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Genetic Interactions Among Components of the Messenger RNA Biogenesis Machinery in the Yeast Saccharomyces Cerevisiae

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Genetic Interactions Among Components of the Messenger RNA Biogenesis Machinery in the Yeast Saccharomyces Cerevisiae Genetic interactions among components of the messenger RNA biogenesis machinery in the yeast Saccharomyces cerevisiae Ian Matthew Donaldson A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Molecular and Medical Genetics University of Toronto O Copyright by Ian Matthew Donaldson 1999 National Library Bibliothéque nationale du Canada Acquisitions and Acquisitions et Bibliographie Services services bibliographiques 395 Wellington Street 395. rue Wellington Ottawa ON K1A ON4 OitawaON KlAW Canada Canada The author has granted a non- L'auteur a accordé une licence non exclusive licence allowing the exclusive permettant à la National Library of Canada to Bibliothèque nationale du Canada de reproduce, loan, disîribute 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 microfiche/£üm, 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 fiom 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. Wer immer strebend sich bemüht, den komen wir erlosen. mm ABSTRACT GENETIC INTERACTIONS AMONG COMPONENTS OF THE MESSENGER RNA BIOGENESIS MACHINERY IN THE YEAST SACCHAROMYCES CEREVISIAE Ian Matthew Donaldson, Degree of Doctor of Philosophy, 1999, Department of Molecular and Medical Genetics, University of Toronto The overall goal of this thesis was to characterize mutations in the zinc-binding domain (ZBD) of the iargest subunit (Rpo2lp) of yeast RNA polymerase iI and then use these mutations to find new genetic interactions with other components of the messenger RNA biogenesis machinery. The first data chapter demonstrates that the zinc stoichiometry of RNA polymerase II (RNAP KI) is 7; consistent with the number of zinc-binding motifs present in the enzyme. Mutations in the Rpo2Ip-ZBD reduced RNAP II activity without visibly altering association of subunits required for this activity. The second data chapter describes the use of an RpoSlp-ZBD mutant in a synthetic- lethal screen designed to identify other components of the transcriptional machinery. Two mutant genes were identified; an allele of SRBS (a known component of the RNAP II holoenzyme) and an allele of GCR3 ( a factor that had previously been implicated in the expression of glycolytic genes). No evidence was found to suggest that Gcr3p is a component of the holoenzyme; its effect on in vitro transcription appeared to be marginal and possibly indirect. Gcr3p was identified (by another group) as the largest subunit of the nuclear cap-binding complex and was shown to play a role in efficient splicing. The allele of GCR3 identified in this synthetic-lethal screen also had an effect on in vitro spiicing. 1 hypothesize that this defect, coupled with the transcriptional defect conferred by the zinc- binding domain mutation is sufficient to explain the synthetic-lethality observed between the two. The third data ctiapicr de.scribes an attempt to determine if SrbSp also ploys a role in ~p!i~-lng€,nrncts of thc mutant SRB5 strain were deficient in splicing activity. This effect u ltlicly an indirect one. possibly mediated by the effect of the SM5 mutant allele on the pnc cspresion of one or more splicing factors. Extracts made from Rpo2lp-ZBD riiutrints also wcre rcduced in splicing activity raising the possibility that splicing activity is w ns i t lvc to de fects in components of the transcriptional machinery . ACAWOWLEDGEMENTS I would l&e to thanlc my supervisor Jim Friesen for his many years of tireless suppoa encouragement and enthusiasm. I would also Like to acknowledge the past and pmcnt members of my cornmittee for their guidance; Tom Yager. Ben Blencowe, Jacqueline Segall and Vincent Giguem. 1 am gratefd to Jacques Archambault, Emmanuel Maicas. Keith Schappert. Shahrzad Nouraini, Mike Drebot, Dave Jansma, Jiusheng Wu, Mark Toone, Sara Petersen-Bjorn, Brian Bobecko, Scott Houliston. Debbie Field, Vicki Lay, Deming Xu, Tina Harrington. Alia Ahmed, Dorian Anglin. Yan Xu, Andreas Zurlinden. Manuela Moser, Siro Trevisanato and Driss Talibi. These were the many members of the Friesen lab, past and present, that 1 got to how. They made the Friesen lab an intereshg and stimulating place to work in. My especial thanks go to Debbie and Shahnad for their encouragement. 1 am also indebted to Chris Koth, Saily Hemming, Steve Orlicky, Don Awry, Johnson Wong and Mike Kobor for al1 their helpful guidance. There are also the indispensable friends who provided a haven; Monis Manoison, Petra Kuehl, Mariano Radaeli, Pascale Rousseau and Keith Neil. 1would especially like to thank Moms for his advice and fkiendship. Lastly, and most importantly 1 would like to achowledge my family. Tney have ail been waiting patiently a long thefor this. Most of aii, 1 wish to thank my wife Katerina who has walked bai& me the whole way. TABLE OF CONTENTS Abstract ...................................................................... ri Acknowiedgements ........... .......................................... iv Table of Contents.......................................................... v List of Tables............................................................... vii List of Figures................. .. .......................................... viii List of Abbreviations .............. .. .................................... x A note on RNA polymerase nomenclature.............................. ai CHAPTER 1 A review of the events of mRNA biogenesis and their coordination Overview and Scope....................................................... ... Transcnptlon initiation- ............................................. Transition from the pre-initiation complex to the elongation complex ................................................. Initiation of transcription and the biogenesis of mRNA........ S'-end capping of the pre-mRNA ........... .. .................. Capping and mRNA biogenesis ................ .................. Splicing. ............................................................... Splicing and mRNA biogenesis ................................... Processing of the pre-mRNA 3'-end............................ 3'-processing and the biogenesis of mRNA ..................... Temination of transcription and mRNA biogenesis ............ RNA export from the nucleus...................................... Summary of mRNA biogenesis .................................. Thesis summary............................................................ References.................................................................. CEIAPTER II Zinc stoichiometry of yeast RNA polymerase II and characterinition of mutations in the zinc-binding domain of the largest subunit Abstract ...................................................................... II-2 Introduction ................................................................. II-3 Matenals and Methods .................................................. 11-8 Results ....................................................................... 11-18 Discussion .................................................................. IL38 References.................................................................. 11-46 CHAPTER m A synthetic-lethal screen for factors that interact huictionally with RPO2l Abstract ...................................................................... III-2 Introduction. ................................................................ III-3 Materials and Methods ................................................... ïïl-6 Results .............,................................................. ïïI-23 Discussion ......... ... .......,. .... .... ..JII-56 References......... ,, ....... ........ ................................... III-64 CHAPTERIV Characterizaiion of a mutant srb5 spking defec t and the effect of an RNAP II carboxyl-terminal domain peptide on yeast in vitro splicing . Abstract ..................................................................... Introduction ................................................................. Materials and Methods ..................................................... Results ...................., ................................................. Discussion .................................................................. References.................. ,.. .............................................. CHAPTER V Thesis Summary and Future Dktions Zinc-binding domain mutants of RPOZI ............. .....,. ...... V-2 Pointers to a successful synthetic-lethal screen ....................... V-3 GCR3 and RNAP II................................................... V-5 GCR3........................................................................ V-6 SRBS ........................................................................ V-9 The RNAP II CTD and splicing ................. ................... V-10 References.................... .. .......................................... V-13 LIST OF TABLES CHAFTER 1 Table 1.1 Components of the yeast basal transcription machinery.......... I-9 Table 1.2 Cornponents of the yeast RNAP II holoenzyme ........... .... 1-12 Table 1.3 Capping enzymes and the cap-binding complex of yeast. ........ 1-27 Table 1.4
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