Jeudi 15 décembre à 11h30

Annick HAREL-BELLAN

Laboratoire Epigénétique et Cancer, FRE 3377 CNRS
SBIGEM - CEA Saclay

When slicing meets splicing

Invitée par François-Xavier Barre (01 69 82 32 24)

Résumé

While Argonaute (AGO) proteins play a major role in heterochromatin formation and transcriptional gene silencing in many organisms1-3, their role in the nucleus of mammalian cells is controversial and still poorly understood. Here, we characterized the chromatin complex associated with both AGO1 and AGO2. It contains previously described AGO-protein partners4-6 as well as chromatin proteins and, quite unexpectedly, spliceosome components and splicing factors. Using the CD44 gene as a model system, we show that depletion of AGO1 or AGO2 hinders the Protein Kinase C (PKC)-dependent inclusion of variant exons. AGO proteins were recruited to CD44 chromatin in a Dicer- and HP1 gamma-dependent manner, thus reminiscent of the mechanisms operating in Schizosaccharomyces pombe to silence heterochromatin repeated sequences1. Importantly, two main features of transcription-coupled alternative splicing, i. e. histone H3 lysine 9 methylation and RNA polymerase II decreased elongation rate, were AGO-dependent. Taken together, our results unravel a physical and functional link between the AGO/RNAi machinery and the spliceosome complex.

Vendredi 9 décembre 2011 à 14h30

Luc BONNEFOND

Dépt. Biologie Structurale Intégrative - IGBMC - Strasbourg

Études structurales et fonctionnelles de partenaires des ARN de transfert

Invité par Dominique Fourmy (01 69 82 38 84 ou 38 83)

Résumé

Les ARN de transfert sont d’abord connus pour leur rôle d’adaptateurs entre codons et acides aminés au cours de la traduction de l’information génétique. Mais un certain nombre d’ARNt sont déviés de cette voie classique pour participer à d’autres mécanismes, telles que la synthèse du peptidoglycane de la paroi bactérienne ou le recyclage de protéines. Les ARNt sont donc amenés à interagir avec de nombreux partenaires protéiques différents.
Pour mieux comprendre cette versatilité des ARNt, je me suis penché sur plusieurs de leurs partenaires. Une aminoacyl-ARNt synthétase, tout d’abord, ces enzymes qui catalysent la fixation d’acides aminés sur l’extrémité 3’ terminale des ARNt. Mais aussi une enzyme modification post-transcriptionnel des ARNt qui modifie l’anticodon. Dans ces deux cas l’enzyme doit reconnaître non seulement l’architecture caractéristique des ARNt, mais aussi les éléments spécifiques de l’ARNt avec lequel elle interagit afin d’éviter d’introduire des erreurs dans la traduction.
Enfin, je présenterai une nouvelle classe d’enzymes qui génèrent des dipeptides cycliques en utilisant des ARNt aminoacylés comme substrats.

Vendredi 2 décembre 2011 à 14h30

Marc BLONDEL

Inserm U613 Brest – Equipe «Levure comme Modèle pour des Pathologies Humaines»

La levure comme modèle pour différentes pathologies humaines : l’exemple des maladies mitochondriales

Invité par Geneviève Dujardin (01 69 82 31 69)

Résumé

Utilisée depuis au moins 6 000 ans pour les applications biotechnologiques majeures que sont la fermentation de sucres en alcool et la panification, la levure Saccharomyces cerevisiae constitue également un organisme modèle très utilisé en biologie du fait de la grande conservation de la plupart des mécanismes de biologie cellulaire de la levure aux mammifères. Ainsi, on estime que au moins un tiers des gènes humains impliqués dans des maladies ont un homologue fonctionnel proche chez la levure.
Pour ces raisons, depuis une dizaine d’années nos projets tournent autour de la création de modèles levure pour des pathologies humaines très diverses, allant du cancer à des maladies génétiques ou neurodégénératives. Dans tous les cas ces modèles permettent différentes approches de criblage, tant pharmacologiques (recherche de candidats médicaments par criblage de banques de molécules bioactives) que génétiques (identification de nouveaux gènes impliqués dans l’apparition des maladies par criblage de banques génomiques ou de mutants) ou biotechnologiques (mise au point de tests de dépistage chez la levure). Ces différents modèles levure s’inscrivent donc à l’interface entre recherche fondamentale et appliquée : les connaissances et outils créés par la recherche fondamentale sont traduisibles en découvertes pour la recherche biomédicale et les découvertes dans le champ de la biomédecine (molécules actives par exemple) peuvent servir d’outils originaux pour revisiter des mécanismes très fondamentaux.
L’exemple de modèles levure pour des maladies mitochondriales sera présenté pour illustrer de façon globale ce genre d’approche dans lesquelles les drogues peuvent être considérées et utilisées comme des mutations.

Jeudi 1er décembre à 11h30

Mireille ANSALDI

Laboratoire de Chimie Bactérienne - Institut de Microbiologie de la Méditerranée
CNRS - Marseille

Host-regulated site-specific recombination of temperate phages and impact on lysogeny maintenance

Invitée par Olivier Espéli (01 69 82 32 14)

Résumé

Temperate phages have the ability to integrate their genome into the host chromosome, a process called lysogeny. In the absence of any stress, prophages remain silent and replicate passively within the host genome. However, when stressful conditions occur, prophages excise themselves and resume a lytic growth. Integration as well as excision of the phage genomes is mediated by regulated site-specific recombination catalyzed by tyrosine and serine recombinases. However, for excision, recombination directionality factors (RDF or excisionase) are required to control the reaction direction and to prevent reintegration in the host genome.
We identified several new levels of regulation by the host on excisive recombination for several (pro)phages that share a similar recombination module, which is different from the canonical lambda module. We describe a new link between the excisive recombination and the heat shock response that involves the general stress chaperon DnaJ (HSP40). Genetics and bioinformatics studies reveal that the regulation of the RDF genes is central to prophage maintenance for numerous (pro)phages. The consequences of these regulations on lysogeny escape will be discussed.

