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. 1992 Dec 1;89(23):11146–11150. doi: 10.1073/pnas.89.23.11146

Evidence that the packaging signal for nodaviral RNA2 is a bulged stem-loop.

W Zhong 1, R Dasgupta 1, R Rueckert 1
PMCID: PMC50506  PMID: 1454792

Abstract

Flock house virus is an insect virus belonging to the family Nodaviridae; members of this family are characterized by a small bipartite positive-stranded RNA genome. The larger genomic segment, RNA1, encodes viral replication proteins, whereas the smaller one, RNA2, encodes coat protein. Both RNAs are packaged in a single particle. A defective-interfering RNA (DI-634), isolated from a line of Drosophila cells persistently infected with Flock house virus, was used to show that a 32-base region of RNA2 (bases 186-217) is required for packaging into virions. RNA folding analysis predicted that this region forms a stem-loop structure with a 5-base loop and a 13-base-pair bulged stem.

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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., Janda M. cDNA cloning and in vitro transcription of the complete brome mosaic virus genome. Mol Cell Biol. 1984 Dec;4(12):2876–2882. doi: 10.1128/mcb.4.12.2876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bernardi A., Spahr P. F. Nucleotide sequence at the binding site for coat protein on RNA of bacteriophage R17. Proc Natl Acad Sci U S A. 1972 Oct;69(10):3033–3037. doi: 10.1073/pnas.69.10.3033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Carey J., Cameron V., de Haseth P. L., Uhlenbeck O. C. Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site. Biochemistry. 1983 May 24;22(11):2601–2610. doi: 10.1021/bi00280a002. [DOI] [PubMed] [Google Scholar]
  4. Carey J., Lowary P. T., Uhlenbeck O. C. Interaction of R17 coat protein with synthetic variants of its ribonucleic acid binding site. Biochemistry. 1983 Sep 27;22(20):4723–4730. doi: 10.1021/bi00289a017. [DOI] [PubMed] [Google Scholar]
  5. Dasgupta R., Ghosh A., Dasmahapatra B., Guarino L. A., Kaesberg P. Primary and secondary structure of black beetle virus RNA2, the genomic messenger for BBV coat protein precursor. Nucleic Acids Res. 1984 Sep 25;12(18):7215–7223. doi: 10.1093/nar/12.18.7215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dasgupta R., Sgro J. Y. Nucleotide sequences of three Nodavirus RNA2's: the messengers for their coat protein precursors. Nucleic Acids Res. 1989 Sep 25;17(18):7525–7526. doi: 10.1093/nar/17.18.7525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dasmahapatra B., Dasgupta R., Ghosh A., Kaesberg P. Structure of the black beetle virus genome and its functional implications. J Mol Biol. 1985 Mar 20;182(2):183–189. doi: 10.1016/0022-2836(85)90337-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dasmahapatra B., Dasgupta R., Saunders K., Selling B., Gallagher T., Kaesberg P. Infectious RNA derived by transcription from cloned cDNA copies of the genomic RNA of an insect virus. Proc Natl Acad Sci U S A. 1986 Jan;83(1):63–66. doi: 10.1073/pnas.83.1.63. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Felgner P. L., Gadek T. R., Holm M., Roman R., Chan H. W., Wenz M., Northrop J. P., Ringold G. M., Danielsen M. Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7413–7417. doi: 10.1073/pnas.84.21.7413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fosmire J. A., Hwang K., Makino S. Identification and characterization of a coronavirus packaging signal. J Virol. 1992 Jun;66(6):3522–3530. doi: 10.1128/jvi.66.6.3522-3530.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Friesen P. D., Rueckert R. R. Black beetle virus: messenger for protein B is a subgenomic viral RNA. J Virol. 1982 Jun;42(3):986–995. doi: 10.1128/jvi.42.3.986-995.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Friesen P. D., Rueckert R. R. Early and late functions in a bipartite RNA virus: evidence for translational control by competition between viral mRNAs. J Virol. 1984 Jan;49(1):116–124. doi: 10.1128/jvi.49.1.116-124.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Friesen P. D., Rueckert R. R. Synthesis of Black Beetle Virus Proteins in Cultured Drosophila Cells: Differential Expression of RNAs 1 and 2. J Virol. 1981 Mar;37(3):876–886. doi: 10.1128/jvi.37.3.876-886.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Friesen P., Scotti P., Longworth J., Rueckert R. Black beetle virus: propagation in Drosophila line 1 cells and an infection-resistant subline carrying endogenous black beetle virus-related particles. J Virol. 1980 Sep;35(3):741–747. doi: 10.1128/jvi.35.3.741-747.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Gallagher T. M., Friesen P. D., Rueckert R. R. Autonomous replication and expression of RNA 1 from black beetle virus. J Virol. 1983 May;46(2):481–489. doi: 10.1128/jvi.46.2.481-489.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Gallagher T. M., Rueckert R. R. Assembly-dependent maturation cleavage in provirions of a small icosahedral insect ribovirus. J Virol. 1988 Sep;62(9):3399–3406. doi: 10.1128/jvi.62.9.3399-3406.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Guarino L. A., Ghosh A., Dasmahapatra B., Dasgupta R., Kaesberg P. Sequence of the black beetle virus subgenomic RNA and its location in the viral genome. Virology. 1984 Nov;139(1):199–203. doi: 10.1016/0042-6822(84)90342-8. [DOI] [PubMed] [Google Scholar]
  20. Guarino L. A., Kaesberg P. Isolation and Characterization of an RNA-Dependent RNA Polymerase from Black Beetle Virus-Infected Drosophila melanogaster Cells. J Virol. 1981 Nov;40(2):379–386. doi: 10.1128/jvi.40.2.379-386.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. Konarska M. M., Padgett R. A., Sharp P. A. Recognition of cap structure in splicing in vitro of mRNA precursors. Cell. 1984 Oct;38(3):731–736. doi: 10.1016/0092-8674(84)90268-x. [DOI] [PubMed] [Google Scholar]
  23. Newman J. F., Matthews T., Omilianowski D. R., Salerno T., Kaesberg P., Rueckert R. In vitro translation of the Two RNAs of Nodamura virus, a novel mammalian virus with a divided genome. J Virol. 1978 Jan;25(1):78–85. doi: 10.1128/jvi.25.1.78-85.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. 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]
  25. SCHNEIDER I. DIFFERENTIATION OF LARVAL DROSOPHILA EYE-ANTENNAL DISCS IN VITRO. J Exp Zool. 1964 Jun;156:91–103. doi: 10.1002/jez.1401560107. [DOI] [PubMed] [Google Scholar]
  26. Saunders K., Kaesberg P. Template-dependent RNA polymerase from black beetle virus-infected Drosophila melanogaster cells. Virology. 1985 Dec;147(2):373–381. doi: 10.1016/0042-6822(85)90139-4. [DOI] [PubMed] [Google Scholar]
  27. Schneider I. Cell lines derived from late embryonic stages of Drosophila melanogaster. J Embryol Exp Morphol. 1972 Apr;27(2):353–365. [PubMed] [Google Scholar]
  28. Scotti P. D., Dearing S., Mossop D. W. Flock House virus: a nodavirus isolated from Costelytra zealandica (White) (Coleoptera: Scarabaeidae). Arch Virol. 1983;75(3):181–189. doi: 10.1007/BF01315272. [DOI] [PubMed] [Google Scholar]
  29. Selling B. H., Rueckert R. R. Plaque assay for black beetle virus. J Virol. 1984 Jul;51(1):251–253. doi: 10.1128/jvi.51.1.251-253.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Turner D. R., Joyce L. E., Butler P. J. The tobacco mosaic virus assembly origin RNA. Functional characteristics defined by directed mutagenesis. J Mol Biol. 1988 Oct 5;203(3):531–547. doi: 10.1016/0022-2836(88)90190-8. [DOI] [PubMed] [Google Scholar]
  31. Weber H. The binding site for coat protein on bacteriophage Qbeta RNA. Biochim Biophys Acta. 1976 Jan 19;418(2):175–183. doi: 10.1016/0005-2787(76)90067-8. [DOI] [PubMed] [Google Scholar]
  32. Witherell G. W., Uhlenbeck O. C. Specific RNA binding by Q beta coat protein. Biochemistry. 1989 Jan 10;28(1):71–76. doi: 10.1021/bi00427a011. [DOI] [PubMed] [Google Scholar]
  33. Wu H. N., Uhlenbeck O. C. Role of a bulged A residue in a specific RNA-protein interaction. Biochemistry. 1987 Dec 15;26(25):8221–8227. doi: 10.1021/bi00399a030. [DOI] [PubMed] [Google Scholar]
  34. Zimmern D., Butler P. J. The isolation of tobacco mosaic virus RNA fragments containing the origin for viral assembly. Cell. 1977 Jul;11(3):455–462. doi: 10.1016/0092-8674(77)90064-2. [DOI] [PubMed] [Google Scholar]
  35. Zimmern D. The nucleotide sequence at the origin for assembly on tobacco mosaic virus RNA. Cell. 1977 Jul;11(3):463–482. doi: 10.1016/0092-8674(77)90065-4. [DOI] [PubMed] [Google Scholar]
  36. Zuidema D., Bierhuizen M. F., Cornelissen B. J., Bol J. F., Jaspars E. M. Coat protein binding sites on RNA 1 of alfalfa mosaic virus. Virology. 1983 Mar;125(2):361–369. doi: 10.1016/0042-6822(83)90208-8. [DOI] [PubMed] [Google Scholar]

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