Skip to main content
PMC home page
RNA logoLink to RNA
. 2001 Sep;7(9):1254–1267. doi: 10.1017/s1355838201012079

Bms1p, a G-domain-containing protein, associates with Rcl1p and is required for 18S rRNA biogenesis in yeast.

T Wegierski 1, E Billy 1, F Nasr 1, W Filipowicz 1
PMCID: PMC1370170  PMID: 11565748

Abstract

Maturation of 18S rRNA and biogenesis of the 40S ribosomes in yeast requires a large number of trans-acting factors, including the U3 small nucleolar ribonucleoprotein (U3 snoRNP), and the recently characterized cyclase-like protein Rcl1p. U3 snoRNP is a key particle orchestrating early 35S rRNA cleavage events. A unique property of Rcl1p is that it specifically associates with U3 snoRNP, but this association appears to occur only at the level of nascent ribosomes and not with the U3 monoparticle. Here we report the characterization of Bms1p, a protein that associates with Rcl1p in multiple structures, including a specific complex sedimenting at around 10S. Like Rcl1p, Bms1p is an essential, evolutionarily conserved, nucleolar protein, and its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. The N-terminal domain of Bms1p has structural features found in regulatory GTPases and we demonstrate that mutations of amino acids implicated in GTP/GDP binding affect Bms1p activity in vivo. The results indicate that Bms1p may act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus.

Full Text

The Full Text of this article is available as a PDF (2.3 MB).

