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研究生：	陳永茂 Chen, Young-Mao
論文名稱：	神經壞死病毒感染石斑魚免疫反應基因體與蛋白質體學之研究 Genomic and proteomic analysis of host response during nodavirus infection in grouper
指導教授：	陳宗嶽 Chen, Tzong-Yueh 楊惠郎 Yang, Huey-Lang
學位類別：	博士 Doctor
系所名稱：	生物科學與科技學院 - 生物科技研究所 Institute of Biotechnology
論文出版年：	2008
畢業學年度：	96
語文別：	英文
論文頁數：	160
中文關鍵詞：	神經壞死病毒、基因體學、蛋白質體學
外文關鍵詞：	nodavirus, Genomic, proteomic
相關次數：	點閱：137 下載：4
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點帶石斑魚 (Epinephelus coioides)，是台灣最重要的經濟養殖魚類之ㄧ，石斑魚的幼魚受到神經壞死病毒 (nodavirus) 感染死亡的情形相當嚴重，但成魚則相對的沒那麼嚴重，因此點帶石斑的成魚體內似乎有一套有效的防禦機制對抗神經壞死病毒的感染。石斑魚感染神經壞死病毒之後，分析宿主的免疫反應，實驗是利用基因體學與蛋白質體學的技術來說明宿主和病毒之間的相互作用所引發宿主的免疫反應。細胞內免疫螢光實驗發現誘導石斑魚的抗病毒蛋白表現可以藉由結合或干擾神經壞死病毒蛋白在魚細胞內的位置及分佈聚集。神經壞死病毒的外殼蛋白可專一性與抗病毒蛋白之作用子區域結合。dsRNA poly[I:C] 誘導石斑魚的抗病毒蛋白表現抑制神經壞死病毒的感染，顯示誘導石斑魚的抗病毒蛋白表現抑制神經壞死病毒抗原的外殼蛋白的聚集和神經壞死病毒 RNA 聚合酶的功能，造成病毒顆粒量減少。在細胞感染後的早期階段，大量表現石斑魚的抗病毒蛋白仍對神經壞死病毒具抗性。在這個研究裡我們證實石斑魚的抗病毒蛋白在抑制神經壞死病毒的感染扮演重要的角色。

Grouper (Epinephelus coioides) is one of the most important economical fishes in Taiwan, but because virus infection in the adult orange-spotted groupers has often been neglected, thus groupers should have an efficient defense system against the nodavirus, but at the same time the antigens of the nodavirus were also taken noticed of, since the groupers were easily infected by the virus at their juvenile and larvae stage. An outline of it is making use of both the genomic and proteomic techniques during the research to illustrate the interaction between the host and the nodavirus, which caused the immune response of the host after which the groupers were infected by the nodavirus. It has been previously found that an overexpression of grouper Mx was proclaimed as a negative regulator of nodavirus activity through direct interaction, such that grouper Mx induction expression might bind and perturb intracellular localization of coat protein. Deletion analysis of grouper Mx indicated that coat protein of nodavirus could bind to the effector domain of Mx. The presence of grouper Mx in dsRNA poly[I:C] interferon system inhibited nodavirus infection, which showed that overexpressing grouper Mx had an inhibitory effect on both coat protein and RdRp of nodavirus antigens, resulting in reducing levels of virus yields. This study demonstrated a key role of grouper Mx in cellular resistance to nodavirus infection.

