Interactions Between Polyomavirus Large T Antigen and the Viral Replication Origin Dna: How and Why

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Interactions Between Polyomavirus Large T Antigen and the Viral Replication Origin Dna: How and Why INTERACTIONS BETWEEN POLYOMAVIRUS LARGE T ANTIGEN AND THE VIRAL REPLICATION ORIGIN DNA: HOW AND WHY by Yu-Cai Peng Department of Microbiology and Immunology McGill University, Montreal April, 1999 A thesis submitted to the Faculty of Craduate Studies and Re3earch in partial fulfullmeat of the requirements of the degree of doctor of philosophy @Yu-Cai Peng, 1999 National Library Biblioth ue nationale 1+1 of Canada du Cana7 a Acquisitions and Acquisitions et Bibliographie Srvices services bibliographiques 395 Wellmgton Street 395, nie Weliingîm Ottawa ON KIA ON4 OrtawaON K1AON4 Canada Canada The author has granted a non- L'auteur a accordé une licence non exclusive Licence ailowing the exclusive permettant à la National Library of Canada to Bibliothèque nationale du Canada de reproduce, loan, distribute or sell reproduire, prêter, distribuer ou copies of this thesis in microform, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfichelfilm, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantial extracts fkom it Ni la thèse ni des extraits substantiels may be printed or othenvise de celle-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. TABLE OF CONTENTS Page Tableofcontents................................................... I Abstract .......................................................... VI Resumé........................................................... VI11 Acknowledgements ................................................. X Claim of contribution to kaowledge ................................... XI Listoffigures ...................................................... XllI Guidelines regarding doctoral thesis ................................... XV CHAPTER 1. INTRODUCTION .................................... 1 1. Overview: Life cycle of polyomavirus and simian virus 40 ........... 1 II .A most multifunctional protein: large T antigen.................... 1. General properties........................................... A) Posttranslational rnodifcations ............................... B) Nuclear locaiization ........................................ C) Oligomerization ........................................... 2 . Functions in viral DNA replication ............................. A) Originsfor viral DNA repiicatbn ............................. B) Large T antigen and viral DNA replication ...................... C) Regulation of DNA replication by phosphorylation of large T antigen . D) Replication factors interacting with large T antigen ............... i) Replication protein A .................................... ii) DNA polymerase a: primase .............................. iii) Topoisomerase I ........................................ E) Zhc-f»>gerand Dnd domains on large T antigen ................. i) Zinc-jnger domain ...................................... ii) Dnal domain .......................................... 3. Functionfi in regulation of transcription ........................ A) Regulation of viral gene expression ........................... B) Interactions between large T antigen and ~ranscriptionfactors ...... 32 4 . Functions in immortalization and transformation of infected cells ... 34 A) TranF/orming activiy of T antigens ............................ 35 B) Cellular targetsfor large T antigen implicated in its transforming uctiviîy ....................................... 38 i) p ................................................... 38 ii) pRb/p107/p130 ......................................... 39 iii) p300/CBP ............................................. 42 III .DNA Binding by large T antigens ............................... 1. Origin specific DNA binding ................................. 2 . Nonorigin DNA binding ..................................... 3. DNA-binding domains on large T antigen ...................... 4 . Formation of large T antigen hexamers in the core origin ......... 5. DNA dbtortioiis associated with large T antigen binding andoligomeriution ......................................... 6. Conditions that affect DNA binding by large T antigen ........... A) nucleotides ............................................... B) phosphorylation ........................................... C) pH ...................................................... IV . Production of large T antigens for in vitro analysis ................. 67 1. Expression with an adenovirus vector system ................... 67 2 . Expression in E. coli ........................................ 69 3 . Expression with a baculovirus system .......................... 70 4 . Expression in yeast: Pichia pastoris system ...................... 71 CHAPTER 2 . MATERIALS AND METHODS ........................ 75 1. Ce11 cultures .................................................. 75 1. Strains .................................................... 75 2. Media and growth conditions ................................. 76 3. Yeast and bacterial transformation ............................ 77 4. Screening for yeast transformants expressing large T antigen ...... 77 II. Nucleicacids ................................................. 78 1. DNA extraction and enzymatic manipulations ................... 78 2 . PCR ampliIication .......................................... 79 3. PIasmid constructs .......................................... 80 III. Protein analysis .............................................. 83 1. Western blottiag and silver staining ........................... 83 2 . Immunoaffinity column prepamtion ........................... 83 3. Expression and purification of polyomavirus large T antigen ...... 84 IV. Assays for protein-DNA interactions ............................. 87 1. Filter binding assay ......................................... 87 2. DNase 1 footprinting analysis ................................. 88 3. Gel electrophoresis mobility shift assay ........................ 89 1. DNA immunoprecipitation assay .............................. 89 5 . Glycerol gradient centrifugation .............................. 90 6. Duplex DNA fragment unwinding assay ........................ 91 CHAPTER 3. Production of active polyomavirus large T antigen inycastPlcliiapmtoris ................................. Absfract ..................................................... Introduction .................................................. Results ...................................................... lntegration of polyomavhs large T antigen gene into yeast Pichia pmris and expression of the large T antigen .............. Specific DNA-binding and purification of the yeast-derived large T antigen ............................................ Purified large T antigen unwinds duplex DNA fragment ........... Discussion .................................................... III CHAPTER 4. Polyomavinis large T mtigen bhds cooperatively to its multiple binding sites in the viral ongin of DNA repücation .. Connecting text ............................................... Introduction ...................................~~...~.~.~.~~.~ Results ....................................................... Specific origin-binding activity of polyomavirus large T antigen is enhanced at pH 7 and below ................................ Large T antigen-DNA complexes are stable at pH 6 to 7 but are unstable at pH 7.6 .......................................... ATP does not affect DNA binding at pH 7 or below but stabilizes a fraction of large T antigen-origin DNA complexes at high pH ...... Stabilization of complexes by ATP depends on the presence of site 112 Binding of large T antigen to origin DNA fragments containing one or more adjacent binding sites ................................ Binding of large T antigen to DNA targets containing mutated binding sites .............................................. DNase 1 footprinting of mutant DNAs in the presence of large T antigen .................................................. ATP specifically enhances protection against DNase 1 digestion of the central 1O to 12 bp of site 112 .............................. Discussion .................................................... CHAPTER 5. Enhanced binding to origin DNA at low pH enables easy detection of polyomavirus large T antigen by gel mobility shift assay of unfucd complexes ......................... 145 Connecting text ............................................... 146 Abstract ..................................................... 147 Introduction .................................................. 148 Results ...................................,.................. 150 Gel mobility shift assay of large T antigen-DNA complexes at pH 6: sensitivity and specificity ............................. 150 Application of gel mobility shift assay to crude lysates of cells expressing large T antigen ................................... Glycerol gradient analysis of large T antigen-DNA complexes ...... Influence of binding sites on gel retardation ..................... Discussion .................................................... CHAPTER 6. SUMMARY AND CONCLUSIONS ..................... 1. Expression of large T antigen in Pichia pasioris .................. II . pH effect on origin DNA binding by large T antigen .............. III . Applications of the pH effect on large T antigen DNA binding ..... IV . ATP effect on ongin DNA binding by large
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