Molecular and Biological Characterization of the Iranian Isolate of the Australian Grapevine Viroid

Authors
M. Zaki-aghl 1
K. Izadpanah 1
A. Niazi 2
S. A. A. Behjatnia 1
A. R. Afsharifar 1
1 Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Islamic Republic of Iran.
2 Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Islamic Republic of Iran.
Abstract
Australian grapevine viroid (AGVd), an apscaviroid of the family Pospiviroidae, was recently identified in vineyards of southern Iran. It had a relatively wide host range and caused stunting, leaf deformation, mottling and vein clearing in experimental hosts upon mechanical inoculation of nucleic acid extracts or agroinfiltration of the viroid infectious cloned DNA. Predicted secondary structure of the AGVD-Ir showed a difference from the predicted structure of the type isolate in the viroid pathogenicity domain. Mutational analyses showed sequence changes introduced into that domain of the AGVD-Ir clone decreased the viroid’s replication efficiency in planta but did not show any effects on its movement.

Keywords

1. Al Rwahnih, M., Daubert, S., Golino, D. and Rowhani, A. 2009. Deep Sequencing Analysis of RNAs from a Grapevine Showing Syrah Decline Symptoms Reveals a Multiple Virus Infection that Includes a Novel Virus. Virol., 387: 395-401.
2. Ding, B. 2009. The Biology of Viroid-host Interactions. Annu. Rev. Phytopathol., 47:105-131.
3. Ding, B. and Itaya, A. 2007. Viroid: A Useful Model for Studying the Basic Principles of Infection and RNA Biology. MPMI, 20: 7–20.
4. Elleuch, A., Fakhfakh, H., Pelchat, M., Landry, P., Marrakchi, M. and Perreault, J. P. 2002. Sequencing of Australian Grapevine Viroid and Yellow Speckle Viroid Isolated from a Tunisian Grapevine without Passage in an Indicator Plant. Eur. J. Plant Pathol., 108: 815–820.
5. Elleuch, A., Marrakchi, M., Perreault, J. P. and Fakhfakh, H. 2003. First report of Australian Grapevine Viroid from the Mediterranean Region. J. Plant Pathol., 85: 53-57.
6. Flores, R., Hernandez, C., Martınez de Alba, A. E., Daros, J. and Di Serio, F. 2005. Viroids and Viroid-host Interactions. Annu. Rev. Phytopathol., 43: 117–139.
7. Gardner, R. C., Chonoles, K. R. and Owens R. A. 1986. Potato Spindle Tuber Viroid Infections Mediated by the Ti Plasmid of Agrobacterium tumefaciens. Plant Mol. Biol., 6: 221-228.
8. Gozmanova, M., Denti, M. A., Minkov, I. N., Tsagris, M. and Tabler, M. 2003. Characterization of the RNA Motif Responsible for the Specifc Interaction of Potato Spindle Tuber Viroid RNA (PSTVd) and the Tomato Protein Virp1. Nucleic Acids Res., 31: 5534-5543.
9. Gora-Sochacka, A. 2004. Viroids: Unusual Small Pathogenic RNAs. Acta Biochim. Pol., 51: 587-607.
10. Hadidi, A., Flores, R., Randles, J. and Semancik, J. 2003. Viroids. CSIRO Publishing, 392 PP.
11. Hammond, R. W. and Owens R. A., 1987. Mutational Analysis of Potato Spindle Tuber Viroid Reveals Complex Relationships between Structure and Infectivity. PNAS., 84: 3967-3971.
12. Hayward-Lester, A., Oefner, P. J., Sabatini, S. and Doris P. A. 1995. Accurate and Absolute Quantitative Measurement of Gene Expression by Single-tube RT-PCR and HPLC. Genome Res., 5: 494-499.
13. Hellens, R., Mullineaux, P. and Klee, H. 2000. A Guide to Agrobacterium Binary Ti Vectors. Trends Plant Sci., 5: 446-451.
14. Jiang, D., Peng, P., Wu, Z., Cheng, Z. and Li, S. 2009. Genetic Diversity and Phylogenetic Analysis of Australian Grapevine Viroid Isolated from Different Grapevines in China. Virus Genes, 38: 178-183.
15. Keese, P. and Symons, R. 1985. Domains in Viroids: Evidence of Intermolecular RNA Rearrangements and Their Contribution to Viroid Evolution. PNAS, 82: 4582-4586.
16. Koltunow, A. M. and Rezaian, M. A. 1988. Grapevine Yellow Speckle Viroid: Structural Features of a New Viroid Group. Nucleic Acids Res., 15: 7040-7052.
17. Mumford, R. A., Walsh, K. and Boonham, N. 2000. A Comparison of Molecular Methods for the Routine Detection of Viroids. Bull. OEPP/EPPO Bull., 30: 431-435.
18. Nakahara, K., Hataya, T., Hayashi, Y., Sugimoto, T., Kimura, I. and Shikata, E. 1998. A Mixture of Synthetic Oligonucleotide Probes Labeled with Biotin for the Sensitive Detection of Potato Spindle Tuber Viroid. J. Virol. Methods, 71: 219–227.
19. Owens, R. A., Chen, W., Hu, Y. and Hsu, Y. H. 1995. Suppression of Potato Spindle Tuber Viroid Replication and Symptom Expressions by Mutations which Stabilize the Pathogenicity Domain. Virol., 208: 554-564.
20. Owens, R. A., Steger, G., Hu, Y., Fels, R., Hammond, R. W. and Riesner, D. 1996. RNA Structural Features Responsible for Potato Spindle Tuber Viroid Pathogenicity. Virol., 222: 144–158.
21. Owens, R. A. and Hammond, R. W. 2009. Viroid Pathogenicity: One Process, Many Faces. Viruses, 1: 298-316.
22. Owens, R. A., Flores, R., Di Serio, F., Li, S., Pallas, V., Randles, J., Sano, T. and Vidalakis, G. 2011. Viroids. In: "Virus Taxonomy", (Eds.): King, A. M., Q. Lefkowitz, E., Adams, M. J. and Carstens, E. B.. Elsevier, Oxford, PP. 1221-1234.
23. Qi, Y. and Ding, B. 2002. Replication of Potato Spindle Tuber Viroid in Cultured Cells of Tobacco and Nicotiana benthamiana: The Role of Specific Nucleotides in Determining Replication Levels for Host Adaptation. Virol., 302: 445–456.
24. Rezaian, M. A., Koltunow, A. M. and Krake, L. R. 1988. Isolation of Three Viroids and a Circular RNA from Grapevines. J. Gen. Virol., 69: 413-422.
25. Rezaian, M. A. 1990. Australian Grapevine Viroid: Evidence for Extensive Recombination between Viroids. Nucleic Acids Res., 18: 1813-1818.
26. Rigden, J. E. and Rezaian, M. A. 1993. Analysis of Sequence Variation in Grapevine Yellow Speckle Viroid 1 Reveals Two Distinct Alternative Structures for Pathogenic Domain. Virol., 193: 474-477.
27. Sanjuan, R. and Daros, J. A. 2007. One-step Site-directed Mutagenesis of Viroid Dimeric cDNA. J. Virol. Methods, 145: 71–75.
28. Sano, T., Candresse, T., Hammond, R. W., Diener, T. O. and Owens, R. A. 1992. Identification of Multiple Structural Domains Regulating Viroid Pathogenicity. PNAS, 89: 10104-10108.
29. Serra, P., Gago, S. and Duran-Vila, N. 2008. A Single Nucleotide Change in Hop Stunt Viroid Modulates Citrus Cachexia Symptoms. Virus Res., 138: 130–134.
30. Szychowski, J. A., Credi, R., Reanwarakorn, K. and Semancik, J. S. 1998. Population Diversity in Grapevine Yellow Speckle Viroid-1 and the Relationship to Disease Expression. Virol, 248: 432–444.
31. Tabler, M. and Tsagris, M. 2004. Viroids: Petite RNA Pathogens with Distinguished Talents. Trends Plant Sci., 9: 339-348.
32. Tamura, K., Dudley, J., Nei, M. and Kumar, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol. Biol. Evol., 24: 1596-1599.
33. Wan Chow Wah, J. and Symons, R. 1997. A Highly Sensitive RT-PCR Assay for the Diagnosis of Grapevine Viroids in Field and Tissue Culture Samples. J. Virol. Methods, 63: 57-69.
34. Wang, K. 2006. Agrobacterium Protocols. Second EditionM Humana Press. 507 p.
35. Wang, A., Doyle, M. and Mark, D. 1989. Quantitation of mRNA by the Polymerase Chain Reaction. PNAS, 86: 9717-9721.
36. Zaki-aghl, M. and Izadpanah, K. 2004. Identification and Transmission of Grapevine Yellow Speckle Disease in Iran. Proc. 16th Iran. Plant Protec. Cong., Tabriz, Iran, 2: 359.
37. Zaki-aghl, M. and Izadpanah, K. 2005. Identification of several different viroids from grapevine in Fars province. Third Iran. Virol. Cong. P. 171.
38. Zaki-aghl, M. and Izadpanah, K. 2006. Sequencing and Genome Analysis of Iranian Isolate of Grapevine Yellow Speckle Viroid 1. Proc. 17th Iran. Plant Protec. Cong., Karaj, Iran, 2: 358.
39. Zaki-aghl, M. and Izadpanah, K. 2009. Identification and Partial Characterization of Grapevine Viroids in Southern Iran. 16th Meeting of the International Council for the Study of Virus and Virus-like Diseases of the Grapevine, Dijon, France. 354 PP.
40. Zhong, X., Archual, A. J., Amin, A. A. and Ding, B. 2008. A Genomic Map of Viroid RNA Motifs Critical for Replication and Systemic Trafficking. Plant Cell, 20: 35–47
Journal of Agricultural Science and Technology
Volume 15, Issue 4
July and August 2013
Pages 855-865