Plant Virology Protocols pp 69-79

Part of the Methods in Molecular Biology™ book series (MIMB, volume 451)

Role of Silencing Suppressor Proteins

  • József Burgyán


RNA silencing suppressors, developed by plant viruses, are potent arms in the arm race between plant and invading viruses. In higher plants, these proteins efficiently inhibit RNA silencing, which has evolved to defend plants against viral infection in addition to regulation of gene expression for growth and development Virus-encoded RNA-silencing suppressors interfere with various steps of the different silencing pathways and the mechanisms of suppression are being progressively unraveled. Our better understanding of action of silencing suppressors at molecular level dramatically improved our basic knowledge about the intimate plant-virus interactions and also provided valuable tools to unravel the diversity, regulation, and evolution of RNA-silencing pathways.


RNA silencing VIGS Plant virus silencing suppressors Mechanism of silencing suppression siRNA pl9 p21 HC-Pro 


  1. 1.
    1. Voinnet, O., Induction and suppression of RNA silencing: insights from viral infections. Nat Rev Genet, 2005. 6(3): p. 206–20.PubMedCrossRefGoogle Scholar
  2. 2.
    2. Lakatos L., C.T., Pantaleo V., Chapman E.J., Carrington J.C., Liu Y.R, Dolja V.V., Fernández Calvino L., López-Moya J.J., Burgyán J., Comparative study of viral encoded silencing suppressors: small RNA binding is a common strategy to suppress RNA silencing. EMBO J, 2006. 25: 2768–2780.PubMedCrossRefGoogle Scholar
  3. 3.
    3. Mérai, Z., Kerenyi, Z., Kertész, S., Magna, M., Lakatos, L., and Silhavy, D., Double-stranded RNA binding could be a general plant RNA viral strategy to suppress RNA silencing. J. Virol. 2006., 80(12): 5747–56.PubMedCrossRefGoogle Scholar
  4. 4.
    4. Baulcombe, D., RNA silencing in plants. Nature, 2004. 431(7006): p. 356–63.PubMedCrossRefGoogle Scholar
  5. 5.
    5. Silhavy, D. and J. Burgyan, Effects and side-effects of viral RNA silencing suppressors on short RNAs. Trends Plant Sci, 2004. 9(2): p. 76–83.PubMedCrossRefGoogle Scholar
  6. 6.
    6. Hamilton, A., et al. Two classes of short interfering RNA in RNA silencing. Embo J, 2002. 21(17): p. 4671–4679.PubMedCrossRefGoogle Scholar
  7. 7.
    7. Hamilton, A.J. and D.C. Baulcombe, A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 1999. 286(5441): p. 950–2.PubMedCrossRefGoogle Scholar
  8. 8.
    8. Plasterk, R.H., RNA silencing: the genome's immune system. Science, 2002. 296(5571): p. 1263–5.PubMedCrossRefGoogle Scholar
  9. 9.
    9. Hannon, G.J. and D.S. Conkhn, RNA interference by short hairpin RNAs expressed in vertebrate cells. Methods Mol Biol. Vol. 257. 2004. 255–66.Google Scholar
  10. 10.
    10. Meister, G. and T Tuschl, Mechanisms of gene silencing by double-stranded RNA. Nature, 2004. 431(7006): p. 343–9.PubMedCrossRefGoogle Scholar
  11. 11.
    11. Voinnet, O., RNA silencing: small RNAs as ubiquitous regulators of gene expression. Curr Opin Plant Biol, 2002. 5(5): p. 444.PubMedCrossRefGoogle Scholar
  12. 12.
    12. Zamore, P.D., Ancient pathways programmed by small RNAs. Science, 2002. 296(5571): p. 1265–9.PubMedCrossRefGoogle Scholar
  13. 13.
    13. Bernstein, E., et al. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 2001. 409(6818): p. 363–6.PubMedCrossRefGoogle Scholar
  14. 14.
    14. Nykanen, A., B. Haley, and P.D. Zamore, ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell, 2001. 107(3): p. 309–21.PubMedCrossRefGoogle Scholar
  15. 15.
    15. Hammond, S.M., et al. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature, 2000. 404(6775): p. 293–6.PubMedCrossRefGoogle Scholar
  16. 16.
    16. Doench, J.G., C.P. Petersen, and PA. Sharp, siRNAs can function as miRNAs. Genes Dev, 2003. 17(4): p. 438–42.PubMedCrossRefGoogle Scholar
  17. 17.
    17. Hutvagner, G. and P.D. Zamore, RNAi: nature abhors a double-strand. Curr Opin Genet Dev, 2002. 12(2): p. 225–32.PubMedCrossRefGoogle Scholar
  18. 18.
    18. Chen, X., A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 2003. 11: p. 11.Google Scholar
  19. 19.
    19. Aukerman, M.J. and H. Sakai, Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell, 2003. 10: p. 10.Google Scholar
  20. 20.
    20. Verdel, A., et al., RNAi-mediated targeting of heterochromatin by the RITS complex. Science, 2004. 303(5658): p. 672–6.PubMedCrossRefGoogle Scholar
  21. 21.
    21. Dalmay, T., et al. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell, 2000. 101(5): p. 543–53.PubMedCrossRefGoogle Scholar
  22. 22.
    22. Mourrain, P., et al., Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell, 2000. 101(5): p. 533–42.PubMedCrossRefGoogle Scholar
  23. 23.
    23. Himber, C, et al. Transitivity-dependent and -independent cell-to-cell movement of RNA silencing. Embo J, 2003. 22(17): p. 4523–33.PubMedCrossRefGoogle Scholar
  24. 24.
    24. Voinnet, O., Non-cell autonomous RNA silencing. FEES Lett, 2005. 579(26): p. 5858–71.CrossRefGoogle Scholar
  25. 25.
    25. Bartel, D.P, MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004. 116(2): p. 281–97.PubMedCrossRefGoogle Scholar
  26. 26.
    26. Chen, X., MicroRNA biogenesis and function in plants. FEES Lett, 2005. 579(26): p. 5923–31.CrossRefGoogle Scholar
  27. 27.
    27. Vazquez, E, et al. Endogenous trans-Acting siRNAs Regulate the Accumulation of Arabidopsis mRNAs. Mol Cell, 2004. 16(1): p. 69–79.PubMedCrossRefGoogle Scholar
  28. 28.
    28. Peragine, A., et al., SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev, 2004. .18(19): p. 2368–79.PubMedCrossRefGoogle Scholar
  29. 29.
    29. Allen, E., et al., microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005. 121(2): p. 207–21.PubMedCrossRefGoogle Scholar
  30. 30.
    30. Gasciolli, V., et al. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol, 2005. 15(16): p. 1494–500.PubMedCrossRefGoogle Scholar
  31. 31.
    31. Dunoyer, P., C. Himber, and O. Voinnet, DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genet, 2005. 37(12): p. 1356–60.PubMedCrossRefGoogle Scholar
  32. 32.
    32. Szittya, G., et al. Short defective interfering RNAs of tombusviruses are not targeted but trigger post-transcriptional gene silencing against their helper virus. Plant Cell, 2002. 14(2): p. 359–72.PubMedCrossRefGoogle Scholar
  33. 33.
    33. Ratcliff, E, B.D. Harrison, and D.C. Baulcombe, A Similarity Between Viral Defense and Gene Silencing in Plants. Science, 1997. 276(5318): p. 1558–60.PubMedCrossRefGoogle Scholar
  34. 34.
    34. Moissiard, G. and O. Voinnet, Viral suppression of RNA silencing in plants. Molecular plant pathology, 2004. 5(1): p. 71–82.PubMedCrossRefGoogle Scholar
  35. 35.
    35. Voinnet, O., Y.M. Pinto, and D.C. Baulcombe, Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci U S A, 1999. 96(24): p. 14147–52.PubMedCrossRefGoogle Scholar
  36. 36.
    36. Li, W.X. and S.W. Ding, Viral suppressors of RNA silencing. Curr Opin Biotechnol, 2001. 12(2): p. 150–4.PubMedCrossRefGoogle Scholar
  37. 37.
    37. Silhavy, D., et al., A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs. Embo J, 2002. 21(12): p. 3070–80.PubMedCrossRefGoogle Scholar
  38. 38.
    38. Pruss, G., et al. Plant viral synergism: the potyviral genome encodes a broad-range pathogenicity enhancer that transactivates rephcation of heterologous viruses. Plant Cell, 1997. 9(6): p. 859–68.PubMedCrossRefGoogle Scholar
  39. 39.
    39. Anandalakshmi, R., et al., A viral suppressor of gene silencing in plants. Proc Natl Acad Sci USA, 1998. 95(22): p. 13079–84.PubMedCrossRefGoogle Scholar
  40. 40.
    40. Brigneti, G., et al. Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. Embo J, 1998. 17(22): p. 6739–46.PubMedCrossRefGoogle Scholar
  41. 41.
    41. Anandalakshmi, R., et al., A calmodulin-related protein that suppresses posttranscriptional gene silencing in plants. Science, 2000. 290(5489): p. 142–4.PubMedCrossRefGoogle Scholar
  42. 42.
    42. Mallory, A.C., et al., HC-Pro suppression of transgene silencing eliminates the small RNAs but not transgene methylation or the mobile signal. Plant Cell, 2001. 13(3): p. 571–83.PubMedCrossRefGoogle Scholar
  43. 43.
    43. Dunoyer, P., et al. Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell, 2004. 16(5): p. 1235–50.PubMedCrossRefGoogle Scholar
  44. 44.
    44. Chapman, E.J., et al. Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev, 2004. 18(10): p. 1179–86.PubMedCrossRefGoogle Scholar
  45. 45.
    45. Lakatos, L., et al. Molecular mechanism of RNA silencing suppression mediated by pl9 protein of tombusviruses. Embo J, 2004. 23(4): p. 876–84. Epub 2004 Feb 19.PubMedCrossRefGoogle Scholar
  46. 46.
    46. Vargason, J., et al. Size selective recognition of siRNA by an RNA silencing suppressor. Cell, 2003. 115(7): p. 799–811.PubMedCrossRefGoogle Scholar
  47. 47.
    47. Ye, K., L. Malinina, and D.J. Patel, Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature, 2003. 3: p. 3.Google Scholar
  48. 48.
    48. Ebhardt, H.A., et al. Extensive 33′ modification of plant small RNAs is modulated by helper component-proteinase expression. Proc Natl Acad Sci U S A, 2005. 102(38): p. 13398–403.PubMedCrossRefGoogle Scholar
  49. 49.
    49. Dolja, V.V., J.F. Kreuze, and J.P Valkonen, Comparative and functional genomics of closteroviruses. Virus Res, 2006. 117(1): p. 38–51.PubMedCrossRefGoogle Scholar
  50. 50.
    50. Koonin, E.V., et al. 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 U S A, 1991. 88(23): p. 10647–51.PubMedCrossRefGoogle Scholar
  51. 51.
    51. Reed, J.C., et al. Suppressor of RNA silencing encoded by Beet yellows virus. Virology, 2003. 306(2): p. 203–9.PubMedCrossRefGoogle Scholar
  52. 52.
    52. Pazhouhandeh, M., et al., F-box-like domain in the polerovirus protein PO is required for silencing suppressor function. Proc Natl Acad Sci U S A, 2006. 103(6): p. 1994–9.PubMedCrossRefGoogle Scholar
  53. 53.
    53. Qu, F., T. Ren, and T.J. Morris, The coat protein of turnip crinkle virus suppresses posttranscriptional gene silencing at an early initiation step. J Virol, 2003. 77(1): p. 511–22.PubMedCrossRefGoogle Scholar
