Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism

Journal of Molecular Biology

Volumn 284, Issue 4, 1998, Pages 975-988

  Chanfreau, Guillaume ^a   Legrain, Pierre ^a   Jacquier, Alain ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

Endonuclease; Nucleolus; Ribonuclease; snoRNA; Tetraloop

Indexed keywords

DOUBLE STRANDED RNA; ENDONUCLEASE; RIBONUCLEASE III; SMALL NUCLEAR RNA;

ARTICLE; BIOGENESIS; CONSENSUS SEQUENCE; CONTROLLED STUDY; IMMUNOPRECIPITATION; MOLECULAR WEIGHT; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; RNA CLEAVAGE; RNA METABOLISM; YEAST; YEAST CELL;

BACTERIA (MICROORGANISMS);

EID: 0032509095     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2237     Document Type: Article

References (48)

1. Abou Elela S. A., Ares M. Jr. Depletion of yeast RNase III blocks correct U2 3′ end formation and results in polyadenylated but functional U2 snRNA. EMBO J. 17:1998;3738-3746.
2. Abou Elela S. A., Igel H., Ares M. Jr. RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell. 85:1996;115-124.
3. Bachellerie J. P., Michot B., Nicoloso M., Balakin A., Ni J., Fournier M. J. Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem. Sci. 20:1995;261-264.
4. Balakin A. G., Smith L., Fournier M. J. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell. 86:1996;823-834.
5. Beltrame M., Tollervey D. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J. 14:1995;4350-4356.
6. Caffarelli E., Arese M., Santoro B., Fragapane P., Bozzoni I. In vitro study of processing of the intron-encoded U16 small nucleolar RNA in Xenopus laevis. Mol. Cell. Biol. 14:1994;2966-2974.
7. Cavaille J., Nicoloso M., Bachellerie J. P. Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature. 383:1996;732-735.
8. Chanfreau G., Jacquier A. An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J. 15:1996;3466-3476.
9. Chanfreau G., Abou Elela S., Ares M. Jr, Guthrie C. Alternative 3′ end processing of U5 snRNA by RNase III. Genes Dev. 11:1997;2741-2751.
10. Chanfreau G., Rotondo G., Legrain P., Jacquier A. Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1. EMBO J. 17:1998;3726-3737.
11. Chelladurai B. S., Li H., Nicholson A. W. A conserved sequence element in ribonuclease III processing signals is not required for accurate in vitro enzymatic cleavage. Nucl. Acids Res. 19:1991;1759-1766.
12. Chelladurai B., Li H., Zhang K., Nicholson A. W. Mutational analysis of a ribonuclease III processing signal. Biochemistry. 32:1993;7549-7558.
13. Court D. RNAse III: a double-strand processing enzyme. Brawerman G., Belasco J. Control of mRNA Stability. 1993;70-116 Academic Press, New York.
14. Fragapane P., Prislei S., Michienzi A., Caffarelli E., Bozzoni I. A novel small nucleolar RNA (U16) is encoded inside a ribosomal protein intron and originates by processing of the pre-mRNA. EMBO J. 12:1993;2921-2928.
15. Ganot P., Bortolin M. L., Kiss T. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell. 89:1997a;799-809.
16. 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. 11:1997b;941-956.
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. 10:1991;4231-4239.
18. Kiss T., Filipowicz W. Small nucleolar RNAs encoded by introns of the human cell cycle regulatory gene RCC1. EMBO J. 12:1993;2913-2920.
19. Kiss T., Filipowicz W. Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. Genes Dev. 9:1995;1411-1424.
20. Kiss-Laszlo Z., Henry Y., Bachellerie J. P., Caizergues-Ferrer M., Kiss T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell. 85:1996;1077-1088.
21. Krainer A. R. Pre-mRNA splicing by complementation with purified human U1, U2, U4/U6 and U5 snRNPs. Nucl. Acids Res. 16:1988;9415-9429.
22. Lafontaine D., Tollervey D. Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing. Biochem. Cell. Biol. 73:1995;803-812.
23. Lafontaine D. L. J., Bousquet-Antonelli C., Henry Y., Caizergues-Ferrer M., Tollervey D. The box H+ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev. 12:1998;527-537.
24. Leader D. J., Sanders J. F., Waugh R., Shaw P., Brown J. W. Molecular characterisation of plant U14 small nucleolar RNA genes: closely linked genes are transcribed as polycistronic U14 transcripts. Nucl. Acids Res. 22:1994;5196-5203.
25. Leader D. J., Clark G. P., Watters J., Beven A. F., Shaw P. J., Brown J. W. Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre-snoRNAs. EMBO J. 16:1997;5742-5751.
26. Leverette R. D., Andrews M. T., Maxwell E. S. Mouse U14 snRNA is a processed intron of the cognate hsc70 heat shock pre-messenger RNA. Cell. 71:1992;1215-1221.
27. 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. 10:1990;1145-1152.
28. Liang W. Q., Fournier M. J. U14 base-pairs with 18S rRNA: a novel snoRNA interaction required for rRNA processing. Genes Dev. 9:1995;2433-2443.
29. Liu J., Maxwell E. S. Mouse U14 snRNA is encoded in an intron of the mouse cognate hsc70 heat shock gene. Nucl. Acids Res. 18:1990;6565-6571.
30. Maxwell E. S., Fournier M. J. The small nucleolar RNAs. Annu. Rev. Biochem. 64:1995;897-934.
31. Myslinski E., Segault V., Branlant C. An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science. 247:1990;1213-1216.
32. Ni J., Tien A. L., Fournier M. J. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell. 89:1997;565-573.
33. Olivas W. M., Muhlrad D., Parker R. Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs. Nucl. Acids Res. 25:1997;4619-4625.
34. Petfalski E., Dandekar T., Henry Y., Tollervey. Processing of precursors to small nucleolar RNAs and ribosomal RNAs requires common components. Mol. Cell. Biol. 18:1998;1181-1189.
35. Prislei S., Michienzi A., Presutti C., Fragapane P., Bozzoni I. Two different snoRNAs are encoded in introns of amphibian and human L1 ribosomal protein genes. Nucl. Acids Res. 21:1993;5824-5830.
36. Qu L. H., Henry Y., Nicoloso M., Michot B., Azum M. C., Renalier M. H., Caizergues-Ferrer M., Bachellerie J. P. U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA. Nucl. Acids Res. 23:1995;2669-2676.
37. Samarsky D. A., Balakin A. G., Fournier M. J. Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34, snR35 and snR36. Nucl. Acids Res. 23:1995;2548-2554.
38. Siegel V., Walter P. Binding sites of the 19-kDa and 68/72-kDa signal recognition particle (SRP) proteins on SRP RNA as determined in protein-RNA "footprinting" Proc. Natl Acad. Sci. USA. 85:1988;1801-1805.
39. Smith C. M., Steitz J. A. Sno storm in the nucleolus: new roles for myriad small RNPs. Cell. 89:1997;669-672.
40. Tollervey D. Small nucleolar RNAs guide ribosomal RNA methylation. Science. 273:1996;1056-1057.
41. Tollervey D., Kiss T. Function and synthesis of small nucleolar RNAs. Curr. Opin. Cell. Biol. 9:1997;337-342.
42. Tycowski K. T., Shu M. D., Steitz J. A. A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. Genes Dev. 7:1993;1176-1190.
43. Tycowski K. T., Shu M. D., Steitz J. A. A mammalian gene with introns instead of exons generating stable RNA products. Nature. 379:1996a;464-466.
44. Tycowski K. T., Smith C. M., Shu M. D., Steitz J. A. A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. Proc. Natl Acad. Sci. U S A. 93:1996b;14480-14485.
45. Umen J. G., Guthrie C. A novel role for a U5 snRNP protein in 3′ splice site selection. Genes Dev. 9:1995;855-868.
46. Villa T., Ceradini F., Presutti C., Bozzoni I. Processing of the intron-encoded U18 small nucleolar RNA in the Yeast Saccharomyces cerevisiae relies on both exo- and endonucleolytic activities. Mol. Cell. Biol. 18:1998;3376-3383.
47. Zhang K., Nicholson A. W. Regulation of ribonuclease III processing by double-helical sequence antideterminants. Proc. Natl Acad. Sci. USA. 94:1997;13437-13441.
48. Zuker M. Prediction of RNA secondary structure by energy minimization. Methods Mol. Biol. 25:1994;267-294.