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研究生:邱曉寧
研究生(外文):Hsiao-Ning Chiu
論文名稱:竹嵌紋病毒負股核酸合成正股基因體的啟動子之研究
論文名稱(外文):The Promoter Analysis of Bamboo Mosaic Potexvirus Plus-Sense Genomic RNA Synthesis by
指導教授:蔡慶修蔡慶修引用關係
指導教授(外文):Ching-Hsiu Tsai
學位類別:碩士
校院名稱:國立中興大學
系所名稱:農業生物科技學研究所
學門:農業科學學門
學類:農業技術學類
論文種類:學術論文
論文出版年:2002
畢業學年度:90
語文別:中文
論文頁數:44
中文關鍵詞:竹嵌紋病毒啟動子
外文關鍵詞:Bamboo Mosaic PotexvirusPromoter
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竹嵌紋病毒(bamboo mosaic virus, BaMV)為potexvirus group的成員之一,基因體為單一正股RNA所構成,一般而言,正股RNA病毒在進行複製時,會由正股的3¢ 端做出負股RNA,再以此負股RNA當作模板,做出新的正股RNA。 目前竹嵌紋病毒已證實其基因體上的3¢ untranslated region (UTR) 存在有特定的結構及序列,可以被病毒的複製酵素所認得以合成出負股;而對於負股RNA上所存在的生合成正股基因體的啟動子則尚不清楚,因此利用電腦程式(MFOLD)預測(-)77RNA的結構,並以具專一性的核酸酵素(ribonucleae)切割具有放射性標定的RNA以做確認,RNase A會切單股RNA上的pyrimidine,RNase T1切單股RNA上的Guanine,RNase T2切單股RNA所有的nucleotides,RNase V1會切所有雙股RNA,綜合實驗結果後顯示,(-)77RNA會形成兩個穩定的stem-loop結構,且其中一個較主要的stem-loop是由上下兩個stem所組成,也根據stem的位置所在而命名lower stem (LS) 以及upper stem (US)。 我們利用in vitro transcription製備了不同長度的3¢ 端負股RNA ((-)39、(-)77、和-173RNA) 轉錄體當作模板,利用實驗室已建立的生體外核酸複製酵素複合體的複製系統來比較複製效率的差異,結果發現(-)39RNA的複製效率不佳,而(-)77RNA與(-)173RNA的複製效率則差異不大,因此推斷啟動子應該位於(-)77RNA上。 因此針對 (-)77RNA上LS及US的結構及序列做改變,來加以確定真正影響複製效率的因子所在;結果顯示在LS上,其序列和結構維持皆對複製效率有很大的影響,而US上結構的破壞會導致複製效率的大幅度下降,倘若改變序列而維持此stem的結構,則可恢復複製效率達到接近野生型的程度。綜合結果顯示合成正股基因體的啟動子應該落在(-)77RNA上主要的那一個stem-loop,並且知道維持stem-loop結構的完整性對病毒的複製有高度的影響力。

Bamboo mosaic potexvirus (BaMV) consists of a single-stranded positive-sense RNA genome. The 3¢ untranslated region (UTR) of BaMV genomic RNA was identified to form a tertiary structure and recognized as template by viral RNA-dependent RNA polymerase (RdRp) complex to synthesize the minus strand RNA. However the promoter on the minus strand RNA for plus strand genomic RNA synthesis is not clear. The secondary structure of (-)77RNA was predicated by MFOLD program and confirmed by specific enzymatic cleavage. Single-strand unpaired nucleotides were probed with ribonuclease A (specific on pyrimidine), T1 (specific on Guanine), T2 (on all four nucleotides) and the paired or stacked nucleotides were cleaved by ribonuclease V1. The probing results indicated that (-)77RNA could form two stable stem-loops in which the major stem-loop contained lower and upper stems. In order to identify the promoter for the plus strand RNA synthesis, we have prepared three different sizes of the minus strand RNA transcripts with co-3¢ end ((-)39, (-)77, and (-)173RNA) as templates for an in vitro RdRp replication assay. We found that (-)39RNA has the lowest replication efficiency, and (-)77RNA has similar replication efficiency with (-)173RNA. This result suggested that the promoter sequence for plus strand RNA synthesis might be located on the last 77 nucleotides of the minus strand RNA, especially the major stem-loop. Mutations were introduced to abolish or revert the major stem structures. Results showed that both sequence and structure of lower stem are necessary for RNA replication and maintaining the upper stem is far more important than the sequence requirement.

壹、 中文摘要---------------------------------------------1
貳、 英文摘要---------------------------------------------2
參、 前人研究---------------------------------------------3
肆、 內文-------------------------------------------------8
Introduction------------------------------------------8
Materials and Methods--------------------------------11
Result-----------------------------------------------15
Discussion-------------------------------------------20
Figures and legends----------------------------------23
伍、參考文獻-------------------------------------------------35
陸、結論-----------------------------------------------------42
柒、附錄-----------------------------------------------------43

1. Abrahams, J. P., Berg, M. V. D., Batengurg, F. H. D., and Pleij, C. W. A. 1990. Prediction of RNA secondary structure, including psedoknotting, by computer simulation. Nucleic Acids Res. 18:3035-3044.
2. Argos, P. 1988. A sequence motif in many polymerase. Nucleic Acids Res. 16:9909-9916.
3. Barrera, I., D. Schuppli, J. M. Sogo, and H. Webber. 1993. Different mechanisms of recognition of bacteriophage Qb replicase. J. Mol. Biol. 232:512-521.
4. Beck, D. L., P. J. Guilford, D. M. Voot, M. T. Andersen, and R. L. S. Forster. 1991. Triple gene block proteins of white clover mosaic potexvirus are required for transport. Virology 183:695-702.
5. Blumenthal, T., and G. G. Carmichael. 1979. RNA replication: function and structure of Qb replicase. Annu. Rev. Biochem. 47:159-251.
6. Cheng, C. -P. and Tsai, C. -H. 1999. Structural and functional analysis of the 3′ untranslated region of bamboo mosaic potexvirus genomic RNA. J. Mol. Biol. 288:555-565.
7. Cheng, J. -H., Ding, M. -P., Hsu, Y. -H. and Tsai, C. -H. 2001. The partial pufiried RNA-dependent RNA polymerases from bamboo mosaic potexvirus and potato virus X infected plants containing the template-dependent activities. Virus Res. 80:41-52.
8. Chiu, W. -W., Hsu, Y. -H. and Tsai, C. -H. 2002. Specificity analysis of the conserved hexanucleotides for the replication of bamboo mosaic potexvirus RNA. Virus Res. (in press).
9. Deiman, B. A. L. M., R. M. Kortlever, and C. W. A. Pleij. 1997. The role of the pseudoknot at the 3¢ end of turnip yellow mosaic virus RNA in minus-strand synthesis by the viral RNA-dependent RNA polymerase. J. Virol. 71:5990-5996.
10. Deiman, B. A. L. M., A. K. Koenen, P. W. G. Verlaan, and C. W. A. Pleij. 1998. Minimal template requirements for initiation of minus-strand synthesis in vitro by the RNA-dependent RNA polymerase of turnip yellow mosaic virus. J. Virol. 72:3965-3972.
11. Dreher, T. W., and T. C. Hall. 1988. Mutation analysis of the sequence and structural requirements in brome mosaic virus RNA for minus strand promoter activity. J. Mol. Biol. 201:31-40.
12. Dreher, T. W. 1999. Functions of the 3′-untranslated regions of positive strand RNA viral genomes. Annu. Rev. Phytopathol. 37:151-174
13. Ferrari, E., J. Wright-Minogue, J. W. S. Fang, B. M. Baroudy, J. Y. N. Lau, and Z. Hong. 1999. Characterization of soluble hepatitis C virus RNA-dependent RNA polymerase expressed in Escherichia coli. J. Virol. 73:1649-1654.
14. Gorbalenya, A. E., and E. V. Koonin. 1989. Viral proteins containing the purine NTP-binding sequence pattern. Nucleic Acids Res. 17:8413-8440.
15. Guilford, P. J., D. L. Beck, and R. L. S. Forster. 1991. Influence of the poly(A) tail and putative polyadenylation signal on the infectivity of white clover mosaic potexvirus. Virology 182:61-67.
16. Hayes, R. J., and K. W. Buck. 1990. Complete replication of a eukaryotic virus RNA in vitro by a purified RNA-dependent RNA polymerase. Cell 63:363-368.
17. Hodgman, T. C. 1988. A new superfamily of replicative proteins. Nature 333:22-23.
18. Hong, Y. and A. G. Hunt. 1996. RNA polymerase activity catalyzed by a potyvirus-encoded RNA-dependent RNA polymerase. Virology 226:146-151.
19. Houser-Scott, F., M. L. Baer, K. F. Liem, J. -M. Cai, and L. Gehrke. 1994. Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein to the 3¢ untranslated region of alfalfa mosaic virus RNA4. J. Virol. 68:2194-2205.
20. Houser-Scott, F., P. Ansel-Mckinney, J. -M. Cai, and L. Gehrke. 1997. In vitro genetic selection analysis of alfalfa mosaic virus coat protein binding to 3¢-terminal AUGC repeats in the viral RNAs. J. Virol. 71:2310-2319.
21. Houwing, C. J., and E. M. J. Jaspars. 1986. Coat protein blocks the in vitro transcription of the virion RNAs of alfalfa mosaic virus. FEBS Lett. 209:284-288.
22. Huang, C. -Y., Huang Y. -L., Meng, M. , Hsu, Y. -H., and Tsai, C. -H. 2001. Sequence at the 3′ untranslated region of the bamboo mosaic potexvirus RNA interacted with the viral RNA-dependent RNA polymerase. J. Virol. 75:2818-2824.
23. Joyce, C. M., and T. A. Steitz. 1995. Polymerase structures and function: variations on a theme? J. Bacteriol. 177:6321-6329.
24. Kao, C. C., and J. -H. Sun. 1996. Initiation of minus-strand RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase :Use of oligoribonucleotide primers. J. Virol. 70:6826-6830.
25. Kao, C. C., Singh, P., and Eckert, D. J. 2001. De nova initiation of viral RNA-dependent RNA synthesis. Virology 287:251-260.
26. Koonin, E. V. 1991. The phylogeny of RNA-dependent RNA polymerase of plus-strand RNA virus. J. Gen. Virol. 72:2197-2206.
27. Li, Y. -I., Cheng, Y. -M., Huang, Y. -L., Tsai, C. -H., Hsu, Y. -H. and Meng, M. 1998. Identification and characterization of the Escherichia coli-expressed RNA-dependent RNA polymerase of bamboo mosaic virus. J. Virol. 72:10093-10099.
28. Lin, M. T., E. W. Kitajima, F. P. Cupertino, and C. L. Costa. 1977. Partial purification and some properties of bamboo mosaic virus. Phytopathology 67:1439-1443.
29. Lin, N. -S., F. -Z. Lin, T. -Y. Huang, and Y. -H. Hsu. 1992. Genome properties of bamboo mosaic virus. Phytopathology 82:731-734.
30. Lin, N. -S., and Y. -H. Hsu. 1994. A satellite RNA associated with bamboo mosaic potexvirus. Virology 202:707-714.
31. Lin, N. -S., B. -Y. Lin, N. -W. Lo, C. -C. Hu, T. -Y. Chow, and Y. -H. Hsu. 1994. Nucleotide sequence of the genomic RNA of bamboo mosaic potexvirus. J. Gen. Virol. 75:2513-2518.
32. Lohmann, V., A. Roos, F. Korner, J. O. Koch, and R. Bartenschlager. 1998. Biochemical and kinetic analyses of NS5B RNA-dependent RNA polymerase of the hepatitis C virus. Virology 249:108-118.
33. McBride, A. E., A. Schlegel, and K. Kirkegaard. 1996. Human protein Sam68 relocalization and interaction with poliovirus RNA polymerase in infected cells. Proc. Natl. Acad. Sci. USA 93:2296-2301.
34. Miller, W. A., Bujarski, J. J., Dreher T. W., Hall, T. C. 1986. Minus-strand initiation by brome mosaic virus replicase within the 3′ tRNA-like structure of native and modified RNA templates. J. Mol. Biol. 187:537-546.
35. Mouches, C., C. Bove, and J. M. Bove. 1974. Turnip yellow mosaic virus RNA replicase: Partial purification of the enzyme from the solubilized enzyme-template complex. Virology 58:409-423.
36. Oh, J. -W., Ito, T., and Lai, M. M. 1999. A recombinant hepatitis C virus RNA-dependent RNA polymerase capable of copying the full-length viral RNA. J. Virol. 73:7694-7702.
37. Osman, T. A. M., and K. W. Buck. 1996. Complete replication in vitro of tobacco mosaic virus RNA by a template-dependent, membrane-bound RNA polymerase. J. Virol. 70:6227-6234.
38. Plante, C. A., Kim, K. H., Pillai-Nair, N., Osman, T. A., Buck, K. W., and Hemenway, C. L. 2000. Soluble, template-dependent extracts from Nicotiana benthamiana plants infected with potato virus X transcribe both plus- and minus-strand RNA templates. Virology 275:444-451.
39. Pogue, G. P. and Hall, T. C. 1992. The requirement for a 5′ stem-loop structure in brome mosaic virus replication supports a new model for viral positive-strand RNA initiation. J. Virol. 66:674-684.
40. Quadt, R., and E. M. J. Jaspars. 1990. Purification and characterization of brome mosaic virus RNA-dependent RNA polymerase. Virology 178:189-194.
41. Quadt, R., H. J. M. Rosdorff, T. W. Hunt, and E. M. J. Japars. 1991. Analysis of the protein composition of alfalfa mosaic virus RNA-dependent RNA polymerase. Virology 182:309-315.
42. Quadt, R., C. C. Kao, K. S. Browning, R. P. Hershberger, and P. Ahlquist. 1993. Characterization of a host protein associated with brome mosaic virus RNA-dependent RNA polymerase. Proc. Natl. Acad. Sci. USA 90:1498-1502.
43. Rao, A. L., T. W. Dreher, L. E. Marsh, and T. C. Hall. 1989. Telomeric function of the tRNA-like structure of brome mosaic virus RNA. Proc. Natl. Acad. Sci. USA 86:5335-5339.
44. Reigadas, S., Ventura, M., Sarih-Cottin, L., Castroviejo, M., Litvak, S, and Astier-Gin, T. 2001. HCV RNA-dependent RNA polymerase replicates in vitro the 3′ terminal region of the minus-strand viral RNA more efficiently than the 3′ terminal region of the plus RNA. Eur. J. Biochem. 268:5857-5867.
45. Reusken, C. B. E. M., and J. F. Bol. 1996. Structural elements of the 3¢-terminal coat protein binding site in alfalfa mosaic virus RNAs. Nucleic Acids Res. 24:2660-2665.
46. Rothstein, M. A., O. C. Richards, C. Amin, and E. Ehrenfeld. 1988. Enzymatic activity of poliovirus RNA polymerase synthesized in Escherichia coli from viral cDNA. Virology 164:301-308.
47. Rozanov, M. N., E. V. Koonon, and A. E. Gorbalenya. 1992. Conservation of the putative methyltransferase domain: a hallmark of the Sindbis-like supergroup of plus-strand RNA viruses. J. Gen. Virol. 73:2129-2134.
48. Siberklang, M., Gillum, A. M. and RajBshandary, U. 1977. The use of nuclease P1 in sequence analysis end group labeled RNA. Nucleic Acids Res. 4:4091-4108.
49. Singh, R. N., and T. W. Dreher. 1997. Turnip yellow mosaic virus RNA-dependent RNA polymerase initiation of minus strand synthesis in vitro. Virology 233:430-439.
50. Sivakumaran, K. and Kao, C. C. 1999. Initiation of genomic plus-strand RNA synthesis from DNA and RNA templates by a viral RNA-dependent RNA polymerase. J. Virol. 73:6415-6423.
51. Song, C., and A. E. Simon. 1994. RNA-dependent RNA polymerase from plants infected with turnip crinkle virus can transcribe (+)- and (-)-strands of virus-associated RNAs. Proc. Natl. Acad. Sci. USA 91:8792-8796.
52. Song, C., and A. E. Simon. 1994. Requirement of a 3¢-terminal stem-loop in in vitro transcription by an RNA-dependent RNA polymerase. J. Mol. Biol. 245:6-14.
53. Sun, J. -H., and C. C. Kao. 1997. RNA synthesis by the brome mosaic virus RNA-dependent RNA polymerase: transition from initiation to elongation. Virology 233:63-73.
54. Tsai, C. H., and T. W. Dreher. 1992. Second-site suppressor mutations assist in studying the function of the 3¢ noncoding region of turnip yellow mosaic virus RNA. J. Virol. 66:5190-5199.
55. Tsai, C. -H., Cheng, C. -P., Pong, C. -W., Lin, B. -Y., Lin, N. -S., and Hsu, Y. -H. 1999. Sufficient length of the poly(A) tail for the formation of a potential pseudoknot is required for an efficient replication of bamboo mosaic potexvirus RNA. J. Virol. 73:2703-2709.
56. Van Duin, J. 1988. Single-stranded RNA bacteriophages, p. 117-167.In R. Callendar (ed.), The bacteriophages. Plenum Press. New York, N. Y.
57. White, K. A., Bancroft, J. B. and Mackie, G. A. 1992. Mutagenesis of a hexanuleotide sequence conserved in potexvirus RNAs. Virology 198:817-820.
58. White, K. A., Rouleau, M., Bancroft, J. B. and Mackie, G. A. 1994. Potexvirus, p.1142-1147. In “Encyclopedia of Virology”(R. G. Webster and A. Granoff, Ed.), Academic Press.
59. Wu, S., and Kaesberg, P. 1991. Synthesis of template-sense, single-strand fluckhouse virus RNA in a cell-free replication system. Virology 183:392-396.
60. Wu, S., Ahlquist, P. and Kaesberg, P. 1992. Active complete in vitro replication of nodavirus RNA requires glycerophosphate. Proc. Natl. Acad. Sci. USA 89:11136-11140.
61. Zuker, M., Mathews, D.H. and Turner, D.H. 1999, p.11-43. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide in RNA biochemistry and biotechnology.

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