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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. <scp> KARRIKIN INSENSITIVE2 </scp> regulates leaf development, root system architecture and arbuscular‐mycorrhizal symbiosis in Brachypodium distachyon

Author: Yongjie Meng, Kartikye Varshney, Norbert Incze, Eszter Badics, Muhammad Kamran, Sabrina F. Davies, Larissa M. F. Oppermann, Kévin Magne, Marion Dalmais, Abdel Bendahmane, Richard Sibout, John Vogel, Debbie Laudencia‐Chingcuanco, Charles S. Bond, Vilmos Soós, Caroline Gutjahr, Mark T. Waters, Sichuan Agricultural University, Technical University of Munich and Helmholtz Center Munich, Institute of Environmental Medicine, WIK Wissenschaftliches Institut für Infrastruktur und Kommunikationsdienste [Bad Honnef]-WIK Wissenschaftliches Institut für Infrastruktur und Kommunikationsdienste [Bad Honnef], Hungarian Acad Sci, Inst Agr, Agr Res Ctr, H-2462 Martonvasar, Hungary, Partenaires INRAE, University of Engineering & Technology Lahore (UET), The University of Western Australia (UWA), 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 de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Joint Genome Institute (JGI), United States Department of Energy, USDA-ARS Western Regional Research Center, Ludwig Maximilian University [Munich] (LMU), Plant Energy Biology, ARC Centre of Excellence, Australian Research Council Future Fellowship (FT150100162) to MTW. PhD scholarship from the China Scholarship Council to YM. Funding from the Hungarian National Research, Development and Innovation Office (NKFIH Grants K128644 and GINOP-2.3.2-15-2016-00029) to VS. Funding from the Emmy Noether program (GU1423/1-1) of the Deutsche Forschungsgemeinschaft (DFG) to CG and a doctoral student fellowship from the German Academic Exchange Service (DAAD) to KV.The Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231., and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: Brachypodium distachyon, strigolactone, arbuscular mycorrhiza, Arabidopsis Proteins, Arabidopsis, Cell Biology, Plant Science, butenolide, karrikin, Plant Leaves, Lactones, Plant Growth Regulators, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, α/β-hydrolase, Furans, Symbiosis, Brachypodium, Pyrans
Abstract: International audience; Karrikins, of which KAR1 and KAR2 are representatives, are a class of abiotic plant growth regulators produced from the partial combustion of plant material (Flematti et al., 2004; Flematti et al., 2009). Released into the soil following wildfires, karrikins can promote seed germination and seedling photomorphogenesis, and thereby facilitate the revegetation process (Nelson et al., 2009; Nelson et al., 2010; Stevens et al., 2007). The butenolide moiety of karrikins is also an essential structural feature of strigolactones (SLs), which are carotenoid-derived plant hormones that regulate a range of developmental processes in plants, and also serve as a rhizosphere signal for arbuscular mycorrhizal fungi and root parasitic weeds (Waters et al., 2016; Bürger and Chory, 2020). Collectively, these butenolides possess wide-ranging biological activities with considerable agricultural and environmental significance.
Published: 2022
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3. 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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4. 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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5. Arabidopsis thaliana 2,3‐bisphosphoglycerate‐independent phosphoglycerate mutase 2 activity requires serine 82 phosphorylation

Author: Edouard Boex-Fontvieille, Marlène Davanture, Guillaume Tcherkez, Michel Zivy, Pauline Duminil, Michael Hodges, Céline Oury, Nathalie Glab, 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), 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), 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 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), Australian National University - Joint College of Sciences, (ANU), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-14-CE19-0015,Regul3P,Régulation de la photorespiration par phosphorylation protéique(2014), 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'Angers (UA)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: phosphopeptide, Arabidopsis, Plant Science, catalytic mechanism, Biology, Glyceric Acids, Arabidopsis thaliana, Serine, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Phosphorylation, Phosphoglycerate Mutase, chemistry.chemical_classification, Phosphoglycerate kinase, Arabidopsis Proteins, Phosphopeptide, Phosphoproteomics, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, transient phosphorylation, Recombinant Proteins, Models, Structural, Plant Leaves, Enzyme, chemistry, Biochemistry, iPGAM, Glycolysis
Abstract: International audience; Phosphoglycerate mutases (PGAMs) catalyse the reversible isomerisation of 3-phosphoglycerate and 2-phosphoglycerate, a step of glycolysis. PGAMs can be sub-divided into 2,3-biphosphoglycerate dependent (dPGAM) and independent (iPGAM) enzymes. In plants, phosphoglycerate isomerisation is carried out by cytosolic iPGAM. Despite its crucial role in catabolism, little is known about post-translational modifications of plant iPGAM. In Arabidopsis thaliana, phosphoproteomics analyses have previously identified a iPGAM phosphopeptide where serine 82 is phosphorylated. Here, we show that this phosphopeptide is less abundant in dark-adapted compared to illuminated Arabidopsis leaves. In silico comparison of iPGAM protein sequences and 3D-structural modelling of AtiPGAM2 based on non-plant iPGAM enzymes suggest a role for phosphorylated serine in the catalytic reaction mechanism. This is confirmed by the activity (or the lack thereof) of mutated recombinant Arabidopsis iPGAM2 forms, affected in different steps of the reaction mechanism. We thus propose that the occurrence of the S82-phosphopeptide reflects iPGAM2 steady-state catalysis. Based on this assumption, the metabolic consequences of a higher iPGAM activity in illuminated versus darkened leaves are discussed.
