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研究生: 洪素珍
Hung, Su-Jhen
論文名稱: 流感病毒核蛋白基因變異對病毒複製特性的影響
Effect of genetic variations of influenza virus nucleoprotein on virus replication
指導教授: 王貞仁
Wang, Jen-Ren
學位類別: 碩士
Master
系所名稱: 醫學院 - 醫學檢驗生物技術學系
Department of Medical Laboratory Science and Biotechnology
論文出版年: 2014
畢業學年度: 102
語文別: 英文
論文頁數: 57
中文關鍵詞: A型流感病毒核蛋白基因變化聚合酶活性
外文關鍵詞: Influenza A virus, NP, genetic variation, polymerase activity
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  • A型流感病毒具有基因片段重配及快速突變的特性,不僅造成歷史上多次嚴重的大流行,更季節性地在全球傳播與流行。病毒RNA基因被病毒核蛋白及聚合酶包裹成RNP的結構,這個結構是做為病毒基因片段轉錄和複製的單元。核蛋白在病毒複製時扮演重要且多重的角色,它利用與聚合酶、RNA以及宿主細胞中的分子交互作用來進行調控。在本篇研究中,我們希望了解病毒不斷改變的過程中核蛋白基因序列的演化情形,並探討這樣的變化對於病毒複製特性是否有影響。我們收集了臨床上分離出的A型流感H3N2亞型病毒株,以定序方式得到核蛋白基因序列,再用演化分析法檢視基因的演變。在分析的時段中 (1999至2014年),核蛋白基因已經延伸出至少六個演化分枝,且造成許多胺基酸的取代。接著,挑選自不同演化分枝的病毒株之核蛋白基因構築在質體上,利用微基因體實驗(mini-genome assay)去分析基因變化對聚合酶活性的影響。結果發現相較於其它來源,來自Taiwan/N1215/07病毒的核蛋白會顯著地有較高的活性;相對地,來自Taiwan/3446/02病毒的核蛋白則有顯著地較低的活性。進一步分析以定點突變法(site-directed mutagenesis)製造的位點突變,發現在攝氏33及37度的溫度條件下,S450G的取代會顯著地增加聚合酶活性,而K31R的取代會降低活性。另外,將它們突變成丙胺酸(alanine)後觀察到聚合酶活性與細胞中病毒生長速度皆亦有顯著地下降,更加確立這兩個位點對病毒複製的影響。綜合以上實驗結果,我們發現了核蛋白演化出的胺基酸變化確實影響了病毒的複製特性,並且證明31及450是可能的重要位點。我們認為持續性的監測核蛋白病毒基因演化對病毒複製特性的影響是非常重要的。

    Influenza A virus causes severe pandemics and annual epidemics through its RNA genome segment reassortment and frequent gene mutations. The RNA together with viral polymerase PB2, PB1, PA and nucleoprotein (NP) form the ribonucleoprotein (RNP) complexes, which are the functional units for viral genome transcription and replication. In RNP, NP plays an important role on polymerase activity by interaction with viral polymerase, vRNA and multiple host factors. Here, we aim to investigate the NP genetic evolution in human and characterize the effect of identified variations. NP genes of randomly selected H3N2 clinical isolates from 1999 to 2014 were sequenced and many genetic variations were identified. Phylogenetic analysis showed NP genes can be divided into 6 clades. Five NP genes from different clades were cloned into plasmid for the mini-genome assay to analyze the effect of NP genetic variations. The results showed that NP of Taiwan/N1215/07 virus had significantly higher polymerase activity than NP from other isolates; in contrast, NP of Taiwan/N3446/02 had significantly lower polymerase activity both at 33℃ and 37℃. By site-directed mutagenesis, we found that S450G of NP gene increased the polymerase activity but K31R decreased the activity. Furthermore, alanine substitutes of 31 and 450 residues significantly decreased the polymerase activity and virus growth in vitro. In conclusions, by analyzing the genetic variations identified from clinical isolates, we demonstrated that residues 31 and 450 of NP contribute to viral polymerase activity as well as virus replication, indicating the evolutionary genetic variations of NP play roles on functional change of influenza virus.

    Chinese Abstract I Abstract II Acknowledgments III Table of contents IV List of tables VII List of figures VIII List of appendix figures IX Abbreviations X Chapter 1 Introduction 1 1.1 Introduction of influenza viruses 1 1.1.1 Classification and structure of influenza viruses 1 1.1.2 Significance and epidemiology of influenza A viruses 1 1.1.3 Evolution of influenza A viruses 2 1.2 Role of gene segments and translated proteins in influenza virus replication 3 1.2.1 Receptor recognition and endocytosis 3 1.2.2 Membrane fusion and RNA genome release 3 1.2.3 RNA transcription and replication 3 1.2.4 Assembly and viral particle budding 4 1.2.5 Resistance to host immune pressure 4 1.3 Significance of genetic changes in influenza A viruses 5 1.3.1 Surface proteins alteration 5 1.3.2 Internal gene evolution 5 1.4 Character of NP in influenza A viruses 6 1.4.1 Sequence, structure and functional domains of NP 6 1.4.2 Multi-functional roles of NP 6 1.5 Specific aims 7 Chapter 2 Materials and Methods 9 2.1 Materials 9 2.1.1Cell lines 9 2.1.2 Bacteria 9 2.1.3 Primers 9 2.1.3.1 For NP gene amplification 9 2.1.3.2 For NP expression plasmids construction 9 2.1.3.3 For site-directed mutagenesis 10 2.1.4 Plasmids 10 2.1.5 Enzymes 11 2.1.6 Chemicals and reagents 11 2.1.7 Buffers and solutions 12 2.1.8 Kits 13 2.1.9 Instruments 14 2.2 Methods 15 2.2.1 Cell lines and virus isolates 15 2.2.2 NP gene amplified and sequenced 15 2.2.3 Phylogenetic and amino acid substitution analysis 15 2.2.4 Construction of NP expression plasmids and site-directed mutagenesis 16 2.2.5 Mini-genome assay 16 2.2.6 Production of reverse genetics viruses 16 2.2.7 Immunofluorescence stain (IF stain) 17 2.2.8 Virus growth kinetics 17 2.2.9 Plaque assay 17 2.2.10 Analysis of sequences from database 18 2.2.11 Structural modeling of NP 18 Chapter 3 Results 19 3.1 Analyze the NP gene evolution of H3N2 virus isolates from NCKUH 19 3.1.1 Collection of NP gene sequences of H3N2 viruses 19 3.1.2 Analysis of NP gene evolution 19 3.1.3 Analysis of NP amino acid substitutions 19 3.2 Evaluate the effect of genetic variations on polymerase activity 20 3.2.1 Establishment of mini-genome assay 20 3.2.2 Investigation of the effect of NP genetic variations on polymerase activity 21 3.3 Identify determinant of NP on polymerase activity 21 3.3.1 Effect of K31R, S377G and S450G substitutions on NP function 21 3.3.2 Inspection of evolutional change on residue 31, 377 and 450 22 3.3.3 Investigation of the residue 31, 377 and 450 by alanine substitutions 22 3.4 Investigate the effect of substitutions on virus replication 23 3.4.1 Production of reverse genetics viruses with NP mutations 23 3.4.2 Comparison of virus replication 23 3.5 Examine the substitutions on functional domain and structure of NP 24 Chapter 4 Discussion and conclusions 25 References 29

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