The RNA binding protein Cwc2 interacts directly with the U6 snRNA to link the nineteen complex to the spliceosome during pre-mRNA splicing

Nucleic Acids Research

Volumn 37, Issue 13, 2009, Pages 4205-4217

  McGrail, Joanne C ^a   Krause, André ^a   O'Keefe, Raymond T ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN; RNA BINDING PROTEIN CWC2; SMALL NUCLEAR RNA; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ARTICLE; CONTROLLED STUDY; DEPLETION; GENE ACTIVATION; GENE MUTATION; INTRON; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CROSS LINKING; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN PURIFICATION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RNA BINDING; RNA SPLICING; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SPLICEOSOME; YEAST CELL;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BINDING SITES; GENE EXPRESSION REGULATION, FUNGAL; MOLECULAR SEQUENCE DATA; MUTATION; RNA PRECURSORS; RNA SPLICING; RNA, MESSENGER; RNA, SMALL NUCLEAR; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPLICEOSOMES; ZINC FINGERS;

EID: 67949106544     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp341     Document Type: Article

References (41)

1. Will,C.L. and Lührmann,R. (2001) Spliceosomal UsnRNP biogenesis, structure and function. Curr. Opin. Cell Biol., 13, 290-301.
2. Moore,M.J., Query,C.C. and Sharp,P.A. (1993) Splicing of precursors to mRNA by the spliceosome. In Gesteland,R.F. and Atkins,J.F. (eds), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 303-357.
3. Nilsen,T.W. (1998) RNA-RNA interactions in nuclear pre-mRNA splicing. In Simons,R.W. and Grunberg-Manago,M. (eds), RNA Structure and Function Cold Spring Harbor Press, Cold Spring Harbor, NY, pp. 279-307.
4. Staley,J.P. and Guthrie,C. (1999) An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p. Mol. Cell, 3, 55-64.
5. Raghunathan,P.L. and Guthrie,C. (1998) RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Curr. Biol., 8, 847-855.
6. Small,E.C., Leggett,S.R., Winans,A.A. and Staley,J.P. (2006) The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. Mol. Cell, 23, 389-399.
7. Chan,S.P. and Cheng,S.C. (2005) The Prp19-associated complex is required for specifying interactions of U5 and U6 with pre-mRNA during spliceosome activation. J. Biol. Chem., 280, 31190-31199.
8. Chan,S.P., Kao,D.I., Tsai,W.Y. and Cheng,S.C. (2003) The Prp19p-associated complex in spliceosome activation. Science, 302, 279-282.
9. Ohi,M.D. and Gould,K.L. (2002) Characterization of interactions among the Cef1p-Prp19p-associated splicing complex. RNA, 8, 798-815.
10. Ben-Yehuda,S., Dix,I., Russell,C.S., McGarvey,M., Beggs,J.D. and Kupiec,M. (2000) Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics, 156, 1503-1517.
11. Makarov,E.M., Makarova,O.V., Urlaub,H., Gentzel,M., Will,C.L., Wilm,M. and Lührmann,R. (2002) Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome. Science, 298 2205-2208.
12. Villa,T. and Guthrie,C. (2005) The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing. Genes Dev, 19, 1894-1904.
13. Ajuh,P., Kuster,B., Panov,K., Zomerdijk,J.C., Mann,M. and Lamond,A.I. (2000) Functional analysis of the human CDC5L complex and identification of its components by mass spectrometry. EMBO J., 19, 6569-6581.
14. Chen,C.H., Kao,D.I., Chan,S.P., Kao,T.C., Lin,J.Y. and Cheng,S.C. (2006) Functional links between the Prp19-associated complex, U4/U6 biogenesis, and spliceosome recycling. RNA, 12, 765-774.
15. Tarn,W.Y., Hsu,C.H., Huang,K.T., Chen,H.R., Kao,H.Y., Lee,K.R. and Cheng,S.C. (1994) Functional association of essential splicing factor(s) with PRP19 in a protein complex. EMBO J., 13, 2421-2431.
16. Sikorski,R.S. and Hieter,P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics, 122, 19-27.
17. Kunkel,T.A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl Acad. Sci. USA, 82, 488-492.
18. O'Keefe,R.T., Norman,C. and Newman,A.J. (1996) The invariant U5 snRNA loop 1 sequence is dispensable for the first catalytic step of pre-mRNA splicing in yeast. Cell, 86, 679-689.
