Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1991 Jan 25;19(2):227–235. doi: 10.1093/nar/19.2.227

An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA.

D L Nickrent 1, M L Sargent 1
PMCID: PMC333584  PMID: 2014163

Abstract

The V4 region of the small subunit (18S) ribosomal RNA was examined in 72 different sequences representing a broad sample eukaryotic diversity. This domain is the most variable region of the 18S rRNA molecule and ranges in length from ca. 230 to over 500 bases. Based upon comparative analysis, secondary structural models were constructed for all sequences and the resulting generalized model shows that most organisms possess seven helices for this region. The protists and two insects show from one to as many as four helices in addition to the above seven. In this report, we summarize secondary structure information presented elsewhere for the V4 region, describe the general features for helical and apical regions, and identify signature sequences useful in helix identification. Our model generally agrees with other current concepts; however, we propose modifications or alternative structures for the start of the V4 region, the large protist inserts, and the sector that may possibly contain a pseudoknot.

Full text

PDF
228

Selected References

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

  1. Atmadja J., Brimacombe R., Maden B. E. Xenopus laevis 18S ribosomal RNA: experimental determination of secondary structural elements, and locations of methyl groups in the secondary structure model. Nucleic Acids Res. 1984 Mar 26;12(6):2649–2667. doi: 10.1093/nar/12.6.2649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Cedergren R., Gray M. W., Abel Y., Sankoff D. The evolutionary relationships among known life forms. J Mol Evol. 1988 Dec;28(1-2):98–112. doi: 10.1007/BF02143501. [DOI] [PubMed] [Google Scholar]
  3. Dams E., Hendriks L., Van de Peer Y., Neefs J. M., Smits G., Vandenbempt I., De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1988;16 (Suppl):r87–173. doi: 10.1093/nar/16.suppl.r87. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Ellis R. E., Sulston J. E., Coulson A. R. The rDNA of C. elegans: sequence and structure. Nucleic Acids Res. 1986 Mar 11;14(5):2345–2364. doi: 10.1093/nar/14.5.2345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Field K. G., Olsen G. J., Lane D. J., Giovannoni S. J., Ghiselin M. T., Raff E. C., Pace N. R., Raff R. A. Molecular phylogeny of the animal kingdom. Science. 1988 Feb 12;239(4841 Pt 1):748–753. doi: 10.1126/science.3277277. [DOI] [PubMed] [Google Scholar]
  6. Gonzalez I. L., Schmickel R. D. The human 18S ribosomal RNA gene: evolution and stability. Am J Hum Genet. 1986 Apr;38(4):419–427. [PMC free article] [PubMed] [Google Scholar]
  7. Gutell R. R., Weiser B., Woese C. R., Noller H. F. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. doi: 10.1016/s0079-6603(08)60348-7. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Haselman T., Camp D. G., Fox G. E. Phylogenetic evidence for tertiary interactions in 16S-like ribosomal RNA. Nucleic Acids Res. 1989 Mar 25;17(6):2215–2221. doi: 10.1093/nar/17.6.2215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hedges S. B., Moberg K. D., Maxson L. R. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. Mol Biol Evol. 1990 Nov;7(6):607–633. doi: 10.1093/oxfordjournals.molbev.a040628. [DOI] [PubMed] [Google Scholar]
  11. Hendriks L., De Baere R., Van Broeckhoven C., De Wachter R. Primary and secondary structure of the 18 S ribosomal RNA of the insect species Tenebrio molitor. FEBS Lett. 1988 May 9;232(1):115–120. doi: 10.1016/0014-5793(88)80398-3. [DOI] [PubMed] [Google Scholar]
  12. Herzog M., Maroteaux L. Dinoflagellate 17S rRNA sequence inferred from the gene sequence: Evolutionary implications. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8644–8648. doi: 10.1073/pnas.83.22.8644. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Neefs J. M., De Wachter R. A proposal for the secondary structure of a variable area of eukaryotic small ribosomal subunit RNA involving the existence of a pseudoknot. Nucleic Acids Res. 1990 Oct 11;18(19):5695–5704. doi: 10.1093/nar/18.19.5695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Neefs J. M., Van de Peer Y., Hendriks L., De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1990 Apr 25;18 (Suppl):2237–2317. doi: 10.1093/nar/18.suppl.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Nelles L., Fang B. L., Volckaert G., Vandenberghe A., De Wachter R. Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs. Nucleic Acids Res. 1984 Dec 11;12(23):8749–8768. doi: 10.1093/nar/12.23.8749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nickrent D. L., Franchina C. R. Phylogenetic relationships of the Santalales and relatives. J Mol Evol. 1990 Oct;31(4):294–301. doi: 10.1007/BF02101124. [DOI] [PubMed] [Google Scholar]
  17. Olsen G. J., McCarroll R., Sogin M. L. Secondary structure of the Dictyostelium discoideum small subunit ribosomal RNA. Nucleic Acids Res. 1983 Nov 25;11(22):8037–8049. doi: 10.1093/nar/11.22.8037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Olsen G. J. Phylogenetic analysis using ribosomal RNA. Methods Enzymol. 1988;164:793–812. doi: 10.1016/s0076-6879(88)64084-5. [DOI] [PubMed] [Google Scholar]
  19. Sogin M. L., Gunderson J. H., Elwood H. J., Alonso R. A., Peattie D. A. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science. 1989 Jan 6;243(4887):75–77. doi: 10.1126/science.2911720. [DOI] [PubMed] [Google Scholar]
  20. Tautz D., Hancock J. M., Webb D. A., Tautz C., Dover G. A. Complete sequences of the rRNA genes of Drosophila melanogaster. Mol Biol Evol. 1988 Jul;5(4):366–376. doi: 10.1093/oxfordjournals.molbev.a040500. [DOI] [PubMed] [Google Scholar]
  21. Vossbrinck C. R., Maddox J. V., Friedman S., Debrunner-Vossbrinck B. A., Woese C. R. Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. 1987 Mar 26-Apr 1Nature. 326(6111):411–414. doi: 10.1038/326411a0. [DOI] [PubMed] [Google Scholar]
  22. Waters A. P., McCutchan T. F. Partial sequence of the asexually expressed SU rRNA gene of Plasmodium vivax. Nucleic Acids Res. 1989 Mar 11;17(5):2135–2135. doi: 10.1093/nar/17.5.2135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Waugh D. S., Green C. J., Pace N. R. The design and catalytic properties of a simplified ribonuclease P RNA. Science. 1989 Jun 30;244(4912):1569–1571. doi: 10.1126/science.2472671. [DOI] [PubMed] [Google Scholar]
  24. Wheeler W. C., Honeycutt R. L. Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol Biol Evol. 1988 Jan;5(1):90–96. doi: 10.1093/oxfordjournals.molbev.a040480. [DOI] [PubMed] [Google Scholar]
  25. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Woese C. R., Magrum L. J., Gupta R., Siegel R. B., Stahl D. A., Kop J., Crawford N., Brosius J., Gutell R., Hogan J. J. Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res. 1980 May 24;8(10):2275–2293. doi: 10.1093/nar/8.10.2275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. doi: 10.1093/nar/9.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Zwieb C., Glotz C., Brimacombe R. Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species. Nucleic Acids Res. 1981 Aug 11;9(15):3621–3640. doi: 10.1093/nar/9.15.3621. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES