Conservation of the Protein Composition and Electron Microscopy Structure of Drosophila melanogaster and Human Spliceosomal Complexes

REFERENCES

• Amero, S. A., M. J. Matunis, E. L. Matunis, J. W. Hockensmith, G. Raychaudhuri, and A. L. Beyer. 1993. A unique ribonucleoprotein complex assembles preferentially on ecdysone-responsive sites in Drosophila melanogaster. Mol. Cell Biol. 13:5323–5330.
   PubMedGoogle Scholar
• Ballut, L., B. Marchadier, A. Baguet, C. Tomasetto, B. Séraphin, and H. Le Hir. 2005. The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nat. Struct. Mol. Biol. 12:861–869.
   PubMed Web of Science ®Google Scholar
• Behzadnia, N., M. M. Golas, K. Hartmuth, B. Sander, B. Kastner, J. Deckert, P. Dube, C. L. Will, H. Urlaub, H. Stark, and R. Lührmann. 2007. Composition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes. EMBO J. 26:1737–1748.
   PubMed Web of Science ®Google Scholar
• Berget, S. M. 1995. Exon recognition in vertebrate splicing. J. Biol. Chem. 270:2411–2414.
   PubMed Web of Science ®Google Scholar
• Bessonov, S., M. Anokhina, C. L. Will, H. Urlaub, and R. Lührmann. 2008. Isolation of an active step I spliceosome and composition of its RNP core. Nature 452:846–850.
   PubMed Web of Science ®Google Scholar
• Black, D. L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72:291–336.
   PubMed Web of Science ®Google Scholar
• Boehringer, D., E. M. Makarov, B. Sander, O. V. Makarova, B. Kastner, R. Lührmann, and H. Stark. 2004. Three-dimensional structure of a pre-catalytic human spliceosomal complex B. Nat. Struct. Mol. Biol. 11:463–468.
   PubMedGoogle Scholar
• Celniker, S. E., and G. M. Rubin. 2003. The Drosophila melanogaster genome. Annu. Rev. Genomics Hum. Genet. 4:89–117.
   PubMedGoogle Scholar
• Chan, S. P., D. I. Kao, W. Y. Tsai, and S. C. Cheng. 2003. The Prp19p-associated complex in spliceosome activation. Science 302:279–282.
   PubMed Web of Science ®Google Scholar
• Chaouki, A. S., and H. K. Salz. 2006. Drosophila SPF45: a bifunctional protein with roles in both splicing and DNA repair. PLoS Genet. 2:1974–1983.
   Google Scholar
• Deckert, J., K. Hartmuth, D. Boehringer, N. Behzadnia, C. L. Will, B. Kastner, H. Stark, H. Urlaub, and R. Lührmann. 2006. Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions. Mol. Cell. Biol. 26:5528–5543.
   PubMed Web of Science ®Google Scholar
• Dignam, J. D., R. M. Lebovitz, and R. G. Roeder. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11:1475–1489.
   PubMed Web of Science ®Google Scholar
• Dube, P., R. Tavares, R. Lurz, and M. van Heel. 1993. The portal protein of bacteriophage SPP1: a DNA pump with 13-fold symmetry. EMBO J. 12:1303–1309.
   PubMedGoogle Scholar
• Förch, P., and J. Valcárcel. 2003. Splicing regulation in Drosophila sex determination. Prog. Mol. Subcell. Biol. 31:127–151.
   PubMedGoogle Scholar
• Fortes, P., D. Bilbao-Cortés, M. Fornerod, G. Rigaut, W. Raymond, B. Séraphin, and I. W. Mattaj. 1999. Luc7p, a novel yeast U1 snRNP protein with a role in 5′ splice site recognition. Genes Dev. 13:2425–2438.
   PubMedGoogle Scholar
• Fribourg, S., D. Gatfield, E. Izaurralde, and E. Conti. 2003. A novel mode of RBD-protein recognition in the Y14-Mago complex. Nat. Struct. Biol. 10:433–439.
   PubMedGoogle Scholar
• Gatfield, D., L. Unterholzner, F. D. Ciccarelli, P. Bork, and E. Izaurralde. 2003. Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J. 22:3960–3970.
   PubMed Web of Science ®Google Scholar
• Guo, M., P. C. Lo, and S. M. Mount. 1993. Species-specific signals for the splicing of a short Drosophila intron in vitro. Mol. Cell. Biol. 13:1104–1118.
   PubMedGoogle Scholar
• Hachet, O., and A. Ephrussi. 2001. Drosophila Y14 shuttles to the posterior of the oocyte and is required for oskar mRNA transport. Curr. Biol. 11:1666–1674.
   PubMed Web of Science ®Google Scholar
• Hartmuth, K., H. Urlaub, H.-P. Vornlocher, C. L. Will, M. Gentzel, M. Wilm, and R. Lührmann. 2002. Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method. Proc. Natl. Acad. Sci. USA 99:16719–16724.
   PubMed Web of Science ®Google Scholar
• Johnstone, O., and P. Lasko. 2001. Translational regulation and RNA localization in Drosophila oocytes and embryos. Annu. Rev. Genet. 35:365–406.
   PubMedGoogle Scholar
• Jurica, M. S., L. J. Licklider, S. R. Gygi, N. Grigorieff, and M. J. Moore. 2002. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA 8:426–439.
   PubMed Web of Science ®Google 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
• Jurica, M. S., D. Sousa, M. J. Moore, and N. Grigorieff. 2004. Three-dimensional structure of C complex spliceosomes by electron microscopy. Nat. Struct. Mol. Biol. 11:265–269.
   PubMedGoogle Scholar
• Kastner, B., and R. Lührmann. 1989. Electron microscopy of U1 small nuclear ribonucleoprotein particles: shape of the particle and position of the 5′ RNA terminus. EMBO J. 8:277–286.
   PubMed Web of Science ®Google Scholar
• Kastner, B., N. Fischer, M. M. Golas, B. Sander, P. Dube, D. Boehringer, K. Hartmuth, J. Deckert, J., F. Hauer, E. Wolf, H. Uchtenhagen, H. Urlaub, F. Herzog, J. M. Peters, D. Poerschke, R. Lührmann, and H. Stark. 2008. GraFix: sample preparation for single-particle electron cryomicroscopy. Nat. Methods 5:53–55.
   PubMed Web of Science ®Google Scholar
• Konarska, M. M. 1989. Analysis of splicing complexes and small nuclear ribonucleoprotein particles by native gel electrophoresis. Methods Enzymol. 180:442–453.
   PubMedGoogle Scholar
• Le Hir, H., E. Izaurralde, L. E. Maquat, and M. J. Moore. 2000. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19:6860–6869.
   PubMed Web of Science ®Google Scholar
• Lim, L. P., and C. Burge. 2001. A computational analysis of sequence features involved in recognition of short introns. Proc. Natl. Acad. Sci. USA 98:11193–11198.
   PubMed Web of Science ®Google Scholar
• Makarov, E. M., O. V. Makarova, H. Urlaub, M. Gentzel, C. L. Will, M. Wilm, and R. Lührmann. 2002. Small nuclear ribonucleoprotein remodelling during catalytic activation of the spliceosome. Science 298:2205–2208.
   PubMed Web of Science ®Google Scholar
• Makarova, O. V., E. M. Makarov, H. Urlaub, C. L. Will, M. Gentzel, M. Wilm, and R. Lührmann. 2004. A subset of human 35S U5 proteins, including Prp19, function prior to catalytic step 1 of splicing. EMBO J. 23:2381–2391.
   PubMed Web of Science ®Google Scholar
• Matunis, M. J., E. L. Matunis, and G. Dreyfuss. 1994. Isolation and characterization of RNA-binding proteins from Drosophila melanogaster. Methods Cell Biol. 44:191–205.
   PubMedGoogle Scholar
• Merz, C., H. Urlaub, C. L. Will, and R. Lührmann. 2007. Protein composition of human mRNPs spliced in vitro and differential requirements for mRNP protein recruitment. RNA 13:116–128.
   PubMed Web of Science ®Google Scholar
• Moore, M. J. 2005. From birth to death: the complex lives of eukaryotic mRNAs. Science 309:1514–1518.
