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Uncovering Ubiquitylation Pathways in Liver Metabolism by a Proteomic Approach Helena Magliarelli

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Uncovering Ubiquitylation Pathways in Liver Metabolism by a Proteomic Approach Helena Magliarelli Uncovering ubiquitylation pathways in liver metabolism by a proteomic approach Helena Magliarelli To cite this version: Helena Magliarelli. Uncovering ubiquitylation pathways in liver metabolism by a proteomic approach. Molecular biology. Université de Strasbourg, 2014. English. NNT : 2014STRAJ083. tel-01413594 HAL Id: tel-01413594 https://tel.archives-ouvertes.fr/tel-01413594 Submitted on 10 Dec 2016 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. UNIVERSITÉ DE STRASBOURG École Doctorale des Sciences de la Vie et de la Santé IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire THÈSE présentée par : Helena MAGLIARELLI soutenue le : 09 Octobre 2014 pour obtenir le grade de : !"#$%&'($')R%+,-$&.,# '($'0#&1.2!%&3 Discipline/ Spécialité : Aspects moléculaires et cellulaires de la biologie Uncovering ubiquitylation pathways in liver metabolism by a proteomic approach Mr RICCI Romeo Directeur de thèse Mr BAUMERT Thomas Examinateur Mme PICHLER Andrea Rapporteur externe Mme POSTIC Catherine Rapporteur externe Acknowledgements Acknowledgements First of all, I would like to thank Romeo for giving me always the very best opportunities to develop and become a better scientist. Thank you for guiding me throught the path that has brought me to this point. Thank you for all the trust, encouragement, help and support that made our work progress. And thanks for making the lab a nice and friendly environment where I spent very enjoyable 4 years. I would also like to very much thank Iza for all your help and support during these years. All of your precious inputs during lab meetings and conversations have contributed to the development of my work and make me grateful. I would like to thank Prof. Thomas Baumert, Prof. Catherine Postic and Dr. Andrea Pichler. Thank you for your time and effort as a member of my jury. I would also like to thank Prof. Ruedi Aebersold and Dr. Mariette Matondo for our collaboration, helpful discussions and for receiving me in Zurich. My acknowledgement goes also to the IGBMC PhD program and for the Fondation pour la Recherche Médicale (FRM) for the financial support. Special thanks go to all current and old members of the lab! Thanks for the scientific and non- scientific discussions, for the nice and friendly atmosphere, for your comments, for your help and your support. Thank you Alex for welcoming me to the lab, it was just the two of us for some weeks when I started. Thank you Gergo for working in projects together and giving me an extra pair of hands to handle the mice. Thank you Michael for being so enthusiastic about the complement project and for helping me with it. Thank you Eric, Adrien and Joelle for helping me with French translations everytime I needed one and for introducing me to the adorable French culture. Thank you Aurelie for the quick chats we had sometimes and the help with qPCR and Europapark. Thank you Zhirong for your help and suggestions with my project and cloning. Thank you Olga for your support and words of encouragement during these months you are in the lab. !"#$%& "'%(& )(& "''& )!*& +*+,*-%& (.& /0"R%& '",& .(-& )!*& #23*& 2#)*-"3)2(#%& "#4& .-52).5''& 42%35%%2(#%& during lab meetings. 2 Acknowledgements À minha familia no Brasil, que mesmo com um oceano de distância, está sempre dentro da minha cabeça e coração. Muito muito muito obrigada pelo apoio, pelo carinho e por tudo que fazem para cada dia eu seja uma pessoa melhor. Parece que finalmente eu vou sair da escola, e já era hora, né? :) Y a ti, muchas gracias por ser parte de mi vida. Gracias por cuidar de mí, por apoyar mis ideas locas, por empujarme a hacer cosas locas (incluyendo nieve, montañas, aviones, árboles...), por estar a mi lado en todas las ocasiones, por hacerme una mejor persona. Muchas muchas gracias por todo!!! Thanks to all my friends in Strasbourg, I will miss you all a lot. All the moments that we spent together will for sure stay in my memory. Special thanks to Ana YSR, thanks for being the bestest BFF, for tolerating my screaming and laughter and for being by my side during the good, the bad and the Ylvis. Thanks Nikolas for your company, for your kind/sarcastic words that make me laugh, and for feeding me with sweets frequently. Thanks Lena for your supp (-)6&7(5-&O95%)& 4(&2)P& approach, for your company in the library and in the water. Thanks to all my friends from Goettingen and from Brazil. Thank you for all your support, all your help and all the effort to keep this friendship alive! Thanks for all the awesome trips and videos. In special, thank you Iris, for your craziness, constant presence in my life and the sweetest box of encouragement. 3 Table of contents Table of contents Acknowledgements ................................................................................................................... 2 Table of contents ....................................................................................................................... 4 Detailed table of contents ......................................................................................................... 5 Table of Figures ....................................................................................................................... 10 Table of Tables ........................................................................................................................ 11 Abstract.................................................................................................................................... 12 Introduction ............................................................................................................................. 13 Aims of the project .................................................................................................................. 72 Materials and Methods ............................................................................................................ 73 Results ..................................................................................................................................... 81 Discussion ............................................................................................................................. 142 Résume de thèse ................................................................................................................... 163 References ............................................................................................................................. 173 4 Detailed table of contents Detailed table of contents Acknowledgements ................................................................................................................... 2 Table of contents ....................................................................................................................... 4 Detailed table of contents ......................................................................................................... 5 Table of Figures ....................................................................................................................... 10 Table of Tables ........................................................................................................................ 11 Abstract.................................................................................................................................... 12 Introduction ............................................................................................................................. 13 1. Energy homeostasis .......................................................................................................... 13 1.1. Pancreas ..................................................................................................................... 13 1.1.1. Insulin ................................................................................................................... 13 1.1.2. Glucagon .............................................................................................................. 14 1.2. Brain ............................................................................................................................ 15 1.3. White adipose tissue ................................................................................................... 15 1.4. Skeletal Muscle ........................................................................................................... 16 1.5. Liver ............................................................................................................................ 17 1.5.1. Postprandial state ................................................................................................. 17 1.5.1.1. Main pathways ............................................................................................... 17 1.5.1.1.1. Glucose metabolism ................................................................................. 17 1.5.1.1.2. Fatty-acid metabolism .............................................................................. 18 1.5.1.2.
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