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. 1999 Aug 1;27(15):3071–3078. doi: 10.1093/nar/27.15.3071

Structural equivalence in the transcribed spacers of pre-rRNA transcripts in Schizosaccharomyces pombe.

A I Lalev 1, R N Nazar 1
PMCID: PMC148532  PMID: 10454602

Abstract

The structure of the internal transcribed spacer 2 (ITS2) in Schizosaccharomyces pombe was re-evaluated with respect to phylogenetically conserved features in yeasts, features in other transcribed spacer regions as well as the binding of transacting factors which potentially play a role in ribosomal maturation. Computer analyses and probes for nuclease protection indicate a very simple core structure consisting of a single extended hairpin which includes the interacting termini of the mature 5.8S and 25S rRNAs. Comparisons with ITS2 sequences in greatly diverging organisms indicate that the same feature also can be recognized. This is especially clear in organisms that contain very short sequences in which the putative structures are much less ambiguous. Diversity between organisms is the result of changes in hairpin length as well as the addition of branched helices. Protein binding and gel retardation studies with the S.pombe ITS2 further indicate that, as observed in the 3" external transcribed spacer (ETS) and ITS1 regions, the extended hairpin is not only the site of intermediate RNA cleavage during rRNA processing but also a site for specific interactions with one or more soluble factors. Taken together with other analyses on transcribed spacer regions, the present data suggest that the spacer regions all may act in a similar fashion, not only to organize the maturing terminal sequences, but also serve to organize specific soluble factors possibly acting with snoRNAs or in a manner which is analogous with that of the free snoRNPs.

