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Phylogénie Et Évolution Du Genre Frankia Imen Nouioui

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Phylogénie Et Évolution Du Genre Frankia Imen Nouioui Phylogénie et évolution du genre Frankia Imen Nouioui To cite this version: Imen Nouioui. Phylogénie et évolution du genre Frankia. Biologie végétale. Université Claude Bernard - Lyon I, 2014. Français. NNT : 2014LYO10087. tel-01089349 HAL Id: tel-01089349 https://tel.archives-ouvertes.fr/tel-01089349 Submitted on 1 Dec 2014 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. N° d’ordre 87 – 2014 Année 2014 THÈSE DE L’UNIVERSITE DE LYON Délivrée par L’UNIVERSITE CLAUDE BERNARD LYON 1 ECOLE DOCTORALE : Evolution Ecosystèmes Microbiologie Modélisation DIPLOME DE DOCTORAT (arrêté du 7 Août 2006) Soutenue publiquement le 23 juin 2014 par Melle Imen NOUIOUI Phylogénie et Évolution du genre Frankia Directeurs de thèse : Maria P. FERNANDEZ & Maher GTARI Jury : M. Abdellatif Boudabous Professeur à l’Université Tunis El Manar Président M. Ridha Mhamdi Professeur au Centre de Biotechnologie de Borj Cédria Rapporteur M. Sergio Svistoonoff Chargé de recherche à l’IRD, Montpellier Rapporteur M. Maher Gtari Professeur à l’Université de Carthage Examinateur Mme. Maria P. Fernandez Professeur à l’Université Lyon 1 Examinateur M. Philippe Normand Directeur de Recherche CNRS à l’Université Lyon 1 Examinateur Dédicaces Je tiens à dédier ce travail : A mes parents Qui m’ont permis de faire les études et qui m’ont toujours soutenue moralement et financièrement Qu’ils trouvent ici le témoignage de ma grande affection et mon éternelle reconnaissance pour leur soutien constant, leur dévouement et leur confiance, Je leurs dois ce que je suis aujourd’hui et ce que je serai demain A mes sœurs et mes frères Pour leurs encouragements tout au long de ces années et pour tous nos bons moments passés ensemble et pour les liens solides qui nous unissent. A toute la famille NOUIOUI et GUEHIOUECHE Enfin à tous ceux qui m’ont aidé à devenir ce que je suis. REMERCIEMENT Ce travail de thèse a été réalisé en cotutelle au sein du Laboratoire Microorganismes et Biomolécules Actives de la Faculté des Sciences de Tunis (LMBA-FST), Université Tunis El Manar et le Laboratoire d’Ecologie Microbienne UMR557 CNRS, à la Faculté des Sciences et Technologies à Lyon, Université Claude Bernard Lyon1, France. J’exprime ici ma profonde reconnaissance à toutes les personnes qui m’ont guidée et soutenue avec amabilité tout au long de ce travail. Je n’oublierai pas de remercier très cordialement les responsables de la coopération universitaire franco-tunisienne aussi bien au niveau du ministère de l’enseignement supérieur et de la recherche scientifique à Tunis qu’au niveau de l’Institut Français de Coopération pour avoir financier mes séjours à Lyon durant mon parcours de thèse. Je tiens tout d'abord à remercier trois personnes : Monsieur Abdellatif Boudabous, Professeur à la Faculté des Sciences Tunis et directeur du Laboratoire Microorganismes et Biomolécules Actives (MBA), Monsieur Philippe Normand, Directeur de recherche CNRS à l'Université Lyon 1 et Monsieur Yvan Moënne-Loccoz, directeurde l’UMR CNRS 5557 d’Ecologie Microbienne, de m'avoir accueillir dans leur équipe de recherche. Qu’ils trouvent ici l'expression de ma reconnaissance et de mon profond respect. Je suis profondément reconnaissante à Monsieur Maher Gtari, Professeur à l’Institut Nationale des Sciences Appliquées et de Technologie et directeur de cette thèse, pour m’avoir plus qu’aidée et soutenue au-delà de toute espérance tout au long de mon travail, depuis mon mastère. Merci de m’avoir fait confiance dès le début. Grâce à vous j’ai appris à aimer ce métier. Merci pour vos conseils judicieux, vos qualités humaines et vos encouragements qui m’ont permis de conduire ce travail jusqu’à son terme. Que vous trouviez ici toute l’expression de mes remerciements et de mon profond respect. Mes sincères remerciements à Madame Maria P. Fernandez, Professeur à l’Université Lyon 1, d’avoir acceptée de co-diriger ce travail, de m’avoir toujours soutenue et de m’avoir fait partagée ses nombreuses connaissances. Je remercie vivement Monsieur Abdellatif Boudabous, Professeur à la Faculté des Sciences de Tunis d'avoir accepté de présider le jury d'évaluation. Toute ma reconnaissance va également à Monsieur Ridha Mhamdi, Professeur au Centre de Biotechnologie de Borj Cédria (CBBC) à Tunis et Monsieur Sergio Svistoonoff, chargé de recherche à l’IRD de Montpelier, rapporteurs de cette thèse, pour leurs conseils précieux. Qu'ils trouvent ici le témoignage de mes sincères remerciements. J’adresse aussi mes vifs remerciements à Monsieur Philippe Normand, Directeur de recherche CNRS à l'Université Lyon 1, d’avoir accepté de juger ce travail. Mes plus vifs remerciements à Mr Atef Jaouani, Mr Ameur Chérif, Mme Imen Ouzari, Mr Karim Ben Slama, Mr. Skander Gharbi et Mme Naouel Klibi du laboratoire de Microorganismes et Biomolécules Actives de Tunis (LMBA) pour leur sympathie et leur soutien. Je remercie également tous mes collègues et les techniciens (es) de LMBA de Tunis sans exception pour la belle ambiance du laboratoire qui restera gravée dans ma mémoire. J'adresse aussi mes remerciements à tous les membres du laboratoire d’Ecologie Microbienne UMR5557 à Lyon sans exception et plus particulièrement à tous mes compagnons de l’équipe symbiose actinorhizienne pour les discussions fructueuses que j’ai eu avec eux durant mes séjours à Lyon et l’ambiance chaleureuse assez particulière. Un grand Merci à Faten, Imen, Imed, Haithem, Mohamed, Olfa, Lorena, Adrien, Aude, Laetitia, Hugo, Hasna, Clément et Pierre pour leur soutien et pour tous les moments de franche insouciance. Enfin je remercie tous ceux qui ont collaboré de près ou de loin à l’élaboration de cette thèse. Qu’ils trouvent tous les termes de remerciement et de gratitude. Ce travail a été financé dans le cadre de programme PHC-Utique CMCU n°09G0916. Sommaire Résumé........................................................................................................................................1 Abstract.......................................................................................................................................2 Liste des figures..........................................................................................................................3 Liste des tableaux........................................................................................................................4 Abréviations................................................................................................................................5 Introduction générale...............................................................................................................6 I. Le genre Frankia.................................................................................................................7 1. Taxonomie du genre Frankia..............................................................................7 2. Plante hôte...........................................................................................................8 3. Morphologie........................................................................................................9 4. Physiologie........................................................................................................11 5. Chimiotaxonomie..............................................................................................13 6. Génétique et génomique....................................................................................14 6.1. Hybridation ADN/ADN.............................................................................15 6.2. Phylogénie moléculaire..............................................................................18 6.2.1. Gènes ribosomiques.....................................................................19 6.2.2. Gènes de la nitrogénase...............................................................21 6.2.3. Gènes de la glutamine synthétase................................................23 II. Intérêt du genre Frankia.................................................................................................23 1. Fixation symbiotique de l’azote........................................................................23 2. Métabolites et activités enzymatiques...............................................................25 Matériel et méthodes I. Origine, culture et conservation des souches de Frankia.................................................27 II. Origine des nodules de Coriaria utilisés.........................................................................27 III. Piégeage..........................................................................................................................27 IV. Manipulation de l’ADN.................................................................................................28 1. Extraction d’ADN génomique à partir des souches de Frankia......................28 2. Extraction d’ADN à partir des nodules............................................................28 3. Dosage d’ADN.................................................................................................29
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