Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1983;2(12):2253–2258. doi: 10.1002/j.1460-2075.1983.tb01731.x

The nucleotide sequence of cowpea mosaic virus B RNA

GP Lomonossoff 1,*, M Shanks 1
PMCID: PMC555442  PMID: 16453487

Abstract

The complete sequence of the bottom component RNA (B RNA) of cowpea mosaic virus (CPMV) has been determined. Restriction enzyme fragments of double-stranded cDNA were cloned in M13 and the sequence of the inserts was determined by a combination of enzymatic and chemical sequencing techniques. Additional sequence information was obtained by primed synthesis on first strand cDNA. The complete sequence deduced is 5889 nucleotides long excluding the 3' poly(A), and contains an open reading frame sufficient to code for a polypeptide of mol. wt. 207 760. The coding region is flanked by a 5' leader sequence of 206 nucleotides and a 3' non-coding region of 82 residues which does not contain a polyadenylation signal.

Keywords: CPMV B RNA, cDNA cloning, M13, nucleotide sequence

Full text

PDF
2254

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ahlquist P., Kaesberg P. Determination of the length distribution of poly(A) at the 3' terminus of the virion RNAs of EMC virus, poliovirus, rhinovirus, RAV-61 and CPMV and of mouse globin mRNA. Nucleic Acids Res. 1979 Nov 10;7(5):1195–1204. doi: 10.1093/nar/7.5.1195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  3. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bruening G., Agrawal H. O. Infectivity of a mixture of cowpea mosaic virus ribonucleoprotein components. Virology. 1967 Jun;32(2):306–320. doi: 10.1016/0042-6822(67)90279-6. [DOI] [PubMed] [Google Scholar]
  5. Cornelissen B. J., Brederode F. T., Moormann R. J., Bol J. F. Complete nucleotide sequence of alfalfa mosaic virus RNA 1. Nucleic Acids Res. 1983 Mar 11;11(5):1253–1265. doi: 10.1093/nar/11.5.1253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cornelissen B. J., Brederode F. T., Veeneman G. H., van Boom J. H., Bol J. F. Complete nucleotide sequence of alfalfa mosaic virus RNA 2. Nucleic Acids Res. 1983 May 25;11(10):3019–3025. doi: 10.1093/nar/11.10.3019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Daubert S. D., Bruening G., Najarian R. C. Protein bound to the genome RNAs of cowpea mosaic virus. Eur J Biochem. 1978 Dec 1;92(1):45–51. doi: 10.1111/j.1432-1033.1978.tb12721.x. [DOI] [PubMed] [Google Scholar]
  8. Davies J. W., Aalbers A. M., Stuik E. J., Van Kammen A. Translation of cowpea mosaic virus RNA in a cell-free extract from wheat germ. FEBS Lett. 1977 May 15;77(2):265–269. doi: 10.1016/0014-5793(77)80248-2. [DOI] [PubMed] [Google Scholar]
  9. Davies J. W., Stanley J., Van Kammen A. Sequence homology adjacent to the 3' terminal poly(A) of cowpea mosaic virus RNAs. Nucleic Acids Res. 1979 Sep 25;7(2):493–500. doi: 10.1093/nar/7.2.493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Duckworth M. L., Gait M. J., Goelet P., Hong G. F., Singh M., Titmas R. C. Rapid synthesis of oligodeoxyribonucleotides VI. Efficient, mechanised synthesis of heptadecadeoxyribonucleotides by an improved solid phase phosphotriester route. Nucleic Acids Res. 1981 Apr 10;9(7):1691–1706. doi: 10.1093/nar/9.7.1691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fields S., Winter G. Nucleotide-sequence heterogeneity and sequence rearrangements in influenza virus cDNA. Gene. 1981 Nov;15(2-3):207–214. doi: 10.1016/0378-1119(81)90130-x. [DOI] [PubMed] [Google Scholar]