Chapter 1: Introduction	                             1
Chapter 2: Grouper Mx confers resistance to nodavirus and interacts with coat protein                              6
Chinese Abstract	                                       7
Abstract	                                                8
1. Introduction	                                       9
2. Materials and Methods                                 19
 2.1. Fish maintenance and collection                    19
 2.2. Cell culture and reagents                          19
 2.3. Virus purification and virus titration             19
 2.4. MTT assay                                          20
 2.5. RNA isolation and RT-PCR                           20
 2.6. Cloning and sequencing                             21
 2.7. Rapid amplification of cDNA ends (RACE) polymerase chain reaction                                           22
 2.8. Construction of Mx promoter-gfp fusion plasmid, cell transfection and reporter gene assay                     22
 2.9. RT-PCR analysis of grouper Mx gene expression      24
 2.10. Western blot analysis                             25
 2.11. Construction of grouper Mx-gfp, Mx-his6 fusion plasmid and generation of stable cell lines              26
 2.12. Production of a polyclonal rabbit anti-grouper Mx antiserum                                                27
 2.13. Construction of glutathione S-transferase or His-tag fusion plasmids                                      28
 2.14. Far Western blotting                              29
 2.15. Expression and purification of GST fusion protein 30
3. Results                                               31
 3.1. Molecular cloning and nucleotide sequencing of grouper Mx cDNA                                          31
 3.2. Analysis of grouper Mx promoter                    31
 3.3. Differential expression of Mx gene in a variety of grouper tissues investigated by RT-PCR                   32
 3.4. Induction of Mx mRNA by nodavirus and iridovirus   33
 3.5. Induction of grouper Mx nodavirus-infected grouper  cells                                                    33
 3.6. Analysis of phylogenetic tree                      34
 3.7. Resistance to nodavirus infection by induction Mx protein in grouper cells                                 35
 3.8. Influence of grouper Mx protein overexpression on viral production                                         37
 3.9. Influence of Mx overexpression of nodavirus gene expression                                               37
 3.10. Detection of the association of nodavirus coat protein and grouper Mx after infection                   38
 3.11. Identification of domains responsible for Mx protein and nodavirus coat protein interaction           38
4. Discussion                                            40
 
Chapter 3:
Myostatin gene organization and nodavirus-influenced expression in orange-spotted grouper (Epinephelus coioides)                                                48
Chinese Abstract	                                       49
Abstract                                                 51
1. Introduction	                                       53
2. Materials and Methods                                 56
 2.1. Fish maintenance and collection                    56
 2.2. RNA isolation and reverse transcriptase chain reaction                                                 56
 2.3. Suppression subtractive hybridization              57
 2.4. Rapid amplification of cDNA ends (RACE) polymerase chain reaction                                           58
 2.5. Cloning of grouper myostatin promoter              58
 2.6. Cloning of introns                                 59
 2.7. Construction of myostatin promoter reporter gene   59
 2.8. Quantitative analysis of grouper myostatin gene expression                                               60
 2.9. Phylogenetic tree analysis                         61
 2.10. Production of a polyclonal grouper myostatin antiserum for Western blotting                           61
 2.11. Two-dimensional (2-D) gel electrophoresis         62
3.Results                                                64
 3.1. Molecular cloning and nucleotide sequencing of grouper myostatin gene                                   64
 3.2. Phylogenetic tree analysis                         65
 3.3. Analysis of grouper myostatin promoter             65
 3.4. Organization of the grouper myostatin gene         66
 3.5. Expression of myostatin RNA transcript in grouper muscle                                                   67
 3.6. Identification of myostatin protein expression     67
 3.7. Influence of nodavirus infection on serum myostatin67
4. Discussion	                                       69

Chapter 4:
Identification of responsive protein of shsp (small heat shock protein) for nervous necrosis virus infection by proteomic approach                                       73
Chinese Abstract	                                       74
Abstract	                                                75
1. Introduction	                                       76
2. Materials and Methods                                 79
 2.1. Two-dimensional (2-D) gel electrophoresis          79
 2.2. RNA isolation and reverse transcriptase chain reaction                                                 79
 2.3. Rapid amplification of cDNA ends (RACE) polymerase chain reaction                                           80
 2.4. Quantitative analysis of grouper shsp gene         81
expression
 2.5. Phylogenetic tree analysis                         82
 2.6. Production of a polyclonal grouper myostatin antiserum for Western                                    82
     blotting
 2.7. Preparation of dityrosine standard                 83
 2.8. Isocratic reverse-phase HPLC                       83

3. Results                                               85
 3.1. Molecular cloning and nucleotide sequencing of grouper shsp gene                                        85
 3.2. Phylogenetic tree analysis                         85
 3.3. Expression of shsp RNA transcript                 85 
 3.4. Identification of small heat shock protein (sHSP) expression                                              86
 3.5. Influence of nodavirus infection on sHSP expression and chaperone-like activity                             86
 3.6. Dityrosine cross-linking promotes formation of stable small heat shock protein polymers                87
4. Discussion                                           87
Chapter 5: Discussion	                            90
Figures, Tables, and Additional Figures	          95
References	                                    138

