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1. Semipermeable species boundaries create opportunities for gene flow and adaptive potential

Author: I. Satokangas, P. Nouhaud, B. Seifert, P. Punttila, R. Schultz, M. M. Jones, J. Sirén, H. Helanterä, J. Kulmuni, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-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), Senckenberg Museum of Natural History Görlitz, Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Finnish Environment Institute (SYKE), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Oulu, Ecology and Genetics Research Unit, University of Oulu, 90014 Oulu, Tvärminne Zoological Station, Zoological Station, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam [Amsterdam] (UvA), and We thank Natural Resources Institute Finland for access to samples collected during the 10th National Forest Inventory (NFI) of Finland, and Leena Finér and Jouni Kilpeläinen for organising the collection of the NFI ant data. NFI and data collection was funded by the Academy of Finland (#200870 and #114380). Timo Domisch, Pirjo Appelgren, Gergely Várkonyi, Riitta Savolainen and Kari Vepsäläinen provided additional ant samples. We would also like to thank Raphal Martin-Roy for helping to collect the within-nest temperature data, Jaakko Kuurne for involvement in the preliminary mitochondrial data analyses, and the SpecIAnt research group and Perttu Seppä for comments and support. Warm thanks for Martyn James and other Biomedicum Functional Genomics Unit personnel for expertise and advice in genome sequencing, and CSC–ITCenter for Science, Finland, for computational resources. Mirkka Jones and Jukka Sirén acknowledge support from the Academy of Finland's ‘Thriving Nature’ research profiling action. Jonna Kulmuni acknowledges support from the Academy of Finland (#328961, #309580). Ina Satokangas was supported by the Doctoral Programme in Integrative Life Science (University of Helsinki), and Societas pro Fauna et Flora Fennica.
Subjects: [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], speciation, mosaic hybrid zone, hybridisation, Genetics, adaptation, Hymenoptera, Ecology, Evolution, Behavior and Systematics, Formica wood ants
Abstract: International audience; Hybridisation and gene flow can have both deleterious and adaptive consequences for natural populations and species. To better understand the extent of hybridisation in nature and the balance between its beneficial and deleterious outcomes in a changing environment, information on naturally hybridising nonmodel organisms is needed. This requires the characterisation of the structure and extent of natural hybrid zones. Here, we study natural populations of five keystone mound-building wood ant species in the Formica rufa group across Finland. No genomic studies across the species group exist, and the extent of hybridisation and genomic differentiation in sympatry is unknown. Combining genome-wide and morphological data, we demonstrate more extensive hybridisation than was previously detected between all five species in Finland. Specifically, we reveal a mosaic hybrid zone between Formica aquilonia, F. rufa and F. polyctena, comprising further generation hybrid populations. Despite this, we find that F. rufa, F. aquilonia, F. lugubris and F. pratensis form distinct gene pools in Finland. We also find that hybrids occupy warmer microhabitats than the nonadmixed populations of cold-adapted F. aquilonia, and suggest that warm winters and springs, in particular, may benefit hybrids over F. aquilonia, the most abundant F. rufa group species in Finland. In summary, our results indicate that extensive hybridisation may create adaptive potential that could promote wood ant persistence in a changing climate. Additionally, they highlight the potentially significant ecological and evolutionary consequences of extensive mosaic hybrid zones, within which independent hybrid populations face an array of ecological and intrinsic selection pressures.
Published: 2023
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2. Multiple evolutionary origins and losses of tooth complexity in squamates

Author: Julien Clavel, Nicolas Di-Poï, Fabien Lafuma, Ian J. Corfe, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Geological Survey of Finland, Équipe 6 - Paléontologie, Paléoécologie, Paléobiogéographie, Évolution (P3E), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Department of Life Sciences, The Natural History Museum [London] (NHM), Vertebrate Evolution, Development and Regeneration Group, Institute of Biotechnology, and Helsinki Institute of Life Science HiLIFE
Subjects: 0106 biological sciences, REPTILES LIZARDS, Evolution, Speciation, Science, Biology, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, TEETH, Extant taxon, stomatognathic system, biology.animal, Genetic algorithm, Animals, R PACKAGE, Dietary change, PHYLOGENIES, Phylogeny, 030304 developmental biology, Mammals, 0303 health sciences, Fossils, Palaeontology, Vertebrate, Phylogenetic comparative methods, FOSSIL RECORD, Biological Evolution, ADAPTIVE RADIATION, Diet, Phylogenetics, stomatognathic diseases, EXTINCTION, Phenotype, Evolutionary biology, 1181 Ecology, evolutionary biology, Vertebrates, Cusp (anatomy), Identification (biology), Mammal, DIVERSIFICATION, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, HERBIVORY, Tooth
Abstract: Teeth act as tools for acquiring and processing food, thus holding a prominent role in vertebrate evolution. In mammals, dental-dietary adaptations rely on tooth complexity variations controlled by cusp number and pattern. Complexity increase through cusp addition has dominated the diversification of mammals. However, studies of Mammalia alone cannot reveal patterns of tooth complexity conserved throughout vertebrate evolution. Here, we use morphometric and phylogenetic comparative methods across fossil and extant squamates to show they also repeatedly evolved increasingly complex teeth, but with more flexibility than mammals. Since the Late Jurassic, multiple-cusped teeth evolved over 20 times independently from a single-cusped common ancestor. Squamates frequently lost cusps and evolved varied multiple-cusped morphologies at heterogeneous rates. Tooth complexity evolved in correlation with changes in plant consumption, resulting in several major increases in speciation. Complex teeth played a critical role in vertebrate evolution outside Mammalia, with squamates exemplifying a more labile system of dental-dietary evolution., Tooth morphology has provided many insights into the tempo and mode of dietary evolution in mammals. A study of fossil and extant squamates shows that this group also repeatedly evolved increasingly complex teeth with more flexibility than mammals, and that higher tooth complexity and herbivory likely led to higher speciation rates.
Published: 2021
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3. Putative pectate lyase PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport in Arabidopsis

Author: Lothar Kalmbach, Matthieu Bourdon, Ilya Belevich, Josip Safran, Adrien Lemaire, Jung-ok Heo, Sofia Otero, Bernhard Blob, Jérôme Pelloux, Eija Jokitalo, Ykä Helariutta, Department of Plant Molecular Biology, Université de Lausanne = University of Lausanne (UNIL), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Biologie du Fruit, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, 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), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-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), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Apollo - University of Cambridge Repository
Subjects: pectin, cell wall, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, symplastic transport, General Agricultural and Biological Sciences, phloem, General Biochemistry, Genetics and Molecular Biology, callose, plant vascular development
Abstract: In plants, the phloem distributes photosynthetic products for metabolism and storage over long distances. It relies on specialized cells, the sieve elements, which are enucleated and interconnected through large so-called sieve pores in their adjoining cell walls. Reverse genetics identified PECTATE LYASE LIKE 12 (PLL12) as critical for plant growth and development. Using genetic complementations, we established that PLL12 is required exclusively late during sieve element differentiation. Structural homology modeling, enzyme inactivation, and overexpression suggest a vital role for PLL12 in sieve element specific pectin remodeling. While short distance symplastic diffusion is unaffected, the pll12 mutant is unable to accommodate sustained plant development due to an incapacity to accommodate increasing hydraulic demands on phloem long distance transport as the plant grows – a defect that is aggravated when combined with another sieve element specific mutant callose synthase 7 (cals7). Establishing CALS7 as a specific sieve pore marker, we investigated the sub36 cellular dynamics of callose deposition in the developing sieve plate. Using fluorescent CALS7 then allowed identifying structural defects in pll12 sieve pores that are moderate at the cellular level but become physiologically relevant due to the serial arrangement of sieve elements in the sieve tube. Overall, pectin degradation through PLL12 appears subtle in quantitative terms. We therefore speculate that PLL12 may act as a regulator to locally remove homogalacturonan thus potentially enabling further extracellular enzymes to access and modify the cell wall during sieve pore maturation.
Published: 2023
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4. A network of transcriptional repressors modulates auxin responses

Author: Simon Bellows, François Parcy, Anthony Bishopp, Etienne Farcot, Siobhan M. Brady, Margot E. Smit, Jekaterina Truskina, Arnaud Stigliani, Malcolm J. Bennett, Anne Maarit Bågman, Teva Vernoux, Géraldine Brunoud, Silvana Porco, Ari Pekka Mähönen, Julien Macé, Jingyi Han, Ondřej Smetana, Elina Chrysanthou, Carlos S. Galvan-Ampudia, Jonathan Legrand, François Roudier, Stéphanie Lainé, University of Nottingham, School of Biosciences, University of Nottingham, UK (UON), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Mathematical Sciences, University of Nottingham, University of California Davis - Department of Plant Biology, University of California (UC), Genome Center [UC Davis], University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsinki Institute of Life Science (HiLIFE), Régulateurs du développement de la fleur (Flo_RE ), 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), Human Frontier Science Program organization (HFSP) grant RPG0054-2013, Royal Society University Research Fellowship and enhancement award (UF110249 and RGF\EA\180308), Aux-ID CNRS PICS grant, ANR-14-CE11-0018,SERRATIONS,Comprendre les mécanismes de signalisation de l'auxine dans la morphogenèse foliaire(2014), ANR-11-IDEX-0007,Avenir L.S.E.,PROJET AVENIR LYON SAINT-ETIENNE(2011), 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-18-CE12-0014,ChromAuxi,Décodage de la réponse auxine à l'interface ARFs-chromatine(2018), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), University of California, University of California-University of California, University of Helsinki-University of Helsinki, and University of Helsinki-University of Helsinki-Helsinki Institute of Life Science (HiLIFE)
Subjects: 0106 biological sciences, Transcription, Genetic, Mutant, Arabidopsis, Gene regulatory network, Down-Regulation, Repressor, Biology, Genes, Plant, 01 natural sciences, 03 medical and health sciences, Gene Expression Regulation, Plant, Auxin, Transcription (biology), Two-Hybrid System Techniques, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulatory Networks, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Gene, 030304 developmental biology, chemistry.chemical_classification, Regulation of gene expression, 0303 health sciences, Multidisciplinary, Indoleacetic Acids, Arabidopsis Proteins, fungi, food and beverages, Chromatin, Cell biology, Repressor Proteins, chemistry, Mutation, 010606 plant biology & botany
Abstract: International audience; The regulation of signalling capacity, combined with the spatiotemporal distribution of developmental signals themselves, is pivotal in setting developmental responses in both plants and animals1. The hormone auxin is a key signal for plant growth and development that acts through the AUXIN RESPONSE FACTOR (ARF) transcription factors2-4. A subset of these, the conserved class A ARFs5, are transcriptional activators of auxin-responsive target genes that are essential for regulating auxin signalling throughout the plant lifecycle2,3. Although class A ARFs have tissue-specific expression patterns, how their expression is regulated is unknown. Here we show, by investigating chromatin modifications and accessibility, that loci encoding these proteins are constitutively open for transcription. Through yeast one-hybrid screening, we identify the transcriptional regulators of the genes encoding class A ARFs from Arabidopsis thaliana and demonstrate that each gene is controlled by specific sets of transcriptional regulators. Transient transformation assays and expression analyses in mutants reveal that, in planta, the majority of these regulators repress the transcription of genes encoding class A ARFs. These observations support a scenario in which the default configuration of open chromatin enables a network of transcriptional repressors to regulate expression levels of class A ARF proteins and modulate auxin signalling output throughout development.
Published: 2020
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5. Inverse Conformational Selection in Lipid–Protein Binding

