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Evolution of Telomerase RNA by Dhenugen Logeswaran A Evolution of Telomerase RNA by Dhenugen Logeswaran A Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy Approved November 2019 by the Graduate Supervisory Committee: Julian Chen, Chair Giovanna Ghirlanda Chad Borges ARIZONA STATE UNIVERSITY December 2019 ABSTRACT The highly specialized telomerase ribonucleoprotein enzyme is composed minimally of telomerase reverse transcriptase (TERT) and telomerase RNA (TR) for catalytic activity. Telomerase is an RNA-dependent DNA polymerase that syntheizes DNA repeats at chromosome ends to maintain genome stability. While TERT is highly conserved among various groups of species, the TR subunit exhibits remarkable divergence in primary sequence, length, secondary structure and biogenesis, making TR identification extremely challenging even among closely related groups of organisms. A unique computational approach combined with in vitro telomerase activity reconstitution studies was used to identify 83 novel TRs from 10 animal kingdom phyla spanning 18 diverse classes from the most basal sponges to the late evolving vertebrates. This revealed that three structural domains, pseudoknot, a distal stem-loop moiety and box H/ACA, are conserved within TRs from basal groups to vertebrates, while group- specific elements emerge or disappear during animal TR evolution along different lineages. Next the corn-smut fungus Ustilago maydis TR was identified using an RNA- immunoprecipitation and next-generation sequencing approach followed by computational identification of TRs from 19 additional class Ustilaginomycetes fungi, leveraging conserved gene synteny among TR genes. Phylogenetic comparative analysis, in vitro telomerase activity and TR mutagenesis studies reveal a secondary structure of TRs from higher fungi, which is also conserved with vertebrates and filamentous fungi, providing a crucial link in TR evolution within the opisthokonta super-kingdom. i Lastly, work by collabarotors from Texas A&M university and others identified the first bona fide TR from the model plant Arabidopsis thaliana. Computational analysis was performed to identify 85 novel AtTR orthologs from three major plant clades: angiosperms, gymnosperms and lycophytes, which facilitated phylogenetic comparative analysis to infer the first plant TR secondary structural model. This model was confirmed using site-specific mutagenesis and telomerase activity assays of in vitro reconstituted enzyme. The structures of plant TRs are conserved across land plants providing an evolutionary bridge that unites the disparate structures of previously characterized TRs from ciliates and vertebrates. ii DEDICATION This dissertation is dedicated to my family whose unconditional love and unwavering support made all this possible in my life. In memory of my beloved father and my first teacher, Caruppiah Logeswaran, who passed away two years ago. My mother, Santhirapavani Logeswaran whose inspiring strength is the driving force that made me reach many milestones. My brother, Lajanugen Logeswaran, my intellectual role model. My wife Nirupa Nagaratnam, who supported me physically, emotionally and intellectually through college and my PhD. Their sacrifices are unmatched, and I will forever be grateful. Finally, our son Ashwick, whose arrival is the single greatest joy in our life. iii ACKNOWLEDGMENTS My deepest gratitude to my advisor Prof. Julian Chen who demanded rigorous and meticulous work instilling in me the passion for scientific glory. He taught me everything about being a great scientist from critical thinking to even managing time. His lessons will forever accompany me in all my future scientific endeavors. I am grateful to my fellow lab members of the Chen lab past and present; Joshua Podlevsky, Dustin Rand, Yinnan Chen, Zhenqiu Huang, Bowen Liu and Yang Li for being great team members and for many insightful discussions. Undergraduate students past and present who performed tedious work to acquire invaluable laboratory training. iv TABLE OF CONTENTS Page LIST OF TABLES ................................................................................................................ viii LIST OF FIGURES ................................................................................................................. ix CHAPTER 1 INTRODUCTION ................................................................................................ 1 1.1 Overview of Telomeres and Telomerase Research .................................... 1 1.2 Telomerase Reverse Transcriptase .............................................................. 6 1.3 Telomerase RNA ......................................................................................... 8 1.4 Recent Advances in Structural Studies of Telomerase Holoenzyme ....... 15 1.5 References .................................................................................................. 17 2 STRUCTURE AND FUNCTION OF METAZOAN TELOMERASE RNA ... 36 2.1 Abstract ...................................................................................................... 36 2.2 Introduction ................................................................................................ 37 2.3 Materials and Methods .............................................................................. 41 2.4 Results ........................................................................................................ 44 2.5 Discussion .................................................................................................. 51 2.6 References .................................................................................................. 59 3 STRUCTURE AND FUNCTION OF USTILAGO FUNGAL TELOMERASE RNA ...................................................................................................................... 74 3.1 Abstract ...................................................................................................... 74 3.2 Introduction ................................................................................................ 75 3.3 Materials and Methods .............................................................................. 79 v CHAPTER Page 3.4 Results ........................................................................................................ 84 3.5 Discussion .................................................................................................. 91 3.6 References .................................................................................................. 97 4 STRUCTURE AND FUNCTION OF LAND PLANTS TELOMERASE RNA .................................................................................................................... 114 4.1 Abstract .................................................................................................... 114 4.2 Introduction .............................................................................................. 115 4.3 Materials and Methods ............................................................................ 118 4.4 Results ...................................................................................................... 120 4.5 Discussion ................................................................................................ 127 4.6 References ................................................................................................ 130 REFERENCES .................................................................................................................... 145 APPENDIX A SPECIES IDENTIFICATION VIA PCR AMPLIFICATIOF OF RIBOSOMAL RNA AND SANGER SEQUENCING .................................................... 162 B PLASMID MAP OF PCM955-3XFLAG-UMATERT ................................... 164 C READ COVERAGE OF U. MAYDIS CANDIDATE #2 LOCUS ................. 166 D UMATR α SEQUENCE AND TEMPLATE ANNOTATION ....................... 168 E MULTIPLE SEQUENCE ALIGNMENT OF UMAG_03168 HOMOLOGS 170 F MULTIPLE SEQUENCE ALIGNMENT OF CAR2-ORNITHINE OXO-ACID TRANSAMINASE (OAT) ...................................................................... 172 G EXPANDED PHYLOGENETIC TREE OF LAND PLANTS ....................... 174 vi APPENDIX Page H CO-AUTHOR APPROVAL .............................................................................. 176 vii LIST OF TABLES Table Page 4.1 Species with Land Plant TRs Identified in this Study ........................................ 142 viii LIST OF FIGURES Figure Page 1.1 Telomere Sequences of Major Eukaryotic Groups ............................................... 29 1.2 Schematic of the End-replication problem ........................................................... 30 1.3 Telomerase adds DNA Repeats to Telomeres de novo ....................................... 31 1.4 Domain Architecture of the Catalytic TERT Protein ......................................... 32 1.5 Conserved Structural Domains of TR from well-studied Groups ....................... 33 1.6 Diverse TR Biogenesis Pathways from Major Organism Groups ...................... 34 1.7 Cryo-EM structures of Tetrahymena and Human Telomerase ............................ 35 2.1 Phylogeny Assisted TR Identification Approach ................................................ 63 2.2 Phylogenetic Tree of Metazoan Kingdom with Number of TRs Identified Shown ............................................................................................................ 65 2.3 Validation and Characterization of Saccoglossus kowalevskii (acorn worm) TR ..................................................................................................................
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