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Thèse Version À Diffuser UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE IGBMC – IGFL – ENS de Lyon THÈSE présentée par Eric SAMARUT soutenue le 16 décembre 2013 pour obtenir le grade de Docteur de l’université de Strasbourg Sciences du Vivant – Aspects Moléculaires et Cellulaires de La Biologie ETUDE FONCTIONNELLE ET EVOLUTIVE DE LA VOIE DE L’ACIDE RETINOIQUE ET DE LA PHOSPHORYLATION DES RECEPTEURS CHEZ LE POISSON ZEBRE Soutenance publique devant le jury composé de DIRECTEURS DE THESE Dr Cécile Rochette-Egly (Université de Strasbourg) Pr Vincent Laudet (ENS de Lyon) RAPPORTEURS Denis Duboule (Ecole Polytechnique Fédérale de Lausanne) Frédéric Michon (University of Helsinki) EXAMINATEUR Julien Vermot (Université de Strasbourg) ii A mes poissons morts pour la Science, A Maurice Star, iii Remerciements Bien évidemment, je tiens en tout premier lieu à remercier mes deux directeurs de thèse avec qui cela a toujours été un plaisir de discuter science, de confronter des idées, et d’imaginer la suite. Cette codirection a été une très bonne balance de « liberté cadrée » entre accompagnement et autonomie, suivi et confiance, choucroute et gratin dauphinois ! Merci au dynamisme et à la réactivité de Cécile, merci à la souplesse et à la confiance de Vincent. Cette codirection a aussi été l’occasion pour moi de découvrir Strasbourg et l’IGBMC. Je ne serai jamais assez reconnaissant de l’accueil qui m’a été réservé à mon arrivée au laboratoire. Un merci particulier à la dinde Christine et au grand steak Sébastien pour leurs conseils techniques, leurs recommandations culinaires et leur bonne-humeur. J’ai passé une première année très agréable au sein de l’équipe aux côtés de Régis, Vanessa, Nathalie, Aleksandr et Gabi. Un grand merci à Lady Samia et Ziad avec qui j’ai passé une grande partie de ma seconde année strasbourgeoise. Les pauses cafés (p’tit caf ?) sur des fonds de discussions plus ou moins scientifiques, les soirées arrosées au Barco Latino et au Seven me resteront en souvenir ! Je remercie également les Vermot et particulièrement Emilie et Stéphane pour m’avoir fourni en poissons et m’avoir fait une petite place à l’animalerie ! Merci aussi à tous les membres des services communs de l’IGBMC dont Mustapha et ses anticorps, Betty et ses cellules, Pascal et ses peptides et plus particulièrement La Blonde et ses vacances (Dear everyone…). Après deux ans passés au grand Nord, c’est le retour sur Lyon. Merci au bureau de m’avoir fait une place et de m’avoir accueilli au sein de leurs délires de chef ligoté et autres élans déchaînés ! J’ai pris un plaisir tout particulier à parler le vieux avec Florent ou encore réapprendre l’espagnol avec Juli avec quelques verres dans le nez ! Un immense merci à Laure le pétoncle, la sirène de l’animalerie, la poissonnière de l’IGFL pour sa gentillesse, sa compréhension, sa naïveté et les passe-droits qu’elle a pu m’accorder ! Un merci tout particulier à Cyril le crazy dude qui m’a été d’une RAR inspiration ! Grâce à lui, je sais que iv mon Mac peut parler, et ce fût un plaisir de passer une grande partie de mon temps au sein de l’équipe GOSAM©…je reste optimiste pour qu’elle se monte un jour dans un labo junior inoccupé! Le déménagement dans le nouvel IGFL a été l’occasion de nouveaux rapprochements, en particulier avec les Volfettes, ex-réfugiées du froid sous-sol. Merci à Domi et sa douceur à toute épreuve ainsi qu’à Dédé, son rire ravageur et sa gentillesse authentique! J’ai beaucoup apprécié les moments en votre compagnie au sein de la DreamTeam avec Roro le puriste et les membres de l’équipe Aïe-Troudp(o)ut’ ! Sandrine, merci d’avoir toujours modéré nos propos masculins, Benj et Romain, merci de toujours les enrichir de nouvelles données (quoi ? un hareng géant ?). Merci également pour cet engouement sportif dans lequel vous avez réussi à m’enliser ! Je souhaite remercier la sympathie et l’aide de nombreuses autres personnes au sein de l’équipe mais aussi des équipes environnantes. En particulier, merci à Marie qui a aidé SamSam dans l’analyse de ses données. Je remercie les Viriot (Manu et al..), les Samarut (Damien, Karine et al.), les Mérabet (Marilyne, Manon et al.), les Flamant (Fabrice et al.), les Vanacker (Violaine et al.), les Volff (Fred, Emilien, Magalie et al.) et les Ruggiero (Elise et al.). Un immense merci à nos chefs financières qui sont Sonia et Fabienne : merci d’avoir accepté avec gentillesse et bonne humeur mes demandes d’achat improbables entre grillage anti-moustique pour fabriquer des pondoirs, à des lots de poissons exotiques dont même le CNRS doutait de leur utilisation à des fins scientifiques ! Enfin, je souhaite remercier mes amis et proches pour m’avoir soutenu et pour être encore aux côtés d’un fou qui travaille sur… …des poissons-zèbres ! Merci à mes parents