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Gene Review

RdRp  -  RNA dependent RNA polymerase

Cymbidium mosaic virus

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Disease relevance of RdRp

  • Similar to other potexviruses, its genome organisation is comprised of five major open reading frames (ORFs 1 to 5), encoding a Mr 160 KDa putative RNA-dependent RNA polymerase (RdRp); a Mr 26KDa/13KDa/10KDa triple-gene-block (TGB) and a Mr 24 KDa coat protein [1].
  • The RNA-dependent RNA polymerase (RdRp) of foxtail mosaic virus (FMV) was partially purified from infected leaves of Chenopodium quinoa [2].
  • The RNA template endogenous to RdRp preparations could be removed using micrococcal nuclease but the resulting fraction was unable to copy added template purified from FMV virions [2].
  • Specific sequences of the tobacco mosaic virus (TMV) RNA-dependent RNA-polymerase (RdRp) gene were investigated for their ability to confer cross-protection [3].
  • In vitro RNA-dependent RNA polymerase (RdRp) transcription assay share an extremely useful system for studying the molecular mechanisms of replication of positive-sense RNA viruses such as Bamboo mosaic virus (BaMV) [4].

High impact information on RdRp

  • During studies of salicylic acid (SA)-induced resistance to viral pathogens, we recently found that the activity of a tobacco RdRP was increased in virus-infected or SA-treated plants [5].
  • Electrophoretic mobility shift and competition assays have now been used to demonstrate that the Escherichia coli-expressed RNA-dependent RNA polymerase domain (Delta 893) derived from BaMV open reading frame 1 could specifically bind to the 3' UTR of BaMV RNA [6].
  • Frameshift mutations that blocked protein expression from RdRp segments disrupted only the high levels of protection derived from POL segments and not the low levels derived from the other segments [3].
  • Three single amino acid changes, glycine to alanine (AKS), lysine to asparagine (GNS) and lysine to glutamate (GES) within the GKS motif of the PVX RdRp were tested for their effect on PVX accumulation [7].
  • Mutation of the GKS motif of the RNA-dependent RNA polymerase from potato virus X disables or eliminates virus replication [7].

Biological context of RdRp


Associations of RdRp with chemical compounds

  • Additional purification was obtained by solubilization of the RdRp using KCl and dodecyl-sucrose and by centrifugation through a glycerol gradient [2].
  • The 3' untranslated regions (UTR) containing a stretch of 40 adenylate residues were shown to be an efficient exogenous RNA template for in vitro RdRp reactions [10].

Analytical, diagnostic and therapeutic context of RdRp

  • Phylogenetic analyses of the 85 CP and 37 RdRp sequences revealed the segregation of the isolates into two congruent monophyletic clusters; however these two subgroups did not cluster in amino sequence analysis because most of the nt mutations were synonymous [8].
  • Recombinant RNA-dependent RNA polymerase (RdRp) of BaMV binds to the pseudoknot poly(A) tail in gel mobility shift assays (C.-Y. Huang, Y.-L. Huang, M. Meng, Y.-H. Hsu, and C.-H. Tsai, J. Virol. 75:2818-2824, 2001) [11].
  • After treatment of the extracts with micrococcal nuclease to remove the endogenous templates, the full-length genomic RNA and the two subgenomic RNAs were efficiently synthesized by the partially purified RdRp complex in vitro [12].


  1. Cymbidium mosaic potexvirus RNA: complete nucleotide sequence and phylogenetic analysis. Wong, S.M., Mahtani, P.H., Lee, K.C., Yu, H.H., Tan, Y., Neo, K.K., Chan, Y., Wu, M., Chng, C.G. Arch. Virol. (1997) [Pubmed]
  2. Partial purification and characterization of foxtail mosaic potexvirus RNA-dependent RNA polymerase. Rouleau, M., Bancroft, J.B., Mackie, G.A. Virology (1993) [Pubmed]
  3. Tobacco mosaic virus replicase-mediated cross-protection: contributions of RNA and protein-derived mechanisms. Goregaoker, S.P., Eckhardt, L.G., Culver, J.N. Virology (2000) [Pubmed]
  4. Characterization of the infectivity of Bamboo mosaic virus with its correlation to the in vitro replicase activities in Nicotiana benthamiana. Lin, J.W., Hsu, Y.H., Tsai, C.H. Virus Res. (2005) [Pubmed]
  5. An important role of an inducible RNA-dependent RNA polymerase in plant antiviral defense. Xie, Z., Fan, B., Chen, C., Chen, Z. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  6. Sequences at the 3' untranslated region of bamboo mosaic potexvirus RNA interact with the viral RNA-dependent RNA polymerase. Huang, C.Y., Huang, Y.L., Meng, M., Hsu, Y.H., Tsai, C.H. J. Virol. (2001) [Pubmed]
  7. Mutation of the GKS motif of the RNA-dependent RNA polymerase from potato virus X disables or eliminates virus replication. Davenport, G.F., Baulcombe, D.C. J. Gen. Virol. (1997) [Pubmed]
  8. Evidence that Cymbidium mosaic virus (CymMV) isolates divide into two subgroups based on nucleotide diversity of coat protein and replicase genes. Moles, M., Delatte, H., Farreyrol, K., Grisoni, M. Arch. Virol. (2007) [Pubmed]
  9. A single amino acid residue of RNA-dependent RNA polymerase in the Potato virus X genome determines the symptoms in Nicotiana plants. Kagiwada, S., Yamaji, Y., Komatsu, K., Takahashi, S., Mori, T., Hirata, H., Suzuki, M., Ugaki, M., Namba, S. Virus Res. (2005) [Pubmed]
  10. The partial purified RNA-dependent RNA polymerases from bamboo mosaic potexvirus and potato virus X infected plants containing the template-dependent activities. Cheng, J.H., Ding, M.P., Hsu, Y.H., Tsai, C.H. Virus Res. (2001) [Pubmed]
  11. The synthesis of minus-strand RNA of bamboo mosaic potexvirus initiates from multiple sites within the poly(A) tail. Cheng, J.H., Peng, C.W., Hsu, Y.H., Tsai, C.H. J. Virol. (2002) [Pubmed]
  12. Significance of the 3'-terminal region in minus-strand RNA synthesis of Hibiscus chlorotic ringspot virus. Wang, H.H., Wong, S.M. J. Gen. Virol. (2004) [Pubmed]
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