1887

Abstract

Summary

The sequence of the 7356 nucleotide [excluding the 3′ poly(A)] RNA-1 of tomato black ring virus (TBRV) was determined from overlapping cDNA clones. A putative initiation codon at nucleotide 261 was considered to be the start of an open reading frame which terminates at a UAG codon at position 7053. The predicted translation product is a protein of 2264 amino acids with an of 253680 (254K). Comparison of the amino acid sequence of this 254K protein with other viral proteins revealed three regions, each having about 60% homology with a region of the three cowpea mosaic virus (CPMV) proteins (58K, 24K, 87K) which are thought to be involved in replication of the CPMV RNAs. The same regions show similarities, although less extended, with proteins 2C, 3C and 3D of picornaviruses. From these results we suggest that the genome organization of TBRV is similar to that of comoviruses and picornaviruses.

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1988-07-01
2022-01-21
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References

  1. AHLQUIST P., DASGUPTA R., KAESBERG P. 1981; Near identity of 3′ RNA secondary structure in bromoviruses and cucumber mosaic virus. Cell 23:183–189
    [Google Scholar]
  2. AHLQUIST P., STRAUSS E. G., RICE C. M., STRAUSS J. H., HASELOFF J., ZIMMERN D. 1985; Sindbis virus proteins nsPl and nsP2 contain homology to nonstructural proteins from several RNA plant viruses. Journal of Virology S3:536–542
    [Google Scholar]
  3. 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]
  4. ARGOS P., KAMER G., NICKLIN 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]
  5. BIRNBOIM H. C., DOLY J. 1979; A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Research 7:1513–1523
    [Google Scholar]
  6. BOUZOUBAA S., GUILLEY H., JONARD G., RICHARDS K., PUTZ C. 1985; Nucleotide sequence analysis of RNA-3 and RNA-4 of beet necrotic yellow vein virus, isolates F2 and G1. Journal of General Virology 66:1553–1564
    [Google Scholar]
  7. BOUZOUBAA S., QUILLET L., GUILLEY H., JONARD G., RICHARDS K. 1987; Nucleotide sequence of beet necrotic yellow vein virus RNA-1. Journal of General Virology 68:615–626
    [Google Scholar]
  8. CARROLL A. R., ROWLANDS D. J., CLARKE B. E. 1984; The complete nucleotide sequence of the RNA coding for the primary translation product of foot and mouth disease virus. Nucleic Acids Research 12:2461–2472
    [Google Scholar]
  9. CORNELISSEN B. J. C, BREDERODE F. T., MOORMANN R. J. M., BOL J. F. 1983; Complete nucleotide sequence of alfalfa mosaic virus RNA 1. Nucleic Acids Research 11:1253–1265
    [Google Scholar]
  10. DAGERT M., EHRLICH S. D. 1979; Prolonged incubation in calcium chloride improves the competence of Escherichia coli cells. Gene 6:23–28
    [Google Scholar]
  11. 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]
  12. DODD S. M., ROBINSON D. J. 1987; Conservation of the 3′-terminal sequences of the genome RNA species of tomato black ring virus. Journal of General Virology 68:973–978
    [Google Scholar]
  13. DOMIER L. L., FRANKLIN K. M., SHAHABUDDIN M., HELLMANN G. M., OVERMEYER J. H., HIREMATH S. T., SIAW M. F. E., LOMONOSSOFF G. P., SHAW J. G., RHOADS R. E. 1986; The nucleotide sequence of tobacco vein mottling virus RNA. Nucleic Acids Research 14:5417–5430
    [Google Scholar]
  14. DOMIER L. L., SHAW J. G., RHOADS R. E. 1987; Potyviral proteins share amino acid sequence homology with picorna-, como-, and caulimoviral proteins. Virology 158:20–27
    [Google Scholar]
  15. FRANSSEN H., GOLDBACH R., BROEKHUUSEN M., MOERMAN M., VAN KAMMEN A. 1982; Expression of middle component RNA of cowpea mosaic virus: in vitro generation of a precursor to both capsid proteins by a bottom component RNA-encoded protease from infected cells. Journal of Virology 41:8–17
    [Google Scholar]
  16. FRITSCH C, MAYO M. A., MURANT A. F. 1978; Translation of the satellite RNA of tomato black ring virus in vitro and in tobacco protoplasts. Journal of General Virology 40:587–593
    [Google Scholar]
  17. FRITSCH C, MAYO M. A., MURANT A. F. 1980; Translation products of genome and satellite RNAs of tomato black ring virus. Journal of General Virology 46:381–389
    [Google Scholar]
  18. GOLDBACH R. W. 1986; Molecular evolution of plant RNA viruses. Annual Review of Phytopathology 24:289–310
    [Google Scholar]
  19. GOLDBACH R. W., VAN KAMMEN A. 1985 Structure, replication and expression of the bipartite genome of cowpea mosaic virus. Molecular Plant Virology 283–120 Edited by Davies J. W. Boca Raton: CRC Press;
    [Google Scholar]
  20. GOLDBACH R. W., REZELMAN G., VAN KAMMEN A. 1980; Independent replication and expression of B component RNA of cowpea mosaic virus. Nature, London 286:297–300
    [Google Scholar]
  21. GORBALENYA A. E., BLINOV V. M., KOONIN E. V. 1985; Prediction of nucleotide-binding properties of virus-specific proteins from their primary structure. Molekuljarnaja Genetika 11:30–36
    [Google Scholar]
  22. HAMILTON W. D. O., BOCCARA M., ROBINSON D. J., BAULCOMBE D. C. 1987; The complete nucleotide sequence of tobacco rattle virus RNA-1. Journal of General Virology 68:2563–2575
    [Google Scholar]
  23. HANECAK R., SEMLER B. L., ANDERSON C. W., WIMMER E. 1982; Proteolytic processing of poliovirus polypeptides: antibodies to polypeptide P3-7C inhibit cleavage at glutamine-glycine pairs. Proceedings of the National Academy of Sciences, U.S.A 79:3973–3977
    [Google Scholar]
  24. HASELOFF J., GOELET P., ZIMMERN D., AHLQUIST P., DASGUPTA R., KAESBERG P. 1984; Striking similarities in amino acid sequence among non-structural 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]
  25. HEIDECKER G., MESSING J. 1983; Sequence analysis of zein cDNAs obtained by an efficient mRNA cloning method. Nucleic Acids Research 11:4891–4906
    [Google Scholar]
  26. HEMMER O., MEYER M., GREIF E., FRITSCH C. 1987; Comparison of the nucleotide sequences of five tomato black ring virus satellite RNAs. Journal of General Virology 68:1823–1833
    [Google Scholar]
  27. 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]
  28. KITAMURA N., ADLER C. J., ROTHBERG P. G., MARTINKO J., NATHENSON S. G., WIMMER E. 1980; The genome-linked protein of picornaviruses. VII. Genetic mapping of poliovirus VPg by protein and RNA sequence studies. Cell 21:295–302
    [Google Scholar]
  29. KITAMURA N., SEMLER B. L., ROTHBERG P. G., LARSEN G. R., ADLER C. J., DORNER A. J., EMINI E. A., HANECAK R., LEE J. J., VAN DER WERF S., ANDERSON C. W., WIMMER E. 1981; Primary structure, gene organization and polypeptide expression of poliovirus RNA. Nature, London 291:547–553
    [Google Scholar]
  30. KOENIG I., FRITSCH C. 1982; A protein linked at the 5′ end of satellite and genomic tomato black ring virus RNAs: study of in vitro translation after protease treatment. Journal of General Virology 60:343–353
    [Google Scholar]
  31. KOZAK M. 1981; Possible role of flanking nucleotides in recognition of the AUG initiation codon by eukaryotic ribosomes. Nucleic Acids Research 9:5233–5252
    [Google Scholar]
  32. KOZAK M. 1984; Compilation and analysis of sequences upstream from translational start in eukaryotic mRNA. Nucleic Acids Research 12:857–872
    [Google Scholar]
  33. LOMONOSSOFF G., SHANKS M. 1983; The nucleotide sequence of cowpea mosaic virus B RNA. EMBO Journal 2:2253–2258
    [Google Scholar]
  34. LÜTCKE H. A., CHOW K. C, MICKEL F. S., MOSS K. A., KERN H. F., SCHEELE G. A. 1987; Selection of AUG initiation codons differs in plants and animals. EMBO Journal 6:43–48
    [Google Scholar]
  35. MAAS R. 1983; An improved colony hybridization method with significantly increased sensitivity for detection of single genes. Plasmid 10:296–298
    [Google Scholar]
  36. MANIATIS T., FRITSCH E. F., SAMBROOK J. 1982 Molecular Cloning: A Laboratory Manual New York: Cold Spring Harbor Laboratory;
    [Google Scholar]
  37. MAXAM A. M., GILBERT W. 1980; Sequencing end-labeled DNA with base-specific chemical cleavages. Methods in Enzymology 65:499–560
    [Google Scholar]
  38. MAYO M. A., BARKER H., HARRISON B. D. 1979; Polyadenylate in the RNA of five nepoviruses. Journal of General Virology 43:603–610
    [Google Scholar]
  39. MAYO M. A., BARKER H., HARRISON B. D. 1982; Specificity and properties of the genome-linked proteins of nepoviruses. Journal of General Virology 59:149–162
    [Google Scholar]
  40. MESSING J. 1983; New M13 vectors for cloning. Methods in Enzymology 101:20–77
    [Google Scholar]
  41. 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]
  42. MURANT A. F., RASCHKÉ J. H. 1982; Specificity of the dependence of satellite RNA on tomato black ring virus (TBRV). Annual Report of the Scottish Crop Research Institute 1981:107–108
    [Google Scholar]
  43. MURANT A. F., TAYLOR M., DUNCAN G. H., RASCHKÉ J. H. 1981; Improved estimates of molecular weight of plant virus RNA by agarose gel electrophoresis and electron microscopy after denaturation with glyoxal. Journal of General Virology 53:321–332
    [Google Scholar]
  44. NOMOTO A., OMATA T., TOYODA H., KUGE S., HORIE H., KATAOKA Y., GENBA Y., NAKANO Y. SI, 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]
  45. PALMENBERG A. C. 1987 Genome organization, translation and processing in picornaviruses. The Molecular Biology of Positive Strand RNA Viruses1–15 Edited by Rowlands D. J., Mayo M. A., Mahy B. W. J. New York & London: Academic Press;
    [Google Scholar]
  46. PALMENBERG A. C, KIRBY E. M., JANDA M. R., DRAKE N. L., DUKE G. M., POTRATZ K. F., COLLETT M. S. 1984; The nucleotide and deduced amino acid sequences of the encephalomyocarditis viral polyprotein coding region. Nucleic Acids Research 12:2969–2985
    [Google Scholar]
  47. PELHAM H. R. B. 1979; Synthesis and proteolytic processing of cowpea mosaic virus proteins in reticulocyte lysates. Virology 96:463–477
    [Google Scholar]
  48. RACANIELLO V. R., BALTIMORE D. 1981; Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proceedings of the National Academy of Sciences, U.S.A 78:4887–4891
    [Google Scholar]
  49. RANDLES J. W., HARRISON B. D., MURANT A. F., MAYO M. A. 1977; Packaging and biological activity of the two essential RNA species of tomato black ring virus. Journal of General Virology 36:187–193
    [Google Scholar]
  50. REZAIAN M. A., WILLIAMS R. H. V., GORDON K. H. J., GOULD A. R., SYMONS R. H. 1984; Nucleotide sequence of cucumber mosaic virus RNA 2 reveals a translation product significantly homologous to corresponding proteins of other viruses. European Journal of Biochemistry 143:277–284
    [Google Scholar]
  51. REZAIAN M. A., WILLIAMS R. H. V., SYMONS R. H. 1985; Nucleotide sequence of cucumber mosaic virus RNA 1. European Journal of Biochemistry 150:331–339
    [Google Scholar]
  52. ROBINSON D. J., BARKER H., HARRISON B. D., MAYO M. A. 1980; Replication of RNA-1 of tomato black ring virus independently of RNA-2. Journal of General Virology 51:317–326
    [Google Scholar]
  53. RUECKERT R. R., WIMMER E. 1984; Systematic nomenclature of Picornavirus proteins. Journal of Virology 50:957–959
    [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. STADEN R. 1982; An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Research 10:2951–2961
    [Google Scholar]
  56. TAKEDA N., KUHN R. J., YANG C, TAKEGAMI T., WIMMER E. 1986; Initiation of poliovirus plus-strand RNA synthesis in a membrane complex of infected HeLa cells. Journal of Virology 60:43–53
    [Google Scholar]
  57. TAKEGAMI T., SEMLER B. L., ANDERSON C. W., WIMMER E. 1983; Membrane fractions active in poliovirus RNA replication contain VPg precursor polypeptides. Virology 128:33–47
    [Google Scholar]
  58. THOMAS P. S. 1980; Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose. Proceedings of the National Academy of Sciences, U.S.A 77:5201–5205
    [Google Scholar]
  59. VERVER J., GOLDBACH R. W., GARCIA J. A., VOS P. 1987; In vitro expression of a full-length DNA copy of cowpea mosaic virus B RNA: identification of the B RNA encoded 24 Kd protein as a viral protease. EMBO Journal 6:549–554
    [Google Scholar]
  60. WELLINK J., REZELMAN G., GOLDBACH R. W., 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]
  61. WU S., RINEHART C. A., KAESBERG P. 1987; Sequence and organization of southern bean mosaic virus genomic RNA. Virology 161:73–80
    [Google Scholar]
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