide the nitrogen required for plant growth in agriculture. The host plants allow the rhizobia to colonize specific symbiotic organs, the nodules, in large numbers in order to produce sufficient reduced nitrogen for the plant needs. Some legumes, including Medicago spp., produce massively antimicrobial peptides to keep this large bacterial population in check. These peptides, known as NCRs, have the potential to kill the rhizobia but in nodules, they rather inhibit the division of the bacteria, which maintain a high nitrogen fixing activity. In this study, we show that the tempering of the antimicrobial activity of the NCR peptides in the Medicago symbiont Sinorhizobium meliloti is multifactorial and requires the YejABEF peptide transporter, the lipopolysaccharide outer membrane composition and the stress response regulator RpoH1.
Published: 2021
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15. Avoidance of detrimental defense responses in beneficial plant–microbe interactions

Author: Pascal Ratet, Benjamin Gourion, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-14-CE19-0003,NOOT,Les gènes NOOT gardiens de l'dentité des nodosités symbiotiques et de l'abscission(2014), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-17-CE20-0013,TrolesInfidels,Compromis dans les symbioses rhizobium-légumineuse, influence de l'immunité et des défenses sur la symbiose et vice versa(2017), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Biomedical Engineering, Bioengineering, Biology, 01 natural sciences, Crop, 03 medical and health sciences, Stress, Physiological, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, Abiotic component, 0303 health sciences, Resistance (ecology), business.industry, fungi, Plant microbe, food and beverages, 15. Life on land, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Biotechnology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, business, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; In the environment microbes interact with plants and provide them with benefits that include protection against biotic and abiotic stresses as well as improved nutrition. However, plants are also exposed to parasites and pathogens. To manage appropriate responses, evolution has resulted in improved tolerance of plants to beneficial microbes while keeping the ability to recognize detrimental ones and to develop defense responses. Here we review the mechanisms involved in these interactions. We also discuss how the interactions might be handled to improve crop resistance to pathogens without losing the ability to establish beneficial interactions.
Published: 2021
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16. The miR166–SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato

Author: Abdelhafid Bendahmane, Gwilherm Brisou, Marion Verdenaud, Ravi Sureshbhai Devani, Grégory Mouille, Halima Morin, Christian Clepet, Rachid Boumlik, Yanwei Hao, Adnane Boualem, Jean-Christophe Lepeltier, Sylvie Citerne, Brahim Mania, Fabien Marcel, Shai Koussevitzky, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), South China Agricultural University (SCAU), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), HM. CLAUSE [France], Hazera – Seeds of Growth, INRAE, Centre National de la Recherche Scientifique (CNRS) European Commission, Horizon 2020 research and innovation program (TOMRES)727929, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and European Project: 0341076(2002)
Subjects: 0106 biological sciences, 0301 basic medicine, Parthenogenesis, Mutant, Plant Science, Biology, Parthenocarpy, 01 natural sciences, heat stress, 03 medical and health sciences, Solanum lycopersicum, Transcription (biology), HD-ZipIII, Allele, Ovule, Molecular Biology, Gene, Transcription factor, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Plant Proteins, 2. Zero hunger, Leucine Zippers, [SDV.GEN]Life Sciences [q-bio]/Genetics, Gene Expression Profiling, miRNA166, food and beverages, Promoter, Cell biology, MicroRNAs, dosage sensitivity, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, RNA, Plant, cold stress, parthenocarpy, Transcription Factors, 010606 plant biology & botany
Abstract: International audience; Fruit set is inhibited by adverse temperatures, with consequences on yield. We isolated a tomato mutant producing fruits under non-permissive hot temperatures and identified the causal gene as SlHB15A, belonging to class III homeodomain leucine-zipper transcription factors. SlHB15A loss-of-function mutants display aberrant ovule development that mimics transcriptional changes occurring in fertilized ovules and leads to parthenocarpic fruit set under optimal and non-permissive temperatures, in field and greenhouse conditions. Under cold growing conditions, SlHB15A is subjected to conditional haploinsufficiency and recessive dosage sensitivity controlled by microRNA 166 (miR166). Knockdown of SlHB15A alleles by miR166 leads to a continuum of aberrant ovules correlating with parthenocarpic fruit set. Consistent with this, plants harboring an Slhb15a–miRNA166-resistant allele developed normal ovules and were unable to set parthenocarpic fruit under cold conditions. DNA affinity purification sequencing and RNA-sequencing analyses revealed that SlHB15A is a bifunctional transcription factor expressed in the ovule integument. SlHB15A binds to the promoters of auxin-related genes to repress auxin signaling and to the promoters of ethylene-related genes to activate their expression. A survey of tomato genetic biodiversity identified pat and pat-1, two historical parthenocarpic mutants, as alleles of SlHB15A. Taken together, our findings demonstrate the role of SlHB15A as a sentinel to prevent fruit set in the absence of fertilization and provide a mean to enhance fruiting under extreme temperatures.
Published: 2021
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17. Progerin impairs 3D genome organization and induces fragile telomeres by limiting the dNTP pools

Author: Vincent Piras, Anna Kychygina, Hilda A. Pickett, Joshua A. M. Allen, Jean-Charles Cadoret, Marina Dall’Osto, Laure Crabbe, Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), The University of Sydney, Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), European Project: 714653,TeloHOOK, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)
Subjects: [SDV]Life Sciences [q-bio], Deoxyribonucleotides, Nuclear envelope, Mice, 0302 clinical medicine, Progeria, Genes, Reporter, Cells, Cultured, Cellular Senescence, Skin, Mice, Knockout, 0303 health sciences, Multidisciplinary, Lamin Type B, integumentary system, Telomere, Lamin Type A, Chromatin, Cell biology, Histone Code, Telomeres, Nuclear lamina, Medicine, Premature aging, Adult, DNA Replication, Recombinant Fusion Proteins, Science, Green Fluorescent Proteins, Biology, Senescence, Article, Telomere organization, 03 medical and health sciences, Telomere Homeostasis, medicine, Animals, Humans, 030304 developmental biology, Replication timing, Nuclear organization, Nuclear Lamina, Infant, Newborn, Fibroblasts, medicine.disease, 030217 neurology & neurosurgery, DNA Damage
Abstract: Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity. A key player in this spatial scattering of chromosomes is the nuclear envelope (NE). The NE tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins. This organization is perturbed in cells from Hutchinson–Gilford progeria syndrome (HGPS), a genetic disorder characterized by premature aging features. Here, we show that HGPS-related lamina defects trigger an altered 3D telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state. The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late. As a consequence, we detected a higher density of replication forks traveling simultaneously on DNA fibers, which relies on limiting cellular dNTP pools to support processive DNA synthesis. Remarkably, increasing dNTP levels in HGPS cells rescued fragile telomeres, and improved the replicative capacity of the cells. Our work highlights a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.
Published: 2021
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18. HAG1 and SWI3A/B control of male germ line development in P. patens suggests conservation of epigenetic reproductive control across land plants

Author: Kristian K. Ullrich, Zhanghai Li, Fabien Nogué, Stefan A. Rensing, Fabian B. Haas, Anne Christina Genau, Rabea Meyberg, Christopher Grosche, Karen S. Renzaglia, Mona Schreiber, Noe Fernandez Pozo, Per K.I. Wilhelmsson, University of Marburg, Southern Illinois University [Carbondale] (SIU), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for Evolutionary Biology, Max-Planck-Gesellschaft, Centre for Biological Signaling Studies [Freiburg] (BIOSS), University of Freiburg [Freiburg], LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Projekt DEAL, MAdLand (http://madland.science, DFG priority program 2237), DFG (RE 1697/15–1, 19–1, 20–1), National Science Foundation (NSF 1758497), National Institutes of Health (NIH 5R25GM107760-07), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, Spermatozoid, Plant Science, Biology, 01 natural sciences, Epigenesis, Genetic, 03 medical and health sciences, Germ line, Marchantia, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Genetics, Gametophyte, 0303 health sciences, Gametangia, Reproduction, Embryo, Sporophyte, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Cell Biology, 15. Life on land, Biological Evolution, Sexual reproduction, Fertilization, Alternation of generations, Physcomitrium, Embryophyta, Original Article, Bryophyte, Germ line development, Germ Cells, Plant, Ploidy, 010606 plant biology & botany
Abstract: Key message Bryophytes as models to study the male germ line: loss-of-function mutants of epigenetic regulators HAG1 and SWI3a/b demonstrate conserved function in sexual reproduction. Abstract With the water-to-land transition, land plants evolved a peculiar haplodiplontic life cycle in which both the haploid gametophyte and the diploid sporophyte are multicellular. The switch between these phases was coined alternation of generations. Several key regulators that control the bauplan of either generation are already known. Analyses of such regulators in flowering plants are difficult due to the highly reduced gametophytic generation, and the fact that loss of function of such genes often is embryo lethal in homozygous plants. Here we set out to determine gene function and conservation via studies in bryophytes. Bryophytes are sister to vascular plants and hence allow evolutionary inferences. Moreover, embryo lethal mutants can be grown and vegetatively propagated due to the dominance of the bryophyte gametophytic generation. We determined candidates by selecting single copy orthologs that are involved in transcriptional control, and of which flowering plant mutants show defects during sexual reproduction, with a focus on the under-studied male germ line. We selected two orthologs, SWI3a/b and HAG1, and analyzed loss-of-function mutants in the moss P. patens. In both mutants, due to lack of fertile spermatozoids, fertilization and hence the switch to the diploid generation do not occur. Pphag1 additionally shows arrested male and impaired female gametangia development. We analyzed HAG1 in the dioecious liverwort M. polymorpha and found that in Mphag1 the development of gametangiophores is impaired. Taken together, we find that involvement of both regulators in sexual reproduction is conserved since the earliest divergence of land plants.
Published: 2021
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19. Mutation of an Arabidopsis Golgi membrane protein ELMO1 reduces cell adhesion

Author: Susan L. Kohorn, Bruce D. Kohorn, Salem Chabout, Grégory Mouille, Frances D H Zorensky, Jacob Dexter-Meldrum, Bowdoin College [Brunswick], Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Science Foundation (NSF) IOS 1556057, Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health P20GM103423, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: 0106 biological sciences, ELMO1, Morphogenesis, Arabidopsis, Golgi Apparatus, Pectin binding, Biology, 01 natural sciences, Extracellular matrix, Cell wall, 03 medical and health sciences, symbols.namesake, Gene Expression Regulation, Plant, Cell Adhesion, Cell adhesion, Molecular Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, 030304 developmental biology, Adaptor Proteins, Signal Transducing, 0303 health sciences, Golgi membrane, Arabidopsis Proteins, fungi, Membrane Proteins, food and beverages, Adhesion, Methyltransferases, Golgi apparatus, Hypocotyl, Cell biology, symbols, Pectins, Mannose, 010606 plant biology & botany, Developmental Biology, Research Article
Abstract: International audience; Plant growth, morphogenesis and development involve cellular adhesion, a process dependent on the composition and structure of the extracellular matrix or cell wall. Pectin in the cell wall is thought to play an essential role in adhesion, and its modification and cleavage are suggested to be highly regulated so as to change adhesive properties. To increase our understanding of plant cell adhesion, a population of ethyl methanesulfonate-mutagenized Arabidopsis were screened for hypocotyl adhesion defects using the pectin binding dye Ruthenium Red that penetrates defective but not wild-type (WT) hypocotyl cell walls. Genomic sequencing was used to identify a mutant allele of ELMO1 which encodes a 20 kDa Golgi membrane protein that has no predicted enzymatic domains. ELMO1 colocalizes with several Golgi markers and elmo1−/− plants can be rescued by an ELMO1-GFP fusion. elmo1−/− exhibits reduced mannose content relative to WT but no other cell wall changes and can be rescued to WT phenotype by mutants in ESMERALDA1, which also suppresses other adhesion mutants. elmo1 describes a previously unidentified role for the ELMO1 protein in plant cell adhesion.
Published: 2021
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20. Evolution-driven versatility of N-terminal acetylation in photoautotrophs

Author: Carmela Giglione, Thierry Meinnel, Maturation des proteines, destinée cellulaire et thérapeutique (PROMTI), Département Biologie des Génomes (DBG), 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), ANR-17-CAPS-0001,KatNat,Elucider les fonctions multifacettes des protéines acétyl transferase en réponse au stress et dans la régulation métabolique(2017), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and European Project: 291864,EC:FP7:KBBE,FP7-ERANET-2011-RTD,ERACAPS(2011)
Subjects: 0106 biological sciences, 0301 basic medicine, Terminal protein, [SDV]Life Sciences [q-bio], Plant Science, Computational biology, Biology, Photosynthesis, N-terminal alpha-acetyltransferase, 01 natural sciences, GNAT, 03 medical and health sciences, Gnat, Protein translocation, Plastids, Plastid, plastid, Acetylation, stress response, Plant development, 030104 developmental biology, lysine epsilon-acetyltransferase, Posttranslational modification, plant development, Protein Processing, Post-Translational, 010606 plant biology & botany
Abstract: International audience; N-terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
Published: 2021
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21. Regulation of photosynthetic electron flow on dark to light transition by ferredoxin:NADP(H) oxidoreductase interactions

Author: Manuela Kramer, Manuel Twachtmann, Melvin Rodriguez-Heredia, Laura Mosebach, Guy Hanke, Giovanni Finazzi, Anja Krieger-Liszkay, Francesco Saccon, Christopher D. P. Duffy, Robert J. Knell, School of Biochemistry and Chemistry, Queen Mary University of London, Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Universität Osnabrück - Osnabrück University, 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), Light Photosynthesis & Metabolism (Photosynthesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Funding from the Deutsche Forschungsgemeinschaft through (Project 2 in the Collaborative Research Center (SFB) 944) and BBSRC (BB/R004838/1), Bayer Science and Education foundation (F-2016-BS-0555), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-10-INTB-1501,BioPol folders,Repliement et stabilisation par des polymeres amphiphiles biocompatibles de fragments scFv marqueurs cellulaires de cancers.(2010), European Project: 833184, ChloroMito, Institute for Plant Biology and Biotechnology,University of Münster, and Department of Plant Physiology, University of Osnabrück
Subjects: 0106 biological sciences, 0301 basic medicine, inorganic chemicals, Chloroplasts, QH301-705.5, Photoperiod, Science, thylakoid, Arabidopsis, Electrons, Photosynthesis, 01 natural sciences, environment and public health, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chloroplast, Oxidoreductase, NADPH, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, electron transport, Biology (General), Ferredoxin, chemistry.chemical_classification, plant biology, photosynthesis, General Immunology and Microbiology, biology, Chemistry, Arabidopsis Proteins, General Neuroscience, Biological Transport, General Medicine, Immunogold labelling, biology.organism_classification, ferredoxin, Electron transport chain, Chloroplast, Ferredoxin-NADP Reductase, 030104 developmental biology, Thylakoid, A. thaliana, Biophysics, Medicine, bacteria, 010606 plant biology & botany, Research Article
Abstract: International audience; During photosynthesis, electron transport is necessary for carbon assimilation and must be regulated to minimize free radical damage. There is a longstanding controversy over the role of a critical enzyme in this process (ferredoxin:NADP(H) oxidoreductase, or FNR), and in particular its location within chloroplasts. Here we use immunogold labelling to prove that FNR previously assigned as soluble is in fact membrane associated. We combined this technique with a genetic approach in the model plant Arabidopsis to show that the distribution of this enzyme between different membrane regions depends on its interaction with specific tether proteins. We further demonstrate a correlation between the interaction of FNR with different proteins and the activity of alternative photosynthetic electron transport pathways. This supports a role for FNR location in regulating photosynthetic electron flow during the transition from dark to light.
Published: 2021
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22. The root‐knot nematode effector MiEFF18 interacts with the plant core spliceosomal protein SmD1 required for giant cell formation

Author: Hervé Vaucheret, Bruno Favery, Jérémie Bazin, Michaël Quentin, Nhat-My Truong, Nathalie Marteu, Nathalie Bouteiller, Joffrey Mejias, Yongpan Chen, Shinichiro Sawa, Pierre Abad, Martin Crespi, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kumamoto University, China Agricultural University (CAU), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRA SPE department, INRA-Syngenta Targetome project, French-Japanese bilateral collaboration programme PHC SAKURA 2016 35891VD, French-Chinese bilateral collaboration program PHC XU GUANGQI 2020 45478PF, French Ministere de lEnseignement Superieur, de la Recherche et de lInnovation (MENRT grant), USTH fellowship, as part of the 911-USTH programme of the Ministry of Education and Training of The Socialist Republic of Vietnam, China Scholarship Council 201806350108, French-Japanese bilateral collaboration programme PHC SAKURA 2019 43006VJ, ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), ANR-16-CE12-0032,SPLISIL,Dialogue épissage et extinction de l'ARN durant l'expression génétique(2016), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Spliceosome, Arabidopsis thaliana, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Giant Cells, Plant Roots, 01 natural sciences, Host-Parasite Interactions, 03 medical and health sciences, alternative splicing, Solanum lycopersicum, medicine, Meloidogyne incognita, Nicotiana benthamiana, Animals, Tylenchoidea, Plant Diseases, Plant Proteins, biology, Effector, Alternative splicing, food and beverages, Helminth Proteins, medicine.disease, biology.organism_classification, Cell biology, 030104 developmental biology, effector, Nematode infection, Giant cell, RNA splicing, Spliceosomes, nucleus, 010606 plant biology & botany
Abstract: International audience; The root-knot nematode Meloidogyne incognita secretes specific effectors (MiEFF) and induces the redifferentiation of plant root cells into enlarged multinucleate feeding 'giant cells' essential for nematode development. Immunolocalizations revealed the presence of the MiEFF18 protein in the salivary glands of M. incognita juveniles. In planta, MiEFF18 localizes to the nuclei of giant cells demonstrating its secretion during plant-nematode interactions. A yeast two-hybrid approach identified the nuclear ribonucleoprotein SmD1 as a MiEFF18 partner in tomato and Arabidopsis. SmD1 is an essential component of the spliceosome, a complex involved in pre-mRNA splicing and alternative splicing. RNA-seq analyses of Arabidopsis roots ectopically expressing MiEFF18 or partially impaired in SmD1 function (smd1b mutant) revealed the contribution of the effector and its target to alternative splicing and proteome diversity. The comparison with Arabidopsis galls data showed that MiEFF18 modifies the expression of genes important for giant cell ontogenesis, indicating that MiEFF18 modulates SmD1 functions to facilitate giant cell formation. Finally, Arabidopsis smd1b mutants exhibited less susceptibility to M. incognita infection, and the giant cells formed on these mutants displayed developmental defects, suggesting that SmD1 plays an important role in the formation of giant cells and is required for successful nematode infection.
Published: 2021
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23. Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

Author: Martin Crespi, Camille Fonouni-Farde, Federico Ariel, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad Nacional del Litoral [Santa Fe] (UNL), Agencia Nacional de Promoción Científica y Tecnológica (PICT), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-19-CE20-0011,PIOSYM,Comprendre le mode d'action d'un facteur de transcription pionnier pendant le développement des nodosités symbiotiques(2019), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Ariel, protein re-localization, lcsh:QH426-470, Computational biology, Review, Biology, 01 natural sciences, Biochemistry, Genome, 03 medical and health sciences, C, Keywords: long noncoding RNA, alternative splicing, Gene expression, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Epigenetics, long noncoding RNA, Molecular Biology, Post-transcriptional regulation, Genome size, Crespi, translation promotion, Regulation of gene expression, [SDV.GEN]Life Sciences [q-bio]/Genetics, Alternative splicing, Long non-coding RNA, target mimicry, lcsh:Genetics, 030104 developmental biology, post-translational modification, F, Fonouni-Farde, M. Plant Long Noncoding long noncoding RNA, 010606 plant biology & botany, post-transcriptional regulation
Abstract: International audience; The first reference to the “C-value paradox” reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.
Published: 2021
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24. Involvement of SUT1 and SUT2 Sugar Transporters in the Impairment of Sugar Transport and Changes in Phloem Exudate Contents in Phytoplasma-Infected Plants

Author: Federica De Marco, Brigitte Batailler, Michael R. Thorpe, Frédérique Razan, Rozenn Le Hir, Françoise Vilaine, Alain Bouchereau, Marie-Laure Martin-Magniette, Sandrine Eveillard, Sylvie Dinant, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Sciences Division, Research School of Biology, The Australian National University, Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), 267196, AgreenSkills, ANR-17-EUR-0007, Agence Nationale de la Recherche, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Mathématiques et Informatique Appliquées (MIA Paris-Saclay)
Subjects: photorespiration, Phytoplasma, Monosaccharide Transport Proteins, plant-pathogen interaction, [SDV]Life Sciences [q-bio], Pathologie végétale, Phloem, Genes, Plant, Article, lcsh:Chemistry, Gene Expression Regulation, Plant, glycolate, sugar metabolism, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Metabolomics, peroxisome, lcsh:QH301-705.5, Plant Diseases, glyoxylate, fungi, Bactérie, Santé des Plantes, food and beverages, Biological Transport, Starch, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Mollicute, defense, Plant Leaves, Phenotype, lcsh:Biology (General), lcsh:QD1-999, carbon allocation, Host-Pathogen Interactions, Carbohydrate Metabolism, metabolome, Sugars, source-sink relationships
Abstract: Phytoplasmas inhabit phloem sieve elements and cause abnormal growth and altered sugar partitioning. However, how they interact with phloem functions is not clearly known. The phloem responses were investigated in tomatoes infected by “Candidatus Phytoplasma solani” at the beginning of the symptomatic stage, the first symptoms appearing in the newly emerged leaf at the stem apex. Antisense lines impaired in the phloem sucrose transporters SUT1 and SUT2 were included. In symptomatic sink leaves, leaf curling was associated with higher starch accumulation and the expression of defense genes. The analysis of leaf midribs of symptomatic leaves indicated that transcript levels for genes acting in the glycolysis and peroxisome metabolism differed from these in noninfected plants. The phytoplasma also multiplied in the three lower source leaves, even if it was not associated with the symptoms. In these leaves, the rate of phloem sucrose exudation was lower for infected plants. Metabolite profiling of phloem sap-enriched exudates revealed that glycolate and aspartate levels were affected by the infection. Their levels were also affected in the noninfected SUT1- and SUT2-antisense lines. The findings suggest the role of sugar transporters in the responses to infection and describe the consequences of impaired sugar transport on the primary metabolism.
Published: 2021
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25. Fungal treatment for the valorization of technical soda lignin

Author: Daou, Mariane, Farfan Soto, Clementina, Majira, Amel, Cézard, Laurent, Cottyn, Betty, Pion, Florian, Navarro, David, Correia, Lydia Oliveira, Drula, Elodie, Record, Eric, Raouche, Sana, Baumberger, Stéphanie, Faulds, Craig B., Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Bio Based Industry Joint Undertaking under the European Union 720303LabEx Saclay Plant Sciences-SPS ANR-10-LABX-552 0040-SPS, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), European Project: 9720303(1998), and AgroParisTech
Subjects: Leiotrametes menziesii, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, fungi, filamentous fungi, technology, industry, and agriculture, food and beverages, Pycnoporus sanguineus, macromolecular substances, Polyporus brumalis, complex mixtures, Article, oxidoreductases, lcsh:Biology (General), technical lignin, secretomic analysis, [CHIM]Chemical Sciences, lcsh:QH301-705.5
Abstract: Technical lignins produced as a by-product in biorefinery processes represent a potential source of renewable carbon. In consideration of the possibilities of the industrial transformation of this substrate into various valuable bio-based molecules, the biological deconstruction of a technical soda lignin by filamentous fungi was investigated. The ability of three basidiomycetes (Polyporus brumalis,Pycnoporus sanguineusandLeiotrametes menziesii) to modify this material, the resultant structural and chemical changes, and the secreted proteins during growth on this substrate were investigated. The three fungi could grow on the technical lignin alone, and the growth rate increased when the media were supplemented with glucose or maltose. The proteomic analysis of the culture supernatants after three days of growth revealed the secretion of numerous Carbohydrate-Active Enzymes (CAZymes). The secretomic profiles varied widely between the strains and the presence of technical lignin alone triggered the early secretion of many lignin-acting oxidoreductases. The secretomes were notably rich in glycoside hydrolases and H2O2-producing auxiliary activity enzymes with copper radical oxidases being induced on lignin for all strains. The lignin treatment by fungi modified both the soluble and insoluble lignin fractions. A significant decrease in the amount of soluble higher molar mass compounds was observed in the case ofP. sanguineus. This strain was also responsible for the modification of the lower molar mass compounds of the lignin insoluble fraction and a 40% decrease in the thioacidolysis yield. The similarity in the activities ofP. sanguineusandP. brumalisin modifying the functional groups of the technical lignin were observed, the results suggest that the lignin has undergone structural changes, or at least changes in its composition, and pave the route for the utilization of filamentous fungi to functionalize technical lignins and produce the enzymes of interest for biorefinery applications.
Published: 2021
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26. A blue-print for gene function analysis through Base Editing in the model plant Physcomitrium (Physcomitrella) patens

Author: Guyon-Debast, Anouchka, Alboresi, Alessandro, Terret, Zoé, Charlot, Florence, Berthier, Floriane, Vendrell-Mir, Pol, Casacuberta, Josep M., Veillet, Florian, Morosinotto, Tomas, Gallois, Jean-Luc, Nogue, Fabien, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universita degli Studi di Padova, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Spanish National Research Council (CSIC), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), French National Research Agency French National Research Agency (ANR) [ANR11-BTBR-0001-GENIUS], LabEx Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS], ANR-11-BTBR-0001,GENIUS,Ingénierie cellulaire : amélioration et innovation technologiques pour les plantes d'une agriculture(2011), University of Padova [Padova, Italy], Centre for Research in Agricultural Genomics (CRAG), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Agence Nationale de la Recherche (France), Institute of Plant Sciences Paris-Saclay, Università degli Studi di Padova = University of Padua (Unipd), and Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest
Subjects: Gene Editing, Physcomitrella patens, Adenine deaminase, Physcomitrium patens, APRT, Base editing, CRISPR, Cas9, Cytosine deaminase, Research, cytosine deaminase, [SDV]Life Sciences [q-bio], food and beverages, Bryopsida, Methods, Mutagenesis, Site-Directed, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems
Abstract: CRISPR-Cas9 has proven to be highly valuable for genome editing in plants, including the model plant Physcomitrium patens. However, the fact that most of the editing events produced using the native Cas9 nuclease correspond to small insertions and deletions is a limitation., CRISPR-Cas9 base editors enable targeted mutation of single nucleotides in eukaryotic genomes and therefore overcome this limitation. Here, we report two programmable base-editing systems to induce precise cytosine or adenine conversions in P. patens., Using cytosine or adenine base editors, site-specific single-base mutations can be achieved with an efficiency up to 55%, without off-target mutations. Using the APT gene as a reporter of editing, we could show that both base editors can be used in simplex or multiplex, allowing for the production of protein variants with multiple amino-acid changes. Finally, we set up a co-editing selection system, named selecting modification of APRT to report gene targeting (SMART), allowing up to 90% efficiency site-specific base editing in P. patens., These two base editors will facilitate gene functional analysis in P. patens, allowing for site-specific editing of a given base through single sgRNA base editing or for in planta evolution of a given gene through the production of randomly mutagenised variants using multiple sgRNA base editing., The work, including study design, data collection, analysis and interpretation and manuscript writing, was supported by the French National Research Agency (ANR11-BTBR-0001-GENIUS). The IJPB benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).
Published: 2021
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27. Bayesian luminescence dating at Ghār-e Boof, Iran, provides a new chronology for Middle and Upper Paleolithic in the southern Zagros

Author: Nicholas J. Conard, Maryam Heydari, Mohsen Zeidi, Guillaume Guérin, IRAMAT-Centre de recherche en physique appliquée à l’archéologie (IRAMAT-CRP2A), Institut de Recherches sur les Archéomatériaux (IRAMAT), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Montaigne-Université de Technologie de Belfort-Montbeliard (UTBM), University of Tübingen, German Research Foundation (DFG) CO 226/30-1, and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 010506 paleontology, Luminescence, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, New Chronology, Iran, 01 natural sciences, Stone Age, Sequence (geology), Cave, Middle Paleolithic, Animals, Humans, 0601 history and archaeology, Ecology, Evolution, Behavior and Systematics, Neanderthals, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, 060102 archaeology, Thermoluminescence dating, Radiometric Dating, Bayes Theorem, 06 humanities and the arts, Archaeology, Caves, Anthropology, Upper Paleolithic, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Chronology
Abstract: International audience; Ghar-e Boof is a Paleolithic cave site in Iran well known for its rich early Upper Paleolithic Rostamian assemblages. The site is located on the edge of the Dasht-e Rostam plain in the southern Zagros. Recent excavations by the members of the Tfibingen-Iranian Stone Age Research Project at Ghar-e Boof also recovered well-stratified Middle Paleolithic assemblages. Here, we provide the first detailed luminescence chronology for the Middle and Upper Paleolithic of the site. More generally, our work is the first luminescence chronology for a Middle and Upper Paleolithic site in the Zagros Mountains region in Iran. The luminescence ages for the Upper Paleolithic of Ghar-e Boof agree with published C-14 dates. We applied Bayesian models specifically designed for luminescence dating using the R package 'BayLum' to incorporate the well-established stratigraphic constraints, as well as the published C-14 ages with our optically stimulated luminescence (OSL) ages to improve the precision of the chronological framework. The Bayesian chronology shows a significantly improved precision of the OSL ages in particular for the upper part of the sequence where C-14 ages were available. The Bayesian OSL ages for the Rostamian horizons, archaeologicalhorizon (AH) III (a-b-c), and AH IV, fall in the range of 37-42 ka (68% credible interval [CI]). Moreover, we determined a series of dates between 45 and 81 ka (68% CI) for the Middle Paleolithic strata from AH IVd to AH VI. Our results point to a demographic shift in the populations responsible for the Middle Paleolithic and the Rostamian within three millennia. This major technological change accompanied by the rise of symbolic artifacts such as personal ornaments, may or may not reflect a replacement of Neanderthals by modern humans. While we are confident that the Rostamian was made by modern humans, available information does not allow us to be sure who made the local Middle Paleolithic.
Published: 2021
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28. Evolution of the distribution area of the Mediterranean Nigella damascena and a likely multiple molecular origin of its perianth dimorphism

Author: Andreas G. Heiss, Natalia Conde E Silva, Léa Chazalviel, Pierre Galipot, Domenica Manicacci, Pierre-Emmanuel Du Pasquier, Catherine Damerval, Martine Le Guilloux, Yves Deveaux, Florian Jabbour, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université de Neuchâtel (UNINE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Systematics, Evolution and Biodiversity, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Österreichischen Archäologischen Instituts (ÖAI), and Grant Agency of the Czech Republic
Subjects: 0106 biological sciences, Genotyping, Locus (genetics), Plant Science, Biology, 010603 evolutionary biology, 01 natural sciences, Mediterranean Basin, Botany, Floral dimorphism, Allele, Nigella damascena, Ecology, Evolution, Behavior and Systematics, NdAP3-3, Nectariferous petal, Ecology, fungi, Herbarium collections, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Museum time series, Herbarium, Petal formation, Perianth, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Literature survey, 010606 plant biology & botany
Abstract: International audience; Nigella damascena (Ranunculaceae) is a common Mediterranean species traditionally used as condiment and healing herb. Its perianth dimorphism has been known since 1591. In all modern accessions examined to date, a single allele of the NdAP3-3 gene characterized by a MITE insertion has been found to be responsible for the mutant morph, lacking a corolla. Based on herbarium collections, we aimed at (i) reconstructing the evolution of the worldwide distribution area of both morphs of N. damascena, and (ii) assessing the diversity in the molecular origin of the mutant allele.We compiled a database of more than 3000 collections of N. damascena across four centuries. When possible, specimens were georeferenced, and distribution maps were built for the wild-type and mutant morphs. Additionally, we genotyped the NdAP3-3 locus, based on DNA extracted from herbarium specimens collected from various localities and at different times.We observe a consistently larger and denser distribution area of wild-type plants in Europe and North Africa compared with the mutant morph. The relative proportions of mutant and wild-type morph plants collected in the last couple of centuries are roughly similar. Interestingly in herbarium specimens, NdAP3-3 alleles without a MITE insertion can be found in plants exhibiting the mutant morph.The diachronic study of the distribution area of N. damascena and a literature survey showed that populations exhibiting the mutant phenotype have been present since the end of the 16th century, though not frequently, in the broad Mediterranean Basin. Our genotyping results indicate that the origin of the mutant morph may be multiple and suggest that the NdAP3-3 allele with the MITE insertion typically found in all modern accessions to date, is only a sample of the variability susceptible to disrupt petal formation and development in Nigella damascena.
Published: 2021
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29. Protein Farnesylation Takes Part in Arabidopsis Seed Development

Author: Vergès, Valentin, Dutilleul, Christelle, Godin, Béatrice, Collet, Boris, Lecureuil, Alain, Rajjou, Loïc, Guimaraes, Cyrille, Pinault, Michelle, Chevalier, Stéphane, Giglioli-Guivarc’h, Nathalie, Eric, Ducos, Biomolécules et biotechnologies végétales (BBV EA 2106), Université de Tours, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nutrition, croissance et cancer (U 1069) (N2C), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Tours, Ministère de l'Enseignement, de la Recherche et de l'Innovation, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Université de Tours (UT), and Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: pollination, ERA1, protein farnesylation, [SDV]Life Sciences [q-bio], food and beverages, gynoecium, lcsh:SB1-1110, Plant Science, fatty acid, lcsh:Plant culture, plant reproduction, Original Research
Abstract: International audience; Protein farnesylation is a post-translational modification regulated by the ERA1 (Enhanced Response to ABA 1) gene encoding the β-subunit of the protein farnesyltransferase in Arabidopsis. The era1 mutants have been described for over two decades and exhibit severe pleiotropic phenotypes, affecting vegetative and flower development. We further investigated the development and quality of era1 seeds. While the era1 ovary contains numerous ovules, the plant produces fewer seeds but larger and heavier, with higher protein contents and a modified fatty acid distribution. Furthermore, era1 pollen grains show lower germination rates and, at flower opening, the pistils are immature and the ovules require one additional day to complete the embryo sac. Hand pollinated flowers confirmed that pollination is a major obstacle to era1 seed phenotypes, and a near wild-type seed morphology was thus restored. Still, era1 seeds conserved peculiar storage protein contents and altered fatty acid distributions. The multiplicity of era1 phenotypes reflects the diversity of proteins targeted by the farnesyltransferase. Our work highlights the involvement of protein farnesylation in seed development and in the control of traits of agronomic interest.
Published: 2021
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30. Plant nitrate supply regulates Erwinia amylovora virulence gene expression in Arabidopsis

Author: Farjad, Mahsa, Clément, Gilles, Launay, Alban, Jeridi, Roua, Jolivet, Sylvie, Citerne, Sylvie, Rigault, Martine, Soulie, Marie‐Christine, Dinant, Sylvie, Fagard, Mathilde, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Carthage - University of Carthage, Sorbonne Université - UFR Sciences de la vie (UFR 927 ), Sorbonne Université (SU), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: defence, Nitrates, nonhost, salicylic acid, fungi, jasmonic acid, Arabidopsis, food and beverages, Cyclopentanes, Gene Expression Regulation, Bacterial, Original Articles, phytopathogenic bacteria, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, nitrogen, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, virulence, Bacterial Proteins, multistress, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Erwinia amylovora, Original Article, Oxylipins, Plant Diseases
Abstract: We showed previously that nitrogen (N) limitation decreases Arabidopsis resistance to Erwinia amylovora (Ea). We show that decreased resistance to bacteria in low N is correlated with lower apoplastic reactive oxygen species (ROS) accumulation and lower jasmonic acid (JA) pathway expression. Consistently, pretreatment with methyl jasmonate (Me‐JA) increased the resistance of plants grown under low N. In parallel, we show that in planta titres of a nonvirulent type III secretion system (T3SS)‐deficient Ea mutant were lower than those of wildtype Ea in low N, as expected, but surprisingly not in high N. This lack of difference in high N was consistent with the low expression of the T3SS‐encoding hrp virulence genes by wildtype Ea in plants grown in high N compared to plants grown in low N. This suggests that expressing its virulence factors in planta could be a major limiting factor for Ea in the nonhost Arabidopsis. To test this hypothesis, we preincubated Ea in an inducing medium that triggers expression of hrp genes in vitro, prior to inoculation. This preincubation strongly enhanced Ea titres in planta, independently of the plant N status, and was correlated to a significant repression of JA‐dependent genes. Finally, we identify two clusters of metabolites associated with resistance or with susceptibility to Ea. Altogether, our data showed that high susceptibility of Arabidopsis to Ea, under low N or following preincubation in hrp‐inducing medium, is correlated with high expression of the Ea hrp genes in planta and low expression of the JA signalling pathway, and is correlated with the accumulation of specific metabolites., Under low nitrate, infection of Arabidopsis thaliana plants with the phytopathogenic bacterium Erwinia amylovora leads to reduced nonhost resistance and increased virulence gene expression.
Published: 2021
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31. DEFECTIVE EMBRYO AND MERISTEMS genes are required for cell division and gamete viability in Arabidopsis

Author: Bernard J. Carroll, Filipe Borges, John L. Bowman, Christopher W. G. Mann, Christopher A. Brosnan, Venkatesan Sundaresan, Thierry G. A. Lonhienne, Chin Hong Lee, Bostjan Kobe, Nial R. Gursanscky, Quy A. Ngo, Nathaniel P. Hawker, Raphael Mercier, Laurence Cromer, Christelle Taochy, Louisa Matthew, Peer M. Schenk, Jonathan R. Peters, Pawlowski, Wojciech P, University of Queensland [Brisbane], University of California [Davis] (UC Davis), University of California, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for Plant Breeding Research (MPIPZ), Monash University [Clayton], DP150104048, DP0559710, DP160100892, FL180100109, and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, Cancer Research, Fruit and Seed Anatomy, Cell division, Messenger, Arabidopsis, Gene Dosage, Plant Science, QH426-470, Genetically Modified Plants, 01 natural sciences, Essential, Animal Cells, Gene Expression Regulation, Plant, 2.1 Biological and endogenous factors, Cell Cycle and Cell Division, Transgenes, Aetiology, Ovule, Flowering Plants, Genetics (clinical), 2. Zero hunger, 0303 health sciences, Genes, Essential, biology, Chromosome Biology, Plant Anatomy, Genetically Modified Organisms, Eukaryota, RNA-Binding Proteins, food and beverages, Embryo, Plants, Cell biology, Meiosis, medicine.anatomical_structure, Experimental Organism Systems, Cell Processes, Organ Specificity, Multigene Family, [SDE]Environmental Sciences, Seeds, Pollen, Engineering and Technology, Gamete, Cellular Types, Genetic Engineering, Cell Division, Research Article, Biotechnology, Evolution, Cell Survival, 1.1 Normal biological development and functioning, Arabidopsis Thaliana, Bioengineering, Brassica, Research and Analysis Methods, Genes, Plant, Ovules, Evolution, Molecular, 03 medical and health sciences, Model Organisms, Underpinning research, Plant and Algal Models, Genetics, medicine, RNA, Messenger, Molecular Biology, Alleles, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Arabidopsis Proteins, Contraception/Reproduction, Meiosis II, Genetic Complementation Test, Organisms, Molecular, Biology and Life Sciences, Plant, Cell Biology, Meristem, biology.organism_classification, Sperm, Germ Cells, ran GTP-Binding Protein, Gene Expression Regulation, Genes, Animal Studies, RNA, Plant Biotechnology, Generic health relevance, Developmental Biology, 010606 plant biology & botany
Abstract: The DEFECTIVE EMBRYO AND MERISTEMS 1 (DEM1) gene encodes a protein of unknown biochemical function required for meristem formation and seedling development in tomato, but it was unclear whether DEM1’s primary role was in cell division or alternatively, in defining the identity of meristematic cells. Genome sequence analysis indicates that flowering plants possess at least two DEM genes. Arabidopsis has two DEM genes, DEM1 and DEM2, which we show are expressed in developing embryos and meristems in a punctate pattern that is typical of genes involved in cell division. Homozygous dem1 dem2 double mutants were not recovered, and plants carrying a single functional DEM1 allele and no functional copies of DEM2, i.e. DEM1/dem1 dem2/dem2 plants, exhibit normal development through to the time of flowering but during male reproductive development, chromosomes fail to align on the metaphase plate at meiosis II and result in abnormal numbers of daughter cells following meiosis. Additionally, these plants show defects in both pollen and embryo sac development, and produce defective male and female gametes. In contrast, dem1/dem1 DEM2/dem2 plants showed normal levels of fertility, indicating that DEM2 plays a more important role than DEM1 in gamete viability. The increased importance of DEM2 in gamete viability correlated with higher mRNA levels of DEM2 compared to DEM1 in most tissues examined and particularly in the vegetative shoot apex, developing siliques, pollen and sperm. We also demonstrate that gamete viability depends not only on the number of functional DEM alleles inherited following meiosis, but also on the number of functional DEM alleles in the parent plant that undergoes meiosis. Furthermore, DEM1 interacts with RAS-RELATED NUCLEAR PROTEIN 1 (RAN1) in yeast two-hybrid and pull-down binding assays, and we show that fluorescent proteins fused to DEM1 and RAN1 co-localize transiently during male meiosis and pollen development. In eukaryotes, RAN is a highly conserved GTPase that plays key roles in cell cycle progression, spindle assembly during cell division, reformation of the nuclear envelope following cell division, and nucleocytoplasmic transport. Our results demonstrate that DEM proteins play an essential role in cell division in plants, most likely through an interaction with RAN1., Author summary Up to half of the genes predicted from genome projects lack a known biological and biochemical function. Many of these genes are likely to play essential roles but it is difficult to reveal their function because minor changes in the genetic sequence can result in lethality and genetic redundancy can obscure analysis. Genome projects predict that flowering plants have at least two DEM genes that encode a protein of unknown cellular and biochemical function. In this paper, we use multiple combinations of dem mutants in Arabidopsis to show that DEM genes are essential for cell division and gamete viability. Interestingly, gamete viability depends not only on the number of functional copies of DEM genes in the gametes, but also on the number of functional copies of DEM genes in the parent plant that produces the gametes. We also show that DEM proteins interact with RAN, a highly conserved protein that controls cell division in all eukaryotic organisms.
Published: 2021
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32. The Seed Development Factors TT2 and MYB5 Regulate Heat Stress Response in Arabidopsis

Author: Jacob, Pierre, Brisou, Gwilherm, Dalmais, Marion, Thévenin, Johanne, van der Wal, Froukje, Latrasse, David, Suresh Devani, Ravi, Benhamed, Moussa, Dubreucq, Bertrand, Boualem, Adnane, Lepiniec, Loic, Immink, Richard G. H., Hirt, Heribert, Bendahmane, Abdelhafid, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen University and Research [Wageningen] (WUR), King Abdullah University of Science and Technology (KAUST), University of Vienna [Vienna], Gautier Semences SA, ANRT (CIFR2012/1125), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, Arabidopsis Proteins, Arabidopsis, HSFA2, Environmental stress, QH426-470, TT2/ MYB5-MBW complex, Article, DNA-Binding Proteins, Heat Shock Transcription Factors, Gene Expression Regulation, Plant, Loss of Function Mutation, Seeds, Genetics, Site II element, Laboratorium voor Moleculaire Biologie, Laboratory of Molecular Biology, BIOS Plant Development Systems, Seed development, Transcriptome, Heat-Shock Response
Abstract: HEAT SHOCK FACTOR A2 (HSFA2) is a regulator of multiple environmental stress responses required for stress acclimation. We analyzed HSFA2 co-regulated genes and identified 43 genes strongly co-regulated with HSFA2 during multiple stresses. Motif enrichment analysis revealed an over-representation of the site II element (SIIE) in the promoters of these genes. In a yeast 1-hybrid screen with the SIIE, we identified the closely related R2R3-MYB transcription factors TT2 and MYB5. We found overexpression of MYB5 or TT2 rendered plants heat stress tolerant. In contrast, tt2, myb5, and tt2/myb5 loss of function mutants showed heat stress hypersensitivity. Transient expression assays confirmed that MYB5 and TT2 can regulate the HSFA2 promoter together with the other members of the MBW complex, TT8 and TRANSPARENT TESTA GLABRA 1 (TTG1) and that the SIIE was involved in this regulation. Transcriptomic analysis revealed that TT2/MYB5 target promoters were enriched in SIIE. Overall, we report a new function of TT2 and MYB5 in stress resistance and a role in SIIE-mediated HSFA2 regulation.
Published: 2021
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33. Variability of stem solidness among miscanthus genotypes and its role on mechanical properties of polypropylene composites

Author: Maryse Brancourt‐Hulmel, Raphaël Raverdy, Jordi Girones, Stéphanie Arnoult, Emilie Mignot, Yves Griveaux, Patrick Navard, Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Centre de Mise en Forme des Matériaux (CEMEF), Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Unité Expérimentale Grandes Cultures Innovation Environnement - Picardie (GCIE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and ANR-11-BTBR-0006,BFF,Biomasse pour le futur(2011)
Subjects: specific weight, biomass, food and beverages, TJ807-830, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Energy industries. Energy policy. Fuel trade, Miscanthus sinensis, composites, Renewable energy sources, cell-wall, genotypes, [SPI.MECA.MEMA]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Mechanics of materials [physics.class-ph], cell wall, HD9502-9502.5
Abstract: International audience; Miscanthus (Miscanthus Andersson) is a perennial grass that is attracting growing interest from the biomaterial industry. Our aim was to compare miscanthus genotypes varying in stem solidness, a measure of degree to which pith fills cavity between the outer walls of the stem, and analyze whether this trait influences the mechanical properties of polypropylene composites reinforced with miscanthus particles. Six contrasting genotypes were chosen from a Miscanthus sinensis population to determine morphological variables, stem solidness, and mechanical properties of polypropylene composites including 30% of milled miscanthus particles of two sizes of 100 < × < 200 μm and 200 < × < 300 μm. Although aboveground biomass of miscanthus was closely related to the aboveground volume of the plant, namely stand volume, a few genotypes showed contrasting aboveground biomass production for similar stand volumes. This generated contrasting ratio between aboveground biomass and stand volume, namely plant-specific weights, for similar plant volumes. A principal component analysis showed that fully pith-filled stems, namely solid stems, were explained by a large stand volume and plant-specific weights as well as small stem cross-sections. Genotypes showing partially filled stems were taller with larger stem cross-sections but smaller plant-specific weights. They revealed high lignin and p-coumaric acid contents. Compared to neat-polypropylene, Young's modulus increased significantly by 139% and 134% and tensile strength by 39% and 36% for genotypes with partially filled stems compared to genotypes with fully pith-filled stems, respectively. This difference in reinforcing capacity was similar to that of two particle sizes (139% and 134% for Young's modulus, 41% and 34% for tensile strength, respectively). A good tensile strength was obtained with large cross-stem section, plant height and lignin and p-coumaric acid contents. It decreased with plant-specific weight, hemicellulose and ferulic acid contents. Wider morphological variations in other progenies or Miscanthus species should be explored further using the techniques reported here.
Published: 2021
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34. The Physcomitrium (Physcomitrella) patens PpKAI2L receptors for strigolactones and related compounds function via MAX2-dependent and independent pathways

Author: Ambre Guillory, Catherine Rameau, Beate Hoffmann, Sandrine Bonhomme, Jean-Bernard Pouvreau, François-Didier Boyer, Mauricio Lopez-Obando, David Cornu, Philippe Delavault, Alexandre de Saint Germain, Philippe Le Bris, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Swedish University of Agricultural Sciences (SLU), Vedas Recherche et Innovation (Vedas CII), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-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), Laboratoire de biologie et pathologie végétales (LBPV), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN), Infrastructures en Biologie Santeet Agronomie grant to SICAPS platform of the Institute for Integrative Biology of the Cell, AgreenSkills award from the European Union in the framework of the MarieCurie FP7 COFUND People Programme, ANR-12-BSV6-0004,StrigoPath,Voies de signalisation des strigolactones (et/ou de dérivés) chez les plantes terrestres(2012), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and ANR-11-LABX-0039,CHARMMMAT,CHimie des ARchitectures MoléculairesMultifonctionnelles et des MATériaux(2011)
Subjects: 0106 biological sciences, Physcomitrella, Mutant, Strigolactone, Plant Science, Physcomitrella patens, 01 natural sciences, 03 medical and health sciences, Lactones, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Receptor, Gene, Research Articles, 030304 developmental biology, 0303 health sciences, biology, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Bryopsida, Karrikin, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Biochemistry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Heterocyclic Compounds, 3-Ring, 010606 plant biology & botany
Abstract: In angiosperms, the α/β hydrolase DWARF14 (D14), along with the F-box protein MORE AXILLARY GROWTH2 (MAX2), perceives strigolactones (SL) to regulate developmental processes. The key SL biosynthetic enzyme CAROTENOID CLEAVAGE DIOXYGENASE8 (CCD8) is present in the moss Physcomitrium patens, and PpCCD8-derived compounds regulate moss extension. The PpMAX2 homolog is not involved in the SL response, but 13 PpKAI2LIKE (PpKAI2L) genes homologous to the D14 ancestral paralog KARRIKIN INSENSITIVE2 (KAI2) encode candidate SL receptors. In Arabidopsis thaliana, AtKAI2 perceives karrikins and the elusive endogenous KAI2-Ligand (KL). Here, germination assays of the parasitic plant Phelipanche ramosa suggested that PpCCD8-derived compounds are likely noncanonical SLs. (+)-GR24 SL analog is a good mimic for PpCCD8-derived compounds in P. patens, while the effects of its enantiomer (−)-GR24, a KL mimic in angiosperms, are minimal. Interaction and binding assays of seven PpKAI2L proteins pointed to the stereoselectivity toward (−)-GR24 for a single clade of PpKAI2L (eu-KAI2). Enzyme assays highlighted the peculiar behavior of PpKAI2L-H. Phenotypic characterization of Ppkai2l mutants showed that eu-KAI2 genes are not involved in the perception of PpCCD8-derived compounds but act in a PpMAX2-dependent pathway. In contrast, mutations in PpKAI2L-G, and -J genes abolished the response to the (+)-GR24 enantiomer, suggesting that PpKAI2L-G, and -J proteins are receptors for moss SLs.
Published: 2021
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35. Luminescent lanthanide nanoparticle-based imaging enables ultra-sensitive, quantitative and multiplexed in vitro lateral flow immunoassays

Author: C. Féraudet Tarisse, Stéphanie Simon, Cedric Bouzigues, Thierry Gacoin, F. Mousseau, Antigoni Alexandrou, Alexandrou, Antigoni, Equipements d'excellence - Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse) - - MORPHOSCOPE 22011 - ANR-11-EQPX-0029 - EQPX - VALID, Développment d'une infrastructure française distribuée coordonnée - - France-BioImaging2010 - ANR-10-INBS-0004 - INBS - VALID, Saclay Plant Sciences - - SPS2010 - ANR-10-LABX-0040 - LABX - VALID, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, Laboratoire de physique de la matière condensée (LPMC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: Lanthanide, chemistry.chemical_classification, Analyte, Materials science, Biomolecule, [SDV]Life Sciences [q-bio], Nanoparticle, Nanotechnology, Multiplexing, [SDV] Life Sciences [q-bio], chemistry, General Materials Science, Sensitivity (control systems), Luminescence, Ultra sensitive
Abstract: International audience; Lateral Flow Assays (LFAs) have been extensively used on-site to rapidly detect analytes, possibly in complex media. However, standard gold nanoparticle-based LFAs lack sensitivity and cannot provide quantitative measurements with high accuracy. To overcome these limitations, we image lanthanidedoped nanoparticles (YVO 4 :Eu 40%) as new luminescent LFA probes, using a homemade reader coupled to a smartphone and propose an original image analysis allowing strip quantification regardless of the shape of the test band signal. This method is demonstrated for the detection of staphylococcal enterotoxins SEA, SEG, SEH, and SEI. A systematic comparison to state-of-the-art gold nanoparticle-based LFA revealed an analytical sensitivity enhancement of at least one order of magnitude. We furthermore provided measurements of absolute toxin concentration over two orders of magnitude and demonstrated simultaneous quantitative detection of multiple toxins with unaltered sensitivity. In particular, we reached concentrations 100 times lower than the ones reported in the literature for on-site multiplexed LFA targeting enterotoxins. Altogether, these results highlight that our luminescent nanoparticle-based method provides a powerful and versatile on-site framework to detect multiple biomolecules with sensitivity approaching that obtained by ELISA. This paves the way to a change of paradigm in the field of analytical immunoassays by providing fast in situ quantitative high sensitivity detection of biomarkers or pathogens.
Published: 2021
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36. Cellular transduction of mechanical oscillations in plants by the plasma-membrane mechanosensitive channel MSL10

Author: Nathalie Leblanc-Fournier, Emmanuel de Langre, Jean-Marie Frachisse, Bruno Moulia, Tiffanie Girault, Marjorie Guichard, Sébastien Thomine, Daniel Tran, Jean-Marc Allain, Agroscope, 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), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'hydrodynamique (LadHyX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Mathematical and Mechanical Modeling with Data Interaction in Simulations for Medicine (M3DISIM), Laboratoire de mécanique des solides (LMS), École polytechnique (X)-Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), ANR-09-BLAN-0245,Senzo(2009), ANR-11-BSV7-0010,CAROLS,Canaux ioniques et espèces actives de l'oxygène dans le poil absorbant de légumineuse: rôle dans la symbiose avec Rhizobium(2011), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), École polytechnique (X)-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)-École polytechnique (X)-MINES ParisTech - École nationale supérieure des mines de Paris
Subjects: 0106 biological sciences, Materials science, Arabidopsis, 01 natural sciences, Mechanotransduction, Cellular, Ion Channels, 03 medical and health sciences, Passive movements, vibration modes, wind, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Mechanotransduction, 030304 developmental biology, mechanotransduction, mechanosensitive channel, 0303 health sciences, Multidisciplinary, Ion Transport, Oscillation, Arabidopsis Proteins, atmsl10 wind, Cell Membrane, Membrane Proteins, Plasma, oscillation, Biological Sciences, Plants, Genetically Modified, Membrane, frequency, ion-channel, Biophysics, Mechanosensitive channels, Transduction (physiology), Mechanoreceptors, 010606 plant biology & botany, Communication channel, Signal Transduction
Abstract: International audience; Plants spend most of their life oscillating around 1–3 Hz due to the effect of the wind. Therefore, stems and foliage experience repetitive mechanical stresses through these passive movements. However, the mechanism of the cellular perception and transduction of such recurring mechanical signals remains an open question. Multimeric protein complexes forming mechanosensitive (MS) channels embedded in the membrane provide an efficient system to rapidly convert mechanical tension into an electrical signal. So far, studies have mostly focused on nonoscillatory stretching of these channels. Here, we show that the plasma-membrane MS channel MscS-LIKE 10 (MSL10) from the model plant Arabidopsis thaliana responds to pulsed membrane stretching with rapid activation and relaxation kinetics in the range of 1 s. Under sinusoidal membrane stretching MSL10 presents a greater activity than under static stimulation. We observed this amplification mostly in the range of 0.3–3 Hz. Above these frequencies the channel activity is very close to that under static conditions. With a localization in aerial organs naturally submitted to wind-driven oscillations, our results suggest that the MS channel MSL10, and by extension MS channels sharing similar properties, represents a molecular component allowing the perception of oscillatory mechanical stimulations by plants.
Published: 2020
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37. The nucellus: between cell elimination and sugar transport

Author: Olivier Coen, Christine Péchoux, Sophie Jasinski, Rozenn Le Hir, Jing Lu, Enrico Magnani, Dennys-Marcela Gómez-Páez, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Doctorale Sciences du Végétal : du Gène à l'Ecosystème, Université Paris-Sud - Paris 11 (UP11), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, Monosaccharide Transport Proteins, Physiology, [SDV]Life Sciences [q-bio], Cell, Arabidopsis, Plant Science, 01 natural sciences, Endosperm, 03 medical and health sciences, Magnoliopsida, Human fertilization, Botany, Genetics, medicine, Sugar, Ovule, Research Articles, 030304 developmental biology, 0303 health sciences, biology, Arabidopsis Proteins, Chalaza, food and beverages, Biological Transport, Starch, biology.organism_classification, medicine.anatomical_structure, Mutation, Seeds, Sink (computing), Sugars, 010606 plant biology & botany
Abstract: The architecture of the seed is shaped by the processes of tissue partitioning, which determines the volume ratio of maternal and zygotic tissues, and nutrient partitioning, which regulates nutrient distribution among tissues. In angiosperms, early seed development is characterized by antagonistic development of the nucellus maternal tissue and the endosperm fertilization product to become the main sugar sink. This process marked the evolution of angiosperms and outlines the most ancient seed architectures. In Arabidopsis, the endosperm partially eliminates the nucellus and imports sugars from the seed coat. Here, we show that the nucellus is symplasmically connected to the chalaza, the seed nutrient unloading zone, and works as both a sugar sink and source alongside the seed coat. After fertilization, the transient nucellus accumulates starch early on and releases it in the apoplasmic space during its elimination. By contrast, the persistent nucellus exports sugars toward the endosperm through the SWEET4 hexose facilitator. Finally, we analyzed sugar metabolism and transport in the transparent testa 16 mutant, which fails to undergo nucellus cell elimination, which shed light on the coordination between tissue and nutrient partitioning. Overall, this study identifies a path of sugar transport in the Arabidopsis seed and describes a link between sugar redistribution and the nucellus cell-elimination program.
Published: 2020
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38. Fast tree aggregation for consensus hierarchical clustering

