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1. IFNγ binding to extracellular matrix prevents fatal systemic toxicity

Author

Josephine Kemna, Evelyne Gout, Leon Daniau, Jessica Lao, Kristoffer Weißert, Sandra Ammann, Ralf Kühn, Matthias Richter, Christine Molenda, Anje Sporbert, Dario Zocholl, Robert Klopfleisch, Hugues Lortat-Jacob, Peter Aichele, Thomas Kammertoens, Thomas Blankenstein, Institut de biologie structurale (IBS - UMR 5075), 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)-Université Grenoble Alpes (UGA), Molecular Epidemiology Research Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany, Institute for Immunodeficiency, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Center of Chronic Immunodeficiency, University Medical Center and University of Freiburg, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], and Institute of Veterinary Pathology

Subjects
MESH: Signal Transduction, MESH: Cytokines, Cancer Research, MESH: Interferon-gamma, [SDV]Life Sciences [q-bio], Immunology, Immunology and Allergy, MESH: Animals, MESH: Neoplasms, MESH: Extracellular Matrix, Technology Platforms, MESH: Mice
Abstract

Interferon-γ (IFNγ) is an important mediator of cellular immune responses, but high systemic levels of this cytokine are associated with immunopathology. IFNγ binds to its receptor (IFNγR) and to extracellular matrix (ECM) via four positively charged C-terminal amino acids (KRKR), the ECM-binding domain (EBD). Across evolution, IFNγ is not well conserved, but the EBD is highly conserved, suggesting a critical function. Here, we show that IFNγ lacking the EBD (IFNγΔKRKR) does not bind to ECM but still binds to the IFNγR and retains bioactivity. Overexpression of IFNγΔKRKR in tumors reduced local ECM binding, increased systemic levels and induced sickness behavior, weight loss and toxicity. To analyze the function of the EBD during infection, we generated IFNγΔKRKR mice lacking the EBD by using CRISPR–Cas9. Infection with lymphocytic choriomeningitis virus resulted in higher systemic IFNγΔKRKR levels, enhanced sickness behavior, weight loss and fatal toxicity. We conclude that local retention of IFNγ is a pivotal mechanism to protect the organism from systemic toxicity during prolonged immune stimulation.

Published
2023

2. Mosaicism due to postzygotic mutations in women with focal dermal hypoplasia

Author

J. Küsel, Julien Thevenon, Emmanuelle Bourrat, Steffen Hörer, Rudolf Happle, Lisa Heinz, Pierre Vabres, Svenja Alter, Alrun Hotz, Andreas Zimmer, Judith Fischer, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Center for Human Genetics Freiburg, Service de dermatologie [Paris], Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Dermatologie (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), FHU TRANSLAD (CHU de Dijon), University of Freiburg [Freiburg], Department of Dermatology, University Medical Center Freiburg, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and FHU TRANSLAD

Subjects
Adult, Zygote, DNA Mutational Analysis, Dermatology, Biology, Postzygotic mutation, medicine.disease_cause, PORCN, Young Adult, 030207 dermatology & venereal diseases, 03 medical and health sciences, 0302 clinical medicine, medicine, Humans, Missense mutation, Goltz syndrome, Skin, Genetics, Mutation, Mosaicism, Mouth Mucosa, Genetic disorder, High-Throughput Nucleotide Sequencing, Membrane Proteins, cutaneous mosaicism, Karyotype, medicine.disease, Focal dermal hypoplasia, 3. Good health, focal dermal hypoplasia, Female, Klinefelter syndrome, Acyltransferases, [SDV.MHEP.DERM]Life Sciences [q-bio]/Human health and pathology/Dermatology
Abstract

International audience; Focal dermal hypoplasia (FDH, Goltz syndrome, MIM: #305600) constitutes a rare multisystem genetic disorder of the skin, skeleton, teeth and eyes with considerable variation in the clinical features. FDH is transmitted as an X-linked dominant trait and is caused by mutations in PORCN. In males, hemizygous PORCN mutations are lethal in utero. Around 300 cases have been reported in the literature to date. About 10% of them are males presenting either Klinefelter syndrome (karyotype 47, XXY) or mosaicism of a postzygotic mutation. Here we describe four cases of women with typical features of FDH, in whom a PORCN mutation was found in DNA from affected cutaneous tissue but not in DNA from peripheral blood. This study suggests that mosaicism caused by a postzygotic mutation occurs more often than assumed to date in female patients with FDH. A negative analysis performed on peripheral blood DNA does not exclude the diagnosis of FDH and it is thereby of practical importance to analyse DNA from the affected skin in order to identify low level mosaicism and thus to improve diagnostic precision. In total, we found two missense variants, one novel indel and one novel splice site variant. Individuals harbouring postzygotic mosaicism run a risk of transmitting the disorder to their daughters, because the maternal mosaic could also affect the gonads. This article is protected by copyright. All rights reserved.

Published
2018

3. A human liver cell atlas reveals heterogeneity and epithelial progenitors

Author

Nadim Aizarani, Josip S. Herman, Sagar, Patrick Pessaux, Dominic Grün, Antonio Saviano, Sarah C. Durand, Laurent Mailly, Thomas F. Baumert, Max Planck Institute of Immunobiology and Epigenetics (MPI-IE), Max-Planck-Gesellschaft, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, International Max Planck Research School for Molecular and Cellular Biology [Freiburg, Germany] (MPRS-MCB), Institut de Recherche sur les Maladies Virales et Hépatiques (IVH), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pôle hépato-digestif [Strasbourg], Nouvel Hôpital Civil, Hospices Civils de Strasbourg-Institut Hospitalo-Universitaire de strasbourg, Centre for Integrative Biological Signaling Studies [Freiburg, Germany], University of Freiburg [Freiburg], This study was supported by the Max Planck Society, the German Research Foundation (DFG) (SPP1937 GR4980/1-1, GR4980/3-1, and GRK2344 MeInBio), the DFG under Germany’s Excellence Strategy (CIBSS – EXC-2189 – Project ID 390939984), and the Behrens-Weise- Foundation (all to D.G.), and by ARC, Paris and Institut Hospital-Universitaire, Strasbourg (TheraHCC, TheraHCC2.0 IHUARC IHU201301187 and IHUARC2019 IHU201901299 to T.F.B.), the European Union (ERC-AdG-2014-671231-HEPCIR, EU H2020-667273-HEPCAR and ERC-PoC-2016- PRELICAN to T.F.B), Agence nationale de recherches sur le sida et les hépatites virales (ANRS, ECTZ35076) and the Foundation of the University of Strasbourg. This work was done under the framework of the LABEX ANR-10-LABX-0028_HEPSYS and Inserm Plan Cancer (Plan Cancer 2014-2019, Action 13.1, appel à projets 2018) and benefits from funding from the state managed by the French National Research Agency as part of the Investments for the future. Institut Universitaire France (IUF) to T.F.B., ANR-10-IDEX-0002,UNISTRA,Functional genomics of viral hepatitis and liver disease(2010), European Project: 671231,H2020,ERC-2014-ADG,HEPCIR(2016), European Project: 667273,H2020,H2020-PHC-2015-two-stage,HEP-CAR(2016), daulny, anne, Initiative d'excellence - Par-delà les frontières, l'Université de Strasbourg - - UNISTRA2010 - ANR-10-IDEX-0002 - IDEX - VALID, Cell circuits as targets and biomarkers for liver disease and cancer prevention - HEPCIR - - H20202016-01-01 - 2020-12-31 - 671231 - VALID, Mechanisms underlying hepatocellular carcinoma pathogenesis and impact of co-morbidities. - HEP-CAR - - H20202016-01-01 - 2019-12-31 - 667273 - VALID, and ANR-10-IDEX-0002,UNISTRA,Par-delà les frontières, l'Université de Strasbourg(2010)

Subjects
Adult, Male, 0301 basic medicine, Cell type, Carcinoma, Hepatocellular, Liver cytology, Cell, Population, Biology, Cholangiocyte, Mice, 03 medical and health sciences, 0302 clinical medicine, Antigens, Neoplasm, RNA, Small Cytoplasmic, medicine, Animals, Humans, RNA-Seq, Progenitor cell, education, Progenitor, education.field_of_study, Multidisciplinary, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Chimera, Stem Cells, Endothelial Cells, Reproducibility of Results, Epithelial Cells, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, medicine.disease, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, 3. Good health, Organoids, 030104 developmental biology, medicine.anatomical_structure, Gene Expression Regulation, Liver, 030220 oncology & carcinogenesis, Hepatocellular carcinoma, Hepatocytes, Cancer research, Female, Cell Adhesion Molecules, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Antonio Saviano and Sagar contributed equally.; International audience; The human liver is an essential multifunctional organ. The incidence of liver diseases is rising and there are limited treatment options. However, the cellular composition of the liver remains poorly understood. Here we performed single-cell RNA sequencing of about 10,000 cells from normal liver tissue from nine human donors to construct a human liver cell atlas. Our analysis identified previously unknown subtypes of endothelial cells, Kupffer cells, and hepatocytes, with transcriptome-wide zonation of some of these populations. We show that the EPCAM+ population is heterogeneous, comprising hepatocyte-biased and cholangiocyte populations as well as a TROP2int progenitor population with strong potential to form bipotent liver organoids. As a proof-of-principle, we used our atlas to unravel the phenotypic changes that occur in hepatocellular carcinoma cells and in human hepatocytes and liver endothelial cells engrafted into a mouse liver. Our human liver cell atlas provides a powerful resource to enable the discovery of previously unknown cell types in normal and diseased livers.

Published
2019

4. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

Author

Cristina Vives, Sebastian N. W. Hoernstein, Dennis W. Stevenson, Anders Larsson, Klaus F. X. Mayer, Fabian B. Haas, Jane Grimwood, Priya Ranjan, Lucas Schneider, Yong Zhang, Ralf Reski, Florian Maumus, Stuart F. McDaniel, Michael Tillich, Thomas Widiez, Carl J. Rothfels, Andreas Zimmer, Daniel S. Rokshar, Yasuko Kamisugi, Heidrun Gundlach, Sean W. Graham, Klaas Vandepoele, Richard D. Hayes, Aikaterini Symeonidi, Omar Abu Saleh, Andrew C. Cuming, Jeremy Schmutz, Jordi Morata, Shengqiang Shu, Jérôme Salse, Joerg Fuchs, Ralph S. Quatrano, Daniel Lang, Juan Carlos Villarreal Aguilar, Kristian K. Ullrich, Gerald A. Tuskan, Fay-Wei Li, Mathieu Piednoël, Pierre-François Perroud, Florent Murat, Ann M. Wymore, Gane Ka-Shu Wong, Manuel Hiss, Jerry Jenkins, Lee E. Gunter, Josep M. Casacuberta, Nico van Gessel, Wellington Muchero, Jeremy Phillips, Michiel Van Bel, Eva L. Decker, Rabea Meyberg, Stefan A. Rensing, Guillaume Blanc, Fritz Thümmler, David Goodstein, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), United States Department of Energy, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Helmholtz-Zentrum München (HZM), Center for Research in Agricultural Genomics, Freiburg Initiative in Systems Biology, University of Freiburg [Freiburg], Laboratoire de Physique Statistique de l'ENS (LPS), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), London School of Hygiene and Tropical Medicine (LSHTM), Luleå University of Technology (LUT), BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, 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), Department of Biological Sciences [Edmonton], University of Alberta, Wolfgang Pauli Institute (WPI), University of Vienna [Vienna], Department of Molecular Psychiatry, Rheinische Friedrich-Wilhelms-Universität Bonn, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Plant Biotechnology, Faculty of Biology, University of Freiburg, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Office of Science of the US Department of Energy [DEAC02-05CH11231], German Research Foundation [DFG RE 837/10-2], Excellence Initiative of the German Federal and State Governments [EXC 294], German Federal Ministry of Education and Research [BMBF FRISYS], US National Science Foundation [IOS339156, IOS-1444490], U.S. National Science Foundation [DBI-0735191, DBI-1265383], UK Biological Sciences and Biotechnology Research Council [BB/F001797/1], Ghent University’s Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’ Project [01MR0410W], Spanish Ministerio de Economıa y Competitividad [AGL2013-43244-R], Alberta Ministry of Innovation and Advanced Education, Alberta Innovates Technology Futures (AITF), Innovates Centres of Research Excellence (iCORE), Musea Ventures, BGI-Shenzhen and China National Genebank (CNGB), EMBO Long-Term Fellowships [ALTF 1166-2011], German Research Foundation [SFB924], German Ministry of Education and Research [BMBF, 031A536/de.NBI], European Project: 267146,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,EMBOCOFUND2010(2011), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum München = German Research Center for Environmental Health, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-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), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Biotechnology and Biological Sciences Research Council (UK), Ministerio de Economía y Competitividad (España), European Commission, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), VIB Department of Plant Systems Biology, Ghent University [Belgium] (UGENT), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), and École normale supérieure - Paris (ENS Paris)

