Sequence analysis of the parsnip yellow fleck virus polyprotein: evidence of affinities with picornaviruses

References

1. Akrigg D., Bleasby A. J., Dix N. IM., Findlay J. BC., North A. CT., Parry-Smith D., Wootton J. C., Blundell T. L., Gardner S. P., Hayes F., Islam S., Sternberg MJ. E, Thornton J. M., Tickle I. J., Murray-Rust P. 1988; A protein sequence/structure database. Nature, London 335:745–746
   [Google Scholar]
2. Allison R., Johnston R. E., Dougherty W. G. 1986; The nucleotide sequence of the coding region of tobacco etch virus genomic RNA: evidence for the synthesis of a single polyprotein. Virology 154:9–20
   [Google Scholar]
3. Argos P., Kamer G., Nicklen MJ. H, Wimmer E. 1984; Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families. Nucleic Acids Research 12:7251–7267
   [Google Scholar]
4. Bae Y. S., Eun H. M., Yoon J. W. 1989; Genomic differences between the diabetogenic and nondiabetogenic variants of encephalomyocarditis virus. Virology 170:282–287
   [Google Scholar]
5. Bazan J. F., Fletterick R. J. 1988; Viral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications. Proceedings of the National Academy of Sciences, U.S.A. 85:7872–7876
   [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. Chang K. H., Day C., Walker J., Hyypia T., Stanway G. 1992; The nucleotide sequences of wild-type coxsackievirus A9 strains imply that an RGD motif in VP1 is functionally significant. Journal of General Virology 73:621–626
   [Google Scholar]
8. Dessens J. T., Lomonossoff G. P. 1991; Mutational analysis of the putative catalytic triad of the cowpea mosaic virus 24K protease. Virology 184:738–746
   [Google Scholar]
9. Deuchler M., Skern T., Sommergruber W., Neubauer C., Gruendler P., Fogy I., Blaas D., Kuechler E. 1987; Evolutionary relationships within the human rhinovirus genus: comparison of serotypes 89, 2 and 14. Proceedings of the National Academy of Sciences, U.S.A. 84:2605–2609
   [Google Scholar]
10. Devereux J., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Research 12:387–395
    [Google Scholar]
11. Dougherty W. G., Parks T. D. 1991; Post-translational processing of the tobacco etch virus 49-kDa small nuclear inclusion polyprotein: identification of an internal cleavage site and delimitation of VPg and proteinase domains. Virology 183:449–156
    [Google Scholar]
12. Dougherty W. G., Parks T. D., Cary S. M., Bazan J. F., Fletterick R. J. 1989; Characterization of the catalytic residues of the tobacco etch virus 49-kDa proteinase. Virology 172:302–310
    [Google Scholar]
13. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
    [Google Scholar]
14. Fox G., Parry N. R., Barnett P. V., McGinn B., Rowlands D. J., Brown F. 1989; The cell attachment site on foot-and-mouth disease virus includes the amino acid sequence RGD (arginine-glycine-aspartic acid). Journal of General Virology 70:625–637
    [Google Scholar]
15. Geysen H. M., Barteling S. J., Meloen R. H. 1985; Small peptides induce antibodies with a sequence and structural requirement for binding antigen comparable to antibodies raised against the native protein. Proceedings of the National Academy of Sciences, U.S.A. 82:178–182
    [Google Scholar]
16. Goldbach R. 1986; Molecular evolution of plant RNA viruses. Annual Review of Phytopathology 24:289–310
    [Google Scholar]
17. Goldbach R. 1987; Genome similarities between plant and animal RNA viruses. Microbiological Sciences 4:197–202
    [Google Scholar]
18. Gorbalenya A. E., Koonin E. V. 1989; Viral proteins containing the purine NTP-binding sequence pattern. Nucleic Acids Research 17:8413–8440
    [Google Scholar]
19. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1988; A conserved NTP-motif in putative helicases. Nature, London 333:22
    [Google Scholar]
20. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1989a; Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Research 17:4713–1730
    [Google Scholar]
21. Gorbalenya A. E., Donchenko A. P., Blinov V. M., Koonin E. V. 1989b; Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. FEBS Letters 243:103–114
    [Google Scholar]
22. Greif C., Hemmer O., Fritsch C. 1988; Nucleotide sequence of tomato black ring virus RNA-1. Journal of General Virology 69:1517–1529
    [Google Scholar]
23. Hämmerle T., Hellen CU. T, Wimmer E. 1991; Site-directed mutagenesis of the putative catalytic triad of poliovirus 3C proteinase. Journal of Biological Chemistry 266:5412–5416
    [Google Scholar]
24. Hemida S. K., Murant A. F. 1989; Particle properties of parsnip yellow fleck virus. Annals of Applied Biology 114:87–100
    [Google Scholar]
25. Higgins D. G., Bleasby A. J., Fuchs R. 1992; CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8:189–191
    [Google Scholar]
26. Hodgman T. C. 1988; A new superfamily of replicative proteins. Nature, London 333:22–23
    [Google Scholar]
27. Hynes R. O. 1987; Integrins: a family of cell surface receptors. Cell 48:549–554
    [Google Scholar]
28. Kamer G., Argos P. 1984; Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Research 12:7269–7282
    [Google Scholar]
29. Kean K. M., Teterina N. L., Marc D., Girard M. 1991; Analysis of putative active site residues of the poliovirus 3C protease. Virology 181:609–619
    [Google Scholar]
30. 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]
31. Laemmli U. K. 1970; Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, London 227:680–685
    [Google Scholar]
32. Lomonossoff G. P., Shanks M. 1983; The nucleotide sequence of cowpea mosaic virus B RNA. EMBO Journal 2:2253–2258
    [Google Scholar]
33. Meshi T., Watanabe Y., Saito T., Sugimoto A., Maeda T., Okada Y. 1987; Function of the 30 kd protein of tobacco mosaic virus: involvement in cell-to-cell movement and dispensability for replication. EMBO Journal 6:2557–2563
    [Google Scholar]
34. Meyer M., Hemmer O., Mayo M. A., Fritsch C. 1986; The nucleotide sequence of tomato black ring virus RNA-2. Journal of General Virology 67:1257–1271
    [Google Scholar]
35. Murant A. F. 1988; Parsnip yellow fleck virus, type member of a proposed new plant virus group, and a possible second member, dandelion yellow mosaic virus. In The Plant Viruses, vol. 3, Polyhedral Virions with Monopartite RNA Genomes pp 273–288 Edited by Koenig R. New York: Plenum Press;
    [Google Scholar]
36. Murant A. F. 1991; Parsnip yellow fleck virus group. In Classification and Nomenclature of Viruses. Fifth Report of the International Committee on Taxonomy of Viruses pp 318–319 Edited by Francki R. IB., Fauquet C. M., Knudson D. L., Brown F. Vienna: Springer-Verlag;
    [Google Scholar]
37. Murant A. F. 1993; Parsnip yellow fleck virus group. In Encyclopedia of Virology Edited by Webster R. G., Granolf A. New York: Academic Press (in press);
    [Google Scholar]
38. Murant A. F., Goold R. A. 1968; Purification, properties and transmission of parsnip yellow fleck, a semi-persistent, aphid-borne virus. Annals of Applied Biology 62:123–137
    [Google Scholar]
39. Murant A. F., Hemida S. K., Mayo M. A. 1987; Plant viruses that resemble picornaviruses. In Abstracts of the 7th International Congress of Virology, Edmonton, Canada p 183 Ottawa: National Research Council Canada;
    [Google Scholar]
40. Najarian R., Caput D., Gee W., Potter S. J., Renard A., Merryweather J., Van Nest G., Dina D. 1985; Primary structure and gene organization of human hepatitis A virus. Proceedings of the National Academy of Sciences, U.S.A. 82:2627–2631
    [Google Scholar]
41. Nomoto A., Omata T., Toyoda H., Kuge S., Horie H., Kataoka Y., Genba Y., Nakano Y., Imura N. 1982; Complete nucleotide sequence of the attenuated poliovirus Sabin 1 strain genome. Proceedings of the National Academy of Sciences, U.S.A. 79:5793–5797
    [Google Scholar]
42. Ohara Y., Stein S., Fu J., Stillman L., Horie H., Klaman L., Roos R. P. 1988; Molecular cloning and sequence determination of DA strain of Theiler’s murine encephalomyelitis viruses. Virology 164:245–255
    [Google Scholar]
43. Palmenberg A. C. 1990; Proteolytic processing of picornaviral polyprotein. Annual Review of Microbiology 44:603–623
    [Google Scholar]
44. Poch O., Sauvaget I., Delarue M., Tordo N. 1989; Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO Journal 8:3867–3874
    [Google Scholar]
45. Robertson B. H., Grubman M. J., Weddell G. N., Moore D. M., Welsh J. D., Fischer T., Dowbenko D. J., Yansura D. G., Small B., Kleid D. G. 1985; Nucleotide and amino acid sequence coding for polypeptides of foot-and-mouth disease virus type A12. Journal of Virology 54:651–660
    [Google Scholar]
46. Rossmann M. G., Arnold E., Erickson J. W., Frankenberger E. A., Griffith J. P., Hecht H. J., Johnson J. E., Kamer G., Luo M., Mosser A. G., Rueckert R. R., Sherry B., Vriend G. 1985; Structure of a human common cold virus and functional relationship to other picornaviruses. Nature, London 317:145–153
    [Google Scholar]
47. Ruoslahti E. 1988; Fibronectin and its receptors. Annual Review of Biochemistry 57:375–113
    [Google Scholar]
48. Ruoslahti E., Pierschbacher M. 1987; New perspectives in cell adhesion: RGD and integrins. Science 238:491–197
    [Google Scholar]
49. Saitou N., Nei M. 1987; Neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406–425
    [Google Scholar]
50. Speicher D. W. 1989; Microsequencing with PVDF membranes. In Techniques in Protein Chemistry pp 24–35 Edited by Hugli T. E. San Diego: Academic Press;
    [Google Scholar]
51. Stanway G., Hughes P. J., Mountford R. C., Minor P. D., Almond J. W. 1984; The complete nucleotide sequence of a common cold vims: human rhinovirus 14. Nucleic Acids Research 12:7859–7875
    [Google Scholar]
52. Turnbull-Ross A. D., Reavy B., Mayo M. A., Murant A. F. 1984; The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus. Journal of General Virology 73:3203–3211
    [Google Scholar]
53. Van Wezenbeek P., Verver J., Harmsen J., Vos P., Van Kammen A. 1983; Primary structure and gene organisation of the middle component RNA of cowpea mosaic virus. EMBO Journal 2:941–946
    [Google Scholar]
54. Verver J., Goldbach R., Garcia J. A., Vos P. 1987; In vitro expression of a full-length DNA copy of cowpea mosaic vims B RNA: identification of the B RNA encoded 24-kd protein as a viral protease. EMBO Journal 6:549–554
    [Google Scholar]