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Natural insertions within the N-terminal region of the coat protein of Maize dwarf mosaic potyvirus (MDMV) have an effect on the RNA stability

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Abstract

A 13 amino acid residue insertion was found in the N-terminal region of the coat protein of several Maize dwarf mosaic virus isolates (MDMV). These insertions seem to be the result of a direct duplication event, but differ in some positions. In order to evaluate the influence of the insertion on the RNA secondary structure and stability, the RNA secondary structures and minimum free energies (MFE) of all existing MDMV coat protein sequences were estimated using three different softwares, the Vienna RNA Package, NUPACK, and UNAFold, and compared to the secondary structure and MFE of various random sequence collections preserving the nucleotide distribution of MDMV. The bioinformatic analysis showed that the insertion stabilizes the RNA structure of the coat protein gene.

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References

  1. P. Simmonds, A. Tuplin, D.J. Evans, RNA 10, 1337–1351 (2004). doi:https://doi.org/10.1261/rna.7640104

    Article  CAS  Google Scholar 

  2. Z. Ullah, B. Chai, S. Hammar, B. Raccah, A. Gal-On, R. Grumat, Physiol. Mol. Plant Pathol. 63, 129–139 (2003). doi:https://doi.org/10.1016/j.pmpp.2003.11.001

    Article  CAS  Google Scholar 

  3. L. Riechmann, S. Laín, A. García, J. Gen. Virol. 73, 1–16 (1992)

    Article  CAS  Google Scholar 

  4. S. Urcuqui-Inchima, A.L. Haenni, F. Bernardi, Virus Res. 74, 157–175 (2001). doi:https://doi.org/10.1016/S0168-1702(01)00220-9

    Article  CAS  Google Scholar 

  5. D.D. Shukla, C.W. Ward, Adv. Virus Res. 36, 273–314 (1989)

    Article  CAS  Google Scholar 

  6. C.W. Ward, D.D. Shukla, Intervirology 32, 269–296 (1991)

    Article  CAS  Google Scholar 

  7. V.V. Dolja, R. Haldeman, N.L. Robertson, W.G. Dougherty, J.C. Carrington, EMBO J. 13, 1482–1491 (1994)

    Article  CAS  Google Scholar 

  8. Y. Zhong, A. Guo, C. Li, B. Zhuang, M. Lai, C. Wei, J. Luo, Y. Li, Virus Genes 30, 75–83 (2005). doi:https://doi.org/10.1007/s11262-004-4584-y

    Article  CAS  Google Scholar 

  9. I. Tóbiás, L. Palkovics, J. Phytopathol. 152, 445–447 (2004). doi:https://doi.org/10.1111/j.1439-0434.2004.00863.x

    Article  Google Scholar 

  10. G. Gell, K. Petrik, E. Balázs, Virus Genes, under submission

  11. K. Thivierge, V. Nicaise, P.J. Dufresne, S. Cotton, J.-F. Laliberté, O. Le Gall, M.G. Fortin, Plant Physiol. 138, 1822–1827 (2005). doi:https://doi.org/10.1104/pp.105.064105

    Article  CAS  Google Scholar 

  12. J.C. McCormack, X. Yuan, Y.G. Yingling, R.E. Zamora, B.A. Shapiro, A.E. Simon, J. Virol. 82, 8706–8720 (2008). doi:https://doi.org/10.1128/JVI.00416-08

    Article  CAS  Google Scholar 

  13. M. Davis, S.M. Sagan, J.P. Pezacki, D.J. Evans, P. Simmonds, J. Virol. 82, 11824–11836 (2008). doi:https://doi.org/10.1128/JVI.01078-08

    Article  CAS  Google Scholar 

  14. L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, P. Schuster, Monatshefte für Chemie/Chemical Monthly 125, 167–188 (1994)

    Article  CAS  Google Scholar 

  15. N.R. Markham, M. Zuker, Methods Mol. Biol. 453, 3–31 (2008)

    Article  CAS  Google Scholar 

  16. R.M. Dirks, N.A. Pierce, J. Comput. Chem. 25, 1295–1304 (2004). doi:https://doi.org/10.1002/jcc.20057

    Article  CAS  Google Scholar 

  17. M. Zuker, P. Stiegler Nucl. Acids Res. 9, 133–148 (1981)

    Article  CAS  Google Scholar 

  18. S.J. Schroeder, J. Virol. 83, 6326–6334 (2008). doi:https://doi.org/10.1128/JVI.00251-09

    Article  Google Scholar 

  19. P. Rice, I. Longden, A. Bleasby, EMBOSS: Trends Genetics 16, 276–277 (2000). doi:https://doi.org/10.1016/S0168-9525(00)02024-2

    CAS  Google Scholar 

Download references

Acknowledgments

This study was supported by grants from the German Academic Exchange Service (DAAD), the Hungarian Scientific Research Fund (OTKA NI 61023) and the EU-FP7-REGPOT 2007-1 (AGRISAFE 203288) project. The authors are grateful to B. Harasztos for the English revision of the manuscript.

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  1. Department of Applied Genomics, Agricultural Research Institute of the Hungarian Academy of Sciences, Brunszvik u. 2, 2462, Martonvásár, Hungary

    Kathrin Petrik, Endre Sebestyén, Gyöngyvér Gell & Ervin Balázs

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  1. Kathrin Petrik
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  2. Endre Sebestyén
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  3. Gyöngyvér Gell
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  4. Ervin Balázs
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Correspondence to Kathrin Petrik.

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Petrik, K., Sebestyén, E., Gell, G. et al. Natural insertions within the N-terminal region of the coat protein of Maize dwarf mosaic potyvirus (MDMV) have an effect on the RNA stability. Virus Genes 40, 135–139 (2010). https://doi.org/10.1007/s11262-009-0425-3

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  • DOI: https://doi.org/10.1007/s11262-009-0425-3

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