Skip to main content
NCBI home page
Elsevier - PMC COVID-19 Collection logoLink to Elsevier - PMC COVID-19 Collection
. 2002 Nov 12;33(2):145–156. doi: 10.1016/0168-1702(94)90051-5

Sequence analysis of the 3' termini of RNA1 and RNA2 of blueberry leaf mottle virus

JW Bacher a,∗, D Warkentin a,b, D Ramsdell b, JF Hancock a
PMCID: PMC7173305  PMID: 7975879

Abstract

The 3' termini of RNA1 and RNA2 of blueberry leaf mottle virus (BBLMV) were cloned and the cDNA sequence of a portion of the putative polymerase gene, the complete coat protein (CP) gene, and the 3' non-coding regions was determined. The N terminus of the coat protein gene was precisely located by comparison with the amino acid sequence determined by the Edman degradation sequencing of the purified coat protein. The coat protein gene encoded a polypeptide of 521 amino acids with a predicted Mr of 57,542. Homology to BBLMV coat protein was highest with tomato ringspot virus (TomRSV) and cherry leaf roll virus (CLRV); two other nepoviruses also belonging to a sub-group defined by the presence of large RNA2 components. The 3' terminal 1390 nt of RNA1 and RNA2 were nearly identical and apparently non-coding. No statistically significant sequence homology was found between the 3' non-coding regions of BBLMV and other nepoviruses. A highly conserved 3' non-coding region of this length is unusual, but has been reported for two other related viruses, TomRSV and CLRV. The biological function of the long 3' non-coding region and how the high level of sequence homology is maintained between RNA1 and RNA2, is unknown. Possible mechanisms for conservation of the 3' terminus are discussed.

Keywords: BBLMV, Nepovirus, 3' Non-coding region, Coat protein, Recombination

References

  1. Bertioli D.J., Harris R.D., Edwards M.L., Cooper J.I., Hawes W.S. Transgenic plants and insect cells expressing the coat protein of arabis mosaic virus produce empty virus-like particles. J. Gen. Virol. 1991;72:1801–1809. doi: 10.1099/0022-1317-72-8-1801. [DOI] [PubMed] [Google Scholar]
  2. Blok V.C., Wardell J., Jolly C.A., Manoukian A., Robinson D.J., Edwards M.L., Mayo M.A. The nucleotide sequence of RNA2 of raspberry ringspot nepovirus. J. Gen. Virol. 1992;73:2189–2194. doi: 10.1099/0022-1317-73-9-2189. [DOI] [PubMed] [Google Scholar]
  3. Bouzoubaa S., Ziegler V., Beck D., Guilley H., Richards K., Jonard G. Nucleotide sequence of beet necrotic yellow vein virus RNA2. J. Virol. 1986;67:1689–1700. [Google Scholar]
  4. Brault V., Hibrand L., Candresse T., Le Gall O., Dunez J. Nucleotide sequence and genetic organization of Hungarian grapevine chrome mosaic nepovirus RNA 2. Nucl. Acids Res. 1989;17(19):7809–7819. doi: 10.1093/nar/17.19.7809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Demangeat G., Greif C., Hemmer O., Fritsch C. Analysis of the in vitro cleavage products of tomato black ring virus RNA-1 encoded 250K polyprotein. J. Gen. Virol. 1990;71:1649–1654. doi: 10.1099/0022-1317-71-8-1649. [DOI] [PubMed] [Google Scholar]
  6. Demangeat G., Hemmer O., Fritsch C., Le Gall O., Candresse T. In vitro processing of the RNA-2-encoded polyprotein of two nepoviruses: tomato black ring virus and grapevine chrome mosaic virus. J. Gen. Virol. 1991;72:247–252. doi: 10.1099/0022-1317-72-2-247. [DOI] [PubMed] [Google Scholar]
  7. Devereux J., Haeberl P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucl. Acids Res. 1984;12(1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Domingo E., Holland J.J. High error rates, population equilibrium and evolution of RNA replication systems. In: Domingo E., Holland J.J., Ahlquist P., editors. Vol 3. CRC Press; Boca Raton, Florida: 1988. pp. 3–36. (RNA Genetics). [Google Scholar]
  9. Doolittle R.R. Similar amino acid sequences: chance or common ancestry? Science. 1981;214(9):149–159. doi: 10.1126/science.7280687. [DOI] [PubMed] [Google Scholar]
  10. Fraenkel-Conrat H., Singer B., Tsugita A. Purification of viral RNA by means of bentonite. Virology. 1961;14:51–58. doi: 10.1016/0042-6822(61)90131-3. [DOI] [PubMed] [Google Scholar]
  11. Greif C., Hemmer O., Fritsch C. Nucleotide sequence of tomato black ring virus RNA 1. J. Gen. Virol. 1988;69:1517–1529. [Google Scholar]
  12. Gubler U., Hoffman B.J. A simple and very efficient method for generating cDNA libraries. Gene. 1983;25:263–269. doi: 10.1016/0378-1119(83)90230-5. [DOI] [PubMed] [Google Scholar]
  13. Harrison B.D., Murant A.F. Kew; Surrey, UK: 1977. Nepovirus group. CMI/AAB Descriptions of Plant Viruses. no. 185, unpaged. [Google Scholar]
  14. Hunkapiller M.W., Lajun E., Ostrander F., Hood L.E. Isolation of microgram quantities of protein from polyacrylamide gels for amino acid sequence analysis. Meth. Enzymol. 1983;91:227–236. doi: 10.1016/s0076-6879(83)91019-4. [DOI] [PubMed] [Google Scholar]
  15. Kamer G., Argos P. Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucl. Acids Res. 1984;12:7269–7782. doi: 10.1093/nar/12.18.7269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lai M.M. Coronaviruses: Organization, replication and expression of genome. Ann. Rev. Microbiol. 1990;44:303–333. doi: 10.1146/annurev.mi.44.100190.001511. [DOI] [PubMed] [Google Scholar]
  17. Le Gall O, Candresse T., Brault V., Dunez J. Nucleotide sequence of Hungarian grapevine chrome mosaic nepovirus RNA1. Nucl. Acids Res. 1989;17:7795–7807. doi: 10.1093/nar/17.19.7795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Martelli G.P. Nematode Vectors of Plant Viruses. In: Lamberti F., Taylor C.E., Seinhorst J.W., editors. 1975. p. 223. London. [Google Scholar]
  19. Matthews R.E.F. Third Edition. 1991. Plant Virology; p. 835. London, UK and New York, USA. [Google Scholar]
  20. Meshi T., Kiyama R., Ohno T., Okada Y. Nucleotide sequence of coat protein cistron and the 3' non-coding region of cucumber green mottle virus (watermelon strain) RNA. Virology. 1983;127:54–64. doi: 10.1016/0042-6822(83)90370-7. [DOI] [PubMed] [Google Scholar]
  21. Meyer M., Hemmer O., Mayo M.A., Fritsch C. The nucleotide sequence of tomato black ring virus RNA 2. J. Gen. Virol. 1986;67:1257–1271. [Google Scholar]
  22. Ramsdell D.C., Stace-Smith R. Physical and chemical properties of the particles of ribonucleic acid of blueberry leaf mottle virus. Phytopathol. 1981;71(4):468–472. [Google Scholar]
  23. Rott M.E., Tremaine J.H., Rochon D.M. Comparison of the 5' and 3' termini of tomato ringspot virus RNA 1 and RNA 2: evidence for RNA recombination. Virology. 1991;185:468–472. doi: 10.1016/0042-6822(91)90801-H. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Rott M.E., Tremaine J.H., Rochon D.M. Nucleotide sequence of tomato ringspot virus RNA2. J. Gen. Virol. 1991;72:1505–1514. doi: 10.1099/0022-1317-72-7-1505. [DOI] [PubMed] [Google Scholar]
  25. Sambrook J., Fritsch E.F., Maniatis T. Cold Springs Harbor Laboratory; Cold Spring Harbor, N.Y: 1991. (Molecular Cloning: A Laboratory Manual). [Google Scholar]
  26. Sanger F. Determination of nucleotide sequence in DNA. Science. 1981;214:1205–1210. doi: 10.1126/science.7302589. [DOI] [PubMed] [Google Scholar]
  27. Scott N.W., Cooper J.I., Liu Y.Y., Hellen C.U.T. A 1.5 kb homology in the 3'-terminal regions of RNA1 and RNA2 of birch isolate of cherry leaf roll nepovirus is also present, in part, in a rhubarb isolate. J. Gen. Virol. 1992;73:481–485. doi: 10.1099/0022-1317-73-2-481. [DOI] [PubMed] [Google Scholar]
  28. Serghini M.A., Fuchs M., Pinck M., Reinbolt J., Walter B., Pinck L. RNA 2 of grapevine fanleaf virus: sequence analysis and coat protein cistron location. J. Gen. Virol. 1990;71:1433–1441. doi: 10.1099/0022-1317-71-7-1433. [DOI] [PubMed] [Google Scholar]
  29. Steinhauer D.A., Holland J.J. Rapid evolution of RNA viruses. Ann. Rev. Microbiol. 1987;41:409–433. doi: 10.1146/annurev.mi.41.100187.002205. [DOI] [PubMed] [Google Scholar]
  30. Vieira J., Messing J. Meth. Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [DOI] [PubMed] [Google Scholar]

Articles from Virus Research are provided here courtesy of Elsevier

RESOURCES