Virus Genes

, Volume 44, Issue 3, pp 513–521 | Cite as

Analysis of two strains of Peanut stunt virus: satRNA-associated and satRNA free

  • Aleksandra Obrępalska-StęplowskaEmail author
  • Marta Budziszewska
  • Przemysław Wieczorek
  • Anna Czerwoniec


Peanut stunt virus (PSV) is a pathogen of legumes, vegetables, trees, and weeds occurring worldwide. The species is characterized by significant genetic variability. PSV strains are classified into four subgroups on the basis of their nucleotide sequence homology. Here, we are presenting two further, fully sequenced PSV strains—PSV-Ag and PSV-G, that could be considered as I subgroup representatives. However, their sequence homology with other typical I subgroups members, similarly as another strain—PSV-P, characterized by our group previously, is lower than 90%. This lead us to propose further subdivision of the I subgroup into IA, IB, and IC units, and to classify PSV-Ag and PSV-G strains to the last one. In this article, we are showing that identity level of PSV-Ag and PSV-G is very high and apart from the presence of satRNA in the first one, they differ only by a few nucleotides in their genomic RNAs. Nevertheless, symptoms they cause on host plants might differ significantly, just as the levels in infected plants. Effect of single amino acid changes between strains on the three-dimensional structure of viral proteins was analyzed. Differences occur mainly on the protein surfaces which can possibly affect protein–protein interaction in infected cells, which is discussed.


PSV Classification satRNA Symptom expression Three-dimensional model structure of viral proteins 



We thank Prof. Henryk Pospieszny for the help with viral strains. The study was supported by the Polish Ministry of Science and Higher Education Grant NN 310 117537 (to AOS) and grant 0067/P01/2010/70 (to AC).


