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Study of the Interactome of UPF1, a Key Factor of Nonsense-Mediated Decay in Arabidopsis Thaliana Clara Chicois

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Study of the Interactome of UPF1, a Key Factor of Nonsense-Mediated Decay in Arabidopsis Thaliana Clara Chicois Study of the interactome of UPF1, a key factor of Nonsense-mediated decay in Arabidopsis thaliana Clara Chicois To cite this version: Clara Chicois. Study of the interactome of UPF1, a key factor of Nonsense-mediated decay in Arabidopsis thaliana. Molecular biology. Université de Strasbourg, 2018. English. NNT : 2018STRAJ005. tel-02918112 HAL Id: tel-02918112 https://tel.archives-ouvertes.fr/tel-02918112 Submitted on 20 Aug 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. UNIVERSIT ! DE!STRASBOURG! COLE!DOCTORALE!DES!SCIENCES!DE!LA!VIE!ET!DE!LA!SANT ! Institut!de!Biologie!Mol"culaire!des!Plantes! –!CNRS! –!UPR2357!! TH#SE!DE!DOCTORAT! !!pr!sent!e par : Clara!CHICOIS! ! ! ! pour obtenir le grade de : Docteur de l’universit! de!Strasbourg Discipline: Sciences de la Vie et de la Sant! Sp!cialit! : Aspects Mol!culaires et Cellulaires de la Biologie Study!of!the!interactome!of!UPF1,!a!key!factor!of! Nonsense-Mediated!Decay!in! Arabidopsis thaliana ! ! ! ! ! ! ! Th"se soutenue le 31 janvier 2018 devant la Commission d’Examen : ! Dr!BOUSQUET-ANTONELLI!C"cile! (CNRS, Universit! de Perpignan) Rapporteur externe Dr!WACHTER!Andreas (Universit! de T#bingen) Rapporteur externe Dr!PFEFFER!S"bastien! ! (CNRS, Universit! de Strasbourg) Examinateur interne Dr!GARCIA!Damien (CNRS, Universit! de Strasbourg) Directeur de th"se Acknowledgments / Remerciements Firstly, I would like to thank the members of the jury C!cile Bousquet-Antonelli, Andreas Wachter and S!bastien Pfeffer for having accepted to evaluate my thesis work. Je souhaite remercier mon directeur de th"se, Damien Garcia pour sa patience et sa pr!sence au cours de ces trois ann!es de th"se. Je remercie !galement Shahinez qui m’a beaucoup appris, pour son soutien ind!fectible et sa bonne humeur. Merci aux membres de mon ancienne !quipe d’accueil, Marco, Thomas, Yerim, Fabrice et Pat ; ainsi que Lucie et R!jane pour leur travail fourni. Je remercie aussi l’!quipe D!gradation des ARNs, notamment Caroline, Marl"ne et H!l"ne S. pour leur aide, leur disponibilit! ainsi que pour nos moments partag!s. Je remercie !galement H!l"ne Z., Heike et Gag pour leurs pr!cieux conseils. J’aimerais !galement remercier les diff!rentes plateformes de l’IBMP, Malek et Sandrine de la plateforme de s!quen"age, J!rome # la plateforme d’imagerie , Mich"le de la laverie mais !galement toute la plateforme de production de plantes, pour avoir pris soin de mes plantes pendant toutes ces ann!es . Je remercie !galement les membres de l’IBMP qui m’ont aid! au cours de ma th"se, par leur mise # disposition de mat!riel et leurs conseils. Enfin, j ’aimerais aussi remercier Laure pour son soutien moral et nos d!couvertes culinaires. $videmment , j’aimerais remercier ma famille et mes amis de m’avoir soutenue , !paul!e et encourag!e pendant toutes ces ann!es. Encore hier je vais … 1 Abbreviation list AD Activation domain Ade Adenine BD Binding domain bp Base pair CaCl 2 Calcium chloride Ci Curie cDNA Complementary DNA Ct Cycle threshold D Aspartic acid DAI Days after infiltration DCP Decapping DNA Desoxyribonucleic Acid dATP Desoxyadenosine triphosphate dCTP Desoxycytidine triphosphate dGTP Desoxyguanine triphosphate dNTP Desoxynucleotide triphosphate DTT Dithiolthreitol dTTP Desoxythymidine triphosphate EDTA Ethylenediaminetetra-acetic acid EGTA ethylene glycol- bis(• -aminoethyl ether)-N,N,N',N'-tetraacetic acid FC Fold change g Centrifuge acceleration GFP Green Fluorescent Protein h Hour HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid His Histidine IP Immunoprecipitation L Liter LB Lysogeny Broth LiAc Lithium acetate Leu Leucine mA Milliampere MgSO 4 Magnesium sulfate min Minute mJ Millijoules mRNA Messenger RNA MS Murashige & Skoog N Alanine NaCl Sodium chloride ng Nanogram 2 nm Nanometer NMD Nonsense Mediated Decay Nt Nucleotide ORF Open Reading Frame PEG Polyethylene Glycol PCR Polymerase Chain Reaction PVX Potato Virus X qPCR Quantitative PCR RFP Red Fluorescent Protein RNA Ribonucleic Acid rpm Rotation per minute RT Reverse transcription SDS Sodium Dodecyl Sulfate Sec Second SSC Sodium saline citrate TBS Tris-buffered saline TE Tris EDTA TCV Turnip Crinkle Virus Trp Tryptophane TuMV Turnip Mosaic Virus UCN UFP1 Co-purified Nuclease UPF1 Up frameshift UV Ultra-violet V Volt v/v Volume/volume XRN Exoribonuclease w/v Weight/volume 3 Table of contents Introduction ................................................................................................................................... 