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研究生:毛乙智
研究生(外文):Yi-Chih Mao
論文名稱:胡瓜嵌紋病毒衛星核酸的移動及其與輔助病毒外鞘蛋白、移動蛋白間的交互作用
論文名稱(外文):The Movement Mechanism of Satellite RNAs Associated with Cucumber Mosaic Virus (CMV) and the Interactions with CMV-encoded Coat Protein and Movement Protein
指導教授:胡仲祺
指導教授(外文):Chung-Chi Hu
學位類別:博士
校院名稱:國立中興大學
系所名稱:生物科技學研究所
學門:生命科學學門
學類:生物科技學類
論文種類:學術論文
畢業學年度:96
語文別:英文
論文頁數:158
中文關鍵詞:胡瓜嵌紋病毒衛星核酸外鞘蛋白移動蛋白系統性移動核酸-蛋白交互作用
外文關鍵詞:CMVCPMPSystemic movementRNA-Protein interaction
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當胡瓜嵌紋病毒(Cucumber mosaic virus, CMV)進行細胞間移動時必須依賴外鞘蛋白(Coat protein, CP)、移動蛋白(Movement protein, MP)與寄主植物因子(Host factors)三者間的交互作用後,以核醣核蛋白複合體(Ribonucleoprotein complex)的型態通過原生質絲(Plasmodesmata)進而感染鄰近的細胞。因此蛋白與核酸間的交互作用在病毒移動機制中扮演著極重要的角色。然而衛星核酸在植物細胞間移動之分子機制至今尚未明瞭,所以本研究主要目的在於探討CMV基因體核酸與衛星核酸與其CP、MP交互作用,以期能了解衛星核酸在植物體內移動之分子機制。為求高效率分析核酸與蛋白分子間之交互作用,以分析系統Nucleoprotein Binding ELISA (NB-ELISA), 並配合核酸與蛋白質交互作用之定量分析與解離常數(Kd)測定,來快速偵測分析衛星核酸,MP與CP分子間之交互作用。利用大腸桿菌中表現CP不同區域片段與衛星核酸進行交互作用,結果顯示CP之N端前30個胺基酸為主要結合衛星核酸之區域。然後利用衛星核酸、CMV基因體核酸及全長MP與MP CΔ84(胺基酸位置199-283)以NB-ELISA方法測試,實驗結果指出全長MP能與CMV 3’NCR正負股和雙股核酸和正單股菸草嵌紋病毒 (Tobacco Mosaic Virus, TMV)的TLS (tRNA-like structure)形成複合體進行結合,但無法與正單股的衛星核酸結合。此外利用MP CΔ84與變性MP做相同的測試,結果發現當MP CΔ84與變性MP會對正單股衛星核酸會有親和力並且對核酸的親和力也會上升。由上述實驗結果得知CMV與衛星核酸可能存有不同的移動機制。藉由單一點突變分子標記W株系衛星核酸,接種在不同植物上去研究衛星核酸移動機制。實驗結果指出單獨W株系衛星核酸能夠在N. benthamiana與N. tabacum進行雙向系統性移動,但在C. quinoa上則否。但是藉由CMV提供外鞘蛋白與移動蛋白在C. quinoa上則可以幫助W株系衛星核酸進行系統性移動。總結全部實驗結果得知衛星核酸移動的分子機制與CMV有所不同,而且藉由瞭解衛星核酸雙向系統性移動可得知RNA運輸的管道可能為篩管(phloem)。
Cell-to-cell movement of plant viruses through plasmodesmata involves specific host and viral factors i.e. coat protein (CP) and movement protein (MP). And the virus is inevitably assisted by cellular mechanisms in MP targeting, plasma membrane anchoring and transporting of the MP through the plasmodesmal pore. Therefore the interactions among the virus factors play an important role in the molecular mechanism of virus movement. Some CMV strains contain satellite RNAs (satRNAs), which are molecular parasites and depend on helper virus for replication, encapsidation, and transmission, but share little or no sequence similarity to the helper virus. Despite the knowledge on the movement mechanisms of viral RNAs, little is known concerning the cell-to-cell and long distance movement of satRNAs in plants. Therefore, the aims of this study are to analyze the molecular interactions among the CP, MP, genomic RNAs and satRNAs. Nucleoprotein Binding-Enzyme Linked Immunosorbent Assay (NB-ELISA) was applied to facilitate detections and analyses of the interactions between nucleic acids and protein molecules. The N-terminal 30 amino acids were shown to be the solely required region to recognize satRNAs. The truncated MP CΔ84, but not wild-type MP, could interact with satRNA to form the nucleoprotein complex, suggesting that CMV genomic RNAs and satRNAs may move from cell to cell by different mechanisms. To examine the possibility, satRNA was transiently expressed in leaves of Nicotiana benthamiana, Nicotiana tabacum, and Chenopodium quinoa infected with engineered Agrobacterium tumefaciens. SatRNA trafficked within the phloem bidirectionally to sink leaves near the apical meristem as well as to the source leaves at the bottom of the plant. These results demonstrate that satRNA can use a CMV-independent movement mechanism to traffic in N. benthamiana and N. tabacum.
