Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Jul 15;24(14):2660–2665. doi: 10.1093/nar/24.14.2660

Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs.

C B Reusken 1, J F Bol 1
PMCID: PMC145989  PMID: 8758992

Abstract

The 3'-terminal of the three genomic RNAs of alfalfa mosaic virus (AIMV) and ilarviruses contain a number of AUGC-motifs separated by hairpin structures. Binding of coat protein (CP) to such elements in the RNAs is required to initiate infection of these viruses. Determinants for CP binding in the 3'-terminal 39 nucleotides (nt) of AIMV RNA 3 were analyzed by band-shift assays. From the 5'- to 3'-end this 39 nt sequence contains AUGC-motif 3, stem-loop structure 2 (STLP2), AUGC-motif 2, stem-loop structure 1 (STLP1) and AUGC-motif 1. A mutational analysis showed that all three AUGC-motifs were involved in CP binding. Mutation of the A- and U-residues of motifs 1 or 3 had no effect on CP binding but similar mutations in motif 2 abolished CP binding. A mutational analysis of the stem of STLP1 and STLP2 confirmed the importance of these hairpins for CP binding. Randomization of the sequence of the stems and loops of STLP1 and STLP2 had no effect on CP binding as long as the secondary structure was maintained. This indicates that the two hairpins are not involved in sequence-specific interactions with CP. They may function in a secondary structure-specific interaction with CP and/or in the assembly of the AUGC-motifs in a configuration required for CP binding.

Full Text

The Full Text of this article is available as a PDF (108.2 KB).

