Skip to main content
NCBI home page
Journal of Virology logoLink to Journal of Virology
. 1981 Jan;37(1):328–335. doi: 10.1128/jvi.37.1.328-335.1981

Stable hairpin structure within the 5'-terminal 85 nucleotides of poliovirus RNA.

G R Larsen, B L Semler, E Wimmer
PMCID: PMC171010  PMID: 6260985

Abstract

The primary sequence of a 5'-terminal fragment of poliovirus type 1 RNA, generated by digestion with RNase III, has been determined. This sequence reveals the presence of a stable hairpin structure beginning nine nucleotides from the terminally linked protein VPg. The sequence does not contain (i) the initiation codons AUG or GUG or (ii) the putative ribosome-binding sequence complementary to the 3' end of eucaryotic ribosomal 18S RNA. The stem-and-loop structure identified can be drawn in either plus or minus RNA strands. It is unclear to which strand functional significance (if any) can be assigned. It is possible that the hairpin structure is involved in ribosomal recognition and translation or in RNA synthesis by interacting with replicase molecules.

Full text

PDF
328

Images in this article

330Image
on p.330
331Image
on p.331
332Image
on p.332
333Image
on p.333

Selected References

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

  1. Alberty H., Raba M., Gross H. J. Isolation from rat liver and sequence of a RNA fragment containing 32 nucleotides from position 5 to 36 from the 3' end of ribosomal 18S RNA. Nucleic Acids Res. 1978 Feb;5(2):425–434. doi: 10.1093/nar/5.2.425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ambros V., Baltimore D. Protein is linked to the 5' end of poliovirus RNA by a phosphodiester linkage to tyrosine. J Biol Chem. 1978 Aug 10;253(15):5263–5266. [PubMed] [Google Scholar]
  3. Baltimore D. Expression of animal virus genomes. Bacteriol Rev. 1971 Sep;35(3):235–241. doi: 10.1128/br.35.3.235-241.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Baralle F. E., Brownlee G. G. AUG is the only recognisable signal sequence in the 5' non-coding regions of eukaryotic mRNA. Nature. 1978 Jul 6;274(5666):84–87. doi: 10.1038/274084a0. [DOI] [PubMed] [Google Scholar]
  5. Borer P. N., Dengler B., Tinoco I., Jr, Uhlenbeck O. C. Stability of ribonucleic acid double-stranded helices. J Mol Biol. 1974 Jul 15;86(4):843–853. doi: 10.1016/0022-2836(74)90357-x. [DOI] [PubMed] [Google Scholar]
  6. Bruenn J. A., Brennan V. E. Yeast viral double-stranded RNAs have heterogeneous 3' termini. Cell. 1980 Apr;19(4):923–933. doi: 10.1016/0092-8674(80)90084-7. [DOI] [PubMed] [Google Scholar]
  7. Donis-Keller H., Maxam A. M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. doi: 10.1093/nar/4.8.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dunn J. J. RNase III cleavage of single-stranded RNA. Effect of ionic strength on the fideltiy of cleavage. J Biol Chem. 1976 Jun 25;251(12):3807–3814. [PubMed] [Google Scholar]
  9. 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]
  10. Fernandez-Munoz R., Darnell J. E. Structural difference between the 5' termini of viral and cellular mRNA in poliovirus-infected cells: possible basis for the inhibition of host protein synthesis. J Virol. 1976 May;18(2):719–726. doi: 10.1128/jvi.18.2.719-726.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Flanegan J. B., Petterson R. F., Ambros V., Hewlett N. J., Baltimore D. Covalent linkage of a protein to a defined nucleotide sequence at the 5'-terminus of virion and replicative intermediate RNAs of poliovirus. Proc Natl Acad Sci U S A. 1977 Mar;74(3):961–965. doi: 10.1073/pnas.74.3.961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hagenbüchle O., Santer M., Steitz J. A., Mans R. J. Conservation of the primary structure at the 3' end of 18S rRNA from eucaryotic cells. Cell. 1978 Mar;13(3):551–563. doi: 10.1016/0092-8674(78)90328-8. [DOI] [PubMed] [Google Scholar]
  13. Harris T. J., Dunn J. J., Wimmer E. Identification of specific fragments containing the 5' end of poliovirus RNA after ribonuclease III digestion. Nucleic Acids Res. 1978 Nov;5(11):4039–4054. doi: 10.1093/nar/5.11.4039. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Harris T. J. The nucleotide sequence at the 5' end of foot and mouth disease virus RNA. Nucleic Acids Res. 1979 Dec 11;7(7):1765–1785. doi: 10.1093/nar/7.7.1765. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hewlett M. J., Florkiewicz R. Z. Sequence of picornavirus RNAs containing a radioiodinated 5'-linked peptide reveals a conserved 5' sequence. Proc Natl Acad Sci U S A. 1980 Jan;77(1):303–307. doi: 10.1073/pnas.77.1.303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hewlett M. J., Rose J. K., Baltimore D. 5'-terminal structure of poliovirus polyribosomal RNA is pUp. Proc Natl Acad Sci U S A. 1976 Feb;73(2):327–330. doi: 10.1073/pnas.73.2.327. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Johnson R. A., Walseth T. F. The enzymatic preparation of [alpha-32P]ATP, [alpha-32P]GTP, [32P]cAMP, and [32P]cGMP, and their use in the assay of adenylate and guanylate cyclases and cyclic nucleotide phosphodiesterases. Adv Cyclic Nucleotide Res. 1979;10:135–167. [PubMed] [Google Scholar]
  18. Keller E. B., Calvo J. M. Alternative secondary structures of leader RNAs and the regulation of the trp, phe, his, thr, and leu operons. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6186–6190. doi: 10.1073/pnas.76.12.6186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kitamura N., Wimmer E. Sequence of 1060 3'-terminal nucleotides of poliovirus RNA as determined by a modification of the dideoxynucleotide method. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3196–3200. doi: 10.1073/pnas.77.6.3196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Krupp G., Gross H. J. Rapid RNA sequencing: nucleases from Staphylococcus aureus and Neurospora crassa discriminate between uridine and cytidine. Nucleic Acids Res. 1979 Aug 10;6(11):3481–3490. doi: 10.1093/nar/6.11.3481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Larsen G. R., Dorner A. J., Harris T. J., Wimmer E. The structure of poliovirus replicative form. Nucleic Acids Res. 1980 Mar 25;8(6):1217–1229. doi: 10.1093/nar/8.6.1217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lee Y. F., Kitamura N., Nomoto A., Wimmer E. Sequence studies of poliovirus RNA. IV. Nucleotide sequence complexities of poliovirus type 1, type 2 and two type 1 defective interfering particles RNAs, and fingerprint of the poliovirus type 3 genome. J Gen Virol. 1979 Aug;44(2):311–322. doi: 10.1099/0022-1317-44-2-311. [DOI] [PubMed] [Google Scholar]
  23. Lee Y. F., Nomoto A., Detjen B. M., Wimmer E. A protein covalently linked to poliovirus genome RNA. Proc Natl Acad Sci U S A. 1977 Jan;74(1):59–63. doi: 10.1073/pnas.74.1.59. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lee Y. F., Nomoto A., Wimmer E. The genome of poliovirus is an exceptional eukaryotic mRNA. Prog Nucleic Acid Res Mol Biol. 1976;19:89–96. doi: 10.1016/s0079-6603(08)60910-1. [DOI] [PubMed] [Google Scholar]
  25. Leung D. W., Browning K. S., Heckman J. E., RajBhandary U. L., Clark J. M., Jr Nucleotide sequence of the 5' terminus of satellite tobacco necrosis virus ribonucleic acid. Biochemistry. 1979 Apr 3;18(7):1361–1366. doi: 10.1021/bi00574a036. [DOI] [PubMed] [Google Scholar]
  26. Lockard R. E., Alzner-Deweerd B., Heckman J. E., MacGee J., Tabor M. W., RajBhandary U. L. Sequence analysis of 5'[32P] labeled mRNA and tRNA using polyacrylamide gel electrophoresis. Nucleic Acids Res. 1978 Jan;5(1):37–56. doi: 10.1093/nar/5.1.37. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lovinger G. G., Schochetman G. 5' terminal nucleotide sequences of type C retroviruses: features common to noncoding sequences of eucaryotic messenger RNAs. Cell. 1980 Jun;20(2):441–449. doi: 10.1016/0092-8674(80)90630-3. [DOI] [PubMed] [Google Scholar]
  28. McReynolds L., O'Malley B. W., Nisbet A. D., Fothergill J. E., Givol D., Fields S., Robertson M., Brownlee G. G. Sequence of chicken ovalbumin mRNA. Nature. 1978 Jun 29;273(5665):723–728. doi: 10.1038/273723a0. [DOI] [PubMed] [Google Scholar]
  29. Nomoto A., Detjen B., Pozzatti R., Wimmer E. The location of the polio genome protein in viral RNAs and its implication for RNA synthesis. Nature. 1977 Jul 21;268(5617):208–213. doi: 10.1038/268208a0. [DOI] [PubMed] [Google Scholar]