 Contents of Figures, Tables, and Additional Figures	 95
Figure 1.	The complete nucleotide and deduced amino acid sequences of the grouper (Epinephelus coioides) Mx gen  96
Figure 2.	Functional characterization of the grouper Mx promoter                                                97
Figure 3.	RT-PCR revealing the overall distribution of Mx expression among different tissues                      98
Figure 4.	Time course of Mx expression in brain of nodavirus experimentally -infectedgrouper detected by RT-PCR                                                     99
Figure 5.	Differential effect of nodavirus on transcription of Mx gene in the grouper. Effects of nodavirus, iridovirus, and Vibro anguillarum infected grouper     100
Figure 6.	Immunological subcellular localization of grouper Mx proteins in nodavirus infected or poly[I:C] induced Mx expressing grouper cells                               101
Figure 7.	Neighbour-joining tree of Mx family of different organisms. The treeis based on an alignment corresponding to the full length of the Mx protein                   102
Figure 8.	Effect of poly[I:C] treatment on protection of cells against nodavirus infection                      104
Figure 9.	Nodavirus activity of the mx-expressing clones 105
Figure 10. Proliferative activity was suppressed to some extent in both clonal cell lines expressing Mx          106
Figure 11.Determination of virus production in Mx-expressing cells. Two independent clonal lines of mx-gfp were used; GF-1 cells expressing grouper Mx-GFP proteins, and mx-his6 GF-1 cells expressing grouper Mx-HIS6 proteins                                                107
Figure 12.Inhibition of nodavirus gene expression in the Mx-expressing stable clones                             108
Figure 13.Delineation of grouper Mx binding regions of nodavirus coat protein                                  109
Figure 14.Interaction between nodavirus coat protein and grouper Mx protein                                      111
Figure 15.Nucleotide sequence of the grouper myostatin gene and predicted amino acid sequence                  112
Figure 16.Neighbour-joining tree of myostatin family of different organisms                                     113
Figure 17.Functional characterization of the grouper myostatin promoter                                      115
Figure 18.Diagram presenting the structure of the myostatin gene determined in bovine and grouper         117
Figure 19 Expression levels of myostatin transcripts in different organs of grouper                             118
Figure 20.Two-dimensional protein profiles and immunoblotting analyses. Analyses were conducted on uninfected and nodavirus naturally-infected grouper at 40-45 dph                                                  119
Figure 21.Western blot of myostatin protein in the grouper serum                                                   120
Figure 22.Large scale of cellular proteins separated in 2D gels. Proteins were focused using pH 3-10 NL, IPG strips, separated in 10% SDS - PAGE gels and stained with silver nitrate                                                 121
Figure 23.(A) The nucleotide and deduced amino acid sequence for grouper shsp. (B) Comparision of grouper shsp amino acid sequence to zebrafish shsp. (C) Phylogenetic tree of shsps in vertebrates                            122
Figure 24.Immunoblot analysis with an anti-sHSP antibody of protein extracted from grouper eye tissue of healthy and nodavirus naturally-infectedgrouper.                124
Figure 25.Expression levels of shsp transcripts in different organs of grouper                             125
Figure 26.Chaperone-like activity of sHSP was also observed by fluorescence microscope after nodavirus infection and thermo challenge                          126
Figure 27.Reversed-phase HPLC analysis of tyrosine and dityrosine. Dityrosine and tyrosine were analyzed by HPLC using a C18 column                                      127
Figure 28.The level of dityrosine forms was examined by Western blot analysis                                   128
		
Figure 29.Analysis of shsp with feton reaction aggregates by PAGE. SDS-PAGE Western blot analysis: the figure indicates the presence of aggregates that did not enter the gel matrix                                          129
		
Table 1:	Position and sequence of synthetic oligonucleotide primers used in the study               130
Table 2:	Consensus sequences of splicing sites of the grouper myostatin gene                                  131
Table 3:	Relative quantification of myostatin expression in healthy grouper by quantitative RT-PCR               132
Table 4:	Relative quantification of myostatin expression in healthy grouper by quantitative RT-PCR               133
Table 5:	2-D PAGE protein expression profile of grouper eye                                                     134
Table 6:	Sequences used in the homology analysis and phylogenetic tree                                       135
Table 7:	Relative quantification of myostatin expression in healthy grouper by quantitative                      136
Table 8:	RT-PCR The fold induction of grouper shsp expression after nodavirus infection by quantitative RT-PCR                                                     137
                                    

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