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Durand Romain Phd 2020.Pdf (14.08Mb) DÉTERMINANTS DE LA MOBILISATION DE L’ILOT GÉNOMIQUE DE RÉSISTANCE SGI1 par Romain Durand Thèse présentée au Département de biologie en vue de l’obtention du grade de docteur ès sciences (Ph.D.) FACULTÉ DES SCIENCES UNIVERSITÉ DE SHERBROOKE Sherbrooke, Québec, Canada, novembre 2020 Le 26 novembre 2020 Le jury a accepté la thèse de Monsieur Romain Durand dans sa version finale. Membres du jury Professeur Vincent Burrus Directeur de recherche Département de biologie Université de Sherbrooke Professeur Sébastien Rodrigue Codirecteur de recherche Département de biologie Université de Sherbrooke Docteur Yoshiharu Yamaichi Évaluateur externe Département de biologie des génomes Institut de Biologie Intégrative de la Cellule Docteur Benoît Leblanc Évaluateur interne Département de biologie Université de Sherbrooke Professeure Pascale B. Beauregard Président-rapporteur Département de biologie Université de Sherbrooke REMERCIEMENTS J’aimerais tout d’abord remercier mon directeur de thèse, Vincent, qui a cru en moi très tôt, m’a transmis sa passion pour la science et m’a toujours poussé à dépasser mes limites. Merci aux Fonds de Recherche du Québec – Nature et Technologies, pour avoir financé une partie de mon doctorat. Merci à Sébastien, Pascale et Benoît pour leurs conseils avisés. Merci aux membres passés et présents du laboratoire, particulièrement Nicolas Carraro pour avoir significativement contribué à lancer ma carrière de jeune chercheur. Merci également à Didier de m’avoir mis sur le chemin de la recherche scientifique. Merci à ceux qui m’ont côtoyé et soutenu au cours de ces 5 dernières années. Merci à ceux qui, malgré la distance, m’ont continuellement supporté. Victor, plus de vingt ans d’amitié ont mis du vent dans mes voiles. Je tiens également à remercier ma (grande) famille qui m’a perpétuellement soutenu au travers des épreuves : mon père Christophe, ma mère Valérie, mes sœurs Lucile et Juliette et mon frère Mathis, ainsi que ma belle-famille de Tahiti pour leur accueil chaleureux. Une petite pensée pour mon chat CRISPR-Cat9, qui m’a (presque) toujours accueilli avec enthousiasme après de longues journées de travail. Enfin, un immense merci à mon épouse Teura. Je n’aurais jamais été capable de gravir cette montagne sans ton soutien infatigable. Je ne compte plus les obstacles que tu m’as aidé à surmonter. Maintenant qu’une page se tourne, je n’ai qu’une seule hâte : voir ce que la vie nous réserve à tous les deux. SOMMAIRE Les plasmides conjugatifs appartenant au groupe d’incompatibilité C (IncC) sont des acteurs majeurs de la dissémination des gènes de résistance aux antibiotiques chez les Gammaprotéobactéries. Malheureusement, bien qu’ils figurent dans des centaines d’études épidémiologiques, ils ne sont à l’affiche que d’une poignée d’études mécanistiques. La caractérisation d’AcaCD, complexe majeur d’activation du transfert des plasmides IncC, a constitué une étape clé dans la compréhension du cycle de vie de ces éléments. La liaison de cet activateur transcriptionnel en amont de nombreux opérons impliqués dans le transfert conjugatif permet de déclencher conjointement l’assemblage d’un système de sécrétion de type IV et l’initiation du transfert conjugatif. Elle permet aussi de déclencher l’excision et la mobilisation subséquente de plusieurs familles distinctes d’ilots génomiques mobilisables. L’ilot génomique de résistance Salmonella Genomic Island 1 (SGI1), initialement isolé à partir de Salmonella enterica, est aujourd’hui considéré comme une large famille d’ilots génomiques mobilisables. Un grand nombre de variants, conférant régulièrement des résistances aux antibiotiques, ont été isolés à partir de nombreuses espèces de Gammaprotéobactéries. Bien qu’il n’encode pas de système de sécrétion de type IV complet, SGI1 peut être spécifiquement mobilisé par un plasmide IncC. L’excision de SGI1 est médiée par un gène dont l’expression est activée par AcaCD. Après circularisation, le transfert conjugatif est initié à l’origine de transfert de l’ilot, qui transloque alors au travers du pore de conjugaison encodé par le plasmide. Ce projet de doctorat a permis de montrer que SGI1 encode trois sous-unités fonctionnelles du système de sécrétion de type IV. Celles-ci sont incorporées à la place des sous-unités homologues encodées par le plasmide IncC. Notre étude a montré que ce remodelage du pore de conjugaison par SGI1 lui permettait d’optimiser sa propagation. Nous avons également montré le rôle clé du complexe SgaCD encodé par l’ilot, homologue au complexe majeur d’activation du transfert des plasmides IncC AcaCD. SgaCD s’est révélé essentiel à l’excision et à la réplication de SGI1, entrainant ultimement une déstabilisation du plasmide IncC résidant dans la même cellule. Enfin, nous présentons des données préliminaires montrant l’existence d’un nouveau déterminant de la mobilisation de SGI1 et d’un répresseur du transfert des plasmides IncC encodé par SGI1. Ensemble, nos résultats participent à caractériser la relation complexe entre deux familles d’éléments génétiques mobiles. Nous avons pu identifier de nombreux acteurs impliqués dans la dissémination de ces éléments, lesquels constituent des cibles potentielles pour le développement de composés visant à freiner la propagation des résistances aux antibiotiques. Mots clés : résistance aux antibiotiques, transfert conjugatif, système de sécrétion de type IV, plasmides conjugatifs, ilots génomiques, régulation transcriptionnelle, Gammaprotéobactéries, IncC, SGI1 x TABLE DES MATIÈRES CHAPITRE 1 Introduction .......................................................................................................... 1 1.1 Transfert horizontal de gènes .............................................................................. 1 1.2 Conjugaison .......................................................................................................... 5 1.2.1. Mécanisme global .................................................................................................. 5 1.2.2. Classification des T4SS .......................................................................................... 7 1.2.3. T4SS de type P ...................................................................................................... 10 1.2.3.1 Structure ........................................................................................................... 10 1.2.3.2 Mécanisme de la conjugaison (type P) ............................................................ 12 1.2.3.3 Pilus ................................................................................................................. 14 1.2.4. T4SS de type F ...................................................................................................... 15 1.2.4.1 Structure ........................................................................................................... 16 1.2.4.2 Pilus ................................................................................................................. 18 1.2.4.3 Mpf et Mps ....................................................................................................... 19 1.2.4.4 Exclusion ......................................................................................................... 20 1.2.4.5 Relaxase TraI du plasmide F ........................................................................... 21 1.3 Les éléments conjugatifs .................................................................................... 22 1.3.1. Régulation ............................................................................................................ 23 1.3.1.1 Régulation du transfert des ICE ....................................................................... 23 1.3.1.2 Cycle de vie des ICE ........................................................................................ 26 1.3.1.3 Régulation du transfert des plasmides conjugatifs .......................................... 28 1.3.2. Éléments modèles au laboratoire ......................................................................... 29 1.3.2.1 Les ICE SXT/R391 .......................................................................................... 29 1.3.2.2 Les plasmides A/C ........................................................................................... 31 1.3.2.3 MGIVchHai6 .................................................................................................... 35 1.3.2.4 SGI1 ................................................................................................................. 36 1.3.3. Bilan des interactions entre différentes familles d’éléments ................................ 39 1.4 Hypothèses du projet de doctorat ..................................................................... 42 1.5 Objectifs du projet de doctorat ......................................................................... 43 CHAPITRE 2 Salmonella Genomic Island 1 (SGI1) Reshapes the Mating Apparatus of IncC Conjugative Plasmids to Promote Self-Propagation ............................................ 45 2.1 Introduction ........................................................................................................ 45 2.1.1. Pertinence ............................................................................................................. 45 2.1.2. Apport des auteurs ............................................................................................... 46 2.1.3. Référence .............................................................................................................
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