  30. Nomoto A., Imura N. A convenient sequencing method for 5' protein-linked RNAs. Nucleic Acids Res. 1979 Nov 10;7(5):1233–1246. doi: 10.1093/nar/7.5.1233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nomoto A., Jacobson A., Lee Y. F., Dunn J., Wimmer E. Defective interfering particles of poliovirus: mapping of the deletion and evidence that the deletions in the genomes of DI(1), (2) and (3) are located in the same region. J Mol Biol. 1979 Feb 25;128(2):179–196. doi: 10.1016/0022-2836(79)90125-6. [DOI] [PubMed] [Google Scholar]
  32. Nomoto A., Kitamura N., Golini F., Wimmer E. The 5'-terminal structures of poliovirion RNA and poliovirus mRNA differ only in the genome-linked protein VPg. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5345–5349. doi: 10.1073/pnas.74.12.5345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Nomoto A., Lee Y. F., Babich A., Jacobson A., Dunn J. J., Wimmer E. Restricted fragmentation of poliovirus type 1, 2 and 3 RNAs by ribonuclease III. J Mol Biol. 1979 Feb 25;128(2):165–177. doi: 10.1016/0022-2836(79)90124-4. [DOI] [PubMed] [Google Scholar]
  34. Nomoto A., Lee Y. F., Wimmer E. The 5' end of poliovirus mRNA is not capped with m7G(5')ppp(5')Np. Proc Natl Acad Sci U S A. 1976 Feb;73(2):375–380. doi: 10.1073/pnas.73.2.375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Oxender D. L., Zurawski G., Yanofsky C. Attenuation in the Escherichia coli tryptophan operon: role of RNA secondary structure involving the tryptophan codon region. Proc Natl Acad Sci U S A. 1979 Nov;76(11):5524–5528. doi: 10.1073/pnas.76.11.5524. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Pettersson R. F., Flanegan J. B., Rose J. K., Baltimore D. 5'-Terminal nucleotide sequences of polio virus polyribosomal RNA and virion RNA are identical. Nature. 1977 Jul 21;268(5617):270–272. doi: 10.1038/268270a0. [DOI] [PubMed] [Google Scholar]
  37. Richardson C. C. Phosphorylation of nucleic acid by an enzyme from T4 bacteriophage-infected Escherichia coli. Proc Natl Acad Sci U S A. 1965 Jul;54(1):158–165. doi: 10.1073/pnas.54.1.158. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Rothberg P. G., Harris T. J., Nomoto A., Wimmer E. O4-(5'-uridylyl)tyrosine is the bond between the genome-linked protein and the RNA of poliovirus. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4868–4872. doi: 10.1073/pnas.75.10.4868. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Rowlands D. J. Sequences of vesicular stomatitis virus RNA in the region coding for leader RNA, N protein mRNA, and their junction. Proc Natl Acad Sci U S A. 1979 Oct;76(10):4793–4797. doi: 10.1073/pnas.76.10.4793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. 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]
  42. Simoncsits A., Brownlee G. G., Brown R. S., Rubin J. R., Guilley H. New rapid gel sequencing method for RNA. Nature. 1977 Oct 27;269(5631):833–836. doi: 10.1038/269833a0. [DOI] [PubMed] [Google Scholar]
  43. Summers D. F., Levintow L. Constitution and function of polyribosomes of poliovirus-infected HeLa cells. Virology. 1965 Sep;27(1):44–53. doi: 10.1016/0042-6822(65)90142-x. [DOI] [PubMed] [Google Scholar]
  44. Summers D. F., Maizel J. V., Jr, Darnell J. E., Jr The decrease in size and synthetic activity of poliovirus polysomes late in the infectious cycle. Virology. 1967 Mar;31(3):427–435. doi: 10.1016/0042-6822(67)90222-x. [DOI] [PubMed] [Google Scholar]
  45. Tinoco I., Jr, Borer P. N., Dengler B., Levin M. D., Uhlenbeck O. C., Crothers D. M., Bralla J. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol. 1973 Nov 14;246(150):40–41. doi: 10.1038/newbio246040a0. [DOI] [PubMed] [Google Scholar]
  46. Yogo Y., Wimmer E. Polyadenylic acid at the 3'-terminus of poliovirus RNA. Proc Natl Acad Sci U S A. 1972 Jul;69(7):1877–1882. doi: 10.1073/pnas.69.7.1877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. de Wachter R., Merregaert J., Vandenberghe A., Contreras R., Fiers W. Studies on the bacteriophage MS2. The untranslated 5'-terminal nucleotide sequence preceding the first cistron. Eur J Biochem. 1971 Oct 14;22(3):400–414. doi: 10.1111/j.1432-1033.1971.tb01558.x. [DOI] [PubMed] [Google Scholar]

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

RESOURCES