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Characterization of Grapevine Vein Clearing Virus Expression CHARACTERIZATION OF GRAPEVINE VEIN CLEARING VIRUS EXPRESSION STRATEGY AND DEVELOPMENT OF CAULIMOVIRUS INFECTIOUS CLONES _______________________________________ A Dissertation presented to the Faculty of the Graduate School at the University of Missouri-Columbia _______________________________________________________ In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in Plant, Insect and Microbial Sciences _____________________________________________________ by YU ZHANG Dr. James E. Schoelz, Dissertation Supervisor DECEMBER 2016 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled CHARACTERIZATION OF GRAPEVINE VEIN CLEARING VIRUS EXPRESSION STRATEGY AND DEVELOPMENT OF CAULIMOVIRUS INFECTIOUS CLONES Presented by Yu Zhang A candidate for the degree of doctor of philosophy In Plant, Insect and Microbial Sciences And hereby certify that, in their opinion, it is worthy of acceptance. Dr. James E. Schoelz, PhD Dr. Wenping Qiu, PhD Dr. David G. Mendoza-Cózatl, PhD Dr. Trupti Joshi, PhD ACKNOWLEDGEMENTS I wish to express my appreciation to my advisor, Dr. James Schoelz, for his constant guidance and support during my doctoral studies. He is a role model to me as an enthusiastic and hard working scientist. Although I will leave MU, I will keep what I learnt from him with my future life. I owe thanks to members of my doctoral committee, Dr. Wenping Qiu, Dr. David G. Mendoza-Cózatl, and Dr. Trupti Joshi, for their helpful comments and suggestions. I also want to thank Dr. Dmitry Korkin, who served in my committee for one year and helped me with bioinformatics and data interpretation. Thanks are due to my colleagues in the lab, Dr. Carlos Angel, Dr. Andres Rodriguez, Mustafa Adhab, and Mohammad Fereidouni, who I really enjoyed working with. In addition, Mustafa Adhab contributed to chapter 5 by helping me with screening vein clearing symptoms on young leaves of N. benthamiana and taking pictures of symptomatic leaves. Mustafa has such a keen eye for early stage viral disease symptoms. Finally, I‟m grateful to my parents, family, and friends for their constant, unconditional support during my studies in Missouri ii TABLE OF CONTENTS ACKNOWLEDGEMENTS ....................................................................................... ii LIST OF TABLES .................................................................................................... vii LIST OF FIGURES .................................................................................................viii ABSTRACT ............................................................................................................. xiv CHAPTER 1: LITERATURE REVIEW ................................................................... 1 1. The family Caulimoviridae ...................................................................... 1 2. The biology of CaMV .............................................................................. 2 2.1. Cauliflower mosaic virus (CaMV) ................................................. 2 2.2. CaMV genome structure and protein functions ............................. 3 2.3. CaMV transcription and replication ............................................. 11 2.4. Translation of the 35S RNA into proteins CaMV proteins ......... 14 2.5. Intracellular, intercellular, and long distance movement of CaMV virions ................................................................................................. ......................................................................................................... 17 3. The genus, Badnavirus ........................................................................... 23 4. Grapevine vein clearing virus (GVCV) ................................................ 25 5. Agroinfiltration and agroinfiltion system for transient gene expression. .................................................................................................................. 34 5.1. The role of A. tumefactions in gene transfer ................................ 35 5.2. Ti plasmid and horizontal gene transfer ....................................... 37 5.3. Binary vector systems .................................................................... 38 6. Characterization of the molecular biology of GVCV. .......................... 41 Reference ........................................................................................................ 42 CHAPTER 2: CHARACTERIZATION OF GRAPEVINE VEIN CLEARING VIRUS (GVCV) PROMOTER ...................................................................... 56 Abstract ........................................................................................................... 56 1. Introduction ............................................................................................. 58 2. Results ..................................................................................................... 60 2.1. The strength of the GVCV promoter is comparable to the CaMV 35S promoter .................................................................................. 60 2.2. Identification of the initiation and termination sites for the major GVCV transcript present in infected grape tissues ...................... 67 2.3. Influence of sORFs in the leader sequence on expression of ORF1 .................................................................................................. ......................................................................................................... 72 3. Discussion ............................................................................................... 77 iii 4. Methods ................................................................................................... 81 4.1. Plasmid Construction ..................................................................... 81 4.2. Agroinfiltration .............................................................................. 82 4.3. GFP ELISA .................................................................................... 82 4.4. 5‟ and 3‟ RACE .............................................................................. 83 4.5. mFold .............................................................................................. 83 Reference ........................................................................................................ 85 CHAPTER 3: A NICOTIANA BENTHAMIANA SYSTEM TO TEST INFECTIVITY OF INFECTIOUS CLONES ............................................... 90 Abstract ........................................................................................................... 90 1. Introduction ............................................................................................. 91 2. Results ..................................................................................................... 93 2.1. CaMV viral DNA was detected from JS215+P6 and JS215+P6-GFP co-infiltration....................................................... 93 2.2. The infectivity of JS215+P6 and JS215+P6-GFP co-infiltration is due to complementation instead of recombination. ..................... 98 2.3. Both P6 and P6-GFP support the expression of CaMV coat protein and virion assembly ........................................................ 101 2.4. CaMV virions form upon co-agroinfiltration of JS215 with P6 or P6-GFP into N. benthamiana leaves ........................................... 101 2.5. JS215+P6 co-infiltration system can be used in other Nicotiana species in addition to N. benthamiana........................................ 103 3. Discussion ............................................................................................. 107 4. Material and methods ........................................................................... 111 4.1. Plasmids ........................................................................................ 111 4.2. Growth and maintenance of plants ............................................. 111 4.3. Agroinfiltration ............................................................................ 113 4.4. Purification of CaMV virions and viral DNA ............................ 113 4.5. PCR ............................................................................................... 114 4.6. Western blotting ........................................................................... 115 4.7. Electron microscopy .................................................................... 116 References .................................................................................................... 117 CHAPTER 4: DEVELOPMENT OF A GRAPEVINE VEIN CLEARING VIRUS INFECTIOUS CLONE AND ANALSYSIS OF PUTATIVE VIRIONS .. 122 Abstract ......................................................................................................... 122 1. Introduction ........................................................................................... 124 2. Results ................................................................................................... 127 2.1. Construction of a terminally redundant GVCV clone ............... 127 iv 2.2. Encapsidated GVCV DNA was detected from Nicotiana benthamiana leaves infiltrated with pGVCV-1 and some plants develop systemic symptoms........................................................ 137 2.3. Attempts to isolate GVCV viral particles from N. benthamiana leaves agroinfiltrated with pGVCV-1 ......................................... 142 2.4. Isolation of flexuous rods
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