臺灣博碩士論文加值系統

胡瓜嵌紋病毒 (cucumber mosaic virus, CMV) 為單股三基因體的RNA植物病毒，有些分離株攜帶有衛星核酸(satellite RNA, satRNA)，需要依賴輔助病毒進行複製、包被及傳播，但與其輔助病毒無核酸序列同源性。本研究以胡瓜嵌紋病毒NT9株系 (CMV-NT9) 及其衛星核酸M-satRNA為材料，利用PCR的方式造成端點序列突變，來探討衛星核酸複製所需之訊息是由序列或者是結構所決定，以進一步了解衛星核酸之複製機制與輔助病毒複製酵素之交互作用。實驗方法主要為利用帶有30個隨機核苷酸序列的引子進行PCR來取代原本衛星核酸的5’端及3’端序列，突變株經生體外轉錄得到的轉錄體，與輔助病毒共同接種至菸草 (Nicotiana tabacum 、N.benthamiana)，再抽取雙股RNA來偵測突變株於植物體中之複製能力，並利用逆轉錄-聚合酵素鏈鎖反應 (RT-PCR) 及核酸定序來確認子代之衛星核酸序列。在實驗進行之前，鑑於隨機序列接種可能出現野生型，因此先將使用的M48 satRNA作修飾，把位於satRNA 164位置上的核苷酸由T修改成A，使其多出一個NdeⅠ切位，方便於判斷獲得的野生型殖株是由於序列隨機度足夠還是接種污染所造成。另外，突變的位置是在端點，無法用端點引子進行RT-PCR，因此以poly (A) polymerase在雙股RNA的3’端加上poly(A) tail以oligo (dT) 進行RT-PCR以得到子代序列。實驗後發現，在雙股RNA正股的3’端可能有未知結構，妨礙poly(A) tail的加入，因此改利用多體的特性，以中間序列引子進行RT-PCR，即得到端點的序列，解序結果發現一突變株，在5’端的序列為5’-GTTTTGTTT-3’ ，與M48 satRNA相比，在5’端多了一個T，在3’ 端少了一個C，但與其他野生型satRNA端點序列差異並不顯著。部分序列多體連接處不完整，經分析後發現缺失序列接點附近具有高度相似性序列，因此研判多體的產生為與同源性序列有關。分析經原生質體接種確定不具複製能力的突變株，及以mfold預測其二級結構，不論其序列和結構皆與原本的衛星核酸差異甚大。另外本實驗比較在自然界存在的胡瓜嵌紋衛星核酸，將mfold預測的最低能量結構直線化，利用叢集分類進行多重序列排列，並與序列分類做比較。結果發現以結構分類與序列分類的的衛星核酸差異甚大，而有些結構在衛星核酸中屬於高度保留。總而言之，在本實驗的環境下，帶有野生型端點序列的衛星核酸最具有競爭力，而分析後發現序列與結構同樣在衛星核酸複製上扮演著重要角色。

Cucumber mosaic virus (CMV) is the type species of the genus Cucumovirus. Some strains of CMV harbor satellite RNAs (satRNAs) that are dependent on CMV for their replication, encapsidation, and transmission. The specific aim of this study is to investigate the 5’- and 3’-terminal signals on satRNAs required for high efficiency replication and to distinguish the effects of nucleotide sequences and structures. The 5’- and/or 3’-terminal 30 nucleotides were replaced by random sequences with synthetic primers in polymerase chain reactions (PCR). The transcripts of mutants were used to inoculate the plants with the helper virus, CMV-NT9. The viabilities of the mutants were analyzed by double-stranded RNA (dsRNA) analyses. The nucleotide sequences of the mutant satRNAs progenies were investigated using RT-PCR followed by DNA sequencing. To differentiate between inoculated transcripts and wild-type satRNA contaminations, a selection marker was introduced into the satRNAs by mutating the Thymine164 into an Adenine to create an NdeI restriction site. Since the 5’- and/or 3’-terminal sequences were randomized, poly(A) polmerase was used to add poly(A) tail at 3’ends of dsRNAs, and oligo(dT) primers were used to amplify the progenies. In addition, the multimeric replication forms of satRNAs were also used as templates for RT-PCR with inverse internal primer pair to amplify the terminal sequences. A viable mutant was recovered from the progenies of 324 inoculation tests. Nucleotide sequencing revealed that the mutant contains an addition of T in the 5’ terminal T stretch region and a deletion of C in the 3’ terminal triple region. The sequence analysis of the multimeric forms revealed that some nucleotides at the junctions between monomers were deleted, and the deletion sites contain similar sequence. The formation of multimers may come from homologous template-switching. Sequence analyses and structural predictions revealed evident differences between viable and non-viable satRNAs. Together, the results indicated that the current wild-type terminal sequences of satRNAs are the most competitive patterns under our experimental conditions. Both structure and sequence may play important roles in the replication of satRNAs.

