The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus

References

1. Acharya R., Fry E., Stuart D., Fox G., Rowlands D., Brown F. 1989; The three-dimensional structure of foot-and-mouth disease virus at 2.9 Å resolution. Nature, London 337:709–716
   [Google Scholar]
2. Agol V. I. 1991; The 5′-untranslated region of picomaviral genomes. Advances in Virus Research 40:103–180
   [Google Scholar]
3. Allison R. F., Sorenson J. C., Kelly M. E., Armstrong F. B., Dougherty W. G. 1985; Sequence determination of the capsid protein gene and flanking regions of tobacco etch virus: evidence for synthesis and processing of a polyprotein in potyvirus genome expression. Proceedings of the National Academy of Sciences, U.S.A. 82:3969–3972
   [Google Scholar]
4. 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]
5. Argos P., Kamer G., Nicklen M. J. 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]
6. Birnboim H. C., Doly J. 1979; A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Research 7:1513–1523
   [Google Scholar]
7. Brinton M. A., Fernandez A. V., Dispoto J. H. 1986; The 3′-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 153:113–121
   [Google Scholar]
8. Buluwela L., Forster A., Boehm T., Rabbitts T. H. 1989; A rapid procedure for colony hybridisation using nylon filters. Nucleic Acids Research 17:452
   [Google Scholar]
9. 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]
10. Chi H.-C., Hsieh J.-C., Tam M. F. 1988; Modified method for double stranded DNA sequencing and synthetic oligonucleotide purification. Nucleic Acids Research 16:10382
    [Google Scholar]
11. Collett M. S., Larson R., Gold C., Strick D., Anderson D. K., Purchio A. F. 1988; Molecular cloning and nucleotide sequence of the pestivirus bovine viral diarrhea virus. Virology 165:191–199
    [Google Scholar]
12. Deborde D. C., Naeve C. W., Herlocher M. L., Maassab H. F. 1986; Resolution of a common RNA sequencing ambiguity by terminal deoxynucleotidyl transferase. Analytical Biochemistry 157:275–282
    [Google Scholar]
13. 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]
14. Donis-Keller H., Maxam A. M., Gilbert W. 1977; Mapping adenines, guanines and pyrimidines in RNA. Nucleic Acids Research 4:2527–2538
    [Google Scholar]
15. Elnagar S., Murant A. F. 1976; Relations of the semi-persistent viruses, parsnip yellow fleck and anthriscus yellows, with their vector Cavariella aegopodii . Annals of Applied Biology 84:153–167
    [Google Scholar]
16. England T. E., Bruce A. G., Uhlenbeck O. C. 1980; Specific labeling of 3′ termini of RNA with T4 RNA ligase. Methods in Enzymology 65:65–74
    [Google Scholar]
17. Forss S., Strebel K., Beck E., Schaller H. 1984; Nucleotide sequence and genomic organization of foot-and-mouth-disease virus. Nucleic Acids Research 12:6587–6601
    [Google Scholar]
18. Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. 1986; Improved free-energy parameters for predictions of RNA duplex stability. Proceedings of the National Academy of Sciences, U.S.A. 83:9373–9377
    [Google Scholar]
19. Gallie D. R., Sleat D. E., Watts J. W., Turner P. C., Wilson T. M. A. 1987; A comparison of eukaryotic viral 5′Teader sequences as enhancers of mRNA expression in vivo . Nucleic Acids Research 15:8693–8711
    [Google Scholar]
20. Geliebeter J. 1987; Dideoxynucleotide sequencing of RNA and uncloned cDNA. Focus 9:5–8
    [Google Scholar]
21. Goldbach R. W. 1986; Molecular evolution of plant RNA viruses. Annual Review of Phytopathology 24:289–310
    [Google Scholar]
22. Goldbach R. 1987; Genome similarities between plant and animal RNA viruses. Microbiological Sciences 4:197–202
    [Google Scholar]
23. Gorbalenya A. E., Koonin E. V. 1989; Viral proteins containing the purine NTP-binding sequence pattern. Nucleic Acids Research 17:8413–8440
    [Google Scholar]
24. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1988; A conserved NTP-motif in putative helicases. London, Nature 333:22
    [Google Scholar]
25. Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. 1989; 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]
26. Grange T., Bouloy M., Girard M. 1985; Stable secondary structure at the 3′ end of the genome of yellow fever virus (17D vaccine strain). FEBS Letters 188:159–163
    [Google Scholar]
27. 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]
28. Hahn C. S., Hahn Y. S., Rice C. M., Lee E., Dalgarno L., Strauss E. G., Strauss J. H. 1987; Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences. Journal of Molecular Biology 198:33–41
    [Google Scholar]
29. Hanahan D. 1983; Studies on transformation of Escherichia coli with plasmids. Journal of Molecular Biology 166:557–580
    [Google Scholar]
30. Haseloff J., Goelet P., Zimmern D., Ahlquist P., Dasgupta R., Kaesberg P. 1984; Striking similarities in amino acid sequence among nonstructural proteins encoded by RNA viruses that have dissimilar genomic organization. Proceedings of the National Academy of Sciences, U.S.A. 81:4358–4362
    [Google Scholar]
31. Hemida S. K., Murant A. F. 1989a; Particle properties of parsnip yellow fleck virus. Annals of Applied Biology 114:87–100
    [Google Scholar]
32. Hemida S. K., Murant A. F. 1989b; Host ranges and serological properties of eight isolates of parsnip yellow fleck virus belonging to the two major serotypes. Annals of Applied Biology 114:101–109
    [Google Scholar]
33. Huynh T. V., Young R. A., Davis R. W. 1985; Constructing and screening cDNA libraries in λgtl0 and λgt11. In DNA Cloning, A Practical Approach vol 1 pp 49–78 Edited by Glover D. M. Oxford: IRL Press;
    [Google Scholar]
34. Jackson R. J., Howell M. T., Kaminski A. 1990; The novel mechanism of initiation of picornavirus RNA translation. Trends in Biochemical Sciences 15:477–483
    [Google Scholar]
35. 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]
36. 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]
37. Kozak M. 1987; At least six nucleotides preceding the AUG initiator codon enhance translation in mammalian cells. Journal of Molecular Biology 196:947–950
    [Google Scholar]
38. Lommel S. A., Weston-Fina M., Xiong Z., Lomonossoff G. P. 1988; The nucleotide sequence and gene organization of red clover mosaic virus RNA-2. Nucleic Acids Research 16:8587–8602
    [Google Scholar]
39. Lomonossoff G. P., Shanks M. 1983; The nucleotide sequence of cowpea mosaic virus B RNA. EMBO Journal 2:2253–2258
    [Google Scholar]
40. Lütcke H. A., Chow R. C., Mickel F. S., Moss K. A., Kern H. F., Sceele G. A. 1987; Selection of AUG initiation codons differs in plants and animals. EMBO Journal 6:43–48
    [Google Scholar]
41. Mandl C. W., Kunz C., Heinz F. X. 1991; Presence of poly(A) in a flavivirus: significant differences between the 3′ noncoding regions of the genomic RNAs of tick-borne encephalitis virus strains. Journal of Virology 65:4070–4077
    [Google Scholar]
42. Maniatis T., Fritsch E. F., Sambrook J. 1982 In Molecular Cloning: A Laboratory Manual pp 464–466 New York: Cold Spring Harbor Laboratory;
    [Google Scholar]
43. 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]
44. Murant A. F. 1988; Parsnip yellow fleck virus, type member of a proposed new 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]
45. 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. I. B., Fauquet C. M., Knudson D. L., Brown F. Vienna: Springer–Verlag;
    [Google Scholar]
46. 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]
47. 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, 1987 p 183
    [Google Scholar]
48. 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]
49. Natsuaki T., Mayo M. A., Jolly C. A., Murant A. F. 1991; Nucleotide sequence of raspberry bushy dwarf virus RNA-2: a bicistronic component of a bipartite genome. Journal of General Virology 72:2183–2189
    [Google Scholar]
50. 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]
51. 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]
52. Rice C. M., Lenches E. M., Eddy S. R., Shin S. J., Sheets R. L., Strauss J. H. 1985; Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution. Science 229:726–733
    [Google Scholar]
53. Saneyoshi M., Ohashi Z., Harada F., Nishimura S. 1972; Isolation and characterization of 2-methyladenosine from Escheri-chia coli tRNA₂^Glu, tRNA₁^Asp, tRNA₁^His and tRNA^Arg. Biochimica et biophysica acta 262:1–10
    [Google Scholar]
54. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, U.S.A. 74:5463–5467
    [Google Scholar]
55. Stanway G., Hughes P. J., Mountford R. C., Minor P. D., Almond J. W. 1984; The complete nucleotide sequence of a common cold virus: human rhinovirus 14. Nucleic Acids Research 12:7859–7875
    [Google Scholar]
56. 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]
57. Vingron M., Argos P. 1991; Motif recognition and alignment for many sequences by comparison of dot-matrices. Journal of Molecular Biology 218:33–43
    [Google Scholar]
58. Wellink J., Rezelman G., Goldbach R., Beyreuther K. 1986; Determination of the proteolytic processing sites in the polyprotein encoded by the bottom-component RNA of cowpea mosaic virus. Journal of Virology 59:50–58
    [Google Scholar]
59. Wengler G., Castle E. 1986; Analysis of structural properties which possibly are characteristic for the 3′-terminal sequence of the genome RNA of flaviviruses. Journal of General Virology 67:1183–1188
    [Google Scholar]