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標題: 胡瓜嵌紋病毒衛星核酸的起源與修復機制之研究
Studies on the origin and repair mechanism of satellite RNAs associated with Cucumber mosaic virus
作者: 游慧玲
You, Huei-Ling
關鍵字: cucumber mosaic virus;胡瓜嵌紋病毒;satellite RNA;衛星核酸
出版社: 生物科技學研究所
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胡瓜嵌紋病毒(Cucumber mosaic virus, CMV)為Bromoviridae科,Cucumovirus屬的三基因體正股植物RNA病毒。有些分離株攜帶有衛星核酸(satellite RNA, satRNA),為一小段線狀的核酸,長度介於330至405核苷酸間,需仰賴輔助病毒進行複製、包被及傳播,但與其輔助病毒並無核酸序列的相似性。先前研究顯示在接種CMV的實驗植物中經常發現satRNA的出現,且接種satRNA序列刪減突變株時,也顯示satRNA經常能自動修補缺失的序列。然而,衛星核酸的起源與其修補缺失所使用的複製模板至今仍然不明。本實驗利用基因庫搜尋比對及人為演化的方法,期能找出其可能的起源或修補來源,所搜尋比對的基因庫有植物(包含真菌)、微生物及無脊椎動物的基因庫,利用SSearch及FASTA的方法搜尋比對;而人為演化的方法則是將序列有缺失的衛星核酸與輔助病毒共同接種至非自然寄主及接種後給予嚴苛的生長壓力來促進其演化。欲接種的satRNA是構築在以CMV RNA 3為基礎的載體上,是將外鞘蛋白的大部分置換成satRNA的cDNA,再將此含有satRNA cDNA序列的RNA 3構築到已含有兩個35S啟動子的質體上,與CMV共同接種至植物,利用CMV複製時不斷產生新的satRNA分子,以做為人為演化的起始。本實驗所構築的satRNA有兩種,第一種是正對照組satNdeI (pd35S-R3-satNdeI),與野生型satRNA只差異一個核苷酸(T164A)使能被限制酵素NdeI水解(張, 2004),第二種是測試組satM26 (pd35S-R3-satM26),其為從第124到第237個核苷酸缺失並多出了12 nt與野生型衛星核酸無關之序列,且發現將satM26與CMV共同接種至Nicotiana benthamiana中,在某些情況下satM26會恢復為野生型satRNA (陳, 2005)。對目前基因庫比對結果進行分析,將搜尋比對到相同satRNA區域之序列進行多序列比對後,再進行共變異分析,發現到有與衛星核酸相似之共變異區域存在,對此區域進行二級結構預測分析,發現有相似之結構,當它們存在同一環境中,有可能在病毒進行複製的時候,被複製相關蛋白辨認且複製,然後一起包被在病毒的外鞘蛋白內,於是衛星核酸有可能就此而產生了,然而,此假設尚待進一步的實驗來證實。在人為演化實驗方面,CMV病毒顆粒與衛星核酸載體共同接種到A. thaliana及N. benthamiana七天後,抽取病毒雙股核酸以電泳進行分析,並無偵測到satRNA,利用反轉錄聚合酵素鏈鎖反應(RT-PCR)則是有偵測到satRNA的存在,但可能是分析到了接種葉上殘留的接種質體,因此繼續在N. tabacum上做接種測試,並採系統葉抽取病毒雙股核酸以電泳進行分析,也無偵測到satRNA的訊號,利用RT-PCR也無法偵測到satRNA的存在,推測可能是接種植物體較複雜,因此以單細胞層次來觀察此載體是否能表現satRNA,於是便構築一個新的重組質體,將增強型綠色螢光蛋白(enhanced green fluorescent protein, EGFP)構築到與satRNA相同位置,命名為pd35S-R3-EGFP,以當作報導基因,對N. benthamiana的原生質體進行接種測試,在接種48小時後,抽取總體蛋白進行西方墨點法分析,有偵測到EGFP的訊號,推測此載體可以表現出在CMV RNA 3 的subgenomic promoter下游之基因。本研究的結果提供了衛星核酸序列與結構之證據可用於追溯衛星核酸的起源及其修復所使用的模版,並研發了可能的分子工具可用來進一步測試上述之假說。

Cucumber mosaic virus (CMV), the type member of the Cucumovirus, is a plant virus with a tripartite, single-stranded positive-sense RNA genome. Some CMV strains contain small RNAs that have been demonstrated to be satellite RNAs (satRNAs), which are dependent on CMV for replication, encapsidation, and transmission, but share little or no sequence similarity with CMV. Previous studies have shown that satRNAs are often found in experimental hosts infected with CMV, and deletion mutants of satRNAs are usually automatically repaired to the wild type. However, the origin and repair mechanism of satRNA remain to be elucidated. The purpose of this study is to explore the possible origin and repair mechanism of CMV associated satRNAs through comprehensive database searches and artificial evolution experiments under environmental stresses. The databases explored include plant, bacteria and invertebrate genomes, using highly sensitive algorithms of SSearch and FASTA. For artificial evolution experiments, the constructs used to inoculate are based on CMV RNA 3 driven by double 35S promoter, with most part of coat protein sequence replaced by those of satRNA variants, including positive control, satRNA-NdeI (pd35S-R3-satNdeI), and test construct, satM26 (pd35S-R3-satM26), a mutant with the nucleotides from 124 to 237 deleted, and 12 additional nucleotides that are not related to satRNAs. Co-inoculation of the constructs with CMV to Nicotiana benthamiana would result in the continuous production of satRNAs for as a start point for evolution or repair. Current database searches revealed several possible candidates, which are subject to multiple alignment analysis. The result revealed that these homologous sequences also shared substantial similarities in their predicted secondary structure models. This finding supported the possibility that satRNAs might have evolved from host genomes, and might be recognized by the viral replicases and assembled into functional replicons during certain rare transposition events. Repeated in plant inoculation tests indicated that satRNAs were not efficiently generated. To test the replication ability and the activity of the subgenomic promoter of the constructs, enhanced green fluorescent protein (EGFP) were used as a reporter and assayed in N. benthamiana protoplasts. EGFP was detected by western blot analysis 48 hrs after inoculation, suggesting that the CMV RNA 3 vector could be used to express foreign genes downstream of the subgenomic promoter. These results presented nucleotide sequence and structure evidence for the possible origins and repair mechanism of CMV satRNAs, and proved possible tools to test these hypotheses. If the EGFP have been detected in protoplast, this vector could be used to test the satRNA repair mechanism and study of origin.
其他識別: U0005-2607200713213600
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