Skip to main content
NCBI home page
RNA logoLink to RNA
. 1996 Feb;2(2):183–197.

The yeast Hansenula wingei U3 snoRNA gene contains an intron and its coding sequence co-evolved with the 5' ETS region of the pre-ribosomal RNA.

F Brulé 1, J Venema 1, V Ségault 1, D Tollervey 1, C Branlant 1
PMCID: PMC1369362  PMID: 8601284

Abstract

The 5' external transcribed spacer (ETS) region of the pre-rRNA in Saccharomyces cerevisiae contains a sequence with 10 bp of perfect complementarity to the U3 snoRNA. Base pairing between these sequences has been shown to be required for 18S rRNA synthesis, although interaction over the full 10 bp of complementarity is not required. We have identified the homologous sequence in the 5' ETS from the evolutionarily distant yeast Hansenula wingei; unexpectedly, this shows two sequence changes in the region predicted to base pair to U3. By PCR amplification and direct RNA sequencing, a single type of U3 snoRNA coding sequence was identified in H. wingei. As in the S. cerevisiae U3 snoRNA genes, it is interrupted by an intron with features characteristic of introns spliced in a spliceosome. Consequently, this unusual property is not restricted to the yeast genus Saccharomyces. The introns of the H. wingei and S. cerevisiae U3 genes show strong differences in length and sequence, but are located at the same position in the U3 sequence, immediately upstream of the phylogenetically conserved Box A region. The 3' domains of the H. wingei and S. cerevisiae U3 snoRNAs diverge strongly in primary sequence, but have very similar predicted secondary structures. The 5' domains, expected to play a direct role in pre-ribosomal RNA maturation, are more conserved. The sequence predicted to base pair to the pre-rRNA contains two nucleotide substitutions in H. wingei that restore 10 bp of perfect complementarity to the 5' ETS. This is a strong phylogenetic evidence for the importance of the U3/pre-rRNA interaction.

Full Text

The Full Text of this article is available as a PDF (3.1 MB).