Vendredi 25 novembre 2011 à 14h00

Salle de conférences, bâtiment 23-24
Centre de Génétique Moléculaire
CNRS Gif-sur-Yvette

Anne de SEPTENVILLE

Rôle des hélicases et des protéines de la recombinaison lors des collisions entre la réplication et la transcription

Soutenance de Thèse de Doctorat - Université Paris VI - Pierre et Marie Curie

Vendredi 25 novembre 2011 à 11h00 - Salle de séminaires du CGM, sous-sol du bâtiment 26

Patrice POLARD

Equipe Transformation du Pneumocoque - LMGM – Toulouse

Insights into the DprA-mediated mechanism of RecA loading during genetic transformation of Streptococcus pneumoniae

Invité par Bénédicte Michel (01 69 82 32 29)

Résumé

Transformation promotes genome plasticity in bacteria via RecA-driven homologous recombination. In the Gram-positive human pathogen Streptococcus pneumoniae, a multiprotein complex, the transformasome, internalizes, protects, and processes transforming DNA into recombinants. Double-stranded DNA is internalized as single strands (ssDNA), onto which we proposed that the transformation-dedicated DprA ensures the loading of RecA to form presynaptic filaments.
We have solved the atomic structure of DprA, which comprises the novel association of a SAM domain and a Rossmann fold. Furthermore, we have demonstrated that DprA forms tail-to-tail dimers and that dimerization is crucial for ssDNA binding and genetic transformation. We have also identified and mutated residues important for DprA-RecA interaction and established this interaction to be equally important for transformation. Positioning of key DprA residues revealed a striking overlap between DprA-DprA and DprA-RecA interaction surfaces. We discuss this overlap in a model in which RecA-induced monomerization of DprA is key for RecA nucleation and loading.

Jeudi 24 novembre 2011 à 11h30

Anne PEYROCHE

iBiTec-S, CEA Saclay

From DNA damage responses to proteasome- dedicated assembly chaperones

Invitée par Olivier Espéli (01 69 82 32 14)

Résumé

Proteasomes are highly conserved multicatalytic protease complexes present in both the nucleus and cytosol in all eukaryotic cells. The proteasome is the central catalytic unit of the Ubiquitin-Proteasome system (UPS). The UPS has become increasingly recognized as a controller of numerous physiological processes, including signal transduction, DNA repair, chromosome maintenance, transcriptional activation, cell cycle progression, cell survival, and certain immune cell functions.
The proteasome is a compartmentalized, ATP-dependent protease composed of more than 30 subunits that recognizes and degrades polyubiquitinated substrates. It consists of two subcomplexes, the 20S catalytic core (CP) and the 19S regulatory complex (RP) itself composed of two subcomplexes, the base and the lid. Proteasome assembly proceeds in a multi-step and orderly fashion.
We uncovered a striking phenotype related to DNA damage responses that allowed us to isolate several proteasome-specialized chaperones in budding yeast. We first showed that Poc1/2 and Poc3/4 form two pairs working at different stages in early 20S proteasome assembly. We next characterized the yeast Hsm3 protein as the first 19S RP dedicated chaperone. We also identified the functional homologs of these chaperones in mammals. These findings shed new light on functional and structural features of chaperone-assisted proteasome assembly and on the relationships between proteasome and DNA damage responses.

Jeudi 17 novembre 2011 à 11h30

Nicolas BUCHON

Host pathogens relationships in D. melanogaster - Ecole Polyctechnique Fédérale de Lausanne, CH

Host/Microbe interactions in the Drosophila gut: a model for tissue homeostasis and mucosal immunity

Invité par Jacques Montagne (01 69 82 32 27)

Résumé

Gut homeostasis is central to whole organism health and its disruption is associated with a broad range of pathologies. Following damage, complex physiological events are required in the gut to maintain proper homeostasis. Recently, we have observed that ingestion of bacteria induces an increase in stem cell proliferation and epithelial renewal in the Drosophila gut and that this response is essential to repair the damages caused by infection. Interestingly, the gut is completely remodeled but still maintains its barrier activity thanks to the tight coordination between delamination of damaged cells and integration of new enterocytes.
Our data suggest that gut homeostasis is maintained through a balance between cell damage due to the collateral effects of bacteria killing and epithelial repair by stem cell division. The Drosophila gut provides a powerful model to study the integration of stress and immunity with pathways associated with stem cell control, and should prove to be a useful resource for such further studies.

Jeudi 10 novembre 2011 à 11h30

Pierre FICHELSON

Epithelial Morphogenesis & Cell Polarity
Medical Research Council, LMCB, Cell Biology Unit, University College London, UK

Orthodenticle cooperates with Ecdysone signalling to regulate polarity remodelling during retinal morphogenesis

Invité par Jacques Montagne (01 69 82 32 27)

Résumé

Terminal differentiation of photoreceptor neurons requires extensive remodelling of epithelial features together with the generation of specialized membrane domains to allow light detection. Very little is known about the molecular and cellular pathways regulating the maturation of this cell type toward the generation of a specialised sensory neuron. We address this question using the fly retina and characterize a new pathway that coordinates photoreceptor maturation, including polarity remodelling, with overall development through hormonal control.

Jeudi 3 novembre 2011 à 11h30

Hakim MIREAU

Equipe organites et reproduction, Institut Jean-Pierre Bourgin
INRA-AgroParisTech, Versailles

The astonishing adaptability of the plant PPR proteins in organelle gene expression

Invité par Nathalie Bonnefoy (01 69 82 31 75)

Résumé

As opposed to many eukaryotes, gene expression in plant mitochondria consists in a complex process involving numerous cascades of post-transcriptional RNA processing and stabilization steps. The PentatricoPeptide Repeat protein (PPR) family has been recently shown to play primordial roles in these maturation processes in plants. PPR proteins are modular proteins composed of highly degenerated 35 amino-acid repeats that organize specific RNA binding interaction surfaces. This family of protein has massively expanded in terrestrial plant as more than 400 of these proteins are encoded in higher plant nuclear genomes. The molecular mode of action of PPR proteins is still enigmatic, but most data support that they might function as RNA chaperones uncovering or structuring transcript domains to allow access of other actors of the RNA processing machinery. PPR proteins might also stabilize RNA transcripts by binding to their extremities, preventing the progression of exoribonucleases.
I will present our latest genetic and biochemical data exemplifying the various functions covered by the PPR proteins in plant mitochondria and will show that these factors can correspond to positive but also negative, or even apparently neutral, actors of gene expression. I will then discuss the potential reasons for PPR massive expansion in plants, their evolution, and the high adaptability of this protein family in recognizing of RNA sequences.

Jeudi 27 octobre 2011 à 11h30

Ludivine WALTER

Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY
Laboratoire de Biologie Moléculaire de Cellule, ENS-Lyon, UMR CNRS 5239, Lyon

Nouvelles facettes du rôle de la mitochondrie dans le vieillissement chez C. elegans

Invitée par Annie Sainsard-Chanet (01 69 82 43 70)

Résumé

La manipulation de certaines voies génétiques et/ou processus physiologiques peut avoir un effet considérable sur le vieillissement d’un animal. Notre étude a consisté à explorer l’influence des mitochondries sur le vieillissement selon deux axes de recherche :
1) Nous nous sommes intéressés à l’effet d’une réduction partielle de l’activité de la chaîne respiratoire qui, chez de nombreuses espèces, peut augmenter la longévité de façon significative. Nous avons émis l’hypothèse qu’une diminution partielle de l’activité de la chaîne respiratoire peut constituer un signal qui va induire des changements du programme  transcriptionnel nucléaire aboutissant à une augmentation de la durée de vie. Pour tester cette hypothèse, nous avons réalisé un crible à l’aide d’ARNs interférents ciblant 387 facteurs de transcription chez C. elegans. Nous avons démontré que la protéine homéobox CEH-23 est un médiateur spécifique des effets des mutations de la chaîne respiratoire sur la durée de vie. De plus, le niveau d’expression de ceh-23 est augmenté lorsque l’activité de la chaîne respiratoire est diminuée, et sur-exprimer ceh-23 chez des vers sauvages suffit à prolonger la longévité. Notre étude suggère qu’une communication entre les mitochondries et le noyau est clé pour déterminer la durée de vie d’un animal et révèle que le facteur de transcription CEH-23 est un déterminant génétique du vieillissement répondant à des altérations de la chaîne respiratoire.
2) Nous nous sommes intéressés à l’implication de la dynamique mitochondriale dans le vieillissement chez C. elegans car la balance entre la fission et la fusion mitochondriale est critique pour de nombreux aspects de la physiologie animale. Nous avons diminué la fission mitochondriale en utilisant des animaux présentant une mutation dans la protéine de fission DRP-1.  Les animaux sauvages et les mutants drp-1 présentent la même longévité suggérant que la fission mitochondriale n’influence pas le vieillissement en conditions contrôles. Cependant, lorsque la voie de signalisation à l’insuline est diminuée, l’inactivation de drp-1 augmente de façon dramatique l’effet d’une réduction des voies à l’insuline sur la longévité.              

Ainsi notre travail révèle de nouvelles facettes du rôle des mitochondries dans le vieillissement d’un animal et peut ouvrir de nouvelles voies de recherche dans le développement de stratégies thérapeutiques contre les maladies liées au vieillissement.

Mercredi 26 octobre 2011 à 11h00

Jérôme CAVAILLÉ

LBME-CNRS UMR 5099, Université de Toulouse

Biogenèse et Fonction des microARN dont les gènes sont régulés par l’empreinte génomique parentale

Invité par Marie-Claire Daugeron (01 69 82 36 40)
dans le cadre du mini-colloque ARN de l'UE "Les multiples facettes de l'ARN"
Master 2 GCDE - Ecole Doctorale "Gènes, Génomes, Cellules" - Université Paris-Sud 11

Résumé

L’activité transcriptionnelle d’un génome de mammifères est bien plus complexe que l’on aurait pu l’imaginer, comme l’atteste l’identification récente d’un grand nombre de transcrits qui sont incapables, en l’état actuel de nos connaissances, de générer des protéines. On parle alors d’ARN non-codant (ARNnc). Bien que la fonction de la grande majorité d’entre eux reste à démontrer, de tels transcrits sont aujourd’hui considérés comme des régulateurs majeurs de l’expression des génomes.
Parmi cette vaste population d’ARNnc, les microARN sont actuellement sur le devant de la scène. Ces petits ARN, d’environ 20 nucléotides, agissent comme des ARN antisens et modulent négativement l’expression des gènes au niveau post-transcriptionnel. Leur mode d’action repose sur des appariements imparfaits avec les ARNm, et ce préférentiellement au niveau des régions 3’ non-traduites. Par des mécanismes encore relativement peu compris, la fixation du microARN sur son ARNm-cible provoque une mise en silence de ce dernier, soit par inhibition de sa traduction, soit par accélération de sa dégradation. Par leur capacité à interagir avec un grand nombre d’ARNm, les microARN exercent des fonctions régulatrices dans quasiment tous les systèmes biologiques examinés à ce jour, y compris dans des contextes pathologiques tels que des cancers.
Nous concentrons nos recherches actuelles sur des centaines de microARN dont les gènes sont regroupés au sein de deux loci chromosomiques: le domaine Dlk1-Dio3 et le cluster C19MC. Ces microARN ont un patron d’expression spécifique, avec une expression marquée dans le cerveau adulte et le placenta. Fait remarquable, leurs gènes sont régulés par l’empreinte génomique parentale, un mécanisme épigénétique conduisant à une expression mono-allélique dépendante de l’origine parentale des allèles. En d’autres termes, pour un locus génique donné, seul l’allèle paternel est exprimé tandis que l’allèle maternel, au sein du même noyau et parfois génétiquement identique, demeure dans un état silencieux.
A travers des approches d’imagerie cellulaire à l’échelle du noyau et des approches fonctionnelles via l’utilisation de modèles murins knock-out, nos travaux en cours visent à disséquer la biogenèse et les fonctions physiologiques des microARN dont les gènes sont régulés par l’empreinte génomique parentale.

Vendredi 14 octobre 2011

Colloque de l'IFR 115 : "Séquençage à haut débit"

La plateforme de séquençage à haut débit IMAGIF organise avec l'IFR 115 une journée consacrée à divers aspects du séquençage à haut débit. Cette journée ouverte à tous présentera des travaux récents utilisant des études basées sur cette technologie : détermination de transcriptomes, détection d’ARNs non-codants et de microRNAs, Chip-seq, séquençage de génomes de novo, détection de mutations, etc. Les orateurs apporteront leur expérience sur les problèmes biologiques qui peuvent être abordés par cette méthodologie, sur sa puissance mais aussi sur certains problèmes rencontrés lors de sa mise en œuvre.

L'inscription est gratuite mais obligatoire : merci d'envoyer un e-mail avec vos coordonnées à Jocelyne Mauger en précisant si vous souhaitez participer au déjeuner sur place.

Programme

9h00 - Accueil des participants

Introduction par Claude Thermes (CGM, Gif-sur-Yvette) : « Plateforme de séquençage IMAGIF : résultats, évolutions »

- Chairman : Domenico Libri

09h45 - Domenico Libri (CGM, Gif-sur-Yvette) : « Identification des séquences de terminaison de la transcription »

10h15 - Jean-Luc Pernodet (IGM, Université Paris-Sud 11) : « Exploration du métabolisme des Streptomyces : apport du séquençage de novo »

10h45 - Pause café

11h15 - Chunlong Chen (CGM, Gif-sur-Yvette) : « XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast »

11h45 - Sean Kennedy (MICALIS, INRA Jouy-en-Josas) : « Quantitative Metagenomics: Understanding the Link between the Human Intestinal Microbiota and Disease »

12h15 - Déjeuner

- Chairman : Eric Meyer

14h00 - Eric Meyer (ENS, Paris) : « Identification de gènes impliqués dans l'ARN interférence chez Paramecium tetraurelia »

14h30 - Stéphane Duigou (CGM, Gif-sur-Yvette) : « Identification et caractérisation d'une mutation supprimant le besoin de HolD chez E. coli »

15h00 - Annick Jacq (IGM, Université Paris-Sud 11) « RNA-seq chez un Vibrio pathogène d'huîtres : une vision de la régulation par les ARN à l'échelle du génome »

15h30 - Pause café

16h00 - Didier Poncet (VMS, Gif-sur-Yvette) : « Recherche de mutations dans un génome viral à ARN double brin »  

16h30 - Laurence Amar (CNPS, Université Paris-Sud 11) : « Profils "miRNA" de noyaux hypothalamiques chez le rat. Variabilité individuelle d’expression ? »

17h00 - Daniel Gautheret (IGM, Université Paris-Sud 11) : « Non-coding RNA-seq in the three domains of life. A comparative perspective »

Téléchargement du programme sur le site de l'IFR 115

Jeudi 13 octobre 2011 à 11h30

Alex DAJKOVIC

Faculté de Médecine Paris Descartes, Génétique Moléculaire Evolutive et Médicale

Organization and Spatial Control of the Bacterial Cytokinetic Apparatus

Invité par François-Xavier Barre (01 69 82 31 58)

Résumé

Vendredi 30 septembre 2011 à 14h00

Salle de conférences, bâtiment 23-24
Centre de Génétique Moléculaire
CNRS Gif-sur-Yvette

François-Xavier LAURENT

Une nouvelle fonction pour la DEAD-box ARN hélicase p68/DDX5 dans la Dystrophie Myotonique de type 1

Soutenance de Thèse de Doctorat - Université Paris-Sud 11

Jeudi 29 septembre 2011 à 14h00

Salle de conférences, bâtiment 23-24
Centre de Génétique Moléculaire
CNRS Gif-sur-Yvette

Chloé LALIGNÉ

Etude de la fonction protéique de Bug22p

Soutenance de Thèse de Doctorat - Université Paris-Sud 11

Vendredi 23 septembre 2011 à 14h30

Salle de conférences, bâtiment 23-24
Centre de Génétique Moléculaire
CNRS Gif-sur-Yvette

Axel THIEL

Organisation á longue distance du chromosome d’Escherichia coli : insulation du macrodomaine Ter

Soutenance de Thèse de Doctorat - Université Paris-Sud 11

Vendredi 23 septembre 2011 à 11h00 - salle de conférences du bâtiment 26

Bernard HALLET

Université de Louvain-la-Neuve, Belgique

"Hi-jacking" as mechanism for recruiting the cellular replication machinery during replicative transposition

Invité par Frédéric Boccard (01 69 82 32 17)

Résumé

Vendredi 16 septembre 2011 à 14h00

Salle de conférences du Centre de Génétique Moléculaire
Bâtiment 23-24, CNRS Gif-sur-Yvette

Delphine RISPAL

du laboratoire de Bertrand Séraphin : Protein networks and complexes regulating eukaryotic mRNA decay, IGBMC, Illkirch

Etude des facteurs impliqués dans la terminaison de la traduction et
la dégradation des ARNm chez Saccharomyces cerevisiae

Soutenance de Thèse de Doctorat - Université Paris-Sud 11
Ecole Doctorale "Gènes, Génomes, Cellules"

Mardi 13 septembre 2011 à 14h00

Luke REINEKE

Baylor College of Medicine, Houston, Texas, USA

Translational activation by the stress granule protein G3BP

Invité par Laurent Chavatte (01 69 82 32 13)

Résumé

My project centers on the tight inverse correlation between stress granule assembly and translational activity.  Stress granules are mRNP aggregates that contain stalled translation initiation factors and translationally silent mRNAs.  Although a strong correlation exists between these translation and stress granule formation, little is known about the signaling between them.  My project focuses on the connection between stress granules and translational regulation using a protein known as Ras-GAP SH3 binding protein (G3BP) as a model.  This protein has been shown to be an integral component of stress granules, and is targeted by poliovirus to disengage stress granules and promote viral translation.  Previous studies have demonstrated that G3BP acts as a translational suppressor.  We hypothesized that G3BP switches between translationally inert and repressive states upon encountering cellular stress.

