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. 1977 Oct;24(1):135–141. doi: 10.1128/jvi.24.1.135-141.1977

Secondary structure of RNA from bacteriophages f2 Qbeta, and PP7.

T D Edlind, A R Bassel
PMCID: PMC515917  PMID: 409852

Abstract

Electron microscopy of RNA-protein monolayers prepared under partial denaturing conditions has been used to compare the secondary structure of coliphage f2 and Qbeta and Pseudomonas aeruginosa phage PP7 RNAs. The secondary structure map of f2 RNA contains a central open loop and four symmetrically placed hairpins, which is similar to the pattern reported by Jacobson (A. B. Jacobson, Proc. Natl. Acad. Sci. U.S.A. 73:307-311, 1976) for the closely related phage MS2. With the same denaturing conditions, Qbeta RNA, which is 20% larger than f2 or PP7 RNA, has a central open loop and a smaller terminal loop. PP7 RNA has two large, closed secondary structures, one of which is nearly central. The base composition of PP7 RNA was determined and is similar to that of the group I coliphage RNAs. Thus, the greater amount of large base-paired structure is not related to an increased guanine-plus-cytosine content of PP7 RNA. With increased denaturing conditions, the central, closed structure of PP7 RNA is converted into an open loop. The central structures of all three phages include about 700 nucleotides. The relevance of these findings to the genetic maps of the coliphage RNAs is discussed.

