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Identification and Characterization of Novel Mtor Splicing Isoforms

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Identification and Characterization of Novel Mtor Splicing Isoforms Identification and Characterization of Novel mTOR Splicing Isoforms Zeyad Mohammad S Alharbi A thesis submitted to the University College of London in fulfilment with the requirements for the degree of Doctor of Philosophy London, January 2015 Research Department of Structural and Molecular Biology University College London Gower Street, London WC1E 6BT, United Kingdom Declaration I, Zeyad M. Raddadi Alharbi, declare that all work presented in this thesis is the result of my own work. The work presented here does not constitute part of any thesis. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. The work herein was carried out while I was a graduate student at the University College London, Research Department of Structural and Molecular Biology under the supervision of Professor Ivan Gout. Zeyad Alharbi 2 Abstract mTOR (mammalian target of rapamycin) is a serine/threonine protein kinase which belongs to the family of phosphoinositide 3-kinase related kinases (PIKK), which also includes ATR, ATM, DNA-PK, SMG1 and TRRAP. mTOR contains several conserved protein-protein interaction modules at the N-terminus and a protein kinase domain at the C-terminus. The regulatory interactions of mTOR are mainly mediated by HEAT (Huntingtin, Elongation factor 3, protein phosphatase 2A, and TOR1) repeats and FAT (FRAP, ATM and TRRAP) domains. In contrast to other PIKK family members, mTOR possesses a unique FRB (FKBP12/Rapamycin Binding) domain which mediates the interaction with the FKBP12/rapamycin inhibitory complex. mTOR is a key component of two distinct multi-protein complexes in mammalian cells, termed mTOR complex 1 (TORC1) and mTOR complex 2 mTORC2). A diverse range of extracellular and intracellular signals stimulate both mTOR complexes to regulate cell growth, survival and proliferation. Dysregulation of mTOR signalling has been implicated in various human pathologies, including cancer, inflammation, neurodegenerative and metabolic disorders. Therefore, mTOR is an attractive target for drug discovery. In cancer research, mTOR inhibitors have shown a potent anti-proliferative activity in pre-clinical studies and several of these are currently being evaluated in clinical trials. There is only one mTOR gene in higher vertebrates, which is known to encode two splicing isoforms: mTORα and mTORβ. In contrast to the full length mTORα protein, mTORβ lacks most of its protein-protein interaction modules, HEAT and FAT, but retains domains responsible for FKBP12/rapamycin binding, protein kinase activity and regulation. Importantly, mTOR was shown to shorten considerably the G1 phase of the cell cycle, to 3 stimulate cell proliferation and to possess oncogenic potential in cell-based and xenograft studies. Like other PIKK family members, there is increasing evidence of the presence of mTOR splicing isoforms. The main aim of this study was to identify new mTOR splicing isoforms and to determine their molecular characterization. In addition we aim to explore the ability of these isoforms to phosphorylate known mTOR targets such as 4E-BP1. Furthermore, we aim to study the role of the new isoforms in the mTOR–mediated cellular processes, such as cell proliferation, and the contribution of the identified isoforms in the oncogenic characteristics of cells. In this study, we have employed bioinformatics, biochemical, cell and molecular techniques to identify and characterize two novel mTOR splicing isoforms, denoted mTORδ and mTOR. When compared to mTORα, the mTORδ splice variant contains only the N-terminal HEAT repeats and a unique C-terminal region, while the mTORγ isoform possesses a 12 amino acid deletion in the kinase domain. The existence of the mTORδ isoform was confirmed at mRNA and protein levels by identifying corresponding EST clones and detecting the splice variant with specific anti–mTORδ antibodies. Furthermore, we have found several EST clones corresponding to the mTORγ splicing variant. In contrast to mTORα, the stably expressed mTORδ and mTOR lack the kinase activity in vitro. It was also found that stable overexpression of mTORδ and mTORγ splice variants in HEK293 cells inhibits cell proliferation and colony formation in soft agar. These findings suggest that identified novel isoforms have the potential to regulate the mTOR signalling pathway in a dominant–negative manner. 4 Acknowledgments I would like to express my sincere gratitude to my supervisor Professor Ivan Gout whose passion for science is truly inspiring, for offering me this PhD position, for the continuous support of my study, as well as for all his help and guidance during the production of my PhD thesis. His guidance helped me in all the time of research and writing of this thesis. I would also like to thank my committee members, Professor Elizabeth Shephard and Professor John Christodoulou for their advice on both research as well as on my career. My sincere thanks also goes to Dr. Alexander Zhyvoloup for enlightening me the first glance of research. My friends and colleagues made the time during the research unforgettable. Special thanks to Ahmed, Pascale, Lena, Yugo, Kamil and Mahmoud for all their help, humour and support. Also, thanks to all the girls and guys I met around the department and shared a joke with from time to time. You all made life more enjoyable. I would also like to thank all of my friends who supported me and encouraged me to strive towards my goal. Last but not the least a special thanks to my family for spurring me on to complete this thesis and for all their support during my studies and in particular my mother who spent sleepless nights praying for me and was always my support in the moments where I needed support. 5 Table of contents Declaration ................................................................................................................................. 2 Abstract ...................................................................................................................................... 3 Acknowledgments ...................................................................................................................... 5 List of Figure ............................................................................................................................ 12 Abbreviations ........................................................................................................................... 17 Chapter 1: General Introduction ........................................................................................ 24 1.1 mTOR, an overview ................................................................................................. 24 1.1.1 The mTOR Structure ............................................................................................ 25 1.1.2 mTOR Complexes in mammalian cells ............................................................... 28 1.1.2.1 mTORC1 ..................................................................................................... 30 1.1.2.2 mTORC2 ..................................................................................................... 31 1.1.2.3 Regulation of mTOR ................................................................................... 32 1.1.2.3.1 mTORC1 regulation ............................................................................... 32 1.1.2.3.2 mTORC2 Regulation .............................................................................. 35 1.2 Role of mTOR in cellular functions ......................................................................... 35 1.2.1 mTOR signalling in the regulation of protein synthesis ...................................... 38 1.2.2 Implication of mTOR signalling in the regulation of cell survival ...................... 39 1.2.3 Role of mTOR signalling in mitochondrial biogenesis ........................................ 42 1.2.4 Regulation of ribosomal biogenesis via the mTOR signalling pathway .............. 42 1.2.5 Role of mTOR signalling in autophagy ............................................................... 43 1.2.6 mTOR signalling and lipid biosynthesis .............................................................. 43 6 1.2.7 Other roles of mTOR in regulating cellular processes ......................................... 46 1.3 FKBP12 – Rapamycin Complex .............................................................................. 46 1.3.1 Overview of Rapamycin ....................................................................................... 46 1.3.2 Overview of FKBP12 ........................................................................................... 47 1.4 Initial evidence for the existence of mTOR splicing isoforms ................................. 48 1.5 Aim of the study ....................................................................................................... 50 1.6 Methods of isolating mTOR ..................................................................................... 50 Chapter 2: Methodology .................................................................................................... 54 2.1 Materials ................................................................................................................... 54 2.1.1 Common laboratory reagents ............................................................................... 54 2.1.2 Molecular cloning materials ................................................................................. 54 2.1.3 Proteins ................................................................................................................
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