中文摘要------------------------------------------------------1
英文摘要------------------------------------------------------2
前言----------------------------------------------------------3
前人研究------------------------------------------------------5
一、胡瓜嵌紋病毒簡介------------------------------------------5
1. 經濟重要性------------------------------------------5
2. 分類地位--------------------------------------------5
二、基因體結構、組成與功能------------------------------------6
1. RNA1與其基因功能------------------------------------6
2. RNA2與其基因功能------------------------------------7
3. RNA3、次基因體RNA 4與其基因功能---------------------8
三、衛星核酸----------------------------------------------9
1. 序列及結構--------------------------------------9
2. 複製模式---------------------------------------11
3. 複製訊號---------------------------------------12
材料與方法---------------------------------------------------14
一、病毒來源------------------------------------------------14
二、病毒的純化-----------------------------------------------14
三、衛星核酸篩選記號之產生-----------------------------------15
四、端點突變株之產生-----------------------------------------18
五、測試端點突變株之隨機度-----------------------------------19
六、接種試驗-------------------------------------------------20
七、轉錄子複製之偵測-----------------------------------------21
八、原生質體的製備及接種-------------------------------------23
九、找出造成反轉錄聚合酵素鏈反應問題的實驗設置---------25
十、衛星核酸多體之偵測與分析-------------------------- 26
十一、電腦輔助核苷酸序列分析-------------------------- 27
結果---------------------------------------------------------28
討論---------------------------------------------------------33
參考文獻-----------------------------------------------------39
圖-----------------------------------------------------------52

陳薇。(1992). 序列刪減突變對胡瓜嵌紋病毒衛星核酸的影響. 國立中興大學分子生物研究所碩士論文。
洪怡芳。(2002). 突變序列對胡瓜嵌紋病毒衛星核酸複製之探討. 國立中興大學農業生物科技學研究所碩士論文。
Al-Kaff, N.S., Covey, S.N., Kreike, M. M., Page, A. M., Pinder, R., and Dale, P. J. (1998). Transcriptional and posttranscriptional plant gene silencing in response to a pathogen. Science 279, 2113-2115.
Altschul, S. F., Thomas, L. M., Alejandro, A. S., Jinghui, Z., Zheng, Z., Webb, M., and David, J. L. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
Aranda, M. A., Fraile, A., Dopazo, J., Malpica, J. M., and Garcia-Arenal, F. (1997). Contribution of mutation and RNA recombination to the evolution of a plant pathogenic RNA. Journal of Molecular Evolution 44(1), 81-88.
Avila-Rincon, M. J., Collmer, C. W., and Kaper, J. M. (1986). In vitro translation of cucumoviral satellites. II. CARNA 5 from cucumber mosaic virus strain S and SP6 transcripts of cloned (S)CARNA 5 cDNA produce electrophoretically comigrating protein products. Virology 152(2), 455-458.
Béclin, C., Berthome, R., Palauqui, J. C., Tepfer, M. & Vaucheret, H. (1998). Infection of tobacco or Arabidopsis plants by CMV counteracts systemic post-transcriptional silencing of nonviral (trans) genes. Virology 252, 313—317.
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Wheeler, D. L. (2004). Genebank. Nucleic Acids Res 32,23-26.
Bernal, J. J., Garcia-Arenal, F. (1994). Complex interactions between several base positions determine phenotypes defective for long distance transport in the satellite RNA of cucumber mosaic cucumovirus. Virology 200, 148-153.
Birnboim, H. C., and Doly, J. (1979). A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7, 1513-1523.
Blackman, M. L., Boevink, P., Santa Cruz, S., Palukaitis, P. & Oparka, K. J. (1998). The movement protein of cucumber mosaic virus traffics into sieve elements in minor veins of Nicotiana clevelandii. Plant Cell 10, 525—537.
Bouhida, M., Lockhart, B. E., and Olszewski, N. E. (1990). An analysis of the complete sequence of a sugarcane bacilliform virus genome infectious to banana and rice. J Gen Virol 74, 15-22.
Brigneti, G., Voinnet, O., Li, W. X., Ji, L. H., Ding, S. W., and Baulcombe, D. C. (1998). Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J 16, 6739-6746.
Buck, K. (1996). Comparison of the replication of positive-stranded RNA viruses of plants and animals. Advances in Virus Research 47, 159-251.
Buck, K. W. (1997). Comparison of the replication of positive-strnaded RNA viruses of plants and animals. Adv Virus Res 47, 159-251.
Burgyan, J., and Garcia-Arenal, F. (1998). Template-independent repair of the 3'' end of cucumber mosaic virus satellite RNA controlled by RNAs 1 and 2 of helper virus. Journal of Virology 72(6), 5061-6.
Canto, T., Prior, D. A. M., Hellwald, K.-H., Oparka, K. J. and Palukaitis, P. (1997). Characterization of cucumber mosaic virus. IV. Movement protein and coat protein are both essential for cell-to-cell movement of cucumber mosaic virus. Virology 237, 237—248.
Citovsky, V., Knorr, D., Schuster, G., and Zambryski, P. (1990). The P30 movement protein of tobacco mosaic virus is a single-strand nucleic acid binding protein. Cell 60, 637-647.
Cohen, J., Loebenstein, G., and Spiegel, S. (1988). Infection of sweet potato by cucumber mosaic virus depends on the presence of sweet potato feathery mottle virus. Plant Dis 72(7), 583-585.
Collmer, C. W., and Kaper, J. M. (1985). Double-stranded RNAs of cucumber mosaic virus and its satellite contain an unpaired terminal guanosine: implications for replication. Virology 145(2), 249-259.
Collmer, C. W., and Kaper, J. M. (1986). Infectious RNA transcripts from cloned cDNAs of cucumber mosaic viral satellites. Biochem Biophys Res Commun 135:290-296.
Collmer, C. W., and Howell, S. H. (1992). Role of satellite RNA in the expression of symptoms caused by plant-viruses. Annual review of phytopathology 30, 419-442.
Collmer, C. W., Tonsignant, M. E., and Kaper, J. M. (1983). Cucumber mosaic virus-associated RNA5: X. The complete nucleotide sequence of CARNA5 incapable of inducing tomato necrosis. Virology 127, 230-234.
Covery, S. N., Al-Kaff, N. S., Langara, A., and Turner, D. S. (1997). Plants combat infection by gene silencing. Nature 385, 781-782.
Dagert, M., and Ehrlich, S. D. (1979). Prolongedincubation in CaCl2 improves the competence of E. coli cells. Gene 6, 23-28.
De Graaf, M. and Jaspars, E. M. J. (1994). Plant viral RNA synthesis in cell-free systems. Annual Review of Phytopathology 32, 261-285.
Deom, C. M., Lapidot, M., and Beachy, R. N. (1992). Plant virus movement proteins. Cell 69, 221-224.
Devereux, J., Haeberli, P., and Smithies, O. (1984). A comprehensive set of nucleotide sequence analysis programs for the VAX. Nucleic Acids Research 12, 387-395.
