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  • Génomes

    • Vendredi 7 février 11:00-12:00 - Laura EME - ESE (Écologie Systématique et Evolution) CNRS - Université Paris-Sud Orsay

      Impact of Lateral Gene Transfer in eukaryotic evolution

      Résumé : Lateral gene transfer (LGT) has been increasingly used to explain the presence of ‘unexpected’ genes in eukaryotes. Despite numerous independent studies on a variety of eukaryote lineages showing what appears to be clear examples of LGT, there is debate over the frequency and impact of laterally acquired genes within eukaryotes. While analyses thus far have suggested LGT occurs less frequently in eukaryotes than in prokaryotes, the apparent rarity compared to LGT in prokaryotes does not mean it should be disregarded as an important factor impacting eukaryotic evolution. Here I will review evidence for potential mechanisms of LGT in eukaryotes and discuss the impact LGT has had on the evolution of microbial eukaryotes in particular, by acting as a catalyst for acquiring novel traits and laying the foundation to explore and thrive in various ecological niches. Finally, I will discuss our current research plans to better understand what favours or hampers the acquisition and maintenance of foreign genes in a genome.

      Contact : Daan NOORDERMEER (daan.noordermeer i2bc.paris-saclay.fr)

      Lieu : Bibliothèque - bâtiment 34 - campus de Gif-sur-Yvette

      Article

    • Vendredi 28 février 10:00-11:00 - Tomio TAKAHASHI - Microbiology Department, I2BC

      Advances in understanding Topoisomerase I molecular mechanisms

      Résumé : Abstract :
      Chromosome structure and dynamics, DNA repair, DNA replication and transcription are all mechanisms that involve changes in the topology of DNA, requiring a set of enzyme called DNA topoisomerases. In particular, human topoisomerase IB (Top1) removes torsional stresses associated with DNA replication and transcription, and is important for the regulation of gene expression. Top1 activity involves one step of DNA cleavage and one step of DNA ligation. The current structural data suggests that Top1 clamps the DNA molecule during these two steps. However, there is little data concerning the mechanisms underlying the entry and the exit of the DNA molecule inside this toroidal structure.
      The topoisomerase IB from one hyperthermophilic archaeon, Caldiarchaeum subterraneum was recently found to be highly similar to the eukaryotic enzyme (1). This highly thermostable enzyme allowed me recently to solve the first structure of Top1 in an open conformation in the absence of DNA. This novel structure reveals that Top1 is a bimodular enzyme, in which one catalytic domain and one core domain are linked with one flexible hinge loop, which allows the opening/closing of the enzyme. Top1 dynamics raises question about the specificity of the enzyme towards specific DNA structures including supercoiled DNA and non-canonical DNA structures such as G-quadruplexes.
      I will also briefly introduce a new family of proteins, homologous with Topoisomerase IIB and Spo11, which are found exclusively in viruses (2).
      References :
      1. Dahmane N, Gadelle D, Delmas S, Criscuolo A, Eberhard S, Desnoues N, et al. TopIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB. Nucleic Acids Res. 2016 ;44(6):2795–805.
      2. Takahashi, T.S., Da Cunha, V., Krupovic, M., Mayer, C., Forterre, P., and Gadelle, D. Expanding the type IIB DNA topoisomerase family : identification of new topoisomerase and topoisomerase-like proteins in mobile genetic elements. NAR Genomics and Bioinformatics 2(1) (2020)
      Contact : Yoshi Yamaichi <Yoshiharu.YAMAICHI i2bc.paris-saclay.fr>

      Lieu : Bibliothèque- bâtiment 34 - Campus CNRS de Gif-sur-Yvette

      Article

  • Microbiologie

    • Vendredi 28 février 11:30-12:30 - Daisuke NAKANE - Gakushuin University, Dpt of Physics, Japan

      How bacteria move ? Pulling, crawling, and drilling

      Résumé : Many bacteria swim freely in a fluid with a rotation of flagella filament. On the other hand, some tiny organisms also develop several varieties of cell motility without flagella. These mysterious movements are widespread in bacteria, and have been very attractive to many researchers for long time. But it had remained unclear how bacteria move without flagella, and what is the machinery for cell propulsion. Recent advance on the visualization techniques of optical microscopy provides us dynamic behaviors of molecular machineries at a single cellular level in detail, and the current understanding of this field have dramatically jumped in the last 10-20 years. In this seminar, I would like to introduce our recent study about a surprising new world of biological movements in the smallest life forms such as Spider-man like motion by the repeated cycles of extension and retraction, a caterpillar like motion by the surface flow along cell membrane, and a corkscrew like motion by mechanical drilling in high viscous environments.


      References :
      - Nakane & Miyata (2007) PNAS 104 : 19518-23
      - Nakane et al. (2013) PNAS 110 : 11145-50
      - Kinosita, Nakane et al. (2014) PNAS 111 : 8601-6
      - Nakane & Nishizaka (2017) PNAS 114 : 6593-98

      Lieu : Bibliothèque - Bâtiment 34, Campus de Gif-sur-Yvette

      Article

  • B3S

    • Lundi 3 février 11:30-13:00 - Alain Roussel - AFMB, UMR7257 CNRS - Aix Marseille Univ., Marseille

      Camelid nanobodies : versatile tools for molecular and structural biology studies

      Résumé :
      In recent years, the use of single-domain camelid immunoglobulins, termed vHHs or nanobodies, has seen increasing growth in biotechnology, pharmaceutical applications and structure/function research. The usefulness of nanobodies in molecular and structural biology is now firmly established whether to solve 3D structures or to perform functional studies. After describing our platform dedicated to the selection and production of nanobodies, I will present the recent results we have obtained in the structural studies of bacterial secretion systems (T2SS, T6SS and T9SS). Finally I will present our current work on the development of neutralizing nanobodies against Ebola virus.
       
      Related publications
      - Desmyter, A., Spinelli, S., Roussel, A., and Cambillau, C. (2015) Camelid nanobodies : killing two birds with one stone. Current opinion in structural biology 32C, 1-8
      - Douzi, B., Trinh, N. T. T., Michel-Souzy, S., Desmyter, A., Ball, G., Barbier, P., Kosta, A., Durand, E., Forest, K. T., Cambillau, C., Roussel, A., and Voulhoux, R. (2017) Unraveling the Self-Assembly of the Pseudomonas aeruginosa XcpQ Secretin Periplasmic Domain Provides New Molecular Insights into Type II Secretion System Secreton Architecture and Dynamics. MBio 8
      - Nguyen, V. S., Logger, L., Spinelli, S., Legrand, P., Huyen Pham, T. T., Nhung Trinh, T. T., Cherrak, Y., Zoued, A., Desmyter, A., Durand, E., Roussel, A., Kellenberger, C., Cascales, E., and Cambillau, C. (2017) Type VI secretion TssK baseplate protein exhibits structural similarity with phage receptor-binding proteins and evolved to bind the membrane complex. Nat Microbiol 2, 17103
      - Leone, P., Roche, J., Vincent, M. S., Tran, Q. H., Desmyter, A., Cascales, E., Kellenberger, C., Cambillau, C., and Roussel, A. (2018) Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space. Nat Commun 9, 429
       
      Short biography
      Alain Roussel, Director of Research CNRS. Deputy director of AFMB, Marseille, France. Head of the « Host-Pathogen Interaction » team. Scientific coordinator of the IbiSA platform of Structural Biology at AFMB, which is supported by the French Infrastructure for Integrated Structural Biology (FRISBI). Member of the executive committee of FRISBI. Specialist of X-ray crystallography. Fields of interest : Innate immunity, Bacterial secretion systems, Monoclonal antibodies.
       
      Invited by Julie Ménétrey
       

      Lieu : Auditorium, building 21 - Avenue de la Terrasse, Gif-sur-Yvette

      Article

    • Vendredi 28 février 11:00-12:00 - Diego F. GAUTO - Institut de Biologie Structurale (IBS), Grenoble

      Atomic-Resolution structure determination and dynamic studies on big macromolecular protein assemblies : Joining strenghts between NMR, CryoEM and Computational Simulations

      Lieu : Auditorium I2BC - Bâtiment 21, Campus de Gif-sur-Yvette

      Article

    • Vendredi 28 février 14:00-15:00 - Volker LOHMANN - University of Heidelberg

      Shaping the lipid composition of viral replication organelles by Hepatitis C virus

      Résumé : Chronic Hepatitis C virus (HCV) infections affect 71 million people worldwide, often resulting in severe liver damage. Since 2014 highly efficient therapies based on direct acting antivirals (DAAs) are available, offering cure rates of almost 100%, if the infection is diagnosed in time. It took more than a decade to discover HCV in 1989 and another decade to establish the first cell culture model, which was essential for therapy development, from drug screening to understanding of mode of action and resistance. More recently we are beginning to understand the molecular basis for efficient HCV replication in cell culture, which is highly dependent on the shaping of the lipid composition of the membranous viral replication organelle, mediated by host factors like PI4KA and SEC14L2. This presentation will summarize our current knowledge on the mechanism of action of host factors contributing to HCV RNA synthesis and provide an outlook on future opportunities based on our increasing understanding of molecular mechanisms governing HCV replication.

      Lieu : Bibliothèque - Bâtiment 34, Campus de Gif-sur-Yvette

      Article

  • cytoskeleton club

    • Mardi 11 février 11:30-12:30 - Christian Poüs - INSERM UMR-S 1193, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry

      Cytoskeleton club - Microtubule dynamics and cell response to stress : the rescue point of view

      Lieu : Bibliothèque - bât. 34

      Article

Soutenance

  • B3S

    • Jeudi 6 février 14:00-17:30 - Thibaud Dieudonné - Laboratoire des Protéines et Systèmes Membranaires, I2BC

      Functional and structural characterization of lipid flippases : the yeast Drs2p/Cdc50p and the disease-related human ATP8B1/CDC50A complexes

      Résumé : Living cells are surrounded by membranes organized in bilayers, separating the intracellular medium from the extracellular environment. A hallmark of eukaryotic membranes from the late secretory/endocytic pathways is the asymmetric distribution of phospholipids between the two leaflets. Indeed, phosphatidylcholine (PC) and sphingolipids (SL) are mainly found in the outer leaflet whereas phosphatidylserine (PS) and phosphatidylethanolamine (PE) are sequestered in the inner leaflet. This asymmetry is maintained thanks to different membrane lipid transporters. Among them, flippases, which are transporters fueled by ATP hydrolysis, translocate lipids from the outer to the inner leaflet. Flippases belong to the P4-ATPase family and have been linked to several diseases. For instance, mutated forms of a human P4-ATPase, ATP8B1, are responsible for intrahepatic cholestasis, a severe liver disease. In this thesis, we investigated the regulatory mechanism of two flippases, the yeast PS-specific flippase complex Drs2p/Cdc50p, and the human disease-related flippase complex ATP8B1/CDC50A. Both proteins were expressed in S. cerevisiae and purified for downstream functional characterization. Our results demonstrate that both flippases are tightly regulated by phosphoinositides and autoinhibited by their N- and C-terminal extensions.

      Lieu : Auditorium I2BC - Bâtiment 21, Campus de GIf-sur-Yvette

      Article

    • Lundi 24 février 13:30-17:30 - Maelenn CHEVREUIL - Equipe Interactions et mécanismes d’assemblage des protéines et des peptides, I2BC

      Phénomènes dynamiques d’auto-assemblage et désassemblage dans des virus icosaédriques

      Résumé : L’auto-assemblage et le désassemblage de la capside des virus, étapes critiques du cycle viral, est un sujet qui suscite beaucoup d’intérêt.
      Cependant, les mécanismes sous-jacents et, en particulier, les chemins cinétiques d’assemblage et de désassemblage des capsides, vides ou pleines, des virus ne sont pas entièrement résolus. La diffusion des rayons X aux petits angles résolue en temps, combinée à la décomposition en valeur singulière, est une technique qui permet d’étudier des processus impliquant des espèces de taille nanométrique avec une résolution temporelle de l’ordre de la milliseconde. De plus, la technique de criblage de thermo-stabilité des protéines par fluorescence, couplée à un modèle théorique de champ moyen, permet d’estimer expérimentalement les énergies d’interactions entre les protéines et la charge effective de celles-ci. Ainsi, dans le cas du virus de la marbrure chlorotique de la cornille (CCMV), nous avons étudié la dynamique d’auto-assemblage des protéines des capsides avec leur matériel génétique.
      Les expériences ont révélé la formation de complexes amorphes via un chemin cinétique appelé en masse tandis que leur relaxation en virions s’effectue via un chemin cinétique dit synchrone. Les énergies de liaison des protéines avec le génome se sont révélées modérées tandis que la barrière d’énergie séparant les complexes des virions est élevée. Des expériences complémentaires ont également montré que cette barrière pouvait être abaissée, de sorte que des capsides pleines se forment directement.
      Dans le cas du virus de l’hépatite B (VHB), nous avons étudié les dynamiques d’assemblage et de désassemblage des capsides vides. Tout d’abord, nous avons pu identifier un chemin cinétique probable de désassemblage avec la présence d’une espèce intermédiaire assimilable à une structure fractale-branchée. Enfin, les expériences d’assemblage ont révélé un chemin cinétique en trois phases, i.e. agglomération, croissance et relaxation, dirigé par l’attraction hydrophobe et modulé par la répulsion électrostatique. De plus, certaines expériences ont également montré que la dernière phase pouvait être facilement inhibée.

      Lieu : Amphithéâtre Blandin - Laboratoire de Physique des Solides (LPS), 1 rue Nicolas Appert, Orsay

      Article

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