Published: 2021
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6. Induced mutations in SlE8 and SlACO1 control tomato fruit maturation and shelf-life

Author: Filomena Carriero, Amandine Cornille, Sophie J M Piquerez, Gwilherm Brisou, Silvia Minoia, Fabien Marcel, Adnane Boualem, Abdelhafid Bendahmane, 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), Gautier semences, Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura (Alsia), 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), Plant Biology and Breeding Department of INRAE, AgenceNationale de Recherche et Technologie (ANRT), 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: 0106 biological sciences, TILLING, Ethylene, fruit shelf-life, Physiology, Population, fruit ripening, Plant Science, tomato, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Negative selection, Solanum lycopersicum, fruit firmness, Gene Expression Regulation, Plant, education, Plant Proteins, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, Genetic diversity, biology, fungi, food and beverages, Ripening, Ethylenes, SlACO1, SlE8, biology.organism_classification, Horticulture, Phenotype, chemistry, Fruit, [SDE]Environmental Sciences, Mutation, Solanum, Climacteric, 010606 plant biology & botany
Abstract: Fruit maturation and softening are critical traits that control fruit shelf-life. In the climacteric tomato (Solanum lycopersicum L.) fruit, ethylene plays a key role in fruit ripening and softening. We characterized two related proteins with contrasting impact on ethylene production, ACC oxidase 1 (SlACO1) and SlE8. We found SlACO1 and SlE8 to be highly expressed during fruit ripening. To identify loss-of-function alleles, we analysed the tomato genetic diversity but we did not find any natural mutations impairing the function of these proteins. We also found the two loci evolving under purifying selection. To engineer hypomorphic alleles, we used TILLING (target-induced local lesions in genomes) to screen a tomato ethylmethane sulfonate-mutagenized population. We found 13 mutants that we phenotyped for ethylene production, shelf-life, firmness, conductivity, and soluble solid content in tomato fruits. The data demonstrated that slaco1-1 and slaco1-2 alleles could be used to improve fruit shelf-life, and that sle8-1 and sle8-2 alleles could be used to accelerate ripening. This study highlights further the importance of SlACO1 and SlE8 in ethylene production in tomato fruit and how they might be used for post-harvest fruit preservation or speeding up fruit maturation.
Published: 2021
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7. SeSAM: software for automatic construction of order-robust linkage maps

Author: Adrien Vidal, Franck Gauthier, Willy Rodrigez, Nadège Guiglielmoni, Damien Leroux, Nicolas Chevrolier, Sylvain Jasson, Elise Tourrette, Olivier C. Martin, Matthieu Falque, 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), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), 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), MARS-WRIGLEY co-funded the salary of AV and WR. The funding bodies did not play any role in the design of the study, collection, analysis, and interpretation of the data, or writing the manuscript., ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010), and Université Paris-Saclay
Subjects: Genetic Markers, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genotype, Linkage, Applied Mathematics, Chromosome Mapping, Genetic mapping, Biochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Polymorphism, Single Nucleotide, Computer Science Applications, Genetic mapping Linkage Automated software Seriation Marker order robustness, Automated software, Marker order robustness, Structural Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Seriation, Molecular Biology, Software
Abstract: Background Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate with the numbers of SNPs available. Thus, guaranteeing a statistically robust marker order requires that maps include only a carefully selected subset of SNPs. Results In this context, the SeSAM software allows automatic genetic map construction using seriation and placement approaches, to produce (1) a high-robustness framework map which includes as many markers as possible while keeping the order robustness beyond a given statistical threshold, and (2) a high-density total map including the framework plus almost all polymorphic markers. During this process, care is taken to limit the impact of genotyping errors and of missing data on mapping quality. SeSAM can be used with a wide range of biparental populations including from outcrossing species for which phases are inferred on-the-fly by maximum-likelihood during map elongation. The package also includes functions to simulate data sets, convert data formats, detect putative genotyping errors, visualize data and map quality (including graphical genotypes), and merge several maps into a consensus. SeSAM is also suitable for interactive map construction, by providing lower-level functions for 2-point and multipoint EM analyses. The software is implemented in a R package including functions in C++. Conclusions SeSAM is a fully automatic linkage mapping software designed to (1) produce a framework map as robust as desired by optimizing the selection of a subset of markers, and (2) produce a high-density map including almost all polymorphic markers. The software can be used with a wide range of biparental mapping populations including cases from outcrossing. SeSAM is freely available under a GNU GPL v3 license and works on Linux, Windows, and macOS platforms. It can be downloaded together with its user-manual and quick-start tutorial from ForgeMIA (SeSAM project) at https://forgemia.inra.fr/gqe-acep/sesam/-/releases
Published: 2022
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8. 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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9. 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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10. A Comparative Study of Maize and Miscanthus Regarding Cell-Wall Composition and Stem Anatomy for Conversion into Bioethanol and Polymer Composites

Author: S. Jaffuel, M.-P. Jacquemont, F. El Hage, Patrick Navard, Matthieu Reymond, Laurent Cézard, Loan T.T. Vo, Jordi Girones, Maryse Brancourt-Hulmel, Stéphanie Arnoult, Yves Griveau, Emilie Mignot, Emilie Gineau, Catherine Lapierre, Frédéric Legée, Valérie Méchin, Grégory Mouille, 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), 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), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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 Montpellier (UM), ANR-11-BTBR-0006,BFF,Biomasse pour le futur(2011), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, 020209 energy, polysaccharides, 02 engineering and technology, Xylose, 01 natural sciences, [SPI.MAT]Engineering Sciences [physics]/Materials, Ferulic acid, chemistry.chemical_compound, 010608 biotechnology, 0202 electrical engineering, electronic engineering, information engineering, Lignin, Cellulose, Stover, lignocellulosic biomass, Plant stem, Energy crop, biology, Renewable Energy, Sustainability and the Environment, enzymatic hydrolysis, Anatomy, Miscanthus, biology.organism_classification, biofuels, [CHIM.POLY]Chemical Sciences/Polymers, chemistry, Pith, Agronomy and Crop Science, biomaterials, Energy (miscellaneous)
Abstract: International audience; Due to an increasing demand for environmentally sustainable products, miscanthus and maize stover represent interesting lignocellulosic resources for conversion into biofuels and biomaterials. The overall purpose was to compare miscanthus and maize regarding cell-wall composition and stem anatomy for conversion into bioethanol and polymer composites using partial least squares regressions. For each of the two crops, six contrasted genotypes were cultivated in complete block design, and harvested. Internodes below the main cob for maize, and on the first aboveground internode for miscanthus, were analyzed for biochemistry and anatomy. Their digestibility was predicted using crop-specific near infrared calibrations, and the mechanical properties were evaluated in stem-based composites. On average, the internode cross-section of miscanthus anatomy was characterized by a thick rind (26.2 %) and few but dense pith-bundles (3.5 nb/mm²), while cell-wall constituted 95.2 % of the dry matter with high lignin (243.2 mg/g) and cellulose concentrations (439.7 mg/g). Maize internode-anatomy showed large cross-sections (397.5 mm²), pith with the presence of numerous bundles and non-lignified-pith fractions (22.3 % of the section). Its cellwall biochemistry displayed high concentrations of hemicelluloses, galactose, arabinose, xylose and ferulic acid. Cell-wall, lignin and cellulose concentrations were positively correlated with rind-fraction and pith-bundle-density, which explained strong mechanical properties as shown in miscanthus. Hemicelluloses, galactose, arabinose and ferulic acid concentrations were positively correlated with pith fraction and stem cross-section, revealing high digestibility as shown in maize. This underlines interesting traits for further comparative genetic studies, as maize represents a good model for digestibility and miscanthus for composites.
