Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 Mar 11;11(5):1253–1265. doi: 10.1093/nar/11.5.1253

Complete nucleotide sequence of alfalfa mosaic virus RNA 1.

B J Cornelissen, F T Brederode, R J Moormann, J F Bol
PMCID: PMC325794  PMID: 6298738

Abstract

Double-stranded cDNA of alfalfa mosaic virus (AlMV) RNA 1 has been cloned and sequenced. From clones with overlapping inserts, and other sequence data, the complete primary sequence of the 3644 nucleotides of RNA 1 was deduced: a long open reading frame for a protein of Mr 125,685 is flanked by a 5'-terminal sequence of 100 nucleotides and a 3' noncoding region of 163 nucleotides, including the sequence of 145 nucleotides the three genomic RNAs of AlMV have in common. The two UGA-termination codons halfway RNA 1, that were postulated by Van Tol et al. (FEBS Lett. 118, 67-71, 1980) to account for partial translation of RNA 1 in vitro into Mr 58,000 and Mr 62,000 proteins, were not found in the reading frame of the Mr 125,685 protein.

Full text

PDF
1253

Images in this article

Selected References

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

  1. 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]
  2. 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]
  3. Bol J. F., Brederode F. T., Janze G. C., Rauh D. K. Studies on sequence homology between the RNA's of alfalfa mosaic virus. Virology. 1975 May;65(1):1–15. doi: 10.1016/0042-6822(75)90002-1. [DOI] [PubMed] [Google Scholar]
  4. Bol J. F., van Vloten-Doting L. Function of top component a RNA in the initiation of infection by alfalfa mosaic virus. Virology. 1973 Jan;51(1):102–108. doi: 10.1016/0042-6822(73)90370-x. [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. Casino A., Cipollaro M., Guerrini A. M., Mastrocinque G., Spena A., Scarlato V. Coding capacity of complementary DNA strands. Nucleic Acids Res. 1981 Mar 25;9(6):1499–1518. doi: 10.1093/nar/9.6.1499. [DOI] [PMC free article] [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. Dasgupta R., Kaesberg P. Complete nucleotide sequences of the coat protein messenger RNAs of brome mosaic virus and cowpea chlorotic mottle virus. Nucleic Acids Res. 1982 Jan 22;10(2):703–713. doi: 10.1093/nar/10.2.703. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Devos R., van Emmelo J., Seurinck-Opsomer C., Gillis E., Fiers W. Addition by ATP: RNA adenylyltransferase from Escherichia coli of 3'-linked oligo(A) to bacteriophage Qbeta RNA and its effect on RNA replication. Biochim Biophys Acta. 1976 Oct 18;447(3):319–327. doi: 10.1016/0005-2787(76)90055-1. [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. Gould A. R., Symons R. H. Alfalfa mosaic virus RNA. Determination of the sequence homology between the four RNA species and a comparison with the four RNA species of cucumber mosaic virus. Eur J Biochem. 1978 Nov 2;91(1):269–278. doi: 10.1111/j.1432-1033.1978.tb20962.x. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Guilley H., Briand J. P. Nucleotide sequence of turnip yellow mosaic virus coat protein mRNA. Cell. 1978 Sep;15(1):113–122. doi: 10.1016/0092-8674(78)90087-9. [DOI] [PubMed] [Google Scholar]
  15. Guilley H., Jonard G., Kukla B., Richards K. E. Sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA. Nucleic Acids Res. 1979 Apr;6(4):1287–1308. doi: 10.1093/nar/6.4.1287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. 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]
  18. Houwing C. J., Jaspars E. M. Coat protein binds to the 3'-terminal part of RNA 4 of alfalfa mosaic virus. Biochemistry. 1978 Jul 11;17(14):2927–2933. doi: 10.1021/bi00607a035. [DOI] [PubMed] [Google Scholar]
  19. 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. Primary structure, gene organization and polypeptide expression of poliovirus RNA. Nature. 1981 Jun 18;291(5816):547–553. doi: 10.1038/291547a0. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. 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]
  22. Koper-Zwarthoff E. C., Lockard R. E., Alzner-deWeerd B., RajBhandary U. L., Bol J. F. Nucleotide sequence of 5' terminus of alfalfa mosaic virus RNA 4 leading into coat protein cistron. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5504–5508. doi: 10.1073/pnas.74.12.5504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kozak M. Analysis of ribosome binding sites from the s1 message of reovirus. Initiation at the first and second AUG codons. J Mol Biol. 1982 Apr 25;156(4):807–820. doi: 10.1016/0022-2836(82)90143-7. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Lomedico P. T., McAndrew S. J. Eukaryotic ribosomes can recognize preproinsulin initiation codons irrespective of their position relative to the 5' end of mRNA. Nature. 1982 Sep 16;299(5880):221–226. doi: 10.1038/299221a0. [DOI] [PubMed] [Google Scholar]
  26. Lomonossoff G. P., Shanks M., Matthes H. D., Singh M., Gait M. J. The location of the first AUG codons in cowpea mosaic virus RNAs. Nucleic Acids Res. 1982 Aug 25;10(16):4861–4872. doi: 10.1093/nar/10.16.4861. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lupker H. S., Dekker B. M. Purification of the sequence-specific endonuclease SinI from Salmonella infantis. Biochim Biophys Acta. 1981 Jul 27;654(2):297–299. doi: 10.1016/0005-2787(81)90185-4. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Mohier E., Hirth L., Le Meur M. A., Gerlinger P. Translation of alfalfa mosaic virus RNA's in mammalian cell-free systems. Virology. 1975 Dec;68(2):349–359. doi: 10.1016/0042-6822(75)90278-0. [DOI] [PubMed] [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. RAUWS A. G., JASPARS E. M., VELDSTRA H. THE BASE COMPOSITION RIBONUCLEIC ACIDS FROM ALFALFA MOSAIC VIRUS COMPONENTS. Virology. 1964 Jun;23:283–286. doi: 10.1016/0042-6822(64)90297-1. [DOI] [PubMed] [Google Scholar]
  34. Racaniello V. R., Baltimore D. Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc Natl Acad Sci U S A. 1981 Aug;78(8):4887–4891. doi: 10.1073/pnas.78.8.4887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Rice C. M., Strauss J. H. Synthesis, cleavage and sequence analysis of DNA complementary to the 26 S messenger RNA of Sindbis virus. J Mol Biol. 1981 Aug 15;150(3):315–340. doi: 10.1016/0022-2836(81)90550-7. [DOI] [PubMed] [Google Scholar]
  36. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. Subramani S., Mulligan R., Berg P. Expression of the mouse dihydrofolate reductase complementary deoxyribonucleic acid in simian virus 40 vectors. Mol Cell Biol. 1981 Sep;1(9):854–864. doi: 10.1128/mcb.1.9.854. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Van Tol R. G., Van Gemeren R., Van Vloten-Doting L. Two leaky termination codons in AMV RNA 1. FEBS Lett. 1980 Aug 25;118(1):67–71. doi: 10.1016/0014-5793(80)81220-8. [DOI] [PubMed] [Google Scholar]
  40. van Tol R. G., van Vloten-Doting L. Translation of alfalfa-mosaic-virus RNA 1 in the mRNA-dependent translation system from rabbit reticulocyte lysates. Eur J Biochem. 1979 Feb 1;93(3):461–468. doi: 10.1111/j.1432-1033.1979.tb12844.x. [DOI] [PubMed] [Google Scholar]
  41. van Vloten-Doting L., Francki R. I., Fulton R. W., Kaper J. M., Lane L. C. Tricornaviridae - a proposed family of plant viruses with tripartite, single-stranded RNA genomes. Intervirology. 1981;15(4):198–203. doi: 10.1159/000149232. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES