Etude Des Effets Des Hautes Pressions Hydrostatiques Sur Pyrococcus Yayanosii , Un Piézophile Extrême Par Une Approche Multi-« Omics »

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Etude Des Effets Des Hautes Pressions Hydrostatiques Sur Pyrococcus Yayanosii , Un Piézophile Extrême Par Une Approche Multi-« Omics » THÈSE / UNIVERSITÉ DE BRETAGNE OCCIDENTALE présentée par sous le sceau de l’Université européenne de Bret agne Grégoire Michoud pour obtenir le titre de DOCTEUR DE L’UNIVERSITÉ DE BRETAGNE OCCIDENTALE Préparée à l'Institut Universitaire Européen Mention : MICROBIOLOGIE de la Mer, au sein du laboratoire de École Doctorale des Sciences de la Mer Microbiologie des Environnements Extrêmes Etude des effets des Thèse soutenue le Lundi 7 Juillet 2014 devant le jury composé de : hautes pressions Jacques OBERTO RAPPORTEUR hydrostatiques sur Chargé de recherche, Université Paris Sud 11 , un Long-Fei WU RAPPORTEUR Pyrococcus yayanosii Directeur de recherche, Aix-Marseille Université piézophile extrême par une Philippe OGER EXAMINATEUR Chargé de recherche, ENS de Lyon approche multi-«omics» Vianney PICHEREAU PRESIDENTEXAMINATEUR Professeur, Université de Bretagne Occidentale Mohamed JEBBAR DIRECTEUR DE THESE Professeur, Université de Bretagne Occidentale La théorie, c’est quand on sait tout et que rien ne fonctionne. La pratique, c’est quand tout fonctionne et que personne ne sait pourquoi. Ici, nous avons réuni théorie et pratique : Rien ne fonctionne... et personne ne sait pourquoi ! Albert Einstein Combien sot, en e ffet, est le voyageur qui, remarquant d’agréables prairies sur son chemin, oublie d’aller où il voulait Anonyme iii REMERCIEMENTS Je tiens tout d’abord à remercier chaleureusement les membres du jury, Jacques Oberto, Long-Fei Wu, Philippe Oger, Vianney Pichereau et Mohamed Jebbar d’avoir accepté d’évaluer ma thèse. Je remercie Mohamed Jebbar, mon directeur de thèse de m’avoir encadré pendant cette thèse. Merci de m’avoir poussé à donner le meilleur de moi-même, en me laissant organiser mon travail comme je le souhaitais et en ayant toujours des idées qui permet- tait d’approfondir le sujet. Tu as fortement contribué à mon envie de poursuivre dans cette voie. Je remercie Pauline Vannier de m’avoir appris la base de la culture des Thermococcales , ainsi que la culture sous pressions, on aura bien galéré avec ces incubateurs mais on s’en est sorti finalement ! ! Merci à Mickael d’avoir entretenu et surtout réparé ces fameux incubateurs pressions sur lesquels j’aurai passé un certains temps. Merci aussi pour m’avoir donné un bon coup de main dans mes di fférentes manipulations notamment protéiques. Je voudrais remercier Stéphane, Stéphanie, Morgane, Alexandre, Nadège et Myriam sans qui le labo ne tournerait pas et qui tentent de contrôler la tendance au désordre inhérente aux stagiaires et doctorants. Un remerciement tout particulier à Stéphane pour son expertise notamment sur la culture de micro-organismes et pour avoir repris le flambeau du développement du bioréacteur. Merci à Yann Moalic et Lois Maignien pour leur expertise en bio-info et pour les discus- sions qui m’ont permis de mieux appréhender la partie analyse de cette thèse. Je remer- cie aussi les chercheurs du laboratoire, Karine Alain, Claire Geslin, Gwenaelle Le Blay, v Fréderique Duthoit et, Marc Le Romancer. Un salut particulier à Odile Vandenabeele- Trambouze, dont la jovialité dès le matin manque au laboratoire, en espérant que tu iras mieux très vite. Mes remerciements à la partie grenobloise de l’ANR Living Deep soit Bruno Franzetti, Vincent Marty et Judith Peters pour avoir tenter de m’expliquer les bases de la di ffusion neutronique malgré mes lacunes importantes dans ce domaine. Je remercie aussi la composante ifremer du laboratoire, notamment la directrice Anne Godfroy, les chercheurs Didier Flament, Ghislaine Henneke, Laurent To ffin, Marie-Anne Cambon-Bonavita ainsi que les thésards, Simon Le Bloa, Gaelle Hogrel, Sandrine Bes- sete. Un de mes regrets aura de ne pas avoir plus interagit avec vous. Je voudrais aussi remercier Jean-Luc Ferat et Guy-Franck Richard, mes anciens en- cadrants de stage de M1 et M2 qui ont façonné mon envie de faire de la microbiologie et de la génomique. Un salut à Jacques Daniel (oui je sais . .) pour ces discussions sur le métier de chercheur. Je souhaite remercier tout particulièrement les stagiaires et surtout doctorants du laboratoire, qui ont rendu cette thèse si agréables. Tout d’abord Julien, avec qui j’ai sympathisé dès le premier jour dans le bureau des stagiaires, et qui avait toujours la petite blague au bon moment. Merci de m’avoir fait découvrir Brest, enfin surtout les bars, ainsi que le whisky, je n’oublierais pas de sitôt ces discussions politiques avec Joonas et Fred jusqu’au bout de la nuit. Je remercie aussi Fred avec qui nous avions des discussions sur la bioinfo et qui n’avait pas son pareil pour lancer des sujets de philosophie dès le matin, je n’aurai qu’un petit reproche, c’est que tu sois un peu trop centriste pour moi. Je pense aussi à Joonas, le finlandais volant qui avait entre autre une belle culture cinématographique et un bon coup de bouteille (de bierre évidemment). Merci à Matthieu (avec deux T !) pour ses jeux de mots, son sens lyrique et sa bonne humeur. Merci aussi aux filles du bureau Coraline et Cécile d’apporter un peu de fraicheur et légèreté dans ce bureau très masculin. Ne t’inquiètes pas Cécile, ça va aller ! ! Je pense aussi aux stagiaires et post-docs notamment Samuel, Axel, Kevin, Sophia, Tiphaine et Gwendoline. Je remercie mes parents et mes frères pour ces petites discussions Skype du dimanche soir plus ou moins stables et plus ou moins compréhensibles lorsque le nombre de parti- cipants augmentaient. Je les remercie aussi pour ces voyages à quelques milliers de km qui étaient sans pareil pour se changer les idées. Je remercie aussi la partie bretonne de la famille Le Den que j’ai en quelque sorte redécouvert avec cette thèse à Brest. Un remerciement tout particulier à mes grands-parents qui m’ont souvent accueilli le di- manche pour des déjeuners parfois un peu arrosé et qui ont ainsi combatu ma tendance vi à l’isolement avec plus ou moins de succès, il faut bien le dire dire. J’espère que vous aller vous remettre très vite. Finalement, je voudrais remercier toutes les personne que j’ai oubliées, notamment mes anciens collègues du M2 et les gens que j’ai côtoyé dans les di fférents laboratoires par lequel je suis passé. vii TABLE DES MATIÈRES I Introduction 1 I.1 Les sources hydrothermales . 1 I.2 La pression hydrostatique . 5 I.3 La piézophilie . 6 I.4 Les micro-organismes piézophiles . 8 I.5 E ffets de la pression hydrostatique sur les composés cellulaires « fonda- mentaux » . 13 I.5.1 La membrane cellulaire . 13 I.5.2 Les protéines . 16 I.5.3 Le biais de codons . 17 I.5.4 Les acides nucléiques . 19 I.6 E ffets de la pression hydrostatique sur les composés cellulaires « complexes » 20 I.6.1 La mobilité . 22 I.6.2 La membrane : transport, respiration, protéines . 27 I.6.3 Induction d’une réponse générale de stress à la pression hydrosta- tique . 33 I.7 Les Thermococcales .............................. 36 I.7.1 Réplication, transcription, traduction . 37 I.7.2 Le métabolisme énergétique . 43 I.7.3 Les voies de biosynthèse . 49 I.7.4 Les transporteurs . 53 I.7.5 La mobilité . 55 I.7.6 L’immunité cellulaire : les CRISPR . 57 I.8 Contexte et objectifs . 58 II Matériel et méthodes 63 II.1 Culture de Thermococcales .......................... 63 II.1.1 Milieu de culture . 63 II.1.2 Culture en condition anaérobie . 64 ix Table des matières II.1.3 Culture sous pression hydrostatique . 64 II.1.4 Cinétique de croissances . 64 II.1.5 Observation en microscopie électronique à transmission . 65 II.2 Acides nucléiques . 66 II.2.1 Extraction d’ADN génomique . 66 II.2.2 Amplification par PCR . 66 II.2.3 Extraction d’ARN total . 67 II.2.4 Purification de l’ARN et vérification . 68 II.2.5 RT-PCR . 68 II.2.6 Migration sur gel . 69 II.2.7 Amorces utilisées . 69 II.2.8 Puces à ADN . 70 II.3 Protéines . 71 II.3.1 Extraction de protéines par la méthode de Lee .......... 71 II.3.2 Dosage des protéines . 72 II.3.3 Migration SDS-PAGE . 72 II.3.4 Analyses en LC-MS/MS « de novo » . 73 II.4 Analyse et comparaison génomique . 74 II.4.1 Analyse des gènes régulés par la pression hydrostatique . 74 III Comparaison de génomes 77 III.1 Analyses phylogéniques . 77 III.2 Physiologie . 81 III.3 Génomique . 81 III.4 CRISPR et CRISPRcas . 98 III.5 Transporteurs . 102 III.6 Métabolisme de l’hydrogène et du formate . 103 III.7 Conclusions . 106 IV Analyse transcriptomique et protéomique des e ffets des HPH 109 IV.1 Résultats généraux . 109 IV.2 Analyse de P. furiosus ............................118 IV.2.1 Mobilité . 118 IV.2.2 Transport . 121 IV.2.3 Traduction . 123 IV.3 Analyse de P. yayanosii ...........................124 IV.3.1 Chimiotactisme . 124 IV.3.2 Tranports . 125 IV.3.3 Traduction . 127 IV.3.4 Respiration et métabolisme énergétique . 129 IV.3.5 CRISPR- cas ..............................134 IV.3.6 ARN non codants . 138 IV.3.7 Régulation diverses . 140 x Table des matières V Discussion générale et conclusion 145 VI Annexes 155 VI.1 Michoud et Jebbar (2014)......................... 155 VI.2 Peters et al. (2014)............................. 190 VI.3 Thiel et al. (2014).............................. 203 Bibliographie 213 xi TABLE DES FIGURES I.1 Coupe schématique de la biosphère profonde . 2 I.2 Localisation des sources hydrothermales . 4 I.3 Croissance de souches piézosensibles, piézotolérantes, piézophiles et piézo- philes strictes . 8 I.4 Adapation des lipides archéens aux conditions environnementales chez M. jannaschii...................................... 15 I.5 Structure des appareils de mobilité bactériennes et archéennes . 23 I.6 Schéma simplifié de la voie du chimiotactisme chez les Bacteria et le phylum archéen des Euryarchaeota ...........................
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