Mutations in the U5 snRNA result in altered splicing of subsets of pre-mRNAs and reduced stability of Prp8

RNA

Volumn 15, Issue 7, 2009, Pages 1292-1304

  Kershaw, Christopher J ^a   David Barrass, J ^b   Beggs, Jean D ^b   O'Keefe, Raymond T ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Microarray; pre mRNA splicing; Prp8; U5 snRNA; Yeast

Indexed keywords

MESSENGER RNA PRECURSOR; PROTEIN PRP8; SMALL NUCLEAR RNA; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CATALYSIS; EXON; GENE MUTATION; GENE SEQUENCE; GENETIC CONSERVATION; GENOME; IN VIVO STUDY; MICROARRAY ANALYSIS; MUTANT; PRIORITY JOURNAL; PROTEIN RNA BINDING; PROTEIN STABILITY; RNA PROCESSING; RNA SPLICING; SPLICEOSOME; WILD TYPE;

ALTERNATIVE SPLICING; BASE SEQUENCE; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; RIBONUCLEOPROTEIN, U4-U6 SMALL NUCLEAR; RIBONUCLEOPROTEIN, U5 SMALL NUCLEAR; RNA PRECURSORS; RNA, SMALL NUCLEAR; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPLICEOSOMES;

EID: 67649373352     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1347409     Document Type: Article

References (46)

1. Abelson J. 2008. Is the spliceosome a ribonucleoprotein enzyme? Nat Struct Mol Biol 15: 1235-1237.
2. Achsel T, Ahrens K, Brahms H, Teigelkamp S, Lührmann R. 1998. The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein. Mol Cell Biol 18: 6756-6766. (Pubitemid 28500563)
3. Alvi RK, Lund M, O'Keefe RT. 2001. ATP-dependent interaction of yeast U5 snRNA loop 1 with the 5′ splice site. RNA 7: 1013-1023. (Pubitemid 32612478)
4. Bacikova D, Horowitz DS. 2005. Genetic and functional interaction of evolutionarily conserved regions of the Prp18 protein and the U5 snRNA. Mol Cell Biol 25: 2107-2116. (Pubitemid 40354611)
5. Brenner TJ, Guthrie C. 2006. Assembly of Snu114 into U5 snRNP requires Prp8 and a functional GTPase domain. RNA 12: 862-871.
6. Burckin T, Nagel R, Mandel-Gutfreund Y, Shiue L, Clark TA, Chong JL, Chang TH, Squazzo S, Hartzog G, Ares M Jr. 2005. Exploring functional relationships between components of the gene expression machinery. Nat Struct Mol Biol 12: 175-182.
7. Chiara MD, Gozani O, Bennett M, Champion-Arnaud P, Palandjian L, Reed R. 1996. Identification of proteins that interact with exon sequences, splice sites, and the branchpoint sequence during each stage of spliceosome assembly. Mol Cell Biol 16: 3317-3326. (Pubitemid 26199851)
8. Chiara MD, Palandjian L, Kramer RF, Reed R. 1997. Evidence that U5 snRNP recognizes the 3′ splice site for the catalytic step II in mammals. EMBO J 16: 4746-4759. (Pubitemid 27326612)
9. Clark TA, Sugnet CW, Ares M. 2002. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296: 907-910. (Pubitemid 34464895)
10. Collins CA, Guthrie C. 2000. The question remains: Is the spliceosome a ribozyme? Nat Struct Biol 7: 850-854.
11. Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: A sequence logo generator. Genome Res 14: 1188-1190. (Pubitemid 38811555)
12. Crotti LB, Bacikova D, Horowitz DS. 2007. The Prp18 protein stabilizes the interaction of both exons with the U5 snRNA during the second step of pre-mRNA splicing. Genes & Dev 21: 1204-1216. (Pubitemid 46789878)
13. Dix I, Russell CS, O'Keefe RT, Newman AJ, Beggs JD. 1998. Protein-RNA interactions in the U5 snRNP of Saccharomyces cerevisiae. RNA 4: 1239-1250. (Pubitemid 28457854)
14. Frank DN, Roiha H, Guthrie C. 1994. Architecture of the U5 small nuclear RNA. Mol Cell Biol 14: 2180-2190. (Pubitemid 24074615)
15. Grainger RJ, Beggs JD. 2005. Prp8 protein: At the heart of the spliceosome. RNA 11: 533-557. (Pubitemid 40594322)
16. Guthrie C, Patterson B. 1988. Spliceosomal snRNAs. Annu Rev Genet 22: 387-419. (Pubitemid 19156671)
17. Ismaili N, Sha M, Gustafson EH, Konarska MM. 2001. The 100-kDa U5 snRNP protein (hPrp28p) contacts the 5′ splice site through its ATPase site. RNA 7: 182-193. (Pubitemid 33590502)
18. Long M, de Souza SJ, Gilbert W. 1997. The yeast splice site revisited: New exon consensus from genomic analysis. Cell 91: 739-740.
19. Longtine MS, McKenzie A, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14: 953-961. (Pubitemid 28328001)
20. Lopez PJ, Séraphin B. 1999. Genomic-scale quantitative analysis of yeast pre-mRNA splicing: Implications for splice-site recognition. RNA 5: 1135-1137. (Pubitemid 29422754)
21. Maroney PA, Romfo CM, Nilsen TW. 2000. Functional recognition of the 5′ splice site by U4/U6•U5 tri-snRNP defines a novel ATP-dependent step in early spliceosome assembly. Mol Cell 6: 317-328.
22. McConnell TS, Steitz JA. 2001. Proximity of the invariant loop of U5 snRNA to the second intron residue during pre-mRNA splicing. EMBO J 20: 3577-3586. (Pubitemid 32634364)
23. McGrail JC, Tatum EM, O'Keefe RT. 2006. Mutation in the U2 snRNA influences exon interactions of U5 snRNA loop 1 during pre-mRNA splicing. EMBO J 25: 3813-3822. (Pubitemid 44300267)
24. McPheeters DS, Muhlenkamp P. 2003. Spatial organization of protein- RNA interactions in the branch site-3′ splice site region during pre-mRNA splicing in yeast. Mol Cell Biol 23: 4174-4186. (Pubitemid 36666422)
25. Moore MJ, Query CC, Sharp PA. 1993. Splicing of precursors to mRNA by the spliceosome. In The RNA world (eds. RF Gesteland and JF Atkins), pp. 303-357. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
26. Newman A, Norman C. 1991. Mutations in yeast U5 snRNA alter the specificity of 5′ splice-site cleavage. Cell 65: 115-123. (Pubitemid 121001219)
27. Newman AJ, Norman C. 1992. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68: 743-754.
28. Newman AJ, Teigelkamp S, Beggs JD. 1995. snRNA interactions at 5′ and 3′ splice sites monitored by photoactivated crosslinking in yeast spliceosomes. RNA 1: 968-980.
29. Nilsen TW. 1998. RNA-RNA interactions in nuclear pre-mRNA splicing. In RNA structure and function (eds. RW Simons and M Grunberg-Manago), pp. 279-307. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
30. O'Keefe RT. 2002. Mutations in U5 snRNA loop 1 influence the splicing of different genes in vivo. Nucleic Acids Res 30: 5476-5484. (Pubitemid 36113925)
31. O'Keefe RT, Newman AJ. 1998. Functional analysis of the U5 snRNA loop 1 in the second catalytic step of yeast pre-mRNA splicing. EMBO J 17: 565-574. (Pubitemid 28045496)
32. O'Keefe RT, Norman C, Newman AJ. 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. (Pubitemid 26299498)
33. Patterson B, Guthrie C. 1987. An essential yeast snRNA with a U5-like domain is required for splicing in vivo. Cell 49: 613-624.
34. Pleiss JA, Whitworth GB, Bergkessel M, Guthrie C. 2007a. Rapid, transcript-specific changes in splicing in response to environmental stress. Mol Cell 27: 928-937. (Pubitemid 47489768)
35. Pleiss JA, Whitworth GB, Bergkessel M, Guthrie C. 2007b. Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol 5: e90. doi: 10.1371/journal.pbio.0050090. (Pubitemid 46631852)
36. Reyes JL, Kois P, Konforti BB, Konarska MM. 1996. The canonical GU dinucleotide at the 5′ splice site is recognized by p220 of the U5 snRNP within the spliceosome. RNA 2: 213-225. (Pubitemid 26371291)
37. Reyes JL, Gustafson EH, Luo HR, Moore MJ, Konarska MM. 1999. The C-terminal region of hPrp8 interacts with the conserved GU dinucleotide at the 5′ splice site. RNA 5: 167-179. (Pubitemid 29079277)
38. Siatecka M, Reyes JL, Konarska MM. 1999. Functional interactions of Prp8 with both splice sites at the spliceosomal catalytic center. Genes & Dev 13: 1983-1993. (Pubitemid 29407365)
39. Sontheimer EJ, Steitz JA. 1993. The U5 and U6 small nuclear RNAs as the active site components of the spliceosome. Science 262: 1989-1996. (Pubitemid 24041876)
40. Teigelkamp S, Newman AJ, Beggs JD. 1995. Extensive interactions of PRP8 protein with the 5′ and 3′ splice sites during splicing suggests a role in stabilization of exon alignment by U5 snRNA. EMBO J 14: 2602-2612.
41. Turner IA, Norman CM, Churcher MJ, Newman AJ. 2006. Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome. RNA 12: 375-386. (Pubitemid 43290866)
42. Umen JG, Guthrie C. 1995. Prp16p, Slu7p, and Prp8p interact with the 3′ splice site in two distinct stages during the second catalytic step of pre-mRNA splicing. RNA 1: 584-597.
43. Vidal VPI, Verdone L, Mayes AE, Beggs JD. 1999. Characterization of U6 snRNA-protein interactions. RNA 5: 1470-1481. (Pubitemid 29530491)
44. Wyatt JR, Sontheimer EJ, Steitz JA. 1992. Site-specific cross-linking of mammalian U5 snRNP to the 5′ splice site before the first step of pre-mRNA splicing. Genes & Dev 6: 2542-2553. (Pubitemid 23052883)
45. 2 test. J R Stat Soc 1: 217-235.
46. Young BP, Craven RA, Reid PJ, Willer M, Stirling CJ. 2001. Sec63p and Kar2p are required for the translocation of SRP-dependent precursors into the yeast endoplasmic reticulum in vivo. EMBO J 20: 262-271. (Pubitemid 32099122)