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. 2002 Jun;8(6):786–797. doi: 10.1017/s1355838202023063

Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast.

Colette A Côté 1, Chris L Greer 1, Brenda A Peculis 1
PMCID: PMC1370297  PMID: 12088151

Abstract

Maturation of the large subunit rRNAs includes a series of cleavages that result in removal of the internal transcribed spacer (ITS2) that separates mature 5.8S and 25/28S rRNAs. Previous work demonstrated that formation of higher order secondary structure within the assembling pre-ribosomal particle is a prerequisite for accurate and efficient pre-rRNA processing. To date, it is not clear which specific sequences or secondary structures are required for processing. Two alternative secondary structure models exist for Saccharomyces cerevisiae ITS2. Chemical and enzymatic structure probing and phylogenetic comparisons resulted in one structure (Yeh & Lee, J Mol Biol, 1990, 211:699-712) referred to here as the "hairpin model." More recently, an alternate folded structure was proposed (Joseph et al., Nucleic Acids Res, 1999, 27:4533-4540), called here the "ring model." We have used a functional genetic assay to examine the potential significance of these predicted structures in processing. Our data indicate that elements of both structural models are important in efficient processing. Mutations that prevent formation of ring-specific structures completely blocked production of mature 25S rRNA, whereas those that primarily disrupt hairpin elements resulted in reduced levels of mature product. Based on these results, we propose a dynamic conformational model for the role of ITS2 in processing: Initial formation of the ring structure may be required for essential, early events in processing complex assembly and may be followed by an induced transition to the hairpin structure that facilitates subsequent processing events. In this model, yeast ITS2 elements may provide in cis certain of the functions proposed for vertebrate U8 snoRNA acting in trans.

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Selected References

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  1. Bakker F. T., Olsen J. L., Stam W. T. Evolution of nuclear rDNA ITS sequences in the Cladophora albida/sericea clade (Chlorophyta). J Mol Evol. 1995 Jun;40(6):640–651. doi: 10.1007/BF00160512. [DOI] [PubMed] [Google Scholar]
  2. Chilton N. B., Hoste H., Newton L. A., Beveridge I., Gasser R. B. Common secondary structures for the second internal transcribed spacer pre-rRNA of two subfamilies of trichostrongylid nematodes. Int J Parasitol. 1998 Nov;28(11):1765–1773. doi: 10.1016/s0020-7519(98)00129-5. [DOI] [PubMed] [Google Scholar]
  3. Côté C. A., Peculis B. A. Role of the ITS2-proximal stem and evidence for indirect recognition of processing sites in pre-rRNA processing in yeast. Nucleic Acids Res. 2001 May 15;29(10):2106–2116. doi: 10.1093/nar/29.10.2106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Fritz G. N., Conn J., Cockburn A., Seawright J. Sequence analysis of the ribosomal DNA internal transcribed spacer 2 from populations of Anopheles nuneztovari (Diptera: Culicidae). Mol Biol Evol. 1994 May;11(3):406–416. doi: 10.1093/oxfordjournals.molbev.a040122. [DOI] [PubMed] [Google Scholar]
  5. Geerlings T. H., Vos J. C., Raué H. A. The final step in the formation of 25S rRNA in Saccharomyces cerevisiae is performed by 5'-->3' exonucleases. RNA. 2000 Dec;6(12):1698–1703. doi: 10.1017/s1355838200001540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hershkovitz M. A., Zimmer E. A. Conservation patterns in angiosperm rDNA ITS2 sequences. Nucleic Acids Res. 1996 Aug 1;24(15):2857–2867. doi: 10.1093/nar/24.15.2857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hung G. C., Chilton N. B., Beveridge I., Gasser R. B. Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference. Int J Parasitol. 1999 Dec;29(12):1949–1964. doi: 10.1016/s0020-7519(99)00155-1. [DOI] [PubMed] [Google Scholar]
  8. Joseph N., Krauskopf E., Vera M. I., Michot B. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Res. 1999 Dec 1;27(23):4533–4540. doi: 10.1093/nar/27.23.4533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Joseph N., Krauskopf E., Vera M. I., Michot B. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Res. 1999 Dec 1;27(23):4533–4540. doi: 10.1093/nar/27.23.4533. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kressler D., Linder P., de La Cruz J. Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol. 1999 Dec;19(12):7897–7912. doi: 10.1128/mcb.19.12.7897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Michot B., Bachellerie J. P., Raynal F. Structure of mouse rRNA precursors. Complete sequence and potential folding of the spacer regions between 18S and 28S rRNA. Nucleic Acids Res. 1983 May 25;11(10):3375–3391. doi: 10.1093/nar/11.10.3375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Mitchell P., Petfalski E., Shevchenko A., Mann M., Tollervey D. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. Cell. 1997 Nov 14;91(4):457–466. doi: 10.1016/s0092-8674(00)80432-8. [DOI] [PubMed] [Google Scholar]
  14. Mitchell P., Petfalski E., Tollervey D. The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. Genes Dev. 1996 Feb 15;10(4):502–513. doi: 10.1101/gad.10.4.502. [DOI] [PubMed] [Google Scholar]
  15. Morgan J. A., Blair D. Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model. J Mol Evol. 1998 Oct;47(4):406–419. doi: 10.1007/pl00006398. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Nogi Y., Vu L., Nomura M. An approach for isolation of mutants defective in 35S ribosomal RNA synthesis in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7026–7030. doi: 10.1073/pnas.88.16.7026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Nogi Y., Yano R., Dodd J., Carles C., Nomura M. Gene RRN4 in Saccharomyces cerevisiae encodes the A12.2 subunit of RNA polymerase I and is essential only at high temperatures. Mol Cell Biol. 1993 Jan;13(1):114–122. doi: 10.1128/mcb.13.1.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Nogi Y., Yano R., Nomura M. Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I. Proc Natl Acad Sci U S A. 1991 May 1;88(9):3962–3966. doi: 10.1073/pnas.88.9.3962. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Peculis B. A., Greer C. L. The structure of the ITS2-proximal stem is required for pre-rRNA processing in yeast. RNA. 1998 Dec;4(12):1610–1622. doi: 10.1017/s1355838298981420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Peculis B. A. The sequence of the 5' end of the U8 small nucleolar RNA is critical for 5.8S and 28S rRNA maturation. Mol Cell Biol. 1997 Jul;17(7):3702–3713. doi: 10.1128/mcb.17.7.3702. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Venema J., Tollervey D. Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet. 1999;33:261–311. doi: 10.1146/annurev.genet.33.1.261. [DOI] [PubMed] [Google Scholar]
  23. Wesson D. M., Porter C. H., Collins F. H. Sequence and secondary structure comparisons of ITS rDNA in mosquitoes (Diptera: Culicidae). Mol Phylogenet Evol. 1992 Dec;1(4):253–269. doi: 10.1016/1055-7903(92)90001-w. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. 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]
  26. van Hoof A., Lennertz P., Parker R. Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast. EMBO J. 2000 Mar 15;19(6):1357–1365. doi: 10.1093/emboj/19.6.1357. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. 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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