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19 results on '"Department of Biology [ETH Zürich] (D-BIOL)"'

1. Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota

Author

Daniel Hoces, Giorgia Greter, Markus Arnoldini, Claudia Moresi, Sara Berent, Isabel Kolinko, Florence Bansept, Aurore Woller, Janine Häfliger, Eric Martens, Wolf-Dietrich Hardt, Claude Loverdo, Emma Slack, Department of Health Sciences and Technology [ETH Zürich] (D-HEST), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Laboratoire Jean Perrin (LJP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-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), University of Michigan Medical School [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Department of Biology [ETH Zürich] (D-BIOL), and Loverdo, Claude

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract

SummaryMany microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. However, we remain largely blind to the quantitative effects of processes determining colonization success. In this study, we used genetically-barcoded Bacteroides thetaiotaomicron (B.theta) strains in combination with mathematical modeling to quantify population bottlenecks experienced by B.theta during gut colonization. Integrating population bottlenecks sizes with careful quantification of net growth rates in vivo and in vitro allows us to build models describing the events during intestinal colonization in the context of gnotobiotic and complex microbiotas. Using these models, we estimated the decrease in niche size for B.theta colonization with increasing microbiota complexity. In addition, our system can be applied to mechanistically dissect colonization defects of mutant strains. As a proof of concept, we demonstrated that the competitive disadvantage of a B.theta mutant lacking capsular polysaccharide is due to a combination of an increased lag-phase before growth initiation in the gut, combined with an increased clearance rate. Crucially, the requirement for the B.theta capsule depended strongly on microbiota composition, suggesting that the dominant role may be protection from bacterial or phage aggression rather than from host-induced bactericidal mechanisms.

Published
2022
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2. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome

Author

Ahmed A, Zayed, James M, Wainaina, Guillermo, Dominguez-Huerta, Eric, Pelletier, Jiarong, Guo, Mohamed, Mohssen, Funing, Tian, Akbar Adjie, Pratama, Benjamin, Bolduc, Olivier, Zablocki, Dylan, Cronin, Lindsey, Solden, Erwan, Delage, Adriana, Alberti, Jean-Marc, Aury, Quentin, Carradec, Corinne, da Silva, Karine, Labadie, Julie, Poulain, Hans-Joachim, Ruscheweyh, Guillem, Salazar, Elan, Shatoff, Ralf, Bundschuh, Kurt, Fredrick, Laura S, Kubatko, Samuel, Chaffron, Alexander I, Culley, Shinichi, Sunagawa, Jens H, Kuhn, Patrick, Wincker, Matthew B, Sullivan, Silvia G, Acinas, Marcel, Babin, Peer, Bork, Emmanuel, Boss, Chris, Bowler, Guy, Cochrane, Colomban, de Vargas, Gabriel, Gorsky, Lionel, Guidi, Nigel, Grimsley, Pascal, Hingamp, Daniele, Iudicone, Olivier, Jaillon, Stefanie, Kandels, Lee, Karp-Boss, Eric, Karsenti, Fabrice, Not, Hiroyuki, Ogata, Nicole, Poulton, Stéphane, Pesant, Christian, Sardet, Sabrinia, Speich, Lars, Stemmann, Shinichi, Sungawa, Department of Microbiology [Columbus], Ohio State University [Columbus] (OSU), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, 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), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Génomique métabolique (UMR 8030), 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), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Physics, The Ohio State University, Department of Statistics, the Ohio State University Columbus, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Université Laval [Québec] (ULaval), Institute of Microbiology, Department of Biology, ETH Zurich, Institute of Microbiology, Department of Microbiology, The Ohio state university, Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, and Nantes Université (Nantes Univ)

Subjects
Multidisciplinary, Virome, Oceans and Seas, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Genome, Viral, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biological Evolution, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDE]Environmental Sciences, Viruses, RNA, RNA Viruses, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem, Phylogeny, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth’s RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. “Species”-rank abundance determination revealed that viruses of the new phyla “ Taraviricota ,” a missing link in early RNA virus evolution, and “ Arctiviricota ” are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.

Published
2022
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3. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition

Author

Caroline Belser, Julie Poulain, Karine Labadie, Frederick Gavory, Adriana Alberti, Julie Guy, Quentin Carradec, Corinne Cruaud, Corinne da Silva, Stefan Engelen, Paul Mielle, Aude Perdereau, Gaelle Samson, Shahinaz Gas, Genoscope Technical Team, Voolstra, Christian R., Galand, Pierre E., Michel Flores, J., Benjamin Cc Hume, Gabriela Perna, Maren Ziegler, Hans-Joachim Ruscheweyh, Emilie Boissin, Sarah Romac, Guillaume Bourdin, Guillaume Iwankow, Clémentine Moulin, Paz García, David A., Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Éric Douville, Didier Forcioli, Paola Furla, Éric Gilson, Fabien Lombard, Stephane Pesant, Stéphanie Reynaud, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Rebecca Vega Thurber, Didier Zoccola, Claude Scarpelli, Krame Jacoby, E., Oliveira, Pedro H., Jean-Marc Aury, Denis Allemand, Serge Planes, Patrick Wincker, 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Universität Konstanz, Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Weizmann Institute of Science [Rehovot, Israël], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Maine, Tara Expéditions, Centro de Investigaciones Biologicas del Noroeste [Mexico] (CONACYT-CIBNOR), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Université de Tsukuba = University of Tsukuba, Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), 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)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université Côte d'Azur (UCA), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory (EMBL), Centre Scientifique de Monaco (CSM), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), Menguy, Caroline, Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), and Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE)

Subjects
FOS: Biological sciences, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Quantitative Biology - Quantitative Methods, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the host coral organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Published
2022
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4. Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging

Author

Guy Schoehn, Clarisse Uwizeye, Gilles Curien, Rachel Templin, Samuel C. Zeeman, Yannick Schwab, Davide Dal Bo, Denis Falconet, Fabien Chevalier, Serena Flori, Christine Moriscot, Florence Courtois, Claire Seydoux, Jean-Baptiste Keck, Benoit Gallet, Johan Decelle, Nicole L. Schieber, Pierre-Henri Jouneau, Giovanni Finazzi, Guillaume Allorent, LIPID, 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), Photosymbiose, Modélisation et Exploration des Matériaux (MEM), 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)-Université Grenoble Alpes (UGA), Light Photosynthesis & Metabolism (Photosynthesis), Institut de biologie structurale (IBS - UMR 5075), Calcul des Variations, Géométrie, Image (CVGI), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory, European Molecular Biology Laboratory [Grenoble] (EMBL), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Défi X-Life grant from CNRS, CEA DRFimpulsion FIB-Bioprogram, Auvergne-Rhône-Alpes Region, Fondation Recherche Medicale (FRM), FEDER and the GIS-Infrastructures en Biologie Santé et Agronomie (IBiSA), 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-17-CE05-0029,MoMix,Modélisation de la Mixotrophie chez l'algue extrêmophile Galdieria sulphuraria(2017), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), European Project: 833184, ChloroMito, and European Project: 654248,H2020,H2020-INFRADEV-1-2014-1,CORBEL(2015)

