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Homologous Recombination in Bacteriophages, Less Fidelity for More Exchanges Geoffrey Hutinet

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Homologous Recombination in Bacteriophages, Less Fidelity for More Exchanges Geoffrey Hutinet Homologous recombination in Bacteriophages, less fidelity for more exchanges Geoffrey Hutinet To cite this version: Geoffrey Hutinet. Homologous recombination in Bacteriophages, less fidelity for more exchanges. Bacteriology. Université Paris Sud - Paris XI, 2014. English. NNT : 2014PA112290. tel-01152135 HAL Id: tel-01152135 https://tel.archives-ouvertes.fr/tel-01152135 Submitted on 15 May 2015 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. UNIVERSITÉ PARIS-SUD ÉCOLE DOCTORALE 435 : AGRICULTURE, ALIMENTATION, BIOLOGIE, ENVIRONNEMENT ET SANTÉ Laboratoire : MICALIS THÈSE DE DOCTORAT SUR TRAVAUX SCIENCES AGRONOMIQUES, BIOTECHNOLOGIES AGRO-ALIMENTAIRES par Geoffrey HUTINET Homologous recombination in Bacteriophages : less fidelity for more exchanges Date de soutenance : 31/10/2014 Composition du jury : Directeur de thèse : Marie-Agnès PETIT Directeur de Recherches (INRA) Président du jury : Cécile FAIRHEAD Professeur (Université Paris Sud XI) Rapporteurs : Mart KRUPOVIC Chargé de Recherches (Institut Pasteur) Stéphanie MARSIN Directeur de Recherches (CEA) Examinateurs : François ENAULT Maitre de Conférences (Université Blaise Pascale) Mauro MODESTI Directeur de Recherches (CNRS) 2 To the truth 3 4 Remerciements Ce que m’a appris ce doctorat sur la recherche peut se résumer par le célèbre adage d’Edward A. Murphy Jr., plus connu sous le nom de loi de Murphy, « Anything that can go wrong, will go wrong » (« Tout ce qui peut mal tourner va mal tourner »). Effectivement, la plupart des expériences menées en laboratoire se soldent par des échecs. Et des échecs j’en ai essuyé de nombreux avant d’arriver au rendu final que vous allez lire. Fort heureusement, on apprend de ses échecs, on peut alors se relever et recommencer grâces aux conseils, aux remontrances ou au réconfort des gens qui nous entourent, à la fois dans notre vie professionnelle et privée, afin de réussir à mener un projet jusqu’à son terme. C’est pourquoi je souhaite remercier les personnes qui m’ont permis de mener à bien ce projet de thèse, et de rentrer dans cet étrange, mais merveilleux, monde qu’est la recherche. Tout d’abord, je souhaite remercier les membres de mon jury de thèse, chargés de m’évaluer pour l’obtention du grade de docteur. Merci à Mart Krupovic et Stéphanie Marsin qui ont accepté de relire et juger mon manuscrit en tant que rapporteurs, et surtout merci pour leurs commentaires plus qu’encourageants. Merci à François Enault et à Mauro Modesti d’avoir accepté d’être examinateurs. Enfin merci à Cécile Fairhead, la présidente du jury. Je souhaite ensuite remercier les membres de mon comité de suivi de thèse, qui m’ont aidé chaque année avec leurs remarques pertinentes et pour les discussions passionnantes qui m’ont permis d’avancer. Merci donc à Xavier Veaute, Bénédicte Michel et Michael Dubow. Merci aux membres de « l’ex‐UBLO » pour m’avoir diverti quand le besoin s’en faisait sentir ! Je remercie plus particulièrement Aurélie Bobillot, Mélanie Guillemet, Renata Matos, Laureen Crouzet et Olivier Telle. Les « potins » et autres discussions, scientifiques ou non, en français ou en anglais, m’ont permis de faire des pauses aux moments nécessaires. Merci à mon équipe d’accueil, l’équipe « phages ». Marianne De Paepe et Colin Tinsley qui ont su me conseiller lors de mes expériences grâce à leurs compétences personnelles, mais aussi pour les blagues et discussion sur tout et rien. Merci à Oussema Souai, Théo Mozzanino, Hadrien Delattre, Jeffrey Cornault et Arnaud Briet d’avoir partagé des moments de rigolade avec moi. Merci à Olivier Son et Elisabeth Moncault de m’avoir aidé à réaliser les expériences en fin de thèse. Merci à Jihane Amarir‐Bouhram pour avoir ouvert le champ de recherche grâce à sa thèse, précédant la mienne. Enfin, merci à mon encadrante, Marie‐Agnès Petit, avec qui il n’a pas été toujours évident de se confronter mais qui, au final, m’a aidé et aiguillé au bon moment pour arriver aux résultats que vous allez lire. Merci à nos collaborateurs du CEA de Gif‐sur‐Yvette, l’équipe « Molecular assemblies and signaling », dirigée par Raphaël Guerois et Françoise Ochsenbein. Ils m’ont accueilli et appris à purifier des protéines. Merci à Nicolas Richet de m’avoir aidé à mettre au point ces purifications. Merci à Arthur Belse qui a fini de les mettre au point et qui purifiait les protéines pour moi. Merci au reste de l’équipe et au reste du bâtiment pour la bonne entente et la bonne