  1. 1.
    R. Adamczak, A. Porollo, J. Meller, Proteins 56, 753–767 (2004)PubMedCrossRefGoogle Scholar
  2. 2.
    G. Brignetti, O. Voinnet, W.X. Li, L.H. Ji, S.W. Ding, D.C. Baulcombe, EMBO J. 17, 6739–6746 (1998)CrossRefGoogle Scholar
  3. 3.
    H.Y. Chen, J. Yang, C. Lin, Y.A. Yuan, EMBO Rep. 9, 754–761 (2008)PubMedCrossRefGoogle Scholar
  4. 4.
    J.A. Cuff, G.J. Barton, Proteins 40, 502–511 (2000)PubMedCrossRefGoogle Scholar
  5. 5.
    W.L. DeLano, The PyMOL user’s manual (DeLano Scientific, San Carlos, 2002)Google Scholar
  6. 6.
    S.W. Ding, B.J. Anderson, H.R. Haase, R.H. Symons, Virology 198, 593–601 (1994)PubMedCrossRefGoogle Scholar
  7. 7.
    S.W. Ding, W.X. Li, R.H. Symons, EMBO J. 14, 5762–5772 (1995)PubMedGoogle Scholar
  8. 8.
    S.W. Ding, B.J. Shi, W.X. Li, R.H. Symons, Proc. Natl. Acad. Sci. USA 93, 7470–7474 (1996)PubMedCrossRefGoogle Scholar
  9. 9.
    C. Fereiro, K. Ostrowka, J.J. Lopez-Moja, J.R. Diaz-Ruiz, Eur. J. Plant Pathol. 102, 779–786 (1996)CrossRefGoogle Scholar
  10. 10.
    A. Gellert, K. Salanki, G. Naray-Szabo, F. Balazs, J. Mol. Graph. Model. 24, 319–327 (2006)PubMedCrossRefGoogle Scholar
  11. 11.
    I. Gonzalez, L. Martinez, D.V. Rakitina, M.G. Lewsey, F.A. Atencio, C. Llave, N.O. Kalinina, J.P. Carr, P. Palukaitis, T. Canto, MPMI 23, 294–303 (2010)PubMedCrossRefGoogle Scholar
  12. 12.
    K. Goto, T. Kobori, Y. Kosaka, T. Natsuaki, C. Masuta, Plant Cell Physiol. 48, 1050–1060 (2007)PubMedCrossRefGoogle Scholar
  13. 13.
    T.A. Hall Nucl, Acids Symp. Ser. 41, 95–98 (1999)Google Scholar
  14. 14.
    C.C. Hu, A.E. Aboul-Ata, R.A. Naidu, S.A. Ghabrial, J. Gen. Virol. 78, 929–939 (1997)PubMedGoogle Scholar
  15. 15.
    M.S. Hwang, K.N. Kim, J.H. Lee, Y.I. Park, J. Gen. Virol. 88, 3445–3451 (2007)PubMedCrossRefGoogle Scholar
  16. 16.
    J.I. Inaba, B.M. Kim, H. Shimura, C. Masuta, Plant Physiol. 156, 2026–2036 (2011)PubMedCrossRefGoogle Scholar
  17. 17.
    L.H. Ji, S.W. Ding, Mol. Plant-Microbe Interact. 14, 715–724 (2001)PubMedCrossRefGoogle Scholar
  18. 18.
    A. Karasawa, K. Nakaho, T. Kakutani, Y. Minobe, Y. Ehara, Virology 185, 464–467 (1991)PubMedCrossRefGoogle Scholar
  19. 19.
    A. Karasawa, K. Nakaho, T. Kakutani, Y. Minobe, Y. Ehara, J. Gen. Virol. 73, 701–707 (1992)PubMedCrossRefGoogle Scholar
  20. 20.
    M.J. Kim, B.K. Ham, H.R. Kim, I.J. Lee, Y.J. Kim, K.H. Ryu, Y.I. Park, K.H. Paek, Plant Mol. Biol. 59, 981–994 (2005)PubMedCrossRefGoogle Scholar
  21. 21.
    M.J. Kim, S.U. Huh, B.K. Ham, K.H. Paek, J. Virol. 82, 4823–4833 (2008)PubMedCrossRefGoogle Scholar
  22. 22.
    S.H. Kim, P. Palukaitis, Y.I. Park, EMBO J. 21, 2292–2300 (2002)PubMedCrossRefGoogle Scholar
  23. 23.
    L. Kiss, E. Sebestyen, E. Laszlo, P. Salamon, E. Balazs, K. Salanki, Arch. Virol. 153, 1373–1377 (2008)PubMedCrossRefGoogle Scholar
  24. 24.
    L. Kiss, E. Balazs, K. Salanki, Eur. J. Plant Pathol. 125, 677–761 (2009)CrossRefGoogle Scholar
  25. 25.
    J. Kosinski, I.A. Cymerman, M. Feder, M.A. Kurowski, J.M. Sasin, J.M. Bujnicki, Proteins 53(Suppl 6), 369–379 (2003)PubMedCrossRefGoogle Scholar
  26. 26.
    J. Kosinski, M.J. Gajda, I.A. Cymerman, M.A. Kurowski, M. Pawlowski, M. Boniecki, A. Obarska, G. Papaj, P. Sroczynska-Obuchowicz, K.L. Tkaczuk, P. Sniezynska, J.M. Sasin, A. Augustyn, J.M. Bujnicki, M. Feder, Proteins 61(Suppl 7), 106–113 (2005)PubMedCrossRefGoogle Scholar
  27. 27.
    E.V. Koonin, V.V. Dolja Crit, Rev. Biochem. Mol. Biol. 28, 375–430 (1993)CrossRefGoogle Scholar
  28. 28.
    S. Kumar, K. Tamura, M. Nei, Brief. Bioinform. 5, 150–163 (2004)PubMedCrossRefGoogle Scholar
  29. 29.
    M.A. Kurowski, J.M. Bujnicki, Nucl. Acids Res. 31, 3305–3307 (2003)PubMedCrossRefGoogle Scholar
  30. 30.
    M.G. Lewsey, I. Gonzalez, N.O. Kalinina, P. Palukaitis, T. Canto, J.P. Carr, Plant Signal Behav. 5, 705–708 (2010)PubMedCrossRefGoogle Scholar
  31. 31.