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Selected References

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  1. Bachellerie J. P., Cavaillé J. Guiding ribose methylation of rRNA. Trends Biochem Sci. 1997 Jul;22(7):257–261. doi: 10.1016/s0968-0004(97)01057-8. [DOI] [PubMed] [Google Scholar]
  2. Borsuk P., Gniadkowski M., Kucharski R., Bisko M., Kanabus M., Stepień P. P., Bartnik E. Evolutionary conservation of the transcribed spacer sequences of the rDNA repeat unit in three species of the genus Aspergillus. Acta Biochim Pol. 1994;41(1):73–77. [PubMed] [Google Scholar]
  3. Chaconas G., van de Sande J. H. 5'-32P labeling of RNA and DNA restriction fragments. Methods Enzymol. 1980;65(1):75–85. doi: 10.1016/s0076-6879(80)65012-5. [DOI] [PubMed] [Google Scholar]
  4. Enright C. A., Maxwell E. S., Eliceiri G. L., Sollner-Webb B. 5'ETS rRNA processing facilitated by four small RNAs: U14, E3, U17, and U3. RNA. 1996 Nov;2(11):1094–1099. [PMC free article] [PubMed] [Google Scholar]
  5. Gonzalez I. L., Chambers C., Gorski J. L., Stambolian D., Schmickel R. D., Sylvester J. E. Sequence and structure correlation of human ribosomal transcribed spacers. J Mol Biol. 1990 Mar 5;212(1):27–35. doi: 10.1016/0022-2836(90)90302-3. [DOI] [PubMed] [Google Scholar]
  6. Good L., Intine R. V., Nazar R. N. Interdependence in the processing of ribosomal RNAs in Schizosaccharomyces pombe. J Mol Biol. 1997 Nov 7;273(4):782–788. doi: 10.1006/jmbi.1997.1351. [DOI] [PubMed] [Google Scholar]
  7. Good L., Intine R. V., Nazar R. N. The ribosomal-RNA-processing pathway in Schizosaccharomyces pombe. Eur J Biochem. 1997 Jul 1;247(1):314–321. doi: 10.1111/j.1432-1033.1997.00314.x. [DOI] [PubMed] [Google Scholar]
  8. Gutell R. R., Fox G. E. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 1988;16 (Suppl):r175–r269. doi: 10.1093/nar/16.suppl.r175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hitchen J., Ivakine E., Melekhovets Y. F., Lalev A., Nazar R. N. Structural features in the 3' external transcribed spacer affecting intragenic processing of yeast rRNA. J Mol Biol. 1997 Dec 12;274(4):481–490. doi: 10.1006/jmbi.1997.1376. [DOI] [PubMed] [Google Scholar]
  10. Jazwinski S. M. Preparation of extracts from yeast. Methods Enzymol. 1990;182:154–174. doi: 10.1016/0076-6879(90)82015-t. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Katiyar S. K., Visvesvara G. S., Edlind T. D. Comparisons of ribosomal RNA sequences from amitochondrial protozoa: implications for processing, mRNA binding and paromomycin susceptibility. Gene. 1995 Jan 11;152(1):27–33. doi: 10.1016/0378-1119(94)00677-k. [DOI] [PubMed] [Google Scholar]
  13. Lalev A. I., Nazar R. N. Conserved core structure in the internal transcribed spacer 1 of the Schizosaccharomyces pombe precursor ribosomal RNA. J Mol Biol. 1998 Dec 18;284(5):1341–1351. doi: 10.1006/jmbi.1998.2222. [DOI] [PubMed] [Google Scholar]
  14. Lee Y., Melekhovets Y. F., Nazar R. N. Termination as a factor in "quality control" during ribosome biogenesis. J Biol Chem. 1995 Nov 24;270(47):28003–28005. doi: 10.1074/jbc.270.47.28003. [DOI] [PubMed] [Google Scholar]
  15. Lee Y., Nazar R. N. Ribosomal 5 S rRNA maturation in Saccharomyces cerevisiae. J Biol Chem. 1997 Jun 13;272(24):15206–15212. doi: 10.1074/jbc.272.24.15206. [DOI] [PubMed] [Google Scholar]
  16. Liang W. Q., Fournier M. J. Synthesis of functional eukaryotic ribosomal RNAs in trans: development of a novel in vivo rDNA system for dissecting ribosome biogenesis. Proc Natl Acad Sci U S A. 1997 Apr 1;94(7):2864–2868. doi: 10.1073/pnas.94.7.2864. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lott T. J., Burns B. M., Zancope-Oliveira R., Elie C. M., Reiss E. Sequence analysis of the internal transcribed spacer 2 (ITS2) from yeast species within the genus Candida. Curr Microbiol. 1998 Feb;36(2):63–69. doi: 10.1007/s002849900280. [DOI] [PubMed] [Google Scholar]
  18. Melekhovets Y. F., Good L., Elela S. A., Nazar R. N. Intragenic processing in yeast rRNA is dependent on the 3' external transcribed spacer. J Mol Biol. 1994 Jun 3;239(2):170–180. doi: 10.1006/jmbi.1994.1361. [DOI] [PubMed] [Google Scholar]
