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Decoding the Translation Initiation Mechanism of Maize Chlorotic Mottle Virus

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Decoding the Translation Initiation Mechanism of Maize Chlorotic Mottle Virus Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2020 Decoding the translation initiation mechanism of maize chlorotic mottle virus Elizabeth Jacqueline Carino Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Recommended Citation Carino, Elizabeth Jacqueline, "Decoding the translation initiation mechanism of maize chlorotic mottle virus" (2020). Graduate Theses and Dissertations. 17962. https://lib.dr.iastate.edu/etd/17962 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Decoding the translation initiation mechanism of maize chlorotic mottle virus by Elizabeth Jacqueline Carino A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Genetics and Genomics Program of Study Committee: Wyatt A. Miller, Major Professor Steven Whitham Thomas Lubberstedt Walter Moss Bing Yang The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2020 Copyright © Elizabeth Jacqueline Carino, 2020. All rights reserved. ii DEDICATION I want to dedicate this thesis to all I hold dear: friends, family, mentors, and colleagues. During my scientific journey at Iowa State University, I had the privilege to cultivate long- lasting friendships from diverse academic fields from bioinformatics, agronomy, business, electrical engineering, physics, chemistry, mechanical engineering, graphic design, genetics and genomics, plant pathology and microbiology, kinesiology, mathematics, chemical engineering, psychology, to the department of education and many others fields. Thank you! I am grateful for all your unwavering support through good times and rough times. Thank you all for being a marvelous council of friends. To my mom: thank you for supplying me with the building blocks I needed to build up my strength and resilience. Unfortunately, you didn’t have the chance to see the final product of this dissertation as your end arrived abruptly during the first stages of my dissertation journey. Nonetheless, I dedicate this thesis to you. I miss you. ¡Lo logramos! To my GMAP people: I would like to thank all of the graduate college staff and the graduate student volunteers who served with me in the GMAP research symposium committee during my four years of service. It was inspiring to be surrounded by brilliant minds who were willing to showcase and support the greatness of others. To all the unsung graduate student heroes with whom I have the opportunity to collaborate and work towards making a greater impact on the ISU campus and the Ames community, this dissertation also goes to you. I look forward to the contributions in your respective fields and society. iii TABLE OF CONTENTS Page LIST OF FIGURES ....................................................................................................................... vi LIST OF TABLES ......................................................................................................................... ix ACKNOWLEDGMENTS ...............................................................................................................x ABSTRACT ................................................................................................................................... xi CHAPTER 1: LITERATURE REVIEW .........................................................................................1 Preface ....................................................................................................................................... 1 Tombusviridae Family ............................................................................................................... 1 Tombusviridae Family- Brief History .................................................................................. 1 General Overview ................................................................................................................. 4 Virus Replication .................................................................................................................. 7 Cap-Independent Translation Elements (CITEs) .................................................................... 14 Cap-independent translation elements classification ......................................................... 15 Maize Lethal Necrosis (MLND) .............................................................................................. 19 What causes Maize Lethal Necrosis Disease? ................................................................... 19 From its origins until now .................................................................................................. 21 Economic Impact ................................................................................................................ 21 Detection and Prevention ................................................................................................... 22 Maize Chlorotic Mottle Virus .................................................................................................. 22 Overview ............................................................................................................................ 22 MCMV Symptoms ............................................................................................................. 23 MCMV transmission .......................................................................................................... 25 MCMV detection ................................................................................................................ 26 Molecular Information ....................................................................................................... 28 References ............................................................................................................................... 31 Figures ..................................................................................................................................... 44 Tables ....................................................................................................................................... 62 CHAPTER 2: THE RNA OF MAIZE CHLOROTIC MOTTLE VIRUS - THE ESSENTIAL VIRUS IN MAIZE LETHAL NECROSIS DISEASE - IS TRANSLATED VIA A PANICUM MOSAIC VIRUS-LIKE CAP-INDEPENDENT TRANSLATION ELEMENT ..........................67 Abstract .................................................................................................................................... 67 Author Summary ..................................................................................................................... 68 Introduction ............................................................................................................................. 69 Results ..................................................................................................................................... 71 Mapping the 3’-cap-independent translation element in MCMV ...................................... 71 Determining the secondary structure of MCMV 3’-CITE ................................................. 73 Comparison of the MTE to PTEs: role of the pseudoknot ................................................. 74 The MTE binds eIF4E ........................................................................................................ 77 Secondary structure of the MCMV 5’-UTR ....................................................................... 79 iv Long distance base pairing of the MTE to the 5’ UTR ...................................................... 79 Effects of mutations on the translation of full-length MCMV genomic RNA ................... 81 Replication of mutant MCMV RNA .................................................................................. 82 Discussion ................................................................................................................................ 84 Identification of the 3’CITE in MCMV genome ................................................................ 84 Long-distance kissing stem-loop interactions .................................................................... 86 Translation of sgRNA1 ...................................................................................................... 87 Efficient replication vs efficient translation? ..................................................................... 88 Toward host resistance to MCMV ..................................................................................... 89 Materials and methods ............................................................................................................. 90 Plasmids.............................................................................................................................. 90 In vitro Transcription.......................................................................................................... 90 In vitro
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