Published: 2021
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11. 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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12. 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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13. Dp71 contribution to the molecular scaffold anchoring aquaporine‐4 channels in brain macroglial cells

Author: Cyrille Vaillend, Jean-Vianney Barnier, Alvaro Rendon, Charlotte Izabelle, Mehdi Belmaati Cherkaoui, Claire Boulogne, Ophélie Vacca, Martine Cohen-Salmon, Cynthia Gillet, Anne-Cécile Boulay, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), 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 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), Microscopie Électronique (MET), 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)-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 la Vision, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR-14-CE13-0037,DYSther,Dystrophines Dans Le Système Nerveux : De la Neurophysiologie à la Thérapie Moléculaire(2014), 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), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Cerebellum, glymphatic system, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Hippocampus, Blood–brain barrier, Dystrophin, Mice, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, Cortex (anatomy), medicine, Animals, Dystroglycans, Aquaporin 4, biology, Brain, Immunogold labelling, blood-brain barrier, Cell biology, 030104 developmental biology, medicine.anatomical_structure, Neurology, Hippocampal Fissure, Astrocytes, intellectual disability, biology.protein, Glymphatic system, gliovascular unit, Neuroglia, 030217 neurology & neurosurgery
Abstract: International audience; Intellectual disability in Duchenne muscular dystrophy has been associated with the loss of dystrophin-protein 71, Dp71, the main dystrophin-gene product in the adult brain. Dp71 shows major expression in perivascular macroglial endfeet, suggesting that dysfunctional glial mechanisms contribute to cognitive impairments. In the present study, we investigated the molecular alterations induced by a selective loss of Dp71 in mice, using semi-quantitative immunogold analyses in electron microscopy and immunofluorescence confocal analyses in brain sections and purified gliovascular units. In macroglial pericapillary endfeet of the cerebellum and hippocampus, we found a drastic reduction (70%) of the polarized distribution of aquaporin-4 (AQP4) channels, a 50% reduction of β-dystroglycan, and a complete loss of α1-syntrophin. Interestingly, in the hippocampus and cortex, these effects were not homogeneous: AQP4 and AQP4ex isoforms were mostly lost around capillaries but preserved in large vessels corresponding to pial arteries, penetrating cortical arterioles, and arterioles of the hippocampal fissure, indicating the presence of Dp71-independent pools of AQP4 in these vascular structures. In conclusion, the depletion of Dp71 strongly alters the distribution of AQP4 selectively in macroglial perivascular endfeet surrounding capillaries. This effect likely affects water homeostasis and blood-brain barrier functions and may thus contribute to the synaptic and cognitive defects associated with Dp71 deficiency.
Published: 2020
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14. OsASN1 Overexpression in Rice Increases Grain Protein Content and Yield under Nitrogen-Limiting Conditions

Author: Dongjin Shin, Jin-Won Lee, Gynheung An, Pyung Ok Lim, Joonheum Park, Sichul Lee, Céline Masclaux-Daubresse, Hong Gil Nam, Anne Marmagne, Center for Plant Aging Research, Institute for Basic Science, Rural Development Administration, National Institute of Horticultural and Herbal Science (NIHHS), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Kyung Hee University (KHU), Institute for Basic Science (IBS-R013-D1), PHC STAR no 34300ZK and 2017K1A3A1A21013795, and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, 0301 basic medicine, Limiting factor, Nitrogen, Overexpression, Physiology, Knockout, Asparagine synthetase, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Plant Science, Asparagine synthetase 1, AcademicSubjects/SCI01180, Photosynthesis, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Quantitative Trait, Heritable, Gene Expression Regulation, Plant, Grain quality and yield, Ammonium, Cultivar, Plant Proteins, 2. Zero hunger, Nitrogen use efficiency, Oryza sativa, biology, AcademicSubjects/SCI01210, Chemistry, Crop yield, Regular Papers, food and beverages, Aspartate-Ammonia Ligase, Oryza, Cell Biology, General Medicine, Plants, Genetically Modified, biology.organism_classification, 030104 developmental biology, Agronomy, Seedlings, Seedling, Rice, Edible Grain, 010606 plant biology & botany
Abstract: Nitrogen (N) is a major limiting factor affecting crop yield in unfertilized soil. Thus, cultivars with a high N use efficiency (NUE) and good grain protein content (GPC) are needed to fulfill the growing food demand and to reduce environmental burden. This is especially true for rice (Oryza sativa L.) that is cultivated with a high input of N fertilizer and is a primary staple food crop for more than half of the global population. Here, we report that rice asparagine synthetase 1 (OsASN1) is required for grain yield and grain protein contents under both N-sufficient (conventional paddy fields) and N-limiting conditions from analyses of knockout mutant plants. In addition, we show that overexpression (OX) of OsASN1 results in better nitrogen uptake and assimilation, and increased tolerance to N limitation at the seedling stage. Under field conditions, the OsASN1 OX rice plants produced grains with increased N and protein contents without yield reduction compared to wild-type (WT) rice. Under N-limited conditions, the OX plants displayed increased grain yield and protein content with enhanced photosynthetic activity compared to WT rice. Thus, OsASN1 can be an effective target gene for the development of rice cultivars with higher grain protein content, NUE, and grain yield under N-limiting conditions.