Author: Matti Javanainen, Salla I. Virtanen, Fernando Favela-Rosales, Chris Papadopoulos, Antonio Peón, Amélie Bacle, Anne M. Kiirikki, Patrick F.J. Fuchs, O. H. Samuli Ollila, Pavel Buslaev, Ángel Piñeiro, Rebeca García-Fandiño, Paula Milán Rodríguez, Tiago Mendes Ferreira, Markus S. Miettinen, Jesper J. Madsen, Josef Melcr, Ivan Gushchin, Thomas J. Piggot, Lipotoxicity and Channelopathies - ConicMeds (LitCh), Signalisation et Transports Ioniques Membranaires (STIM), Université de Poitiers-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Nanoscience Center [Jyväskylä Univ] (NSC@JYU), University of Jyväskylä (JYU), Moscow Institute of Physics and Technology [Moscow] (MIPT), Centro de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS ), Universidade de Santiago de Compostela [Spain] (USC ), Universidade do Porto = University of Porto, Tecnológico Nacional de México (TecNM), Martin-Luther-University Halle-Wittenberg, Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UFR Sciences du Vivant [Sciences] - Université Paris Cité (UFR SDV UPCité), Université Paris Cité (UPCité), Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB / CAS), Czech Academy of Sciences [Prague] (CAS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Chicago, University of South Florida [Tampa] (USF), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen [Groningen], Max Planck Institute of Colloids and Interfaces, Max-Planck-Gesellschaft, 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), University of Southampton, Molecular Dynamics, Institute of Biotechnology, Biophysical chemistry, Gestionnaire, Hal Sorbonne Université, Université Paris Cité - UFR Sciences du Vivant [Sciences] (UPCité - UFR SDV), Université de Poitiers-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Paris - UFR Sciences du Vivant [Sciences] (UP - UFR SDV), Université de Paris (UP), University of Helsinki-University of Helsinki, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: DYNAMICS, ELECTRIC CHARGE, BILAYERS, PHOSPHATIDYLCHOLINE HEADGROUP, Membrane lipids, DEUTERIUM, Plasma protein binding, Molecular Dynamics Simulation, lipidit, 010402 general chemistry, 01 natural sciences, Biochemistry, biomolekyylit, Catalysis, 03 medical and health sciences, Molecular dynamics, kemialliset sidokset, Colloid and Surface Chemistry, Protein structure, PHOSPHOLIPID-BINDING, MAGNETIC-RESONANCE, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, SEGMENTAL ORDER, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Conformational ensembles, Nuclear Magnetic Resonance, Biomolecular, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Chemistry, Biomolecule, MEMBRANE-LIPIDS, Proteins, Phosphatidylglycerols, General Chemistry, computer.file_format, Protein Data Bank, Lipids, 0104 chemical sciences, Biophysics, Phospholipid Binding, Phosphatidylcholines, MAS NMR, 1182 Biochemistry, cell and molecular biology, lipids (amino acids, peptides, and proteins), proteiinit, computer, Protein Binding
Abstract: International audience; Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups exchange between a few rigid structures, or fluctuate freely across a practically continuous spectrum of conformations? Here, we combine solid-state NMR experiments and molecular dynamics simulations from the NMRlipids Project to resolve the conformational ensembles of headgroups of four key lipid types in various biologically relevant conditions. We find that lipid headgroups sample a wide range of overlapping conformations in both neutral and charged cellular membranes, and that differences in the headgroup chemistry manifest only in probability distributions of conformations. Furthermore, the analysis of 894 protein-bound lipid structures from the Protein Data Bank suggests that lipids can bind to proteins in a wide range of conformations, which are not limited by the headgroup chemistry. We propose that lipids can select a suitable headgroup conformation from the wide range available to them to fit the various binding sites in proteins. The proposed inverse conformational selection model will extend also to lipid binding to targets other than proteins, such as drugs, RNA, and viruses.
Published: 2021
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6. GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation

Author: Witkos, Tomasz M., Chan, Wing Lee, Joensuu, Merja, Rhiel, Manuel, Pallister, Ed, Thomas-Oates, Jane, Mould, A. Paul, Mironov, Alex A., Biot, Christophe, Guerardel, Yann, Morelle, Willy, Ungar, Daniel, Wieland, Felix T., Jokitalo, Eija, Tassabehji, May, Kornak, Uwe, Lowe, Martin, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Molecular Biology, Princeton University, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Faculty of Life Sciences [Manchester], University of Manchester [Manchester], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Université de Lille-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Lille, CNRS, University of Manchester Institute of Science and Technology [UMIST], Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Universität Heidelberg [Heidelberg] = Heidelberg University, Department of Chemistry [York, UK], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 [UGSF], Department of Biology [York], Electron Microscopy, Institute of Biotechnology, and Doctoral Programme in Integrative Life Science
Subjects: Glycosylation, 119 Other natural sciences, Science, Golgi Apparatus, Dwarfism, Article, Coat Protein Complex I, ADP-RIBOSYLATION FACTOR, RECESSIVE FORM, OF-FUNCTION MUTATIONS, Humans, SCYL1, lcsh:Science, BETA-COP, Cells, Cultured, ComputingMilieux_MISCELLANEOUS, COATED VESICLES, Bone Diseases, Carrier Proteins, Cells, Cultured, Enzymes, Golgi Matrix Proteins, HEK293 Cells, HeLa Cells, Mutation, Protein Binding, Protein Transport, RNA Interference, Skin Diseases, Genetic, Transcription Factors, COMPLEX, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], COATOMER, Skin Diseases, Genetic, GERODERMIA OSTEODYSPLASTICA, DNA-Binding Proteins, Adaptor Proteins, Vesicular Transport, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], MEMBRANE TRAFFICKING, lcsh:Q
Abstract: COPI is a key mediator of protein trafficking within the secretory pathway. COPI is recruited to the membrane primarily through binding to Arf GTPases, upon which it undergoes assembly to form coated transport intermediates responsible for trafficking numerous proteins, including Golgi-resident enzymes. Here, we identify GORAB, the protein mutated in the skin and bone disorder gerodermia osteodysplastica, as a component of the COPI machinery. GORAB forms stable domains at the trans-Golgi that, via interactions with the COPI-binding protein Scyl1, promote COPI recruitment to these domains. Pathogenic GORAB mutations perturb Scyl1 binding or GORAB assembly into domains, indicating the importance of these interactions. Loss of GORAB causes impairment of COPI-mediated retrieval of trans-Golgi enzymes, resulting in a deficit in glycosylation of secretory cargo proteins. Our results therefore identify GORAB as a COPI scaffolding factor, and support the view that defective protein glycosylation is a major disease mechanism in gerodermia osteodysplastica., COPI is recruited to the membrane by binding to Arf GTPases. Here the authors find that GORAB, a trans-Golgi protein, promotes COPI recruitment by forming membrane domains that also contain the COPI-interacting protein Scyl1, which is required for efficient glycosylation of cargo proteins.
Published: 2019
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7. Root branching toward water involves posttranslational modification of transcription factor ARF7

Author: Emily Morris, José R. Dinneny, Kristine Hill, Andrew P. French, Beatriz Orosa-Puente, Jason Banda, Joop E.M. Vermeer, Tatsuaki Goh, Nicola Leftley, Teva Vernoux, Daniel von Wangenheim, Moumita Srivastava, Malcolm J. Bennett, Ari Sadanandom, Britta M. C. Kümpers, Jekaterina Truskina, Rahul Bhosale, Hidehiro Fukaki, Anthony Bishopp, Anjil Kumar Srivastava, Goethe-Universität Frankfurt am Main, Centre for Plant Integrative Biology, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Graduate School of Science, Department of Biology, Kobe University, ARS/ALARC, United States Department of Agriculture, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, University of Nottingham, UK (UON), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki
Subjects: 0301 basic medicine, DNA, Plant, SUMO-1 Protein, Arabidopsis, SUMO protein, Repressor, Plant Roots, 03 medical and health sciences, Gene Expression Regulation, Plant, Transcription (biology), Auxin, Gene expression, Life Science, Transcription factor, ComputingMilieux_MISCELLANEOUS, Regulation of gene expression, chemistry.chemical_classification, Multidisciplinary, Indoleacetic Acids, Arabidopsis Proteins, Lateral root, Nuclear Proteins, Sumoylation, Water, Laboratorium voor Celbiologie, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cell biology, Laboratory of Cell Biology, 030104 developmental biology, chemistry, Protein Binding, Transcription Factors
Abstract: Rooting out the mechanism of asymmetry Plant roots grow not in response to architectural blueprints but rather in search of scarce resources in the soil. Orosa-Puente et al. show why a new lateral root emerges on the damp side of a root rather than the dry side (see the Perspective by Giehl and von Wirén). The transcription factor ARF7 is found across the whole root but acquires a posttranslational modification on the dry side of the root, which represses its function. ARF7 on the damp side remains functional and is thus able to initiate the signaling cascade that leads to a new lateral root. Science , this issue p. 1407 ; see also p. 1358
Published: 2018
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8. Hard to catch: Experimental evidence supports evasive mimicry

Author: Johanna Mappes, Keith R. Willmott, Marianne Elias, Janne K. Valkonen, Pável Matos-Maraví, Erika Páez, Organismal and Evolutionary Biology Research Programme, 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), Department of Biological and Environmental Science [Jyväskylä Univ] (JYU), University of Jyväskylä (JYU), McGuire Center for Lepidoptera and Biodiversity, Institute of Entomology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki-Helsinki Institute of Life Science (HiLIFE), and University of Helsinki-University of Helsinki
Subjects: prey defence, 0106 biological sciences, Evolution, Computer science, Aposematism, Models, Biological, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Müllerian mimicry, Predation, Songbirds, 03 medical and health sciences, Avoidance learning, Generalization (learning), Animals, Wings, Animal, General Environmental Science, 030304 developmental biology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Wing, convergence, General Immunology and Microbiology, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Biological Mimicry, General Medicine, Adelpha, biology.organism_classification, Biological Evolution, Batesian mimicry, predator learning, Evolutionary biology, Predatory Behavior, 1181 Ecology, evolutionary biology, Mimicry, evasive aposematism, General Agricultural and Biological Sciences, distastefulness, Butterflies
Abstract: Most research on aposematism has focused on chemically defended prey, but the signalling difficulty of capture remains poorly explored. Similar to classical Batesian and Müllerian mimicry related to distastefulness, such ‘evasive aposematism' may also lead to convergence in warning colours, known as evasive mimicry. A prime candidate group for evasive mimicry areAdelphabutterflies, which are agile insects and show remarkable colour pattern convergence. We tested the ability of naive blue tits to learn to avoid and generalizeAdelphawing patterns associated with the difficulty of capture and compared their response to that of birds that learned to associate the same wing patterns with distastefulness. Birds learned to avoid all wing patterns tested and generalized their aversion to other prey to some extent, but learning was faster with evasive prey compared to distasteful prey. Our results on generalization agree with longstanding observations of striking convergence in wing colour patterns amongAdelphaspecies, since, in our experiments, perfect mimics of evasive and distasteful models were always protected during generalization and suffered the lowest attack rate. Moreover, generalization on evasive prey was broader compared to that on distasteful prey. Our results suggest that being hard to catch may deter predators at least as effectively as distastefulness. This study provides empirical evidence for evasive mimicry, a potentially widespread but poorly understood form of morphological convergence driven by predator selection.
Published: 2020
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9. ELIMÄKI Locus Is Required for Vertical Proprioceptive Response in Birch Trees