Vendredi 1er juillet 2011 à 14h30

Pascal BARBRY

Institut de Pharmacologie Moléculaire et Cellulaire
CNRS/UNSA UMR6097, Sophia Antipolis

Specific microRNA promotes multiple cilia formation in vertebrate

Invité par France Koll (01 69 82 31 45)

Résumé

Multiciliated cells lining the surface of some vertebrate epithelia are essential for various physiological processes, such as airway cleansing. Their apical surface is constituted by hundreds of motile cilia, which beat in a coordinated manner to generate directional fluid flow.
We recently reported the identification of microRNAs of the miR-449 family as evolutionary conserved key regulators of vertebrate multiciliogenesis. MicroRNAs are a class of small non-coding RNAs, which regulate several biological processes at a post-transcriptional level. This novel function of miR-449 was established using in vivo and in vitro antisense approaches in two distinct experimental models. miR-449 strongly accumulated in multiciliated cells in human airway epithelium and Xenopus laevis embryonic epidermis, where it triggered centriole multiplication and multiciliogenesis by directly repressing the Delta/Notch pathway.
Our data complement previous reports that showed the blocking action of miR-449 on the cell cycle, and unraveled a novel conserved mechanism whereby Notch signalling must undergo microRNA-mediated inhibition to permit differentiation of ciliated cell progenitors. We review here several important questions regarding the links between microRNAs and the Notch pathway in the control of cell fate.

Jeudi 30 juin 2011 à 11h30

Stephen DOUTHWAITE

Dept. Biochemistry and Molecular Biology, University of Southern Denmark,
Odense, Denmark

Antibiotic resistance by methylation of ribosomal RNA

Invité par Satoko Yoshizawa (01 69 82 38 30)

Résumé

Many types of chemically diverse antibiotics inhibit bacterial growth by binding to the ribosome and blocking protein synthesis. Resistance to these antibiotics can be conferred by small changes in the bacterial ribosome that greatly reduce antibiotic binding. In pathogenic bacteria, resistance to ribosome-targeting antibiotics is often conferred by addition of one or two methyl groups at specific rRNA nucleotides.
In some few cases, resistance is also conferred by loss of one or more natural methylations in the rRNA. This latter mechanism has been seen in multi-drug resistant strains of Mycobacterium tuberculosis that have become additionally resistant to cyclic peptide antibiotics such as capreomycin due to loss of two methylations on the 16S and 23S rRNA. Taking a phylogenetic approach, we will also look at how methyltransferase enzymes might have evolved to confer antibiotic resistance.

Jeudi 23 juin 2011 à 11h30

Anne BLANC-POTARD

Dynamique des Interactions Membranaires Normales et Pathologiques - UMR 5235 CNRS
Université Montpellier 2

Membrane peptides: an emerging class of regulatory molecules in bacteria

Invitée par Nara Figueroa-Bossi (01 69 82 38 11)

Résumé

Identification of short coding sequences is challenging, both experimentally and in silico, and natural small proteins (termed peptides when < 50 amino acids) have been overlooked in bacteria. However, recent studies have converged to highlight the expression and function of small proteins in Gram-negative bacteria as Escherichia coli and Salmonella typhimurium.
Our studies focus on functional hydrophobic peptides that are located at the bacterial membrane. These peptides appear to play a regulatory role by interacting with protein partners and by modulating protein partner activity or stability. Besides the identification of a novel class of regulatory molecules, characterisation of bioactive membrane peptides can provide a basis for engineering membrane protein antagonists.

Jeudi 9 juin 2011 à 11h30

Koen VISSCHER

Depts. of Physics, and Molecular and Cellular Biology - Applied Mathematics, and the College of Optical Sciences
University of Arizona - USA

Want to control gene-expression? Pull here!

Invité par Dominique Fourmy (01 69 82 38 84 / 38 83)

Résumé

It appears that mechanical force or tension may play an important role in controlling gene-expression, not only during transcription but also during translation. Using optical tweezers we have shown that moderate tension in DNA can shut down transcription initiation by T7 RNA polymerase (RNAP), thereby silencing the gene. Force was found to reduce the lifetime of the DNA-RNAP (pre)initiation complex. In the absence of any ribonucleotides, however, we find this effect much reduced, implying that the force-sensitivity predominantly rests with the “open” complex.
Mechanical force may also control translational recoding by -1 frameshifting. Preliminary work on a theoretical model predicting -1 frameshifting will be discussed. Such models rely on the buildup of tension in mRNA when ribosomes fail to unwind a downstream RNA structure. Therefore we have used optical tweezers as well as Steered Molecular Dynamics to investigate the mechanical stability of the Beet Western Yellow Virus (BWYV) pseudoknot known to trigger programmed -1 frameshifting. This work confirms the crucial role of Mg2+ for RNA stability, but also provides new insights into the surprising drop in frameshift efficiency of certain BWYV mutants.

Vendredi 20 mai 2011 à 14h30

Andy BERGLUND

Institute of Molecular Biology - University of Oregon - USA

Understanding Protein-RNA interactions in myotonic dystrophy and a small molecule approach
to target the toxic element in this disease

Invité par Domenico Libri (01 69 82 36 63)

Résumé

I will discuss our progress on understanding the molecular mechanisms of myotonic dystrophy, the most common form of adult onset muscular dystrophy. Mytonic dystrophy is caused by the expansion of non-coding CTG and CCTG repeats expansions. These repeats are toxic at the RNA level and function to sequester a splicing factor (muscleblind-like 1, MBNL1), which leads to many mis-splicing events that are linked to causing many of the symptoms of myotonic dystrophy. The first part of the talk will focus on our studies to understand the molecular function of MBNL1 and the second part of the talk will be about our studies to use small molecules to inhibit the toxic RNA.

Jeudi 19 mai 2011 à 11h30

Fabien DARFEUILLE

INSERM U869, Laboratoire ARNA - IECB - Université de Bordeaux

Etude des modules toxin-antitoxine (TA) chez Helicobacter pylori
or Toxin-antitoxin modules in Helicobacter pylori

Invité par Lionello Bossi (01 69 82 38 02)

Résumé

Helicobacter pylori is a bacterial pathogen that naturally colonizes the human gastric mucosa of more than half of the world’s population. This infection can lead to peptic ulcer diseases, gastritis and gastric cancers.
During the last few years, bacterial small noncoding RNAs appeared as a new class of key regulators of gene expression. Most of the functionally characterized sRNAs target trans-encoded mRNAs by short and imperfect base pairing, and thereby, act as inhibitors or activators of mRNA translation. They regulate many different genes, encoding e.g., membrane proteins, virulence factors, or endogenous toxins.
By using combined bioinformatic and experimental (deep sequencing) approaches, Sharma and colleagues ¹, discovered a novel family of small non coding RNAs in the sequenced 26695 H. pylori strain. This family is composed of six homologous genes (named IsoA), located at different loci in the genome. We also identified a new class of mRNAs, expressed from the opposite strand of these antisense RNAs. Each of these new mRNAs encode a conserved short peptide (30 amino-acids) and thus were renamed Antisense associated peptide A (AapA). The AapA mRNA and its small cis-encoded antisense transcript (Inhibitor of small ORF A, IsoA) are both expressed in vivo, defining a small expression cassette, repeated several times in the genome of different strains. We have shown that the peptides encoded by these mRNAs are toxic for H. pylori growth and that toxicity is prevented by the antisense RNA expressed in cis orientation. Indeed these peptides are positively charged (+5 to +8) and may fold as a-helices with distinct hydrophobic and charged surfaces, making them good candidates for being toxic in H. pylori. Interestingly each cassette seems to be regulated independently. Each IsoA is able to repress the synthesis of its cognate peptide Phylogenetic analysis of these cassettes in 23 sequenced H. pylori strains predicted a high structure conservation of the peptides as well as AapA/Iso folding. Both RNAs fold into highly conserved double stem-loops that might favour the formation of loop-loop “kissing” complexes between the two RNAs.
During my presentation, I will present the data obtained in the transcriptome analysis of H. pylori, including the surprising large number of antisense transcript as well as our recent results obtained during the characterization of the newly discovered type I toxin-antitoxin modules.

¹ Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF & Vogel J (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature, 464 (7286) 250-5.

Vendredi 13 mai 2011 à 14h30

Prof. Nick DIXON

School of Chemistry - University of Wollongong - Australia

Protein–Protein Interactions in Bacterial DNA Replication

Invité par Bénédicte Michel (01 69 82 32 29)

Résumé

Replication of the bacterial chromosome requires the concerted actions of about 30 different proteins that synthesize both DNA strands at replication forks at the same time, in a multiprotein complex called the replisome. The replisome is a dynamic complex that changes conformation and structure at various stages of the replication cycles, especially during the repeated synthesis of Okazaki fragments on the lagging strand. Protein-protein interactions in the replisome include some strong ones that give rise to readily isolable subcomplexes, and many transient interactions that allow some binding sites to be occupied by different proteins at different times during the replication cycles. Many of these weak interactions are mediated by intrinsically unstructured segments of proteins that become structured when they interact with their binding partners. We (i) now know the 3D structures of (the structured parts) of almost all of the individual replisomal proteins and some sub-complexes of them, (ii) have identified and assigned roles to most of their unstructured regions, and (iii) are beginning to understand dynamic events during replisome function. Not only is study of the E. coli replisome revealing how temporally ordered weak and transient protein-protein interactions determine functions of large dynamic molecular machines, but it is also guiding development of new methods to study them.
In this seminar, I will present recent unpublished data concerning two different sets of transient interactions in the replisome. One set of interactions governs repeated initiation of Okazaki fragment synthesis on the lagging strand, while the other governs events that happen when the replicative DNA polymerase is stalled by meeting an impediment to its progression.

Lundi 9 mai 2011 à 11h30

Valérie DE CRECY

Microbiology and Cell Science - University of Florida - USA

A la pêche aux gènes de modifications d'ARN de transfert manquants :
exploration de 1 000 génomes par génomique comparative

Invitée par Domenico Libri (01 69 82 36 63)

Résumé

Site web de Valérie de Crécy

Vendredi 6 mai 2011 à 14h30

David LEACH

Institute of Cell Biology - School of Biological Sciences - University of Edinburgh - UK

Using Inverted and Direct Repeats to Investigate DNA Repair and Chromosome Segregation in vivo

Invité par Bénédicte Michel (01 69 82 32 29)

Résumé

We have been using inverted repeats (DNA palindromes) and (CAG.CTG)n trinucleotide repeats to target DNA lesions to specific locations on the E. coli chromosome. Palindromes are cleaved to induce DNA double-strand breaks and trinucleotide repeats attract the activity of mismatch repair. I will illustrate how making specific DNA lesions at defined chromosomal locations is a powerful way to investigate fundamental events, associated with DNA replication, such as genetic recombination, mismatch repair and chromosome segregation.

Jeudi 28 avril 2011 à 11h30

Christophe ROUILLON

School of Biology - University of St Andrews - Fife, Scotland

Mechanism and evolution of XPD and XPB DNA helicases

Invité par François-Xavier Barre (01 69 82 32 24)

Résumé

In eukaryotes, XPD and XPB are components of TFIIH, a multifunctional 10 subunits complex involved in basal transcription as well as in Nucleotide Excision Repair (NER). XPD and XPB are also found in most of the archaeal prokaryotes. As they do not belong to a complex, they can be easily studied individually. Essential core motifs for helicase and ATPase activities are highly conserved, which suggest the same mechanism from Archaea to human.
XPD characterisation in Sulfolobus has shown the DNA helicase activity dependant of an iron sulphur cluster. Furthermore, the crystal structure resolution twinned to biochemical studies has allowed mapping some mutated conserved residues leading to diseases in human, also giving functional explanations. In Sulfolobus, XPB interacts with the endonuclease Bax1. Using Bax1 endonuclease activity as a proxy, the weak activity of XPB helicase was visualized, thus showing the complex functions as a helicase-nuclease machine. It has never been proved that archaeal XPD and XPB are involved in NER. Recruitment of these two factors to form eukaryotic TFIIH during evolution is the most probable hypothesis. The presence of highly conserved proteins from one organism to another does not systematically imply conservation of the whole pathway.
In Bacteria, DinG the closest homologue of XPD has been shown to be recruited at the replication fork during RNA polymerase and R-loop removal. In the gram + bacteria, DinG seems to have evolved by loosing its iron sulphur cluster but gaining an additional exonuclease domain.
A synthesis of data regarding archaeal XPD and XPB will be discussed and the biochemical characterisation of Staphylococcus aureus DinG presented.

Vendredi 8 avril 2011 à 11h30

Une conférence du Centre de Recherche de Gif

Patrice CODOGNO

Faculté de Pharmacie, Inserm Châtenay-Malabry

Autophagy: self-eating is good for you

Invité par Renaud Legouis - CGM (01 69 82 43 74)
et
Béatrice Satiat-Jeunemaitre - ISV

Résumé

Plus d'information sur P. Codogno

Jeudi 31 mars 2011 à 14h00

Salle de conférences, bâtiment 23-24
Centre de Génétique Moléculaire
CNRS Gif-sur-Yvette

Muhammad Kashif ZAHOOR

Genome wide analysis for novel regulators of growth and lipid metabolism in Drosophila melanogaster

Soutenance de Thèse de Doctorat - Université Paris-Sud 11

Jeudi 31 mars 2011 à 11h30

Michael PRIMIG

Irset - Inserm Avenir lab - Université de Rennes 1

Sex - is it all about inhibiting the inhibitors?

Invité par Domenico Libri (01 69 82 36 63)

Résumé

Sexual reproduction of most eukaryotes requires meiosis, a developmental pathway leading to the production of haploid gametes whereby diploid cells undergo one round of DNA replication followed by two meiotic divisions without an intervening S-phase. Genetics and functional genomics have identified numerous meiotically induced budding yeast genes required for the process. Some of them are repressed in vegetatively growing cells by the conserved Ume6/Rpd3/Sin3 repressor complex the Ume6 DNA binding subunit of which gets degraded when cells enter meiosis. Recent high-resolution transcriptional profiling analyses of mitotic growth in budding yeast have revealed the wide-spread synthesis of Cryptic Unstable Transcripts (CUTs) detectable only in haploid cells lacking the conserved exoribonuclease Rrp6, and Stable Unannotated Transcripts (SUTs). The roles of noncoding RNAs (ncRNAs) during growth and development are only poorly understood but a number of cases where ncRNAs interfere with mRNA expression have been described.
Using DNA strand specific tiling arrays we have identified an extensive meiotic ncRNA expression program interlaced with its protein-coding counterpart via overlapping sense/antisense transcripts and bidirectional promoters driving mRNA/ncRNA or ncRNA/ncRNA pairs. Moreover, we found meiotic ncRNAs which overlap with the regulatory regions of protein-coding genes and others that cover Autonomously Replicating Sequence elements. Many of these novel Meiotic Unannotated Transcripts (MUTs) are mitotic targets of the conserved exosome component Rrp6, which itself is degraded after the onset of meiosis when MUTs, CUTs and SUTs accumulate to high levels in successive waves. Finally, diploid cells lacking Rrp6 fail to initiate premeiotic DNA replication normally and cannot undergo efficient meiotic development.
Preliminary data will be discussed on why Rrp6 is degraded during meiosis and if this pattern is conserved in the case of Rrp6’s mammalian ortholog Exosc10. We propose that the yeast meiotic expression program is established by the simultaneous developmental-stage specific destruction of the DNA binding repressor Ume6 and the exoribonuclease Rrp6.

Site web de Michael Primig

Jeudi 17 mars 2011 à 11h30

Serge PLAZA

Centre de Biologie du Développement (CBD) - UMR5547 CNRS/Université Toulouse 3

Invité par François Agnès (01 69 82 43 85) et Anne-Marie Pret (01 69 82 31 46)

Transcriptional control of epidermal cell shape remodeling in Drosophila

Résumé

Developmental programs are implemented by regulatory interactions between Transcription Factors and their target genes but the nature of the networks involved remains poorly understood. We address these questions by studying the mechanisms involved for the morphological differentiation of embryonic epidermal cells. Epidermal morphogenesis relies on developmental regulatory cascades that ultimately set up the expression of the Shavenbaby transcription factor. Shavenbaby in turn triggers the transcription of genes encoding cellular effectors, which are responsible for localized changes in the shape of epidermal cells leading to denticle formation.
Combining experimental and computational approaches, we aim to decipher the nature of the svb target genes involved and the molecular mechanisms of svb driven target genes control through the cis-regulatory elements that direct specific expression of these cellular effectors in trichome cells. We recently discovered an unexpected function of a putative non coding RNA controlling the Svb protein activity through the production of small peptides directing a proteolytic cleavage to convert Svb from a repressor into an activator.

