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. 1994 Nov 8;91(23):11148–11152. doi: 10.1073/pnas.91.23.11148

Pseudoknot in the central domain of small subunit ribosomal RNA is essential for translation.

A Vila 1, J Viril-Farley 1, W E Tapprich 1
PMCID: PMC45184  PMID: 7526390

Abstract

Phylogenetic comparison of rRNA sequences has suggested that a pseudoknot structure exists in the central domain of small-subunit rRNA. In Escherichia coli 16S rRNA, this pseudoknot would form when positions 570 and 571 pair with positions 865 and 866. Mutations were introduced into this pseudoknot at the phylogenetically invariant nucleotides U571 and A865. Single mutations of U to A at 571 or A to U at 865 dramatically altered the structural stability of the 30S subunit and also impaired the function of the subunit in translation. When the mutations were combined to create a compensatory pairing, the normal structure of the 30S subunit was restored, and the function of the mutant subunit in translation returned to wild-type levels. These results demonstrate the existence of a higher order structure in rRNA that directly affects the folding of the 30S subunit. Given the position of this structure in the three-dimensional model of the small subunit and the additional interactions that are likely to form in the same rRNA region, the central domain pseudoknot appears to contribute to a complex structure of rRNA that controls the conformational state of the ribosome.

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Selected References

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

  1. Brink M. F., Verbeet M. P., de Boer H. A. Formation of the central pseudoknot in 16S rRNA is essential for initiation of translation. EMBO J. 1993 Oct;12(10):3987–3996. doi: 10.1002/j.1460-2075.1993.tb06076.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brosius J., Ullrich A., Raker M. A., Gray A., Dull T. J., Gutell R. R., Noller H. F. Construction and fine mapping of recombinant plasmids containing the rrnB ribosomal RNA operon of E. coli. Plasmid. 1981 Jul;6(1):112–118. doi: 10.1016/0147-619x(81)90058-5. [DOI] [PubMed] [Google Scholar]
  3. Cheong C., Varani G., Tinoco I., Jr Solution structure of an unusually stable RNA hairpin, 5'GGAC(UUCG)GUCC. Nature. 1990 Aug 16;346(6285):680–682. doi: 10.1038/346680a0. [DOI] [PubMed] [Google Scholar]
  4. Cunningham P. R., Nurse K., Weitzmann C. J., Ofengand J. Functional effects of base changes which further define the decoding center of Escherichia coli 16S ribosomal RNA: mutation of C1404, G1405, C1496, G1497, and U1498. Biochemistry. 1993 Jul 20;32(28):7172–7180. doi: 10.1021/bi00079a014. [DOI] [PubMed] [Google Scholar]
  5. Expert-Bezançon A., Wollenzien P. L. Three-dimensional arrangement of the Escherichia coli 16 S ribosomal RNA. J Mol Biol. 1985 Jul 5;184(1):53–66. doi: 10.1016/0022-2836(85)90043-9. [DOI] [PubMed] [Google Scholar]
  6. Godson G. N., Sinsheimer R. L. Use of Brij lysis as a general method to prepare polyribosomes from Escherichia coli. Biochim Biophys Acta. 1967 Dec 19;149(2):489–495. doi: 10.1016/0005-2787(67)90176-1. [DOI] [PubMed] [Google Scholar]
  7. Gutell R. R., Larsen N., Woese C. R. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev. 1994 Mar;58(1):10–26. doi: 10.1128/mr.58.1.10-26.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gutell R. R., Noller H. F., Woese C. R. Higher order structure in ribosomal RNA. EMBO J. 1986 May;5(5):1111–1113. doi: 10.1002/j.1460-2075.1986.tb04330.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gutell R. R., Woese C. R. Higher order structural elements in ribosomal RNAs: pseudo-knots and the use of noncanonical pairs. Proc Natl Acad Sci U S A. 1990 Jan;87(2):663–667. doi: 10.1073/pnas.87.2.663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Heus H. A., Pardi A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science. 1991 Jul 12;253(5016):191–194. doi: 10.1126/science.1712983. [DOI] [PubMed] [Google Scholar]
