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Séminaire

  • Génomes

    • Vendredi 22 juin 10:00-11:00 - Angélique Déléris - Institut de biologie de l’Ecole normale supérieure IBENS, Paris

      Transcriptional control and exploitation of an immune-responsive family of plant retrotransposons

      Résumé : Mobilization of transposable elements (TEs) in plants has been recognized as a driving force of evolution and adaptation, in particular by providing genes with regulatory modules that impact their transcription. In the work that I will present, we employed an ATCOPIA93 Long terminal repeats (LTR) promoter-GUS fusion to show that this retrotransposon behaves like an immune-responsive gene during plant defense in Arabidopsis. We also showed that the reactivation of the endogenous ATCOPIA93 copy “EVD”, in the presence of bacterial stress, is not only negatively regulated by DNA methylation but also by Polycomb-mediated silencing¬—a mode of repression typically found at protein-coding and microRNA genes. Interestingly, one of the ATCOPIA93-derived soloLTRs is located upstream of the disease resistance gene RPP4 and is devoid of either DNA methylation or H3K27m3 marks. Through loss-of-function experiments, we demonstrated that this soloLTR is required for proper expression of RPP4 during plant defense, thus linking the responsiveness of ATCOPIA93 to biotic stress and the co-option of its LTR for plant immunity. I will also introduce the two major follow-up projects that we are currently working on : 1) the identification and characterization of the transcription factors associated with ATCOPIA93 LTR which should allow us to study their interference with the epigenetic and hormonal pathways controlling this TE 2) the extent to which Polycomb is involved in the genome-wide silencing of TEs.
      Contact : BETERMIER Mireille <Mireille.BETERMIER i2bc.paris-saclay.fr>

      Lieu : Bibliothèque Bât. 34 - Campus de Gif-sur-Yvette

      Notes de dernières minutes :  !!CHANGE OF TIME AND LOCATION !! This seminar exceptionally starts at 10h00 so that you can go to the I2BC BBQ at Orsay (Bat 400) after the seminar

      Article

    • Vendredi 22 juin 14:00-16:00 - Dr Alberto Vianelli - University of Varese (Italy) (sabbatical ENS, Paris)

      Overlapping genes in viruses and the de novo origin of proteins

      Résumé : This talk will focus on a genomic feature which looks at first as very specialized, but that in fact might be of general biological interest for different reasons, constituting a fascinating evolutionary puzzle and also possibly shedding some light on the still unsolved problem of the origin of novelty, namely new proteins : overlapping genes (OG) (gènes chevauchants). These are genomic regions of DNA or RNA (in the case of many viruses) which are translated in two (sometimes even three) reading frames to yield two proteins whose amino acid sequence, hence generally their function, is unrelated. It is thought they originate by “overprinting”, in which point mutations in an existing frame allow the expression of a completely new protein from the second frame. In viruses, in which OG are abundant, these new proteins often play a critical role in infection, yet they are frequently overlooked when annotating genomes. Their correct detection is however very important not only when studying viruses since they are now thought to be abundant in eukaryotes as well, with more and more examples being reported in the literature. As noted above, OG are evolutionarily puzzling since each of the two overlapping proteins constrains the freedom to change of the other. To conduct systematic evolutionary studies and to develop better detection methods, we have assembled a high-quality dataset of 80 non-homologous viral OG whose expression is experimentally proven. This allowed us to single out compositional features, that we show to be shared by proven mammalian OG as well, significantly different from non-overlapping genomic regions. We believe these and other features I will describe are relevant for understanding their evolution and their involvement in de novo protein origin not only in viruses. It is likely, in fact, that the new findings on eukaryotic overlapping genes mentioned earlier will eventually have a deep impact on our current vision of genes.

      Lieu : Salle E. Lederer - Bâtiment 430 - Campus d’Orsay

      Notes de dernières minutes : Time and location are exceptionnal : This seminar will take place at Orsay, Bât. 430 at 2 p.m.

      Article

    • Vendredi 29 juin 11:00-12:00 - Edouard Bertrand - Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier

      A dual protein/RNA localization screen reveals specialized translation factories in human cells

      Résumé : Abstract
      Local translation provides a spatial control of gene expression. We performed a dual protein/mRNA localization screen, using smFISH on a collection of 520 HeLa cell lines carrying GFP-tagged genes. We found that 32 RNAs had particular cytoplasmic localizations, with accumulation in P-bodies being to most frequent (17 cases). Eight mRNAs colocalized with their encoded protein, and local translation occurred at various cellular locations, including cytoplasmic extensions, endosomes, and the Golgi apparatus. Interestingly, four mRNAs accumulated in cytoplasmic foci that were not P-bodies and that were distinct from each other. We used the SunTag system to visualize mRNA translation in live cells and at the level of single molecules, and we showed that these four mRNA foci correspond to specialized translation factories. Remarkably, in one case, we found that the factory functions to destruct the nascent protein, and the data further suggest a mechanism for their formation. Extrapolating the results to the entire genome suggests that human cells may contain more than a hundred of such translation factories. They may allow mRNAs to be translated by specialized machineries, including specialized ribosomes.
      Contact : MIRANDE Marc <Marc.MIRANDE i2bc.paris-saclay.fr>