  19. Melton D. A., Krieg P. A., Rebagliati M. R., Maniatis T., Zinn K., Green M. R. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 1984 Sep 25;12(18):7035–7056. doi: 10.1093/nar/12.18.7035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Miller O. L., Jr, Beatty B. R. Visualization of nucleolar genes. Science. 1969 May 23;164(3882):955–957. doi: 10.1126/science.164.3882.955. [DOI] [PubMed] [Google Scholar]
  21. Morrissey J. P., Tollervey D. Birth of the snoRNPs: the evolution of RNase MRP and the eukaryotic pre-rRNA-processing system. Trends Biochem Sci. 1995 Feb;20(2):78–82. doi: 10.1016/s0968-0004(00)88962-8. [DOI] [PubMed] [Google Scholar]
  22. Musters W., Boon K., van der Sande C. A., van Heerikhuizen H., Planta R. J. Functional analysis of transcribed spacers of yeast ribosomal DNA. EMBO J. 1990 Dec;9(12):3989–3996. doi: 10.1002/j.1460-2075.1990.tb07620.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Nazar R. N. A 5.8 S rRNA-like sequence in prokaryotic 23 S rRNA. FEBS Lett. 1980 Oct 6;119(2):212–214. doi: 10.1016/0014-5793(80)80254-7. [DOI] [PubMed] [Google Scholar]
  24. Nazar R. N. Evolutionary relationship between eukaryotic 29--32 S nucleolar rRNA precursors and the prokaryotic 23 S rRNA. FEBS Lett. 1982 Jul 5;143(2):161–162. doi: 10.1016/0014-5793(82)80089-6. [DOI] [PubMed] [Google Scholar]
  25. Nazar R. N., Sitz T. O. Role of the 5'-terminal sequence in the RNA binding site of yeast 5.8 S rRNA. FEBS Lett. 1980 Jun 16;115(1):71–76. doi: 10.1016/0014-5793(80)80729-0. [DOI] [PubMed] [Google Scholar]
  26. Nazar R. N., Wong W. M., Abrahamson J. L. Nucleotide sequence of the 18-25 S ribosomal RNA intergenic region from a thermophile, Thermomyces lanuginosus. J Biol Chem. 1987 Jun 5;262(16):7523–7527. [PubMed] [Google Scholar]
  27. Ni J., Tien A. L., Fournier M. J. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell. 1997 May 16;89(4):565–573. doi: 10.1016/s0092-8674(00)80238-x. [DOI] [PubMed] [Google Scholar]
  28. Peattie D. A. Direct chemical method for sequencing RNA. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1760–1764. doi: 10.1073/pnas.76.4.1760. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Raué H. A., Planta R. J. Ribosome biogenesis in yeast. Prog Nucleic Acid Res Mol Biol. 1991;41:89–129. doi: 10.1016/s0079-6603(08)60007-0. [DOI] [PubMed] [Google Scholar]
  30. Raué H. A., Planta R. J. The pathway to maturity: processing of ribosomal RNA in Saccharomyces cerevisiae. Gene Expr. 1995;5(1):71–77. [PMC free article] [PubMed] [Google Scholar]
  31. Van Ryk D. I., Nazar R. N. Effect of sequence mutations on the higher order structure of the yeast 5 S rRNA. J Mol Biol. 1992 Aug 20;226(4):1027–1035. doi: 10.1016/0022-2836(92)91050-y. [DOI] [PubMed] [Google Scholar]
  32. Veldman G. M., Klootwijk J., van Heerikhuizen H., Planta R. J. The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript. Nucleic Acids Res. 1981 Oct 10;9(19):4847–4862. doi: 10.1093/nar/9.19.4847. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Venema J., Henry Y., Tollervey D. Two distinct recognition signals define the site of endonucleolytic cleavage at the 5'-end of yeast 18S rRNA. EMBO J. 1995 Oct 2;14(19):4883–4892. doi: 10.1002/j.1460-2075.1995.tb00169.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Walker T. A., Johnson K. D., Olsen G. J., Peters M. A., Pace N. R. Enzymatic and chemical structure mapping of mouse 28S ribosomal ribonucleic acid contacts in 5.8S ribosomal ribonucleic acid. Biochemistry. 1982 May 11;21(10):2320–2329. doi: 10.1021/bi00539a008. [DOI] [PubMed] [Google Scholar]
  35. Walter A. E., Turner D. H., Kim J., Lyttle M. H., Müller P., Mathews D. H., Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9218–9222. doi: 10.1073/pnas.91.20.9218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Yeh L. C., Lee J. C. Structural analysis of the internal transcribed spacer 2 of the precursor ribosomal RNA from Saccharomyces cerevisiae. J Mol Biol. 1990 Feb 20;211(4):699–712. doi: 10.1016/0022-2836(90)90071-S. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. 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]
  39. van der Sande C. A., Kwa M., van Nues R. W., van Heerikhuizen H., Raué H. A., Planta R. J. Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA. J Mol Biol. 1992 Feb 20;223(4):899–910. doi: 10.1016/0022-2836(92)90251-e. [DOI] [PubMed] [Google Scholar]

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