Skip to main content
PMC home page
Journal of Virology logoLink to Journal of Virology
. 1997 Mar;71(3):2157–2162. doi: 10.1128/jvi.71.3.2157-2162.1997

In vitro selection of packaging sites in a double-stranded RNA virus.

W Yao 1, K Adelman 1, J A Bruenn 1
PMCID: PMC191321  PMID: 9032349

Abstract

The Saccharomyces cerevisiae double-stranded RNA virus ScVL1 recognizes a small sequence in the viral plus strand for both packaging and replication. Viral particles will bind to this viral binding sequence (VBS) with high affinity in vitro. An in vitro selection procedure has been used to optimize binding, and the sequences isolated have been analyzed for packaging and replication in vivo. The selected sequence consists of a stem with a bulged A residue topped by a loop of several bases. Four residues of the 18 bases are absolutely conserved for tight binding. These all fall in regions that appear to be single stranded. Eight more residues have preferred identities, and six of these are in the stem. The VBS is similar to the R17 bacteriophage coat protein binding site. Packaging and replication require tight binding to viral particles.

Full Text

The Full Text of this article is available as a PDF (679.6 KB).

Selected References

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

  1. Antson A. A., Otridge J., Brzozowski A. M., Dodson E. J., Dodson G. G., Wilson K. S., Smith T. M., Yang M., Kurecki T., Gollnick P. The structure of trp RNA-binding attenuation protein. Nature. 1995 Apr 20;374(6524):693–700. doi: 10.1038/374693a0. [DOI] [PubMed] [Google Scholar]
  2. Bartel D. P., Zapp M. L., Green M. R., Szostak J. W. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell. 1991 Nov 1;67(3):529–536. doi: 10.1016/0092-8674(91)90527-6. [DOI] [PubMed] [Google Scholar]
  3. Baumann C., Otridge J., Gollnick P. Kinetic and thermodynamic analysis of the interaction between TRAP (trp RNA-binding attenuation protein) of Bacillus subtilis and trp leader RNA. J Biol Chem. 1996 May 24;271(21):12269–12274. doi: 10.1074/jbc.271.21.12269. [DOI] [PubMed] [Google Scholar]
  4. Cheng R. H., Caston J. R., Wang G. J., Gu F., Smith T. J., Baker T. S., Bozarth R. F., Trus B. L., Cheng N., Wickner R. B. Fungal virus capsids, cytoplasmic compartments for the replication of double-stranded RNA, formed as icosahedral shells of asymmetric Gag dimers. J Mol Biol. 1994 Dec 2;244(3):255–258. doi: 10.1006/jmbi.1994.1726. [DOI] [PubMed] [Google Scholar]
  5. Diamond M. E., Dowhanick J. J., Nemeroff M. E., Pietras D. F., Tu C. L., Bruenn J. A. Overlapping genes in a yeast double-stranded RNA virus. J Virol. 1989 Sep;63(9):3983–3990. doi: 10.1128/jvi.63.9.3983-3990.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dinman J. D., Icho T., Wickner R. B. A -1 ribosomal frameshift in a double-stranded RNA virus of yeast forms a gag-pol fusion protein. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):174–178. doi: 10.1073/pnas.88.1.174. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. El-Sherbeini M., Tipper D. J., Mitchell D. J., Bostian K. A. Virus-like particle capsid proteins encoded by different L double-stranded RNAs of Saccharomyces cerevisiae: their roles in maintenance of M double-stranded killer plasmids. Mol Cell Biol. 1984 Dec;4(12):2818–2827. doi: 10.1128/mcb.4.12.2818. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Esteban R., Fujimura T., Wickner R. B. Internal and terminal cis-acting sites are necessary for in vitro replication of the L-A double-stranded RNA virus of yeast. EMBO J. 1989 Mar;8(3):947–954. doi: 10.1002/j.1460-2075.1989.tb03456.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Esteban R., Fujimura T., Wickner R. B. Site-specific binding of viral plus single-stranded RNA to replicase-containing open virus-like particles of yeast. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4411–4415. doi: 10.1073/pnas.85.12.4411. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fujimura T., Esteban R., Esteban L. M., Wickner R. B. Portable encapsidation signal of the L-A double-stranded RNA virus of S. cerevisiae. Cell. 1990 Aug 24;62(4):819–828. doi: 10.1016/0092-8674(90)90125-x. [DOI] [PubMed] [Google Scholar]
  11. Fujimura T., Ribas J. C., Makhov A. M., Wickner R. B. Pol of gag-pol fusion protein required for encapsidation of viral RNA of yeast L-A virus. Nature. 1992 Oct 22;359(6397):746–749. doi: 10.1038/359746a0. [DOI] [PubMed] [Google Scholar]
  12. Fujimura T., Wickner R. B. Gene overlap results in a viral protein having an RNA binding domain and a major coat protein domain. Cell. 1988 Nov 18;55(4):663–671. doi: 10.1016/0092-8674(88)90225-5. [DOI] [PubMed] [Google Scholar]
  13. Huan B. F., Shen Y. Q., Bruenn J. A. In vivo mapping of a sequence required for interference with the yeast killer virus. Proc Natl Acad Sci U S A. 1991 Feb 15;88(4):1271–1275. doi: 10.1073/pnas.88.4.1271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Innis M. A., Holland M. J., McCabe P. C., Cole G. E., Wittman V. P., Tal R., Watt K. W., Gelfand D. H., Holland J. P., Meade J. H. Expression, Glycosylation, and Secretion of an Aspergillus Glucoamylase by Saccharomyces cerevisiae. Science. 1985 Apr 5;228(4695):21–26. doi: 10.1126/science.228.4695.21. [DOI] [PubMed] [Google Scholar]
  15. Park C. M., Lopinski J. D., Masuda J., Tzeng T. H., Bruenn J. A. A second double-stranded RNA virus from yeast. Virology. 1996 Feb 15;216(2):451–454. doi: 10.1006/viro.1996.0083. [DOI] [PubMed] [Google Scholar]
  16. Reilly J. D., Bruenn J., Held W. The capsid polypeptides of the yeast viruses. Biochem Biophys Res Commun. 1984 Jun 15;121(2):619–625. doi: 10.1016/0006-291x(84)90227-4. [DOI] [PubMed] [Google Scholar]
  17. Romaniuk P. J., Lowary P., Wu H. N., Stormo G., Uhlenbeck O. C. RNA binding site of R17 coat protein. Biochemistry. 1987 Mar 24;26(6):1563–1568. doi: 10.1021/bi00380a011. [DOI] [PubMed] [Google Scholar]
  18. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Schneider D., Tuerk C., Gold L. Selection of high affinity RNA ligands to the bacteriophage R17 coat protein. J Mol Biol. 1992 Dec 5;228(3):862–869. doi: 10.1016/0022-2836(92)90870-p. [DOI] [PubMed] [Google Scholar]
  21. Shen Y., Bruenn J. A. RNA structural requirements for RNA binding, replication, and packaging in the yeast double-stranded RNA virus. Virology. 1993 Aug;195(2):481–491. doi: 10.1006/viro.1993.1399. [DOI] [PubMed] [Google Scholar]
  22. Tao J., Ginsberg I., Banerjee N., Held W., Koltin Y., Bruenn J. A. Ustilago maydis KP6 killer toxin: structure, expression in Saccharomyces cerevisiae, and relationship to other cellular toxins. Mol Cell Biol. 1990 Apr;10(4):1373–1381. doi: 10.1128/mcb.10.4.1373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Thiele D. J., Hannig E. M., Leibowitz M. J. Multiple L double-stranded RNA species of Saccharomyces cerevisiae: evidence for separate encapsidation. Mol Cell Biol. 1984 Jan;4(1):92–100. doi: 10.1128/mcb.4.1.92. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990 Aug 3;249(4968):505–510. doi: 10.1126/science.2200121. [DOI] [PubMed] [Google Scholar]
  25. Tzeng T. H., Tu C. L., Bruenn J. A. Ribosomal frameshifting requires a pseudoknot in the Saccharomyces cerevisiae double-stranded RNA virus. J Virol. 1992 Feb;66(2):999–1006. doi: 10.1128/jvi.66.2.999-1006.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Valegård K., Murray J. B., Stockley P. G., Stonehouse N. J., Liljas L. Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature. 1994 Oct 13;371(6498):623–626. doi: 10.1038/371623a0. [DOI] [PubMed] [Google Scholar]
  27. Weeks K. M., Crothers D. M. RNA recognition by Tat-derived peptides: interaction in the major groove? Cell. 1991 Aug 9;66(3):577–588. doi: 10.1016/0092-8674(81)90020-9. [DOI] [PubMed] [Google Scholar]
  28. Wickner R. B. Double-stranded RNA viruses of Saccharomyces cerevisiae. Microbiol Rev. 1996 Mar;60(1):250–265. doi: 10.1128/mr.60.1.250-265.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Yao W., Bruenn J. A. Interference with replication of two double-stranded RNA viruses by production of N-terminal fragments of capsid polypeptides. Virology. 1995 Dec 1;214(1):215–221. doi: 10.1006/viro.1995.9938. [DOI] [PubMed] [Google Scholar]
  30. Yao W., Muqtadir K., Bruenn J. A. Packaging in a yeast double-stranded RNA virus. J Virol. 1995 Mar;69(3):1917–1919. doi: 10.1128/jvi.69.3.1917-1919.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES