A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast

RNA

Volumn 9, Issue 7, 2003, Pages 771-779

  Badis, Gwenael ^a   Fromont Racine, Micheline ^a   Jacquier, Alain ^a,b  

^a CNRS   (France)

^b INSTITUT PASTEUR   (France)

Author keywords

H ACA snoRNA; Pseudouridylation; Ribosome; Saccharomyces cerevisiae; Stable RNA

Indexed keywords

GUIDE RNA; NUCLEOTIDE; PSEUDOURIDINE; RIBOSOME RNA; SMALL NUCLEOLAR RNA;

ARTICLE; CELL VIABILITY; CHEMICAL REACTION; CONTROLLED STUDY; EUKARYOTE; FUNGUS GROWTH; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCUS; GENETIC CONSERVATION; INTRON; METHYLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; POLYSOME; PRIORITY JOURNAL; PROTEIN MODIFICATION; PSEUDOURIDYLATION; RNA ANALYSIS; RNA STABILITY; RNA STRUCTURE; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; YEAST;

BASE SEQUENCE; CONSERVED SEQUENCE; DNA PRIMERS; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PLASMIDS; POLYMERASE CHAIN REACTION; PSEUDOURIDINE; RNA, FUNGAL; RNA, RIBOSOMAL; RNA, SMALL NUCLEOLAR; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EUKARYOTA; FUNGI; SACCHAROMYCES CEREVISIAE;

EID: 0038721061     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5240503     Document Type: Article

References (34)

1. Bakin, A. and Ofengand, J. 1993. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: Analysis by the application of a new sequencing technique. Biochemistry 32: 9754-9762.
2. -. 1995. Mapping of the 13 pseudouridine residues in Saccharomyces cerevisiae small subunit ribosomal RNA to nucleotide resolution. Nucleic Acids Res. 23: 3290-3294.
3. Balakin, A.G., Smith, L., and Fournier, M.J. 1996. The RNA world of the nucleolus: Two major families of small RNAs defined by different box elements with related functions. Cell 86: 823-834.
4. Bortolin, M.L. and Kiss, T. 1998. Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding. RNA 4: 445-454.
5. Cherry, J.M., Ball, C., Dolinski, K., Dwight, S., Harris, M., Matese, J.C., Sherlock, G., Binkley, G., Jin, H., Weng, S., et al. 2002. Saccharomyces Genome Database. http://genome-www.stanford.edu/Saccharomyces/.
6. Decatur, W.A. and Fournier, M.J. 2002. rRNA modifications and ribosome function. Trends Biochem. Sci. 27: 344-351.
7. -. 2003. RNA-guided nucleotide modification of ribosomal and other RNAs. J. Biol. Chem. 278: 695-698.
8. Eddy, S.R. 2002. Computational genomics of noncoding RNA genes. Cell 109: 137-140.
9. Fromont-Racine, M., Rain, J.C., and Legrain, P. 1997. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet. 16: 277-282.
10. Ganot, P., Bortolin, M.L., and Kiss, T. 1997a. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89: 799-809.
11. Ganot, P., Caizergues-Ferrer, M., and Kiss, T. 1997b. 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. 11: 941-956.
12. Gietz, R.D., Schiestl, R.H., Willems, A.R., and Woods, R.A. 1995. Studies on the transformation of intact yeast cells by the LiAc/SS-DNA/PEG procedure. Yeast 11: 355-360.
13. Gutgsell, N.S., Del Campo, M.D., Raychaudhuri, S., and Ofengand, J. 2001. A second function for pseudouridine synthases: A point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain. RNA 7: 990-998.
14. King, T.H., Liu, B., McCully, R.R., and Fournier, M.J. 2003. Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center. Mol. Cell 11: 425-435.
15. Kiss, T. 2002. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell 109: 145-148.
16. Kiss, T., Bortolin, M.L., and Filipowicz, W. 1996. Characterization of the intron-encoded U19 RNA, a new mammalian small nucleolar RNA that is not associated with fibrillarin. Mol. Cell Biol. 16: 1391-1400.
17. Lowe, T.M. and Eddy, S.R. 1999. A computational screen for methylation guide snoRNAs in yeast. Science 283: 1168-1171.
18. Ni, J., Tien, A.L., and Fournier, M.J. 1997. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89: 565-573.
19. Ofengand, J. 2002. Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Lett. 514: 17-25.
20. Ofengand, J. and Bakin, A. 1997. Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J. Mol. Biol. 266: 246-268.
21. Ofengand, J., Bakin, A., Wrzesinski, J., Nurse, K., and Lane, B.G. 1995. The pseudouridine residues of ribosomal RNA. Biochem. Cell Biol. 73: 915-924.
22. Ooi, S.L., Samarsky, D.A., Fournier, M.J., and Boeke, J.D. 1998. Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: Intron length effects and activity of a precursor snoRNA. RNA 4: 1096-1110.
23. Racevskis, J., Dill, A., Stockert, R., and Fineberg, S.A. 1996. Cloning of a novel nucleolar guanosine 5′-triphosphate binding protein autoantigen from a breast tumor. Cell Growth Differ. 7: 271-280.
24. Raychaudhuri, S., Conrad, J., Hall, B.G., and Ofengand, J. 1998. A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli. RNA 4: 1407-1417.
25. Ruggero, D., Grisendi, S., Piazza, F., Rego, E., Mari, F., Rao, P.H., Cordon-Cardo, C., and Pandolfi, P.P. 2003. Dyskeratosis congenita and cancer in mice deficient in ribosomal RNA modification. Science 299: 259-262.
26. Saveanu, C., Bienvenu, D., Namane, A., Gleizes, P.E., Gas, N., Jacquier, A., and Fromont-Racine, M. 2001. Nog2p, a putative GTPase associated with pre-60S subunits and required for late 60S maturation steps. EMBO J. 20: 6475-6484.
27. Sayle, R.A. and Milner-White, E.J. 1995. RASMOL: Biomolecular graphics for all. Trends Biochem. Sci. 20: 374.
28. Souciet, J., Aigle, M., Artiguenave, F., Blandin, G., Bolotin-Fukuhara, M., Bon, E., Brottier, P., Casaregola, S., de Montigny, J., Dujon, B., et al. 2000. Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett. 487: 3-12.
29. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
30. Tollervey, D. 1987. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J. 6: 4169-4175.
31. Tollervey, D., Lehtonen, H., Jansen, R., Kern, H., and Hurt, E.C. 1993. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell 72: 443-457.
32. Walter, A.E., Turner, D.H., Kim, J., Lyttle, M.H., Muller, P., Mathews, D.H., and Zuker, M. 1994. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. 91: 9218-9222.
33. Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H., and Noller, H.F. 2001. Crystal structure of the ribosome at 5.5 Å resolution. Science 292: 883-896.
34. Zebarjadian, Y., King, T., Fournier, M.J., Clarke, L., and Carbon, J. 1999. Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA. Mol. Cell Biol. 19: 7461-7472.