  54. 54.
    Deleris et al., A molecular framework for induction and suppression of antiviral RNA silencing in plants. Science, in press.Google Scholar
  55. 55.
    55. Chellappan, P., R. Vanitharani, and C.M. Eauquet, MicroRNA-binding viral protein interferes with Arabidopsis development. Proc Natl Acad Sci U S A, 2005. 102(29): p. 10381–6.PubMedCrossRefGoogle Scholar
  56. 56.
    56. Kasschau, K.D., et al., P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev Cell, 2003. 4(2): p. 205–17.PubMedCrossRefGoogle Scholar
  57. 57.
    57. Thomas, C.L., et al. Turnip crinkle virus coat protein mediates suppression of RNA silencing in Nicotiana benthamiana. Virology, 2003. 306.(1): p. 33–41.PubMedCrossRefGoogle Scholar
  58. 58.
    58. Lu, R., et al. Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome. Proc Natl Acad Sci U S A, 2004. 101(44): p. 15742–7.PubMedCrossRefGoogle Scholar
  59. 59.
    59. Liu, L., et al., Cowpea mosaic virus RNA-1 acts as an amplicon whose effects can be counteracted by a RNA-2-encoded suppressor of silencing. Virology, 2004. 323(1): p. 37–48.PubMedCrossRefGoogle Scholar
  60. 60.
    60. Yehna, N.E., et al. Long-distance movement, virulence, and RNA silencing suppression controlled by a single protein in hordei- and potyviruses: complementary functions between virus families. J Virol, 2002. 76(24): p. 12981–91.CrossRefGoogle Scholar
  61. 61.
    61. Dunoyer, P., et al. Identification, subcellular localzation and some properties of a cysteine-rich suppressor of gene silencing encoded by peanut clump virus. Plant J, 2002. 29(5): p. 555–67.PubMedCrossRefGoogle Scholar
  62. 62.
    62. Pfeffer, S., et al., P0 of beet Western yellows virus is a suppressor of posttranscriptional gene silencing. J Virol, 2002. 76(13): p. 6815–24.PubMedCrossRefGoogle Scholar
  63. 63.
    63. Voinnet, O., C. Lederer, and D.C. Baulcombe, A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell, 2000. 103(1): p. 157–67.PubMedCrossRefGoogle Scholar
  64. 64.
    64. Kasschau, K.D. and J.C. Carrington, A counterdefensive strategy of plant viruses: suppression of posttranscriptional gene silencing. Cell, 1998. 95(4): p. 461–70.PubMedCrossRefGoogle Scholar
  65. 65.
    65. Kubota, K., et al. Tomato mosaic virus replication protein suppresses virus-targeted posttranscriptional gene silencing. J Virol, 2003. 77(20): p. 11016–26.PubMedCrossRefGoogle Scholar
  66. 66.
    66. Chen, J., et al., Viral virulence protein suppresses RNA silencing-mediated defense but upregulates the role of microrna in host gene expression. Plant Cell, 2004. 16(5): p. 1302–13.PubMedCrossRefGoogle Scholar
  67. 67.
    67. Bucher, E., et al. Negative-strand tospoviruses and tenuiviruses carry a gene for a suppressor of gene silencing at analogous genomic positions. J Virol, 2003. 77(2): p. 1329–36.PubMedCrossRefGoogle Scholar
  68. 68.
    68. Cao, X., et al. Identification of an RNA silencing suppressor from a plant double-stranded RNA virus. J Virol, 2005. 79(20): p. 13018–27.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science + Business Media, LLC 2008

Authors and Affiliations

  • József Burgyán
    • 1
  1. 1.Agricultural Biotechnology CenterPlant Biology InstituteHungary

Personalised recommendations