Author: Pasi Rastas, Ari Pekka Mähönen, Lorenz Gerber, Olli-Pekka Smolander, Alexis Peaucelle, Kaisa Nieminen, Hanna Koivula, Hanna Help, Ykä Helariutta, Junko Takahashi, Gugan Eswaran, Omid Safronov, Juan Alonso-Serra, Risto Hagqvist, Chang Su, Juha Immanen, Jarkko Salojärvi, Xueping Shi, Matthieu Bourdon, Sampo Muranen, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Zoology [Cambridge], University of Cambridge [UK] (CAM), Biologie du Fruit, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, NTT Basic Research Laboratories, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Swedish University of Agricultural Sciences (SLU), Department of Plant Molecular Biology, Université de Lausanne (UNIL), Helariutta, Yrjo [0000-0002-7287-8459], Apollo - University of Cambridge Repository, Institute of Biotechnology, Organismal and Evolutionary Biology Research Programme, Food Sciences, Department of Food and Nutrition, Helsinki Institute of Life Science HiLIFE, Materials Physics, Molecular and Integrative Biosciences Research Programme, Plant-Fungal Interactions Group, Bioinformatics for Molecular Biology and Genomics (BMBG), Viikki Plant Science Centre (ViPS), Ari Pekka Mähönen / Principal Investigator, Biosciences, Plant Biology, Yrjö Helariutta / Principal Investigator, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Huazhong Agricultural University [Wuhan] (HZAU), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Natural Resources Institute Finland (LUKE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Tallinn University of Technology (TTÜ), Nanyang Technological University [Singapour], Université de Lausanne = University of Lausanne (UNIL), Academy of Finland Finnish Centre of Excellence in Molecular Biology of Primary Producers (CoE 2014-2019) 271832286404, Gatsby Foundation GAT3395/PR3, University of Helsinki 799992091, and European Project: 323052,EC:FP7:ERC,ERC-2012-ADG_20120314,SYMDEV(2013)
Subjects: 0301 basic medicine, STRESS, [SDV]Life Sciences [q-bio], 119 Other natural sciences, Mutant, Gravitropism, Morphogenesis, Locus (genetics), Stimulus (physiology), Genes, Plant, GRAVITROPISM, General Biochemistry, Genetics and Molecular Biology, BIOMASS, Trees, 03 medical and health sciences, 0302 clinical medicine, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, PLANTS, TRANSCRIPTOME, Betula, COMPLEX, Cambium, biology, Plant Stems, 1184 Genetics, developmental biology, physiology, Xylem, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, Betula pubescens, ARABIDOPSIS, biology.organism_classification, Proprioception, Cell biology, forward genetics, INSIGHTS, radial growth, 030104 developmental biology, CELLULOSE, Mutation, GROWTH, wood formation, mechanosensing, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract: International audience; Tree architecture has evolved to support a top-heavy above-ground biomass, but this integral feature poses a weight-induced challenge to trunk stability. Maintaining an upright stem is expected to require vertical proprioception through feedback between sensing stem weight and responding with radial growth. Despite its apparent importance, the principle by which plant stems respond to vertical loading forces remains largely unknown. Here, by manipulating the stem weight of downy birch (Betula pubescens) trees, we show that cambial development is modulated systemically along the stem. We carried out a genetic study on the underlying regulation by combining an accelerated birch flowering program with a recessive mutation at the ELIMAKI locus (EKI), which causes a mechanically defective response to weight stimulus resulting in stem collapse after just 3 months. We observed delayed wood morphogenesis in eki compared with WT, along with a more mechanically elastic cambial zone and radial compression of xylem cell size, indicating that rapid tissue differentiation is critical for cambial growth under mechanical stress. Furthermore, the touch-induced mechanosensory pathway was transcriptionally misregulated in eki, indicating that the ELIMAKI locus is required to integrate the weight-growth feedback regulation. By studying this birch mutant, we were able to dissect vertical proprioception from the gravitropic response associated with reaction wood formation. Our study provides evidence for both local and systemic responses to mechanical stimuli during secondary plant development.
Published: 2020
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10. Gut microbiota composition is associated with narcolepsy type 1

Author: Lecomte, Alexandre, Barateau, Lucie, Pereira, Pedro, Paulin, Lars, Auvinen, Petri, Scheperjans, Filip, Dauvilliers, Yves, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Département de neurologie [Montpellier], Hôpital Gui de Chauliac [Montpellier]-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Université Montpellier 1 (UM1)-Université de Montpellier (UM), Neuropsychiatrie : recherche épidémiologique et clinique (PSNREC), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Helsinki University Hospital [Finland] (HUS), University of Helsinki, Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Gui de Chauliac [Montpellier]-Université de Montpellier (UM), Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Biotechnology, Department of Neurosciences, Neurologian yksikkö, DNA Sequencing and Genomics, and HUS Neurocenter
Subjects: Adult, Male, Time Factors, Adolescent, Sequence Analysis, RNA, education, Middle Aged, 3124 Neurology and psychiatry, Article, Gastrointestinal Microbiome, Feces, Young Adult, RNA, Ribosomal, 16S, Humans, Female, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Narcolepsy
Abstract: International audience; Objective: To test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.Methods: Thirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.Results: We found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.Conclusion: We provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.
Published: 2020
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11. Occurrence and Molecular Phylogeny of Honey Bee Viruses in Vespids

Author: Hongxia Zhao, Dahe Yang, Elisabeth A. Herniou, Yaojun Wu, Xuejian Jiang, Philippe Gayral, Xinling Wang, Eric Darrouzet, Sa Yang, Chunsheng Hou, Fei Li, Qingyun Diao, Yan-Yan Wu, Diane Bigot, Shuai Deng, Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Institute of Apicultural Research [Beijing, China], Chinese Academy of Agricultural Sciences (CAAS), China Agricultural University (CAU), and Université de Tours-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, viruses, [SDV]Life Sciences [q-bio], Zoology, Insect Viruses, complex mixtures, 01 natural sciences, Article, Virus, Animal Diseases, 03 medical and health sciences, IAPV, AmFV, Virology, Deformed wing virus, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Mite, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Phylogeny, DWV, honeybee viruses, biology, Phylogenetic tree, Vespidae, fungi, hornets, High-Throughput Nucleotide Sequencing, food and beverages, Honey bee, Bees, biology.organism_classification, Insect Vectors, 3. Good health, Phylogeography, 010602 entomology, 030104 developmental biology, Infectious Diseases, Varroa destructor, Molecular phylogenetics, behavior and behavior mechanisms
Abstract: Since the discovery that honey bee viruses play a role in colony decline, researchers have made major breakthroughs in understanding viral pathology and infection processes in honey bees. Work on virus transmission patterns and virus vectors, such as the mite Varroa destructor, has prompted intense efforts to manage honey bee health. However, little is known about the occurrence of honey bee viruses in bee predators, such as vespids. In this study, we characterized the occurrence of 11 honey bee viruses in five vespid species and one wasp from four provinces in China and two vespid species from four locations in France. The results showed that all the species from China carried certain honey bee viruses, notably Apis mellifera filamentous virus (AmFV), Deformed wing virus (DWV), and Israeli acute paralysis virus (IAPV), furthermore, in some vespid colonies, more than three different viruses were identified. In France, DWV was the most common virus, Sacbrood virus (SBV) and Black queen cell virus (BQCV) were observed in one and two samples, respectively. Phylogenetic analyses of IAPV and BQCV sequences indicated that most of the IAPV sequences belonged to a single group, while the BQCV sequences belonged to several groups. Additionally, our study is the first to detect Lake Sinai virus (LSV) in a hornet from China. Our findings can guide further research into the origin and transmission of honey bee viruses in Vespidae, a taxon of ecological, and potentially epidemiological, relevance.
Published: 2020
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12. The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids

Author: Savilammi, Tiina, Primmer, Craig R., Varadharajan, Srinidhi, Guyomard, Rene, Guiguen, Yann, Sandve, Simen Rød, Asbjørn Vøllestad, L., Vøllestad, Leif Asbjørn, Papakostas, Spiros, Lien, Sigbjørn, Department of Biology, University of Memphis, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki-Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, University of Helsinki, Department of Biosciences, University of Kent [Canterbury], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Centre for Integrative Genetics (CIGENE), ANR Blanc SVSE 7 - 2011 (Project SDS), This work was supported by the Academy of Finland (project numbers 287342 and 302873). We thank the Finnish Centre for Scientific Computing for providing computational resources. SV and LAV are supported by Center for Computational Inference in Evolutionary Life Science (CELS) and the Department of Biosciences, University of Oslo. YG and RG contributions were supported by the Agence Nationale de la Recherche (ANR Blanc SVSE 7 2011, project SDS)., ANR-15-CE37-0004,SmellBrain,Dissection fonctionnelle des circuits codant pour la récompense dans le système olfactif(2015), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Helsinki Institute of Sustainability Science (HELSUS), Evolution, Conservation, and Genomics, Institute of Biotechnology, and Organismal and Evolutionary Biology Research Programme
Subjects: 0106 biological sciences, Male, Genetic Linkage, [SDV]Life Sciences [q-bio], génomique fonctionnelle, chromosome evolution, Retrotransposon, QH426-470, 01 natural sciences, Genome, ANNOTATION, poisson, salmonids, DRIVERS, chromosome, ombre commun, Salmo, Genetics (clinical), salmonidae, 0303 health sciences, biology, REARRANGEMENTS, 1184 Genetics, developmental biology, physiology, Chromosome Mapping, karyotype evolution, karyotyping of the cells, Genomics, Thymallus, gène sdY, retrotransposons, ALIGNMENT, séquençage du génome, caryotype, évolution du génome, chromosomal structure, Female, rétrotransposon, Genome evolution, DATABASE, Centromere, Salmo salar, genomic rearrangements, 010603 evolutionary biology, Chromosomes, CLASSIFICATION, thymallus thymallus, Evolution, Molecular, reproduction, 03 medical and health sciences, Genetics, Animals, 14. Life underwater, Molecular Biology, 030304 developmental biology, Synteny, Repetitive Sequences, Nucleic Acid, fish, IDENTIFICATION, Chromosome, Computational Biology, biology.organism_classification, GENE, Genome Report, European grayling, Evolutionary biology, ORIGINS, structure chromosome, évolution chromosomique, SYSTEM
Abstract: Supplemental material available at Figshare: https://doi.org/10.25387/g3.7728512; Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split.
Published: 2019
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13. Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading

Author: Dawei Yan, Shri Ram Yadav, Andrea Paterlini, William J. Nicolas, Jules D. Petit, Lysiane Brocard, Ilya Belevich, Magali S. Grison, Anne Vaten, Leila Karami, Sedeer el-Showk, Jung-Youn Lee, Gosia M. Murawska, Jenny Mortimer, Michael Knoblauch, Eija Jokitalo, Jennifer E. Markham, Emmanuelle M. Bayer, Ykä Helariutta, Yan, Dawei [0000-0001-8256-0279], Paterlini, Andrea [0000-0002-1777-3160], Belevich, Ilya [0000-0003-2190-4909], Mortimer, Jenny [0000-0001-6624-636X], Bayer, Emmanuelle M [0000-0001-8642-5293], Helariutta, Ykä [0000-0002-7287-8459], Apollo - University of Cambridge Repository, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Indian Institute of Technology Roorkee (IIT Roorkee), Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Department of Plant and Soil Sciences, University of Delaware [Newark], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), School of Biological Sciences, Washington State University (WSU), Department of Biochemistry [Lincoln], University of Nebraska [Lincoln], and University of Nebraska System-University of Nebraska System
Subjects: 0106 biological sciences, 0301 basic medicine, Quantitative Biology - Subcellular Processes, Green Fluorescent Proteins, Arabidopsis, Transferases (Other Substituted Phosphate Groups), Plant Science, Plasmodesma, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Phloem, Genes, Plant, 01 natural sciences, Plant Roots, 03 medical and health sciences, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Glucans, Subcellular Processes (q-bio.SC), q-bio.SC, 2. Zero hunger, Sphingolipids, Chemistry, Arabidopsis Proteins, Endoplasmic reticulum, fungi, Plasmodesmata, Membrane Proteins, food and beverages, Plant, Meristem, Sphingolipid, Cell biology, Pericycle, 030104 developmental biology, Genes, Cytoplasm, FOS: Biological sciences, Mutation, Ultrastructure, 010606 plant biology & botany
Abstract: During phloem unloading, multiple cell-to-cell transport events move organic substances to the root meristem. Although the primary unloading event from the sieve elements to the phloem pole pericycle has been characterized to some extent, little is known about post-sieve element unloading. Here, we report a novel gene, PHLOEM UNLOADING MODULATOR (PLM), in the absence of which plasmodesmata-mediated symplastic transport through the phloem pole pericycle--endodermis interface is specifically enhanced. Increased unloading is attributable to a defect in the formation of the endoplasmic reticulum--plasma membrane tethers during plasmodesmal morphogenesis, resulting in the majority of pores lacking a visible cytoplasmic sleeve. PLM encodes a putative enzyme required for the biosynthesis of sphingolipids with very-long-chain fatty acid. Taken together, our results indicate that post-sieve element unloading involves sphingolipid metabolism, which affects plasmodesmal ultrastructure. They also raise the question of how and why plasmodesmata with no cytoplasmic sleeve facilitate molecular trafficking., Comment: Nature Plants, Nature Publishing Group, In press
Published: 2019
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14. A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate

Author: Ranjan Swarup, Meredith T. Hanlon, Darren M. Wells, Bipin K. Pandey, Anja Hartmann, Richard Traini, Ute Voß, Jeonga Yun, Nicola Leftley, Kamal Swarup, Kathleen M. Brown, Malcolm J. Bennett, Nicolaus von Wirén, Jonathan P. Lynch, Teva Vernoux, Anna Stepanova, Ricardo Fabiano Hettwer Giehl, Jose M. Alonso, Anthony Bishopp, Liam Dolan, Jekaterina Truskina, Rahul Bhosale, Karin Ljung, Jitender Giri, Afaf Rashed, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Integrative Biology, University of Nottingham, UK (UON), Department of Genetics, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Umea Plant Science Center, Swedish University of Agricultural Sciences (SLU)-Department of Forest Genetics and Plant Physiology, Department of Plant Science, Pennsylvania State University (Penn State), Penn State System-Penn State System, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Biotechnology and Biological Sciences Research Council BB/G023972/1 BB/R013748/1 BB/L026848/1 BB/M018431/1 BB/PO16855/1 BB/M001806/1 BB/P010520/1, European Research Council FUTUREROOTS Advanced Investigator grant 294729, Leverhulme Trust RPG-2016-409, Royal SocietyWM130021 NA140281, Newton International Fellowship NF140287, British Council Newton Bhabha 228144076, University of Nottingham Future Food Beacon of Excellence Nottingham Research and PhD+ fellowship schemes, Interuniversity Attraction Poles Program, Belgian Science Policy Office P7/29, Swedish Governmental Agency for Innovation Systems (VINNOVA), Swedish Research Council (V.R.), University of Nottingham, Institut National de la Recherche Agronomique (INRA), and NSF-MCB1158181
Subjects: 0106 biological sciences, 0301 basic medicine, Science, Mutant, General Physics and Astronomy, Organogenesis, Root hair, Root hair elongation, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Auxin, Arabidopsis, heterocyclic compounds, lcsh:Science, Transcription factor, ComputingMilieux_MISCELLANEOUS, phosphate, chemistry.chemical_classification, Multidisciplinary, biology, integumentary system, auxine, plasticité, Lateral root, fungi, food and beverages, General Chemistry, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, croissance cellulaire, Cell biology, racine, arabidopsis, 030104 developmental biology, chemistry, plante, lcsh:Q, 010606 plant biology & botany
Abstract: Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
Published: 2018
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15. Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures

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

Author: Howard T. Jacobs, Pierre Rustin, Malgorzata Rak, Riyad El-Khoury, Hyung-Ho Ha, Paule Bénit, Young-Tae Chang, Martin Jastroch, Dominique Chretien, Susanne Keipert, Neuroprotection du Cerveau en Développement / Promoting Research Oriented Towards Early Cns Therapies (PROTECT), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), College of Pharmacy [Suncheon, Corée du Sud], Suncheon National University [Suncheon, Corée du Sud], Institute for Diabetes and Obesity [Neuherberg, Allemagne], German Research Center for Environmental Health - Helmholtz Center München (GmbH), Neuromuscular Diagnostic Laboratory [Beyrouth, Liban], Department of Pathology & Laboratory Medicine [Beyrouth, Liban], American University of Beirut Medical Center [Beyrouth, Liban] (AUBMC), American University of Beirut [Beyrouth] (AUB)-American University of Beirut [Beyrouth] (AUB)-American University of Beirut Medical Center [Beyrouth, Liban] (AUBMC), American University of Beirut [Beyrouth] (AUB)-American University of Beirut [Beyrouth] (AUB), Department of Chemistry [Pohang, Corée du Sud], Pohang University of Science and Technology (POSTECH), Institute of Biosciences and Medical Technology [Tampere, Finlande] (BioMediTech), University of Tampere [Finland], Tampere University Hospital, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Centre National de la Recherche Scientifique (CNRS), European Research Council (grant number 232738). Received by HTJ. Academy Professorship (grant number 256615). Received by HTJ. Academy of Finland (grant number FinMIT CoE 272376). Received by HTJ. Ouvrir Les Yeux (OLY). Received by PB and PR. Association Française contre l'Ataxie de Friedreich (AFAF). Received by PB and PR. Association contre les Maladies Mitochondriales (AMMi). Received by DC, PB, MR, and PR. Association d'Aide aux Jeunes Infirmes (AAJI). Received by PB and PR. E-Rare (grant number E-rare Genomit). Received by DC, PB, MR, and PR. ANR (grant number ANR MITOXDRUGS-DS0403). Received by DC, PB, MR, and PR. ANR (grant number ANR FIFA2-12-BSV1-0010). Received by DC, PB, MR, and PR., ANR-12-BSV1-0010,FiFA2,Combattre l'Ataxie de Friedreich: utilisation de modèles biologiques complémentaires pour le criblage et l'optimisation de nouvelles molécules thérapeutiques(2012), European Project: 232738,EC:FP7:ERC,ERC-2008-AdG,MITO BY-PASS(2009), University of Helsinki-University of Helsinki, Bodescot, Myriam, BLANC - Combattre l'Ataxie de Friedreich: utilisation de modèles biologiques complémentaires pour le criblage et l'optimisation de nouvelles molécules thérapeutiques - - FiFA22012 - ANR-12-BSV1-0010 - BLANC - VALID, and Molecular by-pass therapy for mitochondrial dysfunction - MITO BY-PASS - - EC:FP7:ERC2009-04-01 - 2015-03-31 - 232738 - VALID
Subjects: Hot Temperature, Luminescence, Physiology, Respiratory chain, Mitochondrion, Toxicology, Pathology and Laboratory Medicine, Biochemistry, 0302 clinical medicine, Cytosol, Short Reports, Animal Cells, Medicine and Health Sciences, Uncoupling protein, Biology (General), Uncoupling Protein 1, Energy-Producing Organelles, Plant Proteins, Skin, Connective Tissue Cells, chemistry.chemical_classification, 0303 health sciences, ATP synthase, biology, Physics, Electromagnetic Radiation, Temperature, Thermogenesis, Mitochondria, Electrophysiology, Chemistry, Connective Tissue, Mitochondrial Membranes, Physical Sciences, Cellular Structures and Organelles, Anatomy, Cellular Types, Oxidoreductases, Chemical Elements, Alternative oxidase, QH301-705.5, Primary Cell Culture, Toxic Agents, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Bioenergetics, Membrane Potential, Fluorescence, Mitochondrial Proteins, 03 medical and health sciences, Humans, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, Fluorescent Dyes, Cyanides, HEK 293 cells, Chemical Compounds, Biology and Life Sciences, Kidneys, Metabolism, Cell Biology, Renal System, Fibroblasts, Oxygen, Enzyme, HEK293 Cells, Biological Tissue, chemistry, biology.protein, Biophysics, Salts, 030217 neurology & neurosurgery
Abstract: In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, but a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperature in situ under different physiological conditions. At a constant external temperature of 38 °C, mitochondria were more than 10 °C warmer when the respiratory chain (RC) was fully functional, both in human embryonic kidney (HEK) 293 cells and primary skin fibroblasts. This differential was abolished in cells depleted of mitochondrial DNA or treated with respiratory inhibitors but preserved or enhanced by expressing thermogenic enzymes, such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at or slightly above 50 °C. In view of their potential consequences, these observations need to be further validated and explored by independent methods. Our study prompts a critical re-examination of the literature on mitochondria., Author summary To ensure a stable internal temperature, endothermic species make use of the heat released during the final steps of food burning by the mitochondria present in all cells of the organism. Indeed, only a fraction of the energy released by the oxidation of respiratory substrates is used to generate ATP, while a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured the temperature of active mitochondria in cultured intact human cells. Mitochondria were found to be more than 10 °C warmer when the respiratory chain was functional. This differential was abolished in cells depleted of mitochondrial DNA or by respiratory inhibitors but preserved or enhanced by the expression of thermogenic enzymes such as Ciona alternative oxidase or by uncoupling protein 1. The activity of various respiratory chain enzymes was found to be maximal near 50 °C. Note that in view of their potential consequences, the observations reported here need to be validated and explored further by independent methods.
Published: 2018
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17. A homozygous FANCM mutation underlies a familial case of non-syndromic primary ovarian insufficiency

Author: Baptiste Fouquet, Patrycja Pawlikowska, Sandrine Caburet, Celine Guigon, Marika Mäkinen, Laura Tanner, Marja Hietala, Kaja Urbanska, Laura Bellutti, Bérangère Legois, Bettina Bessieres, Alain Gougeon, Alexandra Benachi, Gabriel Livera, Filippo Rosselli, Reiner A Veitia, Micheline Misrahi, Immunology-Hematology, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Unité de Biologie Fonctionnelle et Adaptative (BFA (UMR_8251 / U1133)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Département d’Histologie-Embryologie-Cytogénétique, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Equipe 4, Tumeurs endocrines digestives : mécanismes de la tumorigenèse et de la progression tumorale, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Léon Bérard [Lyon]-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Mondor de recherche biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), U967, Laboratoire de Développement des Gonades, Institut National de la Santé et de la Recherche Médicale (INSERM), Stabilité Génétique et Oncogenèse (UMR 8200), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11), Hôpital Bicêtre, Université Paris-Sud - Paris 11 - Faculté de médecine (UP11 UFR Médecine), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Turku University Hospital (TYKS), Stabilité génétique, Cellules Souches et Radiations (SCSR (U_967)), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut de Radiobiologie Cellulaire et Moléculaire (IRCM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris-Saclay, Fondation pour la Recherche Médicale (Grant DEQ20150331757), Ligue Contre le Cancer, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Rosselli, Filippo
Subjects: Adult, Male, congenital, hereditary, and neonatal diseases and abnormalities, Genotype, QH301-705.5, [SDV]Life Sciences [q-bio], Science, Young Adult, FANCM, hemic and lymphatic diseases, Mitomycin C, Humans, Genetic Predisposition to Disease, Biology (General), Human Biology and Medicine, Homologous Recombination, ComputingMilieux_MISCELLANEOUS, Chromosome Aberrations, Fanconi Anemia Complementation Group D2 Protein, Homozygote, Ovary, DNA Helicases, Ubiquitination, nutritional and metabolic diseases, Middle Aged, Pedigree, primary ovarian insufficiency, [SDV] Life Sciences [q-bio], Phenotype, replication inhibitor, Medicine, Female, mutation, exome sequencing, Research Article, Human
Abstract: Primary Ovarian Insufficiency (POI) affects ~1% of women under forty. Exome sequencing of two Finnish sisters with non-syndromic POI revealed a homozygous mutation in FANCM, leading to a truncated protein (p.Gln1701*). FANCM is a DNA-damage response gene whose heterozygous mutations predispose to breast cancer. Compared to the mother's cells, the patients’ lymphocytes displayed higher levels of basal and mitomycin C (MMC)-induced chromosomal abnormalities. Their lymphoblasts were hypersensitive to MMC and MMC-induced monoubiquitination of FANCD2 was impaired. Genetic complementation of patient's cells with wild-type FANCM improved their resistance to MMC re-establishing FANCD2 monoubiquitination. FANCM was more strongly expressed in human fetal germ cells than in somatic cells. FANCM protein was preferentially expressed along the chromosomes in pachytene cells, which undergo meiotic recombination. This mutation may provoke meiotic defects leading to a depleted follicular stock, as in Fancm-/- mice. Our findings document the first Mendelian phenotype due to a biallelic FANCM mutation., eLife digest About one in 100 women under the age of 40 experience a condition known as primary ovarian insufficiency, which is sometimes known as premature menopause. Women with this condition may have fewer egg cells and are usually infertile. Women with primary ovarian insufficiency are also more at risk of other diseases, including the bone disorder osteoporosis and cardiovascular diseases. The condition is thought to have a genetic basis in part, although so far its causes are largely unknown. Fouquet, Pawlikowska et al. looked at all the genes in genomes of three women in one Finnish family: two sisters and their mother. Both of the sisters had primary ovarian insufficiency, but were otherwise healthy. Their mother did not have the condition. The genetic analysis identified a mutation in a gene called FANCM, which is involved in the cell’s repair response to DNA damage and has recently been linked to breast cancer. This gene is mostly active in egg cells within the ovary. The sisters’ protein made from this mutated copy of the gene was cut short compared with the protein produced by the mother’s FANCM gene. Due to the mutation, the sisters were more sensitive to chemicals that can damage the DNA, effectively making their genome less stable. The affected sisters also had higher levels of abnormalities in the chromosomes compared with their unaffected mother. Fouquet, Pawlikowska et al. then inserted a healthy version of the FANCM gene into the sisters’ cells. This reversed the sensitivity of the sisters’ cells to DNA-damaging chemicals. The findings confirm a genetic link between primary ovarian insufficiency and genes responsible for DNA repair. Mutations in these genes can also make people more at risk of certain cancers. The findings point towards offering some women who have primary ovarian insufficiency in-depth genetic counselling with a long-term follow-up, when alterations of cancer-susceptibility genes are responsible for their condition.
Published: 2017
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18. 2BC Non-Structural Protein of Enterovirus A71 Interacts with SNARE Proteins to Trigger Autolysosome Formation