Subjects
0106 biological sciences, 0301 basic medicine, Cell biology, Light, Bioenergetics, MESH: Mitochondria, Acclimatization, Science, General Physics and Astronomy, MESH: Acclimatization, MESH: Imaging, Three-Dimensional, Cellular imaging, Photosynthesis, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Pyrenoid, MESH: Microalgae, 03 medical and health sciences, Imaging, Three-Dimensional, Phytoplankton, Microalgae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plastids, Plastid, Cellular microbiology, Trophic level, Biomass (ecology), Multidisciplinary, biology, Ecology, MESH: Energy Metabolism, fungi, MESH: Plastids, General Chemistry, biology.organism_classification, MESH: Light, Mitochondria, 030104 developmental biology, Diatom, MESH: Subcellular Fractions, Energy Metabolism, Subcellular Fractions, MESH: Phytoplankton, 010606 plant biology & botany
Abstract

Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO2-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales., Nature Communications, 12 (1), ISSN:2041-1723

Published
2021
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5. Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR

Author

Beat H. Meier, Pengzhi Wu, Thomas Wiegand, Loïc Salmon, Denis Lacabanne, Julien Boudet, Riccardo Cadalbert, Frédéric H.-T. Allain, Alexander A. Malär, Laboratory of Physical Chemistry [ETH Zürich] (LPC), Department of Chemistry and Applied Biosciences [ETH Zürich] (D-CHAB), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Biochemistry [Netherlands] (DB), and Department of Biochemistry-Medical Faculty, Erasmus University Medical Centre-Erasmus University Rotterdam

Subjects
Fast magic-angle spinning, Magnetic Resonance Spectroscopy, 1 H-detection, Noncovalent interactions, Stereochemistry, 010402 general chemistry, 01 natural sciences, Article, chemistry.chemical_compound, Molecular recognition, pRN1 primase, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, 0103 physical sciences, Materials Chemistry, Magic angle spinning, Non-covalent interactions, Physical and Theoretical Chemistry, DNA binding, Nuclear Magnetic Resonance, Biomolecular, chemistry.chemical_classification, 010304 chemical physics, Hydrogen bond, Proteins, Hydrogen Bonding, Magnetic Resonance Imaging, 3. Good health, 0104 chemical sciences, Surfaces, Coatings and Films, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], chemistry, Proton NMR, Nucleic acid, Primase, Protons, DNA
Abstract

The journal of physical chemistry / B 124(49), 11089-11097 (2020). doi:10.1021/acs.jpcb.0c08150 special issue: "Hellmut Eckert Festschrift : virtual issue", Published by American Chemical Society, Washington, DC

Published
2020
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6. Activity of Tumor Necrosis Factor α Is Modulated by Dynamic Conformational Rearrangements

Author

Daniela Hofmann, Loïc Salmon, Gerhard Wider, Department of Biology [ETH Zürich] (D-BIOL), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)

Subjects
0301 basic medicine, Chemistry, medicine.medical_treatment, Regulator, General Chemistry, Nuclear magnetic resonance spectroscopy, Ligand (biochemistry), Biochemistry, Solution structure, Catalysis, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 03 medical and health sciences, 030104 developmental biology, Colloid and Surface Chemistry, Immune system, Cytokine, medicine, Biophysics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Tumor necrosis factor alpha, Tumor necrosis factor α, ComputingMilieux_MISCELLANEOUS
Abstract

The homotrimeric ligand tumor necrosis factor α (TNFα) is a key cytokine and immune regulator; however, when deregulated, it leads to several major chronic inflammatory diseases. Perturbation of the protein-protein interface has proven to be an efficient strategy to inactivate TNFα, but the atomic-resolution mechanism of its inactivation remains poorly understood. Here, we probe the solution structure and dynamics of active and inactive TNFα using NMR spectroscopy. The data reveal that TNFα undergoes motions on different time scales. Furthermore, by site-directed mutagenesis of residues at the trimerization interface and by targeting the interface with a low molecular weight inhibitor, we show that TNFα retains its overall structure and trimeric state. However, upon perturbation, TNFα exhibits increased conformational dynamics spanning from the trimerization interface to the regions mediating receptor binding. These findings provide novel insights into the inactivation mechanism of TNFα and the basis for strategies to target TNFα activity.

Published
2017
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7. Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5

Author

Asokan Ananbandam, Hisashi Yoshida, Florian Stengel, Mahmoud L. Nasr, Brytteny Thompson, Takeshi Urano, Fan Zhang, Philip Gao, Haribabu Arthanari, Takashi Nagata, Riccardo Pellarin, Gerhard Wagner, Alan G. Hinnebusch, Jacob Morris, Rafael E. Luna, Katsura Asano, Evangelos Papadopoulos, Chelsea Moore, Eric Aube, Pilar Martin-Marcos, Hiroyuki Hiraishi, Eiji Obayashi, Eddie Dagraca, Jan P. Erzberger, Chingakham Ranjit Singh, Satoru Unzai, Ian Harmon, Samantha Hustak, Berkeley California Institute for Quantitative Biosciences [Berkeley], University of California (UC), University of California [San Francisco] (UC San Francisco), Institute for Molecular Systems Biology [ETH Zurich] (IMSB), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Division of Biology, Kansas State University, Kansas State University, This work was supported by a grant from the NIH (R01 GM64781), a pilot grant from University of Kansas COBRE-PSF (P30 GM 110761), NSF Research Grant (1412250), and an Innovative Award from KSU Terry Johnson Cancer Center to K.A., CA68262 and GM47467 to G.W., an intramural grant from NICHD, NIH, to A.G.H., and JSPS KAKENHI 15H01634 and 26440026 to T.N., We thank Hiroshi Matsuo and Erin Adamson for comments, Ivan Topisirovic for proofreading, and Michaela Flax and Speed Rogers for technical assistance., University of California, and University of California [San Francisco] (UCSF)

