Mcewan, William (2010) Factors Affecting Replication and Cross-Species Transmission of Feline Immunodeficiency Virus
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McEwan, William (2010) Factors affecting replication and cross-species transmission of feline immunodeficiency virus. PhD thesis. http://theses.gla.ac.uk/1388/ Copyright and moral rights for this thesis are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the Author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the Author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Glasgow Theses Service http://theses.gla.ac.uk/ [email protected] Factors affecting replication and cross-species transmission of feline immunodeficiency virus Submitted in fulfilment of the requirements of the degree of DOCTOR OF PHILOSOPHY by William McEwan, B.Sc., M.Res. Institute of Comparative Medicine Faculty of Veterinary Medicine University of Glasgow September 2009 Abstract In order to successfully invade a new species, lentiviruses must overcome restriction factors, dominant blocks to replication, and be able to make use of available host factors such as entry receptors for replication. Human immunodeficiency virus (HIV-1) infection is blocked at a post-entry stage by rhesus macaque TRIM5α, an effect that is enhanced by host factor cyclophilin A (CypA), but largely evades restriction by the human TRIM5α variant. HIV-1 replication is also inhibited by simian APOBEC3G but is able to evade restriction by human APOBEC3G by inducing its degradation through expression of accessory protein Vif. Viral entry and tissue tropism are determined by an interaction of the viral Env glycoprotein with a cell surface receptor and a seven transmembrane domain co-receptor. The feline immunodeficiency virus (FIV) infects diverse felid species including the African lion, where infection has likely been endemic since at least the late Pleistocene, and the domestic cat, a more recent host. For domestic cat strains of FIV (FIV-Fca), entry is mediated by host proteins CD134 and CXCR4, but the identity of receptors in non-domestic strains of FIV is unknown. This thesis demonstrates that two strains of FIV isolated from lions (FIV-Ple subtypes B and E) differ in their receptor tropism and that subtype E shares entry receptors with FIV-Fca. The findings suggest that alternative receptor usage is a strategy employed by FIV in this species and has implications for the disputed pathology and tissue tropism of infection in African lions. Next, we tested the hypothesis that species which have harboured lentiviral infection for a long time are better able to prevent viral replication than recent hosts. Whilst we found that TRIM5α is non-functional in all felid species tested, evidence of potent APOBEC3 activity was found and, in lion cells, potently restricts production of infectious FIV. Moreover, lion primary T-cells prevent 2 replication of diverse FIV strains and restrict primate lentiviruses at post-entry stages, suggesting that co-evolution with lentiviruses has driven the selection of broad-ranging restriction factors. Structural and biophysical analyses suggest that whilst FIV’s interaction with CypA appears to be conserved in affinity with HIV-1, the interaction does not appear to be crucial for replication and, in the absence of restriction by TRIM5α, the role of the capsid-CypA interaction is discussed. Overall the study explains the permissivity of domestic cat cells to retroviral infection and identifies FIV infection of lions as an example of host adaptation driven by current lentiviral infection. 3 4 Table of Contents Abstract ............................................................................... 2 Table of Contents .......................................................................... 5 List of Tables and Figures ................................................................ 10 List of Abbreviations ...................................................................... 13 Acknowledgements ........................................................................ 17 Chapter 1. Introduction ............................................................... 18 1.1 Preface ......................................................................... 18 1.2 Retroviruses .................................................................... 19 1.3 Cross-species transmission of lentiviruses in the primates and felids . 23 1.4 Lentiviral entry ................................................................ 26 1.4.1 Receptors for HIV-1 entry .................................................... 26 1.4.2 Molecular mechanism of HIV-1 entry ....................................... 27 1.4.3 Variable tropism of HIV-1 .................................................... 28 1.4.4 Receptors for FIV-Fca entry ................................................. 30 1.4.5 Receptor tropism of non-domestic cat FIV ................................ 33 1.5 Post-entry restriction ......................................................... 34 1.5.1 Murine Fv 1 system ............................................................ 35 1.5.2 TRIM5α restriction ............................................................ 36 1.5.3 Virus interaction maps to TRIM5 B30.2 or CypA domain ................ 37 1.5.4 Adaptive evolution of TRIM5α ............................................... 40 1.5.5 Contribution of RBCC domain to restriction .............................. 42 1.6 The role of Cyclophilin A in lentiviral replication ........................ 46 1.6.1 Cyclophilin A and its inhibitors.............................................. 46 1.6.2 CypA is a cofactor of HIV-1 replication .................................... 47 1.6.3 CypA can have alternative effects on lentiviral replication ............ 48 1.7 Induction of hypermutation by APOBEC3 .................................. 50 1.7.1 Discovery of human APOBEC3G ............................................. 50 5 1.7.2 Antiviral activity of human APOBEC3G ..................................... 51 1.7.3 Encapsidation of human APOBEC3G ........................................ 53 1.7.4 Antiviral activity of other human APOBEC3 genes ....................... 54 1.7.5 The role of Vif in overcoming APOBEC3G and 3F restriction ........... 55 1.7.6 Positive selection of APOBECs ............................................... 56 1.7.7 An expanded cluster of feline APOBEC3 genes ........................... 57 1.7.8 Vif of Feline Immunodeficiency Virus ...................................... 59 1.8 Scope of this thesis ........................................................... 59 Chapter 2. Materials and Methods ................................................... 61 2.1 Molecular cloning ............................................................. 61 2.1.1 Nucleic acid extraction and PCR ............................................ 61 2.1.2 Cloning techniques ............................................................ 62 2.1.3 Sequencing of DNA ............................................................ 63 2.1.4 FIV Envelopes .................................................................. 63 2.1.5 CD134 and CXCR4 ............................................................. 64 2.1.6 TRIM5 ........................................................................... 64 2.1.7 Capsid and cyclophilin A ..................................................... 65 2.1.8 APOBEC3 and vif .............................................................. 66 2.2 Cells and viruses .............................................................. 67 2.2.1 Adherent cells ................................................................. 67 2.2.2 Suspension cells ............................................................... 67 2.2.3 Primary T-cells ................................................................ 68 2.2.4 Replication-competent FIV .................................................. 69 2.2.5 Tissue culture infection with replication competent FIV ............... 70 2.2.6 Drugs and inhibitors .......................................................... 71 2.2.7 Stable transduction of cell lines ............................................ 72 2.2.8 Pseudotype production ....................................................... 73 2.2.9 Pseudotype assay ............................................................. 75 2.2.10 RNA interference ............................................................ 77 6 2.3 Quantitative techniques and immunoloblotting .......................... 78 2.3.1 p24 ELISA ....................................................................... 78 2.3.2 Quantification of reverse transcriptase activity .......................... 78 2.3.3 Real-time PCR ................................................................. 79 2.3.4 SDS-PAGE & Immunoblotting ................................................ 79 2.3.5 Far western blot .............................................................. 80 2.4 Biophysical and structural techniques ..................................... 81 2.4.1 Recombinant protein purification .......................................... 81 2.4.2 Isothermal Titration Calorimetry ........................................... 83 2.4.3 X-ray crystallography ......................................................... 84 2.5 In silico techniques ..........................................................