Invariant U2 RNA Sequences Bordering the Branchpoint Recognition Region Are Essential for Interaction with Yeast SF3a and SF3b Subunits

REFERENCES

• Abovich, N., P. Legrain, and M. Rosbash. 1990. The yeast PRP6 gene encodes a U4/U6 small nuclear ribonucleoprotein particle (snRNP) protein, and the PRP9 gene encodes a protein required for U2 snRNP binding. Mol. Cell. Biol. 10:6417–6425.
   PubMedGoogle Scholar
• Abovich, N., X. C. Liao, and M. Rosbash. 1994. The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes Dev. 8:843–854.
   PubMed Web of Science ®Google Scholar
• Arenas, J. E., and J. N. Abelson. 1993. The Saccharomyces cerevisiae PRP21 gene product is an integral component of the prespliceosome. Proc. Natl. Acad. Sci. USA 90:6771–6775.
   PubMedGoogle Scholar
• Ares, M., Jr. Unpublished data.
   Google Scholar
• Ares, M., Jr., and A. H. Igel. 1989. Phylogenetic comparison of U2 small nuclear RNA sequences suggests a pseudoknotted structure. UCLA Symp. Mol. Cell. Biol. 94:13–23.
   Google Scholar
• Ares, M., Jr., and A. H. Igel. 1990. Lethal and temperature-sensitive mutations and their suppressors identify an essential structure element in U2 small nuclear RNA. Genes Dev. 4:2132–2145.
   PubMed Web of Science ®Google Scholar
• Ares, M., Jr., and B. Weiser. 1995. Rearrangement of snRNA structure during assembly and function of the spliceosome. Prog. Nucleic Acid Res. Mol. Biol. 50:131–159.
   PubMedGoogle Scholar
• Behrens, S.-E., F. Galisson, P. Legrain, and R. Luhrmann. 1993. Evidence that the 60-kDa protein of 17S U2 small nuclear ribonucleoprotein is immunologically and functionally related to the yeast PRP9 splicing factor and is required for the efficient formation of prespliceosomes. Proc. Natl. Acad. Sci. USA 90:8229–8233.
   PubMed Web of Science ®Google Scholar
• Behrens, S.-E., K. Tyc, B. Kastner, J. Reichelt, and R. Luhrmann. 1993. Small nuclear ribonucleoprotein (RNP) U2 contains numerous additional proteins and has a bipartite RNP structure under splicing conditions. Mol. Cell. Biol. 13:307–319.
   PubMedGoogle Scholar
• Bennett, M., and R. Reed. 1993. Correspondence between a mammalian spliceosome component and an essential yeast splicing factor. Science 262:105–108.
   PubMedGoogle Scholar
• Boeke, J. D., J. Trueheart, G. Natsoulis, and G. R. Fink. 1987. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 154:164–175.
   PubMed Web of Science ®Google Scholar
• Brosi, R., K. Groning, S.-E. Behrens, R. Luhrmann, and A. Kramer. 1993. Interaction of mammalian splicing factor SF3a with U2 snRNP and relation of its 60-kD subunit to yeast PRP9. Science 262:102–105.
   PubMed Web of Science ®Google Scholar
• Brosi, R., H.-P. Hauri, and A. Kramer. 1993. Separation of splicing factor SF3 into two components and purification of SF3a activity. J. Biol. Chem. 268:17640–17646.
   PubMed Web of Science ®Google Scholar
• Brow, D. A., and R. M. Vidaver. 1995. An element in human U6 RNA destabilizes the U4/U6 spliceosomal RNA complex. RNA 1:122–131.
   PubMed Web of Science ®Google Scholar
• Cech, T. R. 1985. RNA splicing: three themes with variations. Cell 43:713–716.
   Google Scholar
• Chang, T.-H., M. W. Clark, A. J. Lustig, M. E. Cusick, and J. Abelson. 1988. RNA 11 protein is associated with the yeast spliceosome and is localized in the periphery of the cell nucleus. Mol. Cell. Biol. 8:2379–2393.
   PubMedGoogle Scholar
• Chapon, C., and P. Legrain. 1992. A novel gene, spp91-1, suppresses the splicing defect and the pre-mRNA nuclear export in the prp9-1 mutant. EMBO J. 11:3279–3288.
   PubMedGoogle Scholar
• Chattoo, B., F. Sherman, T. Fejellstedt, D. Menhnert, and M. Ogur. 1979. Selection of lys2 mutants of the yeast Saccharomyces cerevisiae by the utilization of alpha-aminoadipate. Genetics 93:51–65.
   PubMed Web of Science ®Google Scholar
• Datta, B., and A. M. Weiner. 1991. Genetic evidence for base pairing between U2 and U6 snRNA in mammalian mRNA splicing. Nature (London) 352:821–824.
   PubMed Web of Science ®Google Scholar
• Datta, B., and A. M. Weiner. 1993. The phylogenetically invariant ACAG AGA and AGC sequence of U6 small nuclear RNA are more tolerant of mutation in human cells than in Saccharomyces cerevisiae. Mol. Cell. Biol. 13:5377–5382.
   PubMedGoogle Scholar
• Dower, W. J., J. F. Miller, and C. W. Ragsdale. 1988. High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 16:6127–6145.
   PubMed Web of Science ®Google 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
• Fabrizio, P., D. S. McPheeters, and J. Abelson. 1989. In vitro assembly of yeast U6 snRNP: a functional assay. Genes Dev. 3:2137–2150.
   PubMedGoogle Scholar
• Fortner, D. M., R. G. Troy, and D. A. Brow. 1994. A stem/loop in U6 RNA defines a conformational switch required for pre-mRNA splicing. Genes Dev. 8:221–233.
   PubMed Web of Science ®Google Scholar
• Frank, D., B. Patterson, and C. Guthrie. 1992. Synthetic lethal mutations suggest interactions between U5 small nuclear RNA and four proteins required for the second step of splicing. Mol. Cell. Biol. 12:5197–5205.
   PubMed Web of Science ®Google Scholar
• Ghetti, A., M. Company, and J. Abelson. 1995. Specificity of Prp24 binding to RNA: a role for Prp24 in the dynamic interaction of U4 and U6 snRNAs. RNA 1:132–145.
   PubMedGoogle Scholar
• Gozani, O., J. G. Patton, and R. Reed. 1994. A novel set of spliceosome-associated proteins (SAPs) and the essential splicing factor PSF bind stably to pre-mRNA prior to catalytic step II of the splicing reaction. EMBO J. 13:3356–3367.
   PubMedGoogle Scholar
• Guthrie, C., and B. Patterson. 1988. Spliceosomal snRNAs. Annu. Rev. Genet. 22:387–419.
   PubMedGoogle Scholar
• Hausner, T. P., L. M. Giglio, and A. M. Weiner. 1990. Evidence for basepairing between mammalian U2 and U6 small nuclear ribonucleoprotein particles. Genes Dev. 4:2146–2156.
   PubMedGoogle Scholar
• Hodges, P. E., and J. D. Beggs. 1994. U2 fulfills a commitment. Curr. Biol. 4:264–267.
   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
• Igel, A. H., and M. Ares, Jr. 1988. Internal sequences that distinguish yeast from metazoan U2 are unnecessary for pre-mRNA splicing. Nature (London) 334:450–453.
   PubMed Web of Science ®Google Scholar
• Ito, H., Y. Fakuda, K. Murata, and A. Kimura. 1983. Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 153:163–168.
   PubMed Web of Science ®Google Scholar
• Jacquier, A., J. R. Rodriguez, and M. Rosbash. 1985. A quantitative analysis of the effects of 5′ junction and TACTAAC box mutants and mutant combinations on yeast mRNA splicing. Cell 43:423–430.
   PubMed Web of Science ®Google Scholar
• Jandrositz, A., and C. Guthrie. 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.
   PubMedGoogle Scholar
• Kandels-Lewis, S., and B. Seraphin. 1993. Role of U6 snRNA in 5′ splice site selection. Science 262:2035–2039.
   PubMedGoogle Scholar
• Kunkel, T. 1985. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA 82:488–492.
   PubMed Web of Science ®Google Scholar
• Legrain, P., C. Chapon, and F. Galisson. 1993. Interactions between PRP9 and SPP91 splicing factors identify a protein complex required in presplice-osome assembly. Genes Dev. 7:1390–1399.
   PubMedGoogle Scholar
• Lesser, C. F., and C. Guthrie. 1993. Mutations in U6 snRNA that alter splice site specificity: implications for the active site. Science 262:1982–1988.
   PubMedGoogle Scholar
• Lin, R.-J., A. J. Lustig, and J. Abelson. 1987. Splicing of yeast nuclear pre-mRNA in vitro requires a functional 40S spliceosome and several extrinsic factors. Genes Dev. 1:7–18.
   PubMedGoogle Scholar
• Madhani, H. D., R. Bordonne, and C. Guthrie. 1990. Multiple roles for U6 snRNA in the splicing pathway. Genes Dev. 4:2264–2277.
   PubMedGoogle Scholar
• Madhani, H. D., and C. Guthrie. 1992. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell 17:803–817.
   Google Scholar
• Madhani, H. D., and C. Guthrie. 1994. Randomization-selection analysis of snRNAs in vivo: evidence for a tertiary interaction in the spliceosome. Genes Dev. 8:1071–1086.
   PubMed Web of Science ®Google Scholar
• Madhani, H. D., and C. Guthrie. 1994. Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet. 28:1–26.
   PubMedGoogle 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
• Miller, A. 1984. The yeast MATa1 gene contains two introns. EMBO J. 3:1061–1065.
   PubMedGoogle Scholar
• Miraglia, L., S. Steiwert, A. H. Igel, and M. Ares, Jr. 1991. Limited functional equivalence of phylogenetic variation in small nuclear RNA: yeast U2 RNA with altered branchpoint complementarity inhibits splicing and produces a dominant lethal phenotype. Proc. Natl. Acad. Sci. USA 88:7061–7065.
   PubMed Web of Science ®Google Scholar
• Moore, M. J., C. C. Query, and P. A. Sharp. 1993. Splicing of precursors to mRNA by the spliceosome, p. 303–357. In R. Gesteland and J. Atkins (ed.), The RNAworld. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
   Google Scholar
• Newman, A. 1994. Small nuclear RNAs and pre-mRNA splicing. Curr. Opin. Cell Biol. 6:360–367.
   PubMedGoogle Scholar
• Nilsen, T. W. 1994. RNA-RNA interactions in the spliceosome: unraveling the ties that bind. Cell 78:1–4.
   PubMedGoogle Scholar
• Orum, H., H. Nielsen, and J. Engberg. 1991. Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA basepairing interactions. J. Mol. Biol. 222:219–232.
   PubMedGoogle Scholar
• Parker, R. A., P. G. Siliciano, and C. Guthrie. 1987. Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. Cell 49:229–239.
   PubMed Web of Science ®Google Scholar
• Ruby, S. W., T.-H. Chang, and J. Abelson. 1993. Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA. Genes Dev. 7:1909–1925.
   PubMed Web of Science ®Google Scholar
• Sawa, H., and J. Abelson. 1992. Evidence for a base-pairing interaction between U6 small nuclear RNA and 5′ splice site during the splicing reaction in yeast. Proc. Natl. Acad. Sci. USA 89:11269–11273.
   PubMedGoogle Scholar
• Shannon, K. W., and C. Guthrie. 1991. Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA-binding motif. Genes Dev. 5:773–785.
   PubMedGoogle Scholar
• Sharp, P. A. 1985. On the origin of RNA splicing and introns. Cell 42:397–400.
   PubMed Web of Science ®Google Scholar
• Sherman, F., G. Fink, and J. Hicks. 1986. Methods in yeast genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Shuster, E. O., and C. Guthrie. 1988. Two conserved domains of yeast U2 snRNA are separated by 945 nonessential nucleotides. Cell 55:41–48.
   PubMed Web of Science ®Google Scholar
• Staknis, D., and R. Reed. 1994. Direct interactions between pre-mRNA and six U2 small nuclear ribonucleoproteins during spliceosome assembly. Mol. Cell. Biol. 14:2994–3005.
   PubMedGoogle Scholar
• Sun, J., and J. L. Manley. 1994. A novel U2-U6 snRNA structure is necessary for mammalian mRNA splicing. Genes Dev. 9:843–854.
   Google Scholar
• Takahashi, Y., S. Urushiyama, T. Tani, and Y. Ohshima. 1993. An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene. Mol. Cell. Biol. 13:5613–5619.
   PubMedGoogle Scholar
• Vankan, P., C. McGuigan, and I. W. Mattaj. 1990. Domains of U4 and U6 snRNAs required for snRNP assembly and splicing complementation in Xenopus oocytes. EMBO J. 9:3397–3404.
   PubMedGoogle Scholar
• Wassarman, D. A., and J. A. Steitz. 1992. Interactions of small nuclear RNAs with precursor messenger RNA during in vitro splicing. Science 257:1918–1925.
   PubMed Web of Science ®Google Scholar
• Wells, S. E., and Ares, M., Jr. 1994. Interactions between highly conserved U2 small nuclear RNA structures and Prp5p, Prp9p, Prp11p, and Prp21p proteins are required to ensure integrity of the U2 small nuclear ribonuleo-protein in Saccharomyces cerevisiae. Mol. Cell. Biol. 14:6337–6349.
   PubMed Web of Science ®Google Scholar
• Wells, S. E., M. Neville, M. Haynes, J. Wang, H. Igel, and M. Ares, Jr. CUS1, a suppressor of cold sensitive U2 snRNA mutations, is a novel yeast splicing factor homologous to human SAP145. Genes Dev., in press.
   Google Scholar
• Wolff, T., R. Menssen, J. Hammel, and A. Bindereif. 1994. Splicing function of mammalian U6 small nuclear RNA: conserved positions in central domain and helix I are essential during the first and second step of pre-mRNA splicing. Proc. Natl. Acad. Sci. USA 91:903–907.
   PubMedGoogle Scholar
• Wu, J., and J. L. Manley. 1989. Mammalianpre-mRNAbranch site selection by U2 snRNP involves base pairing. Genes Dev. 3:1553–1561.
   PubMed Web of Science ®Google Scholar
• Wu, J., and J. L. Manley. 1991. Base pairing between U2 and U6 snRNs is necessary for splicing of a mammalian pre-mRNA. Nature (London) 352:818–821.
   PubMedGoogle Scholar
• Wu, J., and J. L. Manley. 1992. Multiple functional domains of human U2 small nuclear RNA: strengthening conserved stem I can block splicing. Mol. Cell. Biol. 12:5464–5473.
   PubMed Web of Science ®Google Scholar
• Zavanelli, M., J. Britton, H. Igel, and M. Ares, Jr. 1994. Mutations in an essential U2 small nuclear RNA structure cause cold sensitive U2 small nuclear ribonucleoprotein function by favoring competing U2 RNA structures. Mol. Cell. Biol. 14:1689–1697.
   PubMed Web of Science ®Google Scholar
• Zavanelli, M. I., and M. Ares, Jr. 1991. Efficient association of U2 snRNPs with pre-mRNA requires an essential U2 RNA structural element. Genes Dev. 5:2521–2533.
   PubMed Web of Science ®Google Scholar
• Zhuang, Y., and A. M. Weiner. 1989. A compensatory base change in human U2 snRNA can suppress a branch site mutation. Genes Dev. 3:1545–1552.
   PubMed Web of Science ®Google Scholar