Author: Jeffrey K.F. Lai, I-Ching Sam, Pauline Verlhac, Mathias Faure, Eeva-Liisa Eskelinen, Joël Baguet, Yoke Fun Chan, Biosciences, Biochemistry and Biotechnology, Autophagy, Faculty of Medicine, University of Malaya [Kuala Lumpur, Malaisie], University of Malaya [Kuala Lumpur, Malaisie], Autophagie infection et immunité - Autophagy Infection Immunity (APY), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, University of Malaya = Universiti Malaya [Kuala Lumpur, Malaisie] (UM), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki
Subjects: 0301 basic medicine, Picornavirus, Autolysosome, lcsh:QR1-502, Viral Nonstructural Proteins, Virus Replication, lcsh:Microbiology, Protein Interaction Mapping, HOPS COMPLEX, 1183 Plant biology, microbiology, virology, Tumor, LAMP1, Qa-SNARE Proteins, enterovirus, synaptosome-associated protein of 29 kDa, Qb-SNARE Proteins, VIRUS-REPLICATION, autolysosome, Cell biology, Infectious Diseases, enterovirus A71, SNARE, Host-Pathogen Interactions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, MACHINERY, Microtubule-Associated Proteins, Human, Protein Binding, replication, autophagy, Immunoprecipitation, Biology, Article, MATURATION, Cell Line, MECHANISMS, picornavirus, syntaxin-17, 2BC, 03 medical and health sciences, Cell Line, Tumor, Virology, Two-Hybrid System Techniques, Humans, Qc-SNARE Proteins, POLIOVIRUS REPLICATION COMPLEX, Autophagy, Lysosome-Associated Membrane Glycoproteins, biology.organism_classification, Molecular biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Enterovirus A, Human, 030104 developmental biology, AUTOPHAGOSOME-LYSOSOME FUSION, Viral replication, Membrane protein, CELLS, Enterovirus A, Lysosomes, SYNTAXIN 17, INHIBITORS
Abstract: International audience; Viruses have evolved unique strategies to evade or subvert autophagy machinery. Enterovirus A71 (EV-A71) induces autophagy during infection in vitro and in vivo. In this study, we report that EV-A71 triggers autolysosome formation during infection in human rhabdomyosarcoma (RD) cells to facilitate its replication. Blocking autophagosome-lysosome fusion with chloroquine inhibited virus RNA replication, resulting in lower viral titres, viral RNA copies and viral proteins. Overexpression of the non-structural protein 2BC of EV-A71 induced autolysosome formation. Yeast 2-hybrid and co-affinity purification assays showed that 2BC physically and specifically interacted with a N-ethylmaleimide-sensitive factor attachment receptor (SNARE) protein, syntaxin-17 (STX17). Co-immunoprecipitation assay further showed that 2BC binds to SNARE proteins, STX17 and synaptosome associated protein 29 (SNAP29). Transient knockdown of STX17, SNAP29, and microtubule-associated protein 1 light chain 3B (LC3B), crucial proteins in the fusion between autophagosomes and lysosomes) as well as the lysosomal-associated membrane protein 1 (LAMP1) impaired production of infectious EV-A71 in RD cells. Collectively, these results demonstrate that the generation of autolysosomes triggered by the 2BC non-structural protein is important for EV-A71 replication, revealing a potential molecular pathway targeted by the virus to exploit autophagy. This study opens the possibility for the development of novel antivirals that specifically target 2BC to inhibit formation of autolysosomes during EV-A71 infection.
Published: 2017
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19. The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth

Author: Winnok H. De Vos, Sébastjen Schoenaers, Grégory Mouille, Ive De Smet, Dirk Adriaensen, Claire S. Grierson, Ranjan Swarup, Natalia Nikonorova, Gordon Breen, Jaesung Oh, Isabel Pintelon, Malcolm J. Bennett, Malgorzata Zdanio, Daria Balcerowicz, Kristine Hill, Lam Dai Vu, Michael Wilson, Tara J. Holman, Kris Vissenberg, University of Antwerp (UA), School of Biological Sciences, University of Bristol [Bristol], HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Centre National de la Recherche Scientifique (CNRS), Department of plant Biotechnology and Bioinformatics, University of Gent, Flanders Institute for Biotechnology, Center for Medical Biotechnology, Universität Duisburg-Essen [Essen], Department of Biochemistry, Universiteit Gent = Ghent University [Belgium] (UGENT), Technological Educational Institute of Crete, Research Foundation-Flanders (FWO) [G039815N, G009412N, G0.602.11.N.10, 1.5.091.11.N.00], Interuniversity Attraction Poles Programme-Belgian State-Belgian Science Policy (IUAP) [VI/33], Biotechnology and Biological Sciences Research Council (BBSRC), University of Antwerp [TTBOF/29267, DOCPRO4/28300, BOFNOI/23154], BBSRC [G19475], Engineering and Physical Sciences Research Council (EPSRC) [BB/D019613/1], BBSRC Professional Research Fellowship [BB/G023972/1], Royal Society-Wolfson Merit Award, BBSRC Strategic Studentship [BS/S/H/2005/12044], Royal Society of London Research Grant 'Arabidopsis Root Hair Functional Genomics', R&D program of 'Plasma Advanced Technology for Agriculture and Food (Plasma Farming)' through the National Fusion Research Institute of Korea (NFRI) - government funds, VIB International PhD program fellowship, and Hercules Foundation [AUHA 09/001]
Subjects: 0301 basic medicine, kinase, Catharanthus, Arabidopsis, Root hair, Plant Roots, General Biochemistry, Genetics and Molecular Biology, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Organogenesis, Plant, Plant Growth Regulators, Auxin, Cell Wall, Gene Expression Regulation, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Tip growth, Biology, Transcription factor, Plant Proteins, pectin, chemistry.chemical_classification, biology, Indoleacetic Acids, tip growth, food and beverages, Cell Differentiation, FERONIA, biology.organism_classification, Plants, Genetically Modified, Cell biology, Xyloglucan, Chemistry, 030104 developmental biology, chemistry, CrRLK1L, cell wall, Human medicine, Plant hormone, auxin, AUXIN RESPONSE FACTOR, General Agricultural and Biological Sciences, root hair
Abstract: Root hairs facilitate a plant's ability to acquire soil anchorage and nutrients. Root hair growth is regulated by the plant hormone auxin and dependent on localized synthesis, secretion, and modification of the root hair tip cell wall. However, the exact cell wall regulators in root hairs controlled by auxin have yet to be determined. In this study, we describe the characterization of ERULUS (ERU), an auxin-induced Arabidopsis receptor-like kinase, whose expression is directly regulated by ARF7 and ARF19 transcription factors. ERU belongs to the Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) subfamily of putative cell wall sensor proteins. Imaging of a fluorescent fusion protein revealed that ERU is localized to the apical root hair plasma membrane. ERU regulates cell wall composition in root hairs and modulates pectin dynamics through negative control of pectin methylesterase (PME) activity. Mutant eru (−/−) root hairs accumulate de-esterified homogalacturonan and exhibit aberrant pectin Ca2+-binding site oscillations and increased PME activity. Up to 80% of the eru root hair phenotype is rescued by pharmacological supplementation with a PME-inhibiting catechin extract. ERU transcription is altered in specific cell wall-related root hair mutants, suggesting that it is a target for feedback regulation. Loss of ERU alters the phosphorylation status of FERONIA and H+-ATPases 1/2, regulators of apoplastic pH. Furthermore, H+-ATPases 1/2 and ERU are differentially phosphorylated in response to auxin. We conclude that ERULUS is a key auxin-controlled regulator of cell wall composition and pectin dynamics during root hair tip growth. Root hair growth increases root surface area for nutrient uptake. Schoenaers et al. report that auxin regulates the receptor-like kinase ERULUS, which localizes to the apical root hair plasma membrane, where it controls cell wall composition through pectin methylesterases and phosphorylation of cell-elongation regulators FERONIA and H+-ATPase 1/2.
Published: 2017
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20. Stromal Lkb1 deficiency leads to gastrointestinal tumorigenesis involving the IL-11-JAK/STAT3 pathway

Author: Tomi P. Mäkelä, Kari Vaahtomeri, Yajing Gao, Sushil Tripathi, Iris P. L. Wong, Benoit Viollet, Eva Domenech-Moreno, Yan Yan, Nalle Pentinmikko, Timothy C. Wang, Gustavo Leone, Elina H. Niemelä, Saara Ollila, Kaisa Laajanen, Pekka Katajisto, Viollet, Benoit, Research Programs [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, HiLIFE - Neuroscience Center (NC), Helsinki Institute of Life Science (HiLIFE), Division of Digestive and Liver Diseases [New York, NY, USA] ( Department of Medicine), Columbia University Irving Medical Center (CUIMC)-Irving Cancer Research Center [New York, NY, USA], HiLIFE - Institute of Biotechnology [Helsinki] (BI), [Institut Cochin] Département Endocrinologie, métabolisme, diabète (EMD) (EMD), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Ohio State University [Columbus] (OSU), Department of Biosciences and Nutrition [Stockholm, Sweden], Karolinska Institutet [Stockholm], University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, and Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: MESH: Signal Transduction, MESH: Neoplasm Proteins, 0301 basic medicine, MESH: Interleukin-11, Cell, MESH: Janus Kinase 1, AMP-Activated Protein Kinases, Mouse models, medicine.disease_cause, MESH: Mice, Knockout, MESH: Janus Kinase 2, Mice, MESH: Animals, Juvenile polyposis syndrome, skin and connective tissue diseases, [SDV.MHEP.EM] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Mice, Knockout, Kinase, Gastroenterology, MESH: STAT3 Transcription Factor, MESH: Stomach Neoplasms, General Medicine, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Interleukin-11, 3. Good health, Neoplasm Proteins, medicine.anatomical_structure, Cell Transformation, Neoplastic, Oncology, Signal transduction, Signal Transduction, Research Article, STAT3 Transcription Factor, congenital, hereditary, and neonatal diseases and abnormalities, MESH: Mutation, Stromal cell, Tumor suppressors, Biology, Protein Serine-Threonine Kinases, MESH: Protein-Serine-Threonine Kinases, 03 medical and health sciences, Germline mutation, Stomach Neoplasms, Intestinal Neoplasms, medicine, Animals, MESH: Intestinal Neoplasms, MESH: Mice, Mesenchymal stem cell, Janus Kinase 1, Janus Kinase 2, medicine.disease, 030104 developmental biology, MESH: Cell Transformation, Neoplastic, Mutation, Cancer research, Gastric cancer, Carcinogenesis
Abstract: International audience; Germline mutations in the gene encoding tumor suppressor kinase LKB1 lead to gastrointestinal tumorigenesis in Peutz-Jeghers syndrome (PJS) patients and mouse models; however, the cell types and signaling pathways underlying tumor formation are unknown. Here, we demonstrated that mesenchymal progenitor- or stromal fibroblast-specific deletion of Lkb1 results in fully penetrant polyposis in mice. Lineage tracing and immunohistochemical analyses revealed clonal expansion of Lkb1-deficient myofibroblast-like cell foci in the tumor stroma. Loss of Lkb1 in stromal cells was associated with induction of an inflammatory program including IL-11 production and activation of the JAK/STAT3 pathway in tumor epithelia concomitant with proliferation. Importantly, treatment of LKB1-defcient mice with the JAK1/2 inhibitor ruxolitinib dramatically decreased polyposis. These data indicate that IL-11-mediated induction of JAK/STAT3 is critical in gastrointestinal tumorigenesis following Lkb1 mutations and suggest that targeting this pathway has therapeutic potential in Peutz-Jeghers syndrome.
Published: 2017
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21. From jellyfish to biosensors: the use of fluorescent proteins in plants