Subjects
Models, Molecular, MESH: Eukaryotic Initiation Factor-5, 0301 basic medicine, Magnetic Resonance Spectroscopy, MESH: Eukaryotic Initiation Factor-3, Eukaryotic Initiation Factor-3, ribosomal pre-initiation complex, Eukaryotic Initiation Factor-1, MESH: Amino Acid Sequence, MESH: Saccharomyces cerevisiae Proteins, Start codon, Eukaryotic initiation factor, Eukaryotic Initiation Factor-5, Peptide Chain Initiation, Translational, lcsh:QH301-705.5, Shine-Dalgarno sequence, MESH: Protein Subunits, MESH: Saccharomyces cerevisiae, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, EIF1, ribosome, eIF1, eIF3, MESH: Eukaryotic Initiation Factor-1, eIF5, MESH: Models, Molecular, Protein Binding, MESH: Peptide Chain Initiation, Translational, Saccharomyces cerevisiae Proteins, MESH: Mutation, Saccharomyces cerevisiae, Biology, start codon selection, translation initiation, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, ddc:570, MESH: Protein Binding, Initiation factor, Amino Acid Sequence, RNA, Messenger, MESH: RNA, Messenger, Binding Sites, MESH: Magnetic Resonance Spectroscopy, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Molecular biology, Ribosomal binding site, Protein Subunits, A-site, Internal ribosome entry site, 030104 developmental biology, lcsh:Biology (General), MESH: Binding Sites, Ribosomal pre-initiation complex, Ribosome, Start codon selection, Translation initiation, Mutation, Biophysics, Ribosomes, MESH: Ribosomes
Abstract

During eukaryotic translation initiation, eIF3 binds the solvent-accessible side of the 40S ribosome and recruits the gate-keeper protein eIF1 and eIF5 to the decoding center. This is largely mediated by the N-terminal domain (NTD) of eIF3c, which can be divided into three parts: 3c0, 3c1, and 3c2. The N-terminal part, 3c0, binds eIF5 strongly but only weakly to the ribosome-binding surface of eIF1, whereas 3c1 and 3c2 form a stoichiometric complex with eIF1. 3c1 contacts eIF1 through Arg-53 and Leu-96, while 3c2 faces 40S protein uS15/S13, to anchor eIF1 to the scanning pre-initiation complex (PIC). We propose that the 3c0:eIF1 interaction diminishes eIF1 binding to the 40S, whereas 3c0:eIF5 interaction stabilizes the scanning PIC by precluding this inhibitory interaction. Upon start codon recognition, interactions involving eIF5, and ultimately 3c0:eIF1 association, facilitate eIF1 release. Our results reveal intricate molecular interactions within the PIC, programmed for rapid scanning-arrest at the start codon., Cell Reports, 18 (11), ISSN:2666-3864, ISSN:2211-1247

Published
2017
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8. Alpha diversity of vascular plants in European forests

Author

Valerijus Rašomavičius, Emiliano Agrillo, Jens-Christian Svenning, Marcela Řezníčková, Thomas Wohlgemuth, Grzegorz Swacha, Jonathan Lenoir, Roberto Venanzoni, Urban Šilc, Ilona Knollová, Joop H.J. Schaminée, Milan Chytrý, Wolfgang Willner, Adrian Indreica, Panayotis Dimopoulos, Federico Fernández-González, Kiril Vassilev, Mirjana Ćuk, Juan Antonio Campos, Andraž Čarni, Jean Claude Gégout, Jan Divíšek, Martin Večeřa, Idoia Biurrun, John S. Rodwell, Borja Jiménez-Alfaro, Ute Jandt, Florian Jansen, Guillermo Crespo Jiménez, Jörg Ewald, Zygmunt Kącki, Masaryk University [Brno] (MUNI), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), University of Oviedo, Department of Plant Biology and Ecology, University of the Basque Country UPV/ EHU, Bilbao, Spain, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], National Institute of Biology [Ljubljana] (NIB), University of Castilla-La Mancha (UCLM), University of Novi Sad, University of Patras [Patras], Institute for Molecular Systems Biology [ETH Zurich] (IMSB), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), SILVA (SILVA), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)-AgroParisTech, Transilvania University of Brasov, Philips Research Europe - Hamburg, Sector Medical Imaging Systems, Philips Research, Martin-Luther-University Halle-Wittenberg, University of Rostock, University of Wrocław [Poland] (UWr), Nature Research Centre [Vilnius], Centre for Ecosystem Studies, University of Wageningen, Wageningen University and Research [Wageningen] (WUR), Aarhus University [Aarhus], Bulgarian Academy of Sciences (BAS), Dept Appl Biol, Università degli Studi di Perugia (UNIPG), Vienna Institute for Nature Conservation and Analyses (VINCA), and Swiss Federal Institute for Forest, Snow and Landscape Research WSL