Selected References

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

  1. Bachellerie J. P., Michot B., Raynal F. Recognition signals for mouse pre-rRNA processing. A potential role for U3 nucleolar RNA. Mol Biol Rep. 1983 May;9(1-2):79–86. doi: 10.1007/BF00777477. [DOI] [PubMed] [Google Scholar]
  2. Barton G. J. ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 1993 Jan;6(1):37–40. doi: 10.1093/protein/6.1.37. [DOI] [PubMed] [Google Scholar]
  3. Bayev A. A., Georgiev O. I., Hadjiolov A. A., Kermekchiev M. B., Nikolaev N., Skryabin K. G., Zakharyev V. M. The structure of the yeast ribosomal RNA genes. 2. The nucleotide sequence of the initiation site for ribosomal RNA transcription. Nucleic Acids Res. 1980 Nov 11;8(21):4919–4926. doi: 10.1093/nar/8.21.4919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beltrame M., Henry Y., Tollervey D. Mutational analysis of an essential binding site for the U3 snoRNA in the 5' external transcribed spacer of yeast pre-rRNA. Nucleic Acids Res. 1994 Oct 11;22(20):4057–4065. doi: 10.1093/nar/22.20.4057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Beltrame M., Tollervey D. Identification and functional analysis of two U3 binding sites on yeast pre-ribosomal RNA. EMBO J. 1992 Apr;11(4):1531–1542. doi: 10.1002/j.1460-2075.1992.tb05198.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Branlant C., Krol A., Machatt M. A., Pouyet J., Ebel J. P., Edwards K., Kössel H. Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs. Nucleic Acids Res. 1981 Sep 11;9(17):4303–4324. doi: 10.1093/nar/9.17.4303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brimacombe R., Mitchell P., Osswald M., Stade K., Bochkariov D. Clustering of modified nucleotides at the functional center of bacterial ribosomal RNA. FASEB J. 1993 Jan;7(1):161–167. doi: 10.1096/fasebj.7.1.8422963. [DOI] [PubMed] [Google Scholar]
  8. Brow D. A., Guthrie C. Splicing a spliceosomal RNA. Nature. 1989 Jan 5;337(6202):14–15. doi: 10.1038/337014a0. [DOI] [PubMed] [Google Scholar]
  9. Calvet J. P., Pederson T. Base-pairing interactions between small nuclear RNAs and nuclear RNA precursors as revealed by psoralen cross-linking in vivo. Cell. 1981 Nov;26(3 Pt 1):363–370. doi: 10.1016/0092-8674(81)90205-1. [DOI] [PubMed] [Google Scholar]
  10. Craig N., Kass S., Sollner-Webb B. Nucleotide sequence determining the first cleavage site in the processing of mouse precursor rRNA. Proc Natl Acad Sci U S A. 1987 Feb;84(3):629–633. doi: 10.1073/pnas.84.3.629. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Crouch R. J., Kanaya S., Earl P. L. A model for the involvement of the small nucleolar RNA (U3) in processing eukaryotic ribosomal RNA. Mol Biol Rep. 1983 May;9(1-2):75–78. doi: 10.1007/BF00777476. [DOI] [PubMed] [Google Scholar]
  12. Eichler D. C., Craig N. Processing of eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1994;49:197–239. doi: 10.1016/s0079-6603(08)60051-3. [DOI] [PubMed] [Google Scholar]
  13. Epstein P., Reddy R., Busch H. Multiple states of U3 RNA in Novikoff hepatoma nucleoli. Biochemistry. 1984 Nov 6;23(23):5421–5425. doi: 10.1021/bi00318a007. [DOI] [PubMed] [Google Scholar]
  14. Filipowicz W., Kiss T. Structure and function of nucleolar snRNPs. Mol Biol Rep. 1993 Aug;18(2):149–156. doi: 10.1007/BF00986770. [DOI] [PubMed] [Google Scholar]
  15. Fournier M. J., Maxwell E. S. The nucleolar snRNAs: catching up with the spliceosomal snRNAs. Trends Biochem Sci. 1993 Apr;18(4):131–135. doi: 10.1016/0968-0004(93)90020-n. [DOI] [PubMed] [Google Scholar]
  16. Frendewey D., Barta I., Gillespie M., Potashkin J. Schizosaccharomyces U6 genes have a sequence within their introns that matches the B box consensus of tRNA internal promoters. Nucleic Acids Res. 1990 Apr 25;18(8):2025–2032. doi: 10.1093/nar/18.8.2025. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hughes J. M., Ares M., Jr Depletion of U3 small nucleolar RNA inhibits cleavage in the 5' external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J. 1991 Dec;10(13):4231–4239. doi: 10.1002/j.1460-2075.1991.tb05001.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hughes J. M., Konings D. A., Cesareni G. The yeast homologue of U3 snRNA. EMBO J. 1987 Jul;6(7):2145–2155. doi: 10.1002/j.1460-2075.1987.tb02482.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kass S., Tyc K., Steitz J. A., Sollner-Webb B. The U3 small nucleolar ribonucleoprotein functions in the first step of preribosomal RNA processing. Cell. 1990 Mar 23;60(6):897–908. doi: 10.1016/0092-8674(90)90338-f. [DOI] [PubMed] [Google Scholar]
  20. Lacroute F. Regulation of pyrimidine biosynthesis in Saccharomyces cerevisiae. J Bacteriol. 1968 Mar;95(3):824–832. doi: 10.1128/jb.95.3.824-832.1968. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Li H. D., Zagorski J., Fournier M. J. Depletion of U14 small nuclear RNA (snR128) disrupts production of 18S rRNA in Saccharomyces cerevisiae. Mol Cell Biol. 1990 Mar;10(3):1145–1152. doi: 10.1128/mcb.10.3.1145-1152.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lygerou Z., Mitchell P., Petfalski E., Séraphin B., Tollervey D. The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins. Genes Dev. 1994 Jun 15;8(12):1423–1433. doi: 10.1101/gad.8.12.1423. [DOI] [PubMed] [Google Scholar]
  23. Madhani H. D., Guthrie C. Dynamic RNA-RNA interactions in the spliceosome. Annu Rev Genet. 1994;28:1–26. doi: 10.1146/annurev.ge.28.120194.000245. [DOI] [PubMed] [Google Scholar]
  24. Maser R. L., Calvet J. P. U3 small nuclear RNA can be psoralen-cross-linked in vivo to the 5' external transcribed spacer of pre-ribosomal-RNA. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6523–6527. doi: 10.1073/pnas.86.17.6523. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mougey E. B., O'Reilly M., Osheim Y., Miller O. L., Jr, Beyer A., Sollner-Webb B. The terminal balls characteristic of eukaryotic rRNA transcription units in chromatin spreads are rRNA processing complexes. Genes Dev. 1993 Aug;7(8):1609–1619. doi: 10.1101/gad.7.8.1609. [DOI] [PubMed] [Google Scholar]
  26. Myslinski E., Ségault V., Branlant C. An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science. 1990 Mar 9;247(4947):1213–1216. doi: 10.1126/science.1690452. [DOI] [PubMed] [Google Scholar]
  27. Parker K. A., Steitz J. A. Structural analysis of the human U3 ribonucleoprotein particle reveal a conserved sequence available for base pairing with pre-rRNA. Mol Cell Biol. 1987 Aug;7(8):2899–2913. doi: 10.1128/mcb.7.8.2899-2913.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Peebles C. L., Gegenheimer P., Abelson J. Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease. Cell. 1983 Feb;32(2):525–536. doi: 10.1016/0092-8674(83)90472-5. [DOI] [PubMed] [Google Scholar]
  29. Petes T. D., Hereford L. M., Skryabin K. G. Characterization of two types of yeast ribosomal DNA genes. J Bacteriol. 1978 Apr;134(1):295–305. doi: 10.1128/jb.134.1.295-305.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Pikielny C. W., Teem J. L., Rosbash M. Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing. Cell. 1983 Sep;34(2):395–403. doi: 10.1016/0092-8674(83)90373-2. [DOI] [PubMed] [Google Scholar]
  31. Porter G. L., Brennwald P. J., Holm K. A., Wise J. A. The sequence of U3 from Schizosaccharomyces pombe suggests structural divergence of this snRNA between metazoans and unicellular eukaryotes. Nucleic Acids Res. 1988 Nov 11;16(21):10131–10152. doi: 10.1093/nar/16.21.10131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Qu H. L., Michot B., Bachellerie J. P. Improved methods for structure probing in large RNAs: a rapid 'heterologous' sequencing approach is coupled to the direct mapping of nuclease accessible sites. Application to the 5' terminal domain of eukaryotic 28S rRNA. Nucleic Acids Res. 1983 Sep 10;11(17):5903–5920. doi: 10.1093/nar/11.17.5903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Saffer L. D., Miller O. L., Jr Electron microscopic study of Saccharomyces cerevisiae rDNA chromatin replication. Mol Cell Biol. 1986 Apr;6(4):1148–1157. doi: 10.1128/mcb.6.4.1148-1157.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Skryabin K. G., Eldarov M. A., Larionov V. L., Bayev A. A., Klootwijk J., de Regt V. C., Veldman G. M., Planta R. J., Georgiev O. I., Hadjiolov A. A. Structure and function of the nontranscribed spacer regions of yeast rDNA. Nucleic Acids Res. 1984 Mar 26;12(6):2955–2968. doi: 10.1093/nar/12.6.2955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Stroke I. L., Weiner A. M. The 5' end of U3 snRNA can be crosslinked in vivo to the external transcribed spacer of rat ribosomal RNA precursors. J Mol Biol. 1989 Dec 5;210(3):497–512. doi: 10.1016/0022-2836(89)90126-5. [DOI] [PubMed] [Google Scholar]
  36. Ségault V., Mougin A., Grégoire A., Banroques J., Branlant C. An experimental study of Saccharomyces cerevisiae U3 snRNA conformation in solution. Nucleic Acids Res. 1992 Jul 11;20(13):3443–3451. doi: 10.1093/nar/20.13.3443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Tabor S., Richardson C. C. DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4767–4771. doi: 10.1073/pnas.84.14.4767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Tague B. W., Gerbi S. A. Processing of the large rRNA precursor: two proposed categories of RNA-RNA interactions in eukaryotes. J Mol Evol. 1984;20(3-4):362–367. doi: 10.1007/BF02104742. [DOI] [PubMed] [Google Scholar]
  39. Takahashi Y., Urushiyama S., Tani T., Ohshima Y. An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene. Mol Cell Biol. 1993 Sep;13(9):5613–5619. doi: 10.1128/mcb.13.9.5613-5619.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Tani T., Ohshima Y. The gene for the U6 small nuclear RNA in fission yeast has an intron. Nature. 1989 Jan 5;337(6202):87–90. doi: 10.1038/337087a0. [DOI] [PubMed] [Google Scholar]
  41. Tani T., Ohshima Y. mRNA-type introns in U6 small nuclear RNA genes: implications for the catalysis in pre-mRNA splicing. Genes Dev. 1991 Jun;5(6):1022–1031. doi: 10.1101/gad.5.6.1022. [DOI] [PubMed] [Google Scholar]
  42. Tiollais P., Galibert F., Boiron M. Evidence for the existence of several molecular species in the "45S fraction" of mammalian ribosomal precursor RNA. Proc Natl Acad Sci U S A. 1971 Jun;68(6):1117–1120. doi: 10.1073/pnas.68.6.1117. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Tollervey D. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J. 1987 Dec 20;6(13):4169–4175. doi: 10.1002/j.1460-2075.1987.tb02763.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Tollervey D., Lehtonen H., Carmo-Fonseca M., Hurt E. C. The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J. 1991 Mar;10(3):573–583. doi: 10.1002/j.1460-2075.1991.tb07984.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Tollervey D., Lehtonen H., Jansen R., Kern H., Hurt E. C. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell. 1993 Feb 12;72(3):443–457. doi: 10.1016/0092-8674(93)90120-f. [DOI] [PubMed] [Google Scholar]
  46. Tyc K., Steitz J. A. A new interaction between the mouse 5' external transcribed spacer of pre-rRNA and U3 snRNA detected by psoralen crosslinking. Nucleic Acids Res. 1992 Oct 25;20(20):5375–5382. doi: 10.1093/nar/20.20.5375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Verbeet M. P., van Heerikhuizen H., Klootwijk J., Fontijn R. D., Planta R. J. Evolution of yeast ribosomal DNA: molecular cloning of the rDNA units of Kluyveromyces lactis and Hansenula wingei and their comparison with the rDNA units of other Saccharomycetoideae. Mol Gen Genet. 1984;195(1-2):116–125. doi: 10.1007/BF00332733. [DOI] [PubMed] [Google Scholar]
  48. Yeh L. C., Lee J. C. Structure analysis of the 5' external transcribed spacer of the precursor ribosomal RNA from Saccharomyces cerevisiae. J Mol Biol. 1992 Dec 5;228(3):827–839. doi: 10.1016/0022-2836(92)90867-j. [DOI] [PubMed] [Google Scholar]
  49. Zieve G., Penman S. Small RNA species of the HeLa cell: metabolism and subcellular localization. Cell. 1976 May;8(1):19–31. doi: 10.1016/0092-8674(76)90181-1. [DOI] [PubMed] [Google Scholar]
  50. van Nues R. W., Rientjes J. M., Morré S. A., Mollee E., Planta R. J., Venema J., Raué H. A. Evolutionarily conserved structural elements are critical for processing of Internal Transcribed Spacer 2 from Saccharomyces cerevisiae precursor ribosomal RNA. J Mol Biol. 1995 Jun 30;250(1):24–36. doi: 10.1006/jmbi.1995.0355. [DOI] [PubMed] [Google Scholar]
  51. van Nues R. W., Rientjes J. M., van der Sande C. A., Zerp S. F., Sluiter C., Venema J., Planta R. J., Raué H. A. Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA. Nucleic Acids Res. 1994 Mar 25;22(6):912–919. doi: 10.1093/nar/22.6.912. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES