Abstract
The nucleotide sequences of the RNA 3 of fifteen isolates of Prunus necrotic ringspot virus (PNRSV) varying in the symptomatology they cause in six different Prunus spp. were determined. Analysis of the molecular variability has allowed, in addition to study the phylogenetic relationships among them, to evaluate the minimal requirements for the synthesis of the subgenomic RNA in Ilarvirus genus and their comparison to other members of the Bromoviridae family. Computer assisted comparisons led recently to Jaspars (Virus Genes 17, 233–242, 1998) to propose that a hairpin structure in viral minus strand RNA is required for subgenomic promoter activity of viruses from at least two, and possibly all five, genera in the family of Bromoviridae. For PNRSV and Apple mosaic virus two stable hairpins were proposed whereas for the rest of Ilarviruses and the other four genera of the Bromoviridae family only one stable hairpin was predicted. Comparative analysis of this region among the fifteen PNRSV isolates characterized in this study revealed that two of them showed a 12-nt deletion that led to the disappearance of the most proximal hairpin to the initiation site. Interestingly, the only hairpin found in these two isolates is very similar in primary and secondary structure to the one previously shown in Brome mosaic virus to be required for the synthesis of the subgenomic RNA. In this hairpin, the molecular diversity was concentrated mostly at the loop whereas compensatory mutations were observed at the base of the stem strongly suggesting its functional relevance. The evolutionary implications of these observations are discussed.
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van Regenmortel M.H.V., Fauquet C.M., Bishop D.H.L., Carstens E.B., Estes M.K., Lemon S.M., McGeoch D.J., Maniloff J., Mayo M.A., Pringle C.R., Wickner R.B. (eds), Virus Taxonomy. Classification and Nomenclature of Viruses. Wien Seventh ICTV Report. Academic Press, 2000, pp.
Bol J.F., J Gen Virol 80, 1089–1102, 1999.
Jaspars E.M.J., Arch Virol 144, 843–863, 1999.
Aparicio F., Sánchez-Pina M.A., Sánchez-Navarro J.A., and Pallás V., Eur J Plant Pathol 105, 623–627, 1999.
Uyemoto J.K. and Scott S.W., Plant Dis 76, 5–11, 1992.
Hammond R.W. and Crosslin J.M., J Gen Virol 79, 1815–1823, 1998.
Aparicio F., Myrta A., Di Terlizzi B., and Pallás V., Phytopathology 89, 991–999, 1999.
Scott S.W., Zimmerman M.T., Ge X., and MacKenzie D.J., Eur J Plant Pathol 104, 155–161, 1998.
Vašková D., Petrzik K., and Karešová R., Arch Virol 145, 699–709, 2000.
Miller W.A. and Koev G., Virology 273, 1–8, 2000.
Adkins S., Siegel R.W., Sun J.-H., and Kao C.C., RNA 3, 634–647, 1997.
Chen M.H., Roossinick M.J., and Kao C.C., J Virol 74, 11201–11209, 2000.
Haasnoot P.C.J., Brederode F.Th., Olsthoorn R.C.L., and Bol J.F., RNA 6, 708–716, 2000.
Marsh L.E., Dreher T.W., and Hall T.C., Nucleic Acids Res 16, 981–995, 1988.
Adkins S. and Kao C.C., Virology 252, 1–8, 1998.
Siegel R.W., Adkins S., and Kao C.C., Proc Natl Acad Sci USA 94, 11238–11243, 1997.
Jaspars E.M.J., Virus Genes 17, 233–242, 1998.
Sánchez-Navarro J.A. and Pallás V., Arch Virol 142, 749–763, 1997.
Pallás V., Más P., and Sánchez-Navarro J.A., in Foster G. and Taylor S. (eds), Detection of Plant RNA Viruses by Non-Isotopic Dot-Blot Hybridization. Humana Press, Totowa, 1998.
Pallás V., Sánchez-Navarro J.A., and Díez J., Arch Virol 144, 797–803, 1999.
Thompson J.D., Higgins D.G., and Gibson T.J., Nucleic Acids Res 22, 4673–4680, 1994.
Felsenstein J., Cladistic 5, 164–166, 1989.
Citovsky V., Wong M.L., Shaw A.L., Venkataram P.B.V., and Zambryski P., Plant Cell 4, 397–411, 1992.
Jansen K.A.J., Wolfs C.J.A.M., Lohuis H., Goldbach R.W., and Benedictus J.M.V., Virology 242, 387–394, 1998.
Marcos J.F., Vilar M., Pérez-Payá E., and Pallás V., Virology 255, 354–365, 1999.
Schoumacher F., Giovane C., Maira M., Poirson A., Godefroy-Colburn T., and Berna A., J Gen Virol 75, 3199–3202, 1994.
Vaquero C., Liao Y.-C., Nähring J., and Fisher R., J Gen Virol 78, 2095–2099, 1997.
Fujita M., Mise K., Kajiura Y., Dohi K., and Furusawa I., J Gen Virol 79, 1273–1280, 1998.
Sánchez-Navarro J.A., Reusken C.B.E.M., Bol J.F., and Pallás V., J Gen Virol 78, 3171–3176, 1997.
Candresse T., Revers F., Le Gall O., Kofalvi S., Marcos J., and Pallás V., in Tepfer M. and Balázs E. (ed.) Systematic Search for Recombination Events in Plant Viruses and Viroids. Springer-Verlag, Berlin, pp. 20–25, 1997.
Roossinck M.J., Zhang L., and Hellwald K.-H., J Virol 73, 6752–6758, 1999.
Bujarski J.J. and Kaesberg P., Nucleic Acids Res 15, 1337–1337, 1987.
Marsh L.E., Pogue G.P., and Hall T.C., Virology 172, 415–427, 1989.
Pogue G.P., Marsh L.E., Connell J.P., and Hall T.C., Virology 188, 741–753, 1992.
Boccard F. and Baulcombe D.C., Virology 193, 563–578, 1993.
Dugall R. and Hall T.C., Virology 214, 638–641, 1995.
van der Vossen E.A.G., Neeleman L., and Bol J.F., Nucleic Acids Res 6, 1361–1367, 1993.
van der Vossen E.A.G. and Bol J.F., Virology 220, 539–543, 1996.
Shiel P.J., Alrefai R.H., Domier L.L., Korban S.S., and Berger P.H., Arch Virol 140, 1247–1256, 1995.
Aparicio F., Sánchez-Navarro J.A., Olsthoorn R.C.L., Pallás V., and Bol J.F., J Gen Virol 82, 9947–9951, 2001.
Hammond R.W. and Crosslin J.M., Virology 208, 349–353, 1995.
Guo D., Maiss E., Adam G., and Casper R., J Gen Virol 76, 1073–1079, 1995.
Sánchez-Navarro J.A. and Pallás V., J Gen Virol 75, 1441–1445, 1994.
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Aparicio, F., Pallás, V. The Molecular Variability Analysis of the RNA 3 of Fifteen Isolates of Prunus Necrotic Ringspot Virus Sheds Light on the Minimal Requirements for the Synthesis of its Subgenomic RNA. Virus Genes 25, 75–84 (2002). https://doi.org/10.1023/A:1020126309692
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DOI: https://doi.org/10.1023/A:1020126309692