Subjects
0301 basic medicine, Sequence assembly, Plant Biology, plant, Plant Science, Genome, Gene duplication, chromosome, ComputingMilieux_MISCELLANEOUS, Recombination, Genetic, biology, synteny, food and beverages, Single Nucleotide, Biological Evolution, Chromatin, ddc:580, duplication, Evolution, Chromosome, Plant, Moss, Methylation, Duplication, Synteny, Physcomitrella Patens, Physcomitrellapatens, Genome, Plant, Biotechnology, Transposable element, Centromere, Plant Biology & Botany, Physcomitrella patens, Polymorphism, Single Nucleotide, Chromosomes, Plant, Chromosomes, moss, 03 medical and health sciences, Genetic, evolution, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Polymorphism, Gene, genome, Human Genome, Genetic Variation, Cell Biology, DNA Methylation, biology.organism_classification, Bryopsida, Recombination, 030104 developmental biology, Evolutionary biology, DNA Transposable Elements, Biochemistry and Cell Biology, methylation
Abstract

et al., The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes., 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. Support to RR and SAR by the German Research Foundation (DFG RE 837/10-2), the Excellence Initiative of the German Federal and State Governments (EXC 294), and by the German Federal Ministry of Education and Research (BMBF FRISYS), is highly appreciated. CoGe is supported by the US National Science Foundation under Award Numbers IOS-339156 and IOS-1444490, CyVerse is supported by the U.S. National Science Foundation under Award Numbers DBI-0735191 and DBI-1265383. YK and ACC are grateful for support from the UK Biological Sciences and Biotechnology Research Council (Grant BB/F001797/1). KV acknowledges the Multidisciplinary Research Partnership ‘Bioinformatics: from nucleotides to networks’ Project (no 01MR0410W) of Ghent University. JC is grateful for support from the Spanish Ministerio de Economía y Competitividad (Grant AGL2013-43244-R). RSQ is grateful to Monsanto (St. Louis, MO, USA) for sequencing genomic DNA of P. patens accession Kaskaskia. The 1000 Plants (1 KP) initiative, led by GKSW, is funded by the Alberta Ministry of Innovation and Advanced Education, Alberta Innovates Technology Futures (AITF), Innovates Centres of Research Excellence (iCORE), Musea Ventures, BGI-Shenzhen and China National Genebank (CNGB). TW was supported by EMBO Long-Term Fellowships (ALTF 1166-2011) and by Marie Curie Actions (European Commission EMBOCOFUND2010, GA-2010-267146). The work conducted at PGSB was supported by the German Research Foundation (SFB924) and German Ministry of Education and Research (BMBF, 031A536/de.NBI).

Published
2018

5. Structural and functional characterization of tree proteins involved in redox regulation: a new frontier in forest science

Author

Jean-Pierre Jacquot, Jérémy Couturier, Nicolas Rouhier, Mélanie Morel-Rouhier, Christophe Plomion, Eric Gelhaye, Desirée D. Gütle, Arnaud Hecker, Claude Didierjean, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Cristallographie, Résonance Magnétique et Modélisations (CRM2), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de la Recherche Agronomique (INRA), Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg [Freiburg], Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)

Subjects
0301 basic medicine, Systems biology, [SDV]Life Sciences [q-bio], Glutaredoxin, Genomics, populus, Biology, Genome, 3D protein structure, genome sequence, glutaredoxin, redox, thioredoxin, poplar, thioredoxine, Redox, 03 medical and health sciences, Protein structure, structure 3d, Thioredoxin, Ecology, Forestry, Orphan gene, séquence du génome, 030104 developmental biology, Biochemistry, Structural biology, Genome sequence, Poplar
Abstract

Key message This paper describes how the combination of genomics, genetic engineering, and 3D structural characterization has helped clarify the redox regulatory networks in poplar with consequences not only in system biology in plants but also in bacteria and mammalian systems.[br/] Context Tree genomes are increasingly available with a large number of orphan genes coding for proteins, the function of which is still unknown.[br/] Aims and methods Modern techniques of genome analysis coupled with recombinant protein technology and massive 3D structural determination of tree proteins should help elucidate the function of many of the proteins encoded by orphan genes. X-ray crystallography and NMR will be the methods of choice for protein structure determination.[br/] Results In this review, we provide examples illustrating how the above-mentioned techniques improved our understanding of redox regulatory circuits in poplar, the first forest tree species sequenced. We showed that poplar peroxiredoxins use either thioredoxin or glutaredoxin as electron donors to reduce hydrogen peroxide. That glutaredoxin could be a reductant was unknown at the time of this discovery even in other biological organisms and was later confirmed notably by the observation that the two genes are fused in some bacteria and by the resolution of the structure of the bacterial hybrid protein. Similarly, genome analysis coupled to in vitro analysis of enzymatic properties led to the discovery that some plant methionine sulfoxide reductases can also use both thioredoxins and glutaredoxins as electron donors. Besides their disulfide reductase activity, it has been demonstrated that some poplar glutaredoxins are also involved in iron-sulfur center biogenesis and assembly. The original 3D structure determination has been made with poplar glutaredoxin C1 and then confirmed in a variety of other biological organisms including human. Our work also showed that in plants, so-called glutathione peroxidases use thioredoxins and not glutathione as electron donors. This is true for all non-selenocysteine-containing glutathione peroxidases. Finally, connections between the thioredoxin and glutaredoxin systems have been elucidated through the study of atypical poplar thioredoxins.[br/] Conclusion Altogether, these data illustrate how the combination of genetic engineering and structural biology improves our understanding of biological processes and helps fuel systems biology for trees and other biological species.

