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. 1994 Jul 1;13(13):3158–3165. doi: 10.1002/j.1460-2075.1994.tb06614.x

Structure of influenza virus RNP. I. Influenza virus nucleoprotein melts secondary structure in panhandle RNA and exposes the bases to the solvent.

F Baudin 1, C Bach 1, S Cusack 1, R W Ruigrok 1
PMCID: PMC395207  PMID: 8039508

Abstract

The influenza virus genome consists of eight segments of negative-sense RNA, i.e. the viral (v) RNA forms the template for the mRNA. Each segment is encapsidated by the viral nucleoprotein to form a ribonucleoprotein (RNP) particle and each RNP carries its own polymerase complex. We studied the interaction of purified nucleoprotein with RNA in vitro, by using a variety of enzymatic and chemical probes for RNA conformation. Our results suggest that the nucleoprotein binds to the vRNA backbone without apparent sequence specificity, exposing the bases to the outside and melting all secondary structure. In this way, the viral polymerase may transcribe the RNA without the need for dissociating the nucleoprotein and without being stopped by RNA secondary structure, and the viral RNPs are ready to start transcription as soon as they enter the host cell.

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Selected References

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

  1. Baudin F., Ehresmann C., Romby P., Mougel M., Colin J., Lempereur L., Bachellerie J. P., Ebel J. P., Ehresmann B. Higher-order structure of domain III in Escherichia coli 16S ribosomal RNA, 30S subunit and 70S ribosome. Biochimie. 1987 Oct;69(10):1081–1096. doi: 10.1016/0300-9084(87)90008-3. [DOI] [PubMed] [Google Scholar]
  2. Baudin F., Marquet R., Isel C., Darlix J. L., Ehresmann B., Ehresmann C. Functional sites in the 5' region of human immunodeficiency virus type 1 RNA form defined structural domains. J Mol Biol. 1993 Jan 20;229(2):382–397. doi: 10.1006/jmbi.1993.1041. [DOI] [PubMed] [Google Scholar]
  3. Baudin F., Mougel M., Romby P., Eyermann F., Ebel J. P., Ehresmann B., Ehresmann C. Probing the phosphates of the Escherichia coli ribosomal 16S RNA in its naked form, in the 30S subunit, and in the 70S ribosome. Biochemistry. 1989 Jul 11;28(14):5847–5855. doi: 10.1021/bi00440a022. [DOI] [PubMed] [Google Scholar]
  4. Baudin F., Romaniuk P. J., Romby P., Brunel C., Westhof E., Ehresmann B., Ehresmann C. Involvement of "hinge" nucleotides of Xenopus laevis 5 S rRNA in the RNA structural organization and in the binding of transcription factor TFIIIA. J Mol Biol. 1991 Mar 5;218(1):69–81. doi: 10.1016/0022-2836(91)90874-6. [DOI] [PubMed] [Google Scholar]
  5. Beaton A. R., Krug R. M. Transcription antitermination during influenza viral template RNA synthesis requires the nucleocapsid protein and the absence of a 5' capped end. Proc Natl Acad Sci U S A. 1986 Sep;83(17):6282–6286. doi: 10.1073/pnas.83.17.6282. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Blumberg B. M., Giorgi C., Kolakofsky D. N protein of vesicular stomatitis virus selectively encapsidates leader RNA in vitro. Cell. 1983 Feb;32(2):559–567. doi: 10.1016/0092-8674(83)90475-0. [DOI] [PubMed] [Google Scholar]
  7. Compans R. W., Content J., Duesberg P. H. Structure of the ribonucleoprotein of influenza virus. J Virol. 1972 Oct;10(4):795–800. doi: 10.1128/jvi.10.4.795-800.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Desselberger U., Racaniello V. R., Zazra J. J., Palese P. The 3' and 5'-terminal sequences of influenza A, B and C virus RNA segments are highly conserved and show partial inverted complementarity. Gene. 1980 Feb;8(3):315–328. doi: 10.1016/0378-1119(80)90007-4. [DOI] [PubMed] [Google Scholar]
  9. Duesberg P. H. Distinct subunits of the ribonucleoprotein of influenza virus. J Mol Biol. 1969 Jun 28;42(3):485–499. doi: 10.1016/0022-2836(69)90237-x. [DOI] [PubMed] [Google Scholar]
  10. Ehresmann C., Baudin F., Mougel M., Romby P., Ebel J. P., Ehresmann B. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109–9128. doi: 10.1093/nar/15.22.9109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. England T. E., Uhlenbeck O. C. 3'-terminal labelling of RNA with T4 RNA ligase. Nature. 1978 Oct 12;275(5680):560–561. doi: 10.1038/275560a0. [DOI] [PubMed] [Google Scholar]
  12. Gish G., Eckstein F. DNA and RNA sequence determination based on phosphorothioate chemistry. Science. 1988 Jun 10;240(4858):1520–1522. doi: 10.1126/science.2453926. [DOI] [PubMed] [Google Scholar]
  13. Goldstein E. A., Pons M. W. The effect of polyvinylsulfate on the ribonucleoprotein of influenza virus. Virology. 1970 Jun;41(2):382–384. doi: 10.1016/0042-6822(70)90093-0. [DOI] [PubMed] [Google Scholar]
  14. Heinemann U., Saenger W. Specific protein-nucleic acid recognition in ribonuclease T1-2'-guanylic acid complex: an X-ray study. Nature. 1982 Sep 2;299(5878):27–31. doi: 10.1038/299027a0. [DOI] [PubMed] [Google Scholar]
