Genetic and functional interaction of evolutionarily conserved regions of the Prp18 protein and the U5 snRNA

Molecular and Cellular Biology

Volumn 25, Issue 6, 2005, Pages 2107-2116

  Bačíková, Dagmar ^a   Horowitz, David S ^a  

^a UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA PRECURSOR; PROTEIN PRP 18; SMALL NUCLEAR RNA; UNCLASSIFIED DRUG;

ALLELE; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; GENE INTERACTION; GENE MUTATION; GENE REPRESSION; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; RNA SPLICING;

ALLELES; AMINO ACID SEQUENCE; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GENES, FUNGAL; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; NUCLEIC ACID CONFORMATION; POINT MUTATION; RNA SPLICING; RNA, FUNGAL; RNA, MESSENGER; RNA, SMALL NUCLEAR; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SUPPRESSION, GENETIC;

EID: 14844355531     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.6.2107-2116.2005     Document Type: Article

References (61)

1. Alvi, R. K., M. Lund, and R. T. O'Keefe. 2001. ATP-dependent interaction of yeast U5 snRNA loop 1 with the 5′ splice site. RNA 7:1013-1023.
2. Bačíková, D., and D. S. Horowitz. 2002. Mutational analysis identifies two separable roles of the Saccharomyces cerevisiae splicing factor Prp18. RNA 8:1280-1293.
3. Beggs, J. D., S. Teigelkamp, and A. J. Newman. 1995. The role of PRP8 protein in nuclear pre-mRNA splicing in yeast. J. Cell Sci. 19(Suppl):101-105.
4. Bousquet-Antonelli, C., C. Presutti, and D. Tollervey. 2000. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102:765-775.
5. Brow, D. A. 2002. Allosteric cascade of spliceosome activation. Annu. Rev. Genet. 36:333-360.
6. Brys, A., and B. Schwer. 1996. Requirement for SLU7 in yeast pre-mRNA splicing is dictated by the distance between the branchpoint and the 3′ splice site. RNA 2:707-717.
7. Burge, C. B., T. H. Tuschl, and P. A. Sharp. 1999. Splicing of precursors to mRNAs by the spliceosomes, p. 525-560. In R. F. Gesteland, T. R. Cech, and J, F. Atkins (ed.), RNA World II. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
8. Caponigro, G., D. Muhlrad, and R. Parker. 1993. A small segment of the MATα1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role for rare codons. Mol. Cell. Biol. 13:5141-5148.
9. Cheng, S.-C., and J. Abelson. 1987. Spliceosome assembly in yeast. Genes Dev. 1:1014-1027.
10. Chua, K., and R. Reed. 1999. The RNA splicing factor hSlu7 is required for correct 3′ splice-site choice. Nature 402:207-210.
11. Clark, T. A., C. W. Sugnet, and M. Ares, Jr. 2002. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296:907-910.
12. Collart, M. A., and S. Oliviero. 2000. Preparation of yeast RNA by extraction with hot acidic phenol, p. 13.12.1-13.12.2. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.), Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y.
13. Collins, C. A., and C. Guthrie. 2000. The question remains: is the spliceosome a ribozyme? Nat. Struct. Biol. 7:850-854.
14. Company, M., J. Arenas, and J. Abelson. 1991. Requirement of the RNA helicase-like protein PRP22 for release of messenger RNA from spliceosomes. Nature 349:487-493.
15. Cortes, J. J., E. J. Sontheimer, S. D. Seiwert, and J. A. Steitz. 1993. Mutations in the conserved loop of human U5 snRNA generate use of novel cryptic 5′ splice sites in vivo. EMBO J. 12:5181-5189.
16. Dix, I., C. S. Russell, R. T. O'Keefe, A. J. Newman, and J. D. Beggs. 1998. Protein-RNA interactions in the U5 snRNP of Saccharomyces cerevisiae. RNA 4:1675-1686.
17. Fabrizio, P., and J. Abelson. 1990. Two domains of yeast U6 small nuclear RNA required for both steps of nuclear precursor messenger RNA splicing. Science 250:404-409.
18. Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabelling DNA restriction fragments to high specific activity. Anal. Biochem. 132:6-13.
19. Frank, D., and C. Guthrie. 1992. An essential splicing factor, SLU7, mediates 3′ splice site choice in yeast. Genes Dev. 6:2112-2124.
20. Frank, D., B. Patterson, and C. Guthrie. 1992. Synthetic lethal mutations identify interactions between U5 snRNA and four proteins required for the second step of splicing. Mol. Cell. Biol. 12:5197-5205.
21. Frank, D. N., H. Roiha, and C. Guthrie. 1994. Architecture of the U5 small nuclear RNA. Mol. Cell. Biol. 14:2180-2190.
22. Gottschalk, A., G. Neubauer, J. Banroques, M. Mann, R. Lührmann, and P. Fabrizio. 1999. Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6 52 U5] tri-snRNP. EMBO J. 18:4535-4548.
23. Guarente, L. 1993. Synthetic enhancement in gene interaction: a genetic tool come of age. Trends Genet. 9:362-366.
24. Hill, J., K. A. Ian, G. Donald, and D. E. Griffiths. 1991. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 19:5791.
25. Hilleren, P. J., and R. Parker. 2003. Cytoplasmic degradation of splicedefective pre-mRNAs and intermediates. Mol. Cell. 12:1453-1465.
26. Horowitz, D. S., and J. Abelson. 1993. Stages in the second reaction of pre-mRNA splicing: the final step is ATP independent. Genes Dev. 7:320-329.
27. Horowitz, D. S., and J. Abelson. 1993. A U5 small nuclear ribonucleoprotein particle protein involved only in the second step of splicing in Saccharomyces cerevisiae. Mol. Cell. Biol. 13:2959-2970.
28. Horowitz, D. S., and A. R. Krainer. 1997. A human protein required for the second step of pre-mRNA splicing is functionally related to a yeast splicing factor. Genes Dev. 11:139-151.
29. Hotz, H. R., and B. Schwer. 1998. Mutational analysis of the yeast DEAH-Box splicing factor prp16. Genetics 149:807-815.
30. Huffaker, T. C., M. A. Hoyt, and D. Botstein. 1987. Genetic analysis of the yeast cytoskeleton. Annu. Rev. Genet. 21:259-284.
31. James, S. A., W. Turner, and B. Schwer. 2002. How Slu7 and Prp18 cooperate in the second step of yeast pre-mRNA splicing. RNA 8:1068-1077.
32. Jiang, J., D. S. Horowitz, and R.-M. Xu. 2000. Crystal structure of the functional domain of the splicing factor Prp18. Proc. Natl. Acad. Sci. USA 97:3022-3027.
33. Jones, M. H., D. N. Frank, and C. Guthrie. 1995. Characterization and functional ordering of Slu7p and Prp17p during the second step of pre-mRNA splicing in yeast. Proc. Natl. Acad. Sci. USA 92:9687-9691.
34. Jurica, M. S., and M. J. Moore. 2003. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell 12:5-14.
35. McPheeters, D. S., and J. Abelson. 1992. Mutational analysis of the yeast U2 snRNA suggests a structural similarity to the catalytic core of group I introns. Cell 71:819-831.
36. McPheeters, D. S., and P. Muhlenkamp. 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.
37. Newman, A., and C. Norman. 1991. Mutations in yeast U5 snRNA alter the specificity of 5′ splice-site cleavage. Cell 65:115-123.
38. Newman, A. J. 1997. The role of U5 snRNP in pre-mRNA splicing. EMBO J. 16:5797-5800.
39. Newman, A. J., and C. Norman. 1992. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68:743-754.
40. Newman, A. J., S. Teigelkamp, and J. D. Beggs. 1995. snRNA interactions at 5′ and 3′ splice sites monitored by photoactivated crosslinking in yeast spliceosomes. RNA 1:968-980.
41. O'Keefe, R. T. 2002. Mutations in U5 snRNA loop I influence the splicing of different genes in vivo. Nucleic Acids Res. 30:5476-5484.
42. O'Keefe, R. T., and A. J. Newman. 1998. Functional analysis of the U5 snRNA loop 1 in the second catalytic step of yeast pre-mRNA splicing. EMBO J. 17:565-574.
43. O'Keefe, R. T., C. Norman, and A. J. Newman. 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.
44. Patterson, B., and C. Guthrie. 1987. An essential yeast snRNA with a U5-like domain is required for splicing in vivo. Cell 49:613-624.
45. Query, C. C., and M. M. Konarska. 2004. Suppression of multiple substrate mutations by spliceosomal prp8 alleles suggests functional correlations with ribosomal ambiguity mutants. Mol. Cell 14:343-354.
46. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning, a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
47. Sapra, A. K., Y. Arava, P. Khandelia, and U. Vijayraghavan. 2004. Genome-wide analysis of pre-mRNA splicing: intron features govern the requirement for the second-step factor Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. J. Biol. Chem. 279:52437-52446.
48. Schwer, B., and C. H. Gross. 1998. Prp22, a DExH RNA helicase, plays two distinct roles in yeast pre-mRNA splicing. EMBO J. 17:2086-2094.
49. Schwer, B., and C. Guthrie. 1992. A conformational rearrangement in the spliceosome is dependent on PRP16 and ATP hydrolysis. EMBO J. 11:5033-5039.
50. Schwer, B., and C. Guthrie. 1991. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 349:494-499.
51. Ségault, V., C. L. Will, M. Polycarpou-Schwarz, I. W. Mattaj, C. Branlant, and R. Lührmann. 1999. Conserved loop I of U5 small nuclear RNA is dispensable for both catalytic steps of pre-mRNA splicing in HeLa nuclear extracts. Mol. Cell. Biol. 19:2782-2790.
52. Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
53. Sontheimer, E. J., and J. A. Steitz. 1993. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262:1989-1996.
54. Staley, J. P., and C. Guthrie. 1998. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92:315-326.
55. Teigelkamp, S., A. J. Newman, and J. D. Beggs. 1995. Extensive interactions of PRP8 protein with the 5′ and 3′ splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA. EMBO J. 14:2602-2612.
56. Thomas, B. J., and R. Rothstein. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56:619-630.
57. Turner, I. A., C. M. Norman, M. J. Churcher, and A. J. Newman. 2004. Roles of the U5 snRNP in spliceosome dynamics and catalysis. Biochem. Soc. Trans. 32:928-931.
58. Umen, J. G., and C. Guthrie. 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.
59. Vijayraghavan, U., M. Company, and J. Abelson. 1989. Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev. 3:1206-1216.
60. Wach, A. 1996. PCR synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12:259-265.
61. Zhang, X., and B. Schwer. 1997. Functional and physical interaction between the yeast splicing factors Slu7 and Prp18. Nucleic Acids Res. 25:2146-2152.