de m’avoir initié à la science dès mon plus jeune âge en observant le développement d’œufs de grenouille pêchés dans une marre autour de Saint-Christophe, à Sylvain pour m’avoir donné le goût de l’aquariophilie et à Camille qui s’intéresse à mon travail en ressassant des vieux mots de TP de S.V.T ! v Merci aux belles-sœurs et beaux-frères de tous horizons (Marion, Marlène, Chloé, Marine, Arthur, Tiébo) ainsi qu’à ma nouvellement belle-famille Dufour qui se sont toujours interrogés sur le pourquoi du comment je travaille sur le poisson- zèbre. Un merci tout particulier à ma femme Liselotte qui m’a supporté dans les durs moments de désespoir de la thèse et pour sa relecture attentive de ce manuscrit ! Nous aurons finalement réussi à combiner avec brio un mariage, une thèse et un départ prochain dans les grands froids canadiens ! Merci pour ton enthousiasme et pour m’avoir toujours soutenu et suivi dans ces projets d’éloignements géographiques ! Merci également à mes amis, les futurs Enderlin, Alcaras, Galopin, Sanchiz et Brunon pour leur présence et pour s’être toujours intéressés de près ou de loin à ce que je pouvais bien « rechercher »… Un grand merci à JazzRadio reprise, à ChromaRadio, à Illy, à Coca-Cola Zéro et à Dinausorus, qui m’ont soutenu au sens propre du terme tout au long de cette rédaction ! Pour finir, je remercie par avance tous ceux que j’aurais pu oublier, dans la précipitation du dernier jour de rédaction, de m’excuser de cette étourderie ! vi Publications Samarut E, Fraher D, Laudet V, Gibert Y. (2014) zebRA : an overview of retinoic acid effects during zebrafish development. Soumis, Biochim Biophys Acta……………………….......page 66 Samarut E*, Gaudin C*, Hughes S, Gillet B, De Bernard S, Jouve P.E, Buffat L, Alliot A, Lecompte O, Rochette-Egly C, Laudet V. (2013) RAR-subtype specific transcriptotypes in early zebrafish embryos. Soumis, Mol Endo. ……………………………………….................page 93 Samarut E*, Gibert Y*, Pasco-Viel E, Bernard L, Schulte-Merker S, Labbe C, Viriot L, Laudet V. (2013) Retinoic acid controls tooth morphology and number in Cypriniformes. Soumis, Cell reports.....................................................................................................................................page 177 Tohmé M, Prud’homme S.M, Boulahtouf A, Samarut E, Brunet F, Bernard L, Gibert Y, Balaguer, P and Laudet V. (2013) ERRγ is an in vivo receptor of bisphenol A. En révision, FASEB J. Seritrakul P, Samarut E, Lama TT, Gibert Y, Laudet V, Jackman WR. (2012) Retinoic acid expands the evolutionarily reduced dentition of zebrafish. FASEB J. 26(12):5014- 24………………………………………………………………………………………………………page 166 Samarut E, Rochette-Egly C. (2012) Nuclear retinoic acid receptors: Conductors of the retinoic acid symphony during development. Mol Cell Endocrinol. 348(2):348-60…….page 52 Ferry C, Gaouar S, Fischer B, Boeglin M, Paul N, Samarut E, Piskunov A, Pankotai-Bodo G, Brino L, and Rochette-Egly C. (2011) Cullin 3 mediates SRC-3 ubiquitination and degradation to control the retinoic acid response. PNAS 108(51):20603-8. ........................................page 221 Lalevée S, Anno Y. N, Chatagnon A, Samarut E, Poch O, Laudet V, Benoit G, Lecompte O and Rochette-Egly C. (2011) Genome-wide in silico identification of conserved and functional DR5 retinoic acid receptors response elements. J Biol Chem. 286(38):33322- 34. ...........................................................................................................................................page 207 Samarut E, Amal I, Markov GV, Stote R, Dejaegere A, Laudet V, Rochette-Egly C. (2011) Evolution of nuclear retinoic acid receptor alpha phosphorylation sites. Serine gain provides fine-tuned regulation. Mol Biol Evol. 28(7):2125-37. .........................................................page 142 Grijota-Martínez C, Samarut E, Scanlan TS, Morte B, Bernal J. (2011) In vivo activity of the thyroid hormone receptor beta- and _-selective agonists GC-24 and CO23 on rat liver, heart, and brain. Endocrinology 152(3):1136-42. Lalevée S, Bour G, Quinternet M, Samarut E, Kessler P, Vitorino M, Bruck N, Delsuc MA, Vonesch JL, Kieffer B, Rochette-Egly C. (2010) Vinexinß, an atypical "sensor" of retinoic acid receptor gamma signaling:union and sequestration, separation, and phosphorylation. FASEB J. 24(11):4523-34. ..................................................................................................................page 195 vii Introduction – Etat de l’Art ............................. 1 A. ASPECTS MOLECULAIRES DE LA VOIE DE L’ACIDE RETINOIQUE ..... 2 I. METABOLISME DE L’ACIDE RETINOIQUE ....................................................................... 2 II. RAR et RXR: UNE STRUCTURE MODULAIRE ..................................................................
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