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Selected References

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

  1. Adams J. M., Cory S. Untranslated nucleotide sequence at the 5'-end of R17 bacteriophage RNA. Nature. 1970 Aug 8;227(5258):570–574. doi: 10.1038/227570a0. [DOI] [PubMed] [Google Scholar]
  2. Ball L. A., Kaesberg P. A polarity gradient in the expression of the replicase gene of RNA bacteriophage Q beta. J Mol Biol. 1973 Mar 15;74(4):547–562. doi: 10.1016/0022-2836(73)90046-6. [DOI] [PubMed] [Google Scholar]
  3. Bassel B. A., Jr, Spiegelman S. Specific cleavage of Qbeta-RNA and identification of the fragment carrying the 3'-OH terminus. Proc Natl Acad Sci U S A. 1967 Sep;58(3):1155–1161. doi: 10.1073/pnas.58.3.1155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bassel B. A., Walsh E. C., Chi J. Y., Curry M. E., Brown J. G. Translation of Pseudomonas aeruginosa bacteriophage PP7 RNA by a cell-free amino acid incorporating system from Escherichia coli. J Virol. 1974 Jun;13(6):1326–1330. doi: 10.1128/jvi.13.6.1326-1330.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Benike C., McClements W., Davies J. W. The molecular size of the RNA genome of Pseudomonas aeruginosa bacteriophage PP7. Virology. 1975 Aug;66(2):625–628. doi: 10.1016/0042-6822(75)90236-6. [DOI] [PubMed] [Google Scholar]
  6. Boedtker H. The reaction of ribonucleic acid with formaldehyde. I. Optical absorbance studies. Biochemistry. 1967 Sep;6(9):2718–2727. doi: 10.1021/bi00861a011. [DOI] [PubMed] [Google Scholar]
  7. Chi Y. Y., Bassel A. R. Electron microscopy of viral RNA: molecular weight determination of bacterial and animal virus RNAs. J Virol. 1974 Jun;13(6):1194–1199. doi: 10.1128/jvi.13.6.1194-1199.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Davies J. W., Benike C. Translation of virus mRNA: synthesis of bacteriophage PP7 proteins in cell-free extracts from Pseudomonas aeruginosa. Virology. 1974 Oct;61(2):450–457. doi: 10.1016/0042-6822(74)90281-5. [DOI] [PubMed] [Google Scholar]
  9. Fiers W., Contreras R., Duerinck F., Haegeman G., Iserentant D., Merregaert J., Min Jou W., Molemans F., Raeymaekers A., Van den Berghe A. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature. 1976 Apr 8;260(5551):500–507. doi: 10.1038/260500a0. [DOI] [PubMed] [Google Scholar]
  10. Fiers W., Contreras R., Duerinck F., Haegmean G., Merregaert J., Jou W. M., Raeymakers A., Volckaert G., Ysebaert M., Van de Kerckhove J. A-protein gene of bacteriophage MS2. Nature. 1975 Jul 24;256(5515):273–278. doi: 10.1038/256273a0. [DOI] [PubMed] [Google Scholar]
  11. Gralla J., DeLisi C. mRNA is expected to form stable secondary structures. Nature. 1974 Mar 22;248(446):330–332. doi: 10.1038/248330a0. [DOI] [PubMed] [Google Scholar]
  12. Isenberg H., Cotter R. I., Gratzer W. B. Secondary structure and interaction of RNA and protein in a bacteriophage. Biochim Biophys Acta. 1971 Feb 25;232(1):184–191. doi: 10.1016/0005-2787(71)90502-8. [DOI] [PubMed] [Google Scholar]
  13. Jacobson A. B. Studies on secondary structure of single-stranded RNA from bacteriophage MS2 by electron microscopy. Proc Natl Acad Sci U S A. 1976 Feb;73(2):307–311. doi: 10.1073/pnas.73.2.307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Jou W. M., Fiers W. Studies on the bacteriophages MS2. XXXIII. Comparison of the nucleotide sequences in related bacteriophage RNAs. J Mol Biol. 1976 Oct 5;106(4):1047–1060. doi: 10.1016/0022-2836(76)90352-1. [DOI] [PubMed] [Google Scholar]
  15. Kozak M., Nathans D. Translation of the genome of a ribonucleic acid bacteriophage. Bacteriol Rev. 1972 Mar;36(1):109–134. doi: 10.1128/br.36.1.109-134.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kung H. J., Hu S., Bender W., Bailey J. M., Davidson N., Nicolson M. O., McAllister R. M. RD-114, baboon, and woolly monkey viral RNA's compared in size and structure. Cell. 1976 Apr;7(4):609–620. doi: 10.1016/0092-8674(76)90211-7. [DOI] [PubMed] [Google Scholar]
  17. Min Jou W., Haegeman G., Ysebaert M., Fiers W. Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein. Nature. 1972 May 12;237(5350):82–88. doi: 10.1038/237082a0. [DOI] [PubMed] [Google Scholar]
  18. Mitra S., Enger M. D., Kaesberg P. PHYSICAL AND CHEMICAL PROPERTIES OF RNA FROM THE BACTERIAL VIRUS R17. Proc Natl Acad Sci U S A. 1963 Jul;50(1):68–75. doi: 10.1073/pnas.50.1.68. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ricard B., Salser W. Secondary structures formed by random RNA sequences. Biochem Biophys Res Commun. 1975 Apr 7;63(3):548–554. doi: 10.1016/s0006-291x(75)80419-0. [DOI] [PubMed] [Google Scholar]
  20. Staples D. H., Hindley J., Billeter M. A., Weissmann C. Localization of Q-beta maturation cistron ribosome binding site. Nat New Biol. 1971 Sep 15;234(50):202–204. doi: 10.1038/newbio234202a0. [DOI] [PubMed] [Google Scholar]
  21. Strauss J. H., Jr, Sinsheimer R. L. Initial kinetics of degradation of MS2 ribonucleic acid by ribonuclease, heat and alkali and the presence of configurational restraints in this ribonucleic acid. J Mol Biol. 1968 Jun 28;34(3):453–465. doi: 10.1016/0022-2836(68)90172-1. [DOI] [PubMed] [Google Scholar]
  22. Vandenberghe A., Min Jou W., Fiers W. 3'-Terminal nucletide sequence (n equals 361) of bacteriophage MS2 RNA. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2559–2562. doi: 10.1073/pnas.72.7.2559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Wellauer P. K., Dawid I. B. Secondary structure maps of RNA: processing of HeLa ribosomal RNA. Proc Natl Acad Sci U S A. 1973 Oct;70(10):2827–2831. doi: 10.1073/pnas.70.10.2827. [DOI] [PMC free article] [PubMed] [Google Scholar]

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