TABLE OF CONTENTS
Abstract in Chinese---------------------------------------------------------------------------1
Abstract in English----------------------------------------------------------------------------2
Literature review------------------------------------------------------------------------------3
A) Introduction--------------------------------------------------------------------------------3
B) Taxonomy-----------------------------------------------------------------------------------3
C) Biological properties----------------------------------------------------------------------4
D) Genome structure, organization and function---------------------------------------4
1. Tripartite genome-------------------------------------------------------------------------5
2. RNA 1 and its gene function------------------------------------------------------------5
3. RNA 2 and its gene function------------------------------------------------------------7
4. RNA 3 and function of its genes--------------------------------------------------------8
5. Subgenomic RNAs-----------------------------------------------------------------------9
E) Satellite RNAs (satRNAs) associated with cucumoviruses------------------------12
1. Introduction------------------------------------------------------------------------------12
2. Effect on host plants and helper viruses----------------------------------------------13
3. Potential utilities of satRNAs----------------------------------------------------------14
F) The movement of plant viruses in general--------------------------------------------15
G) Cell to cell movement---------------------------------------------------------------------16
H) Long distance movement----------------------------------------------------------------17
I) Movement of small, non-coding RNAs-------------------------------------------------18
J) Canonical methods for studying Protein-RNA interactions-----------------------20
K) Summary for literature review---------------------------------------------------------21

CHAPTER I. Analyses of Molecular Interactions between the Coat Proteins of Cucumber Mosaic Virus and the Associated Satellite RNAs by a High-Throughput Method Based on ELISA---------------------------------------------23
A) Abstract--------------------------------------------------------------------------------------24
B) Introduction--------------------------------------------------------------------------------25
C) Materials and Methods-------------------------------------------------------------------29
D) Results---------------------------------------------------------------------------------------35
1. Development and optimization of NB-ELISA----------------------------------------35
2. Calculation of Apparent Dissociation Constant (Kd) using NB-ELISA Readings-----------------------------------------------------------------------------------36
3. Interactions between CP and gRNA3 in liquid phase or on solid support--------36
4. Comparison of the interaction of satRNA with CP purified from virions and expressed from E. coli.------------------------------------------------------------------37
5. Analyses of Kd’s for interactions between CMV CP and CMV gRNA3, satRNA, or 3’ NCR of TMV-----------------------------------------------------------------------38
6. Effect of reaction time and virion concentration on the interaction between CMV CPs and satRNAs------------------------------------------------------------------------39
7. Interactions between intact CMV virions and satRNAs-----------------------------40
8. Specificity of the interaction between CMV CPs and satRNAs--------------------41
1). Delineation of regions in CMV CPs interacting with satRNAs----------------42
2).Confirmation of the results of NB-ELISA by Northwestern Hybridization analyses---------------------------------------------------------------------------------43
E) Discussion-----------------------------------------------------------------------------------45

CHAPTER II. Molecular Interactions of Movement Proteins, Coat Proteins, Genomic RNAs and Satellite RNA of Cucumber Mosaic virus----------------------63
A) Abstract--------------------------------------------------------------------------------------64
B) Introduction--------------------------------------------------------------------------------65
C) Materials and Methods-------------------------------------------------------------------68
D) Results---------------------------------------------------------------------------------------72
1. Production and purification of the CMV movement proteins (MPs) -------------72
2. Analysis of interactions between MP and 3’ NCR of CMV------------------------72
3. Analysis of interactions between CMV MP and SatRNAs--------------------------73
4. Analysis of the influence of MP on the nucleic acid-binding capability of CP---74
5. Analysis of the affinity of MP to (+)-, negative-sense [(-)-], or double stranded (ds-) CMV 3’ NCR and SatRNA-------------------------------------------------------75
6. Analysis of the influence of C-terminal deletion of MP on the interactions with CMV 3’ NCR, SatRNA, and TMV 3’ NCR------------------------------------------75
7. Analysis of the effect of increased concentration of SatRNA on the affinity to CMV MP----------------------------------------------------------------------------------76
E) Discussion-----------------------------------------------------------------------------------77


CHAPTER III. Studies on the Systemic Movement Mechanism of Satellite RNAs Associated Cucumber Mosaic Virus-------------------------------------------------------93
A) Abstract--------------------------------------------------------------------------------------94
B) Introduction--------------------------------------------------------------------------------95
C) Materials and Methods-------------------------------------------------------------------99
D) Results--------------------------------------------------------------------------------------103
1. Generation of mutant SatRNA by point mutation----------------------------------103
2. Confirmation of the conservation of biological characteristics in W-SatRNA-103
3. Expression of W-SatRNA in plant cells using Agrobacterium-mediated transient expression system----------------------------------------------------------------------104
4. Systemic movement of W-SatRNA in plants----------------------------------------104
5. Agrobacterium could not move systemically to the un-inoculated leaves of N. benthamiana-----------------------------------------------------------------------------105
6. CMV W-SatRNA cold perform bi-directional systemic movement in N. benthamiana and N. tabacum independent of CMV-------------------------------105
7. CMV W-SatRNA alone could not move systemically in C. quinoa--------------107
8. When co-inoculated, W-SatRNA RNAs, but not CMV-NT9, could move systemically to the un-inoculated leaves in C. quinoa-----------------------------108
E) Discussion----------------------------------------------------------------------------------109
F) References---------------------------------------------------------------------------------125
G) Appendix-----------------------------------------------------------------------------------157
H) List of abbreviations--------------------------------------------------------------------158


LIST OF FIGURES AND TABLES
Figure 1.1. Schematic representation of the NB-ELISA workflow. ---------------------51
Figure 1.2. Binding of CMV CP to CMV gRNA3 as assayed by NB-ELISA. --------52
Figure 1.3. Comparison of the affinity between CMV CP and DIG-labeled CMV gRNA3 in solid and liquid phases as determined using NB-ELISA. ------53
Figure 1.4. The binding of single strand satRNA to CMV CP purified from virions or expressed by bacteria as determined by NB-ELISA. ------------------------54
Figure 1.5. Comparison of the affinities between CMV CP and DIG-labeled CMV gRNA3, SatRNA, or TMV 3’NCR. --------------------------------------------55
Figure 1.6. The interaction between satRNAs and intact CMV virions as measured by NB-ELISA. ------------------------------------------------------------------------56
Figure 1.7. Time course analysis of the interaction between CMV virions and satRNAs as measured by NB-ELISA. -----------------------------------------57
Figure 1.8. Analysis of virion integrity in different buffers by sucrose density gradient centrifugation. ------------------------------------------------------------------58
Figure 1.9. Mapping of domains on CMV CPs responsible for the interaction with satRNAs by NB-ELISA. --------------------------------------------------------59
Figure 1.10. Confirmation of the interactions between various portions of CMV CPs and DIG-labeled satRNAs by northwestern hybridization analyses. ------60
Figure S1. Optimization of conditions for interactions between satRNA and CMV CP as measured by NB-ELISA. --------------------------------------------------61
Figure S2. Specificity of interactions between different proteins and satRNAs as measured by NB-ELISA. -----------------------------------------------------62
Figure 2.1. SDS-PAGE analysis of CMV MP expressed in E. coli. --------------------82
Figure 2.2. Alignment of highly conserved domains of CMV MP and MP CΔ84. ---83
Figure 2.3. Comparison of the affinity between CMV MP and DIG-labeled CMV gRNA3 in solid and liquid phases as determined using NB-ELISA. ---84
Figure 2.4. Comparison of interactions between CMV MP and DIG-labeled CMV gRNA3 and SatRNA. ----------------------------------------------------------85
Figure 2.5. Effect of MP conformation on its ability to interact with SatRNA as measured by NB-ELISA. -----------------------------------------------------86
Figure 2.6. Effect of CMV MP on the binding of CMV CP to various RNAs. -------87
Figure 2.7. Comparison of the binding of full-length CMV MP to various types of RNAs by using NB-ELISA. --------------------------------------------------88
Figure 2.8. Comparison the binding of CMV MP CΔ84 to CMV 3’NCR, SatRNA, and TMV 3’NCR as determined by NB-ELISA. ---------------------------89
Figure 2.9. Comparison of the binding of full-length CMV MP to various RNAs. ---90
Figure 3.1. Schematic representation of the pBin19-WsatRNA, pBin19-EGFP, and pBin19-HcPro constructs. ------------------------------------------------------112
Figure 3.2. Confirmation of the sequence of satRNA mutant, Wsat. ------------------113
Figure 3.3. Biological characteristics of the mutant satRNA, Wsat, used in this study. --------------------------------------------------------------------------------------114
Figure 3.4. Agarose gel electrophoretic analysis of RT-PCR amplified products of WsatRNA in different leaves of N. bemthamiana (N. b.) and N. tabacum (N. t.). -----------------------------------------------------------------------------115
Figure 3.5. Analysis of the movement of mRNAs in plants. ---------------------------116
Figure 3.6. Examination of upward systemic movement of WsatRNA by RT-PCR or strand-specific PCR programmed with RNAs extracted from different leaves of N. bemthamiana. -----------------------------------------------------117
Figure 3.7. Examination of downward systemic movement of WsatRNA by RT-PCR or strand-specific PCR programmed with RNAs extracted from different leaves of N. bemthamiana. -----------------------------------------------------118
Figure 3.8. Examination of upward systemic movement of WsatRNA in N. tabacum. --------------------------------------------------------------------------------------119
Figure 3.9. Examination of downward systemic movement of WsatRNA in N. tabacum. --------------------------------------------------------------------------120
Figure 3.10. Examination of systemic movement of WsatRNA in Chenopodium quinoa without the presence of CMV. -------------------------------------121
Figure 3.11. Examination of systemic movement of WsatRNA in Chenopodium quinoa with the helper virus CMV. -----------------------------------------122
Table 1. Binding parameters for the interaction of CP, MP with DIG-labeled transcripts RNAs--------------------------------------------------------------------91
Table 2: Sequences of the oligonucleotide primers---------------------------------------123
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