Comparisons of the genomic sequences of erysimum latent virus and other tymoviruses: a search for the molecular basis of their host specificities

References

1. Ahlquist P., Janda M. 1984; cDNA cloning and in vitro transcription of the complete brome mosaic virus genome. Molecular and Cellular Biology 4:2876–2882
   [Google Scholar]
2. Ahlquist P., Dasgupta R., Kaesberg P. 1984; Nucleotide sequence of the brome mosaic virus genome and its implications for viral replication. Journal of Molecular Biology 172:369–383
   [Google Scholar]
3. Bonnet J., Ebel J. P., Dirheimer G., Shershneva L. P. 1974; The corrected nucleotide sequence of valine tRNA from baker’s yeast. Biochimie 561211–1213
   [Google Scholar]
4. Both G. W., Air G. M. 1979; Nucleotide sequence coding for the N-terminal region of the matrix protein of influenza virus. European Journal of Biochemistry 96:363–372
   [Google Scholar]
5. Bujarski J. J., Ahlquist P., Hall T. C., Dreher T. W., Kaesberg P. 1986; Modulation of replication, aminocylation, and adenylation in vitro and infectivity in vivo of BMV RNAs containing deletions within the multifunctional 3′ end. EMBO Journal 5:1769–1774
   [Google Scholar]
6. Candresse T., Morch M. D., Dunez J. 1990; Multiple alignment and hierarchical clustering of conserved amino acid sequences in the replication-associated proteins of plant RNA viruses. Research in Virology 141:315–329
   [Google Scholar]
7. Dayhoff M. O., Schwartz R. M., Chen H. R., Orcutt B. C. 1978; A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure vol 5 supplement 3 Edited by Dayhoff M. O. Washington, D.C.: National Biomedical Research Foundation;
   [Google Scholar]
8. Ding S., Keese P., Gibbs A. 1989; Nucleotide sequence of the genome of ononis yellow mosaic tymovirus. Virology 172:555–563
   [Google Scholar]
9. Ding S., Howe J., Keese P., Mackenzie A., Meek D., Osorio-Keese M., Skotnicki M., Srifah P., Torronen M., Gibbs A. 1990a; Nucleotide sequence of the virion protein gene of belladonna mottle tymovirus. Nucleic Acids Research 18:1181–1187
   [Google Scholar]
10. Ding S., Howe J., Keese P., Mackenzie A., Skotnicki M., Gibbs A. 1990b; Nucleotide sequence of the virion protein gene of belladonna mottle tymovirus. Nucleic Acids Research 18:6138
    [Google Scholar]
11. Ding S., Keese P., Gibbs A. 1990c; The nucleotide sequence of the genomic RNA of kennedya yellow mosaic tymovirus-Jervis Bay isolate: relationships with potex- and carlaviruses. Journal of General Virology 71:925–931
    [Google Scholar]
12. Ding S., Mackenzie A., Torronen M., Gibbs A. 1990d; Nucleotide sequence of the virion protein gene of cacao yellow mosaic tymovirus. Nucleic Acids Research 19:5886
    [Google Scholar]
13. Dreher T. W., Hall T. C. 1988a; RNA replication of brome mosaic virus and related viruses. In RNA Genetics vol 1 pp 91–113 Edited by Domingo E., Holland J. J., Ahlquist P. Boca Raton: CRC Press;
    [Google Scholar]
14. Dreher T. W., Hall T. C. 1988b; Mutational analysis of the tRNA mimicry of brome mosaic virus RNA: sequence and structural requirements for aminoacylation and 3′ adenylation. Journal of Molecular Biology 201:41–55
    [Google Scholar]
15. Feng D. F., Doolittle R. F. 1987; Progressive sequence alignment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution 25:351–360
    [Google Scholar]
16. Feng D. F., Johnson M. S., Doolittle R. F. 1985; Aligning amino acid sequences: comparison of commonly used methods. Journal of Molecular Evolution 21:112–125
    [Google Scholar]
17. Forman M. A., Dush M. K., Martin G. R. 1988; Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proceedings of the National Academy of Sciences, U.S.A. 85:8998–9002
    [Google Scholar]
18. Gibbs A. J., Hecht-Poinar E., Woods R. D., McKee R. K. 1966; Some properties of three related viruses: Andean potato latent, dulcamara mottle and ononis yellow mosaic. Journal of General Microbiology 44:177–193
    [Google Scholar]
19. Gorbalenya A. E., Blinov V. M., Donchenko A. P., Koonin E. V. 1989a; An NTP-binding motif is the most conserved sequence in a highly diverged monophylogenetic group of proteins involved in a positive strand RNA viral replication. Journal of Molecular Evolution 28:256–268
    [Google Scholar]
20. Gorbalenya A. E., Blinov V. M., Donchenko A. P., Koonin E. V. 1989b; Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Research 17:4713–4730
    [Google Scholar]
21. Gough K. H., Lilley G. G., Shukla D. D., Woods E. F. 1982; Some physicochemical properties of erysimum latent virus. Australian Journal of Biological Sciences 35:5–11
    [Google Scholar]
22. Gubler U., Hoffman B. J. 1983; A simple and very efficient method for generating cDNA libraries. Genes 25:263–269
    [Google Scholar]
