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A Core Promoter Hairpin is Essential for Subgenomic RNA Synthesis in Alfalfa Mosaic Alfamovirus and is Conserved in other Bromoviridae

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Abstract

The nucleotide sequence immediately in front of the initiation site for subgenomic RNA 4 synthesis on RNA 3 minus strand, which has been proved to function as a core promoter, was inspected for secondary structure in 26 species of the plant virus family Bromoviridae. In 23 cases a stable hairpin could be predicted at a distance of 3 to 8 nucleotides from the initiation site of RNA 4. This hairpin contained several conserved nucleotides that are essential for core promoter activity in brome mosaic virus (R.W. Siegel, S. Adkins and C.C. Kao, Proc. Natl. Acad. Sci. USA 94, 11238–11243, 1997). Phylogenetic evidence and evidence from the effect of artificial mutations reported in the literature (E.A.G. van der Vossen, T. Notenboom and J.F. Bol, Virology 212, 663–672, 1995) indicate that the stem-loop structure is essential for promoter activity in alfalfa mosaic virus and probably in other Bromoviridae. Stability of the hairpin is most pronounced in the genera Alfamovirus and Ilarvirus which display genome activation by coat protein. The hypothesis is put forward that with these viruses the coat protein is needed for the viral RNA polymerase to interact with the core promoter hairpin leading to access for the enzyme to the initiation site of RNA 4.

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References

  1. Rybicki E.P., in Murphy F.A., Fauquet C.M., Bishop D.H.L., Ghabrial S.A., Jarvis A.W., Martelli G.P., Mayo M.A., and Summers M.D. (eds.). Virus taxonomy. Classification and nomenclature of viruses. Sixth report of the international committee on taxonomy of viruses. Springer, Wien, New York, 1995, pp. 450-457.

    Google Scholar 

  2. Miller W.A., Dreher T.W., and Hall T.C., Nature 313, 68-70, 1985.

    Google Scholar 

  3. Marsh L.E., Dreher T.W., and Hall T.C., Nucleic Acids Res 16, 981-995, 1988.

    Google Scholar 

  4. Adkins S., Siegel R.W., Sun J.-H., and Kao C.C., RNA 3, 634- 647, 1997.

    Google Scholar 

  5. Van der Kuyl A.C., Langereis K., Houwing C.J., Jaspars E.M.J., and Bol J.F., Virology 176, 346-354, 1990.

    Google Scholar 

  6. French R., Janda M., and Ahlquist P., Science 231, 1294-1297, 1986.

    Google Scholar 

  7. French R. and Ahlquist P., J Virol 62, 2411-2420, 1988.

    Google Scholar 

  8. Pacha R.F., Allison R.F., and Ahlquist P., Virology 174, 436- 443, 1990.

    Google Scholar 

  9. Boccard F. and Baulcombe D., Virology 193, 563-578, 1993.

    Google Scholar 

  10. Van der Vossen E.A.G., Notenboom T., and Bol J.F., Virology 212, 663-672, 1995.

    Google Scholar 

  11. Siegel R.W., Adkins S., and Kao C.C., Proc Natl Acad Sci USA 94, 11238-11243, 1997.

    Google Scholar 

  12. De Graaff M., Thorburn C., and Jaspars E.M.J., Virology 213, 650-654, 1995.

    Google Scholar 

  13. Reusken C.B.E.M., Neeleman L., Brederode F.T., and Bol J.F., J Virol 71, 8385-8391, 1997.

    Google Scholar 

  14. Marsh L.E., Pogue G.P., and Hall T.C., Virology 172, 415-427, 1989.

    Google Scholar 

  15. Pogue G.P. and Hall T.C., J Virol 66, 674-684, 1992.

    Google Scholar 

  16. Van der Vossen E.A.G. and Bol J.F., Virology 220, 539-543, 1996.

    Google Scholar 

  17. Van Rossum C.M.A., Reusken C.B.E.M., Brederode F.T., and Bol J.F., J Gen Virol 78, 3045-3049, 1997.

    Google Scholar 

  18. Reusken C.B.E.M., Neeleman L., and Bol J.F., J Virol 69, 4552-4555, 1995.

    Google Scholar 

  19. Koper-Zwarthoff E.C., Brederode F.T., Veeneman G., Van Boom J.H., and Bol J.F., Nucleic Acids Res 8, 5635-5647, 1980.

    Google Scholar 

  20. Ahlquist P., Dasgupta R., and Kaesberg P., J Mol Biol 172, 369- 383, 1984.

    Google Scholar 

  21. Dreher T.W. and Hall T.C., in Domingo E., Holland J.J., and Ahlquist P. (eds.). RNA genetics. Vol. I. RNA-directed virus replication. CRC, Boca Raton, FL, 1988, pp. 91-113.

    Google Scholar 

  22. Romero J., Dzianott A.M., and Bujarski J.J., Virology 187, 671-681, 1992.

    Google Scholar 

  23. Van der Kuyl A.C., Neeleman L., and Bol J.F., Virology 185, 496-499, 1991.

    Google Scholar 

  24. Van der Vossen E.A.G., Neeleman L., and Bol J.F., Virology 202, 891-903, 1994.

    Google Scholar 

  25. Houwing C.J. and Jaspars E.M.J., Biochimie 75, 617-621, 1993.

    Google Scholar 

  26. De Graaff M., Man in 't Veld M.R., and Jaspars E.M.J., Virology 208, 583-589, 1995.

    Google Scholar 

  27. Houwing C.J., Van de Putte P., and Jaspars E.M.J., Arch Virol 143, 489-500, 1998.

    Google Scholar 

  28. Jaspars E.M.J., in Davies J.W. (ed.). Molecular plant virology. Vol. I. CRC Press, Boca Raton, FL, 1985, pp. 155- 221.