Published: 2020
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15. 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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16. 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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17. N-acetylation of secreted proteins in Apicomplexa is widespread and is independent of the ER acetyl-CoA transporter AT1

Author: Mary Akinyi Nyonda, Jean-Baptiste Boyer, Lucid Belmudes, Aarti Krishnan, Paco Pino, Yohann Couté, Mathieu Brochet, Thierry Meinnel, Dominique Soldati-Favre, Carmela Giglione, Meinnel, Thierry, Elucider les fonctions multifacettes des protéines acétyl transferase en réponse au stress et dans la régulation métabolique - - KatNat2017 - ANR-17-CAPS-0001 - ERA-CAPS - VALID, Saclay Plant Sciences - - SPS2010 - ANR-10-LABX-0040 - LABX - VALID, Impact des modifications cotranslationnelles N-terminales plastidiales lors de la réponse au stress - - CANMORE2020 - ANR-20-CE92-0040 - AAPG2020 - VALID, Université de Genève = University of Geneva (UNIGE), 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), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Université Grenoble Alpes (UGA), Fondation ARC (ARCPJA32020060002137), 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), and ANR-20-CE92-0040,CANMORE,Impact des modifications cotranslationnelles N-terminales plastidiales lors de la réponse au stress(2020)
Subjects: Male, Mammals, Proteome, Plasmodium berghei, Toxoplasma gondii, Acetylation, Cell Biology, Secretory pathway, Endoplasmic Reticulum, Acetyl Coenzyme A, Animals, Acetyl-CoA transporter, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Female, Parasites, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Protein Processing, Post-Translational, Toxoplasma, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
Abstract: Acetyl-CoA participates in post-translational modification of proteins and in central carbon and lipid metabolism in several cell compartments. In mammals, acetyl-CoA transporter 1 (AT1, also known as SLC33A1) facilitates the flux of cytosolic acetyl-CoA into the endoplasmic reticulum (ER), enabling the acetylation of proteins of the secretory pathway, in concert with the activity of dedicated acetyltransferases such as NAT8. However, the involvement of the ER acetyl-CoA pool in acetylation of ER-transiting proteins in Apicomplexa is unknown. Here, we identified homologs of AT1 and NAT8 in Toxoplasma gondii and Plasmodium berghei parasites. Proteome-wide analyses revealed widespread N-terminal acetylation of secreted proteins in both species. Such extensive acetylation of N-terminally processed proteins has not been observed previously in any other organism. Deletion of AT1 homologs in both T. gondii and P. berghei resulted in considerable reductions in parasite fitness. In P. berghei, AT1 was found to be important for growth of asexual blood stages, production of female gametocytes and male gametocytogenesis, implying its requirement for parasite transmission. In the absence of AT1, lysine acetylation and N-terminal acetylation in T. gondii remained globally unaltered, suggesting an uncoupling between the role of AT1 in development and active acetylation occurring along the secretory pathway.
Published: 2022
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18. 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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19. 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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20. 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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21. 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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22. $Sinorhizobium\ meliloti$ 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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23. 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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24. 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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25. NatB-Mediated N-Terminal Acetylation Affects Growth and Biotic Stress Responses

Author: Irmgard Sinning, Laura Armbruster, Carsten Sticht, Thierry Meinnel, Carmela Giglione, Dominik Layer, Markus Wirtz, Ruediger Hell, Willy V. Bienvenut, Iwona Stephan, Eric Linster, Monika Huber, Karine Lapouge, 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), 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: 0106 biological sciences, NatB complex, Proteome, Physiology, [SDV]Life Sciences [q-bio], Protein subunit, Mutant, Arabidopsis, Plant Science, In Vitro Techniques, medicine.disease_cause, 01 natural sciences, Biochemistry and Metabolism, Acetyltransferases, Osmotic Pressure, Stress, Physiological, Catalytic Domain, Protein targeting, Genetics, medicine, Arabidopsis thaliana, N-Terminal Acetyltransferase B, 2. Zero hunger, biology, Arabidopsis Proteins, Chemistry, Gene Expression Profiling, Computational Biology, Acetylation, Biotic stress, biology.organism_classification, Mutagenesis, Insertional, Gene Ontology, Biochemistry, Seedlings, 010606 plant biology & botany
Abstract: International audience; N-terminal acetylation (NTA) is one of the most abundant protein modifications in eukaryotes. In humans, NTA is catalyzed by seven Nα-acetyltransferases (NatA-F and NatH). Remarkably, the plant Nat machinery and its biological relevance remain poorly understood, although NTA has gained recognition as a key regulator of crucial processes such as protein turnover, protein-protein interaction, and protein targeting. In this study, we combined in vitro assays, reverse genetics, quantitative N-terminomics, transcriptomics, and physiological assays to characterize the Arabidopsis NatB complex. We show that the plant NatB catalytic (NAA20) and auxiliary subunit (NAA25) form a stable heterodimeric complex that accepts canonical NatB-type substrates in vitro. In planta, NatB complex formation was essential for enzymatic activity. Depletion of NatB subunits to 30% of the wild-type level in three Arabidopsis T-DNA insertion mutants (naa20-1, naa20-2, and naa25-1) caused a 50% decrease in plant growth. A complementation approach revealed functional conservation between plant and human catalytic NatB subunits, whereas yeast NAA20 failed to complement naa20-1. Quantitative N-terminomics of approximately 1,000 peptides identified 32 bona fide substrates of the plant NatB complex. In vivo, NatB was seen to preferentially acetylate N-termini starting with the initiator methionine followed by acidic amino acids and contributed 20% of the acetylation marks in the detected plant proteome. Global transcriptome and proteome analyses of NatB-depleted mutants suggested a function of NatB in multiple stress responses. Indeed, loss of NatB function, but not NatA, increased plant sensitivity towards osmotic and high-salt stress, indicating that NatB is required for tolerance of these abiotic stressors.
Published: 2019
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26. A Mutant Allele Uncouples the Brassinosteroid-Dependent and Independent Functions of BRASSINOSTEROID INSENSITIVE 1

Author: Friederike Wanke, Herman Höfte, Eleonore Holzwart, Nina Glöckner, Sebastian Wolf, Klaus Harter, Department of Cell Biology, Centre for Organismal Studies Heidelberg, Heidelberg University-Heidelberg University, Plant Physiology, Center for Plant Molecular Biology, University of Tübingen-University of Tübingen, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), German Research Foundation (DFG)WO 1660/6-1HA2146/22-1CRC 1101-D02German Research Foundation (DFG)WO1660/2, and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, Receptor complex, Physiology, Arabidopsis, Network, Expression, Growth, Plant Science, Cell fate determination, Gene, 01 natural sciences, Bri1, chemistry.chemical_compound, Cell surface receptor, Brassinosteroids, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, Brassinosteroid, Receptor, Alleles, Research Articles, Receptor Kinase, biology, Arabidopsis Proteins, Chemistry, Protein, fungi, Plants, Genetically Modified, biology.organism_classification, Cell biology, Signal transduction, Protein Kinases, Plasma-Membrane, Signal Transduction, Bak1, 010606 plant biology & botany
Abstract: Plants depend on various cell surface receptors to integrate extracellular signals with developmental programs. One of the best-studied receptors is BRASSINOSTEROID INSENSITIVE 1 (BRI1) in Arabidopsis (Arabidopsis thaliana). Upon binding of its hormone ligands, BRI1 forms a complex with a shape-complementary coreceptor and initiates a signal transduction cascade, which leads to a variety of responses. At the macroscopic level, brassinosteroid (BR) biosynthetic and receptor mutants have similar growth defects, which initially led to the assumption that the signaling pathways were largely linear. However, recent evidence suggests that BR signaling is interconnected with several other pathways through various mechanisms. We recently described that feedback from the cell wall is integrated at the level of the receptor complex through interaction with RECEPTOR-LIKE PROTEIN 44 (RLP44). Moreover, BRI1 is required for another function of RLP44: the control of procambial cell fate. Here, we report a BRI1 mutant, bri1(cnu4), which differentially affects canonical BR signaling and RLP44 function in the vasculature. Although BR signaling is only mildly impaired, bri1(cnu4) mutants show ectopic xylem in place of procambium. Mechanistically, this is explained by an increased association between RLP44 and the mutated BRI1 protein, which prevents the former from acting in vascular cell fate maintenance. Consistent with this, the mild BR response phenotype of bri1(cnu4) is a recessive trait, whereas the RLP44-mediated xylem phenotype is semidominant. Our results highlight the complexity of plant plasma membrane receptor function and provide a tool to dissect BR signaling-related roles of BRI1 from its noncanonical functions.
Published: 2019
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27. 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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28. 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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29. 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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30. BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon

Author: Sakai, Kaori, Citerne, Sylvie, Antelme, Sébastien, Le Bris, Philippe, Daniel, Sylviane, Bouder, Axelle, D'Orlando, Angelina, Cartwright, Amy, Tellier, Frédérique, Pateyron, Stéphanie, Delannoy, Etienne, Laudencia-Chingcuanco, Debbie, Mouille, Gregory, Palauqui, Jean Christophe, Vogel, John, Sibout, Richard, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-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), United States Department of Energy Joint Genome Institute, 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), USDA-ARS Western Regional Research Center, United States Department of Energy (DOE) : DE-AC02-05CH11231., ANR-14-CE19-0012,BRAVO,Ontogénie des tissus vasculaires chez les graminées(2014), 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: Crop and Pasture Production, Research, [SDV]Life Sciences [q-bio], fungi, Plant Biology & Botany, Botany, food and beverages, Plant Biology, Receptors, Cell Surface, Protein Serine-Threonine Kinases, Phloem, Protein-Serine-Threonine Kinases, Microbiology, Hormones, Xylem, QK1-989, [SDE]Environmental Sciences, Receptors, Cell Surface, Genetics, ERECTA, Plant Proteins, Brachypodium
Abstract: Background The vascular system of plants consists of two main tissue types, xylem and phloem. These tissues are organized into vascular bundles that are arranged into a complex network running through the plant that is essential for the viability of land plants. Despite their obvious importance, the genes involved in the organization of vascular tissues remain poorly understood in grasses. Results We studied in detail the vascular network in stems from the model grass Brachypodium distachyon (Brachypodium) and identified a large set of genes differentially expressed in vascular bundles versus parenchyma tissues. To decipher the underlying molecular mechanisms of vascularization in grasses, we conducted a forward genetic screen for abnormal vasculature. We identified a mutation that severely affected the organization of vascular tissues. This mutant displayed defects in anastomosis of the vascular network and uncommon amphivasal vascular bundles. The causal mutation is a premature stop codon in ERECTA, a LRR receptor-like serine/threonine-protein kinase. Mutations in this gene are pleiotropic indicating that it serves multiple roles during plant development. This mutant also displayed changes in cell wall composition, gene expression and hormone homeostasis. Conclusion In summary, ERECTA has a pleiotropic role in Brachypodium. We propose a major role of ERECTA in vasculature anastomosis and vascular tissue organization in Brachypodium. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-021-02970-2.
Published: 2021
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31. 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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32. 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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33. 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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34. Is there a unique integration mechanism of Agrobacterium T-DNA into a plant genome?

Author: Denis Faure, 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), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, Genetics, DNA, Bacterial, 0303 health sciences, biology, Physiology, Agrobacterium, DNA repair, Mechanism (biology), [SDV]Life Sciences [q-bio], Plant Science, DNA-Directed DNA Polymerase, biology.organism_classification, 01 natural sciences, Genome, 03 medical and health sciences, chemistry.chemical_compound, chemistry, DNA, ComputingMilieux_MISCELLANEOUS, Genome, Plant, 030304 developmental biology, 010606 plant biology & botany
Abstract: International audience; Agrobacterium evolved the capability to transfer a DNA fragment (T-DNA) of their own genome into the nuclear genome of plants (Gelvin, 2017). This natural process of interkingdom horizontal gene transfer (HGT) contributes to exploitation of the plant host by Agrobacterium bacterial pathogens (Gonzalez-Mula et al., 2018 and 2019). This unique HGT process also inspired the development of a wide spectrum of tools and technologies dedicated to genetic engineering of plants and some other eukaryotes (Sardesai & Subramanyam, 2018). In spite of a popular usage of these tools in basic science and genetic engineering, the ultimate step of the HGT process, namely integration of the T-DNA into nuclear genome of plants remains in a grey zone of knowledge (Singer, 2018). In this issue of New phytologist, Nishizawa-Yokoi et al. (pp. 000-000) suggest that host factors controlling TDNA integration are different in somatic and germinal plnt cells. This article invites the scientific community to debate about the existence of different molecular machineries allowing T-DNA integration in plant genome.