Jeudi 10 février 2011 à 11h30

Tanneke DEN BLAAUWEN

Swammerdam Institute for Life Sciences
Amsterdam, The Netherlands

Invitée par François-Xavier Barre (01 69 82 31 58)

Morphogenesis of Escherichia coli

Résumé

Bacteria proliferate via elongation and binary fission. However, how they determine and maintain their shape that can vary from spherical, rod-shaped, spirals to branched with thin extensions remains mysterious. The cytoskeletal protein MreB, a homolog of eukaryotic actin, forms a helix, which is thought to function as a track for the protein complexes (elongasomes) that synthesize the cylindrical cell wall during length growth. Filaments of FtsZ, a tubulin homolog, form a ring at midcell that acts as the scaffold for the divisome protein complexes that synthesize the poles of the new daughter cells.
Our today’s understanding of how the cell accomplishes the random insertion of cell wall material by the elongasomes and how cell poles of completely new cell wall can be synthesized by the divisome will be discussed. Examples of the use of immunofluorescence microscopy, quantitative image analysis and Förster resonance Energy transfer to study morphogenesis will be shown.

Jeudi 27 janvier 2011 à 11h30

Magali SUZANNE

Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération
UMR 5088 CNRS, Université Paul Sabatier, Toulouse

Invitée par Anne-Marie Pret et François Agnès (01 69 82 43 85)

Rôle et régulation de l'apoptose pendant le développement de la Drosophile

Résumé

L’apoptose est requise au cours du développement pour l'élimination de cellules potentiellement dangereuses, de cellules surnuméraires ou de cellules devenues inutiles, et participe aussi à des mouvements morphogénétiques.
Nous utilisons la formation des articulations de la patte de Drosophile comme modèle d'étude afin de comprendre les causes et les conséquences de l'apoptose au niveau cellulaire, dans un contexte où l'apoptose n'est pas induite artificiellement. Ce modèle est un cas de régulation stricte de l'apoptose qui survient toujours au même endroit au même moment. De plus, cette apoptose est essentielle à la morphogenèse des articulations et est activement impliquée dans la modification de la forme des cellules voisines. Quand l'apoptose est bloquée, l'articulation présomptive tout comme l'articulation adulte n'est pas formée.
Nous cherchons à identifier les signaux amont qui régulent l'apoptose au niveau de l'articulation présomptive et qui conduisent à la mort d’un petit groupe de cellules, localisées au coeur de l'articulation, à un stade précis de son développement.

Role and regulation of apoptosis during development in Drosophila

Abstract

Apoptosis is required during development to eliminate potentially harmful cells, to regulate cell number, to delete cells that are no longer required, but also to participate in morphogenetic events.
We are using the formation of the leg joint in Drosophila as a developmental model in order to understand both the causes and the consequences of apoptosis at a cellular level, in a context in which apoptosis is not artificially induced. This model is a case of strictly regulated apoptosis, occurring always at the same time and at the same place. Furthermore, this apoptosis has been shown to be essential for the morphogenesis of the joint and is actively involved in shape modifications of the surrounding cells. When apoptosis is blocked, both the presumptive joint and the adult joint are impaired.
We are trying to identify the upstream signals that regulate apoptosis in the presumptive joint leading to the death of a small group of cells localized in the joint, at a specific developmental stage.

Jeudi 20 janvier 2011 à 11h30

Shixin YE

Institut de Neuroscience, Département de Biologie
École Normale Supérieure, Paris

Invitée par Gilles Truan (01 69 82 36 65)

Tracking rhodopsin activation using genetically encoded infrared probes

Résumé

In the past two decades, site-directed mutagenesis with non-natural amino acids has emerged as a novel tool in studies of protein function.  This technique allows one to introduce unique chemical probes into proteins at a desired site by means of engineered transfer RNA (tRNA) reading through the amber stop codon.  In this talk, I will overview the development of the mutagenesis technique and focus on applications to the studies of rhodopsin (a prototypical G protein-coupled receptor associated with dim-light vision).  We successfully incorporated an infrared amino acid p-azido-L-phenylalanine at various positions in rhodopsin.  This allows the application of FTIR to track conformational changes during rhodopsin activation process.

Jeudi 13 janvier 2011 à 11h30

Olivier ESPÉLI

CGM, Gif-sur-Yvette

Invité par Bénédicte Michel pour le "Search Commitee" du CGM (01 69 82 32 29)

Sister chromatid cohesion and segregation

Résumé

Sister-chromatid cohesion is an essential step of the cell cycle of eukaryotic cells. This step has recently been described in bacteria, however its role and determinants remain poorly characterized. In Eukaryotic cells, establishment of the cohesion is dependent upon loading of cohesins on the sister-chromatid. In bacteria, cohesins are not present and a combination of proteic factors and DNA untangling are believed to promote cohesion. The extent of the cohesion step is measured in term of co-localization of two sister tags.
We have developed, in E. coli, two alternative genetic assays allowing to measure distance between sister-chromatids and catenation of the sister-chromatids in a more direct way. These assay revealed that sister-chromatid remained in close proximity for short period following replication. We called this step molecular cohesion. The extent of molecular cohesion differs from that of sister foci co-localization. Topoisomerases activity seems to modulate the extent of the cohesion period. Using this assay we have been able to identify a new protein involved in the cohesion step (SciA). The genetic assays will serve as platform to survey sister chromatid organization in E. coli and the yeast S. pombe at the whole genome scale via  high-throughput sequencing technology.
Perspectives for these projects will be discussed.

Web site

Mercredi 5 janvier 2011 à 14h00

Salle de conférences, bâtiment 23-24
Centre de Génétique Moléculaire
CNRS Gif-sur-Yvette

Abderazak DJEDDI

Caractérisation cellulaire et fonctionnelle de l'autophagie chez C. elegans :
interactions avec la voie de maturation endosomale

Soutenance de Thèse de Doctorat - Université Paris-Sud 11