Selected References

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

  1. Aris J. P., Blobel G. Identification and characterization of a yeast nucleolar protein that is similar to a rat liver nucleolar protein. J Cell Biol. 1988 Jul;107(1):17–31. doi: 10.1083/jcb.107.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Barale J. C., Attal-Bonnefoy G., Brahimi K., Pereira da Silva L., Langsley G. Plasmodium falciparum asparagine and aspartate rich protein 2 is an evolutionary conserved protein whose repeats identify a new family of parasite antigens. Mol Biochem Parasitol. 1997 Aug;87(2):169–181. doi: 10.1016/s0166-6851(97)00065-0. [DOI] [PubMed] [Google Scholar]
  3. Baudin A., Ozier-Kalogeropoulos O., Denouel A., Lacroute F., Cullin C. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 1993 Jul 11;21(14):3329–3330. doi: 10.1093/nar/21.14.3329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beltrame M., Tollervey D. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J. 1995 Sep 1;14(17):4350–4356. doi: 10.1002/j.1460-2075.1995.tb00109.x. [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. Billy E., Wegierski T., Nasr F., Filipowicz W. Rcl1p, the yeast protein similar to the RNA 3'-phosphate cyclase, associates with U3 snoRNP and is required for 18S rRNA biogenesis. EMBO J. 2000 May 2;19(9):2115–2126. doi: 10.1093/emboj/19.9.2115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bonneaud N., Ozier-Kalogeropoulos O., Li G. Y., Labouesse M., Minvielle-Sebastia L., Lacroute F. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast. 1991 Aug-Sep;7(6):609–615. doi: 10.1002/yea.320070609. [DOI] [PubMed] [Google Scholar]
  8. Borovjagin A. V., Gerbi S. A. The spacing between functional Cis-elements of U3 snoRNA is critical for rRNA processing. J Mol Biol. 2000 Jun 30;300(1):57–74. doi: 10.1006/jmbi.2000.3798. [DOI] [PubMed] [Google Scholar]
  9. Bourne H. R., Sanders D. A., McCormick F. The GTPase superfamily: conserved structure and molecular mechanism. Nature. 1991 Jan 10;349(6305):117–127. doi: 10.1038/349117a0. [DOI] [PubMed] [Google Scholar]
  10. Colley A., Beggs J. D., Tollervey D., Lafontaine D. L. Dhr1p, a putative DEAH-box RNA helicase, is associated with the box C+D snoRNP U3. Mol Cell Biol. 2000 Oct;20(19):7238–7246. doi: 10.1128/mcb.20.19.7238-7246.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cosentino G. P., Schmelzle T., Haghighat A., Helliwell S. B., Hall M. N., Sonenberg N. Eap1p, a novel eukaryotic translation initiation factor 4E-associated protein in Saccharomyces cerevisiae. Mol Cell Biol. 2000 Jul;20(13):4604–4613. doi: 10.1128/mcb.20.13.4604-4613.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dunbar D. A., Wormsley S., Agentis T. M., Baserga S. J. Mpp10p, a U3 small nucleolar ribonucleoprotein component required for pre-18S rRNA processing in yeast. Mol Cell Biol. 1997 Oct;17(10):5803–5812. doi: 10.1128/mcb.17.10.5803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fabrizio P., Laggerbauer B., Lauber J., Lane W. S., Lührmann R. An evolutionarily conserved U5 snRNP-specific protein is a GTP-binding factor closely related to the ribosomal translocase EF-2. EMBO J. 1997 Jul 1;16(13):4092–4106. doi: 10.1093/emboj/16.13.4092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fu H., Subramanian R. R., Masters S. C. 14-3-3 proteins: structure, function, and regulation. Annu Rev Pharmacol Toxicol. 2000;40:617–647. doi: 10.1146/annurev.pharmtox.40.1.617. [DOI] [PubMed] [Google Scholar]
  15. Ganot P., Caizergues-Ferrer M., Kiss T. The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev. 1997 Apr 1;11(7):941–956. doi: 10.1101/gad.11.7.941. [DOI] [PubMed] [Google Scholar]
  16. Gelperin D., Horton L., Beckman J., Hensold J., Lemmon S. K. Bms1p, a novel GTP-binding protein, and the related Tsr1p are required for distinct steps of 40S ribosome biogenesis in yeast. RNA. 2001 Sep;7(9):1268–1283. doi: 10.1017/s1355838201013073. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hughes J. M. Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. J Mol Biol. 1996 Jun 21;259(4):645–654. doi: 10.1006/jmbi.1996.0346. [DOI] [PubMed] [Google Scholar]
  18. Jansen R., Tollervey D., Hurt E. C. A U3 snoRNP protein with homology to splicing factor PRP4 and G beta domains is required for ribosomal RNA processing. EMBO J. 1993 Jun;12(6):2549–2558. doi: 10.1002/j.1460-2075.1993.tb05910.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jenny A., Minvielle-Sebastia L., Preker P. J., Keller W. Sequence similarity between the 73-kilodalton protein of mammalian CPSF and a subunit of yeast polyadenylation factor I. Science. 1996 Nov 29;274(5292):1514–1517. doi: 10.1126/science.274.5292.1514. [DOI] [PubMed] [Google Scholar]
  20. Kjeldgaard M., Nyborg J., Clark B. F. The GTP binding motif: variations on a theme. FASEB J. 1996 Oct;10(12):1347–1368. [PubMed] [Google Scholar]
  21. 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]
  22. Lee S. J., Baserga S. J. Imp3p and Imp4p, two specific components of the U3 small nucleolar ribonucleoprotein that are essential for pre-18S rRNA processing. Mol Cell Biol. 1999 Aug;19(8):5441–5452. doi: 10.1128/mcb.19.8.5441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lewis J. D., Tollervey D. Like attracts like: getting RNA processing together in the nucleus. Science. 2000 May 26;288(5470):1385–1389. doi: 10.1126/science.288.5470.1385. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Méreau A., Fournier R., Grégoire A., Mougin A., Fabrizio P., Lührmann R., Branlant C. An in vivo and in vitro structure-function analysis of the Saccharomyces cerevisiae U3A snoRNP: protein-RNA contacts and base-pair interaction with the pre-ribosomal RNA. J Mol Biol. 1997 Oct 31;273(3):552–571. doi: 10.1006/jmbi.1997.1320. [DOI] [PubMed] [Google Scholar]
  26. Palm G. J., Billy E., Filipowicz W., Wlodawer A. Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology. Structure. 2000 Jan 15;8(1):13–23. doi: 10.1016/s0969-2126(00)00076-9. [DOI] [PubMed] [Google Scholar]
  27. Powers T., Walter P. Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae. Mol Biol Cell. 1999 Apr;10(4):987–1000. doi: 10.1091/mbc.10.4.987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Séraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 1999 Oct;17(10):1030–1032. doi: 10.1038/13732. [DOI] [PubMed] [Google Scholar]
  29. Roll-Mecak A., Cao C., Dever T. E., Burley S. K. X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Cell. 2000 Nov 22;103(5):781–792. doi: 10.1016/s0092-8674(00)00181-1. [DOI] [PubMed] [Google Scholar]
  30. Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Séraphin B. Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. EMBO J. 1999 Jun 15;18(12):3451–3462. doi: 10.1093/emboj/18.12.3451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Schmelzle T., Hall M. N. TOR, a central controller of cell growth. Cell. 2000 Oct 13;103(2):253–262. doi: 10.1016/s0092-8674(00)00117-3. [DOI] [PubMed] [Google Scholar]
  32. Sharma K., Tollervey D. Base pairing between U3 small nucleolar RNA and the 5' end of 18S rRNA is required for pre-rRNA processing. Mol Cell Biol. 1999 Sep;19(9):6012–6019. doi: 10.1128/mcb.19.9.6012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Song H., Parsons M. R., Rowsell S., Leonard G., Phillips S. E. Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution. J Mol Biol. 1999 Jan 22;285(3):1245–1256. doi: 10.1006/jmbi.1998.2387. [DOI] [PubMed] [Google Scholar]
  34. Sprang S. R. G protein mechanisms: insights from structural analysis. Annu Rev Biochem. 1997;66:639–678. doi: 10.1146/annurev.biochem.66.1.639. [DOI] [PubMed] [Google Scholar]
  35. Sprinzl M., Brock S., Huang Y., Milovnik P., Nanninga M., Nesper-Brock M., Rütthard H., Szkaradkiewicz K. Regulation of GTPases in the bacterial translation machinery. Biol Chem. 2000 May-Jun;381(5-6):367–375. doi: 10.1515/BC.2000.049. [DOI] [PubMed] [Google Scholar]
  36. Sánchez R., Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13597–13602. doi: 10.1073/pnas.95.23.13597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. 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]
  38. Watkins N. J., Ségault V., Charpentier B., Nottrott S., Fabrizio P., Bachi A., Wilm M., Rosbash M., Branlant C., Lührmann R. A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell. 2000 Oct 27;103(3):457–466. doi: 10.1016/s0092-8674(00)00137-9. [DOI] [PubMed] [Google Scholar]
  39. Wiederkehr T., Prétôt R. F., Minvielle-Sebastia L. Synthetic lethal interactions with conditional poly(A) polymerase alleles identify LCP5, a gene involved in 18S rRNA maturation. RNA. 1998 Nov;4(11):1357–1372. doi: 10.1017/s1355838298980955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Yaffe M. P., Schatz G. Two nuclear mutations that block mitochondrial protein import in yeast. Proc Natl Acad Sci U S A. 1984 Aug;81(15):4819–4823. doi: 10.1073/pnas.81.15.4819. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES