Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host

Journal of General Virology

Volumn 80, Issue 8, 1999, Pages 2239-2252

  Ambros S ^a   Hernandez C ^a   Flores, R ^a  

^a Ciudad Politécnica de la Innovación   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; VIRUS RNA;

ARTICLE; GENETIC HETEROGENEITY; NUCLEOTIDE SEQUENCE; PEACH LATENT MOSAIC VIROID; PHENOTYPE; PLANT VIRUS; PRIORITY JOURNAL; VIROID;

PEACH LATENT MOSAIC VIROID; POTATO SPINDLE TUBER VIROID; PRUNUS PERSICA; RNA VIRUSES; SOLANUM TUBEROSUM; VIROIDS;

EID: 0345540644     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/0022-1317-80-8-2239     Document Type: Article

References (57)

1. Ambrós, S. & Flores, R. (1998). In vitro and in vivo self-cleavage of a viroid RNA with a mutation in the hammerhead catalytic pocket. Nucleic Acids Research 26, 1877-1883.
2. Ambrós, S., Desvignes, J. C., Llácer, G. & Flores, R. (1995). Peach latent mosaic and pear blister canker viroids: detection by molecular hybridization and relationships with specific maladies affecting peach and pear trees. Acta Horticulturae 396, 515-521.
3. Ambrós, S., Hernández, C., Desvignes, J. C. & Flores, R. (1998). Genomic structure of three phenotypically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasispecies. Journal of Virology 72, 7397-7406.
4. Aranda, M. A., Fraile, A. & García-Arenal, F. (1993). Genetic variability and evolution of the satellite RNA of cucumber mosaic virus during natural epidemics. Journal of Virology 67, 5896-5901.
5. Bonfiglioli, R. G., McFadden, G.I. & Symons, R. H. (1994). In situ hybridization localizes avocado sunblotch viroid on chloroplast thylakoid membranes and coconut cadang-cadang viroid in the nucleus. Plant Journal 6, 99-103.
6. Bonfiglioli, R. G., Webb, D. R. & Symons, R. H. (1996). Tissue and intracellular distribution of coconut cadang-cadang viroid and citrus exocortis viroid determined by in situ hybridization and confocal laser scanning and transmission electron microscopy. Plant Journal 9, 457-465.
7. Bruening, G. (1989). Compilation of self-cleaving sequences from plant virus satellite RNAs and other sources. Methods in Enzymology 180, 546-558.
8. Desvignes, J. C. (1976). The virus diseases detected in greenhouse and in field by the peach seedling GF 305 indicator. Acta Horticulturae 67, 315-323.
9. Diener, T. O. (1991). Subviral pathogens of plants: viroids and viroidlike satellite RNAs. FASEB Journal 5, 2808-2813.
10. Diener, T. O. (1996). Origin and evolution of viroids and viroid-like satellite RNAs. Virus Genes 11, 47-59.
11. Di Serio, F., Darós, J. A., Ragozzino, A. & Flores, R. (1997). A 451-nucleotide circular RNA from cherry with hammerhead ribozymes in its strands of both polarities. Journal of Virology 71, 6603-6610.
12. Domingo, E. & Holland, J. J. (1994). Mutation rates and rapid evolution of RNA viruses. In The Evolutionary Biology of Viruses, pp. 161-184. Edited by S. S. Morse. New York: Raven Press.
13. Domingo, E., Martínez-Salas, E., Sobrino, F., de la Torre, J. C., Portela, A., Ortín, J., López-Galíndez, C., Pérez-Breña, P., Villanueva, N., Nájera, R., Vandepol, S., Steinhauer, D., Depolo, N. & Holland, J. J. (1985). The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance - a review. Gene 40, 1-8.
14. Eigen, M. (1993). The origin of genetic information: virus as models. Gene 135, 37-47.
15. Elena, S. F., Dopazo, J., Flores, R., Diener, T. O. & Moya, A. (1991). Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis δ virus RNA. Proceedings of the National Academy of Sciences, USA 88, 5631-5634.
16. Flores, R., Hernández, C., Desvignes, J. C. & Llácer, G. (1990). Some properties of the viroid inducing peach latent mosaic disease. Research in Virology 141, 109-118.
17. Flores, R., Di Serio, F. & Hernández, C. (1997). Viroids: the non coding genomes. Seminars in Virology 8, 65-73.
18. Flores, R., Randles, J. W., Bar-Joseph, M. & Diener, T. O. (1998). A proposed scheme for viroid classification and nomenclature. Archives of Virology 143, 623-629.
19. Forster, A. C. & Symons, R. H. (1987). Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 49, 211-220.
20. Góra, A., Candresse, T. & Zagórski, W. (1994). Analysis of the population structure of three phenotypically different PSTVd isolates. Archives of Virology 138, 223-245.
21. Góra-Sochacka, A., Kierzek, A., Candresse, T. & Zagórski, W. (1997). The genetic stability of potato spindle tuber viroid (PSTVd) molecular variants. RNA 3, 68-74.
22. Hammond, R. W. & Owens, R. A. (1987). Mutational analysis of potato spindle tuber viroid reveals complex relationships between structure and infectivity. Proceedings of the National Academy of Sciences, USA 84, 3967-3971.
23. Harders, J., Lukacs, N., Robert-Nicoud, M., Jovin, J. M. & Riesner, D. (1989). Imaging of viroids in nuclei from tomato leaf tissue by in situ hybridization and confocal laser scanning microscopy. EMBO Journal 8, 3941-3949.
24. Hernández, C. & Flores, R. (1992). Plus and minus RNAs of peach latent mosaic self-cleave in vitro via hammerhead structures. Proceedings of the National Academy of Sciences, USA 89, 3711-3715.