Author: Florence Jaffrezic, Julien Chiquet, Audrey Hulot, Guillem Rigaill, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, Infection et inflammation (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ATIGE grant from Genopole, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Rigaill, Guillem, and Saclay Plant Sciences - - SPS2010 - ANR-10-LABX-0040 - LABX - VALID
Subjects: Proteomics, Computer science, Omics, computer.software_genre, lcsh:Computer applications to medicine. Medical informatics, Biochemistry, Unsupervised learning, Hierarchical clustering, 03 medical and health sciences, 0302 clinical medicine, Structural Biology, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Consensus clustering, Cluster (physics), Cluster Analysis, Humans, Cluster analysis, Molecular Biology, lcsh:QH301-705.5, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], 030304 developmental biology, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 0303 health sciences, Applied Mathematics, Methodology Article, Gene Expression Profiling, Partition (database), Computer Science Applications, Data set, Tree structure, lcsh:Biology (General), lcsh:R858-859.7, Data integration, Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, 030217 neurology & neurosurgery, Algorithms
Abstract: Background In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several research areas. For instance in omics analysis, dozen of clustering methods have been developed in the past decade. When a single source of data is at play, hierarchical clustering (HC) is extremely popular, as a tree structure is highly interpretable and arguably more informative than just a partition of the data. However, applying blindly HC to multiple sources of data raises computational and interpretation issues. Results We propose mergeTrees, a method that aggregates a set of trees with the same leaves to create a consensus tree. In our consensus tree, a cluster at height h contains the individuals that are in the same cluster for all the trees at height h. The method is exact and proven to be $\mathcal {O}(nq\log (n))$O(nqlog(n)), n being the individuals and q being the number of trees to aggregate. Our implementation is extremely effective on simulations, allowing us to process many large trees at a time. We also rely on mergeTrees to perform the cluster analysis of two real -omics data sets, introducing a spectral variant as an efficient and robust by-product. Conclusions Our tree aggregation method can be used in conjunction with hierarchical clustering to perform efficient cluster analysis. This approach was found to be robust to the absence of clustering information in some of the data sets as well as an increased variability within true clusters. The method is implemented in / and available as an package named , which makes it easy to integrate in existing or new pipelines in several research areas.
Published: 2020
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39. DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models

Author: Ilana Lambert, Marie-Laure Martin-Magniette, Stefano Colella, Christine Paysant-Le Roux, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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 des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-16-CE20-0009,PSYCHE,Réponses systémiques des plantes aux changements environnementaux(2016), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay
Subjects: 0106 biological sciences, 0301 basic medicine, Generalized linear model, Process (engineering), Computer science, media_common.quotation_subject, RNA-Seq, Plant Science, lcsh:Plant culture, computer.software_genre, 01 natural sciences, 03 medical and health sciences, Differential expression, Genetics, Quality (business), lcsh:SB1-1110, Differential (infinitesimal), lcsh:QH301-705.5, Analysis workspace, media_common, Contrast (statistics), Statistical model, Co-expression, 030104 developmental biology, lcsh:Biology (General), Benchmark (computing), Data mining, Contrasts, RNA-seq, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software, 010606 plant biology & botany, Biotechnology
Abstract: Background RNAseq is nowadays the method of choice for transcriptome analysis. In the last decades, a high number of statistical methods, and associated bioinformatics tools, for RNAseq analysis were developed. More recently, statistical studies realised neutral comparison studies using benchmark datasets, shedding light on the most appropriate approaches for RNAseq data analysis. Results DiCoExpress is a script-based tool implemented in R that includes methods chosen based on their performance in neutral comparisons studies. DiCoExpress uses pre-existing R packages including FactoMineR, edgeR and coseq, to perform quality control, differential, and co-expression analysis of RNAseq data. Users can perform the full analysis, providing a mapped read expression data file and a file containing the information on the experimental design. Following the quality control step, the user can move on to the differential expression analysis performed using generalized linear models thanks to the automated contrast writing function. A co-expression analysis is implemented using the coseq package. Lists of differentially expressed genes and identified co-expression clusters are automatically analyzed for enrichment of annotations provided by the user. We used DiCoExpress to analyze a publicly available RNAseq dataset on the transcriptional response of Brassica napus L. to silicon treatment in plant roots and mature leaves. This dataset, including two biological factors and three replicates for each condition, allowed us to demonstrate in a tutorial all the features of DiCoExpress. Conclusions DiCoExpress is an R script-based tool allowing users to perform a full RNAseq analysis from quality controls to co-expression analysis through differential analysis based on contrasts inside generalized linear models. DiCoExpress focuses on the statistical modelling of gene expression according to the experimental design and facilitates the data analysis leading the biological interpretation of the results.
Published: 2020
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40. Dynamic control of the high-affinity iron uptake complex in root epidermal cells

Author: Guillaume Dubeaux, Julien Spielmann, Enric Zelazny, Grégory Vert, Amanda Martín-Barranco, Approches intégratives du Transport Ionique (MINION), 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), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of California [San Diego] (UC San Diego), University of California, Signalisation Cellulaire et Ubiquitination, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Département Plateforme (PF I2BC), Marie Skłodowska-Curie Actions (grant no. PCIG–GA–2012–334021), European Molecular Biology Organization long-term post-doctoral fellowship (grant no. ALTF334–2018), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-18-CE20-0008,NUTRIR,Protéines HIR des microdomaines membranaires : contrôle de la machinerie d'acquisition du fer et nouvelles fonctions chez Arabidopsis(2018), ANR-13-JSV2-0004,Ubi63,Exploration du role de la polyubiquitination K63 en utilisant les plantes comme modèle(2013), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of California (UC), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0106 biological sciences, Genotype, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Reductase, Endocytosis, Plant Roots, 01 natural sciences, Interactome, Metal, iron, Ubiquitin, Genetics, endocytosis, News and Views, biology, Arabidopsis Proteins, Chemistry, phosphorylation, Genetic Variation, Biological Transport, Transporter, biology.organism_classification, Epidermal Cells, visual_art, transport, biology.protein, visual_art.visual_art_medium, Biophysics, Phosphorylation, IRT1, 010606 plant biology & botany
Abstract: International audience; In plants, iron uptake from the soil is tightly regulated to ensure optimal growth and development. Iron absorption in Arabidopsis root epidermal cells requires the IRT1 transporter that also allows the entry of certain non-iron metals, such as Zn, Mn, and Co. Recent work demonstrated that IRT1 endocytosis and degradation are controlled by IRT1 non-iron metal substrates in an ubiquitin-dependent manner. To better understand how metal uptake is regulated, we identified IRT1-interacting proteins in Arabidopsis roots by mass spectrometry and established an interactome of IRT1. Interestingly, the AHA2 proton pump and the FRO2 reductase, both of which work in concert with IRT1 in the acidification-reduction-transport strategy of iron uptake, were part of this interactome. We confirmed that IRT1, FRO2, and AHA2 associate through co-immunopurification and split-ubiquitin analyses, and uncovered that they form tripartite direct interactions. We characterized the dynamics of the iron uptake complex and showed that FRO2 and AHA2 ubiquitination is independent of the non-iron metal substrates transported by IRT1. In addition, FRO2 and AHA2 are not largely endocytosed in response to non-iron metal excess, unlike IRT1. Indeed, we provide evidence that the phosphorylation of IRT1 in response to high levels of non-iron metals likely triggers dissociation of the complex. Overall, we propose that a dedicated iron-acquisition protein complex exists at the cell surface of Arabidopsis root epidermal cells to optimize iron uptake.
Published: 2020
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41. EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome

Author: Gonzalez‐Fuente, Manuel, Carrere, Sébastien, Monachello, Dario, Marsella, Benjamin, Cazalé, Anne‐Claire, Zischek, Claudine, Mitra, Raka, RÉZÉ, NATHALIE, Cottret, Ludovic, Mukhtar, M. Shahid, Lurin, Claire, Noël, Laurent D., Peeters, Nemo, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Alabama at Birmingham [ Birmingham] (UAB), Carleton College, National Science Foundation (IOS-1557796) to M.S.M, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Xanthomonas, Proteome, Arabidopsis Proteins, Virulence Factors, Arabidopsis, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Original Articles, Ralstonia, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Xanthomonas campestris, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Bacterial Proteins, Host-Pathogen Interactions, network, Original Article, Protein Interaction Maps, interactomics, Databases, Chemical, Software, database, Disease Resistance, Plant Diseases, effectors
Abstract: Pathogens deploy effector proteins that interact with host proteins to manipulate the host physiology to the pathogen's own benefit. However, effectors can also be recognized by host immune proteins, leading to the activation of defence responses. Effectors are thus essential components in determining the outcome of plant–pathogen interactions. Despite major efforts to decipher effector functions, our current knowledge on effector biology is scattered and often limited. In this study, we conducted two systematic large‐scale yeast two‐hybrid screenings to detect interactions between Arabidopsis thaliana proteins and effectors from two vascular bacterial pathogens: Ralstonia pseudosolanacearum and Xanthomonas campestris. We then constructed an interactomic network focused on Arabidopsis and effector proteins from a wide variety of bacterial, oomycete, fungal, and invertebrate pathogens. This network contains our experimental data and protein–protein interactions from 2,035 peer‐reviewed publications (48,200 Arabidopsis–Arabidopsis and 1,300 Arabidopsis–effector protein interactions). Our results show that effectors from different species interact with both common and specific Arabidopsis interactors, suggesting dual roles as modulators of generic and adaptive host processes. Network analyses revealed that effector interactors, particularly “effector hubs” and bacterial core effector interactors, occupy important positions for network organization, as shown by their larger number of protein interactions and centrality. These interactomic data were incorporated in EffectorK, a new graph‐oriented knowledge database that allows users to navigate the network, search for homology, or find possible paths between host and/or effector proteins. EffectorK is available at www.effectork.org and allows users to submit their own interactomic data., EffectorK (www.effectorK.org) is an open database compiling newly generated and literature‐curated interactomic data from various Arabidopsis pathogen effectors.
Published: 2020
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42. Hypomethylation of the aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala mimics the adaptive transition into the terrestrial morphotype

Author: Julien Genitoni, Alain Delaunay, Solenn Stoeckel, Marie-Pierre Etienne, Luis Lemus, Danièle Vassaux, Dominique Barloy, Sylvie Citerne, David Renault, Stéphane Maury, Écologie et santé des écosystèmes (ESE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche Mathématique de Rennes (IRMAR), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique. Grant Number: PI EFPA 2016, Région Bretagne, RTP3E CNRS, ONEMA, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest
Subjects: 0106 biological sciences, 0301 basic medicine, Physiology, Onagraceae, Introduced species, Plant Science, Biology, 01 natural sciences, Invasive species, 03 medical and health sciences, Genetics, Ecosystem, Epigenetics, Transition (genetics), Ecology, Cell Biology, General Medicine, DNA Methylation, Plants, 15. Life on land, biology.organism_classification, 030104 developmental biology, DNA methylation, Adaptation, Introduced Species, [STAT.ME]Statistics [stat]/Methodology [stat.ME], 010606 plant biology & botany
Abstract: International audience; Ongoing global changes affect ecosystems and open up new opportunities for biological invasion. The ability of invasive species to rapidly adapt to new environments represents a relevant model for studying short‐term adaptation mechanisms. The aquatic invasive plant, Ludwigia grandiflora subsp. hexapetala, is classified as harmful in European rivers. In French wet meadows, this species has shown a rapid transition from aquatic to terrestrial environments with emergence of two distinct morphotypes in 5 years. To understand the heritable mechanisms involved in adjustment to such a new environment, we investigate both genetic and epigenetic as possible sources of flexibility involved in this fast terrestrial transition. We found a low overall genetic differentiation between the two morphotypes arguing against the possibility that terrestrial morphotype emerged from a new adaptive genetic capacity. Artificial hypomethylation was induced on both morphotypes to assess the epigenetic hypothesis. We analyzed global DNA methylation, morphological changes, phytohormones and metabolite profiles of both morphotype responses in both aquatic and terrestrial conditions in shoot and root tissues. Hypomethylation significantly affected morphological variables, phytohormone levels and the amount of some metabolites. The effects of hypomethylation depended on morphotypes, conditions and plant tissues, which highlighted differences among the morphotypes and their plasticity. Using a correlative integrative approach, we showed that hypomethylation of the aquatic morphotype mimicked the characteristics of the terrestrial morphotype. Our data suggest that DNA methylation rather than a new adaptive genetic capacity is playing a key role in L. grandiflora subsp. hexapetala plasticity during its rapid aquatic to terrestrial transition.
Published: 2020
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43. Specialized phenolic compounds in seeds: structures, functions, and regulations

Author: Loïc Lepiniec, François Perreau, Massimiliano Corso, Grégory Mouille, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: 0106 biological sciences, 0301 basic medicine, Plant Science, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, 01 natural sciences, 03 medical and health sciences, Phenols, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Flavonoid regulation, Domestication, 2. Zero hunger, Abiotic component, Flavonoids, business.industry, Biological networks, food and beverages, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], General Medicine, 15. Life on land, Phenylpropanoid landscape, Biotechnology, Specialized metabolites, Metabolic pathway, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, Omic techniques, Seeds, business, Agronomy and Crop Science, Biological network, Metabolic Networks and Pathways, 010606 plant biology & botany
Abstract: International audience; Plants produce a huge diversity of specialized metabolites (SM) throughout their life cycle that play important physiological and ecological functions. SM can protect plants and seeds against diseases, predators, and abiotic stresses, or support their interactions with beneficial or symbiotic organisms. They also have strong impacts on human nutrition and health. Despite this importance, the biosynthesis and biological functions of most of the SM remain elusive and their diversity and/or quantity have been reduced in most crops during domestication. Seeds present a large number of SM that are important for their physiological, agronomic, nutritional or industrial qualities and hence, provide interesting models for both studying biosynthesis and producing large amounts of specialized metabolites. For instance, phenolics are abundant and widely distributed in seeds. More specifically, flavonoid pathway has been instrumental for understanding environmental or developmental regulations of specialized metabolic pathways, at the molecular and cellular levels. Here, we summarize current knowledge on seed phenolics as model, and discuss how recent progresses in omics approaches could help to further characterize their diversity, regulations, and the underlying molecular mechanisms involved.
Published: 2020
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44. Dual lysine and N‐terminal acetyltransferases reveal the complexity underpinning protein acetylation

Author: Julian Seidel, Annika Brünje, Gautier Bernal, Dirk Schwarzer, Iris Finkemeier, Laura K Schyrba, Eric Linster, Thierry Meinnel, Ines Lassowskat, Paula Mulo, Jürgen Eirich, Jens Stephan Mühlenbeck, Minna M. Koskela, Aiste Ivanauskaite, Jean-Baptiste Boyer, Markus Wirtz, Trinh V. Dinh, Carmela Giglione, Willy V. Bienvenut, Vincent A. Jung, Cyril Dian, Rüdiger Hell, 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), Maturation des proteines, destinée cellulaire et thérapeutique (PROMTI), Département Biologie des Génomes (DBG), 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), University of Muenster, Hartmut Hoffmann-Berling International Graduate School, Heidelberg University, Heidelberg Institute of Plant Sciences, Universität Heidelberg [Heidelberg] = Heidelberg University, Interfaculty Institute for biochemistry, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, University of Turku, Plant Proteomics Group, Max Planck Institute for Plant Breeding Research (MPIPZ), Universität Heidelberg [Heidelberg], ANR-13-BSV6-0004,eNergiome,N-terminome des organelles de conversion de l'énergie: Une meilleure comprehension de la maturation des protéines impliquées dans ces organelles(2013), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: Proteomics, Medicine (General), Chloroplasts, [SDV]Life Sciences [q-bio], Lysine, Arabidopsis, Plant Biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], N-Terminal Acetyltransferases, Epigenome, Gene Knockout Techniques, 0302 clinical medicine, Tandem Mass Spectrometry, Gnat, Plastids, Biology (General), plastid, Chromatography, High Pressure Liquid, Phylogeny, Plant Proteins, chemistry.chemical_classification, 0303 health sciences, acetylome, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Applied Mathematics, Acetylation, Articles, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Recombinant Proteins, acetyltransferase, Computational Theory and Mathematics, Biochemistry, co‐ and post‐translational modifications, Acetyltransferase, General Agricultural and Biological Sciences, Genome, Plant, Information Systems, Escherichia, quantitative proteomics, QH301-705.5, Quantitative proteomics, quantitative proteomics Subject Categories Plant Biology, In Vitro Techniques, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, R5-920, Post-translational Modifications & Proteolysis, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plastid, co-and post-translational modifications, 030304 developmental biology, General Immunology and Microbiology, Post-translational Modifications, Proteolysis & Proteomics, Enzyme, chemistry, co- and post-translational modifications, Peptides, 030217 neurology & neurosurgery, Chromatography, Liquid
Abstract: Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N‐α‐acetylation (NTA) and ε‐lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5‐related N‐acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid‐localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities., A novel protein acetyltransferase family localized or associated to plant plastids is identified and characterised. These GCN5‐related N‐acetyltransferases (GNATs) have unique amino acid sequence characteristics and unambiguously possess dual N‐α‐ and ε‐lysine acetylation activities.
Published: 2020
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45. Omics data reveal putative regulators of einkorn grain protein composition under sulfur deficiency

Author: Titouan Bonnot, Victor Hatte, Philippe Leroy, Catherine Ravel, Pierre Martre, Annick Moing, Marie Pailloux, Mireille Dardevet, Emmanuelle Bancel, Yves Gibon, Camille Bénard, Catherine Deborde, Marie-Laure Martin-Magniette, Natalia Falagán, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California [Riverside] (UC Riverside), University of California (UC), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Ministère de l'Enseignement Supérieur et de la Recherche, France AgriMer, French Fund Supporting Plant 46 Breeding (FSOV), ANR-10-BTBR-0003,BREEDWHEAT,Développer de nouvelles variétés de blé pour une agriculture durable(2010), ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), European Project: 613556,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,WHEALBI(2014), University of California [Riverside] (UCR), University of California, Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, and Ecole Nationale Supérieure des Mines de St Etienne-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Triticum monococcum, Physiology, [SDV]Life Sciences [q-bio], Sulfur metabolism, Plant Science, Biology, Einkorn (Triticum monococcum), Composition de la protéine du grain, 01 natural sciences, Nitrogen 69 and sulphur nutrition, Transcriptome, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Gene Expression Regulation, Plant, Genetics, Metabolome, Grain Proteins, Gene, Triticum, Research Articles, Plant Proteins, 2. Zero hunger, Regulation of gene expression, Grain protein composition, Plant physiology, food and beverages, Réseau de régulation, Metabolism, Diploidy, Regulatory networks, Métabolome, Biochemistry, Ploidy, Sulfur, 010606 plant biology & botany
Abstract: International audience; Understanding the molecular mechanisms controlling the accumulation of grain storage proteins in response to nitrogen (N) and sulfur (S) nutrition is essential to improve cereal grain nutritional and functional properties. Here, we studied the grain transcriptome and metabolome responses to postanthesis N and S supply for the diploid wheat einkorn (Triticum monococcum). During grain filling, 848 transcripts and 24 metabolites were differentially accumulated in response to N and S availability. The accumulation of total free amino acids per grain and the expression levels of 241 genes showed significant modifications during most of the grain filling period and were upregulated in response to S deficiency. Among them, 24 transcripts strongly responded to S deficiency and were identified in coexpression network analyses as potential coordinators of the grain response to N and S supply. Sulfate transporters and genes involved in sulfate and Met metabolism were upregulated, suggesting regulation of the pool of free amino acids and of the grain N-to-S ratio. Several genes highlighted in this study might limit the impact of S deficiency on the accumulation of grain storage proteins.Sulfur deficiency in einkorn grain leads to upregulation of genes acting in sulfur transport and metabolism that may coordinate the pool of free amino acids necessary for storage protein synthesis.
Published: 2020
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46. The Arabidopsis lnc RNA ASCO modulates the transcriptome through interaction with splicing factors

Author: Martin Crespi, Jérémie Bazin, Aurélie Christ, Stéphanie Huguet, Michaël Moison, Leandro Exequiel Lucero, Celine Charon, Moussa Benhamed, Natali Romero-Barrios, Federico Ariel, Thomas Blein, Richard Rigo, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), NPCyT (PICT2016-0289and -0007, Argentina), CNRS (Laboratoire International Associé NOCOSYM), the'Laboratoire d’Excellence (LABEX)' Saclay Plant Sciences (SPS, ANR-10-LABX-40), the Ministère Français de l’Enseignement Supérieur et de la Recherche (RR), and the ANR grants (ANR-15-CE20-0002-01 EPISYM and ANR16-CE20-0003-04 SPLISIL), the EPIMMUNITY International project between IPS2, France and KAUST University, Saudi Arabia., ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-15-CE20-0002,EPISYM,Régulations épigénétiques dans le développement de nodules symbiotiques racinaires chez les légumineuses(2015), ANPCyTPICT 2016-0289-0007CNRS (Laboratoire International Associe NOCOSYM) 'Laboratoire d'Excellence (LABEX)' Saclay Plant Sciences (SPS) ANR-10-LABX-40Ministere Francais de l'Enseignement Superieur et de la Recherche French National Research Agency (ANR)ANR-15-CE20-0002-01 EPISYMANR 16-CE20-0003-04 SPLISILIPS2, France KAUST University, Saudi Arabia LabEx Saclay Plant Sciences-SPS ANR-10-LABX-0040-SPS, and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: SmD1b, Spliceosome, FLAGELLIN, Arabidopsis, CORE SPLICING FACTORS, Computational biology, Biology, core splicing factors, Biochemistry, flagellin, Transcriptome, purl.org/becyt/ford/1 [https], 03 medical and health sciences, SMD1B, 0302 clinical medicine, PRP8A, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, long noncoding RNA, purl.org/becyt/ford/1.6 [https], Molecular Biology, Gene, 030304 developmental biology, Ribonucleoprotein, 2. Zero hunger, 0303 health sciences, Arabidopsis Proteins, Alternative splicing, LONG NONCODING RNA, Articles, biology.organism_classification, Long non-coding RNA, Alternative Splicing, PRP8a, RNA splicing, RNA, Long Noncoding, RNA Splicing Factors, 030217 neurology & neurosurgery
Abstract: Alternative splicing (AS) is a major source of transcriptome diversity. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through different molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRs interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyze the effect of the knock-down and overexpression of ASCO at the genome-wide level and find a large number of deregulated and differentially spliced genes related to flagellin responses and biotic stress. In agreement, ASCO-silenced plants are more sensitive to flagellin. However, only a minor subset of deregulated genes overlaps with the AS defects of the nsra/b double mutant, suggesting an alternative way of action for ASCO. Using biotin-labeled oligonucleotides for RNA-mediated ribonucleoprotein purification, we show that ASCO binds to the highly conserved spliceosome component PRP8a. ASCO overaccumulation impairs the recognition of specific flagellin-related transcripts by PRP8a. We further show that ASCO also binds to another spliceosome component, SmD1b, indicating that it interacts with multiple splicing factors. Hence, lncRNAs may integrate a dynamic network including spliceosome core proteins, to modulate transcriptome reprogramming in eukaryotes. Fil: Rigo, Richard. Centre National de la Recherche Scientifique; Francia Fil: Bazin, Jérémie. Centre National de la Recherche Scientifique; Francia Fil: Romero Barrios, Natali. Centre National de la Recherche Scientifique; Francia Fil: Moison, Michael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Lucero, Leandro Exequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Christ, Aurelie. Centre National de la Recherche Scientifique; Francia Fil: Benhamed, Moussa. Centre National de la Recherche Scientifique; Francia Fil: Blein, Thomas. Centre National de la Recherche Scientifique; Francia Fil: Huguet, Stephanie. Centre National de la Recherche Scientifique; Francia Fil: Charon, Celine. Centre National de la Recherche Scientifique; Francia Fil: Crespi, Martin. Centre National de la Recherche Scientifique; Francia Fil: Ariel, Federico Damian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
Published: 2020
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47. Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum

Author: Jérémy Just, Peter M. Rogowsky, Asher Pasha, José Caïus, Aurélie Grimault, Eddi Esteban, Nicholas J. Provart, Nicolas M. Doll, Thomas Widiez, Véronique Brunaud, Gwyneth C. Ingram, Nathalie Depège-Fargeix, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Violences, Innovations, Politiques, Socialisations et Sports (VIPS2), Le Mans Université (UM)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2), University of Toronto, Plant Science and Breeding Division of the Institut National de la Recherche en Agriculture et Alimentation et Environnement (BAP, INRAE, Project SeedCom), Estonian Research Council, French National Research Agency (ANR), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Le Mans Université (UM)-École normale supérieure - Rennes (ENS Rennes), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, INRA BAP, 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 de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, 0106 biological sciences, Transcription, Genetic, maïs, [SDV]Life Sciences [q-bio], Plant Science, Biology, maize, 01 natural sciences, Zea mays, In Brief, Endosperm, Transcriptome, endosperm, 03 medical and health sciences, Cell Wall, Gene Expression Regulation, Plant, Aleurone, Compartment (development), [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Plant Proteins, Regulation of gene expression, 0303 health sciences, endosperme, Cell Death, Gene Expression Profiling, transcriptomique, Gene Expression Regulation, Developmental, Reproducibility of Results, food and beverages, Embryo, Cell Biology, Scutellum, Embryonic stem cell, Cell biology, Up-Regulation, 030104 developmental biology, Gene Ontology, Mutation, seed, seed albumins, 010606 plant biology & botany
Abstract: International audience; A population of endosperm cells adjacent to the embryo scutellum shows transcriptomic enrichment in transport functions and is influenced by embryo development.Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm, and maternal tissues). However, the complexity of the kernel makes it difficult to understand intercompartment interactions without access to spatially accurate information. Here, we took advantage of the large size of the maize (Zea mays) kernel to characterize genome-wide expression profiles of tissues at different embryo/endosperm interfaces. Our analysis identifies specific transcriptomic signatures in two interface tissues compared with whole seed compartments: the scutellar aleurone layer and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 d after pollination and persists for around 11 d, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in an embryo specific mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated and to which additional endosperm cells are recruited as the embryo grows.
Published: 2020
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48. Correction to 'Dynamic Contrast for Plant Phenotyping'

Author: Yannick Bellec, Lionel Gissot, Zsolt Kelemen, Ruikang Zhang, Raja Chouket, Ludovic Jullien, Vincent Croquette, Jean-Denis Faure, Thomas Le Saux, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), ABCD : Biophysique des Biomolécules, Laboratoire de physique de l'ENS - ENS Paris (LPENS (UMR_8023)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Fondation pour la Recherche Medicale FRM DEI201512440, IJPBs Plant Observatory, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Laboratoire de physique de l'ENS - ENS Paris (LPENS), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-École normale supérieure - Paris (ENS Paris), 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, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: [PHYS]Physics [physics], General Chemical Engineering, MEDLINE, 02 engineering and technology, General Chemistry, Computational biology, Biology, 010402 general chemistry, 021001 nanoscience & nanotechnology, Plant phenotyping, 01 natural sciences, 0104 chemical sciences, Dynamic contrast, Chemistry, [CHIM]Chemical Sciences, 0210 nano-technology, QD1-999, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020
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49. CATION-CHLORIDE CO-TRANSPORTER 1 (CCC1) Mediates Plant Resistance against Pseudomonas syringae

Author: Jianing Mi, M. Rob G. Roelfsema, Heribert Hirt, Guoxin Cui, Salim Al-Babili, Baoda Han, Julien Sechet, Manuel Aranda, Yunhe Jiang, Grégory Mouille, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST)-King Abdullah University of Science and Technology (KAUST), Department of Molecular Plant Physiology and Biophysics, Biocenter University of Würzburg = Biozentrum der Universität Würzburg, Julius-Maximilians-Universität Würzburg (JMU)-Julius-Maximilians-Universität Würzburg (JMU), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Perutz Laboratories, University of Vienna [Vienna], Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdullah University of Science & Technology BAS/01/1062-01-01 URF/1/2965, European Commission 267196, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU)-Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Triggered Immunity, Physiology, Antimicrobial peptides, Plant Immunity, Plant Science, Trans-golgi Network, 01 natural sciences, Pv. Tomato Dc3000, Arabidopsis-thaliana, Arabidopsis, Metabolic Gene Clusters, Genetics, Camalexin, Pseudomonas syringae, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Lipid Transfer Proteins, Acyl-coenzyme, biology, Chemistry, fungi, food and beverages, Depolarization, biology.organism_classification, Cell biology, Disease Susceptibility, Cotransporter, Pathogenesis-related Proteins, 010606 plant biology & botany, Transcription Factors
Abstract: International audience; Plasma membrane (PM) depolarization functions as an initial step in plant defense signaling pathways. However, only a few ion channels/transporters have been characterized in the context of plant immunity. Here, we show that the Arabidopsis (Arabidopsis thaliana) Na+:K+:2Cl(-) (NKCC) cotransporter CCC1 has a dual function in plant immunity. CCC1 functions independently of PM depolarization and negatively regulates pathogen-associated molecular pattern-triggered immunity. However, CCC1 positively regulates plant basal and effector-triggered resistance to Pseudomonas syringae pv. tomato (Pst) DC3000. In line with the compromised immunity to Pst DC3000, ccc1 mutants show reduced expression of genes encoding enzymes involved in the biosynthesis of antimicrobial peptides, camalexin, and 4-OH-ICN, as well as pathogenesis-related proteins. Moreover, genes involved in cell wall and cuticle biosynthesis are constitutively down-regulated in ccc1 mutants, and the cell walls of these mutants exhibit major changes in monosaccharide composition. The role of CCC1 ion transporter activity in the regulation of plant immunity is corroborated by experiments using the specific NKCC inhibitor bumetanide. These results reveal a function for ion transporters in immunity-related cell wall fortification and antimicrobial biosynthesis.
Published: 2020
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50. NAA50 is an enzymatically active Nα-acetyltransferase that is crucial for development and regulation of stress responses

Author: Eric Linster, Willy V. Bienvenut, Markus Wirtz, Carmela Giglione, Thierry Meinnel, Jürgen Eirich, Jonas Weidenhausen, Iris Finkemeier, Ruediger Hell, Jean-Baptiste Boyer, Iwona Stephan, Irmgard Sinning, Laura Armbruster, Annika Brünje, Universität Heidelberg [Heidelberg] = Heidelberg University, Hartmut Hoffmann-Berling International Graduate School, Heidelberg University, Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Maturation des proteines, destinée cellulaire et thérapeutique (PROMTI), Département Biologie des Génomes (DBG), 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), Heidelberg University Biochemistry Center, Heidelberger Institut für Pflanzenwissenschaften (HIP), ANR-13-BSV6-0004,eNergiome,N-terminome des organelles de conversion de l'énergie: Une meilleure comprehension de la maturation des protéines impliquées dans ces organelles(2013), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Centre for Organismal Studies, Heidelberg University (COS), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Institute for Plant Biology and Biotechnology,University of Münster, COS - Centre for Organismal Studies, Heidelberg University, Universität Heidelberg [Heidelberg], University of Muenster, Centre for Organismal Studies, Plant Proteomics Group, Max Planck Institute for Plant Breeding Research (MPIPZ), and Heidelberg Institute of Plant Sciences
Subjects: 0106 biological sciences, NatA complex, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Physiology, Chemistry, Protein subunit, [SDV]Life Sciences [q-bio], Saccharomyces cerevisiae, Plant Science, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], biology.organism_classification, 01 natural sciences, Ribosome, Cell biology, Acetylation, Acetyltransferase, Arabidopsis, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, NAA15, 010606 plant biology & botany
Abstract: International audience; N a-terminal acetylation (NTA) is a prevalent protein modification in eukaryotes. In plants, the biological function of NTA remains enigmatic. The dominant N-acetyltransferase (Nat) in Arabidopsis (Arabidopsis thaliana) is NatA, which cotranslationally catalyzes acetylation of ;40% of the proteome. The core NatA complex consists of the catalytic subunit NAA10 and the ribosome-anchoring subunit NAA15. In human (Homo sapiens), fruit fly (Drosophila melanogaster), and yeast (Saccharomyces cerevisiae), this core NatA complex interacts with NAA50 to form the NatE complex. While in metazoa, NAA50 has N-acetyltransferase activity, yeast NAA50 is catalytically inactive and positions NatA at the ribosome tunnel exit. Here, we report the identification and characterization of Arabidopsis NAA50 (AT5G11340). Consistent with its putative function as a cotranslationally acting Nat, AtNAA50-EYFP localized to the cytosol and the endoplasmic reticulum but also to the nuclei. We demonstrate that purified AtNAA50 displays N a-terminal acetyltransferase and lysine-«-autoacetyltransferase activity in vitro. Global N-acetylome profiling of Escherichia coli cells expressing AtNAA50 revealed conservation of NatE substrate specificity between plants and humans. Unlike the embryo-lethal phenotype caused by the absence of AtNAA10 and AtNAA15, loss of NAA50 expression resulted in severe growth retardation and infertility in two Arabidopsis transfer DNA insertion lines (naa50-1 and naa50-2). The phenotype of naa50-2 was rescued by the expression of HsNAA50 or AtNAA50. In contrast, the inactive ScNAA50 failed to complement naa50-2. Remarkably, loss of NAA50 expression did not affect NTA of known NatA substrates and caused the accumulation of proteins involved in stress responses. Overall, our results emphasize a relevant role of AtNAA50 in plant defense and development, which is independent of the essential NatA activity.
Published: 2020
Full Text: View/download PDF

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