Genetic and Functional Interaction of Evolutionarily Conserved Regions of the Prp18 Protein and the U5 snRNA

REFERENCES

• 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.
   PubMedGoogle Scholar
• Bačíková, D., and D. S. Horowitz. 2002. Mutational analysis identifies two separable roles of the Saccharomyces cerevisiae splicing factor Prp18. RNA 8:1280–1293.
   PubMedGoogle Scholar
• 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.
   Google Scholar
• Bousquet-Antonelli, C., C. Presutti, and D. Tollervey. 2000. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102:765–775.
   PubMed Web of Science ®Google Scholar
• Brow, D. A. 2002. Allosteric cascade of spliceosome activation. Annu. Rev. Genet. 36:333–360.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Cheng, S.-C., and J. Abelson. 1987. Spliceosome assembly in yeast. Genes Dev. 1:1014–1027.
   PubMed Web of Science ®Google Scholar
• Chua, K., and R. Reed. 1999. The RNA splicing factor hSlu7 is required for correct 3′ splice-site choice. Nature 402:207–210.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   Google Scholar
• Collins, C. A., and C. Guthrie. 2000. The question remains: is the spliceosome a ribozyme. Nat. Struct. Biol. 7:850–854.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabelling DNA restriction fragments to high specific activity. Anal. Biochem. 132:6–13.
   PubMed Web of Science ®Google Scholar
• Frank, D., and C. Guthrie. 1992. An essential splicing factor, SLU7, mediates 3′ splice site choice in yeast. Genes Dev. 6:2112–2124.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Frank, D. N., H. Roiha, and C. Guthrie. 1994. Architecture of the U5 small nuclear RNA. Mol. Cell. Biol. 14:2180–2190.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Guarente, L. 1993. Synthetic enhancement in gene interaction: a genetic tool come of age. Trends Genet. 9:362–366.
   PubMed Web of Science ®Google Scholar
• Hill, J., K. A. Ian, G. Donald, and D. E. Griffiths. 1991. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 19:5791.
   PubMed Web of Science ®Google Scholar
• Hilleren, P. J., and R. Parker. 2003. Cytoplasmic degradation of splice-defective pre-mRNAs and intermediates. Mol. Cell. 12:1453–1465.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• Hotz, H. R., and B. Schwer. 1998. Mutational analysis of the yeast DEAH-Box splicing factor prp16. Genetics 149:807–815.
   PubMedGoogle Scholar
• Huffaker, T. C., M. A. Hoyt, and D. Botstein. 1987. Genetic analysis of the yeast cytoskeleton. Annu. Rev. Genet. 21:259–284.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• Jurica, M. S., and M. J. Moore. 2003. Pre-mRNA splicing: awash in a sea of proteins. Mol. Cell 12:5–14.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Newman, A., and C. Norman. 1991. Mutations in yeast U5 snRNA alter the specificity of 5′ splice-site cleavage. Cell 65:115–123.
   PubMed Web of Science ®Google Scholar
• Newman, A. J. 1997. The role of U5 snRNP in pre-mRNA splicing. EMBO J. 16:5797–5800.
   PubMedGoogle Scholar
• Newman, A. J., and C. Norman. 1992. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68:743–754.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Schwer, B., and C. Guthrie. 1992. A conformational rearrangement in the spliceosome is dependent on PRP16 and ATP hydrolysis. EMBO J. 11:5033–5039.
   PubMed Web of Science ®Google Scholar
• Schwer, B., and C. Guthrie. 1991. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 349:494–499.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Staley, J. P., and C. Guthrie. 1998. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92:315–326.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Thomas, B. J., and R. Rothstein. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56:619–630.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• Vijayraghavan, U., M. Company, and J. Abelson. 1989. Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev. 3:1206–1216.
   PubMed Web of Science ®Google Scholar
• Wach, A. 1996. PCR synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12:259–265.
   PubMed Web of Science ®Google Scholar
• Zhang, X., and B. Schwer. 1997. Functional and physical interaction between the yeast splicing factors Slu7 and Prp18. Nucleic Acids Res. 25:2146–2152.
   PubMedGoogle Scholar