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INTERACTIONS BETWEEN TWO NATURALLY CO-INFECTING MYCOVIRUSES in the CHESTNUT BLIGHT FUNGUS Cryphonectria Parasitica

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INTERACTIONS BETWEEN TWO NATURALLY CO-INFECTING MYCOVIRUSES in the CHESTNUT BLIGHT FUNGUS Cryphonectria Parasitica INTERACTIONS BETWEEN TWO NATURALLY CO-INFECTING MYCOVIRUSES IN THE CHESTNUT BLIGHT FUNGUS Cryphonectria parasitica March, 2020 ANNISA’ AULIA Graduate School of Environmental and Life Science (Doctor’s Course) OKAYAMA UNIVERSITY TABLE OF CONTENTS LIST OF FIGURES ...................................................................................................................... V LIST OF TABLES ...................................................................................................................... VI GENERAL INTRODUCTION ............................................................................ 1 A. VIRUSES INFECTING FUNGI .............................................................................................. 1 B. MYCOVIRUS TAXONOMY ................................................................................................. 2 C. CHESTNUT BLIGHT DISEASE AND DISCOVERY OF HYPOVIRULENCE ................... 3 D. VIRUSES INFECTING CRYPHONECTRIA PARASITICA ............................................................. 4 E. VIRUS/VIRUS INTERACTIONS........................................................................................... 5 1. Synergistic Interactions ....................................................................................................... 5 2. Mutualistic Interactions ...................................................................................................... 6 3. Antagonistic Interactions .................................................................................................... 6 F. RESEARCH OBJECTIVE....................................................................................................... 7 CO-INFECTION OF DOUBLE-STRANDED RNA VIRUS AND A POSITIVE STRAND RNA VIRUS IN CRYPHONECTRIA PARASITICA STRAIN C18 .. 8 A. INTRODUCTION ................................................................................................................... 8 1. Family Reoviridae............................................................................................................... 8 2. Family Hypoviridae ............................................................................................................ 9 3. Virus co-infection in fungi ................................................................................................ 10 B. MATERIAL METHODS ....................................................................................................... 11 1. Fungal strains and culturing .............................................................................................. 11 2. RNA preparation ............................................................................................................... 11 3. Next-generation sequencing ............................................................................................. 11 4. Terminal sequence determination ..................................................................................... 12 5. Asexual sporulation assays ............................................................................................... 14 6. One-step RT-PCR ............................................................................................................. 14 7. Spheroplast preparation .................................................................................................... 14 8. Transformation of C. parasitica spheroplast .................................................................... 15 C. RESULTS .............................................................................................................................. 16 1. C. parasitica C18 strain is co-infected with a mycoreovirus and a hypovirus ................. 16 2. Comparison of CHV4 genome sequence that infects strain C18 with previously reported CHV4-SR2 sequence ............................................................................................................. 17 ii 3. Isolation of virus-free and singly infected fungal strains with the C18 genetic background 20 D. DISCUSSION ........................................................................................................................ 22 STABLE MAINTENANCE OF MYRV2 IN C. PARASITICA C18 IS FACILITATED BY CHV4-C18 THROUGH SUPPRESSION OF HOST ANTIVIRAL DEFENSE ..................................................................................................................................... 24 A. INTRODUCTION....................................................................................................................... 24 1. RNA interference (RNAi) ................................................................................................. 24 2. RNAi in fungi (RNA silencing) ........................................................................................ 26 3. RNAi as an antiviral defense in fungi ............................................................................... 27 4. Mycovirus transmission .................................................................................................... 27 B. MATERIAL METHODS ............................................................................................................. 28 1. Fungal strain and culturing ............................................................................................... 28 2. Northern blot analysis ....................................................................................................... 29 3. The dcl2 knockout assay ................................................................................................... 29 4. Virus particle purification ................................................................................................. 31 5. Virus Transfection ............................................................................................................ 31 C. RESULTS ................................................................................................................................. 33 1. CHV4-C18 facilitates stable maintenance of MyRV2 infection during subculturing ...... 33 2. MyRV2 vertical transmission via asexual spores ............................................................. 34 3. Development of dcl2 knock-out strain in C18 strain (C18 dcl2) ................................... 35 4. Antiviral RNA silencing target MyRV2 and reduces its stability .................................... 38 5. CHV4-C18 suppresses host antiviral defense mechanism and leads to stable accumulation level of MyRV2 ............................................................................................... 40 6. MyRV2 is susceptible toward host antiviral defense and its induced state impairs replication and horizontal transmission. ................................................................................ 42 7. Constitutive expression of dcl2 transcript limits MyRV2 replication .............................. 45 D. DISCUSSION ............................................................................................................................ 46 INVESTIGATION OF THE HOST ANTIVIRAL SUPPRESSOR ENCODED BY CHV4-C18 ......................................................................................................... 48 A. INTRODUCTION....................................................................................................................... 48 1. Viral antiviral RNA silencing suppressor ......................................................................... 48 2. Mechanism of antiviral suppressor ................................................................................... 49 B. MATERIAL METHODS ............................................................................................................. 52 1. Fungal strain and culturing ............................................................................................... 52 iii 2. Green fluorescent protein observation .............................................................................. 52 3. Protein expression and purification .................................................................................. 54 4. SDS-PAGE ....................................................................................................................... 54 5. Amino acid sequence ........................................................................................................ 54 6. Small RNA analysis .......................................................................................................... 55 C. RESULT ................................................................................................................................... 55 1. Development of a method for assessing RNA silencing suppressor activities ................. 55 2. Viral small RNA profiles of CHV4-C18 and MyRV2 in single and double infections ... 58 3. Mapping of the functional domain of papain-like protease encoded by CHV4-C18 ....... 59 4. The p24 papain-like protease of CHV4-C18 functions as an RSS ................................... 61 5. CHV4-C18 p24 facilitates MyRV2 stable infection ......................................................... 63 D. DISCUSSION ............................................................................................................................ 64 GENERAL DISCUSSION AND SUMMARY .................................................. 66 REFERENCES ............................................................................................................................ 69 iv LIST
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