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Super-resolution light microscopy studies of the organisation and architecture of the hepatitis C virus RNA replication complex Christopher Paul Bartlett Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds Astbury Centre for Structural Biology School of Molecular and Cellular Biology September 2016 The candidate confirms that the work submitted is his own, except where work which has formed part of jointly-authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. Chapter 4 within this thesis has been based on work from a jointly-authored publication: Mohl, B.-P., Bartlett, C., Mankouri, J., Harris, M. (2016). Early events in the generation of autophagosomes are required for the formation of membrane structures involved in hepatitis C virus genome replication. Journal of General Virology. DOI: 10.1099/jgv.0.000387. - Dr B.-P. Mohl performed experiments for figures 1, 2, 3, 4a, 6 and 7 and co-authored the paper. - C. Bartlett performed experiments for figures 4b-c, 5 and 8 and co-authored the paper. - Dr J. Mankouri provided supervision and co-authored the paper. - Prof. M. Harris provided supervision and co-authored the paper. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. 2016 The University of Leeds Christopher Paul Bartlett The right of Christopher Paul Bartlett to be identified as Author of this work has been asserted by him in accordance with the Copyright, Designs and Patents Act 1988. i ii Acknowledgements I would like to firstly thank my supervisors Prof. Mark Harris and Prof. Michelle Peckham for their continued expertise, advice, enthusiasm and support throughout the last four years. Secondly, to all members past and present of the Harris and Peckham research groups who have always provided helpful discussion as well as a lively and enjoyable workplace. In particular, thanks to Jamel Mankouri, Douglas Ross-Thriepland and Joe Lattimer for thought provoking ideas and taking my mind off science from time to time. A special thanks to Alistair Curd and Dmitry Ushakov who managed to teach a biologist some physics. I would also like to thanks all my friends and family for their continued support, especially during the more frustrating times, A special mention to Anne-Marie for her constant enthusiasm and the continued supply of cups of tea! Finally, I would like to thank the Wellcome Trust for funding, without which this project would never have developed. iii iv Abstract Hepatitis C virus causes a chronic infection in ~3% of the world’s population and is a leading cause of liver diseases such as cirrhosis and hepatocellular carcinoma. It is a positive-sense single-stranded RNA virus that persists in ~85% of infections. Viral genome replication occurs within a specialised membranous compartment, termed replication factories. This provides an environment suitable for the production of infectious virus, and correct formation and maintenance is critical for virus replication. The process is coordinated by the non-structural proteins in a macromolecular protein assembly, but the precise mechanisms of biogenesis and protein organisation within replication factories are unknown. New super-resolution light microscopy approaches allow resolutions of tens of nanometres, 10-fold higher than standard wide-field or confocal microscopy. The goal of this research was to use these techniques to determine the organisation and architecture of proteins within replication factories. Super-resolution imaging revealed clusters of viral proteins that were equivalent to the diffraction limited puncta observed by wide-field microscopy. A detailed analysis of protein clusters identified significant differences in size and organisation between the non-structural proteins NS3 and NS5A with a defined minimum distance to the cluster centroid. Additional investigations into the functions of NS5A revealed altered cluster phenotypes with both pharmacological inhibition and mutants defective in phosphorylation. A number of strategies were also explored to facilitate fluorescence labelling of viral components in replication factories. In parallel, investigations into the biogenesis of replication factories were explored by characterising interactions between hepatitis C virus and autophagy. This study identified a requirement of HCV replication for early steps in the formation of autophagosomes. The findings from this research are the first descriptions using super-resolution microscopy to understand the hepatitis C virus replication complex and provide insight into the organisation and architecture of the non-structural proteins during infection. v vi Table of Contents Chapter 1 - Introduction ....................................................................................... 1 1.1 Hepatitis C virus ....................................................................................... 3 1.1.1 Identification and classification ...................................................... 3 1.1.2 Epidemiology and transmission .................................................... 5 1.1.3 Pathology ..................................................................................... 6 1.1.4 HCV therapies .............................................................................. 9 1.2 Molecular biology ................................................................................... 13 1.2.1 Genome organisation ................................................................. 13 1.2.2 Virion architecture ....................................................................... 14 1.2.3 HCV entry ................................................................................... 16 1.2.4 Polyprotein translation ................................................................ 19 1.2.5 Genome replication ..................................................................... 20 1.2.6 Assembly and release ................................................................ 21 1.3 Individual HCV proteins .......................................................................... 24 1.3.1 Core – nucleocapsid protein ....................................................... 24 1.3.2 E1 and E2 – envelope glycoproteins ........................................... 24 1.3.3 p7 – viroporin .............................................................................. 25 1.3.4 NS2 – autoprotease .................................................................... 25 1.3.5 NS3/4A – protease/helicase ....................................................... 25 1.3.6 NS4B – transmembrane protein .................................................. 26 1.3.7 NS5A – multifunctional phosphoprotein ...................................... 26 1.3.7.1 Structure of NS5A ........................................................... 26 1.3.7.2 Roles of NS5A during HCV infection ............................... 27 1.3.7.3 Interaction partners ......................................................... 30 1.3.7.4 Phosphorylation of NS5A ................................................ 33 1.3.7.5 NS5A as a target for direct acting antivirals ..................... 34 1.3.8 NS5B – RNA-dependent RNA polymerase ................................. 35 1.4 HCV replication complex ........................................................................ 36 1.4.1 HCV membrane rearrangements ................................................ 36 1.4.2 Formation of double membrane vesicles .................................... 38 1.4.3 HCV replication factory composition ........................................... 39 vii 1.5 Light microscopy ..................................................................................... 42 1.5.1 History of light microscopy .......................................................... 42 1.5.2 Diffraction in light microscopy ...................................................... 42 1.5.3 Extending the optical image resolution ........................................ 44 1.5.4 Breaking the diffraction limit ........................................................ 45 1.5.4.1 Localisation microscopy ................................................... 47 1.5.4.1.1 Principle ................................................................................... 47 1.5.4.1.2 Multi-colour and three dimensional super-resolution imaging ... 48 1.5.4.1.3 Resolution in SMLM ................................................................. 50 1.6 Aims and objectives ................................................................................ 55 Chapter 3 - Materials and Methods .................................................................... 57 3.1 General materials ................................................................................... 59 3.1.1 Bacterial strains .......................................................................... 59 3.1.2 Mammalian cell lines ................................................................... 59 3.1.3 Antibodies – Primary ................................................................... 60 3.1.4 Secondary antibodies and fluorescent reagents .......................... 61 3.1.5 SGR and virus constructs ...........................................................