  12. Franssen H., Goldbach R., Broekhuijsen M., Moerman M., van Kammen A. 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. J Virol. 1982 Jan;41(1):8–17. doi: 10.1128/jvi.41.1.8-17.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gay N. J., Walker J. E. Homology between human bladder carcinoma oncogene product and mitochondrial ATP-synthase. Nature. 1983 Jan 20;301(5897):262–264. doi: 10.1038/301262a0. [DOI] [PubMed] [Google Scholar]
  14. Goelet P., Lomonossoff G. P., Butler P. J., Akam M. E., Gait M. J., Karn J. Nucleotide sequence of tobacco mosaic virus RNA. Proc Natl Acad Sci U S A. 1982 Oct;79(19):5818–5822. doi: 10.1073/pnas.79.19.5818. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Goldbach R. W., Schilthuis J. G., Rezelman G. Comparison of in vivo and in vitro translation of cowpea mosaic virus RNAs. Biochem Biophys Res Commun. 1981 Mar 16;99(1):89–94. doi: 10.1016/0006-291x(81)91716-2. [DOI] [PubMed] [Google Scholar]
  16. Goldbach R., Rezelman G. Orientation of the cleavage map of the 200-kilodalton polypeptide encoded by the bottom-component RNA of cowpea mosaic virus. J Virol. 1983 May;46(2):614–619. doi: 10.1128/jvi.46.2.614-619.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gopo J. M., Frist R. H. Location of the gene specifying the smaller protein of the cowpea mosaic virus capsid. Virology. 1977 Jun 15;79(2):259–266. doi: 10.1016/0042-6822(77)90353-1. [DOI] [PubMed] [Google Scholar]
  18. Gould A. R., Symons R. H. Cucumber mosaic virus RNA 3. Determination of the nucleotide sequence provides the amino acid sequences of protein 3A and viral coat protein. Eur J Biochem. 1982 Aug;126(2):217–226. [PubMed] [Google Scholar]
  19. Hong G. F. A method for sequencing single-stranded cloned DNA in both directions. Biosci Rep. 1981 Mar;1(3):243–252. doi: 10.1007/BF01114911. [DOI] [PubMed] [Google Scholar]
  20. Kitamura N., Wimmer E. Sequence of 1060 3'-terminal nucleotides of poliovirus RNA as determined by a modification of the dideoxynucleotide method. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3196–3200. doi: 10.1073/pnas.77.6.3196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Klootwijk J., Klein I., Zabel P., van Kammen A. Cowpea mosaic virus RNAs have neither m7GpppN ... nor mono-, di- or triphosphates at their 5' ends. Cell. 1977 May;11(1):73–82. doi: 10.1016/0092-8674(77)90318-x. [DOI] [PubMed] [Google Scholar]
  22. Kohli J., Grosjean H. Usage of the three termination codons: compilation and analysis of the known eukaryotic and prokaryotic translation termination sequences. Mol Gen Genet. 1981;182(3):430–439. doi: 10.1007/BF00293932. [DOI] [PubMed] [Google Scholar]
  23. Kozak M. Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes. Nucleic Acids Res. 1981 Oct 24;9(20):5233–5252. doi: 10.1093/nar/9.20.5233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Maizels N. Dictyostelium 17S, 25S, and 5S rDNAs lie within a 38,000 base pair repeated unit. Cell. 1976 Nov;9(3):431–438. doi: 10.1016/0092-8674(76)90088-x. [DOI] [PubMed] [Google Scholar]
  25. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  26. Messing J., Vieira J. A new pair of M13 vectors for selecting either DNA strand of double-digest restriction fragments. Gene. 1982 Oct;19(3):269–276. doi: 10.1016/0378-1119(82)90016-6. [DOI] [PubMed] [Google Scholar]
