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. 1983 May 11;11(9):2881–2891. doi: 10.1093/nar/11.9.2881

Complete nucleotide sequence of alfalfa mosaic virus RNA3.

R F Barker, N P Jarvis, D V Thompson, L S Loesch-Fries, T C Hall
PMCID: PMC325930  PMID: 6856479

Abstract

A full-length cDNA clone of alfalfa mosaic virus (AMV) RNA3 was prepared and sequenced. The 2,037 base sequence contains two open reading frames of 903 and 666 nucleotides that code for a 32,400 dalton protein (32.4K protein) and the 24,380 dalton coat protein, respectively. A 5'-noncoding sequence of 240 bases preceeding the 32.4K protein contains homologous regions that may have a function in its translation. The intercistronic junction is 49 bases long, the last 36 bases representing the 5'-end of the subgenomic RNA4. The remaining 179 bases comprise the 3'-terminal noncoding sequence.

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Selected References

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

  1. Ahlquist P., Dasgupta R., Shih D. S., Zimmern D., Kaesberg P. Two-step binding of eukaryotic ribosomes to brome mosaic virus RNA3. Nature. 1979 Sep 27;281(5729):277–282. doi: 10.1038/281277a0. [DOI] [PubMed] [Google Scholar]
  2. Ahlquist P., Luckow V., Kaesberg P. Complete nucleotide sequence of brome mosaic virus RNA3. J Mol Biol. 1981 Nov 25;153(1):23–38. doi: 10.1016/0022-2836(81)90524-6. [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. Brakke M. K., Van Pelt N. Linear-log sucrose gradients for estimating sedimentation coefficients of plant viruses and nucleic acids. Anal Biochem. 1970 Nov;38(1):56–64. doi: 10.1016/0003-2697(70)90155-7. [DOI] [PubMed] [Google Scholar]
  5. Brederode F. T., Koper-Zwarthoff E. C., Bol J. F. Complete nucleotide sequence of alfalfa mosaic virus RNA 4. Nucleic Acids Res. 1980 May 24;8(10):2213–2223. doi: 10.1093/nar/8.10.2213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Briand J. P., Keith G., Guilley H. Nucleotide sequence at the 5' extremity of turnip yellow mosaic virus genome RNA. Proc Natl Acad Sci U S A. 1978 Jul;75(7):3168–3172. doi: 10.1073/pnas.75.7.3168. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cooke N. E., Coit D., Weiner R. I., Baxter J. D., Martial J. A. Structure of cloned DNA complementary to rat prolactin messenger RNA. J Biol Chem. 1980 Jul 10;255(13):6502–6510. [PubMed] [Google Scholar]
  8. Dagert M., Ehrlich S. D. Prolonged incubation in calcium chloride improves the competence of Escherichia coli cells. Gene. 1979 May;6(1):23–28. doi: 10.1016/0378-1119(79)90082-9. [DOI] [PubMed] [Google Scholar]
  9. Filipowicz W., Haenni A. L. Binding of ribosomes to 5'-terminal leader sequences of eukaryotic messenger RNAs. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3111–3115. doi: 10.1073/pnas.76.7.3111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Garoff H., Ansorge W. Improvements of DNA sequencing gels. Anal Biochem. 1981 Aug;115(2):450–457. doi: 10.1016/0003-2697(81)90031-2. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Grunstein M., Wallis J. Colony hybridization. Methods Enzymol. 1979;68:379–389. doi: 10.1016/0076-6879(79)68027-8. [DOI] [PubMed] [Google Scholar]
  13. Gunn M. R., Symons R. H. Sequence homology at the 3'-termini of the four RNAs of alfalfa mosaic virus. FEBS Lett. 1980 Jan 1;109(1):145–150. doi: 10.1016/0014-5793(80)81330-5. [DOI] [PubMed] [Google Scholar]
  14. Heijtink R. A., Houwing C. J., Jaspars E. M. Molecular weights of particles and RNAs of alfalfa mosaic virus. Number of subunits in protein capsids. Biochemistry. 1977 Oct 18;16(21):4684–4693. doi: 10.1021/bi00640a024. [DOI] [PubMed] [Google Scholar]
  15. Houwing C. J., Jaspars E. M. Protein binding sites in nucleation complexes of alfalfa mosaic virus RNA 4. Biochemistry. 1982 Jul 6;21(14):3408–3414. doi: 10.1021/bi00257a025. [DOI] [PubMed] [Google Scholar]
  16. Koper-Zwarthoff E. C., Bol J. F. 3'-Terminal nucleotide sequence of alfalfa mosaic virus RNA 4. Proc Natl Acad Sci U S A. 1979 Mar;76(3):1114–1117. doi: 10.1073/pnas.76.3.1114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Koper-Zwarthoff E. C., Bol J. F. Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus. Nucleic Acids Res. 1980 Aug 11;8(15):3307–3318. doi: 10.1093/nar/8.15.3307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Koper-Zwarthoff E. C., Brederode F. T., Veeneman G., van Boom J. H., Bol J. F. Nucleotide sequences at the 5'-termini of the alfalfa mosaic virus RNAs and the intercistronic junction in RNA 3. Nucleic Acids Res. 1980 Dec 11;8(23):5635–5647. doi: 10.1093/nar/8.23.5635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Koper-Zwarthoff E. C., Brederode F. T., Walstra P., Bol J. F. Nucleotide sequence of the 3'-noncoding region of alfalfa mosaic virus RNA 4 and its homology with the genomic RNAs. Nucleic Acids Res. 1979 Dec 11;7(7):1887–1900. doi: 10.1093/nar/7.7.1887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kozak M. How do eucaryotic ribosomes select initiation regions in messenger RNA? Cell. 1978 Dec;15(4):1109–1123. doi: 10.1016/0092-8674(78)90039-9. [DOI] [PubMed] [Google Scholar]
  21. Land H., Grez M., Hauser H., Lindenmaier W., Schütz G. 5'-Terminal sequences of eucaryotic mRNA can be cloned with high efficiency. Nucleic Acids Res. 1981 May 25;9(10):2251–2266. doi: 10.1093/nar/9.10.2251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Pinck L., Pinck M. Sequence homology at the 3'-ends of alfalfa mosaic virus RNAs. FEBS Lett. 1979 Nov 1;107(1):61–65. doi: 10.1016/0014-5793(79)80463-9. [DOI] [PubMed] [Google Scholar]
  24. Pinck M., Fritsch C., Ravelonandro M., Thivent C., Pinck L. Binding of ribosomes to the 5' leader sequence (N = 258) of RNA 3 from alfalfa mosaic virus. Nucleic Acids Res. 1981 Mar 11;9(5):1087–1100. doi: 10.1093/nar/9.5.1087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sippel A. E. Purification and characterization of adenosine triphosphate: ribonucleic acid adenyltransferase from Escherichia coli. Eur J Biochem. 1973 Aug 1;37(1):31–40. doi: 10.1111/j.1432-1033.1973.tb02953.x. [DOI] [PubMed] [Google Scholar]
  26. Van Vloten-Doting L., Jaspars E. M. The uncoating of alfalfa mosaic virus by its own RNA. Virology. 1972 Jun;48(3):699–708. doi: 10.1016/0042-6822(72)90154-7. [DOI] [PubMed] [Google Scholar]
  27. Vloten-Doting L. V. Similarities and differences between viruses with a tripartite genome. Ann Microbiol (Paris) 1976 Jan;127A(1):119–129. [PubMed] [Google Scholar]

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