23. Gupta K., Kingsbury D. 1984; Complete sequences of the intergenic and mRNA start signals in the Sendai virus genome: homologies with the genome of vesicular stomatitis virus. Nucleic Acids Research 12:3829–3841
    [Google Scholar]
24. Guy P. L., Dale J. L., Adena M. A., Gibbs A. 1984; A taxonomic study of the host ranges of tymoviruses. Plant Pathology 33:337–346
    [Google Scholar]
25. Hall T. C. 1979; Transfer RNA-like structures in viral genomes. International Review of Cytology 60:1–26
    [Google Scholar]
26. Keese P., Mackenzie A., Gibbs A. 1989; Nucleotide sequence of an Australian isolate of turnip yellow mosaic tymovirus. Virology 172:536–546
    [Google Scholar]
27. Klein C., Fritsch C., Briand J. P., Richards K. E., Jonard G., Hirth L. 1976; Physical and functional heterogeneity in TYMV RNA: evidence for the existence of an independent messenger coding for the coat protein. Nucleic Acids Research 3:3043–3061
    [Google Scholar]
28. Koonin E. V. 1991; The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. Journal of General Virology 72:2197–2206
    [Google Scholar]
29. Mi S., Durbin R., Huang H. R., Rice C. M., Stollar V. 1989; Association of the Sindbis virus RNA methyltransferase activity with the nonstructural protein nsPl. Virology 170:385–391
    [Google Scholar]
30. Miller W. A., Dreher T. W., Hall T. C. 1985; Synthesis of brome mosaic virus subgenomic RNA in vitro by internal initiation on (–)-sense genomic RNA. Nature, London 313:68–70
    [Google Scholar]
31. Morch M. D., Boyer J. C., Haenni A.-L. 1988; Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA. Nucleic Acids Research 16:6157–6173
    [Google Scholar]
32. Osorio-Keese M. E., Keese P., Gibbs A. 1989; Nucleotide sequence of eggplant mosaic tymovirus genome. Virology 172:547–554
    [Google Scholar]
33. Pleu C. W. A., Needleman A., van Vloten-Doting L., Bosch L. 1976; Translation of turnip yellow mosaic virus RNA in vitro’, a closed and open coat protein cistron. Proceedings of the National Academy of Sciences, U.S.A. 73:4437–4441
    [Google Scholar]
34. Rietveld K., van Poelgeest R., Pleu C. W. A., van Bloom J. H., Bosch L. 1982; The tRNA-like structure at the 3′ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Research 10:1929–1946
    [Google Scholar]
35. Rozanov M. N., Morozov S. Y., Skryabin K. G. 1990; Unexpected close relationship between the large non-virion proteins of filamentous potexviruses and spherical tymoviruses. Genes 3:373–379
    [Google Scholar]
36. Saito N., Nei M. 1987; The neighbour-joining method: a new method for reconstructing phylogenetic trees.. Molecular Biology and Evolution 4:406–425
    [Google Scholar]
37. Salomon R., Sela I., Soreq H., Giveon D., Littauer U. Z. 1976; Enzymatic acylation of histidine to tobacco mosaic virus RNA. Virology 71:74–84
    [Google Scholar]
38. Sanger F., Coulson A. R., Barrell B. G., Smith A. J. H., Roe B. A. 1980; Cloning in a single-stranded bacteriophage as an aid to rapid DNA sequencing. Journal of Molecular Biology 143:161–178
    [Google Scholar]
39. Shukla D. D., Gough K. H. 1980; Erysimum latent virus. CMfAAB Descriptions of Plant viruses no. 222
    [Google Scholar]
40. Shukla D. D., Schmelzer K. 1972; Studies on viruses and virus diseases of cruciferous plants. IV. The previously undescribed erysimum latent virus. Acta phytopathologica academiae scientiarum Hungaricae 7:157–167
    [Google Scholar]
41. Shukla D. D., Proll E., Schmelzer K., Schmidt H. B. 1973; Studies on viruses and virus diseases of cruciferous plants. VIII. Purification, properties and serology of erysimum latent virus. Acta phytopathologica academiae scientiarum Hungaricae 8:91–103
    [Google Scholar]
42. Shukla D. D., Koenig R., Gough K. H., Huth W., Lesemann D.-E. 1980; Erysimum latent virus - further characterization as a tymovirus. Phytopathology 70:382–384
    [Google Scholar]
43. Srifah P., Keese P., Shukla D. D., Gibbs A. 1990; The primary structure of the virion protein gene and encoded protein of erysimum latent tymovirus. Journal of General Virology 71:3085–3088
    [Google Scholar]
44. Studier J. A., Keppler K. L. 1988; A note on neighbour joining algorithm of Saito and Nei. Molecular Biology and Evolution 5:729–731
    [Google Scholar]
45. van Belkum A., Verlaan P., Jiang B., Pleu C., Bosch L. 1987; Temperature dependent chemical and enzymatic probing of the tRNA-like structure of TYMV RNA. Nucleic Acids Research 16:1931–1950
    [Google Scholar]
46. Young D. J., Watson L. 1970; The classification of dicotyledons: a study of the upper levels of the hierarchy. Australian Journal of Botany 18:387–133
    [Google Scholar]
47. Zuker M., Steigler P. 1981; Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9:133–148
    [Google Scholar]