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Structural Studies of Human Telomerase Complexes by Cryo‑Electron Microscopy This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Structural studies of human telomerase complexes by cryo‑electron microscopy Jin, Yibo 2020 Jin, Y. (2020). Structural studies of human telomerase complexes by cryo‑electron microscopy. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/139941 https://doi.org/10.32657/10356/139941 This work is licensed under a Creative Commons Attribution‑NonCommercial 4.0 International License (CC BY‑NC 4.0). Downloaded on 27 Sep 2021 17:34:36 SGT STRUCTURAL STUDIES OF HUMAN TELOMERASE COMPLEXES BY CRYO-ELECTRON MICROSCOPY YIBO JIN SCHOOL OF BIOLOGICAL SCIENCES 2020 STRUCTURAL STUDIES OF HUMAN TELOMERASE COMPLEXES BY CRYO-ELECTRON MICROSCOPY YIBO JIN SCHOOL OF BIOLOGICAL SCIENCES A thesis submitted to the Nanyang Technological University in partial fulfilment of the requirement for the degree of Doctor of Philosophy 2020 ii Statement of Originality I hereby certify that the work embodied in this thesis is the result of original research done by me except where otherwise stated in this thesis. The thesis work has not been submitted for a degree or professional qualification to any other university or institution. I declare that this thesis is written by myself and is free of plagiarism and of sufficient grammatical clarity to be examined. I confirm that the investigations were conducted in accord with the ethics policies and integrity standards of Nanyang Technological University and that the research data are presented honestly and without prejudice. 24.01.2020 Date Yibo Jin iii Supervisor Declaration Statement I have reviewed the content and presentation style of this thesis and declare it of sufficient grammatical clarity to be examined. To the best of my knowledge, the thesis is free of plagiarism and the research and writing are those of the candidate’s except as acknowledged in the Author Attribution Statement. I confirm that the investigations were conducted in accord with the ethics policies and integrity standards of Nanyang Technological University and that the research data are presented honestly and without prejudice. 24.01.2020 Date Prof. Daniela Rhodes iv Authorship Attribution Statement This thesis does not contain any materials from papers published in peer-reviewed journals or from papers accepted at conferences in which I am listed as an author. 24.01.2020 Date Yibo Jin v Acknowledgement First, I would like to thank my supervisor Professor Daniela Rhodes for her guidance and support in the development of my scientific career. It was a wonderful experience to take on this challenging project, through which there were tears as well as joys. Without her help, it would have not been possible to work through such a tough project. I would also like to thank my co-supervisor Sara Sandin, for her helpful suggestions and guidance on electron microscopy work. Importantly, I need to express my gratitude for Dr David Gill and Dr Simon Lattman for training me to work as a scientist. I would also like to thank my thesis advisory committee, Peter Droge and Shashi Bhushan for their generous help throughout my PhD life. I wish to thank all my colleague in NTU. I would like to express my special thanks to Ziqi Long, who I spent cheerful five years together as friend and colleague. I wish to thank Qin Gong, Chenrui Xu for useful scientific and general discussions. I wish to thank Dr Andrew Wong and Dr Emmanuel Smith for critical discussion on EM techniques. I would also like to thank all my friends for the emotional supports received. Special thanks to Yishen Wang who helps me to get out of my miserable times. Above all, I would like to thank my parents for their upbringing and support when I chose to study biology during my bachelors and staring a PhD journey far from home. Without their support, I wouldn’t be able to follow my passion for life. Lastly, I would like to thank Nanyang Technological University (NTU) and the Ministry of Education (MOE) for financial support during my course. vi Contents List of abbreviations ............................................................................................................................ ix Summary ................................................................................................................................................ x Chapter 1 Introduction ......................................................................................................................... 1 1.1 Telomerase is a solution to the end replication problem ......................................................... 1 1.1.1 The telomere is at the linear end of eukaryotic chromosomes ........................................ 1 1.1.2 Semi-conservative replication and End replication problem .......................................... 3 1.1.3 Telomere binding complexes .......................................................................................... 6 1.1.4 Telomerase biological function and regulation ............................................................. 11 1.1.5 Human telomerase biogenesis and recruitment ............................................................. 15 1.1.6 Telomerase recruitment and the catalytic cycle ............................................................ 19 1.1.7 Telomerase structure analysis ....................................................................................... 26 1.2 The era of “Resolution Revolution” in biological cryo-electron microscopy ....................... 32 1.2.1 History of transmission electron microscope ................................................................ 32 1.2.2 Electron microscope objective system enhances image contrast .................................. 35 1.2.3 Development of detectors in electron microscopes....................................................... 36 1.2.4 Electron microscopy for biological specimens ............................................................. 38 1.2.5 Cryo-EM sample preparation ........................................................................................ 41 1.2.6 Single-particle cryo-EM and processing ....................................................................... 45 1.2.7 Cryo-electron tomography – directly studying proteins from cell ................................ 51 1.2.8 Resolution revolution .................................................................................................... 54 1.3 Research aim ............................................................................................................................... 56 Chapter 2 Materials and methods ............................................................................................... 58 2.1 Biochemical methods ............................................................................................................ 58 2.2 Electron microscopy methods ............................................................................................... 65 Chapter 3 Overexpression and purification of human telomerase complexes from the mammalian expression system ........................................................................................................... 69 3.1 Introduction ........................................................................................................................... 69 3.2 New telomerase expression system ....................................................................................... 71 3.3 Telomerase expression and cell line selection ....................................................................... 73 3.4 Telomerase purification protocol optimisation ...................................................................... 80 3.5 Substrate-based human telomerase purification .................................................................... 84 3.6 Purification of the telomerase complex containing HSP90 ................................................... 86 3.7 Sucrose gradient characterisation of the human telomerase .................................................. 91 3.8 Characterisation of the purified human telomerase complex ................................................ 94 3.9 Telomerase activity ............................................................................................................... 96 vii 3.10 Shelterin proteins increase telomerase processivity .............................................................. 99 3.11 Conclusions and discussions ............................................................................................... 102 Chapter 4 Structural analysis of human telomerase by using electron microscopy ............. 107 4.1 Introduction ......................................................................................................................... 107 4.2 Optimisation of grid preparation to capture human telomerase sample on grids ................ 108 4.3 Cryo-EM analysis of human telomerase on graphene oxide grids ...................................... 110 4.4 Cryo-EM analysis of human telomerase on holey grids ...................................................... 113 4.5 Negative stain EM analysis of oligo-pull down human telomerase .................................... 118 4.6 Cryo-EM analysis of substrate-based purified human telomerase on holey grids with phase plate ..................................................................................................................................... 120 4.7
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