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標題: I. 建立竹嵌紋病毒於酵母菌中之複製系統 II. 巴氏芽孢桿菌對水庫淤泥固結的可行性探討
I.Establishing Yeast as a Model Host to Study Replication of Bamboo Mosaic Virus II. Potential Use of Sporosarcina pasteurii to Promote the Solidification of Reservoir Sludge
作者: 黃郁婷
Huang, Yu-Ting
關鍵字: Bamboo mosaic virus;竹嵌紋病毒;yeast screen system;Sporosarcina pasteurii;Microbial-induced calcium precipitation;Air-lift;Reservoir sludge;酵母篩選系統;巴氏芽孢桿菌;微生物誘導碳酸鈣;氣舉式;水庫淤泥
出版社: 生物科技學研究所
引用: Part 1: 中文文獻: 張雅婷。2003。I.竹嵌紋病毒戴帽酵素中參與受質 SAM 結合與催化甲基轉移能力之氨基酸探討II.建立竹嵌紋病毒於酵母菌中之完整複製系統。國立中興大學生物科技學研究所碩士論文。 西文文獻: Ahlquist, P., Noueiry, A. O., Lee, W. M., Kushner, D. B., and Dye, B. T. (2003). Host Factors in Positive-Strand RNA Virus Genome Replication. Journal of Virology 77(15), 8181-8186. Chang, B. Y., Lin, N. S., Liou, D. Y., Chen, J. P., Liou, G. G., and Hsu, Y. H. (1997). Subcellular localization of the 28 kDa protein of the triple-gene-block of bamboo mosaic potexvirus. Journal of General Virology 78, 1175-1179. Cheng, C. W., Hsiao, Y. Y., Wu, H. C., Chuang, C. M., Chen, J. S., Tsai, C. H., Hsu, Y. H., Wu, Y. C., Lee, C. C., and Meng, M. S. (2009). Suppression of Bamboo Mosaic Virus Accumulation by a Putative Methyltransferase in Nicotiana benthamiana. Journal of Virology 83(11), 5796-5805. Cheng, J. H., Ding, M. P., Hsu, Y. H., and Tsai, C. H. (2001). The partial purified RNA-dependent RNA polymerases from bamboo mosaic potexvirus and potato virus X infected plants containing the template-dependent activities. Virus Research 80, 41-52. Cheng, S. F., Huang, Y. P., Wu, Z. R., Hu, C. C., Hsu, Y. H., and Tsai, C. H. (2010). Identification of differentially expressed genes induced by Bamboo mosaic virus infection in Nicotiana benthamiana by cDNA-amplified fragment length polymorphism. BioMed Central Plant Biology 10:286. Chiu, M.-H., Chen, I. H., Baulcombe, D. C., and Tsai, C.-H. (2010). The silencing suppressor P25 of Potato virus X interacts with Argonaute1 and mediates its degradation through the proteasome pathway. Molecular Plant Pathology, 11(5),641–649 Faitar, S. L., Brodie, S. A., and Ponticelli, A. S. (2001). Promoter-Specific Shifts in Transcription Initiation Conferred by Yeast TFIIB Mutations Are Determined by the Sequence in the Immediate Vicinity of the Start Sites. Molecular and Cellular Biology 21(14), 4427-4440. Guthrie, C. (1991). Messenger RNA Splicing in Yeast: Clues to why the Spliceosome is a Ribonucleoprotein. Science 253(5016), 157-163 .Huang, Y. L., Han, Y. T., Chang, Y. T., Hsu, Y. H., and Meng, M. S.(2004). Critical Residues for GTP Methylation and Formation of the Covalent m7GMP-Enzyme Intermediate in the Capping Enzyme Domain of Bamboo Mosaic Virus. Journal of Virology 78(3), 1271-1280. Janda, M., and Ahlquist, P. (1993). RNA-dependent replication, transcription, and persistence of brome mosaic virus RNA replicons in S. cerevisiae. Cell Host & Microbe 72(6), 961-970. Jiang, Y., Serviene, E., Gal, J., Panavas, T., and Nagy, P. D. (2006). Identification of Essential Host Factors Affecting Tombusvirus RNA Replication Based on the Yeast Tet Promoters Hughes Collection. Journal of Virology 80(15), 7394-7404. Johnston, M., and Davis, R. W. (1984). Sequences That Regulate the Divergent GAL1-GAL10 Promoter in Saccharomyces cerevisiae. Molecular and Cellular Biology 4(8), 1440-1448. Kushner, D. B. (2003). Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus. Proceedings of the National Academy of Sciences 100(26), 15764-15769. Lai, M. M. (1998). Cellular factors in the transcription and replication of viral RNA genomes : a parallel to DNA-dependent RNA transcription. Virology 244(1), 1-12. Li, Y. I., Cheng, Y. M., Huang, Y. L., Tsai, C. H., Hsu, Y. H., and Meng, M. S.(1998). Identification and Characterization of the Escherichia coli-Expressed RNA-Dependent RNA Polymerase of Bamboo Mosaic Virus. Journal of Virology 72(12), 10093-10099. Li, Y. I., Chen, Y. J., Hsu, Y. H., and Meng, M. (2001a). Characterization of the AdoMet-dependent guanylytransferase activity that is associated with the N terminus of bamboo mosaic virus replicase. Journal of Virology 75, 782-788. Li, Y. I., Shih, T. W., Hsu, Y. H., Han, Y. T., Huang, Y. L., and Meng, M. (2001b). The Helicase-Like Domain of Plant Potexvirus Replicase Participates in Formation of RNA 5'' Cap Structure by Exhibiting RNA 5''-Triphosphatase Activity. Journal of Virology 75(24), 12114-12120. Lin, J. W., Ding, M. P., Hsu, Y. H., and Tsai, C. H. (2007). Chloroplast phosphoglycerate kinase, a gluconeogenetic enzyme, is required for efficient accumulation of Bamboo mosaic virus. Nucleic Acids Research 35(2), 424-432. Lin, M. K. (2004). Arg-16 and Arg-21 in the N-terminal region of the triple-gene-block protein 1 of Bamboo mosaic virus are essential for virus movement. Journal of General Virology 85(1), 251-259. Lin, M. K. (2006). Movement of potexviruses requires species-specific interactions among the cognate triple gene block proteins, as revealed by a trans-complementation assay based on the bamboo mosaic virus satellite RNA-mediated expression system. Journal of General Virology 87(5), 1357-1367. Lin, M. T., W, K. E., P., C. F., and L., C. C. (1977). Partial purification and some properties of bamboo mosaic virus. Phytopathology 67, 1439-1443. Lin, N. S., Chai, Y. J., Huang, T. Y., Chang, T. Y., And Hsu, Y. H. (1993). Incidence of bamboo mosaic potexvirus in Taiwan. Plant disease 77(5), 448-450. Lin, N. S., Lin, B. Y., Lo, N. W., Hu, C. C., Chow, T. Y., and Hsu, Y. H. (1994). Nucleotide sequence of the genomic RNA of bamboo mosaic potexvirus. Journal of General Virology 75, 2513-251. Lin, N. S., and Hsu, Y. H. (1994). A satellite RNA associated with bamboo mosaic potexvirus. Virology 202, 707-714. Lin, N., Lin, F., Huang, T., and Hsu, Y. (1992). Genome properties of bamboo mosaic virus. Phytopathology 82, 731-734. Janda M and Ahlquist P. (1993). RNA-dependent replication, transcription, and persistence of brome mosaic virus RNA replicons in S. cerevisiae. Cell Host & Microbe 72, 961-970. Nagy, P. D. (2008). Yeast as a Model Host to Explore Plant Virus-Host Interactions. Annual Review of Phytopathology 46(1), 217-242. Naito, T., Kiyasu, Y., Sugiyama, K., Kimura , A., and Nakano, R., et al. (2007). An influenza virus replicon system in yeast identified Tat-SF1 as a stimulatory host factor for viral RNA synthesis. Proceedings of the National Academy of Sciences 104, 18235-18240. Panavas, T., and Nagy, P. D. (2003). Yeast as a model host to study replication and recombination of defective interfering RNA of Tomato bushy stunt virus. Virology 314(1), 315-325. Panaviene, Z., Panavas, T., and Nagy, P. D. (2005). Role of an Internal and Two 3''-Terminal RNA Elements in Assembly of Tombusvirus Replicase. Journal of Virology 79(16), 10608-10618. Pantaleo, V., Rubino, L., and Russo, M. (2003). Replication of Carnation Italian ringspot virus defective interfering RNA in Saccharomyces cerevisiae. Journal of Virology 77, 2116-2123. Pleiss, J. A., Whitworth, G. B., Bergkessel, M., and Guthrie, C. (2007). Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components. PLoS Biology 5(4), 745-757 Prasanth, K. R., Huang, Y. W., Liou, M. R., Wang, R. Y., Hu, C. C., Tsai, C. H., Meng, M., Lin, N. S., and Hsu, Y. H. (2011). Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) negatively regulates the replication of Bamboo mosaic virus and its associated satellite RNA. Journal of Virology [Epub ahead of print] Raghavan, V., Malik, P., Choudhury, N., and Mukherjee, S. (2004). The DNA-A component of a plant geminivirus (Indian mung bean yellow mosaic virus) replicates in budding yeast cells. Journal of Virology 78, 2405-2413. T, N., Y, K., K, S., A, K., and Nakano R.(2007). An influenza virus repliconsystem in yeast identified Tat-SF1 as a stimulatory host factor for viral RNA synthesis. Proceedings of the National Academy of Sciences USA 104, 18235-18240. Panavas T, Hawkins CM, Panaviene Z, Nagy PD. (2005). The role of the p33/p92 interactiondomain in RNA replication and intracellular localization of p33 and p92 proteins of Cucumber necrosis tombusvirus. Virology 338, 81-95. Voinnet, O., Lederer, C., and Baulcombe, D. C. (2000). A Viral Movement Protein Prevents Spread of the Gene Silencing Signal in Nicotiana benthamiana. Cell 103(1), 157-167. Pantaleo V., Rubino L., and Russo M.. (2003). Replication of Carnation Italian ringspot virus defectiveinterfering RNA in Saccharomyces cerevisiae. Journal of Virology 77, 2116-2123. Raghavan V., Malik P. S., Choudhury N. R., Mukherjee S. K. (2004). The DNA-A component of aplant geminivirus (Indian mung bean yellow mosaic virus) replicates in budding yeast cells. Journal of Virology 78, 2405-2413. Wung, C.-H., Hsu, Y.-H., Liou, D.-Y., Huang, W.-C., Lin, N.-S., and Chang, B.-Y. (1999). Identification of the RNA-binding sites of the triple gene block protein 1 of bamboo mosaic potexvirus. Journal of General Virology 80, 1119-1126. Yang, C. C., Liu, J. S., Lin, C. P., and Lin, N. S. (1997). Nucleotide sequence and phylogenetic analysis of bamboo mosaic potexvirus isolate from common bamboo (Bambusa vulgaris McClure). Botanical Bulletin of Academia Sinica 38(2), 77-84. Zeenko, V. V., Ryabova, L. A., Spirin, A. S., Rothnie, H. M., Hess, D., Browning, K. S., and Hohn, T. (2002). Eukaryotic elongation factor 1A interactions with the upstream pseudoknot domain in the 3'' untranslated region of tobacco masaic virus RNA. Journal of Virology 76(11), 5678-5691. Part 2: 中文文獻: 中興工程顧問股份有限公司。(2008).石門水庫淤泥多元化處置方案評估規劃綜合報告。經濟部水利署北區水資源局,桃園縣龍潭鄉。 吳素禎、陳移章、曾逸楨、謝國正、曾慶恩、李淳昌。1999。水庫淤泥固化與棄置。中興工程顧問社,臺北市。 陳豪吉、孟孟孝、陳建易、蔡文博、張永璇。2011。細菌應用於混凝土修復及淤泥固結之開發研究總報。經濟部水利署,台北市。 