25. Hu, Y., Feldstein, P. A., Hammond, J., Hammond, R. W., Bottino, P. J. & Owens, R. A. (1997). Destabilization of potato spindle tuber viroid by mutations in the left terminal loop. Journal of General Virology 78, 1199-1206.
26. Hutchins, C. J., Rathjen, P. D., Forster, A. C. & Symons, R. H. (1986). Self-cleavage of plus and minus RNA transcripts of avocado sunblotch viroid. Nucleic Acids Research 14, 3627-3640.
27. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
28. Keese, P. & Symons, R. H. (1985). Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proceedings of the National Academy of Sciences, USA 82, 4582-4586.
29. Keese, P., Visvader, J. E. & Symons, R. H. (1988). Sequence variability in plant viroid RNAs. In RNA Genetics, vol. III, Variability of RNA Genomes, pp. 71-98. Edited by E. Domingo, J. J. Holland & P. Ahlquist. Boca Raton, FL: CRC
30. Kofalvi, S. A., Marcos, J. F., Cañizares, M. C., Pallás, V. & Candresse, T. (1997). Hop stunt viroid (HSVd) sequence variants from Prunus species: evidence for recombination between HSVd isolates. Journal of General Virology 78, 3177-3186.
31. Koltunow, A. M. & Rezaian, M. A. (1988). Grapevine yellow speckle viroid: structural features of a new viroid group. Nucleic Acids Research 16, 849-864.
32. Kore, A. R., Vaish, N. K., Kutzke, U. & Eckstein, F. (1998). Sequence specificity of the hammerhead ribozyme revisited; the NHH rule. Nucleic Acids Research 26, 4116-4120.
33. Kurath, G. & Palukaitis, P. (1989). RNA sequence heterogeneity in natural populations of three satellite RNAs of cucumber mosaic virus. Virology 173, 231-240.
34. Lakshman, D.K. & Tavantzis, S. M. (1992). RNA progeny of an infectious two-base deletion cDNA mutant of potato spindle tuber viroid (PSTV) acquire two nucleotides in planta. Virology 187, 565-572.
35. Lakshman, D. K. & Tavantzis, S. M. (1993). Primary and secondary structure of a 360-nucleotide isolate of potato spindle tuber viroid. Archives of Virology 128, 319-331.
36. Lima, M. I., Fonseca, M. E. N., Flores, R. & Kitajima, E. W. (1994). Detection of avocado sunblotch viroid in chloroplasts of avocado leaves by in situ hybridization. Archives of Virology 138, 285-390.
37. Loss, P., Schimtz, M., Steger, G. & Riesner, D. (1991). Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA. EMBO Journal 10, 719-727.
38. Miller, W. A., Hercus, T., Waterhouse, P. M. & Gerlach, W. L. (1991). A satellite RNA of barley yellow dwarf virus contains a novel hammerhead structure in the self-cleavage domain. Virology 183, 711-720.
39. Navarro, B. & Flores, R. (1997). Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes. Proceedings of the National Academy of Sciences, USA 94, 11262-11267.
40. Nei, M. (1987). Molecular Evolutionary Genetics. New York: Columbia University Press.
41. Owens, R. A., Thomsom, S. M. & Steger, G. (1991). Effects of random mutagenesis upon potato spindle tuber viroid replication and symptom expression. Virology 185, 18-31.
42. Pallás, V., García-Luque, I., Domingo, E. & Flores, R. (1988). Sequence variability in avocado sunblotch viroid (ASBV). Nucleic Acids Research 16, 9864.
43. Qu, F., Heinrich, C., Loss, P., Steger, G., Tien, P. & Riesner, D. (1993). Multiple pathways of reversion in viroid conservation of structural domains. EMBO Journal 12, 2129-2139.
44. Rakowski, A. G. & Symons, R. H. (1989). Comparative sequence studies of variants of avocado sunblotch viroid. Virology 173, 352-356.
45. Rozas, J. & Rozas, R. (1995). DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetic parameters from DNA sequence data. Computer Applications in the Biosciences 11, 621-625.
46. Ruffner, D. E., Stormo, G. D. & Uhlenbeck, O. C. (1990). Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 29, 10695-10702.
47. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406-425.
48. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain terminating inhibitors. Proceedings of the National Academy of Sciences, USA 74, 5463-5467.
49. Semancik, J. S. & Szyehowski, J. A. (1994). Avocado sunblotch disease: a persistent viroid infection in which variants are associated with differential symptoms. Journal of General Virology 75, 1543-1549.
50. Sheldon, C. C. & Symons, R. H. (1989). Mutagenesis analysis of a self-cleaving RNA. Nucleic Acids Research 17, 5679-5685.
51. Sheldon, C. C. & Symons, R. H. (1993). Is hammerhead self-cleavage involved in the replication of a virusoid in vivo? Virology 194, 463-474.
52. Sudhir, K., Tamura, K. & Nei, M. (1993). MEGA: molecular evolutionary genetics analysis, version 1.01. The Pennsylvania State University, University Park, PA, USA.
53. Symons, R. H. (1997). Plant pathogenic RNAs and RNA catalysis. Nucleic Acids Research 20, 2683-2689.
54. Thomson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.
55. Visvader, J. E. & Symons, R. H. (1985). Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with the pathogenicity. Nucleic Acids Research 13, 2907-2920.
56. Wassenegger, M., Heimes, S. & Sänger, H. L. (1994). An infectious viroid RNA replicon evolved from an in vitro-generated non-infectious viroid deletion mutant via a complementary deletion in vivo. EMBO Journal 13, 6172-6177.
57. Zuker, M. (1989). On finding all suboptimal foldings of an RNA molecule. Science 244, 48-52.