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Towards Combinatorial Biosynthesis of Pyrrolamide Antibiotics in Streptomyces Celine Aubry

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Towards Combinatorial Biosynthesis of Pyrrolamide Antibiotics in Streptomyces Celine Aubry Towards combinatorial biosynthesis of pyrrolamide antibiotics in Streptomyces Celine Aubry To cite this version: Celine Aubry. Towards combinatorial biosynthesis of pyrrolamide antibiotics in Streptomyces. Bio- chemistry [q-bio.BM]. Université Paris Saclay (COmUE), 2019. English. NNT : 2019SACLS245. tel-02955510 HAL Id: tel-02955510 https://tel.archives-ouvertes.fr/tel-02955510 Submitted on 2 Oct 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Towards combinatorial biosynthesis of pyrrolamide antibiotics in Streptomyces Thèse de doctorat de l'Université Paris-Saclay préparée à l’Université Paris-Sud École doctorale n°577 Structure et Dynamique des Systèmes Vivants (SDSV) Spécialité de doctorat : Sciences de la vie et de la Santé Thèse présentée et soutenue à Orsay, le 30/09/19, par Céline AUBRY Composition du Jury : Matthieu Jules Professeur, Agroparistech (MICALIS) Président du Jury Yanyan Li Chargée de recherche, MNHN (MCAM) Rapportrice Stéphane Cociancich Chercheur, CIRAD (BGPI) Rapporteur Annick Méjean Professeure, Université Paris-Diderot (LIED) Examinatrice Hasna Boubakri Maitre de conférences, Université Claude Bernard Lyon I (Ecologie microbienne) Examinatrice Sylvie Lautru Chargée de recherche, CNRS (I2BC) Directrice de thèse Acknowledgements J’ai insisté pour rédiger l’ensemble de ma thèse en anglais. La logique voudrait donc que cette section soit écrite en anglais également, mais je n’ai pas pu m’y résoudre. Je vous présente mes excuses pour cette entorse linguistique. Si le doctorat est l’occasion de creuser un projet principalement réalisé par le doctorant, ce n’est en aucun cas un travail individuel qui s’accomplit seul. De nombreuses personnes, par leur aide sur tous les aspects d’un projet doctoral, qu’ils soient scientifiques, administratifs, sociaux ou émotionnels, m’ont permis de vivre pleinement cette expérience. Ces personnes sont trop nombreuses pour être toutes citées ici, mais sachez que les moments partagés font partie des souvenirs irremplaçables que je garde de ces quatre années dans l’équipe de Microbiologie Moléculaire des Actinomycètes (MMA) à l’Institut de Biologie Intégrative de la Cellule. Je souhaite exprimer toute ma reconnaissance à Sylvie Lautru, ma directrice de thèse. Tout au long du projet, tu m’as encadrée avec beaucoup de patience et de disponibilité. Tu m’as témoigné une grande confiance concernant la réalisation des expériences et m’as encouragée à gagner en autonomie. Tu as toujours écouté mes suggestions avant de me donner ta vision des choses, puis de discuter ensemble de la suite. Tu as également été présente pour écouter mes doutes et me rassurer dans les moments plus difficiles. Merci de m’avoir guidée tout en me laissant libre de choisir mon chemin et ma manière de faire les choses. Je remercie les membres de mon jury de thèse, Yanyan Li, Stéphane Cociancich, Annick Méjean, Hasna Boubakri et Matthieu Jules, d’avoir accepté de consacrer du temps à évaluer mes travaux de recherche. Annick Méjean a également fait partie de mes comités de suivi de thèse, avec Muriel Gondry, Christiane Elie et Jean-Luc Pernodet, et je les remercie pour leurs conseils et leur bienveillance concernant mon projet. Concernant les procédures administratives, j’ai bénéficié de l’aide toujours efficace de Muriel Decraëne et de Catherine Drouet, ainsi que de Marie-Hélène Sarda et de Martine Denis, et de Blandine Champion-Grosjean. Votre expertise des multiples procédures m’a permis de gagner un temps précieux. Je tiens également à remercier Paolo Clérici, qui a réalisé la synthèse chimique d’un précurseur de l’anthelvencine spécialement pour une de mes expériences, mais aussi Laurent Micouin et son équipe, qui se sont penchés et se penchent encore aujourd’hui sur la caractérisation structurale de l’anthelvencine avec beaucoup de ténacité. Un grand merci également à Zhilai Hong, Yanyan Li et Soizic Prado, qui ont permis l’analyse en spectrométrie de masse à haute résolution des anthelvencines, et m’ont donné les clefs nécessaires à la compréhension des résultats. 1 D’autres petites mains ont directement participé à mon projet, celles de mes stagiaires Jennifer Perrin et Yacine Sellah. Merci beaucoup, d’une part vous m’avez aidée à faire avancer mon projet, et d’autre part, j’ai beaucoup appris en vous encadrant. Jennifer, tu as été ma première stagiaire, et j’ai été impressionnée par ta vivacité d’esprit et ta motivation. Tu t’es aussi très bien intégrée à l’équipe et je me rappelle la période de ton stage comme un moment plein de rires et de bonne humeur. Yacine, ton projet portait sur des parties plus difficiles de ma thèse, mais tu n’as jamais abandonné et ta persévérance a porté ses fruits, merci d’avoir souhaité autant que moi la réussite de ce projet. Mon implication dans l’encadrement de l’équipe iGEM GO-Paris-Saclay 2018 a également consisté une expérience inestimable. Merci aux encadrants, Stéphanie, Philippe et Mahnaz, j’ai apprécié le résultat de notre coopération ! Merci aussi à tous les étudiants, pour leur enthousiasme et leur créativité, je remercie en particulier les étudiants que j’ai accompagnés à Boston pour présenter les résultats, une aventure pleine de rebondissements et de bons souvenirs. J’aimerais également remercier tous les membres passés et présents des équipes MES et MMA, nos interactions ont rendu mon séjour ici inestimable. Merci en particulier à Jean-Luc, pour ton oreille attentive et ta connaissance incroyable des évènements qui méritent un apéritif, à Christiane pour les anecdotes invraisemblables et les conseils pragmatiques, à Laetitia pour tous les jeudis aux expériences ratées et ta fidélité presque sans faille aux repas du CESFO, à Luisa pour ton efficacité et pour oser aborder les problèmes sans détours, à Alba pour les soirées au dehors et la complicité en 105, à Jerzy pour les petites astuces de labo et les pauses « café » chez Sylvain, à Laura, pour le partage paisible de l’espace et du projet pyrrolamides, à Sylvain, pour l’accueil dans ta cuisine et les discussions aux sujets divers, à Armel, pour les connaissances sur tout et les bonbons, à Manue, pour ta prévenance à mon égard et la gestion infatigable des soucis de séquençage, à Soumaya, pour les conseils spécial doctorants qui facilitent la vie, à Mathieu, pour les bonjours impromptus et le cactus, à Brittany, pour ta gaieté contagieuse et le voyage à Boston, à Corinne, pour la bonne humeur et la musique, à Stéphanie, pour ton dynamisme et cette incroyable capacité à remotiver les gens, à Hervé, pour ton dévouement à toujours ressusciter « mamie » et ton recul sur la science, à Marc, pour ne pas avoir jeté l’HPLC par la fenêtre malgré la tentation, à Aaron, pour des barbecues mémorables, et à Marie-Joëlle et Michelle, pour avoir toujours eu froid pour moi. Merci aussi à Nelly, pour avoir repris le flambeau en l’absence de Sylvain, et m’avoir permis de poursuivre mes expériences en toute sérénité. Il a fait bon vivre au bâtiment 400, où les gens sont toujours prêts à apporter leur aide sur un appareil, ou à partager un moment convivial autour d’un repas ou d’un verre. Merci à tous pour cette ambiance des plus agréables ! Merci aussi aux « anciens » de l’équipe MMA qui sont restés dans les environs, Audrey, Florence et Drago, pour leurs conseils avisés. Un énorme merci à Clara, ma voisine de palier. A nous deux, nous avons égayé le couloir, parfois un peu bruyamment, et acheté les vivres nécessaires aux apéritifs du vendredi soir. Mais bien plus que ça, tu es devenue une véritable amie, et les activités en dehors qui ont commencé par des sessions piscines se sont bien vite diversifiées. Je ne compte plus nos multiples discussions, ni les sorties à l’Opéra ou au cinéma. Ma vie pendant le doctorat n’aurait pas été la même sans toi ! 2 Je souhaite adresser un remerciement spécial à Lucile. Sans toi, cette aventure n’aurait jamais commencé. Merci de m’avoir conseillée ce projet que tu avais initié pendant ton stage ! Je souhaite aussi exprimer une reconnaissance toute particulière à Valentin T., un chercheur en génétique et linguistique des populations humaines exceptionnel. Nos discussions sur le milieu de la recherche scientifique m’ont permis de prendre du recul, et d’élargir ma vision du monde. Tes réflexions sur l’éthique et le sens de la vie ont également généré en moi beaucoup de questions, le genre de questions qu’on ne peut pas se permettre d’ignorer. Je continue à chercher mes réponses. Merci aux amis de tous horizons qui ont manifesté de l’intérêt pour mon projet, et de l’empathie pour mes mésaventures. Merci surtout à ma famille, pour toute sa patience, alors que je ruminais mes problèmes techniques ou partais dans des divagations impossibles à suivre. Merci d’avoir été un soutien sans faille, à tout moment, pendant ces années d’études qui aboutissent maintenant. Ces quelques mots ne sauraient exprimer tout l’amour que j’éprouve pour vous. 3 Index Acknowledgements .................................................................................................................................. 1 Index
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