Selected References

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

  1. Alrefai R. H., Shiel P. J., Domier L. L., D'Arcy C. J., Berger P. H., Korban S. S. The nucleotide sequence of apple mosaic virus coat protein gene has no similarity with other Bromoviridae coat protein genes. J Gen Virol. 1994 Oct;75(Pt 10):2847–2850. doi: 10.1099/0022-1317-75-10-2847. [DOI] [PubMed] [Google Scholar]
  2. Bachman E. J., Scott S. W., Xin G., Vance V. B. The complete nucleotide sequence of prune dwarf ilarvirus RNA 3: implications for coat protein activation of genome replication in ilarviruses. Virology. 1994 May 15;201(1):127–131. doi: 10.1006/viro.1994.1272. [DOI] [PubMed] [Google Scholar]
  3. Burd C. G., Dreyfuss G. Conserved structures and diversity of functions of RNA-binding proteins. Science. 1994 Jul 29;265(5172):615–621. doi: 10.1126/science.8036511. [DOI] [PubMed] [Google Scholar]
  4. Chastain M., Tinoco I., Jr Structural elements in RNA. Prog Nucleic Acid Res Mol Biol. 1991;41:131–177. doi: 10.1016/S0079-6603(08)60008-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cornelissen B. J., Janssen H., Zuidema D., Bol J. F. Complete nucleotide sequence of tobacco streak virus RNA 3. Nucleic Acids Res. 1984 Mar 12;12(5):2427–2437. doi: 10.1093/nar/12.5.2427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. De Graaff M., Man in't Veld M. R., Jaspars E. M. In vitro evidence that the coat protein of alfalfa mosaic virus plays a direct role in the regulation of plus and minus RNA synthesis: implications for the life cycle of alfalfa mosaic virus. Virology. 1995 Apr 20;208(2):583–589. doi: 10.1006/viro.1995.1189. [DOI] [PubMed] [Google Scholar]
  7. Draper D. E. Protein-RNA recognition. Annu Rev Biochem. 1995;64:593–620. doi: 10.1146/annurev.bi.64.070195.003113. [DOI] [PubMed] [Google Scholar]
  8. Gonsalves D., Fulton R. W. Activation of Prunus necrotic ringspot virus and rose mosaic virus by RNA 4 components of some Ilarviruses. Virology. 1977 Sep;81(2):398–407. doi: 10.1016/0042-6822(77)90155-6. [DOI] [PubMed] [Google Scholar]
  9. Gonsalves D., Garnsey S. M. Functional equivalence of an RNA component and coat protein for infectivity of citrus leaf rugose virus. Virology. 1975 Mar;64(1):23–31. doi: 10.1016/0042-6822(75)90075-6. [DOI] [PubMed] [Google Scholar]
  10. Gonsalves D., Garnsey S. M. Infectivity of the multiple nucleoprotein and RNA components of citrus leaf rugose virus. Virology. 1974 Oct;61(2):343–353. doi: 10.1016/0042-6822(74)90272-4. [DOI] [PubMed] [Google Scholar]
  11. Gonsalves D., Garnsey S. M. Nucleic acid components of citrus variegation virus and their activation by coat protein. Virology. 1975 Oct;67(2):311–318. doi: 10.1016/0042-6822(75)90432-8. [DOI] [PubMed] [Google Scholar]
  12. Houser-Scott F., Baer M. L., Liem K. F., Jr, Cai J. M., Gehrke L. Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3' untranslated region of alfalfa mosaic virus RNA 4. J Virol. 1994 Apr;68(4):2194–2205. doi: 10.1128/jvi.68.4.2194-2205.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. 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]
  15. Kaper J. M. Arrangement and identification of simple isometric viruses according to their dominating stabilizing interactions. Virology. 1973 Sep;55(1):299–304. doi: 10.1016/s0042-6822(73)81035-9. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. 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]
  18. Kruseman J., Kraal B., Jaspars E. M., Bol J. F., Brederode F. T., Veldstra H. Molecular weight of the coat protein of alfalfa mosaic virus. Biochemistry. 1971 Feb 2;10(3):447–455. doi: 10.1021/bi00779a015. [DOI] [PubMed] [Google Scholar]
  19. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Neeleman L., Van der Vossen E. A., Bol J. F. Infection of tobacco with alfalfa mosaic virus cDNAs sheds light on the early function of the coat protein. Virology. 1993 Oct;196(2):883–887. doi: 10.1006/viro.1993.1551. [DOI] [PubMed] [Google Scholar]
  21. Quadt R., Rosdorff H. J., Hunt T. W., Jaspars E. M. Analysis of the protein composition of alfalfa mosaic virus RNA-dependent RNA polymerase. Virology. 1991 May;182(1):309–315. doi: 10.1016/0042-6822(91)90674-z. [DOI] [PubMed] [Google Scholar]
  22. Quigley G. J., Gehrke L., Roth D. A., Auron P. E. Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):347–366. doi: 10.1093/nar/12.1part1.347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Reusken C. B., Neeleman L., Bol J. F. Ability of tobacco streak virus coat protein to substitute for late functions of alfalfa mosaic virus coat protein. J Virol. 1995 Jul;69(7):4552–4555. doi: 10.1128/jvi.69.7.4552-4555.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Reusken C. B., Neeleman L., Bol J. F. The 3'-untranslated region of alfalfa mosaic virus RNA 3 contains at least two independent binding sites for viral coat protein. Nucleic Acids Res. 1994 Apr 25;22(8):1346–1353. doi: 10.1093/nar/22.8.1346. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Scott S. W., Ge X. The complete nucleotide sequence of RNA 3 of citrus leaf rugose and citrus variegation ilarviruses. J Gen Virol. 1995 Apr;76(Pt 4):957–963. doi: 10.1099/0022-1317-76-4-957. [DOI] [PubMed] [Google Scholar]
  26. Scott S. W., Ge X. The complete nucleotide sequence of the RNA 3 of lilac ring mottle ilarvirus. J Gen Virol. 1995 Jul;76(Pt 7):1801–1806. doi: 10.1099/0022-1317-76-7-1801. [DOI] [PubMed] [Google Scholar]
  27. Sánchez-Navarro J. A., Pallás V. Nucleotide sequence of apple mosaic ilarvirus RNA 4. J Gen Virol. 1994 Jun;75(Pt 6):1441–1445. doi: 10.1099/0022-1317-75-6-1441. [DOI] [PubMed] [Google Scholar]
  28. Van der Kuyl A. C., Neeleman L., Bol J. F. Role of alfalfa mosaic virus coat protein in regulation of the balance between viral plus and minus strand RNA synthesis. Virology. 1991 Nov;185(1):496–499. doi: 10.1016/0042-6822(91)90807-n. [DOI] [PubMed] [Google Scholar]
  29. van Vloten-Doting L. Coat protein is required for infectivity of tobacco streak virus: biological equivalence of the coat proteins of tobacco streak and alfalfa mosaic viruses. Virology. 1975 May;65(1):215–225. doi: 10.1016/0042-6822(75)90022-7. [DOI] [PubMed] [Google Scholar]
  30. van der Kuyl A. C., Neeleman L., Bol J. F. Deletion analysis of cis- and trans-acting elements involved in replication of alfalfa mosaic virus RNA 3 in vivo. Virology. 1991 Aug;183(2):687–694. doi: 10.1016/0042-6822(91)90997-p. [DOI] [PubMed] [Google Scholar]
  31. van der Vossen E. A., Neeleman L., Bol J. F. Early and late functions of alfalfa mosaic virus coat protein can be mutated separately. Virology. 1994 Aug 1;202(2):891–903. doi: 10.1006/viro.1994.1411. [DOI] [PubMed] [Google Scholar]

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

RESOURCES