  27. Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981 Apr 9;290(5806):470–474. doi: 10.1038/290470a0. [DOI] [PubMed] [Google Scholar]
  28. Pelham H. R. Leaky UAG termination codon in tobacco mosaic virus RNA. Nature. 1978 Mar 30;272(5652):469–471. doi: 10.1038/272469a0. [DOI] [PubMed] [Google Scholar]
  29. Pelham H. R. Synthesis and proteolytic processing of cowpea mosaic virus proteins in reticulocyte lysates. Virology. 1979 Jul 30;96(2):463–477. doi: 10.1016/0042-6822(79)90104-1. [DOI] [PubMed] [Google Scholar]
  30. Rezelman G., Goldbach R., Van Kammen A. Expression of bottom component RNA of cowpea mosaic virus in cowpea protoplasts. J Virol. 1980 Nov;36(2):366–373. doi: 10.1128/jvi.36.2.366-373.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sanger F., Coulson A. R., Barrell B. G., Smith A. J., Roe B. A. Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. J Mol Biol. 1980 Oct 25;143(2):161–178. doi: 10.1016/0022-2836(80)90196-5. [DOI] [PubMed] [Google Scholar]
  32. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Shinnick T. M., Lerner R. A., Sutcliffe J. G. Nucleotide sequence of Moloney murine leukaemia virus. Nature. 1981 Oct 15;293(5833):543–548. doi: 10.1038/293543a0. [DOI] [PubMed] [Google Scholar]
  34. Staden R. A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res. 1980 Aug 25;8(16):3673–3694. doi: 10.1093/nar/8.16.3673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Stanley J., Rottier P., Davies J. W., Zabel P., Van Kammen A. A protein linked to the 5' termini of both RNA components of the cowpea mosaic virus genome. Nucleic Acids Res. 1978 Dec;5(12):4505–4522. doi: 10.1093/nar/5.12.4505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Stanley J., Van Kammen A. Nucleotide sequences adjacent to the proteins covalently linked to the cowpea mosaic virus genome. Sequence determination after labelling in vitro using RNA ligase. Eur J Biochem. 1979 Nov 1;101(1):45–49. doi: 10.1111/j.1432-1033.1979.tb04214.x. [DOI] [PubMed] [Google Scholar]
  37. Thongmeearkom P., Goodman R. M. Complementation and pseudorecombination between ribonucleic acids from two natural isolates of cowpea mosaic virus (severe subgroup). Virology. 1978 Mar;85(1):75–83. doi: 10.1016/0042-6822(78)90412-9. [DOI] [PubMed] [Google Scholar]
  38. Volckaert G., Tavernier J., Derynck R., Devos R., Fiers W. Molecular mechanisms of nucleotide-sequence rearrangements in cDNA clones of human fibroblast interferon mRNA. Gene. 1981 Nov;15(2-3):215–223. doi: 10.1016/0378-1119(81)90131-1. [DOI] [PubMed] [Google Scholar]
  39. Zimmern D. The 5' end group of tobacco mosaic virus RNA is m7G5' ppp5' Gp. Nucleic Acids Res. 1975 Jul;2(7):1189–1201. doi: 10.1093/nar/2.7.1189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. el-Manna M. M., Bruening G. Polyadenylate sequences in the ribonucleic acids of cowpea mosaic virus. Virology. 1973 Nov;56(1):198–206. doi: 10.1016/0042-6822(73)90299-7. [DOI] [PubMed] [Google Scholar]
  41. van Kammen A. Purification and properties of the components of cowpea mosaic virus. Virology. 1967 Apr;31(4):633–642. doi: 10.1016/0042-6822(67)90192-4. [DOI] [PubMed] [Google Scholar]
  42. van Wezenbeek P., Verver J., Harmsen J., Vos P., van Kammen A. Primary structure and gene organization of the middle-component RNA of cowpea mosaic virus. EMBO J. 1983;2(6):941–946. doi: 10.1002/j.1460-2075.1983.tb01525.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES