Skip to main content

Advertisement

SpringerLink
Log in

Sequence and structure prediction of RNA-dependent RNA polymerase of lily symptomless virus isolated from L. × ‘Casablanca’

  • Original Article
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

The DNA sequence of the RNA-dependent RNA polymerase (RdRp) gene of lily symptomless virus (LSV), a lily-infecting member of the genus Carlavirus, was determined from nine overlapping cDNA fragments of different sizes. The complete sequence of this RdRp gene (HM070294) consisted of 5,847 nucleotides coding for a protein of 220 kDa. It had 97-98% sequence identity with RdRps of other known isolates at both the DNA and the amino acid level. Phylogenetic analysis indicated that this RdRp (designated as RdRp-DL) was closely related to the RdRp of the Korean isolate (AM516059), as well as to the RdRps from Passiflora latent virus (PLV) and Kalanchoe latent virus (KLV) of the genus Carlavirus. Hydrophobic analysis of RdRp-DL revealed a hydrophobic N-terminus and a hydrophilic C-terminus. Helices and Loops were the major secondary structures of RdRp-DL. In addition, RdRp-DL also had three coil structures. Four conserved domains were identified: typoviral methyltransferase, RNA-dependent RNA polymerase, P-loop-containing nucleoside triphosphate hydrolases and carlavirus endopeptidase. A model of the tertiary structure predicted by I-TASSER was obtained for each of these conserved domains. This is the first report of a detailed phylogenetic analysis of LSV RdRp with those of other members of the genus Carlavirus, and the first to predict the domain structures of LSV RdRp.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Ahn HI, Ryu JH, Kim JK, Lee SY, Choi JK, Park WM, Ryu KH (1999) Nucleotide sequence analysis of the 3′-terminal region of two Korean isolates of Lily symptomless carlavirus and expression of the coat protein in E. coli. Mol Cells 9:338–343

    PubMed  CAS  Google Scholar 

  2. Allen TC (1972) Lily symptomless virus. CMI/AAB Descriptions of Plant Viruses No. 96. Kew, Surrey, UK

    Google Scholar 

  3. Asjes CJ (2000) Control of aphid-borne lily symptomless virus and lily mottle virus in Lilium in the Netherlands. Virus Res 71:23–32

    Article  PubMed  CAS  Google Scholar 

  4. Choi SA, Ryu KH (2003) The complete nucleotide sequence of the genome RNA of Lily symptomless virus and its comparison with that of other carlaviruses. Arch Virol 148:1945–1955

    Article  Google Scholar 

  5. Derks AFLM (1995) Lily. In: Loebenstein G, Lawson RH, Brunt AA (eds) Virus and virus-like diseases of bulb and flower crops. John Wiley & Sons, Chichester, UK, pp 313–321

    Google Scholar 

  6. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) In: Walker JM (ed) The proteomics protocols handbook. Humana Press, pp. 571–607

  7. Lawson RH (1981) Controlling virus diseases in major national flower and bulb crops. Plant Dis 65:780–786

    Article  Google Scholar 

  8. Lupas A, Van Dyke M, Stock J (1991) Predicting coiled coils from protein sequences. Science 252:1162–1164

    Article  CAS  Google Scholar 

  9. Mason JB, Arndt KM (2004) Coiled coil domains: stability, specificity, and biological implications. Chembiochem 5(2):170–176

    Article  PubMed  CAS  Google Scholar 

  10. Raju BC, Olsen CJ (1985) Indexing systems for producing clean stock for disease control in commercial floriculture. Plant Dis 69:189–192

    Google Scholar 

  11. Rost B, Yachdav G, Liu J (2003) The PredictProtein Server. Nucleic Acids Res 32(Web Server issue):W321-W326

  12. Singh AK, Mahinghara BK, Hallan V, Ram R, Zaidi AA (2008) Recombination and phylogeographical analysis of Lily symptomless virus. Virus Genes 36:421–427

    Article  PubMed  CAS  Google Scholar 

  13. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  14. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882

    Article  Google Scholar 

  15. Wu S, Skolnick J, Zhang Y (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 5:17

    Article  PubMed  Google Scholar 

  16. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinform 9:40

    Article  Google Scholar 

  17. Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 8:108–117

    Article  Google Scholar 

  18. Zheng HY, Chen J, Zhao MF, Lin L, Chen JP, Antoniw JF, Adams MJ (2003) Occurrence and sequence of Lily symptomless virus in plants grown from imported bulbs in Zhejiang province, China. Arch Virol 148:2419–2428

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank the Institute of Gene Engineering of Dalian University of Technology (DUT) for providing the necessary facilities. This project was supported by the National Natural Science Foundation of China (31070621). We are especially grateful to Alan K Chang at DUT for his critical review of the manuscript and helpful suggestions.

Author information

Authors and Affiliations

  1. School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Ganjingzi District, Dalian City, 116024, Liaoning Province, People’s Republic of China

    Pinsan Xu, Huangai Li, Jiwen Liu, Yushi Luan, Yalei Yin & Jianfang Bai

Authors
  1. Pinsan Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Huangai Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jiwen Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yushi Luan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yalei Yin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jianfang Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Huangai Li.

Additional information

National Natural Science Foundation of China (NSFC) (No. 31070621).

The nucleotide sequence data reported in this paper have been deposited in GenBank under accession number HM070294.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Xu, P., Li, H., Liu, J. et al. Sequence and structure prediction of RNA-dependent RNA polymerase of lily symptomless virus isolated from L. × ‘Casablanca’. Arch Virol 156, 939–943 (2011). https://doi.org/10.1007/s00705-011-0928-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-011-0928-9

Keywords

Search

Navigation