Author: Antoine Larrieu, Darren M. Wells, Ute Voss, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Biotechnology and Biological Sciences Research Council, Engineering and Physical Sciences Research Council, University of Helsinki-University of Helsinki, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)
Subjects: 0106 biological sciences, Embryology, Jellyfish, Time Factors, [SDV]Life Sciences [q-bio], Green Fluorescent Proteins, Arabidopsis, Design elements and principles, Biosensing Techniques, Computational biology, Biology, Cell fate determination, 01 natural sciences, law.invention, Green fluorescent protein, 03 medical and health sciences, Confocal microscopy, law, biology.animal, Protein Interaction Mapping, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Animals, 030304 developmental biology, 0303 health sciences, Microscopy, Confocal, Indoleacetic Acids, Models, Genetic, business.industry, Plants, Anthozoa, Plants, Genetically Modified, biology.organism_classification, Fluorescence, DII-VENUS, Biotechnology, Hydrozoa, Microscopy, Fluorescence, Aequorea victoria, business, Biosensor, 010606 plant biology & botany, Developmental Biology
Abstract: International audience; The milestone discovery of green fluorescent protein (GFP) from the jellyfish Aequorea victoria, its optimisation for efficient use in plantae, and subsequent improvements in techniques for fluorescent detection and quantification have changed plant molecular biology research dramatically. Using fluorescent protein tags allows the temporal and spatial monitoring of dynamic expression patterns at tissue, cellular and subcellular scales. Genetically-encoded fluorescence has become the basis for applications such as cell-type specific transcriptomics, monitoring cell fate and identity during development of individual organs or embryos, and visualising protein-protein interactions in vivo. In this article, we will give an overview of currently available fluorescent proteins, their applications in plant research, the techniques used to analyse them and, using the recent development of an auxin sensor as an example, discuss the design principles and prospects for the next generation of fluorescent plant biosensors.
Published: 2013
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22. Tropomyosin Isoforms Specify Functionally Distinct Actin Filament Populations In Vitro

Author: Laurène Gressin, Theresia Reindl, Pekka Lappalainen, Peter W. Gunning, Gergana Gateva, Alphée Michelot, Konstantin Kogan, Elena Kremneva, Tommi Kotila, Dietmar J. Manstein, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Institute Biophysical Chemistry, Hanover Medical School, Faculty of Social Sciences, Bar-Ilan University [Israël], Physiologie cellulaire et végétale (LPCV), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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 de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Institute of Biotechnology, Pekka Lappalainen / Principal Investigator, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), School Medical Science, Oncology Research Unity, University of New South Wales [Sydney] (UNSW), Centre National de la Recherche Scientifique (CNRS), Academy of Finland Center of Excellence Program 272130, Sigrid Juselius Foundation, Jane and Aatos Erkko Foundation, NHMRC APP1004188, Kids Cancer Network, Deutsche Forschungsgemeinschaft MA 1081/22-1, Ella and Georg Ehrnrooth Foundation, ERC 638376, Labex INFORM (Investissements d'Avenir French Government Program) ANR-11-LABX-0054, Institute Biotechnology, University of Helsinki, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), University of New South Wales [Sydney] ( UNSW ), Institut de Biologie du Développement de Marseille ( IBDM ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: 0301 basic medicine, myosine, cell migration, [SDV]Life Sciences [q-bio], Arp2/3 complex, Tropomyosin, myosin, Myosin head, Actin remodeling of neurons, Stress Fibers, BINDING, Protein Isoforms, SPECIFICATION, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Agricultural and Biological Sciences(all), biology, F-ACTIN, actine f, in vitro, cytoskeleton, Cofilin, 3. Good health, Cell biology, NETWORKS, MODULATE, Actin Cytoskeleton, adhesion, General Agricultural and Biological Sciences, actin, Protein Binding, TIRF microscopy, RECRUITMENT, beta tropomyosine, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, macromolecular substances, cofilin, cofiline, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Report, Humans, YEAST, Actin-binding protein, Amino Acid Sequence, levure, [ SDV ] Life Sciences [q-bio], Biochemistry, Genetics and Molecular Biology(all), MYOSIN-II, Actin remodeling, α-actinin, 030104 developmental biology, Actin filament binding, biology.protein, 1182 Biochemistry, cell and molecular biology, MDia1, stress fiber
Abstract: Summary Actin filaments assemble into a variety of networks to provide force for diverse cellular processes [1]. Tropomyosins are coiled-coil dimers that form head-to-tail polymers along actin filaments and regulate interactions of other proteins, including actin-depolymerizing factor (ADF)/cofilins and myosins, with actin [2, 3, 4, 5]. In mammals, >40 tropomyosin isoforms can be generated through alternative splicing from four tropomyosin genes. Different isoforms display non-redundant functions and partially non-overlapping localization patterns, for example within the stress fiber network [6, 7]. Based on cell biological studies, it was thus proposed that tropomyosin isoforms may specify the functional properties of different actin filament populations [2]. To test this hypothesis, we analyzed the properties of actin filaments decorated by stress-fiber-associated tropomyosins (Tpm1.6, Tpm1.7, Tpm2.1, Tpm3.1, Tpm3.2, and Tpm4.2). These proteins bound F-actin with high affinity and competed with α-actinin for actin filament binding. Importantly, total internal reflection fluorescence (TIRF) microscopy of fluorescently tagged proteins revealed that most tropomyosin isoforms cannot co-polymerize with each other on actin filaments. These isoforms also bind actin with different dynamics, which correlate with their effects on actin-binding proteins. The long isoforms Tpm1.6 and Tpm1.7 displayed stable interactions with actin filaments and protected filaments from ADF/cofilin-mediated disassembly, but did not activate non-muscle myosin IIa (NMIIa). In contrast, the short isoforms Tpm3.1, Tpm3.2, and Tpm4.2 displayed rapid dynamics on actin filaments and stimulated the ATPase activity of NMIIa, but did not efficiently protect filaments from ADF/cofilin. Together, these data provide experimental evidence that tropomyosin isoforms segregate to different actin filaments and specify functional properties of distinct actin filament populations., Graphical Abstract, Highlights • Stress-fiber-associated tropomyosin isoforms segregate to different actin filaments • Tropomyosin isoforms bind F-actin with different dynamics • Dynamic tropomyosin isoforms activate non-muscle myosin II • Stable tropomyosin isoforms protect actin filaments from ADF/cofilin, Gateva et al. report that distinct tropomyosin isoforms segregate to different actin filaments and can specify functional properties of distinct actin filament populations. They also provide evidence that functions of tropomyosins in myosin II activation and actin filament stabilization correlate with the dynamics of their actin interactions.
Published: 2016
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23. Expression of X-chromosome linked inhibitor of apoptosis protein in mature purkinje cells and in retinal bipolar cells in transgenic mice induces neurodegeneration

Author: Eija Jokitalo, Gilberto Fisone, Dan Lindholm, Laura Korhonen, Constantino Sotelo, Isabelle Dusart, Rosine Wehrlé, Inga Hansson, Minna Kairisalo, C Maugras, Anders Borgkvist, Neurobiologie des processus adaptatifs (NPA), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Cátedra de Neurobiología del Desarrollo 'Remedios Caro Almela', Universidad Miguel Hernández [Elche] (UMH)-Instituto de Neurociencias de Alicante, Sigrid Juselius Foundation, Academy of Finland, European Commission, Uppsala University, Minerva Foundation, The Ohio State University, and University of Helsinki-University of Helsinki
Subjects: Retinal Bipolar Cells, Programmed cell death, Cell signaling, Proto-Oncogene Proteins c-jun, Green Fluorescent Proteins, Purkinje cell, Mice, Transgenic, X-Linked Inhibitor of Apoptosis Protein, Biology, Endoplasmic Reticulum, Transfection, Inhibitor of apoptosis, Mice, Purkinje Cells, 03 medical and health sciences, 0302 clinical medicine, Cerebellum, medicine, Animals, Humans, Phosphorylation, bcl-2-Associated X Protein, 030304 developmental biology, 0303 health sciences, Behavior, Animal, [SCCO.NEUR]Cognitive science/Neuroscience, General Neuroscience, Neurodegeneration, Age Factors, Gene Expression Regulation, Developmental, medicine.disease, Cell biology, XIAP, Mice, Inbred C57BL, medicine.anatomical_structure, Animals, Newborn, Apoptosis, Nerve Degeneration, Immunology, Microscopy, Electron, Scanning, Ataxia, 030217 neurology & neurosurgery, Immunostaining
Abstract: Transgenic mice with overexpression of the caspase-inhibitor, X-chromosome-linked inhibitor of apoptosis protein (XIAP) in Purkinje cell (PC) and in retinal bipolar cells (RBCs) were produced to study the regulation of cell death. Unexpectedly, an increased neurodegeneration was observed in the PCs in these L7-XIAP mice after the third postnatal week with the mice exhibiting severe ataxia. The loss of PCs was independent of Bax as shown by crossing the L7-XIAP mice with Bax gene–deleted mice. Electron microscopy revealed intact organelles in PCs but with the stacking of ER cisterns indicative of cell stress. Immunostaining for cell death proteins showed an increased phosphorylation of c-Jun in the PCs, suggesting an involvement in cell degeneration. Apart from PCs, the number of RBCs was decreased in adult retina in line with the expression pattern for the L7 promoter. The data show that overexpression of the anti-apoptotic protein XIAP in vulnerable neurons leads to enhanced cell death. The mechanisms underlying this neurodegeneration can be related to the effects of XIAP on cell stress and altered cell signaling., Supported by Sigrid Juselius Foundation, Academy of Finland, EU Biotech Grant, Liv och Hälsa, Maud Kuistila, Ylppö Foundation, Uppsala University and Minerva Foundation. We thank Dr. Urmas Arumäe for discussions, and Dr. Patrik Ernfors for the Bax KO mice, and Eeva Lehto for technical assistance. L7AUG was a kind gift from Dr. J. Oberdick, Ohio State University, USA.
Published: 2008
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24. The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana

Author: Peter D. Gould, Tatsuaki Goh, Angus S. Murphy, Darren M. Wells, Mikaël Lucas, Benjamin Péret, Fiona C. Robertson, Wendy Ann Peer, Tara J. Holman, Michael Wilson, Anthony Hall, Hidehiro Fukaki, Karen J. Halliday, Laurent Laplaze, Alex A. R. Webb, Ilda Casimiro, Malcolm J. Bennett, Karin Ljung, Ute Voß, Kamal Swarup, Kim Kenobi, T. Charlie Hodgman, Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), Institut de Recherche pour le Développement (IRD), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, 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), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), University of Helsinki-University of Helsinki, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Webb, Alex [0000-0003-0261-4375], and Apollo - University of Cambridge Repository
Subjects: Time Factors, root apical meristem, arabidopsis proteins, [SDV]Life Sciences [q-bio], Gravitropism, Circadian clock, Arabidopsis, General Physics and Astronomy, circadian clocks, Plant Roots, time factors, General Biochemistry, Genetics and Molecular Biology, Article, Auxin, Gene Expression Regulation, Plant, Circadian Clocks, Arabidopsis thaliana, heterocyclic compounds, Circadian rhythm, chemistry.chemical_classification, Genetics, Multidisciplinary, biology, Indoleacetic Acids, Arabidopsis Proteins, Lateral root, fungi, food and beverages, cell signalling, General Chemistry, plant roots, plant genetics, Meristem, biology.organism_classification, oxidoreductases, arabidopsis, chemistry, circadian rhythms, Mutation, transcription Factors, Oxidoreductases, Transcriptome, transcriptome, Transcription Factors
Abstract: The endogenous circadian clock enables organisms to adapt their growth and development to environmental changes. Here we describe how the circadian clock is employed to coordinate responses to the key signal auxin during lateral root (LR) emergence. In the model plant, Arabidopsis thaliana, LRs originate from a group of stem cells deep within the root, necessitating that new organs emerge through overlying root tissues. We report that the circadian clock is rephased during LR development. Metabolite and transcript profiling revealed that the circadian clock controls the levels of auxin and auxin-related genes including the auxin response repressor IAA14 and auxin oxidase AtDAO2. Plants lacking or overexpressing core clock components exhibit LR emergence defects. We conclude that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence., In Arabidopsis, lateral root emergence requires the penetration of overlying tissues by stem cells deep within the root. Voß et al. reveal that changes in auxin signalling required for this process are mediated by local rephasing of the circadian clock.
Published: 2015
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25. IRSp53 senses negative membrane curvature and phase separates along membrane tubules

Author: Andrew Callan-Jones, Emmanuel Lemichez, John Manzi, Hongxia Zhao, Pekka Lappalainen, Patricia Bassereau, Coline Prévost, Physico-Chimie-Curie (PCC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC), Université Paris Diderot - Paris 7 (UPD7), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Matière et Systèmes Complexes (MSC (UMR_7057)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), This work was supported by Institut Curie, Centre National de la Recherche Scientifique (CNRS) and the Agence Nationale pour la Recherche (grant ANR-11-BSV2-014). C.P. received a PhD grant from the Université Paris Diderot and support from the Fondation pour la Recherche Médicale. P.B. group belongs to the CNRS consortium CellTiss, to the Labex CelTisPhyBio (ANR-11-LABX0038) and to Paris Sciences et Lettres (ANR-10-IDEX-0001_02). P.L. and H.Z were supported by grants from Academy of Finland., We thank Essi Koskela for help during protein purification. We also thank Guy Tran van Nhieu for carefully reading the manuscript., ANR-11-LABX-0038,CelTisPhyBio,Des cellules aux tissus: au croisement de la Physique et de la Biologie(2011), ANR-11-BSV2-0014,RetroWASH,Remodelage des membranes endosomales par deux machines moléculaires en interaction, le Retromer et le complexe WASH(2011), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Matière et Systèmes Complexes (MSC), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR: 11-LABX-0038,CelTisPhyBio,Des cellules aux tissus: au croisement de la Physique et de la Biologie(2011), Institute of Biotechnology, Hongxia Zhao / Principal Investigator, Pekka Lappalainen / Principal Investigator, and Mitochondrial Morphogenesis
Subjects: MECHANISM, Low protein, [SDV]Life Sciences [q-bio], General Physics and Astronomy, 02 engineering and technology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Quantitative Biology::Cell Behavior, MESH: Cell Membrane/physiology, Membrane proteins, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], ENDOPHILIN N-BAR, BAR domain, FILOPODIUM FORMATION, Pseudopodia, Filopodia, 0303 health sciences, Quantitative Biology::Biomolecules, Multidisciplinary, Vesicle, CDC42, 021001 nanoscience & nanotechnology, HOMOLOGY DOMAIN, Cell biology, Membrane, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Membrane curvature, SHAPE, 0210 nano-technology, STRUCTURAL BASIS, GIANT UNILAMELLAR VESICLES, DYNAMIN, MESH: Cell Line, Tumor, PROTEINS, Nerve Tissue Proteins, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Curvature, General Biochemistry, Genetics and Molecular Biology, Article, Quantitative Biology::Subcellular Processes, 03 medical and health sciences, Cell Line, Tumor, Humans, MESH: Pseudopodia/physiology, 030304 developmental biology, MESH: Humans, Cell Membrane, General Chemistry, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Nerve Tissue Proteins/metabolism, Biophysics, 1182 Biochemistry, cell and molecular biology, Elasticity of cell membranes
Abstract: BAR domain proteins contribute to membrane deformation in diverse cellular processes. The inverted-BAR (I-BAR) protein IRSp53, for instance, is found on the inner leaflet of the tubular membrane of filopodia; however its role in the formation of these structures is incompletely understood. Here we develop an original assay in which proteins are encapsulated in giant unilamellar vesicles connected to membrane nanotubes. Our results demonstrate that I-BAR dimers sense negative membrane curvature. Experiment and theory reveal that the I-BAR displays a non-monotonic sorting with curvature, and expands the tube at high imposed tension while constricting it at low tension. Strikingly, at low protein density and tension, protein-rich domains appear along the tube. This peculiar behaviour is due to the shallow intrinsic curvature of I-BAR dimers. It allows constriction of weakly curved membranes coupled to local protein enrichment at biologically relevant conditions. This might explain how IRSp53 contributes in vivo to the initiation of filopodia., The inverted-BAR domain protein IRSp53 associates with the inner leaflet of tubular membranes such as filopodia. Here, Prévost et al. demonstrate that the I-BAR domain of IRSp53 senses negative membrane curvature, and undergoes phase separation which may aid its clustering upon filopodia generation.
Published: 2015
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26. Cofilin-2 controls actin filament length in muscle sarcomeres

Author: Pekka Lappalainen, Aneta Skwarek-Maruszewska, Alphée Michelot, Roberto Dominguez, Gergana Gateva, Elena Kremneva, Maarit Makkonen, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Department of Physiology, University of Pennsylvania, University of Pennsylvania [Philadelphia], Grants from the Academy of Finland and Finnish Foundation for Cardiovascular Research - NIH grant R01 GM073791., Institut of Biotechnology, National Autonomous University of Mexico, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania, Academy of Finland, Finnish Foundation for Cardiovascular Research, GPBM graduate program, VGSB graduate program, NIH R01 GM073791, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: [SDV]Life Sciences [q-bio], Arp2/3 complex, Actinin, environment and public health, Adenosine Triphosphate, 0302 clinical medicine, Myocytes, Cardiac, RNA, Small Interfering, Cells, Cultured, Cytoskeleton, 0303 health sciences, F-ACTIN, CARDIOMYOCYTE SARCOMERES, Cofilin, Cell biology, Adenosine Diphosphate, Muscle sarcomeres, Actin Cytoskeleton, Treadmilling, SKELETAL-MUSCLE, RNA Interference, Myopathies, NUCLEOTIDE STATE, Muscle Contraction, Protein Binding, Cofilin 1, Sarcomeres, Cofilin 2, DEPOLYMERIZING FACTOR, Molecular Sequence Data, macromolecular substances, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, FACTOR HOMOLOGY DOMAIN, STRIATED-MUSCLE, N-COFILIN, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, Actin-binding protein, Molecular Biology, actin filaments dynamics, 030304 developmental biology, Actin remodeling, Cell Biology, Actin binding protein, D-BINDING-PROTEIN, Actin cytoskeleton, Actins, Rats, ATP, biology.protein, CAENORHABDITIS-ELEGANS, Sequence Alignment, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Developmental Biology
Abstract: International audience; ADF/cofilins drive cytoskeletal dynamics by promoting the disassembly of "aged" ADP-actin filaments. Mammals express several ADF/cofilin isoforms, but their specific biochemical activities and cellular functions have not been studied in detail. Here, we demonstrate that the muscle-specific isoform cofilin-2 promotes actin filament disassembly in sarcomeres to control the precise length of thin filaments in the contractile apparatus. In contrast to other isoforms, cofilin-2 efficiently binds and disassembles both ADP- and ATP/ADP-Pi-actin filaments. We mapped surface-exposed cofilin-2-specific residues required for ATP-actin binding and propose that these residues function as an "actin nucleotide-state sensor" among ADF/cofilins. The results suggest that cofilin-2 evolved specific biochemical and cellular properties that allow it to control actin dynamics in sarcomeres, where filament pointed ends may contain a mixture of ADP- and ATP/ADP-Pi-actin subunits. Our findings also offer a rationale for why cofilin-2 mutations in humans lead to myopathies.
Published: 2014
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27. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots

Author: Jérôme Chopard, Nathan Mellor, Anthony Bishopp, Michael P. Pound, Christophe Godin, Mikaël Lucas, Daniele Muraro, John R. King, T. Charlie Hodgman, Helen M. Byrne, Hanna Help, Tony P. Pridmore, Yrjö Helariutta, Malcolm J. Bennett, Helariutta, Yrjo [0000-0002-7287-8459], Apollo - University of Cambridge Repository, Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), The Weatherall Institute of Molecular Medicine, University of Oxford [Oxford], HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Biotechnology and Biological Sciences Research Council, Engineering and Physical Sciences Research Counci, King Abdullah University of Science and Technology (KAUST) [KUK-013-04], Royal Society, Wolfson Foundation, Royal Society University Research Fellowship, Institut de Biologie Computationnelle de Montpellier, Morphogenetics Inria Project-Lab, Equipe Rhizogenèse (RHIZOGéNèSE- UMR DIA-PC), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), University of Oxford, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institute of Biotechnology, Genetics, Plant Biology, Viikki Plant Science Centre (ViPS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM), and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: 0106 biological sciences, Arabidopsis, 01 natural sciences, Plant Roots, Plant Growth Regulators, CYTOKININ, 1183 Plant biology, microbiology, virology, Vascular tissue, chemistry.chemical_classification, 0303 health sciences, DIVISION, Multidisciplinary, Microscopy, Confocal, biology, mathematical modeling, PERMEASE AUX1, Biological Sciences, Modélisation et simulation, plant development, Cell biology, DIFFERENTIATION, MERISTEM, Stele, Modeling and Simulation, GROWTH, CELL-FATE, Signal Transduction, Cell type, education, Cell fate determination, CROSS-REGULATION, Models, Biological, 03 medical and health sciences, Auxin, Transcription factor, 030304 developmental biology, Homeodomain Proteins, Arabidopsis Proteins, QK, POLAR AUXIN TRANSPORT, biology.organism_classification, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, MicroRNAs, chemistry, Polar auxin transport, Plant Vascular Bundle, 010606 plant biology & botany, Transcription Factors
Abstract: International audience; As multicellular organisms grow, positional information is continually needed to regulate the pattern in which cells are arranged. In the Arabidopsis root, most cell types are organized in a radially symmetric pattern; however, a symmetry-breaking event generates bisymmetric auxin and cytokinin signaling domains in the stele. Bidirectional cross-talk between the stele and the surrounding tissues involving a mobile transcription factor, SHORT ROOT (SHR), and mobile microRNA species also determines vascular pattern, but it is currently unclear how these signals integrate. We use a multicellular model to determine a minimal set of components necessary for maintaining a stable vascular pattern. Simulations perturbing the signaling network show that, in addition to the mutually inhibitory interaction between auxin and cytokinin, signaling through SHR, microRNA165/6, and PHABULOSA is required to maintain a stable bisymmetric pattern. We have verified this prediction by observing loss of bisymmetry in shr mutants. The model reveals the importance of several features of the network, namely the mutual degradation of microRNA165/6 and PHABULOSA and the existence of an additional negative regulator of cytokinin signaling. These components form a plausible mechanism capable of patterning vascular tissues in the absence of positional inputs provided by the transport of hormones from the shoot.
Published: 2013
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28. Genome Mining Expands the Chemical Diversity of the Cyanobactin Family to Include Highly Modified Linear Peptides

Author: Jouni Jokela, Matti Wahlsten, Niina Leikoski, Muriel Gugger, Alexandra Calteau, Liwei Liu, Perttu Permi, David P. Fewer, Cheryl A. Kerfeld, Kaarina Sivonen, Department of Food and Environmental Sciences, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Collection des Cyanobactéries, Institut Pasteur [Paris] (IP), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Plant and Microbial Biology [Berkeley], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), US Department of Energy, Joint Genome Institute (JGI), This research was supported by grants from the Academy of Finland to K.S. (118637, 258827) and D.P.F. (259505), and a Helsinki University Research grant (788/51/2010) to D.P.F.. N.L. is a student and L.L. is a matching funds student at Viikki Doctoral Programme in Molecular Biosciences. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. We are grateful to Lyudmila Saari for her valuable help in handling the cultures., University of Helsinki, Institut Pasteur [Paris], 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 Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), University of Helsinki-University of Helsinki, University of California [Berkeley], and University of California-University of California
Subjects: Cyanobacteria, Evolution, Clinical Biochemistry, Molecular Sequence Data, 01 natural sciences, Biochemistry, Genome, Evolution, Molecular, 03 medical and health sciences, Drug Discovery, [CHIM]Chemical Sciences, Amino Acid Sequence, Molecular Biology, Peptide sequence, Gene, 030304 developmental biology, Pharmacology, chemistry.chemical_classification, Genetics, 0303 health sciences, biology, 010405 organic chemistry, General Medicine, Ribosomal RNA, biology.organism_classification, 0104 chemical sciences, Amino acid, Metabolism, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Multigene Family, Horizontal gene transfer, Molecular Medicine, Genome mining, Peptides, Protein Processing, Post-Translational, Ribosomes, Genome, Bacterial
Abstract: International audience; Ribosomal peptides are produced through the posttranslational modification of short precursor peptides. Cyanobactins are a growing family of cyclic ribosomal peptides produced by cyanobacteria. However, a broad systematic survey of the genetic capacity to produce cyanobactins is lacking. Here we report the identification of 31 cyanobactin gene clusters from 126 genomes of cyanobacteria. Genome mining suggested a complex evolutionary history defined by horizontal gene transfer and rapid diversification of precursor genes. Extensive chemical analyses demonstrated that some cyanobacteria produce short linear cyanobactins with a chain length ranging from three to five amino acids. The linear peptides were N-prenylated and O-methylated on the N and C termini, respectively, and named aeruginosamide and viridisamide. These findings broaden the structural diversity of the cyanobactin family to include highly modified linear peptides with rare posttranslational modifications.
Published: 2013
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29. Human single-chain urokinase is activated by the omptins PgtE of Salmonella enterica and Pla of Yersinia pestis despite mutations of active site residues

Author: Hanna M, Järvinen, Liisa, Laakkonen, Johanna, Haiko, Tiira, Johansson, Katri, Juuti, Marjo, Suomalainen, Carmen, Buchrieser, Nisse, Kalkkinen, Timo K, Korhonen, University of Helsinki, Department of Bacteriology and Immunology [Helsinki], Haartman Institute [Helsinki], Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki-Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Biologie des bactéries intracellulaires, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), This work received financial support from the University of Helsinki, the Academy of Finland (ERA-NET Pathogenomics grant number 1130202), the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS), and the Institut Carnot-Pasteur MI., European Project: Pathomics, Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Faculty of Medecine [Helsinki], Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: MESH: Urokinase-Type Plasminogen Activator/metabolism, MESH: Humans, Yersinia pestis, MESH: Salmonella enterica/enzymology, Serine Endopeptidases, Salmonella enterica, MESH: Catalytic Domain/genetics, MESH: Salmonella enterica/genetics, MESH: Plasminogen Activators/genetics, Plasminogen, MESH: Proteolysis, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Urokinase-Type Plasminogen Activator, MESH: Yersinia pestis/enzymology, Plasminogen Activators, Bacterial Proteins, MESH: Plasminogen/metabolism, Catalytic Domain, Proteolysis, Humans, Point Mutation, MESH: Serine Endopeptidases/genetics, MESH: Yersinia pestis/genetics, MESH: Bacterial Proteins/genetics, MESH: Point Mutation
Abstract: International audience; Fibrinolysis is important in cell migration and tightly regulated by specific inhibitors and activators; of the latter, urokinase (uPA) associates with enhancement of cell migration. Active uPA is formed through cleavage of the single-chain uPA (scuPA). The Salmonella enterica strain 14028R cleaved human scuPA at the peptide bond Lys158-Ile159, the site cleaved also by the physiological activator human plasmin. The cleavage led to activation of scuPA, while no cleavage or activation were detected with the mutant strain 14028R lacking the omptin protease PgtE. Complementation and expression studies confirmed the role of PgtE in scuPA activation. Similar cleavage and activation of scuPA were detected with recombinant Escherichia coli expressing the omptin genes pla from Yersinia pestis, ompT and ompP from E. coli, sopA from Shigella flexneri, and leo from Legionella pneumophila. For these omptins the activation of scuPA is the only shared function so far detected. Only poor cleavage and activation of scuPA were seen with YcoA of Y. pestis and YcoB of Yersinia pseudotuberculosis that are considered to be proteolytically inactive omptin variants. Point mutations of active site residues in Pla and PgtE had different effects on the proteolysis of plasminogen and of scuPA, indicating versatility in omptin proteolysis. © 2013 John Wiley & Sons Ltd.
Published: 2013
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30. Cytokinin signalling inhibitory fields provide robustness to phyllotaxis

Author: Pierre Chambrier, Fabrice Besnard, Jonathan Legrand, Yann Guédon, Frédérique Rozier, Emmanuel Thévenon, Christophe Godin, Vincent Mirabet, François Parcy, Benjamin Marteaux, Géraldine Brunoud, Teva Vernoux, Yassin Refahi, Anthony Bishopp, Etienne Farcot, Stéphanie Lainé, Yrjö Helariutta, Jan Traas, Renaud Dumas, Valérie Morin, Pradeep Das, Arezki Boudaoud, Coralie Cellier, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire Joliot Curie, École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), University of Helsinki-University of Helsinki, École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Cytokinins, F60 - Physiologie et biochimie végétale, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Meristem, Arabidopsis, F62 - Physiologie végétale - Croissance et développement, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Plant Growth Regulators, Auxin, Botany, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, biology, Indoleacetic Acids, Arabidopsis Proteins, fungi, Spatiotemporal pattern, Robustness (evolution), food and beverages, Biological Transport, Phyllotaxis, biology.organism_classification, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Cell biology, chemistry, Cytokinin, Plant hormone, Plant Shoots, 010606 plant biology & botany, Signal Transduction
Abstract: How biological systems generate reproducible patterns with high precision is a central question in science1. The shoot apical meristem (SAM), a specialized tissue producing plant aerial organs, is a developmental system of choice to address this question. Organs are periodically initiated at the SAM at specific spatial positions and this spatiotemporal pattern defines phyllotaxis. Accumulation of the plant hormone auxin triggers organ initiation2, 3, 4, 5, whereas auxin depletion around organs generates inhibitory fields that are thought to be sufficient to maintain these patterns and their dynamics4, 6, 7, 8, 9, 10, 11, 12, 13. Here we show that another type of hormone-based inhibitory fields, generated directly downstream of auxin by intercellular movement of the cytokinin signalling inhibitor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6)14, is involved in regulating phyllotactic patterns. We demonstrate that AHP6-based fields establish patterns of cytokinin signalling in the meristem that contribute to the robustness of phyllotaxis by imposing a temporal sequence on organ initiation. Our findings indicate that not one but two distinct hormone-based fields may be required for achieving temporal precision during formation of reiterative structures at the SAM, thus indicating an original mechanism for providing robustness to a dynamic developmental system.
Published: 2013
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31. Overexpression of Man2C1 leads to protein underglycosylation and upregulation of endoplasmic reticulum-associated degradation pathway

Author: René Cacan, Anne-Marie Mir, Jean-Claude Michalski, Marie-Christine Slomianny, Sandrine Duvet, Pirkko Heikinheimo, Frédéric Krzewinski, Elina Kuokkanen, Yoann Carre, François Foulquier, Willy Morelle, Coralie Bernon, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Developmental Biology Program, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: Mannosidase, Uridine Diphosphate Glucose, Proteasome Endopeptidase Complex, Glycosylation, Oligosaccharides, macromolecular substances, Biology, Endoplasmic-reticulum-associated protein degradation, Endoplasmic Reticulum, Transfection, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, N-linked glycosylation, Downregulation and upregulation, alpha-Mannosidase, Mannosidases, Humans, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Mannosephosphates, Endoplasmic reticulum, 030302 biochemistry & molecular biology, ta1182, Cell biology, Up-Regulation, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], carbohydrates (lipids), Cytosol, chemistry, Glycoprotein, HeLa Cells
Abstract: International audience; Unfolded glycoproteins retained in the endoplasmic reticulum (ER) are degraded via the ER-associated degradation (ERAD) pathway. These proteins are subsequently transported to the cytosol and degraded by the proteasomal complex. Although the sequential events of ERAD are well described, its regulation remains poorly understood. The cytosolic mannosidase, Man2C1, plays an essential role in the catabolism of cytosolic free oligomannosides, which are released from the degraded proteins. We have investigated the impact of Man2C1 overexpression on protein glycosylation and the ERAD process. We demonstrated that overexpression of Man2C1 led to modifications of the cytosolic pool of free oligomannosides and resulted in accumulation of small Man 2-4GlcNAc1 glycans in the cytosol. We further correlated this accumulation with incomplete protein glycosylation and truncated lipidlinked glycosylation precursors, which yields an increase in N-glycoprotein en route to the ERAD. We propose a model in which high mannose levels in the cytosol interfere with glucose metabolism and compromise N-glycan synthesis in the ER. Our results show a clear link between the intracellular mannose-6-phosphate level and synthesis of the lipid-linked precursors for protein glycosylation. Disturbance in these pathways interferes with protein glycosylation and upregulated ERAD. Our findings support a new concept that regulation of Man2C1 expression is essential for maintaining efficient protein N-glycosylation.
Published: 2011
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32. Characterization and subcellular localization of human neutral class II alpha-mannosidase cytosolic enzymes

Author: Kuokkanen, Elina, Smith, Wesley, Mäkinen, Marika, Tuominen, Heidi, Puhka, Maija, Jokitalo, Eija, Duvet, Sandrine, Berg, Thomas, Heikinheimo, Pirkko, Department of Biochemistry and Food Chemistry, Unive, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Department of Medical Biochemistry, Uni, Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: alpha-mannosidase, MAN2C1, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract: A glycosyl hydrolase family 38 enzyme, neutral alpha-mannosidase, has been proposed to be involved in hydrolysis of cytosolic free oligosaccharides originating either from ER-misfolded glycoproteins or the N-glycosylation process. Although this enzyme has been isolated from the cytosol, it has also been linked to the ER by subcellular fractionations. We have studied the subcellular localization of neutral alpha-mannosidase by immunofluorescence microscopy and characterized the human recombinant enzyme with natural substrates to elucidate the biological function of this enzyme. Immunofluorescence microscopy showed neutral alpha-mannosidase to be absent from the ER, lysosomes, and autophagosomes, and being granularly distributed in the cytosol. In experiments with fluorescent recovery after photo bleaching, neutral alpha-mannosidase had slower than expected two-phased diffusion in the cytosol. This result together with the granular appearance in immunostaining suggests that portion of the neutral alpha-mannosidase pool is somehow complexed. The purified recombinant enzyme is a tetramer and has a neutral pH optimum for activity. It hydrolyzed Man(9)GlcNAc to Man(5)GlcNAc in the presence of Fe(2+), Co(2+), and Mn(2+), and uniquely to neutral alpha-mannosidases from other organisms, the human enzyme was more activated by Fe(2+) than Co(2+). Without activating cations the main reaction product was Man(8)GlcNAc, and Cu(2+) completely inhibited neutral alpha-mannosidase. Our findings from enzyme-substrate characterizations and subcellular localization studies support the suggested role for neutral alpha-mannosidase in hydrolysis of soluble cytosolic oligomannosides.
Published: 2007

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32 results on '"HiLIFE - Institute of Biotechnology [Helsinki] (BI)"'

1. Semipermeable species boundaries create opportunities for gene flow and adaptive potential

2. Multiple evolutionary origins and losses of tooth complexity in squamates

3. Putative pectate lyase PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport in Arabidopsis

4. A network of transcriptional repressors modulates auxin responses

5. Inverse Conformational Selection in Lipid–Protein Binding

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7. Root branching toward water involves posttranslational modification of transcription factor ARF7

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

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31. Overexpression of Man2C1 leads to protein underglycosylation and upregulation of endoplasmic reticulum-associated degradation pathway

32. Characterization and subcellular localization of human neutral class II alpha-mannosidase cytosolic enzymes

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