  11. Hubbard J. M., Hearst J. E. Computer modeling 16 S ribosomal RNA. J Mol Biol. 1991 Oct 5;221(3):889–907. doi: 10.1016/0022-2836(91)80182-t. [DOI] [PubMed] [Google Scholar]
  12. Jacob W. F., Santer M., Dahlberg A. E. A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4757–4761. doi: 10.1073/pnas.84.14.4757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kooi E. A., Rutgers C. A., Mulder A., Van't Riet J., Venema J., Raué H. A. The phylogenetically conserved doublet tertiary interaction in domain III of the large subunit rRNA is crucial for ribosomal protein binding. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):213–216. doi: 10.1073/pnas.90.1.213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Makosky P. C., Dahlberg A. E. Spectinomycin resistance at site 1192 in 16S ribosomal RNA of E. coli: an analysis of three mutants. Biochimie. 1987 Aug;69(8):885–889. doi: 10.1016/0300-9084(87)90216-1. [DOI] [PubMed] [Google Scholar]
  16. Noller H. F. Ribosomal RNA and translation. Annu Rev Biochem. 1991;60:191–227. doi: 10.1146/annurev.bi.60.070191.001203. [DOI] [PubMed] [Google Scholar]
  17. Pleij C. W. Pseudoknots: a new motif in the RNA game. Trends Biochem Sci. 1990 Apr;15(4):143–147. doi: 10.1016/0968-0004(90)90214-v. [DOI] [PubMed] [Google Scholar]
  18. Powers T., Noller H. F. A functional pseudoknot in 16S ribosomal RNA. EMBO J. 1991 Aug;10(8):2203–2214. doi: 10.1002/j.1460-2075.1991.tb07756.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ryan P. C., Draper D. E. Detection of a key tertiary interaction in the highly conserved GTPase center of large subunit ribosomal RNA. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6308–6312. doi: 10.1073/pnas.88.14.6308. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. Schüler D., Brimacombe R. The Escherichia coli 30S ribosomal subunit; an optimized three-dimensional fit between the ribosomal proteins and the 16S RNA. EMBO J. 1988 May;7(5):1509–1513. doi: 10.1002/j.1460-2075.1988.tb02970.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Sigmund C. D., Ettayebi M., Borden A., Morgan E. A. Antibiotic resistance mutations in ribosomal RNA genes of Escherichia coli. Methods Enzymol. 1988;164:673–690. doi: 10.1016/s0076-6879(88)64077-8. [DOI] [PubMed] [Google Scholar]
  23. Sigmund C. D., Ettayebi M., Morgan E. A. Antibiotic resistance mutations in 16S and 23S ribosomal RNA genes of Escherichia coli. Nucleic Acids Res. 1984 Jun 11;12(11):4653–4663. doi: 10.1093/nar/12.11.4653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Stern S., Weiser B., Noller H. F. Model for the three-dimensional folding of 16 S ribosomal RNA. J Mol Biol. 1988 Nov 20;204(2):447–481. doi: 10.1016/0022-2836(88)90588-8. [DOI] [PubMed] [Google Scholar]
  25. Tapprich W. E., Dahlberg A. E. A single base mutation at position 2661 in E. coli 23S ribosomal RNA affects the binding of ternary complex to the ribosome. EMBO J. 1990 Aug;9(8):2649–2655. doi: 10.1002/j.1460-2075.1990.tb07447.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Thompson J., Cundliffe E., Dahlberg A. E. Site-directed mutagenesis of Escherichia coli 23 S ribosomal RNA at position 1067 within the GTP hydrolysis centre. J Mol Biol. 1988 Sep 20;203(2):457–465. doi: 10.1016/0022-2836(88)90012-5. [DOI] [PubMed] [Google Scholar]
  27. Woese C. R., Gutell R. R. Evidence for several higher order structural elements in ribosomal RNA. Proc Natl Acad Sci U S A. 1989 May;86(9):3119–3122. doi: 10.1073/pnas.86.9.3119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Woese C. R., Winker S., Gutell R. R. Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops". Proc Natl Acad Sci U S A. 1990 Nov;87(21):8467–8471. doi: 10.1073/pnas.87.21.8467. [DOI] [PMC free article] [PubMed] [Google Scholar]

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