    L.J. McGuffin, K. Bryson, D.T. Jones, Bioinformatics 16, 404–405 (2000)PubMedCrossRefGoogle Scholar
  32. 32.
    L.I. Miller, J.L. Troutman, Plant Dis. 50, 139–143 (1966)Google Scholar
  33. 33.
    A.R. Mushegian, E.V. Koonin, Arch. Virol. 133, 239–257 (1993)PubMedCrossRefGoogle Scholar
  34. 34.
    R.A. Naidu, G.B. Collins, S.A. Ghabrial, Plant Mol. Biol. 17, 175–177 (1991)PubMedCrossRefGoogle Scholar
  35. 35.
    R.A. Naidu, C.C. Hu, R.E. Pennington, S.A. Ghabrial, Phytopathology 85, 502–507 (1995)CrossRefGoogle Scholar
  36. 36.
    O. Netsu, K. Hiratsuka, S. Kuwata, T. Hibi, M. Ugaki, M. Suzuki, Arch. Virol. 153, 1731–1735 (2008)PubMedCrossRefGoogle Scholar
  37. 37.
    A. Obrepalska-Steplowska, M. Budziszewska, H. Pospieszny, Acta Biochim. Pol. 55, 731–739 (2008)PubMedGoogle Scholar
  38. 38.
    A. Obrepalska-Steplowska, K. Nowaczyk, M. Budziszewska, A. Czerwoniec, H. Pospieszny, Virus Genes 36, 221–229 (2008)PubMedCrossRefGoogle Scholar
  39. 39.
    A. Obrepalska-Steplowska, A scientific dissertations of Institute of Plant Protection, National Research Institute 22, 1–110 (2010)Google Scholar
  40. 40.
    E.K. O’Reilly, Z. Wang, R. French, C.C. Kao, J. Virol. 72, 7160–7169 (1998)PubMedGoogle Scholar
  41. 41.
    E.K. O’Reilly, J.D. Paul, C.C. Kao, J. Virol. 71, 7526–7532 (1997)PubMedGoogle Scholar
  42. 42.
    M. Ouali, R.D. King, Protein Sci. 9, 1162–1176 (2000)PubMedCrossRefGoogle Scholar
  43. 43.
    P. Palukaitis, P. Mol, Plant Microbe. Interact. 1, 175–181 (1988)CrossRefGoogle Scholar
  44. 44.
    M. Pawlowski, M.J. Gajda, R. Matlak, J.M. Bujnicki, BMC Bioinf. 29, 403 (2008)CrossRefGoogle Scholar
  45. 45.
    M. Pelczyk, A. Obrepalska-Steplowska, H. Pospieszny, Postepy Biochem. 52, 212–221 (2006)PubMedGoogle Scholar
  46. 46.
    M.W. Pfaffl, G.W. Horgan, L. Dempfle NAR 30, e36 (2002)CrossRefGoogle Scholar
  47. 47.
    H. Pospieszny, J. Plant. Protect. Res. 28, 27–75 (1988)Google Scholar
  48. 48.
    U.J. Rashid, J. Hoffmann, B. Brutschy, J. Piehler, J.C. Chen, Biochemistry 47, 12655–12657 (2008)PubMedCrossRefGoogle Scholar
  49. 49.
    B. Rost, G. Yachdav, J. Liu, Nucl. Acids Res. 32, 321–326 (2004)CrossRefGoogle Scholar
  50. 50.
    M.N. Rozanov, E.V. Koonin, A.E. Gorbalenya, J. Gen. Vir. 73, 2129–2134 (1992)CrossRefGoogle Scholar
  51. 51.
    N. Saitou, M. Nei Mol, Evol. Biol. 4, 406–425 (1987)Google Scholar
  52. 52.
    J. Sambrook, E.F. Fritsch, T. Maniatis (eds.), Molecular cloning: a laboratory manual, 2nd edn. (Cold Spring Harbor Laboratory Press, New York, 1989), pp. 743–745Google Scholar
  53. 53.
    A.E. Simon, M.J. Roosinck, Z. Havelda, Annu. Rev. Phytopathol. 42, 415–437 (2004)PubMedCrossRefGoogle Scholar
  54. 54.
    D. Szilassy, K. Salanki, E. Balazs, Mol. Plant Microbe. Interact. 12, 1105–1113 (1999)PubMedCrossRefGoogle Scholar
  55. 55.
    K. Tamura, J. Dudlmy, M. Nei, S. Kumar, Mol. Biol. Evol. 24, 1596–1599 (2007)PubMedCrossRefGoogle Scholar
  56. 56.
    J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, D.G. Higgins, Nucl. Acids Res. 25, 4876–4882 (1997)PubMedCrossRefGoogle Scholar
  57. 57.
    B. Wallner, A. Elofsson, Protein Sci. 12, 1073–1086 (2003)PubMedCrossRefGoogle Scholar
  58. 58.
    L.Y. Yan, X.Y. Xu, R. Goldbach, C. Kunrong, M. Prins, Arch. Virol. 150, 1203–2111 (2005)PubMedCrossRefGoogle Scholar
  59. 59.
    X. Zhang, Y.R. Yuan, Y. Pei, S.S. Lin, T. Tuschl, D.J. Patel, N. H. Chua Genes Dev. 20, 3255–3268 (2006)CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Aleksandra Obrępalska-Stęplowska
    • 1
    Email author
  • Marta Budziszewska
    • 1
  • Przemysław Wieczorek
    • 1
  • Anna Czerwoniec
    • 2
  1. 1.Interdepartmental Laboratory of Molecular BiologyInstitute of Plant Protection—National Research InstitutePoznanPoland
  2. 2.Bioinformatics Laboratory, Institute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityPoznanPoland

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