Devic, M., Jaegle, M., and Baulcombe, D. (1990). Cucumber mosaic virus satellite RNA (strain Y): analysis of sequences which affect systemic necrosis on tomato. J Gen Virol 71(pt.7), 1443-1449.
Diaz-Ruiz, J. R., and Kaper, J. M. (1983). Nucleotide sequence relationships among thirty peanut stunt virus isolates determined by competition hybridization. Arch Virol 75(4), 277-281.
Ding, S. W., Li, W. X., and Symons, R. H. (1995). A novel naturally occurring gene encoded by a plant RNA virus facilitates long distance virus movement. EMBO J 14(23),5762-5772.
Ding, S. W., Anderson, B. J., Haase, H. R., and Symons, R. H. (1994). New overlapping gene encoded by the cucumber mosaic virus genome. Virology 198(2), 593-601.
Ding, S. W., Shi, B.-J., Li, W.-X., and Symons, R. H. (1996). An interspecies hybrid RNA virus is significantly more virulent than either parental virus. Proc. Natl. Acad. Sci. USA 93, 7470-7474.
Doolittle, S. P. (1916). Phytopathology 6, 145-147.
Dreher, T. W., Bujarski, J. J., and Hall, T. C. (1984). Mutant viral RNAs synthesized in vitro show altered aminoacylation and replicase template activities. Nature 311(5982), 171-5.
Ewardson, J. R., Christie, R. G. (1991). Cucumovirus. CRC Handbook of viruses Infecting Legumes. J. R. Ewardson and R.G. Christie, eds. CRC Press Boca Raton, FL, U.S.A. 293-319.
Fraile A, Garcia-Arenal, F. (1991). Secondary structure as a constraint on the evolution of a plant viral satellite RNA. J Mol Biol. 1991 Oct 20;221(4):1065-9.
Francki, R. I. B., Mossop, D. W., and Hatta, T. (1979). Cucumber mosaic virus [world-wide, especially in temperate regions]. Descr Plant Viruses Commw Mycol Inst(set 13), sheet 213, 6.
Garcia-Arenal, F., Zaitlin, M., and Palukaitis, P. (1987). Nucleotide sequence analysis of six satellite RNAs of cucumber mosaic virus: primary sequence and secondary structure alterations do not correlate with differences in pathogenicity. Virology 158(2), 339-347.
Gorbalenya, A. E., Koonin, E. V., Donchenko, A. P., and Blinov, V. M. (1989). Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res 17(12), 4713-4730.
Gordon, K. H., and Symons, R. H. (1983). Satellite RNA of cucumber mosaic virus forms a secondary structure with partial 3''-terminal homology to genomal RNAs. Nucleic Acids Res 11(4), 947-960.
Gould, A. R., and Symons, R. H. (1982). Cucumber mosaic virus RNA 3. Determination of the nucleotide sequence provides the amino acid sequences of protein 3A and viral coat protein. Eur J Biochem 126(2), 217-226.
Gould, A. R., Palukaitis, P., Symons, R. H., and Mossop, D. W. (1978). Characterization of a satellite RNA associated with cucumber mosaic virus. Virology 84(2), 443-455.
Guan, H., Song, C. and Simon, A. E. (1997). RNA promoters located on (-)-strand of a subviral RNA associated with turnip crinkle virus. RNA, 3, 1401-1412.
Habili, N., and Francki, R. I. (1974). Comparative studies on tomato aspermy and cucumber mosaic viruses. I. Physical and chemical properties. Virology 57(2), 392-401.
Habili, N., and Symons, R. H. (1989). Evolutionary relationship between luteoviruses and other RNA plant viruses based on sequence motifs in their putative RNA poymerases and nucleic acid helicases. Nucleic Acids Res 17, 9543-9555.
Hayes, R. J., Tousch, D., Jacquemond, M., Pereira, V. C., Buck, K. W., and Tepfer, M. (1992). Complete replication of a satellite RNA in vitro by a purified RNA-dependent RNA polymerase. J Gen Virol 73(pt.6), 1597-1600.
Hidaka, S., Hanada, K. & Ishikawa, K. (1990). In vitro messenger properties of a satellite RNA of cucumber mosaic virus. J Gen Virol 71, 439-442.
Hidaka, S., Hanada, K., Ishikawa, K., and Miura, K. (1984). Complete nucleotide sequence of RNA5 from cucumber mosaic virus (strain Y). Virology 164, 326-333.
Hidaka, S., Hanada, K., Ishikawa, K., and Miura, K. (1988). Complete nucleotide sequence of two new satellite RNAs associated with cucumber mosaic virus. Virology 164(2), 326-333.
Higgins, D., Thompson, J., Gibson, T.Thompson J.D., Higgins, D.G.., and Gibson T.J.(1994).CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
Hsu, Y. H., Hu, C. C., Lin, N. S., and Chiu, R. J. (1988). Symptom determinant of two Taiwan strains of cucumber mosaic virus is on RNA3. Bot. Bull. Academia Sinica 29:231-237.
Hsu, Y. H., Lin, F. Z., Hu, C. C. & Yin, S. C. (1989). Host reaction, serology and RNA pattern of cucumber mosaic virus isolates. Pl. Prot. Bull. 31, 51-59.
Ish-Horowicz, D., and Burke, J. F. (1981). Rapid and efficient cosmid cloning. Nucleic Acids Res 9, 2989-2998.
Jacquemond, M., and Leroux, J. P. (1982). Cucumber mosaic virus-associated RNA. II. Virus-satellite RNA relationship in various host plants. L''ARN satellite du virus de la mosaique du concombre. II. Etude de la relation virus-ARN satellite chez divers hotes. Agron Sci Prod Veg Environ 2(1), 55-62.
Kadare, G., and Haenni, A. (1997). Virus-encoded RNA helicases. J. Virol. 71, 2583-2590.
Kamer, G., and Argos, P. (1984). Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 12(18), 7269-7282.
Kao, C. C., and Ahlquist, P. (1992). Identification of the domains required for direct interaction of the helicase-like and polymerase-like RNA replication proteins of brome mosaic virus. J Virol 66(12), 7293-7302.
Kaper, J. M. (1982). Rapid synthesis of double-stranded cucumber mosaic virus-associated RNA 5: mechanism controlling viral pathogenesis. Biochem Biophys Res Commun 105(3), 1014-1022.
Kaper, J. M., and Diaz-Ruiz, J. R. (1977). Molecular weights of the double-stranded RNAs of cucumber mosaic virus strain S and its associated RNA 5. Virology 80(1), 214-217.
Kaper, J. M. & Tousignant, M. E. (1977). Cucumber mosaic virus-associating RNA 5. I. Role of host plant and helper strain in determining amount of associated RNA 5 with virions. Virology 80, 186-95.
Kaper, J. M., and Waterworth, H. E. (1981). Cucumoviruses Cucumber mosaic virus, peanut swine virus, tomato aspermy virus. Handb Plant Virus Infect. Amsterdam, Elsevier/North Holland 1981, 257-332.
Kaplan, I. B., Zhang, L. & Palukaitis, P. (1998). Characterization of cucumber mosaic virus. V. Cell-to-cell movement requires capsid protein but not virions. Virology 246, 221—231.
Kaplan, I. B., Shintaku, M. H., Li, Q., Zhang, L., Marsh, L. E. & Palukaitis, P. (1995). Complementation of virus movement in transgenic tobacco expressing the cucumber mosaic virus 3a gene. Virology 10, 188—199.
Kasschau, K. D., and Carrington, J. C. (1998). A counterdefensive strategy of plant viruses: suppression of posttranscriptional gene silencing. Cell 95, 461-470.
Kim, S. H., Palukaitis, P., and Park, Y. I. (2002). Phosphorylation of cucumber mosaic virus RNA polymerase 2a protein inhibits formation of replicase complex. EMBO J 21(9), 2292-2300.
Koev, G.., and Miller, W. A., (2000). A positive-strand RNA virus with three very different subgenomic RNA promoters. J Gen Virol 74, 5988-5996.
Kohl, R. J., and Hall, T. C. (1974). Amino acylation of RNA from several viruses: amino acid specificity and differential activity of plant, yeast and bacterial synthetase. J Gen Virol 25, 231-257.
Koonin, E. V., and Dolja, V. V. (1993). Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences [published erratum appears in Crit Rev Biochem Mol Biol 1993;28(6):546]. Crit Rev Biochem Mol Biol 28(5), 375-430.
Koonin, E. V., Choi, G. H., Nuss, D. L., Shapira, R., and Carrington, J. C. (1991). Evidence for common ancestry of a chestnut blight hypovirulence-associated double-stranded RNA and a group of positive-strand RNA plant viruses. Proc Natl Acad Sci USA 88(23), 10647-10651.
Kroner, P. A., Young, B. M., and Ahlquist, P. (1990). Analysis of the role of brome mosaic virus 1a protein domains in RNA replication, using linker insertion mutagenesis. J Virol 64(12), 6110-6120.
Kuhn, C. (1990). Cowpea Research: A U.S. Perspective. pp.7-23. Texas A&M Univ. Press, College Station.
Kurath, G., and Palukaitis, P. (1987). Biological activity of T7 transcripts of a prototype clone and a sequence variant clone of a satellite RNA of cucumber mosaic virus. Virology 159(2), 199-208.
Kuroda, T., Natsuaki, T., Wang, W.Q and Qkuda, S. (1997). Formation of multimers of cucumber mosaic virus satellite RNA. J Gen Virol 78, 941-946.
Lai, M. M. C. (1998). Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependdent RNA transcription. Virology 244, 1-12.
Lehto, K., and Dawson, W. O. (1990). Replication, stability, and gene expression of tobacco mosaic virus mutants with a second 30K ORF. Virology 175, 30-40.
Li, Q. and Palukaitis, P. (1996). Comparison of the nucleic acid- and NTP-binding properties of the movement protein of cucumber mosaic cucumovirus and tobacco mosaic tobamovirus. Virology 216, 71—79.
Linthorst, H. J. M., and Kaper, J. M. (1984). Circular satellite-RNA molecules in satellite of tobacco ringspot virus-infected tissue. Virology 137(1), 206-210.
Linthorst, H. J. M., and Kaper, J. M. (1984). Replication of peanut stunt virus and its associated RNA 5 in cowpea protoplasts. Virology 139(2), 317-329.
Linthorst, H. J. M., and Kaper, J. M. (1985). Cucumovirus satellite RNAs cannot replicate autonomously in cowpea protoplasts. J. Gen Virol 66:1839-1842.
Luis-Arteaga, M., Rodriguez-Cerezo, E., and Garcia-Arenal, F. (1988). Plant Dis 72, 265-267.
Masuta, C. & Takanami, Y. (1989). Determination of sequence and structural requirements for pathogenicity of a cucumber mosaic virus satellite RNA (Y-satRNA). Plant Cell 1, 1165-1173.
Masuta, C., Kuwata, S., and Takanami, Y. (1987). In vitro synthesis of infectious RNAs from cDNA of cucumber mosaic virus satellite RNA (strain Y) after removal of non-viral bases with ribonuclease H. Nucleic Acids Res 15:10048.
Matthews, R. E. F. (1991). “Plant Virology.” Third Edition ed. Academic Press Ltd., San Diego.
Mead, K. A., Szxzesna- Skorupa, E., and Kemper, B. (1986). Single-stranded DNA ''''blue'''' T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering. Prot. Eng 1, 67-74.
Melcher, U. (1990). Similarities between putative transport proteins of plant viruses. J Gen Virol 71, 1009—1018.
Morris, T. J., and Dodds, J. A. (1979). Isolation and analysis of double-stranded RNA from virus infected plant and fungal tissue. Phytopathology 69, 854-858.
Mossop, D. W., and Francki, R. I. B. (1979). Comparative studies on two satellite RNAs of cucumber mosaic virus. Virology 95(2), 395-404.
Mullis, K., Faloona F., Scharf S., Saiki R., Horn G., and Erlich. H. (1986). Specific emzymatic amplification of DNA in Vitro: The polymerase chain reaction. Cold Spring Harbor Symp Quant Biol 51, 263.
Murphy, F. A., Fauquet, C. M., Bishop, D. H. L., A., G. S., Jarvis, A. W., Martelli, G. P., Mayo, M. A., and Summers, M. D. (1995). “Virus taxonomy. Classifi cation and nomeclature of viruses.”. Arch. Virol., Suppl. 10, Springer-Verlag Wien, New York.
Naidu, R. A., Collins, G. B., and Ghabrial, S. A. (1991). Sympton-modulating properties of peanut stunt virus satellite RNA sequence variants. Mol Plant Microb Interact MPMI 4(3), 268-275.
Nitta, N., Takanami, Y., Kuwata, S., and Kubo, S. (1988). Inoculation with RNAs 1 and 2 of cucumber mosaic virus induces viral RNA replicase activity in tobacco mesophyll protoplasts. J Gen Virol 69(10), 2695-2700.
Nurkiyanova, K. M., Ryabov, E. V., Kalinina, N. O., Fan, Y., Andreev, I., Fitzgerald, A. G., Palukaitis, P. & Taliansky, M. (2001). Umbravirus-encoded movement protein induces tubule formation on the surface of protoplasts and binds RNA incompletely and non-cooperatively. J Gen Virol 82, 2579—2588.
Owens, R. A. & Kaper, J. M. (1977). Cucumber mosaic virus-associated RNA 5. II. In vitro translation in a wheat germ protein-synthesis system. Virology 80, 196-203.
Palukaitis, P. (1988). Pathogenicity regulation by satellite RNAs of cucumber mosaic virus: minor nucleotide sequence changes alter host responses. Mol Plant Microbe Interact 1(4), 175-81.
Palukaitis, P., Roossinck, M. J., Dietzgen, R. G., and Francki, R. I. B. (1992). Cucumber mosaic virus. Adv Virus Res. San Diego, Calif. : Academic Press 41, 281-348.
Peden, K. W., and Symons, R. H. (1973). Cucumber mosaic virus contains a functionally divided genome. Virology 53(2), 487-92.
Piazzolla, P., Tousignant, M. E., and Kaper, J. M. (1982). Cucumber mosaic virus-associated RNA 5. IX. The overtaking of viral RNA synthesis by CARNA 5 cucumber mosaic virus-associated RNA 5 and dsCARNA 5 in tobacco. Virology 122(1), 147-157.
Ratcliff , F., Harrison, B. D. (1997). A simility between viral defense and gene silencing in plants. Science 276, 1558-1560.
Richard, K. E., Jonard, G., Jacquemond, M., and Lot, H. (1978). Nucleotide sequence of cucumber mosaic virus-associated RNA 5. Virology 89(2), 395-408.
Rietveld, K., Pleij, C. W., and Bosch, L. (1983). Three-dimensional models of the tRNA-like 3'' termini of some plant viral RNAs. Embo J 2(7), 1079-85.
Roossinck, M. J., Sleat, D., and Palukaitis, P. (1992). Satellite RNAs of plant viruses: structures and biological effects. Microbiol. Rev. 56, 265-279.
Roossinck, M. J., Zhang L., and Hellwald K.H.. (1999). Rearrangements in the 5’nontranslated region and phylogenetic analyses of cucumber mosaic
virus RNA 3 indicate radial evolution of three subgroups. J. Virol. 73:6752—
6758.
Ryabov, E. V., Roberts, I. M., Palukaitis, P. and Taliansky, M. (1999). Host-specific cell-to-cell and long-distance movements of cucumber mosaic virus are facilitated by the movement protein of groundnut rosette virus. Virology 260, 98—108.
Schwinghamer, M. W., and Symons, R. H. (1975). Fractionation of cucumber mosaic virus RNA and its translation in a wheat embryo cell-free system. Virology 63(1), 252-262.
Schwinghamer, M. W., and Symons, R. H. (1977). Translation of the four major RNA species of cucumber mosaic virus in plant and animal cell-free systems and in toad oocytes. Virology 79(1), 88-108.
Shi, B. J., Miller, J., Symons, R. H. & Palukaitis, P. (2003). The 2b protein of cucumoviruses has a role in promoting the cell-to-cell movement of pseudorecombinant viruses. Mol Plant Microbe Interact 16, 261—267.
Soards, A. J., Murphy, A. M., Palukaitis, P. & Carr, J. P. (2002). Virulence and differential local and systemic spread of cucumber mosaic virus in tobacco are affected by the CMV 2b protein. Mol Plant Microbe Interact 15, 647—653.
Suzuki, M., Kuwata, S., Kataoka, J., Masuta, C., Nitta, N., and Takanami, Y. (1991). Functional analysis of deletion mutants of cucumber mosaic virus RNA3 using an in vitro transcription system. Virology 183(1), 106-113.
Takamatsu, N., Watanabe, Y., Yanagi, H., Meshi, T., Shiba, T., and Okada, Y. (1990). Production of enkephalin in tobacco protoplasts using tobacco mosaic virus RNA vector. FEBS Letters 269(1), 73-6.
Takanami, Y., Kubo, S., and Imaizumi, S. (1977). Synthesis of single- and double-stranded cucumber mosaic virus RNAs in tobacco mesophyll protoplasts. Virology 80(2), 376-389.
Tasi, C.-H. and Dreher, T. W. (1991). Turnip yellow mosaic virus RNAs with anticodon loop substitutions that result in decreased valylation fail to replicate efficiently. J. Virol. 65:3060-3067.
Tien, P., and Wu, G. S. (1991). Satellite RNA for the biocontrol of plant disease. Advances in Virus Research 39, 321-339.
Tousch, D., Jacquemond, M., and Tepfer, M. (1994). Replication of cucumber mosaic virus satellite RNA from negative-sense transcripts produced either in vitro or in transgenic plants. J gen virol 75(pt.5), 1009-1014.
Wang, MB., Bian, XY., Wu, LM., Liu, LX., Smith, NA., Isenegger, D., Wu, RM., Masuta, C., Vance, VB., Watson, JM., Rezaian, A., Dennis, ES., Waterhouse, PM. (2004). On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proc Natl Acad Sci U S A 101, 3275-80.
Waterworth, H. E., Kaper, J. M., and Tousignant, M. E. (1979). CARNA 5, the small cucumber mosaic virus-dependent replicating RNA causal agent of lethal tomato necrosis, regulates disease expression. Science 204(4395), 845-847.
Wu, G., and Kaper, J. M. (1992).Widely seprarated sequence elements within cucumber mosaic virus satellites contribute to their ability to induce lethal tomato necrosis. J Gen Virol 73, 2805-2812.
Wu, G., and Kaper, J. M. (1994). Requirement of 3''-terminal guanosine in (-)-stranded RNA for in vitro replication of cucumber mosaic virus satellite RNA by viral RNA-dependent RNA polymerase. J Mol Biol 238(5), 655-657.
Young, N. D., Palukaitis, P., and Zaitlin M. (1987). Characterization of multimeric forms of cucumber mosaic virus satellite RNA. Proceedings of the UCLA symposium. ln: Arntzen CJ. Ryan C (eds.) Molecular strategies for crop protection. Liss. New York. pp 243-252.
Zuker M. (1998). Using reliability information to annotate RNA secondary structures. RNA. 4(6):669-79.
Zhang, G and Simon, A.E. , (2003). A multifunctional turnip crinkle virus replication enhancer revealed by in vivo functional SELEX. J Mol Biol. 2003 Feb 7;326(1):35-48.