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Comparative Study of the Proteome of S. Coelicolor M145 and S

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Comparative Study of the Proteome of S. Coelicolor M145 and S Comparative study of the proteome of S. coelicolor M145 and S. lividans TK24, two phylogenetically closely related strains with very different abilities to accumulate TAG and produce antibiotics Aaron Millan Oropeza To cite this version: Aaron Millan Oropeza. Comparative study of the proteome of S. coelicolor M145 and S. lividans TK24, two phylogenetically closely related strains with very different abilities to accumulate TAG and produce antibiotics. Genomics [q-bio.GN]. Université Paris Saclay (COmUE), 2017. English. NNT : 2017SACLS160. tel-01782398v2 HAL Id: tel-01782398 https://tel.archives-ouvertes.fr/tel-01782398v2 Submitted on 14 May 2018 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. NNT : 2017SACLS160 THESE DE DOCTORAT DE L‟UNIVERSITE PARIS-SACLAY PREPAREE A L‟UNIVERSITE PARIS-SUD ECOLE DOCTORALE N° 581 Agriculture, alimentation, biologie, environnement et santé (ABIES) Spécialité de doctorat : Microbiologie Par M. Aarón Millán Oropeza Comparative study of the proteome of S. coelicolor M145 and S. lividans TK24, two phylogenetically closely related strains with very different abilities to accumulate TAG and produce antibiotics Thèse présentée et soutenue à Orsay, le 23 juin 2017 : Composition du Jury : Mme Fabienne Malagnac Prof. Université Paris-Saclay Présidente M. Sébastien Rigali Prof. Université de Liège Rapporteur M. Bertrand Aigle Prof. Université de Lorraine Rapporteur Mme Warren Albertin MCF. ENSCP de Bordeaux Examinatrice M. Ivan Mijakovic Prof. Chalmers University of Technology Examinateur Mme Marie-Jöelle Virolle DR. Université Paris-Saclay Directrice de thèse Mme Céline Henry IE. Université Paris-Saclay- INRA Co-encadrante de thèse i Dedicated to our little angel Ian ii ACKNOWLEDGMENTS Je tiens à remercier à la France pour m‟avoir accueilli pendant ma formation Doctorale dans un environnement international et unique, c‟était une toute première expérience à l‟étranger très enrichissante. Également je remercie à CONACyT et à l‟Ambassade de France au Mexique pour le support économique tout au long de mes études à l‟Université Paris-Sud. J‟exprime ma gratitude aux membres du jury qui m‟ont fait l‟honneur de juger ce travail de thèse ainsi pour les échanges très enrichissantes lors de ma soutenance que je n‟oublierai jamais. Je suis très reconnaissant à ma directrice de thèse Marie-Jöelle Virolle pour m‟avoir accueilli dans son laboratoire de recherche. Cette opportunité m‟a permis d‟apprendre beaucoup des choses du milieu professionnel et surtout du développement personnel. Je vous remercie pour vos recommandations, votre soutien pendant la thèse et votre passion pour les Streptomyces. Un grand merci à ma co-encadrante de thèse Céline Henry pour sa gentillesse, complicité et soutien tout au long de mon séjour en France. Les expériences vécues dans les réunions, formations et congrès ont été des apprentissages significatifs pour mon projet professionnel et personnel. Merci Céline pour être une formidable encadrante et une excellente personne. C‟était un grand plaisir de travailler en collaboration avec les tous les gens de PAPPSO et du bâtiment 526, une expérience exceptionnelle au niveau scientifique, technique et culturel. Merci beaucoup! Spécialement à Mélisande Blein-Nicolas pour m‟avoir encouragé et formé au monde de la bio-informatique où je suis toujours motivé. Je remercie à mes collègues du laboratoire pour les moments vécus ensemble. À Michelle pour m‟avoir formé à la manipulation des Streptomyces et aussi pour ta gentillesse et support inconditionnel. À Marc pour les conseils pragmatiques dans les situations les plus invraisemblables au labo. À Clara pour avoir toujours un sourire et une histoire drôle à raconter, Euro2016 inclus. Également, je remercie aux autres iii membres qui ont fait partie du groupe MES : Anthony, Chlöe, Maxime, Ahmed, Imen, Ines, Catherine, Esma, Jade, Benjamin, Marc-Antoine et Morgane. C‟était un plaisir de travailler à côte de vous. Également, je remercie aux voisins du couloir pour son agréable compagnie jour après jour et pour les afterworks « Picon-bière ». Merci à Jean- Luc, Sylvie, Armel, Emmanuelle, Soumaya, Laura, Luisa, Laetitia, Sylvain, Florence, Jerzy, Drago, Mathieu, Mauro, Babil, Brittany, Céline, Antoine et Christiane. Je remercie également aux gens du LCP, du LETIAM pour son agréable compagnie et collaboration pendant une partie importante de ma thèse. Merci énormément Jean Bleton pour ton soutien et ton aide, tu es un chercheur et une personne formidable. Merci à Fathi, Naira, Philippe, Aurélien, Sanaz, Doura, Marine, Myriam, Ariane, Alex et Rolando. Grâce à cette collaboration j‟ai trouvé des personnes très importantes pour moi. Thanks to my good friends Rolando and Nga for the great moments spent together including running to catch a night bus in the middle of Palaiseau or falling from the “easier” and scarier ski station ;-P Muito obrigado ao meu amor, à minha paixão, Diana, pelos momentos juntos nesta etapa profissional e pessoal. Estou muito contente de ter tido a sorte de conhecer o urso mais jeitoso e lindíssimo do mundo... Nossa! Gracias especiales al club de los “sabrosos” Leticia, Marta, Karen, Adriana, Nicolas, Edgar, David, Elodie, Proxy, Romain, Antoine y Robin por las noches en Paris que hicieron mi estancia más feliz. Muchas gracias a Abuelo, Alan, Pakún, J-Lu, Pablo, Pam, Angie y Sr. Tavo por llenar de memes mi móvil y de alegría mis tardes. Gracias a mi linda familia por apoyarme en todas mis decisiones así como en ésta etapa de mi vida. Los amo mamá, papá, Emi, Maga, Geraldine e Ian. iv TABLE OF CONTENTS INTRODUCTION ............................................................................................................ 1 CHAPTER I. BIBLIOGRAPHIC STUDY ................................................................... 6 1.1. The genus Streptomyces ..................................................................................... 6 1.2. Development cycle of Streptomyces .................................................................. 8 1.3. Genome architecture of Streptomyces ............................................................. 11 1.4. Primary metabolism in Streptomyces............................................................... 13 1.4.1. Central carbon metabolism ....................................................................... 13 1.4.1.1. Glycolysis and gluconeogenesis ........................................................... 14 1.4.1.2. Pentose phosphate pathway .................................................................. 17 1.4.1.3. Krebs cycle ........................................................................................... 19 1.4.1.4. Anaplerotic reactions ............................................................................ 21 1.4.1.5. Glycerol metabolism ............................................................................. 22 1.4.1.6. Fatty acids biosynthesis ........................................................................ 22 1.4.2. Nitrogen metabolism ................................................................................ 24 1.4.3. Phosphate metabolism .............................................................................. 27 1.4.4. Respiratory chain ...................................................................................... 29 1.4.5. Storage compounds .................................................................................. 31 1.4.5.1. Glycogen and trehalose ......................................................................... 31 1.4.5.1. Triacylglycerols .................................................................................... 32 1.4.5.2. Polyphosphates ..................................................................................... 34 1.5. Secondary metabolism in the model specie Streptomyces coelicolor and its regulation .................................................................................................................... 35 1.5.1. Polyketides and fatty acids ....................................................................... 39 1.5.2. Non-ribosomal Peptides (NRP) biosynthesis ........................................... 41 1.5.3. Terpenoids ................................................................................................ 42 v 1.5.4. Regulation of secondary metabolites in S. coelicolor .............................. 43 1.6. Towards the understanding of links between primary and secondary metabolism .................................................................................................................. 49 CHAPTER II. METHODS OF LABEL-FREE RELATIVE QUANTITATIVE PROTEOMICS ......................................................................................................... 52 2.1. Shotgun proteomic preparation ........................................................................ 53 2.2. Nano separation - Mass Spectrometry ............................................................. 54 2.2.1. LC-MS/MS ..............................................................................................
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