Published: 2021
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35. Systemic control of nodule formation by plant nitrogen demand requires autoregulation-dependent and independent mechanisms

Author: Marie-Laure Martin-Magniette, Martha Nigg, Marc Lepetit, Stefano Colella, Marjorie Pervent, Marie-Françoise Jardinaud, Alicia Karouani, Dany Severac, Marc Tauzin, Ilana Lambert, 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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM), 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), 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), ANR-16-CE20-0009,PSYCHE,Réponses systémiques des plantes aux changements environnementaux(2016), and ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010)
Subjects: 0106 biological sciences, Physiology, Nitrogen, Mutant, Plant Science, 01 natural sciences, Plant Root Nodulation, Rhizobia, Transcriptome, 03 medical and health sciences, Nitrogen Fixation, Medicago truncatula, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Homeostasis, Symbiosis, Gene, 030304 developmental biology, Plant Proteins, systemic signalling, 2. Zero hunger, 0303 health sciences, biology, nodule formation, fungi, food and beverages, biology.organism_classification, Phenotype, Legume, Cell biology, Nitrogen fixation, Root Nodules, Plant, Reprogramming, 010606 plant biology & botany, Rhizobium
Abstract: In legumes interacting with rhizobia, the formation of symbiotic organs involved in the acquisition of atmospheric nitrogen gas (N2) is dependent on the plant nitrogen (N) demand. We used Medicago truncatula plants cultivated in split-root systems to discriminate between responses to local and systemic N signaling. We evidenced a strong control of nodule formation by systemic N signaling but obtained no clear evidence of a local control by mineral nitrogen. Systemic signaling of the plant N demand controls numerous transcripts involved in root transcriptome reprogramming associated with early rhizobia interaction and nodule formation. SUPER NUMERIC NODULES (SUNN) has an important role in this control, but we found that major systemic N signaling responses remained active in the sunn mutant. Genes involved in the activation of nitrogen fixation are regulated by systemic N signaling in the mutant, explaining why its hypernodulation phenotype is not associated with higher nitrogen fixation of the whole plant. We show that the control of transcriptome reprogramming of nodule formation by systemic N signaling requires other pathway(s) that parallel the SUNN/CLE (CLAVATA3/EMBRYO SURROUNDING REGION-LIKE PEPTIDES) pathway.
Published: 2021
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36. 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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37. Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity

Author: Axel Mithöfer, Emmanuelle Lastrucci, Maria A. Schlöffel, Delphine Pflieger, Marilia Almeida-Trapp, Kiruthiga Mariappan, Hanna Alhoraibi, Jean Bigeard, Andrea A. Gust, Heribert Hirt, Aala A. Abulfaraj, Ludovic Bonhomme, Mai Jarad, Ronny Völz, Stefan T. Arold, Naganand Rayapuram, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Centre for Research in Agricultural Genomics (CRAG), Department of Biochemistry, FAculty of science, King Abdulaziz University-King Abdulaziz University, 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), Department of Biological Sciences, College of Sciences and Arts-Rabigh Campus, Plant Immunity Research Center, Seoul National University [Seoul] (SNU), Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Center for Plant Molecular Biology, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Santé et de la Recherche Médicale (INSERM), 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), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Computational Bioscience Research Center, Laboratoire Analyse, Modélisation et Matériaux pour la Biologie et l'Environnement (LAMBE - UMR 8587), Université d'Évry-Val-d'Essonne (UEVE)-Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CY Cergy Paris Université (CY), Infrastructure Nationale de Protéomique, FR2048 ProFI, Max Perutz Laboratories, University of Vienna [Vienna], French National Research Agency (ANR)European CommissionANR-2010-JCJC-1608ANR-14-CE19-0014French National Research Agency (ANR)ANR10-INBS-08King Abdullah University of Science & TechnologyBAS/1/1062-01-01, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Lallemant, Christopher, Saclay Plant Sciences - - SPS2010 - ANR-10-LABX-0040 - LABX - VALID, Agence Nationale de la Recherche (France), Centre Européen de Recherche en Biologie et en Médecine (France), King Abdullah University of Science and Technology, Institute of Plant Sciences Paris-Saclay, 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, Arabidopsis, Constitutively active, Library science, MAPK signaling, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, Political science, [INFO.INFO-ET] Computer Science [cs]/Emerging Technologies [cs.ET], Plant Immunity, Phosphorylation, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Arabidopsis Proteins, Pathogen-Associated Molecular Pattern Molecules, Phosphoproteomics, phosphoproteomics, Biological Sciences, Phosphoproteins, immunity, Chromatin, 3. Good health, Mapk signaling, AT-hook motif transcription factor, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], Mitogen-Activated Protein Kinases, AT-Hook Motifs, 010606 plant biology & botany
Abstract: In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis. The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions., This work was supported by Agence Nationale de la Recherche ANR-2010-JCJC-1608 and ANR-14-CE19-0014 (to D.P.); Investissement d’Avenir Infrastructures Nationales en Biologie et Santé program (ProFI project, ANR-10-INBS-08); and by King Abdullah University of Science and Technology BAS/1/1062-01-01 (to H.H.). The Institute of Plant Sciences Paris-Saclay benefits from the support of the LabEx Saclay Plant Sciences (ANR-10-LABX-0040-SPS). M.A.-T. was supported by a Humboldt-Capes fellowship.
Published: 2021
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38. 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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39. 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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40. 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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41. 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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42. 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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43. 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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44. 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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45. 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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46. 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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47. 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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48. 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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49. 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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50. 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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