19. Gietz,R.D. and Woods,R.A. (2006) Yeast transformation by the LiAc/SS Carrier DNA/PEG method. Methods Mol. Biol., 313, 107-120.
20. Boeke,J.D., LaCroute,F. and Fink,G.R. (1984) A positive selection for mutants lacking orotidine-50-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet., 197, 345-346.
21. Longtine,M.S., McKenzie,A., Demarini,D.J., Shah,N.G., Wach,A., Brachat,A., Philippsen,P. and Pringle,J.R. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast, 14, 953-961.
22. Janke,C., Magiera,M.M., Rathfelder,N., Taxis,C., Reber,S., Maekawa,H., Moreno-Borchart,A., Doenges,G., Schwob,E., Schiebel,E. et al. (2004) A versatile toolbox for PCR-based tagging of yeast genes: New fluorescent proteins, more markers and promoter substitution cassettes. Yeast, 21, 947-962.
23. Dobbyn,H.C. and O'Keefe,R.T. (2004) Analysis of Snu13p mutations reveals differential interactions with the U4 snRNA and U3 snoRNA. RNA, 10, 308-320.
24. Ansari,A. and 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.
25. Lin,R.J., Newman,A.J., Cheng,S.C. and Abelson,J. (1985) Yeast mRNA splicing in vitro. J. Biol. Chem., 260, 14780-14792.
26. Li,Z. and Brow,D.A. (1993) A rapid assay for quantitative detection of specific RNAs. Nucleic Acids Res., 21, 4645-4646.
27. McGrail,J.C. and O'Keefe,R.T. (2008) The U1, U2 and U5 snRNAs crosslink to the 5′ exon during yeast pre-mRNA splicing. Nucleic Acids Res. 36, 814-825.
28. McGrail,J.C., Tatum,E.M. and O'Keefe,R.T. (2006) Mutation in the U2 snRNA influences exon interactions of U5 snRNA loop 1 during pre-mRNA splicing. EMBO J., 25, 3813-3822.
29. Kielkopf,C.L., Lucke,S. and Green,M.R. (2004) U2AF homology motifs: protein recognition in the RRM world. Genes Dev., 18, 1513-1526.
30. Bessonov,S., Anokhina,M., Will,C.L., Urlaub,H. and Lührmann,R. (2008) Isolation of an active step I spliceosome and composition of its RNP core. Nature, 452, 846-850.
31. Rigaut,G., Shevchenko,A., Rutz,B., Wilm,M., Mann,M. and Seraphin,B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol., 17 1030-1032.
32. Tarn,W.Y., Lee,K.R. and Cheng,S.C. (1993) The yeast PRP19 protein is not tightly associated with small nuclear RNAs, but appears to associate with the spliceosome after binding of U2 to the pre-mRNA and prior to formation of the functional spliceosome. Mol. Cell Biol., 13 1883-1891.
33. Cheng,S.C. (1994) Formation of the yeast splicing complex A1 and association of the splicing factor PRP19 with the pre-mRNA are independent of the 3′ region of the intron. Nucleic Acids Res., 22, 1548-1554.
34. Vijayraghavan,U., Parker,R., Tamm,J., Iimura,Y., Rossi,J., Abelson,J. and Guthrie,C. (1986) Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome. EMBO J., 5, 1683-1695.
35. Clery,A., Blatter,M. and Allain,F.H. (2008) RNA recognition motifs: boring? Not quite. Curr. Opin. Struct. Biol., 18, 290-298.
36. Tarn,W.Y., Lee,K.R. and Cheng,S.C. (1993) Yeast precursor mRNA processing protein PRP19 associates with the spliceosome concomitant with or just after dissociation of U4 small nuclear RNA. Proc. Natl Acad. Sci. USA, 90, 10821-10825.
37. Aravind,L. and Koonin,E.V. (2000) The U box is a modified RING finger - a common domain in ubiquitination. Curr. Biol., 10, R132-R134.
38. Kerscher,O., Felberbaum,R. and Hochstrasser,M. (2006) Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu. Rev. Cell Dev. Biol., 22, 159-180.
39. Loscher,M., Fortschegger,K., Ritter,G., Wostry,M., Voglauer,R., Schmid,J.A., Watters,S., Rivett,A.J., Ajuh,P., Lamond,A.I. et al. (2005) Interaction of U-box E3 ligase SNEV with PSMB4, the beta7 subunit of the 20 S proteasome. Biochem. J., 388, 593-603.
40. Ohi,M.D., Vander Kooi,C.W., Rosenberg,J.A., Chazin,W.J. and Gould,K.L. (2003) Structural insights into the U-box, a domain associated with multi-ubiquitination. Nat. Struct. Biol., 10, 250-255.
41. Konarska,M.M., Vilardell,J. and Query,C.C. (2006) Repositioning of the reaction intermediate within the catalytic center of the spliceosome. Mol. Cell, 21, 543-553.