10 I. General mRNA degradation ............................................................................................................... 12 1. Degrada tion pathway from 3’ to 5’ ................................................................................................. 13 1.1. Deadenylation ......................................................................................................................... 13 1.2. mRNA uridylation .................................................................................................................... 14 1.3. 3’ -5’ exoribonucleolytic decay ................................................................................................ 14 2. Degradation pathway from 5’ to 3’ ................................................................................................. 15 2.1. Decapping ............................................................................................................................... 15 2.2. 5’ to 3’ exoribonucleolytic decay ............................................................................................ 15 3. Endoribonucleolytic decay .............................................................................................................. 16 4. Processing-bodies, at the crossroad between mRNA decay, storage and translation ................... 16 4.1. Processing-body composition ................................................................................................. 16 4.2. Processing-body functions ...................................................................................................... 17 4.3. The central role of the P-body factor Dhh1/DDX6 in translation repression ......................... 18 4.4. Other key factors involved in translation repression.............................................................. 18 4.5. Processing-bodies are highly dynamic structures ................................................................... 19 II. Nonsense-mediated decay ................................................................................................................. 19 The quality control of translation ........................................................................................................... 19 1. Biological roles of NMD ................................................................................................................... 21 2. NMD-inducing features ................................................................................................................... 21 3. Mechanistic models of NMD ........................................................................................................... 22 3.1. EJC-mediated NMD ................................................................................................................. 22 3.2. The faux 3’ -UTR model ............................................................................................................ 23 3.3. A new unifying NMD model: the ribosome release model..................................................... 24 4. Special features of NMD in plants .................................................................................................. 24 5. NMD in the fine-tuning of gene expression .................................................................................... 25 5.1. Alternative splicing coupled-NMD .......................................................................................... 26 5.2. Sequence-dependent NMD inhibition .................................................................................... 26 6. NMD functions in host-pathogen interactions ............................................................................... 27 6.1. NMD and viruses ..................................................................................................................... 27 6.2. NMD orchestrates plant antibacterial defense ...................................................................... 29 4 III. The Up Frameshift 1 (UPF1) protein .............................................................................................. 29 1. The UPF1 interactome .................................................................................................................... 30 2. UPF1 localization ............................................................................................................................. 32 3. UPF1-dependent but NMD-independent pathways ....................................................................... 32 3.1. UPF1-mediated
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