A conserved Lsm-interaction motif in Prp24 required for efficient U4/U6 di-snRNP formation

RNA

Volumn 8, Issue 11, 2002, Pages 1378-1392

  Rader, Stephen D ^a   Guthrie, Christine ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Annealing; p110nrb; RRM; SART3; Splicing; U4 U6

Indexed keywords

MEMBRANE ANTIGEN; PROTEIN; PROTEIN LSM; PROTEIN PRP 24; SMALL NUCLEAR RIBONUCLEOPROTEIN; SMALL NUCLEAR RNA; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; FUNGUS GROWTH; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN MOTIF; RNA SPLICING; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; TWO HYBRID SYSTEM;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BINDING SITES; BLOTTING, NORTHERN; CONSENSUS SEQUENCE; DNA PRIMERS; FUNGAL PROTEINS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHENOTYPE; POLYMERASE CHAIN REACTION; PRECIPITIN TESTS; RIBONUCLEOPROTEIN, U4-U6 SMALL NUCLEAR; RIBONUCLEOPROTEINS, SMALL NUCLEAR; RNA SPLICING; RNA, FUNGAL; RNA, SMALL NUCLEAR; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SUPPRESSION, GENETIC; TWO-HYBRID SYSTEM TECHNIQUES;

FUNGI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 0036849242     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838202020010     Document Type: Article

References (42)

1. Achsel T, Brahms H, Kastner B, Bachi A, Wilm M, Lührmann R. 1999. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3′ end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. EMBO J 18:5789-5802.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403-410.
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402.
4. Ansari A, Schwer B. 1995. SLU7 and a novel activity, SSF1, act during the PRP16-dependent step of yeast pre-mRNA splicing. EMBO J 14:4001-4009.
5. Bell M, Schreiner S, Damianov A, Reddy R, Bindereif A. 2002. p110, a novel human U6 snRNP protein and U4/U6 snRNP recycling factor. EMBO J 21:2724-2735.
6. Boeke JD, Trueheart J, Natsoulis G, Fink GR. 1987. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol 154:164-175.
7. Bouveret E, Rigaut G, Shevchenko A, Wilm M, Seraphin B. 2000. A Sm-like protein complex that participates in mRNA degradation. EMBO J 19:1661-1671.
8. Bucher P, Bairoch A. 1994. A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. Proc Int Conf Intell Syst Mol Biol 2:53-61.
9. Cooper M, Johnston LH, Beggs JD. 1995. Identification and characterization of Uss1p (Sdb23p): A novel U6 snRNA-associated protein with significant similarity to core proteins of small nuclear ribonucleoproteins. EMBO J 14:2066-2075.
10. Elledge SJ, Davis RW. 1988. A family of versatile centromeric vectors for use in the sectoring-shuffle mutagenesis assay in Saccharomyces cerevisiae. Gene 70:303-312.
11. Fabrizio P, McPheeters DS, Abelson J. 1989. In vitro assembly of yeast U6 snRNP: A functional assay. Genes & Dev 3:2137-2150.
12. Fortner DM, Troy RG, Brow DA. 1994. A stem/loop in U6 RNA defines a conformational switch required for pre-mRNA splicing. Genes & Dev 8:221-233.
13. Fromont-Racine M, Mayes AE, Brunet-Simon A, Rain JC, Colley A, Dix I, Decourty L, Joly N, Ricard F, Beggs JD, Legrain P. 2000. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast 17:95-110.
14. Fromont-Racine M, Rain J-C, Legrain P. 1997. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet 16:277-282.
15. Ghetti A, Company M, Abelson J. 1995. Specificity of Prp24 binding to RNA: A role for Prp24 in the dynamic interaction of U4 and U6 snRNAs. RNA 1:132-145.
16. Gu J, Shimba S, Nomura N, Reddy R. 1998. Isolation and characterization of a new 110 kDa human nuclear RNA-binding protein (p110nrb). Biochim Biophys Acta 1399:1-9.
17. He W, Parker R. 2000. Functions of Lsm proteins in mRNA degradation and splicing. Curr Opin Cell Biol 12:346-350.
18. Jandrositz A, Guthrie C. 1995. Evidence for a Prp24 binding site in U6 snRNA and in a putative intermediate in the annealing of U6 and U4 snRNAs. EMBO J 14:820-832.
19. Johnson TL, Abelson J. 2001. Characterization of U4 and U6 interactions with the 5′ splice site using a S. cerevisiae in vitro transsplicing system. Genes & Dev 15:1957-1970.
20. Kenan DJ, Query CC, Keene JD. 1991. RNA recognition: Towards identifying determinants of specificity. Trends Biochem Sci 16:214-220.
21. Li Z, Brow DA. 1993. A rapid assay for quantitative detection of specific RNAs. Nucleic Acids Res 21:4645-4646.
22. Lin R-J, Newman AJ, Cheng S-C, Abelson J. 1985. Yeast mRNA splicing in vitro. J Biol Chem 260:14780-14792.
23. Lockhart SR, Rymond BC. 1994. Commitment of yeast pre-mRNA to the splicing pathway requires a novel U1 small nuclear ribonucleoprotein polypeptide, Prp39p. Mol Cell Biol 14:3623-3633.
24. Madhani HD, Guthrie C. 1992. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell 71:803-817.
25. Mayes AE, Verdone L, Legrain P, Beggs JD. 1999. Characterization of Sm-like proteins in yeast and their association with U6 snRNA. EMBO J 18:4321-4331.
26. Miller JH. 1972. Experiments in Molecular Genetics. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
27. Pannone BK, Xue D, Wolin SL. 1998. A role for the yeast La protein in U6 snRNP assembly: Evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts. EMBO J 17:7442-7453.
28. Preker PJ, Keller W. 1998. The HAT helix, a repetitive motif implicated in RNA processing. Trends Biochem Sci 23:15-16.
29. Raghunathan PL, Guthrie C. 1998. A spliceosomal recycling factor that reanneals U4 and U6 small nuclear ribonucleoprotein particles. Science 279:857-860.
30. a in spliceosome assembly. RNA 8:997-1010.
31. Ryan DE, Stevens SW, Abelson J. 2002. The 5′ and 3′ domains of yeast U6 snRNA: Lsm proteins facilitate binding of Prp24 protein to the U6 telestem region. RNA 8:1011-1033.
32. Shannon KW, Guthrie C. 1991. Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA-binding motifs. Genes & Dev 5:773-785.
33. Staley JP, Guthrie C. 1998. Mechanical devices of the spliceosome: Motors, clocks, springs, and things. Cell 92:315-326.
34. Staley JP, Guthrie C. 1999. An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol Cell 3:55-64.
35. Stevens SW, Barta I, Ge HY, Moore RE, Young MK, Lee TD, Abelson J. 2001. Biochemical and genetic analyses of the U5, U6, and U4/U6 x U5 small nuclear ribonucleoproteins from Saccharomyces cerevisiae. RNA 7:1543-1553.
36. Thompson JD, Higgins DG, Gibson TJ. 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.
37. Vidal VP, Verdone L, Mayes AE, Beggs JD. 1999. Characterization of U6 snRNA-protein interactions. RNA 5:1470-1481.
38. Vidaver RM, Fortner DM, Loos-Austin LS, Brow DA. 1999. Multiple functions of Saccharomyces cerevisiae splicing protein Prp24 in U6 RNA structural rearrangements. Genetics 153:1205-1218.
39. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Davis RW, et al. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906.
40. Wolff T, Bindereif A. 1993. Conformational changes of U6 RNA during the spliceosome cycle: An intramolecular helix is essential both for initiating the U4-U6 interaction and for the first step of slicing. Genes & Dev 7:1377-1389.
41. Yang D, Nakao M, Shichijo S, Sasatomi T, Takasu H, Matsumoto H, Mori K, Hayashi A, Yamana H, Shirouzu K, Itoh K. 1999. Identification of a gene coding for a protein possessing shared tumor epitopes capable of inducing HLA-A24-restricted cytotoxic T lymphocytes in cancer patients. Cancer Res 59:4056-4063.
42. Zhang Z, Schaffer AA, Miller W, Madden TL, Lipman DJ, Koonin EV, Altschul SF. 1998. Protein sequence similarity searches using patterns as seeds. Nucleic Acids Res 26:3986-3990.