Published
2016

6. Molecular and chemical characterization of a Sphagnum palustre clone: Key steps towards a standardized and sustainable moss bag technique

Author

Fiore Capozzi, Aridane G. González, Roberto Bargagli, Ralf Reski, Oleg S. Pokrovsky, D. Crespo Pardo, Simonetta Giordano, A. Di Palma, Paola Adamo, Anna K. Beike, Valeria Spagnuolo, Mauro Tretiach, D. Cafasso, Z. Varela, Jesús R. Aboal, DI PALMA, Anna, CRESPO PARDO, David, Spagnuolo, Valeria, Adamo, Paola, Bargagli, R., Cafasso, Donata, Capozzi, Fiore, Aboal, J. R., González, A. G., Pokrovsky, O., Beike, A. K., Reski, R., Tretiach, M., Varela, Z., Giordano, Simonetta, Università di Bologna [Bologna] (UNIBO), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Mécanismes et Transfert en Géologie (LMTG), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université Polytechnique Hauts-de-France (UPHF)-Ecole Centrale de Lille-Université Polytechnique Hauts-de-France (UPHF)-Institut supérieur de l'électronique et du numérique (ISEN), Di Palma, A., Crespo Pardo, D., Spagnuolo, V, Adamo, P., Cafasso, D., Tretiach, Mauro, Giordano, S., University of Naples Federico II, Department of Physical Sciences, Earth and Environment [Siena] (DSFTA), Università degli Studi di Siena = University of Siena (UNISI), Dipartimento di Scienze della Vita [Trieste], Università degli studi di Trieste, Universidade de Santiago de Compostela [Spain] (USC ), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Tomsk State University [Tomsk], Russian Academy of Sciences [Moscow] (RAS), Stuttgart State Museum of Natural History, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Centre for Biological Signaling Studies [Freiburg] (BIOSS), University of Freiburg [Freiburg], European Project: 282952,EC:FP7:ENV,FP7-ENV-2011-ECO-INNOVATION-TwoStage,MOSSCLONE(2012), University of Naples Federico II = Università degli studi di Napoli Federico II, Università degli studi di Trieste = University of Trieste, Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)

Subjects
010504 meteorology & atmospheric sciences, Evolution, Moss bags, urban areas, Clone (cell biology), General Decision Sciences, Sphagnum palustre, 010501 environmental sciences, Biology, lichen, 01 natural sciences, Sphagnum, deposition, Behavior and Systematics, Botany, monitoring devices, pollution, Atmospheric pollution, Biomonitoring, DNA molecular markers, Trace elements, Decision Sciences (all), Ecology, Evolution, Behavior and Systematics, Ecology, 0105 earth and related environmental sciences, particulate matter, ACL, trace-elements, biology.organism_classification, Moss, Ecology, Evolution, Behavior and Systematic, RAPD, Moss bag, Genetic marker, Trace element, Microsatellite, metal concentrations, Composition (visual arts), genetic-variation, DNA molecular marker, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, element accumulation
Abstract

00002 ăWOS:000388157900039; International audience; This work aimed to define the molecular and chemical signature of a S. palustre clone developed in the framework of the EU-FP7 Mossclone project to improve the standardization and reliability of the moss bag technique. The molecular characterization was performed by a set of DNA molecular markers (RAPD, ISJ, PCR-RFLP, sequencing and microsatellites) to tag the clone produced within the project. Molecular characterization also provided new DNA markers that can be applied in systematic analyses of Sphagnum, and gave new insights to implement well established techniques. The elemental composition of the clone was measured by ICP-MS analysis of 54 major and trace elements, with and without commonly applied pre-exposure treatments (oven devitalization and EDTA washing). Concentrations of almost all analyzed elements were significantly lower (from 10 to 100 times) in the clone than in conspecific field moss, apart from some elements (K, Mo, P and Na) deriving from the culture medium or EDTA treatment. Oven devitalization and EDTA washing did not significantly affect the clone composition. A comparison between the elemental composition of the clone with that of naturally growing Sphagnum species proved the particularly low elemental content of the clone. Therefore, in view of a rigorously standardized moss-bag protocol for the monitoring of persistent atmospheric pollutants, the use of the S. palustre clone, a biomaterial with very low and constant element composition, and homogenous morphological characteristics is strongly recommended. (C) 2016 Elsevier Ltd. All rights reserved.