    Google Scholar 

  29. Quadt R., Rosdorff H.J.M., Hunt T.W., and Jaspars E.M.J., Virology 182, 309-315, 1991.

    Google Scholar 

  30. Reusken C.B.E.M. and Bol J.F., Nucleic Acids Res 24, 2660- 2665, 1996.

    Google Scholar 

  31. Baer M.L., Houser F., Loesch-Fries L.S., and Gehrke L., EMBO J 13, 727-735, 1994.

    Google Scholar 

  32. Zuidema D., Ph.D. Thesis, University of Leiden, 1983.

  33. Grieco F., Martelli G.P., and Savino V., J Gen Virol 76, 929- 937, 1995.

    Google Scholar 

  34. Ding S.-W., Anderson B.J., Haase H.R., and Symons R.H., Virology 198, 593-601, 1994.

    Google Scholar 

  35. Shi B.-J., Ding S.-W., and Symons R.H., J Gen Virol 78, 237- 241, 1997.

    Google Scholar 

  36. Shi B.-J., Ding S.-W., and Symons R.H., J Gen Virol 78, 505- 510, 1997.

    Google Scholar 

  37. Ahlquist P., Luckow V., and Kaesberg P., J Mol Biol 153, 23- 38, 1981.

    Google Scholar 

  38. Allison R.F., Janda M., and Ahlquist P., Virology 172, 321-330, 1989.

    Google Scholar 

  39. Palukaitis P., Roossinck M.J., Dietzgen R.G., and Francki R.I.B., Advan Virus Res 41, 281-348, 1992.

    Google Scholar 

  40. Shi B.-J., Ding S.W., and Symons R.H., Gen Bank accession number U64435, 1996.

  41. Salánki K., Balázs E., and Burgyán J., Virus Res 33, 281-289, 1994.

    Google Scholar 

  42. O'Reilly D., Thomas C.J.R., and Coutts R.H.A., Virus Genes 8, 79-81, 1994.

    Google Scholar 

  43. Moriones E., Roossinck M.J., and García-Arenal F., J Gen Virol 72, 779-783, 1991.

    Google Scholar 

  44. Karasawa A., Nakaho K., Kakutani T., Minobe Y., and Ehara Y., Virology 185, 464-467, 1991.

    Google Scholar 

  45. Barker R.F., Jarvis N.P., Thompson D.V., Loesch-Fries L.S., and Hall T.C., Nucleic Acids Res 11, 2881-2891, 1983.

    Google Scholar 

  46. Langereis K., Mugnier M.-A., Cornelissen B.J.C., Pinck L., and Bol J.F., Virology 154, 409-414, 1986.

    Google Scholar 

  47. Ravelonandro M., Pinck M., and Pinck L., Biochimie 66, 395- 402, 1984.

    Google Scholar 

  48. Neeleman L., Van der Kuyl A.C., and Bol J.F., Virology 181, 687-693, 1991.

    Google Scholar 

  49. Cornelissen B.J.C., Janssen H., Zuidema D., and Bol J.F., Nucleic Acids Res 12, 2427-2437, 1984.

    Google Scholar 

  50. Ge X. and Scott S.W., Virus Res 40, 57-63, 1996.

    Google Scholar 

  51. Scott S.W. and Ge X., J Gen Virol 76, 957-963, 1995.

    Google Scholar 

  52. Scott S.W. and Ge X., J Gen Virol 76, 1801-1806, 1995.

    Google Scholar 

  53. Rafael-Martin M. and Rivera-Bustamante R.F., Gen Bank accession number X86352, 1995.

  54. Ge X., Scott S.W., and Zimmerman M.T., Arch Virol 142, 1213-1226, 1997.

    Google Scholar 

  55. Guo D., Maiss E., Adam G., and Casper R., J Gen Virol 76, 1073-1079, 1995.

    Google Scholar 

  56. Sánchez-Navarro J.A. and Pallás V., Arch Virol 142, 749-763, 1997.

    Google Scholar 

  57. Hammond R.W. and Crosslin J.M., Virology 208, 349-353, 1995.

    Google Scholar 

  58. Shiel P.J., Alrefai R.H., Domier L.L., Korban S.S., and Berger P.H., Arch Virol 140, 1247-1256, 1995.

    Google Scholar 

  59. Bachman E.J., Scott S.W., Ge X., and Vance V.B., Virology 201, 127-131, 1994.

    Google Scholar 

  60. Freier S.M., Kierzek R., Jaeger J.A., Sugimoto N, Caruthers M.H., Neilson T., and Turner D.H., Proc Natl Acad Sci USA 83, 9373-9377, 1986.

    Google Scholar 

  61. Jaeger J.A., Turner D.H., and Zuker M., Proc Natl Acad Sci USA 86, 7706-7710, 1989.

    Google Scholar 

  62. Francki R.I.B., in Francki R.I.B. (ed.). The plant viruses. Vol. 1. Polyhedral virions with tripartite genomes. Plenum Press, New York, 1985, pp. 1-18.

    Google Scholar 

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  1. Institute of Molecular Plant Sciences, Gorlaeus Laboratories, Leiden University, The Netherlands

    E.M.J. Jaspars

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Jaspars, E. A Core Promoter Hairpin is Essential for Subgenomic RNA Synthesis in Alfalfa Mosaic Alfamovirus and is Conserved in other Bromoviridae. Virus Genes 17, 233–242 (1998). https://doi.org/10.1023/A:1008065704102

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