西文文獻: Achal, V., Mukherjee, A., Basu, P. C., and Reddy, M. S. (2009). Strain improvement of Sporosarcina pasteurii for enhanced urease and calcite production. Journal of Industrial Microbiology & Biotechnology 36(7), 981-988. APHA (1989). Standard methods for the examination of water and wastewater, 17th ed. American Public Health Association (APHA), Washington, DC. . Bachmeier, K. L., Williams, A. E., Warmington, J. R., and Bang, S. S. (2002). Urease activity in microbiologically-induced calcite precipitation. Journal of Biotechnology 93, 171-181. Bang, S. S., Galinat, J. K., and Ramakrishnan, V. (2001). Calcite precipitation induced by polyurethane-immobilized Bacillus pasteurii. Enzyme and Microbial Technology 28, 404-409. Bennett, R. H., Bryant, W. R., and Hulbert, M. H. (1991). Microstructure of fine-grained sediments. Springer, New York. De Muynck, W., De Belie, N., and Verstraete, W. (2010). Microbial carbonate precipitation in construction materials: A review. Ecological Engineering 36(2), 118-136. DeJong, J. T., Fritzges, M. B., and Nusslein, K. (2006). Microbially induced cementation to control sand response to undrained shear. J. Geotech. Geoenv. Engineering. 132, 1381-1392. Ferris, F. G., Beveridge, T. J., and Fyfe, W. S. (1986). Iron-silica crystallite nucleation by bacteria in a geothermal sediment. Nature 320, 609-611. Ferris, F. G., Fyfe, W. S., and Beveridge, T. J. (1987). Bacteria as nucleation sites for authigenic minerals in metal-contaminated lake sediment. Chemical Geology 63, 225-232. Kaltwasser, H., and Schlegel, H. G. (1966). NADH-dependent coupled enzyme assay for urease and other ammonia-producing systems. Analytical Biochemistry16, 132-138. Michihisa, M., Makoto, H., Akira, N., Haruhiko, M., And Takeshi, U. (1994). Cloning, Sequencing, and Expression of Thermophilic Bacillus sp. Strain TB-90 Urease Gene Complex in Escherichia coli. Journal of Bacteriology 176(2), 432-442. Muynck, W., Cox, K., and Beli, N. (2007). Bacterial carbonate precipitation as an alternative surface treatment for concrete Constr Build Mater. Construction and Building Materials 22(5), 875-885 Okwadha, G. D. O., and Li, J. (2010). Optimum conditions for microbial carbonate precipitation. Chemosphere 81(9), 1143-1148. Ramachandran, S. K., Ramakrishnan, V., and Bang, S. S. (2001). Remediation of concrete using micro-organisms. American Concrete Institute Materials Journal 98(1), 3-9. Schultze-Lam, S., Fortin, D., and Beveridge, T. J. (1996). Mineralization of bacterial surfaces. Chem. Geol. 132, 171-181. Stocks-Fischer, S., Galinat, J. K., and Bang, S. S. (1999). Microbiological precipitation of CaCO3. Soil biology and biochemistry 31, 1563-1571. Tiano, P. (1995). Stone reinforcement by calcite crystals precipitation induced by organic mat rix macromolecules. Studies in Conservation 40(3), 171-176. De Muyncka W. , Coxa K., De Beliea N. and Verstraete W. (2007). Bacterial carbonate precipitation as an alternative surface treatment for concrete. Construction and Building Materials 22 (5), 875-885. Zeshan, H., and Yulin, D. (2003). Supersaturation control in aragonite synthesis using sparingly soluble calcium sulfate as reactants. Journal of Colloid and Interface Science 266, 359-365.
第一部分 : 植物病毒為絕對寄生的微生物,由於病毒基因體大小的限制,導致病毒本身所轉譯的蛋白是有限的,因此在病毒複製時,需要依賴宿主因子的幫助,但是在植物體內研究病毒與宿主之間的交互作用並不容易。由於酵母菌僅有約6000個左右的基因,更有超過60 %的基因已被定義,從基因體或蛋白質體的觀點來看,它是一個很好的模式宿主,適合用來研究病毒與宿主因子之間交互作用的實驗系統。本實驗的目的欲建立竹嵌紋病毒於酵母菌中的複製系統。竹嵌紋病毒是一支隸屬於Flexividiae科Potexvirus屬的正股RNA病毒,含有單股6.4 kb的RNA,其基因體包含5’端甲基帽,五個轉譯區(ORFs)及3’端的poly(A)尾部。首先,我們將glyceraldehydes 3-phosphate dehydrogenase (GAP) promoter置換掉酵母雙雜交用之載體pHybLex/Zeo中的promoter,再把竹嵌紋病毒的基因置入GAP promoter之後,並轉型到酵母菌中進行蛋白質的表現。接著主要使用西方墨點法偵測鞘蛋白質來觀察竹嵌紋病毒在酵母菌中的複製情況。結果顯示,在酵母菌INVSc1、L40、BY4739、BY4741中,均偵測到外鞘蛋白的訊號,而在酵母菌BY4741中,竹嵌紋病毒複製酵素GDD motif 的突變使鞘蛋白可被偵測到的量很微弱,暗示著竹嵌紋病毒能在酵母菌BY4741中複製並轉譯蛋白質,是與病毒複製酵素的能力有關。
第二部分 : 水庫蓄水量與經濟發展息息相關,快速的清淤並確保水庫安全與壽命,是全世界關注的議題,但水庫淤泥顆粒的細小 (< 0.01 mm) 使得淤泥的清運、儲存與再利用難以達成。國際研究報告已經提出Sporosarcina pasteurii (Bacillus pasteurii) 可以分解尿素,產生鹼性環境並提供二氧化碳與鈣離子產生碳酸鈣結晶,填補晶粒之間的空隙。因此本實驗欲利用這樣概念來增加水庫淤泥的粒徑,解決水庫淤泥清運不易的困擾。首先將S. pasteurii培養進行調整測試並發現魚骨粉與雞糞肥可作為適合的經濟培養基,而且本實驗也找到台灣本土之S. pasteurii相似菌株Sporosarcina sp. CN3及Sporosarcina sp. CN6。在S. pasteurii固結淤泥實驗方面,發現高濃度氯化鈣可以促進淤泥的固結效果,並利用氣舉式模式,增加深水區的空氣通透量,擴大S. pasteurii應用於沉澱池中固結水庫淤泥的可能性,也觀察水庫淤泥在掃描式電子顯微鏡和X-ray粉末晶體繞射,發現淤泥顆粒上有碳酸鈣結晶的產生。

Part 1 : Interactions between virus-encoded proteins and host factors are crucial for virus replication in host. On the other hand, the interactions may initiate host defense mechanisms counteracting the viral accumulation. However, identifying such interactions between plant virus and its host is a time-consuming and tedious job. Yeast is a great model system if the studied virus could replicate in yeast from the genome-wide and proteomic viewpoint, because it contains only about 6000 genes, of which over 60% have been characterized. In this study, I tried to establish a replication system of Bamboo mosaic virus (BaMV) in yeast. BaMV is a positive-sense RNA virus belonging to the genus of Potexvirus. The 6.4-kb genome contains five open reading frames (ORFs), a 5’ methyl cap, and a 3’ poly(A). To achieve the goal, the entire cDNA of BaMV was placed downstream the glyceraldehydes 3-phosphate dehydrogenase (GAP) promoter in a yeast episomal vector derived from pHybLex/Zeo (Invitrogen), and the plasmid was named pHGB. pHGB was then transformed into Saccharomyces cerevisiae, INVSc1、L40、BY4739、BY4741. The ability of BaMV replication in yeast was monitored by the expression of coat protein (CP) using Western blotting assay. When GDD motif of RdRp activity site was deleted at pHGB, CP couldn’t be detected in BY4741. Compare to the mutant and the wile type, CP could be accumulated in yeast only when functional BaMV replicase existed. In the future, the replication of BaMV in yeast will be further confirmed and then the host factor-hunting experiment can be carried out.
Part 2 : Reservoir storage capacity affects economic development very significantly. Keeping the reservoir security storage level is a worldwide issue; however the reservoir sludge is so small that the precipitation is almost impossible. The previous studies showed that Sporosarcina pasteurii (Bacillus pasteurii) could decomposed urea to produce carbon dioxide and alkaline environment, providing the crystallization of calcium carbonate and fill the gap between the grains. Therefore, this study intended to use this concept to increase the size of the reservoir sludge. We optimized the S. pasteurii growth condition, and found the S. pasteurii analogous organism, Sporosarcina sp. CN3 and Sporosarcina sp. CN6 in Taiwan. For the consolidation experiments of the sludge in S. pasteurii, I found that high concentrations of calcium chloride (250 mM) can promote the efficiency of consolidation. In the air-lift model experiments, high air permeability rising the opportunity of S. pasteurii-mediated the solidification of reservoir sludge in deep water. Furthermore , it was found that the crystallization of calcium carbonate on treated reservoir sludge was increased in the scanning electron microscope and X-ray powder diffraction.
其他識別: U0005-2106201115525000
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