Subjects
0106 biological sciences, Random Forests, plant community, Bos- en Landschapsecologie, Biodiversity, 01 natural sciences, Vegetation-plot database, Forest and Landscape Ecology, vascular plants, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Diversity, Ecology, biology, European Vegetation Archive, Vegetation, PE&RC, Europe, Geography, Plantenecologie en Natuurbeheer, Forest vegetation, Vegetatie, Bos- en Landschapsecologie, species-richness patterns, Vascular plant, forest vegetation, Gamma diversity, [SDE.MCG]Environmental Sciences/Global Changes, Plant Ecology and Nature Conservation, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Plant community, 010603 evolutionary biology, diversity, 03 medical and health sciences, Species-richness patterns, Ecology, Evolution, Behavior and Systematics, Vegetatie, 030304 developmental biology, European Vegetation Archive (EVA), predictive modelling, vegetation-plot database, Vascular plants, Predictive modelling, Species diversity, 15. Life on land, biology.organism_classification, Alpha diversity, Vegetation, Forest and Landscape Ecology, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Aim The former continental‐scale studies modelled coarse‐grained plant species‐richness patterns (gamma diversity). Here we aim to refine this information for European forests by (a) modelling the number of vascular plant species that co‐occur in local communities (alpha diversity) within spatial units of 400 m2; and (b) assessing the factors likely determining the observed spatial patterns in alpha diversity. Location Europe roughly within 12°W–30°E and 35–60°N. Taxon Vascular plants. Methods The numbers of co‐occurring vascular plant species were counted in 73,134 georeferenced vegetation plots. Each plot was classified by an expert system into deciduous broadleaf, coniferous or sclerophyllous forest. Random Forest models were used to map and explain spatial patterns in alpha diversity for each forest type separately using 19 environmental, land‐use and historical variables. Results Our models explained from 51.0% to 70.9% of the variation in forest alpha diversity. The modelled alpha‐diversity pattern was dominated by a marked gradient from species‐poor north‐western to species‐rich south‐eastern Europe. The most prominent richness hotspots were identified in the Calcareous Alps and adjacent north‐western Dinarides, the Carpathian foothills in Romania and the Western Carpathians in Slovakia. Energy‐related factors, bedrock types and terrain ruggedness were identified as the main variables underlying the observed richness patterns. Alpha diversity increases especially with temperature seasonality in deciduous broadleaf forests, on limestone bedrock in coniferous forests and in areas with low annual actual evapotranspiration in sclerophyllous forests. Main conclusions We provide the first predictive maps and analyses of environmental factors driving the alpha diversity of vascular plants across European forests. Such information is important for the general understanding of European biodiversity. This study also demonstrates a high potential of vegetation‐plot databases as sources for robust estimation of the number of vascular plant species that co‐occur at fine spatial grains across large areas., M.V., J.D., I.K., M.Ř. and M.C. were supported by the Czech Science Foundation (Centre of Excellence Pladias; project no. 14–36079G). I.B. and J.A.C. were supported by the Basque Government (IT936‐16). B.J.‐A. was supported by the Marie Curie Clarín‐COFUND program of the Principate of Asturias and the European Union (ACB17‐26). J.‐C.S. considers this work a contribution to his VILLUM Investigator project “Biodiversity Dynamics in a Changing World” funded by VILLUM FONDEN (grant 16549) and his Danish Council for Independent Research | Natural Sciences TREECHANGE project (grant 6108‐00078B).

Published
2019
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9. Diverse activation pathways in class A GPCRs converge near the G protein-coupling region

Author

Tamara Miljuš, Michel Bouvier, Franziska M. Heydenreich, AJ Venkatakrishnan, M. Madan Babu, Tilman Flock, Christopher G. Tate, Guillaume Lebon, S. Balaji, Dmitry B. Veprintsev, Xavier Deupi, Gebhard F. X. Schertler, Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, Condensed Matter Theory Group and Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Immunologie et en Cancérologie [UdeM-Montréal] (IRIC), Université de Montréal (UdeM), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Laboratory of Molecular Biology [Cambridge], and Medical Research Council

Subjects
0301 basic medicine, Models, Molecular, Receptors, Vasopressin, G protein, Biology, Ligands, Rhodopsin-like receptors, Article, Protein Structure, Secondary, Receptors, G-Protein-Coupled, 03 medical and health sciences, Protein structure, Humans, Binding site, Conserved Sequence, G protein-coupled receptor, Multidisciplinary, Binding Sites, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Heterotrimeric GTP-Binding Proteins, Cell biology, Transmembrane domain, 030104 developmental biology, Membrane protein, Structural Homology, Protein, Signal transduction, Signal Transduction
Abstract

International audience; Class A G-protein-coupled receptors (GPCRs) are a large family of membrane proteins that mediate a wide variety of physiological functions, including vision, neurotransmission and immune responses. They are the targets of nearly one-third of all prescribed medicinal drugs such as beta blockers and antipsychotics. GPCR activation is facilitated by extracellular ligands and leads to the recruitment of intracellular G proteins. Structural rearrangements of residue contacts in the transmembrane domain serve as 'activation pathways' that connect the ligand-binding pocket to the G-protein-coupling region within the receptor. In order to investigate the similarities in activation pathways across class A GPCRs, we analysed 27 GPCRs from diverse subgroups for which structures of active, inactive or both states were available. Here we show that, despite the diversity in activation pathways between receptors, the pathways converge near the G-protein-coupling region. This convergence is mediated by a highly conserved structural rearrangement of residue contacts between transmembrane helices 3, 6 and 7 that releases G-protein-contacting residues. The convergence of activation pathways may explain how the activation steps initiated by diverse ligands enable GPCRs to bind a common repertoire of G proteins.

Published
2016
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10. In situ and high-resolution Cryo-EM structure of the Type VI secretion membrane complex

Author

Riccardo Pellarin, Victoria Schmidt, Yassine Cherrak, Laureen Logger, Rémi Fronzes, Romain Kooger, Chiara Rapisarda, Eric Durand, Eric Cascales, Martin Pilhofer, Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Institute of Biochemistry [ETH Zürich], Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Bioinformatique structurale - Structural Bioinformatics, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), European Institute of Chemistry and Biology, Université Sciences et Technologies - Bordeaux 1, This work was funded by the Centre National de la Recherche Scientifique, the Aix‐Marseille Université, and grants from the Agence Nationale de la Recherche (ANR‐14‐CE14‐0006‐02, ANR‐17‐CE11‐0039‐01) and the Fondation pour la Recherche Médicale (DEQ20180339165) to EC. ED was supported by the INSERM and an EMBO short‐term fellowship (ASTF 417 – 2015). YC is supported by a Doctoral school PhD fellowship from the FRM (ECO20160736014). VS is supported by a post‐doctoral fellowship from the association Espoir contre la Mucoviscidose. LL was supported by a fourth year PhD fellowship from the FRM (FDT20160435498). MP is funded by the European Research Council, the Swiss National Science Foundation and the Helmut Horten Foundation. RF and CR were supported by IDEX Bordeaux through a 'chaire d'excellence' to RF., ANR-17-CE11-0039,T6-PLATFORM,Une approche multidisciplinaire et intégrative pour comprendre l'assemblage, la structure et la dynamique d'une plateforme de queue contractile(2017), ANR-14-CE14-0006,B-War,Guerre bactérienne: Architecture et Fonction du Système de Sécrétion de Type VI(2014), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Sciences et Technologies - Bordeaux 1 (UB), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)-Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Bioinformatique structurale, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
In situ, MESH: Protein Structure, Quaternary, Cryo-electron microscopy, [SDV]Life Sciences [q-bio], MESH: Type VI Secretion Systems, Single particle analysis, MESH: Escherichia coli Proteins, law.invention, 03 medical and health sciences, law, MESH: Protein Binding, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Secretion, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH: Bacterial Secretion Systems, 030304 developmental biology, Type VI secretion system, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], MESH: Escherichia coli, 030306 microbiology, Chemistry, Negative stain, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Membrane, Biophysics, MESH: Cryoelectron Microscopy, MESH: Membrane Proteins, Electron microscope, MESH: Models, Molecular, MESH: Cell Membrane
Abstract

Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is related to Myoviridae phages. The T6SS is composed of a baseplate that contains a spike onto which an inner tube is built, surrounded by a contractile sheath. Unlike phages that are released to and act in the extracellular medium, the T6SS is an intracellular machine inserted in the bacterial membranes by a trans-envelope complex. This membrane complex (MC) comprises three proteins: TssJ, TssL and TssM. We previously reported the low-resolution negative stain electron microscopy structure of the enteroaggregative Escherichia coli MC and proposed a rotational 5-fold symmetry with a TssJ:TssL:TssM stoichiometry of 2:2:2. Here, cryo-electron tomography analysis of the T6SS MC confirmed the 5-fold symmetry in situ and identified the regions of the structure that insert into the bacterial membranes. A high resolution model obtained by single particle cryo-electron microscopy reveals its global architecture and highlights new features: five additional copies of TssJ, yielding a TssJ:TssL:TssM stoichiometry of 3:2:2, a 11-residue loop in TssM, protruding inside the lumen of the MC and constituting a functionally important periplasmic gate, and hinge regions. Based on these data, we revisit the model on the mechanism of action of the MC during T6SS assembly and function.

Published
2018
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11. The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein

Author

Frédéric H.-T. Allain, Stanislaw Dunin-Horkawicz, Inna Grishina, Christophe Maris, Janusz M. Bujnicki, Stéphane Thore, Timm Maier, Albrecht Bindereif, Markus Blatter, Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), International Institute of Molecular and Cell Biology, Warsaw and Faculty of Chemistry, University of Warsaw (UW), Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)

Subjects
Genetics, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], RNA recognition motif, 030302 biochemistry & molecular biology, Alternative splicing, RNA, RNA-binding protein, Biology, 03 medical and health sciences, Exon, Structural Biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, ComputingMilieux_MISCELLANEOUS, Function (biology), 030304 developmental biology, Binding domain, Heterogeneous-Nuclear Ribonucleoprotein L
Abstract

The RNA recognition motif (RRM) is the far most abundant RNA binding domain. In addition to the typical β1α1β2β3α2β4 fold, various sub-structural elements have been described and reportedly contribute to the high functional versatility of RRMs. The heterogeneous nuclear ribonucleoprotein L (hnRNP L) is a highly abundant protein of 64 kDa comprising four RRM domains. Involved in many aspects of RNA metabolism, hnRNP L specifically binds to RNAs containing CA repeats or CA-rich clusters. However, a comprehensive structural description of hnRNP L including its sub-structural elements is missing. Here, we present the structural characterization of the RRM domains of hnRNP L and demonstrate their function in repressing exon 4 of SLC2A2. By comparison of the sub-structural elements between the two highly similar paralog families of hnRNP L and PTB, we defined signatures underlying interacting C-terminal coils (ICCs), the RRM34 domain interaction and RRMs with a C-terminal fifth β-strand, a variation we denoted vRRMs. Furthermore, computational analysis revealed new putative ICC-containing RRM families and allowed us to propose an evolutionary scenario explaining the origins of the ICC and fifth β-strand sub-structural extensions. Our studies provide insights of domain requirements in alternative splicing mediated by hnRNP L and molecular descriptions for the sub-structural elements. In addition, the analysis presented may help to classify other abundant RRM extensions and to predict structure–function relationships.

Published
2015
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12. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

Author

Markus Metz, Vadim Cherezov, Peter Berntsen, Dingjie Wang, Richard Neutze, Wenting Wu, Gebhard F. X. Schertler, Linda C. Johansson, Isabel Moraes, Dominik Oberthuer, Thomas A. White, Henry N. Chapman, Valerie Panneels, Kathrin Jaeger, Petra Båth, Daniel James, Anastasya Shilova, Michael Heymann, Manfred Burghammer, Cecilia Wickstrand, Garrett Nelson, Uwe Weierstall, Joerg Standfuss, Nadia A. Zatsepin, Przemyslaw Nogly, Haiguang Liu, John David Spence, Paul Scherrer Inst, Lab Biomol Res, CH-5232 Villigen, Switzerland, Arizona State University [Tempe] (ASU), DESY, Ctr Free Electron Laser Sci, D-22607 Hamburg, Germany, European Synchrotron Radiation Facility (ESRF), Scripps Research Institute, Ctr Ultrafast Imaging, D-22607 Hamburg, Germany, University of Gothenburg (GU), Univ Hamburg, Dept Phys, D-22607 Hamburg, Germany, Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Physics [Tempe], Diamond Light Source, Membrane Prot Lab, Chilton OX11 0DE, Oxon, England, Rutherford Appleton Lab, Didcot OX11 0FA, Oxon, England, Univ London Imperial Coll Sci Technol & Med, Dept Life Sci, London, England, and Universiteit Gent = Ghent University [Belgium] (UGENT)

Subjects
Materials science, Physics::Optics, Synchrotron radiation, 02 engineering and technology, Biochemistry, law.invention, Quantitative Biology::Subcellular Processes, 03 medical and health sciences, law, protein crystallography, Proton transport, [CHIM]Chemical Sciences, ddc:530, General Materials Science, lcsh:Science, 030304 developmental biology, Physics::Biological Physics, Quantitative Biology::Biomolecules, 0303 health sciences, Millisecond, biology, bacteriorhodopsin, lipidic cubic phases, XFEL, Resolution (electron density), Bacteriorhodopsin, General Chemistry, equipment and supplies, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Research Papers, Synchrotron, Crystallography, Lipidic cubic phases, Protein crystallography, biological sciences, X-ray crystallography, Femtosecond, biology.protein, Physics::Accelerator Physics, lcsh:Q, lipids (amino acids, peptides, and proteins), 0210 nano-technology
Abstract

Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway., IUCrJ, 2 (2), ISSN:2052-2525

Published
2015
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13. Peroxisome Proliferator Activated Receptor Gamma Controls Mature Brown Adipocyte Inducibility through Glycerol Kinase

Author

Lukas Varga, Pirjo Nuutila, Wenfei Sun, Sven Enerbäck, Patrik Stefanicka, Christian Wolfrum, Walter Wahli, Bettina Tall, Nicola Zamboni, Kirsi A. Virtanen, Elke Kiehlmann, Petra Krznar, Ez-Zoubir Amri, Lennart Opitz, Jozef Ukropec, Miroslav Balaz, Matthias Rosenwald, Martin E. Lidell, David Lasar, DNA Microarray Facility, Georg-August-University [Göttingen], Institute for Molecular Systems Biology [ETH Zurich] (IMSB), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Turku PET Centre, University of Turku, Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (... - 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)-Centre National de la Recherche Scientifique (CNRS), Center for Integrative Genomics - Institute of Bioinformatics, Génopode (CIG), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL)-Université de Lausanne (UNIL), University of Zurich, Wolfrum, Christian, and Lee Kong Chian School of Medicine (LKCMedicine)

Subjects
0301 basic medicine, Adult, Male, Glycerol kinase, [SDV]Life Sciences [q-bio], Peroxisome proliferator-activated receptor, Adipose tissue, 610 Medicine & health, 10071 Functional Genomics Center Zurich, ta3111, General Biochemistry, Genetics and Molecular Biology, PPAR Gamma, 03 medical and health sciences, chemistry.chemical_compound, Mice, Adipose Tissue, Brown, 1300 General Biochemistry, Genetics and Molecular Biology, Glycerol Kinase, Brown adipose tissue, medicine, Adipocytes, Animals, Humans, PPAR alpha, Receptor, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Fatty acid metabolism, Chemistry, non-shivering thermogenesis, brown adipose tissue, Thermogenesis, Peroxisome, Cell biology, Mice, Inbred C57BL, PPAR gamma, 030104 developmental biology, medicine.anatomical_structure, lcsh:Biology (General), Brown Adipose Tissue, 570 Life sciences, biology, Female, Adipocytes/cytology, Adipocytes/enzymology, Adipocytes/metabolism, Adipose Tissue, Brown/cytology, Adipose Tissue, Brown/enzymology, Adipose Tissue, Brown/metabolism, Glycerol Kinase/metabolism, PPAR gamma/metabolism, glycerol kinase
Abstract

Peroxisome proliferator-activated receptors (PPARs) have been suggested as the master regulators of adipose tissue formation. However, their role in regulating brown fat functionality has not been resolved. To address this question, we generated mice with inducible brown fat-specific deletions of PPARα, β/δ, and γ, respectively. We found that both PPARα and β/δδ are dispensable for brown fat function. In contrast, we could show that ablation of PPARγ in vitro and in vivo led to a reduced thermogenic capacity accompanied by a loss of inducibility by β-adrenergic signaling, as well as a shift from oxidative fatty acid metabolism to glucose utilization. We identified glycerol kinase (Gyk) as a partial mediator of PPARγ function and could show that Gyk expression correlates with brown fat thermogenic capacity in human brown fat biopsies. Thus, Gyk might constitute the link between PPARγ-mediated regulation of brown fat function and activation by β-adrenergic signaling. Published version

Published
2017
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14. Genome-wide small interfering RNA screens reveal VAMP3 as a novel host factor required for Uukuniemi virus late penetration

Author

Christian von Mering, Peter Horvath, Roger Meier, Ari Helenius, Marilou Tétard, Pierre-Yves Lozach, Andrea Franceschini, Roberta Mancini, Institute of Biochemistry [ETH Zürich], Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), This work was supported by grants from InfectX to C.V.M., from theEuropean Research Council, the Swiss National Foundation for Research,ETH Zurich, and LipidX to A.H., and from the Natural Sciences andEngineering Research Council of Canada and the Banting Research Foundationto P.Y.L., and University of Zurich

Subjects
Small interfering RNA, 1109 Insect Science, Time Factors, Vesicle-Associated Membrane Protein 3, [SDV]Life Sciences [q-bio], Immunology, Endosomes, Biology, Microbiology, Virus, UFSP13-7 Evolution in Action: From Genomes to Ecosystems, Virology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], microRNA, Gene silencing, Humans, Gene Silencing, Genetic Testing, RNA, Small Interfering, Host factor, 2403 Immunology, Uukuniemi virus, 2404 Microbiology, Lysosome-Associated Membrane Glycoproteins, Epithelial Cells, Virus Internalization, biology.organism_classification, 10124 Institute of Molecular Life Sciences, 3. Good health, Cell biology, Virus-Cell Interactions, Viral replication, Insect Science, Host-Pathogen Interactions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 2406 Virology, 570 Life sciences, biology, Bunyaviridae, U7 Systems Biology / Functional Genomics, HeLa Cells
Abstract

The Bunyaviridae constitute a large family of enveloped animal viruses, many of which are important emerging pathogens. How bunyaviruses enter and infect mammalian cells remains largely uncharacterized. We used two genome-wide silencing screens with distinct small interfering RNA (siRNA) libraries to investigate host proteins required during infection of human cells by the bunyavirus Uukuniemi virus (UUKV), a late-penetrating virus. Sequence analysis of the libraries revealed that many siRNAs in the screens inhibited infection by silencing not only the intended targets but additional genes in a microRNA (miRNA)-like manner. That the 7-nucleotide seed regions in the siRNAs can cause a perturbation in infection was confirmed by using synthetic miRNAs (miRs). One of the miRs tested, miR-142-3p, was shown to interfere with the intracellular trafficking of incoming viruses by regulating the v-SNARE VAMP3, a strong hit shared by both siRNA screens. Inactivation of VAMP3 by the tetanus toxin led to a block in infection. Using fluorescence-based techniques in fixed and live cells, we found that the viruses enter VAMP3 + endosomal vesicles 5 min after internalization and that colocalization was maximal 15 min thereafter. At this time, LAMP1 was associated with the VAMP3 + virus-containing endosomes. In cells depleted of VAMP3, viruses were mainly trapped in LAMP1-negative compartments. Together, our results indicated that UUKV relies on VAMP3 for penetration, providing an indication of added complexity in the trafficking of viruses through the endocytic network. IMPORTANCE Bunyaviruses represent a growing threat to humans and livestock globally. Unfortunately, relatively little is known about these emerging pathogens. We report here the first human genome-wide siRNA screens for a bunyavirus. The screens resulted in the identification of 562 host cell factors with a potential role in cell entry and virus replication. To demonstrate the robustness of our approach, we confirmed and analyzed the role of the v-SNARE VAMP3 in Uukuniemi virus entry and infection. The information gained lays the basis for future research into the cell biology of bunyavirus infection and new antiviral strategies. In addition, by shedding light on serious caveats in large-scale siRNA screening, our experimental and bioinformatics procedures will be valuable in the comprehensive analysis of past and future high-content screening data.

Published
2014
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15. A high-throughput metabolomics method to predict high concentration cytotoxicity of drugs from low concentration profiles

Author

Stéphanie Heux, Uwe Sauer, Thomas J. Fuchs, Nicola Zamboni, Joachim M. Buhmann, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute for Molecular Systems Biology [ETH Zurich] (IMSB), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), and Marie Curie Intra-European Fellowships F6P-2005

Subjects
Drug, [SDV]Life Sciences [q-bio], Endocrinology, Diabetes and Metabolism, media_common.quotation_subject, Clinical Biochemistry, Off-target drug effects, Method, Biology, Pharmacology, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, Metabolomics, Yeast metabolism, Metabolome, Drug enzyme interaction, Cytotoxicity, Machine-learning, 030304 developmental biology, media_common, 0303 health sciences, Robustness (evolution), Orders of magnitude (mass), 3. Good health, Toxicity, 030217 neurology & neurosurgery, Intracellular
Abstract

Metabolomics 943SV Times Cited:5 Cited References Count:37; International audience; A major source of drug attrition in pharmacological development is drug toxicity, which eventually manifests itself in detrimental physiological effects. These effects can be assessed in large sample cohorts, but generating rich sets of output variables that are necessary to predict toxicity from lower drug dosages is problematic. Currently the throughput of methods that enable multi-parametric cellular readouts over many drugs and large ranges of concentrations is limited. Since metabolism is at the core of drug toxicity, we develop here a high-throughput intracellular metabolomics platform for relative measurement of 50–100 targeted metabolites by flow injection-tandem mass spectrometry. Specifically we focused on central metabolism of the yeast Saccharomyces cerevisiae because potential cytotoxic effects of drugs can be expected to affect this ubiquitous core network. By machine learning based on intracellular metabolite responses to 41 drugs that were administered at seven concentrations over three orders of magnitude, we demonstrate prediction of cytotoxicity in yeast from intracellular metabolome patterns obtained at much lower drug concentrations that exert no physiological toxicity. Furthermore, the 13C-determined intracellular response of metabolic fluxes to drug treatment demonstrates the functional performance of the network to be rather robust, until growth was compromised. Thus we provide evidence that phenotypic robustness to drug challenges is achieved by a flexible make-up of the metabolome.

Published
2011
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16. CcpN Controls Central Carbon Fluxes in Bacillus subtilis

Author

Eliane Fischer, Dominique Le Coq, Emmanuel Jamet, Thierry Doan, Stéphane Aymerich, Simon Tännler, Uwe Sauer, Institute for Molecular Systems Biology [ETH Zurich] (IMSB), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)-Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Microbiologie et Génétique Moléculaire (MGM), Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)

Subjects
Mutant, flux métaboliques, Genetics and Molecular Biology, Pentose phosphate pathway, Biology, métabolisme carboné, Microbiology, Pentose Phosphate Pathway, 03 medical and health sciences, Bacterial Proteins, Glyceraldehyde-3-Phosphate Dehydrogenase (NADP+)(Phosphorylating), régulation, CcpN, Glycolysis, Molecular Biology, Derepression, 030304 developmental biology, Carbon Isotopes, 0303 health sciences, 030306 microbiology, Gene Expression Profiling, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Gene Expression Regulation, Bacterial, Pyruvate carboxylase, DNA-Binding Proteins, Repressor Proteins, Citric acid cycle, Glucose, Phenotype, Biochemistry, Phosphoenolpyruvate carboxykinase, transcriptome, Phosphoenolpyruvate Carboxykinase (ATP), Pyruvate kinase, Bacillus subtilis
Abstract

The transcriptional regulator CcpN of Bacillus subtilis has been recently characterized as a repressor of two gluconeogenic genes, gapB and pckA , and of a small noncoding regulatory RNA, sr1 , involved in arginine catabolism. Deletion of ccpN impairs growth on glucose and strongly alters the distribution of intracellular fluxes, rerouting the main glucose catabolism from glycolysis to the pentose phosphate (PP) pathway. Using transcriptome analysis, we show that during growth on glucose, gapB and pckA are the only protein-coding genes directly repressed by CcpN. By quantifying intracellular fluxes in deletion mutants, we demonstrate that derepression of pckA under glycolytic condition causes the growth defect observed in the ccpN mutant due to extensive futile cycling through the pyruvate carboxylase, phosphoenolpyruvate carboxykinase, and pyruvate kinase. Beyond ATP dissipation via this cycle, PckA activity causes a drain on tricarboxylic acid cycle intermediates, which we show to be the main reason for the reduced growth of a ccpN mutant. The high flux through the PP pathway in the ccpN mutant is modulated by the flux through the alternative glyceraldehyde-3-phosphate dehydrogenases, GapA and GapB. Strongly increased concentrations of intermediates in upper glycolysis indicate that GapB overexpression causes a metabolic jamming of this pathway and, consequently, increases the relative flux through the PP pathway. In contrast, derepression of sr1 , the third known target of CcpN, plays only a marginal role in ccpN mutant phenotypes.

Published
2008
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17. YtsJ Has the Major Physiological Role of the Four Paralogous Malic Enzyme Isoforms in Bacillus subtilis

Author

Nicola Zamboni, Guillaume Lerondel, Thierry Doan, Stéphane Aymerich, Uwe Sauer, Microbiologie et Génétique Moléculaire (MGM), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS), Institute for Molecular Systems Biology [ETH Zurich] (IMSB), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich)-Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), EU Quality of Life and Management of Living Resources program grant QL GZ-CT-1999-O1455, and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)

Subjects
MESH: Malate Dehydrogenase, Physiology and Metabolism, Mutant, Malates, Malic enzyme, Bacillus subtilis, Biology, medicine.disease_cause, Microbiology, Malate dehydrogenase, 03 medical and health sciences, Bacterial Proteins, Malate Dehydrogenase, medicine, Malic enzyme activity, MESH: Bacterial Proteins, Molecular Biology, Escherichia coli, MESH: Malates, 030304 developmental biology, chemistry.chemical_classification, MESH: Gene Expression Regulation, Bacterial, 0303 health sciences, 030306 microbiology, Bacterial, MESH: NAD, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Gene Expression Regulation, Bacterial, MESH: Bacillus subtilis, NAD, biology.organism_classification, Molecular biology, Culture Media, MESH: Glucose, Glucose, Enzyme, Genes, Gene Expression Regulation, chemistry, Biochemistry, Genes, Bacterial, Multigene Family, MESH: Culture Media, MESH: Multigene Family, NAD+ kinase, MESH: Genes, Bacterial, MESH: NADP, NADP
Abstract

The Bacillus subtilis genome contains several sets of paralogs. An extreme case is the four putative malic enzyme genes maeA , malS , ytsJ , and mleA. maeA was demonstrated to encode malic enzyme activity, to be inducible by malate, but also to be dispensable for growth on malate. We report systematic experiments to test whether these four genes ensure backup or cover different functions. Analysis of single- and multiple-mutant strains demonstrated that ytsJ has a major physiological role in malate utilization for which none of the other three genes could compensate. In contrast, maeA , malS , and mleA had distinct roles in malate utilization for which they could compensate one another. The four proteins exhibited malic enzyme activity; MalS, MleA, and MaeA exhibited 4- to 90-fold higher activities with NAD + than with NADP + . YtsJ activity, in contrast, was 70-fold higher with NADP + than with NAD + , with K m values of 0.055 and 2.8 mM, respectively. lacZ fusions revealed strong transcription of ytsJ , twofold higher in malate than in glucose medium, but weak transcription of malS and mleA . In contrast, mleA was strongly transcribed in complex medium. Metabolic flux analysis confirmed the major role of YtsJ in malate-to-pyruvate interconversion. While overexpression of the NADP-dependent Escherichia coli malic enzyme MaeB did not suppress the growth defect of a ytsJ mutant on malate, overexpression of the transhydrogenase UdhA from E. coli partially suppressed it. These results suggest an additional physiological role of YtsJ beyond that of malate-to-pyruvate conversion.

Published
2006
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18. Different phosphatase-dependent mechanisms mediate long-term depression and depotentiation of long-term potentiation in mouse hippocampal CA1 area

Author

Ursula Haditsch, A. Jouvenceau, Patrick Dutar, Jean-Marie Billard, Isabelle M. Mansuy, Neurobiologie de la Croissance et de la Senescence, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Mobilités : Vieillissement, Pathologie, Santé (COMETE), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Brain Research Institute and Swiss Federal Institute of Technology, University of Zürich [Zürich] (UZH), Institut de psychiatrie et neurosciences (U894 / UMS 1266), and Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
N-Methylaspartate, Time Factors, Long-Term Potentiation, Presynaptic Terminals, Hippocampus, Mice, Transgenic, In Vitro Techniques, Biology, Tacrolimus, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Okadaic Acid, Excitatory Amino Acid Agonists, Animals, Enzyme Inhibitors, Long-term depression, alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Long-Term Synaptic Depression, General Neuroscience, Excitatory Postsynaptic Potentials, Neural Inhibition, Long-term potentiation, Protein phosphatase 2, Okadaic acid, Electric Stimulation, Phosphoric Monoester Hydrolases, Electrophysiology, Calcineurin, Synaptic fatigue, chemistry, Mutation, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Depotentiation, Neuroscience, 030217 neurology & neurosurgery
Abstract

Two types of synaptic depression have been described in the hippocampus, long-term depression and depotentiation of long-term potentiation known to recruit the serine/threonine protein phosphatases PP1, PP2A and PP2B (calcineurin). The contribution of each of these protein phosphatases is controversial. To examine the role of the Ca2+/calmodulin-dependent protein phosphatase calcineurin in long-term depression and depotentiation, we analysed the effect of genetically inhibiting calcineurin reversibly in the hippocampus, using the doxycycline-dependent rtTA system in transgenic mice. We show that reducing calcineurin activity has no effect on long-term depression but reversibly affects depotentiation. Consistently, the calcineurin inhibitor FK-506 reproduces the depotentiation impairment observed in the mutant mice but does not affect long-term depression in control animals. In contrast, the PP1/PP2A inhibitor okadaic acid fully blocks both long-term depression and depotentiation. These data demonstrate that the nature of signalling cascades induced by synaptic activity depends on the initial synaptic state. While depression of potentiated synaptic responses requires activation of PP1/PP2A and/or calcineurin, depression of basal synaptic responses depends only on PP1/PP2A activation.

Published
2003
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19. Towards high-throughput identification of endocrine disrupting compounds with mass spectrometry

Author

Renato Zenobi, Sylvia Eiler, Cédric Bovet, Benoit Plet, Marc Ruff, Alexis Nazabal, Dino Moras, Andreas Panagiotidis, Florence Granger, Ryan J. Wenzel, Department of Analytical Chemistry, Laboratory of Organic Chemistry, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institute for Molecular Systems Biology [ETH Zurich] (IMSB), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), and Peney, Maité

Subjects
Estrogen receptor, Endocrine Disruptors, Toxicology, Mass spectrometry, Ligands, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Endocrine system, Humans, Ionization mass spectrometry, Receptor, 030304 developmental biology, 0303 health sciences, Chromatography, Binding Sites, 010401 analytical chemistry, Estrogen Receptor alpha, General Medicine, Ligand binding domain, 0104 chemical sciences, Biochemistry, chemistry, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Quercetin, Dimerization
Abstract

International audience; High-mass matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with chemical cross-linking has the ability to monitor the ligand-dependent dimerization of the human estrogen receptor alpha ligand binding domain (hERalpha LBD) in solution. Because only ER ligands enhance the homodimer abundance, we evaluated the ability of this label-free approach for identifying endocrine disrupting compounds (EDCs) in a high-throughput manner. This was achieved by combining an automated liquid handler with an automated MS acquisition procedure, which allowed a five-fold gain in operator time compared to a fully manual approach. To detect ligand binding with enough confidence, the receptor has to be incubated with at least a 10muM concentration of the test compound. Based on the increase of the measured homodimer intensity, eight compounds with a relative binding affinity (RBA, relative to the natural hormone estradiol) >7% were identified as ER ligands among the 28 chemicals tested. Two other compounds, quercetin and 4-tert-amylphenol, were also identified as ER ligands, although their RBAs have been reported to be only 0.01% and 0.000055%, respectively. This suggests that these two ligands have a higher affinity for hERalpha LBD than reported in the literature. The high-mass MALDI approach thus allows identifying high affinity EDCs in an efficient way.

Published
2008
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