Published
2016

7. The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Author

Jean-Marc Aury, Frithjof C. Küpper, Diego Miranda-Saavedra, John H. F. Bothwell, Claire Jubin, Chris Bowler, Bernhard Gschloessl, James W. Tregear, Andrés Ritter, Andrew E. Allen, Carolyn A. Napoli, Ludovic Delage, Bernard Kloareg, Takahiro Yamagishi, Pi Nyvall-Collén, Svenja Heesch, Julia Morales, Gaelle Samson, Kei Kimura, Ga Youn Cho, Grigoris D. Amoutzias, Yves Van de Peer, Simon M. Dittami, Kenny Billiau, Julie Poulain, François Artiguenave, Sylvie Doulbeau, Marek Eliáš, Bank Beszteri, Carl J. Carrano, Daniel Lang, Florian Maumus, Stefan A. Rensing, Jonathan H. Badger, Béatrice Segurens, Martina Strittmatter, Sylvie Rousvoal, Hervé Moreau, Patrice Lerouge, Colin Brownlee, Betsy Read, Akira F. Peters, J. Mark Cock, Corinne Da Silva, Declan C. Schroeder, Catherine Boyen, Pierre Rouzé, Eric Bonnet, Jonas Collén, Susana M. Coelho, Aude Le Bail, Kamel Jabbari, David R. Nelson, Thierry Tonon, Pascal J. Lopez, Véronique Anthouard, Hadi Quesneville, Manoj P. Samanta, Delphine Scornet, Klaus Valentin, Nicolas Delaroque, Bénédicte Charrier, Cindy Martens, Peter von Dassow, Martin Lohr, Garry Farnham, Chikako Nagasato, Claire M. M. Gachon, Gurvan Michel, Lieven Sterck, Philippe Potin, Erwan Corre, Catherine Leblanc, Taizo Motomura, Cyril Pommier, Patrick Wincker, Hiroshi Kawai, Publica, Végétaux marins et biomolécules, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, State University of Ghent, J Craig Venter Institute, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Marine Biological Association, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), San Diego State University (SDSU), Phophorylation de protéines et Pathologies Humaines (P3H), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Charles University [Prague], Scottish Association for Marine Science (SAMS), Kobe University, Institute of Algological Research [Muroran], Hokkaido University, Fakultät für Biologie = Faculty of Biology [Freiburg], Albert-Ludwigs-Universität Freiburg, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Johannes Gutenberg - Universität Mainz (JGU), École normale supérieure - Paris (ENS Paris), Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Haematology, University of Cambridge [UK] (CAM), Mer et santé (MS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Arizona, The University of Tennessee Health Science Center [Memphis] (UTHSC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), California State University [Los Angeles] (CAL STATE LA), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Systemix Institute, Savelli, Bruno, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), J. Craig Venter Institute, Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Charles University [Prague] (CU), Hokkaido University [Sapporo, Japan], Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris

Subjects
0106 biological sciences, Lineage (evolution), Molecular Sequence Data, Phaeophyta, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Algae, [SDV.BDD] Life Sciences [q-bio]/Development Biology, Botany, BIOLOGIE CELLULAIRE, Animals, 14. Life underwater, [SDV.BDD]Life Sciences [q-bio]/Development Biology, flore marine, Phylogeny, Organism, ComputingMilieux_MISCELLANEOUS, phéophycées, 030304 developmental biology, 0303 health sciences, Multidisciplinary, biology, Ectocarpus siliculosus, Algal Proteins, Eukaryota, Pigments, Biological, Ectocarpus, 15. Life on land, biology.organism_classification, Biological Evolution, Brown algae, Multicellular organism, Evolutionary biology, algues brunes, Biologie, Signal Transduction, 010606 plant biology & botany
Abstract

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. © 2010 Macmillan Publishers Limited. All rights reserved.

Published
2010

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