ambiance. Je souhaite aussi remercier toute la troupe de théâtre du centre de Jouy‐en‐Josas : Abdel Boukadiri, Aline Viel, Annie Mathieu, Emmanelle Bourneuf, Deborah Jardet, Elisabetta Giuffra, Evelyne Lhoste, Olivier Telle, Setha Ketavong, Pierre‐Yves Holtzmann, Elodie Poumerol, Guillaume Piton, François 5 Deniau et surtout notre metteur en scène Jean‐Marc Mollines. Les séances du jeudi soir me permettaient vraiment de sortir de la thèse, et les pièces montées et jouées étaient vraiment divertissantes et enrichissantes. Merci à tous mes amis, qui m’ont littéralement supporté à plusieurs moments. Merci à Marc Descrimes, Cecile Pereira, Drago Haas, Kevin Verstraete pour les plus présents et merci à tous les autres, présents ponctuellement. Un grand merci surtout à Aurélien Lancien qui à su, coûte que coûte, me faire sourire à chaque instant de ma dernière année de thèse. Enfin, merci à mes parents, Johny et Véronique Hutinet, pour m’avoir mis au monde, aidé, tant sentimentalement que financièrement, et conseillé tout au long de ma vie. Je sais que je pourrai toujours compter sur eux si besoin. Merci au reste de ma famille qui croit en moi et me soutient en permanence pour que je puisse réaliser mes rêves et mes projets personnels. On a tous beaucoup d’attentes, dans la thèse comme dans la vie, mais finalement la thèse c’est comme la vie, on rame beaucoup et, à la fin, on te dit que tu as été génial. 6 Table of contents Chapter I: Introduction .......................................................................................................................... 13 I) Bacterial genomes ..................................................................................................................... 16 II) Bacteriophage genomes ............................................................................................................ 19 1) History and definition ............................................................................................................ 19 2) Genome organization ............................................................................................................ 21 3) Ways to exchanges genomes fragments ............................................................................... 23 III) Homologous recombination ...................................................................................................... 30 1) History and definition ............................................................................................................ 30 2) RecA ....................................................................................................................................... 33 3) Phage recombinases .............................................................................................................. 40 IV) All the questionings ................................................................................................................... 48 Chapter II: Rad52 recombinases and mosaicism ................................................................................... 49 Abstract ..............................................................................................................................................51 Introduction .......................................................................................................................................51 Results ................................................................................................................................................52 A recombination assay to measure formation of mosaics in phage λ ...........................................52 Mosaicism is produced by homologous recombination .................................................................54 Recombination genes involved in mosaism ....................................................................................55 Role of other phage encoded recombination promoting genes ....................................................55 Homologous recombination‐dependant gene shuffling also occurs with phage Φ80 ..................56 Like Redβ and RecTΦ80, ErfD3 and RecTRac recombinases are efficient on diverged sequences ...... 56 Genomic analysis reaveals abundant mosaics amond and between phage genomes ..................56 Discussion ........................................................................................................................................... 57 Mosaic formation is driven by Rad52‐like phage recombinases ....................................................57 Contribution of accessory proteins Orf and Rap to recombination ...............................................59
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