Substrate recognition by a eukaryotic RNase III: The double-stranded RNA-binding domain of Rnt1p selectively binds RNA containing a 5'-AGNN-3' tetraloop

RNA

Volumn 6, Issue 8, 2000, Pages 1142-1156

  Nagel, Roland ^a   Ares Jr , Manuel ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DsRBD; Endoribonuclease; Pre rRNA processing

Indexed keywords

DOUBLE STRANDED RNA; RIBONUCLEASE III;

ARTICLE; CONTROLLED STUDY; DIMERIZATION; DNA FLANKING REGION; ENZYME ACTIVITY; ENZYME BINDING; ENZYME SPECIFICITY; GENE MUTATION; GENE SEQUENCE; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; START CODON; STOP CODON; YEAST;

BASE SEQUENCE; BINDING SITES; CENTRIFUGATION, DENSITY GRADIENT; DOSE-RESPONSE RELATIONSHIP, DRUG; ENDORIBONUCLEASES; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASE III; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, DOUBLE-STRANDED; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SUBSTRATE SPECIFICITY; TIME FACTORS;

EID: 0033868624     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838200000431     Document Type: Article

References (33)

1. Abou Elela S, Ares M Jr. 1998. Depletion of yeast RNase III blocks correct U2 3′ end formation and results in polyadenylated but functional U2 snRNA. EMBO J 17:3738-3746.
2. Abou Elela SA, Igel H, Ares M Jr. 1996. RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell 85:115-124.
3. Allmang C, Kufel J, Chanfreau G, Mitchell P, Petfalski E, Tollervey D. 1999. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J 18:5399-5410.
4. Allmang C, Tollervey D. 1998. The role of the 3′ external transcribed spacer in yeast pre-rRNA processing. J Mol Biol 278:67-78.
5. Ares M, Igel H. 1990. Lethal and temperature-sensitive mutations and their suppressors identify an essential structural element in U2 small nuclear RNA. Genes & Dev 4:2132-2145.
6. Bevilacqua PC, George CX, Samuel CE, Cech TR. 1998. Binding of the protein kinase PKR to RNAs with secondary structure defects: Role of the tandem A-G mismatch and noncontiguous helixes. Biochemistry 37:6303-6316.
7. Cadwell RC, Joyce GF. 1992. Randomization of genes by PCR mutagenesis. PCR Methods Appl 2:28-33.
8. Chanfreau G, Buckle M, Jacquier A. 2000. Recognition of a conserved class of RNA tetraloops by Saccharomyces cerevisiae RNase III. Proc Natl Acad Sci USA 97:3142-3147.
9. Chanfreau G, Elela SA, Ares M Jr, Guthrie C. 1997. Alternative 3′-end processing of U5 snRNA by RNase III. Genes & Dev 11: 2741-2751.
10. Chanfreau G, Legrain P, Jacquier A. 1998a. Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism. J Mol Biol 284:975-988.
11. Chanfreau G, Rotondo G, Legrain P, Jacquier A. 1998b. Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1. EMBO J 17:3726-3737.
12. Conrad C, Rauhut R, Klug G. 1998. Different cleavage specificities of RNases III from Rhodobacter capsulatus and Escherichia coli. Nucleic Acids Res 26:4446-4453.
13. Hughes JM, Ares M Jr. 1991. 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 10:4231-4239.
14. Jucker FM, Pardi A. 1995. GNRA tetraloops make a U-turn. RNA 1:219-222.
15. Kufel J, Dichtl B, Tollervey D. 1999. Yeast Rnt1p is required for cleavage of the pre-ribosomal RNA in the 3′ ETS but not the 5′ ETS. RNA 5:909-917.
16. Lamontagne B, Tremblay A, Abou Elela S. 2000. The N-terminal domain that distinguishes yeast from bacterial RNase III contains a dimerization signal required for efficient double-stranded RNA cleavage. Mol Cell Biol 20:1104-1115.
17. Lehmann KA, Bass BL. 1999. The importance of internal loops within RNA substrates of ADAR1. J Mol Biol 297:1-13.
18. Li HD, Zagorski J, Fournier MJ. 1990. Depletion of U14 small nuclear RNA (snR128) disrupts production of 18S rRNA in Saccharomyces cerevisiae. Mol Cell Biol 10:1145-1152.
19. Milligan JF, Uhlenbeck OC. 1989. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180:51-62.
20. Nagel RJ, Lancaster AM, Zahler AM. 1998. Specific binding of an exonic splicing enhancer by the pre-mRNA splicing factor SRp55. RNA 4:11-23.
21. Nicholson AW. 1999. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol Rev 23:371-390.
22. Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y, Caizergues-Ferrer M, Bachellerie JP. 1999. Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast. Mol Cell Biol 19:1144-1158.
23. Ramos A, Grunert S, Adams J, Micklem DR, Proctor MR, Freund S, Bycroft M, St Johnston D, Varani G. 2000. RNA recognition by a Staufen double-stranded RNA-binding domain. EMBO J 19:997-1009.
24. Rotondo G, Frendewey D. 1996. Purification and characterization of the Pad ribonuclease of Schizosaccharomyces pombe. Nucleic Acids Res 24:2377-2386.
25. Rotondo G, Gillespie M, Frendewey D. 1995. Rescue of the fission yeast snRNA synthesis mutant snm1 by overexpression of the double-strand-specific Pad ribonuclease. Mol Gen Genet 247: 698-708.
26. Rotondo G, Huang JY, Frendewey D. 1997. Substrate structure requirements of the Pad ribonuclease from Schizosaccharmyces pombe. RNA 3:1182-1193.
27. Ryter JM, Schultz SC. 1998. Molecular basis of double-stranded RNA-protein interactions: Structure of a dsRNA-binding domain complexed with dsRNA. EMBO J 17:7505-7513.
28. Samarsky DA, Fournier MJ. 1999. A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae. Nucleic Acids Res 27:161-164.
29. Seipelt RL, Zheng B, Asuru A, Rymond BC. 1999. U1 snRNA is cleaved by RNase III and processed through an Sm site-dependent pathway. Nucleic Acids Res 27:587-595.
30. St Johnston D, Brown NH, Gall JG, Jantsch M. 1992. A conserved double-stranded RNA-binding domain. Proc Natl Acad Sci USA 89:10979-10983.
31. Studier FW, Rosenberg AH, Dunn JJ, Dubendorff JW. 1990. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol 185:60-89.
32. Zhang K, Nicholson AW. 1997. Regulation of ribonuclease III processing by double-helical sequence antideterminants. Proc Natl Acad Sci USA 94:13437-13441.
33. Zhou D, Frendewey D, Lobo Ruppert SM. 1999. Pac1p, an RNase III homolog, is required for formation of the 3′ end of U2 snRNA in Schizosaccharomyces pombe. RNA 5:1083-1098.