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Functional Studies of New Protein-Protein Interactions Potentially Involved in Homologous Recombination in Hyperthermophilic Archaea

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Functional Studies of New Protein-Protein Interactions Potentially Involved in Homologous Recombination in Hyperthermophilic Archaea THESE DE DOCTORAT DE L'UNIVERSITE DE BRETAGNE OCCIDENTALE COMUE UNIVERSITE BRETAGNE LOIRE ECOLE DOCTORALE N° 598 Sciences de la Mer et du littoral Spécialité : Microbiologie Par Yang LU Functional studies of new protein-protein interactions potentially involved in homologous recombination in hyperthermophilic archaea. Study of interactions between PCNA and Mre11-Rad50 complex & Primase and RadA Thèse présentée et soutenue à Brest, le 30 novembre 2018 Unité de recherche : Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), UMR6197, Ifremer, CNRS, UBO Rapporteurs avant soutenance : Composition du Jury : Bruno FRANZETTI Directeur de recherche, IBS, Grenoble Président du Jury Marc BLONDEL Professeur, UBO, Brest Tamara BASTA-LE BERRE Maître de conférences, I2BC, Paris Bruno FRANZETTI Directeur de recherche, IBS, Grenoble Tamara BASTA-LE BERRE Maître de conférences, I2BC, Paris Directeur de thèse Didier FLAMENT Chercheur, LMEE/Ifremer/UBO, Brest Invité(s) Mohamed JEBBAR Professeur, LM2E/UBO, Brest Acknowledgement Firstly, I would like to express my sincere gratitude to my advisor Didier FLAMENT for the continuous support of my Ph.D study and related research, to thank him for his patience, motivation, and immense knowledge. His guidance helped me all throughout my research and my writing of this thesis. I could not have imagined a better advisor and mentor to have for my Ph.D study. Besides my advisor, I would like to thank the other members of my thesis jury: Bruno FRANZETTI, Tamara BASTA-LE BERRE and Mohamed JEBBAR, special thanks for Marc BLONDEL for my thesis committee and my thesis jury, their insightful comments and encouragement, but also for the hard question which drove me to widen my research to various perspectives. Also thanks to another member of my thesis committee, Charlotte CORPOREAU. I would like to express my gratitude to all of the staff of laboratory LMEE for the last minute favors. I am also grateful to Ifremer and Region de Bretagne for their financial support until the end of this thesis, and Elisabeth Bondu and Frédéric Jean of the EDSML for their administrative supports during these three years of thesis. My sincere thanks also go to my “replication team”, who provided me with an opportunity to join their team as an intern, and who gave access to the laboratory and research facilities. Ghislaine, my internship supervisor of Master 2, thanks to her help and scientific guidelines, I opened the door of Archaeal World. I would like to thank Audrey BOSSE, who always gave me technical and moral support when I needed it. I would also like to thank Etienne, Sebastien, Remi, who gave me lots of valuable tips on their professional technics such as FRET, SPR and Genetic transformation in vivo, to realize different experiments in order to accomplish my research project. I would also like to thank Gaëlle, my important labmate, thanks for all the stimulating discussions, for the days we worked together, for all the helps before deadlines. Without their precious support it would not be possible to conduct this research. I would also like to thank my intern, Damien HUBERDEAU, who helped me to push my research forward. Also I’m grateful to group members from Clouet d’Orval group (LMGM, Toulouse) for all the help of several experimentations. I am grateful to our secretaries, Christine and Christel, you were always there when I needed to process documents required for administration. Thank you also for all the organization for lab. A super big thanks goes to all the past and present members of LMEE. In particular, I am grateful to Melanie and Charlene, we started as “office-mates” and finished as “family”, all of the precious memories and your support have been essential throughout these years. Thanks to Marion, thank you to have encouraged and supported me every time when I felt stressed out. A special thanks to my friends and colleagues, Sebastien, Simon, Caroline, Jordan, Sarah, Florian, Clarisse, Marc, Blandine, Johanne, Thomas, Dingding, Huan, Manman, thank you to have been with me in the most important moments of all lab’s life and outside the lab. Last but not the least, I would like to thank my family: first, my husband, Francis, thank you for standing up for me and supporting me during all these years, to my parents, my grandparents, and my in-laws, Didier and Sylvie, for supporting me spiritually throughout writing this thesis and my life in general. Table of contents INTRODUCTION .............................................................................................................................................. 1 I. HYPERTHERMOPHILIC ARCHAEA (HA) ......................................................................................................................... 2 1) Extremophiles .................................................................................................................................................... 2 2) Hyperthermophiles ............................................................................................................................................ 5 3) Archaea ............................................................................................................................................................. 9 II. GENOMIC INTEGRITY MAINTENANCE IN HA ............................................................................................................... 12 1) DNA replication and repair .............................................................................................................................. 12 2) Biological role of homologous recomBination in the repair of DNA ................................................................ 17 a) Heat stress-induced DNA douBle-strand Breaks (DSBs) ..................................................................................................... 17 b) DNA repair .......................................................................................................................................................................... 21 3) Biological role of homologous recomBination in DNA replication ................................................................... 25 a) Replication restart after Fork arrest ................................................................................................................................... 25 b) RecomBination-dependent replication (RDR) ..................................................................................................................... 28 III. PROTEINS INTERACTION NETWORK IN GENOME MAINTENANCE IN HA ............................................................................. 30 CHAPTER 1: PCNA & MRE11-RAD50 .............................................................................................................. 33 I. PRESENTATION OF STUDIED PROTEINS ...................................................................................................................... 34 1) PCNA ............................................................................................................................................................... 34 a) “Clamp-loaders” in all three domains of life ....................................................................................................................... 34 b) “Dancer” With many partners ............................................................................................................................................. 37 2) Mre11-rad50 complex ..................................................................................................................................... 43 a) Conserved in all three domains of life and virus ................................................................................................................. 43 b) Structural analysis of the Mre11-rad50 complex ................................................................................................................ 44 c) Biochemical in vitro activities of Mre11-rad50 complex .................................................................................................... 56 d) Third component of the MR complex in eukaryote ............................................................................................................ 59 e) The Mre11-rad50 complex in douBle-strand Break repair and replication fork ................................................................. 60 f) Diseases linked With mutations in Mre11-rad50 ................................................................................................................ 64 3) Aim .................................................................................................................................................................. 65 II. ARTICLE .............................................................................................................................................................. 67 III. SUPPLEMENTARY STUDY: GENETIC STUDY IN VIVO ....................................................................................................... 90 1) Context ............................................................................................................................................................ 90 2) Materials & methods ....................................................................................................................................... 92 a) Strains and GroWth media .................................................................................................................................................
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