  15. Honda A., Uéda K., Nagata K., Ishihama A. Identification of the RNA polymerase-binding site on genome RNA of influenza virus. J Biochem. 1987 Nov;102(5):1241–1249. doi: 10.1093/oxfordjournals.jbchem.a122163. [DOI] [PubMed] [Google Scholar]
  16. Honda A., Uéda K., Nagata K., Ishihama A. RNA polymerase of influenza virus: role of NP in RNA chain elongation. J Biochem. 1988 Dec;104(6):1021–1026. doi: 10.1093/oxfordjournals.jbchem.a122569. [DOI] [PubMed] [Google Scholar]
  17. Hsu M. T., Parvin J. D., Gupta S., Krystal M., Palese P. Genomic RNAs of influenza viruses are held in a circular conformation in virions and in infected cells by a terminal panhandle. Proc Natl Acad Sci U S A. 1987 Nov;84(22):8140–8144. doi: 10.1073/pnas.84.22.8140. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jennings P. A., Finch J. T., Winter G., Robertson J. S. Does the higher order structure of the influenza virus ribonucleoprotein guide sequence rearrangements in influenza viral RNA? Cell. 1983 Sep;34(2):619–627. doi: 10.1016/0092-8674(83)90394-x. [DOI] [PubMed] [Google Scholar]
  19. Kingsbury D. W., Jones I. M., Murti K. G. Assembly of influenza ribonucleoprotein in vitro using recombinant nucleoprotein. Virology. 1987 Feb;156(2):396–403. doi: 10.1016/0042-6822(87)90419-3. [DOI] [PubMed] [Google Scholar]
  20. Kingsbury D. W., Webster R. G. Some properties of influenza virus nucleocapsids. J Virol. 1969 Sep;4(3):219–225. doi: 10.1128/jvi.4.3.219-225.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lamb R. A., Choppin P. W. The gene structure and replication of influenza virus. Annu Rev Biochem. 1983;52:467–506. doi: 10.1146/annurev.bi.52.070183.002343. [DOI] [PubMed] [Google Scholar]
  22. McCauley J. W., Mahy B. W. Structure and function of the influenza virus genome. Biochem J. 1983 May 1;211(2):281–294. doi: 10.1042/bj2110281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Palese P. The genes of influenza virus. Cell. 1977 Jan;10(1):1–10. doi: 10.1016/0092-8674(77)90133-7. [DOI] [PubMed] [Google Scholar]
  24. Philippe C., Portier C., Mougel M., Grunberg-Manago M., Ebel J. P., Ehresmann B., Ehresmann C. Target site of Escherichia coli ribosomal protein S15 on its messenger RNA. Conformation and interaction with the protein. J Mol Biol. 1990 Jan 20;211(2):415–426. doi: 10.1016/0022-2836(90)90362-P. [DOI] [PubMed] [Google Scholar]
  25. Pons M. W., Schulze I. T., Hirst G. K., Hauser R. Isolation and characterization of the ribonucleoprotein of influenza virus. Virology. 1969 Oct;39(2):250–259. doi: 10.1016/0042-6822(69)90045-2. [DOI] [PubMed] [Google Scholar]
  26. Robertson J. S. 5' and 3' terminal nucleotide sequences of the RNA genome segments of influenza virus. Nucleic Acids Res. 1979 Aug 24;6(12):3745–3757. doi: 10.1093/nar/6.12.3745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Romby P., Westhof E., Moras D., Giegé R., Houssier C., Grosjean H. Studies on anticodon-anticodon interactions: hemi-protonation of cytosines induces self-pairing through the GCC anticodon of E. coli tRNA-Gly. J Biomol Struct Dyn. 1986 Oct;4(2):193–203. doi: 10.1080/07391102.1986.10506339. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Schatz D., Leberman R., Eckstein F. Interaction of Escherichia coli tRNA(Ser) with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phosphorothioate-containing tRNA transcripts. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6132–6136. doi: 10.1073/pnas.88.14.6132. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Scholtissek C., Becht H. Binding of ribonucleic acids to the RNP-antigen protein of influenza viruses. J Gen Virol. 1971 Jan;10(1):11–16. doi: 10.1099/0022-1317-10-1-11. [DOI] [PubMed] [Google Scholar]
  31. Shapiro G. I., Krug R. M. Influenza virus RNA replication in vitro: synthesis of viral template RNAs and virion RNAs in the absence of an added primer. J Virol. 1988 Jul;62(7):2285–2290. doi: 10.1128/jvi.62.7.2285-2290.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Silberklang M., Gillum A. M., RajBhandary U. L. The use of nuclease P1 in sequence analysis of end group labeled RNA. Nucleic Acids Res. 1977 Dec;4(12):4091–4108. doi: 10.1093/nar/4.12.4091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Skehel J. J., Hay A. J. Nucleotide sequences at the 5' termini of influenza virus RNAs and their transcripts. Nucleic Acids Res. 1978 Apr;5(4):1207–1219. doi: 10.1093/nar/5.4.1207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Stoeckle M. Y., Shaw M. W., Choppin P. W. Segment-specific and common nucleotide sequences in the noncoding regions of influenza B virus genome RNAs. Proc Natl Acad Sci U S A. 1987 May;84(9):2703–2707. doi: 10.1073/pnas.84.9.2703. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Winter G., Fields S. The structure of the gene encoding the nucleoprotein of human influenza virus A/PR/8/34. Virology. 1981 Oct 30;114(2):423–428. doi: 10.1016/0042-6822(81)90223-3. [DOI] [PubMed] [Google Scholar]

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