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

      Article

  • Biologie Cellulaire

    • Vendredi 15 juin 11:00-12:30 - Nicolas OLIVIER - Ecole Polytechnique, invité par A.M. Tassin

      Super-resolution Microscopy by Localization of Single Molecules : from Microtubules to Centrioles

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

      Article

  • I2BC

    • Lundi 4 juin 15:00-16:00 - Fabienne Malagnac - Département Biologie des Génomes, I2BC

      Epigeneticsand sexual development in filamentous ascomycetes

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

      Article

    • Lundi 18 juin 14:00-15:00 - Scott Blanchard - Department of Physiology & Biophysics, Weill Cornell Medical College, New York, USA

      Single-molecule imaging reveals the rate-determining steps of substrate translocation on the bacterial ribosome

      Résumé : Directional translocation of the ribosome through the mRNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of tRNA and mRNA substrates with respect to the large and small ribosomal subunits. Using pre–steady state, single-molecule fluorescence resonance energy transfer imaging, we tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations revealed direct evidence of structurally and kinetically distinct late intermediates during substrate movement, whose resolution determines the rate of translocation. These steps involve intramolecular events within the EF-G–GDP–bound ribosome, including exaggerated, reversible fluctuations of the small-subunit head domain, which ultimately facilitate peptidyl-tRNA’s movement into its final post-translocation position.
      https://www.scottcblanchardlab.com

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

      Article

  • Microbiologie

    • Mardi 5 juin 11:30-12:30 - Dr. Yoshiaki Kinosita - Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan. Present address: Institute for Biology II, Freiburg University, Germany

      Biophysical approaches to grasp the motility mechanism of microorganisms

      Lieu : Salle Kalogeropoulos, Bât 400, Université Paris sud - Campus Orsay

      Article

    • Mardi 5 juin 11:30-13:00 - Yoshiaki Kinosita - Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan

      Biophysical approaches to grasp the motility mechanism of microorganisms

      Résumé : The motility of organisms is driven by nano-sized molecular machines that convert chemical energy into mechanical work. The ‘conventional’ motile systems of myosin, kinesin and bacterial flagella have been studied extensively over the last several decades using various approaches such as crystal structure, gene manipulation, and functional analysis. In contrast, I have focused only on the unconventional motile system such as walking of Mycoplasma (1) and swimming archaea (2) using a single-molecular approach for 7 years. In my talk, I will show you the application of microscopic techniques to the molecular motors.
      Additionally, I will also introduce the unforeseen swimming motility of a symbiotic bacterium, Burkholderia sp. RPE64 (3). A bean bug symbiont, Burkholderia sp. RPE64, selectively colonizes the gut crypts by flagella-mediated motility : however, the mechanism for this colonization remains unclear. Remarkably, staining of the flagellar filaments with fluorescent dye Cy3 revealed that the flagellar filaments wrap around the cell body with a motion like that of a ribbon streamer in rhythmic gymnastics. Furthermore, the wrapping motion was also observed in a symbiotic bacterium of the Bobtail squid, Aliivibrio fischeri, suggesting that this motility mode may contribute to migration on the mucus-filled narrow passage connecting to the symbiotic organ.
      (1) Kinosita Y, Nakane D, Sugawa M, Masaike T, Mizutani K, Miyata M, Nishizaka T.
      Unitary step of gliding machinery in Mycoplasma mobile. Proc. Natl. Acad. Sci. USA 111, 8601-8606 (2014)
      (2) Kinosita Y., Uchida, N., Nakane, D. & Nishizaka, T. Direct observation of rotation and steps of the archaellum in the swimming halophilic archaeon Halobacterium salinarum. Nature Microbiology 1, 16148 (2016).
      (3) Kinosita Y, Kikuchi Y, Mikami N, Nakane D & Nishizaka T. Unforeseen swimming and gliding mode of an insect gut symbiont, Burkholderia sp. RPE64, with wrapping of the flagella around its cell body. ISME J 12,838-848 (2017)
      Contact : (Peter Mergaert)

      Lieu : Salle Kalogeropoulos, Bât 400, Université Paris sud - Campus Orsay

      Article

    • Mercredi 6 juin 11:30-13:00 - Dr. Marianne Ilbert - « Métabolisme énergétique des bactéries extrémophiles » Bioénergétique et Ingénierie des Protéines (BIP), Marseille

      Bacterial life in acid ? Toward a better understanding of an iron respiratory chain working at pH 2

      Résumé : Microorganisms are found in various ecosystems, where they have this incredible ability to adapt to challenging conditions. Acidithiobacillus ferrooxidans, a gram negative bacterium, is the most studied and relevant model to understand how to survive in harmful environments with pH as low as pH 2 and high level of toxic metals, getting energy source from minerals containing iron and sulfur. This remarkable ability to gain energy through oxidation of ferrous iron at low pH has driven a lot of interest because of application in microbial leaching. We are currently studying the iron respiratory chain of this acidophilic organism by a multidisciplinary approach. Several metalloproteins have been identified and characterized, but the electron transfer pathway from the outer membrane to the inner membrane cytochrome c oxidase is still obscure.
      During this seminar, we will first focus our attention on the newly identified cupredoxin, AcoP, which contains a green-type copper center. We will present the crystal structure of AcoP and will discuss its spectroscopic features underlying some unexpected properties. Key residues were targeted by site directed mutagenesis to better understand the determinants driving these unusual properties. In addition, we are currently reconstituting parts of the respiratory chain with the aim to determine step by step the electron transfer pathway. The strategy is to study purified AcoP, di-heme cytochrome c and cytochrome c oxidase alone or incubated together in solution or in the immobilized state at an electrode mimicking one of the partner. Beyond thermodynamic data for each protein, this methodology offers the opportunity to decipher the molecular basis of protein-protein interaction favorable to electron transfer at low pH (A. ferrooxidans periplasmic compartment is estimated at pH 2.5). This should allow us to further describe the function of each protein in this energy chain.
      Invitée par l’équipe Adaptation bactérienne aux changements environnementaux
      Contact : Anne Durand

      Lieu : Salle Kalogeropoulos - Bâtiment 400, Campus d’Orsay

      Article

  • cytoskeleton club

    • Mardi 12 juin 11:30-12:30 - Hong Wang

      Cytoskeleton club

      Résumé : Talin inhibits actin polymerization - Focal adhesions (FAs) play a major role in many physiological functions. Focal adhesions mechanically couple the extracellular matrix (ECM) to the dynamic and contractile actomyosin cytoskeleton, via transmembrane receptors of the integrin family and actin-binding proteins (ABPs). Among these ABPs, talin plays a major role, including activating integrins and anchoring cytoskeleton to FAs. Talin recruits the ABP vinculin in response to force which also associate to the ABP VASP. Although the ability of vinculin and VASP to regulate actin assembly is known, talin activity has never been studied. Our project is to understand the ability of the talin-vicnulin-VASP complex to regulate actin assembly. As preliminary step, we characterized talin activity. Talin contains three actin-binding domains (ABDs). ABD1 spans along the F2 and F3 subdomains of the FERM domain. ABD2 is located in the center of the rod. ABD3, is located at the C-terminus of the protein. Here we use kinetic assay of actin polymerization in fluorescence spectroscopy and actin filament observation in Total Internal Reflection Fluorescence Microscopy (TIRF) to study talin activity. The detail characterization of talin ABD1 demonstrates that it blocks actin filament barbed end elongation.

      Lieu : Bibliothèque - Bâtiment 34, Campus de Gif

      Article

Soutenance

  • Biologie Cellulaire

    • Mercredi 20 juin 14:00-17:00 - Julie Hodin - Département de Biologie Cellulaire, I2BC

      Le couplage nitrate/proton au sein de l’échangeur AtClCa est essentiel à la physiologie de la plante en réponse aux fluctuations environnementales

      Résumé : Chez les plantes, le nitrate est un élément essentiel mais sa disponibilité dans le sol est fluctuante. Il est donc stocké dans la vacuole grâce à un échangeur nitrate/proton appelé AtClCa. La famille de protéines ClCs comporte à la fois des échangeurs mais aussi des canaux suggérés comme issus de l’évolution des échangeurs par une conversion mécanistique. Chez Arabidopsis thaliana, seuls des ClCs échangeurs assurent la gestion du nitrate. Deux glutamates très conservés, E203 et E270 dans AtClCa, sont essentiels pour le transport des protons chez les ClCs échangeurs. La mutation du résidu E203 en une alanine, un acide aminé non protonable (E203A) a permis de produire artificiellement une telle conversion mécanistique. Afin de mieux comprendre l’importance physiologique du mécanisme d’échange, une analyse a été conduite sur des plantes exprimant la forme mutée d’AtClCa pour ce glutamate. Chez ces plantes, le stockage vacuolaire est fortement réduit au profit d’une importante assimilation accroissant la teneur en protéines. En dépit de cela, elles présentent un défaut de production de biomasse résultant en grande partie d’une perturbation de l’homéostasie hydrique. Elles sont également plus sensibles aux stress hydrique et probablement azoté. La conservation d’un échangeur est donc requise pour croitre en dépit des fluctuations environnementales. En parallèle, la mutation E270A a été introduite en plante afin d’étudier son importance sur la physiologie d’Arabidopsis. Une analyse préliminaire de la biomasse et des contenus en nitrate et eau de plantes exprimant la forme mutée de ce glutamate est donc présentée dans la seconde partie de cette thèse.

      Lieu : Amphithéatre de l'ICSN - bâtiment 28, CNRS Gif-sur-Yvette

      Article

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