   PubMed Web of Science ®Google Scholar
• Mount, S. M., C. Burks, G. Hertz, G. D. Stormo, O. White, and C. Fields. 1992. Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res. 20:4255–4262.
   PubMed Web of Science ®Google Scholar
• Mount, S. M., and H. K. Salz. 2000. Pre-messenger RNA processing factors in the Drosophila genome. J. Cell Biol. 150:F37–F44.
   PubMed Web of Science ®Google Scholar
• Nilsen, T. W. 1998. RNA-RNA interactions in nuclear pre-mRNA splicing, p. 279-307. In R. W. Simons and M. Grunberg-Manago (ed.), RNA structure and function. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
   Google Scholar
• Palacios, I. M., D. Gatfield, D. St. Johnston, and E. Izaurralde. 2004. An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay. Nature 427:753–757.
   PubMed Web of Science ®Google Scholar
• Park, J. W., and B. R. Graveley. 2007. Complex alternative splicing. Adv. Exp. Med. Biol. 623:50–63.
   PubMedGoogle Scholar
• Rappsilber, J., U. Ryder, A. I. Lamond, and M. Mann. 2002. Large-scale proteomic analysis of the human spliceosome. Genome Res. 12:1231–1245.
   PubMed Web of Science ®Google Scholar
• Reed, R. 1996. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr. Opin. Genet. Dev. 6:215–220.
   PubMed Web of Science ®Google Scholar
• Reed, R., and H. Cheng. 2005. TREX, SR proteins and export of mRNA. Curr. Opin. Cell Biol. 17:269–273.
   PubMed Web of Science ®Google Scholar
• Reed, R., and T. Maniatis. 1985. Intron sequences involved in lariat formation during pre-mRNA splicing. Cell 41:95–105.
   PubMed Web of Science ®Google Scholar
• Rehwinkel, J., A. Herold, K. Gari, T. Köcher, M. Rode, F. L. Ciccarelli, M. Wilm, and E. Izaurralde. 2004. Genome-wide analysis of mRNAs regulated by the THO complex in Drosophila melanogaster. Nat. Struct. Mol. Biol. 11:558–566.
   PubMed Web of Science ®Google Scholar
• Rio, D. C. 1988. Accurate and efficient pre-mRNA splicing in Drosophila cell-free extracts. Proc. Natl. Acad. Sci. USA 85:2904–2908.
   PubMedGoogle Scholar
• Sander, B., M. M. Golas, E. M. Makarov, H. Brahms, B. Kastner, R. Lührmann, and H. Stark. 2006. Organization of core spliceosomal components U5 snRNA loop I and U4/U6 di-snRNP within U4/U6.U5 tri-snRNP as revealed by electron cryomicroscopy. Mol. Cell 24:267–278.
   PubMedGoogle Scholar
• Sanford, J. R., J. Ellis, and J. F. Cáceres. 2005. Multiple roles of arginine/serine-rich splicing factors in RNA processing. Biochem. Soc. Trans. 33:443–446.
   PubMedGoogle Scholar
• Sheth, N., X. Roca, M. L. Hastings, T. Roeder, A. R. Krainer, and R. Sachidanandam. 2006. Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res. 34:3955–3967.
   PubMed Web of Science ®Google Scholar
• Shi, H., and R. M. Xu. 2003. Crystal structure of the Drosophila Mago nashi-Y14 complex. Genes Dev. 17:971–976.
   PubMed Web of Science ®Google Scholar
• Spikes, D., and P. M. Bingham. 1992. Analysis of spliceosome assembly and the structure of a regulated intron in Drosophila in vitro splicing extracts. Nucleic Acids Res. 20:5719–5727.
   PubMedGoogle 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
• Talerico, M., and S. M. Berget. 1994. Intron definition in splicing of small Drosophila introns. Mol. Cell. Biol. 14:3434–3445.
   PubMed Web of Science ®Google Scholar
• Tange, T. Ø., T. Shibuya, M. S. Jurica, and M. J. Moore. 2005. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 11:1869–1883.
   PubMed Web of Science ®Google Scholar
• Tange, T. Ø., A. Nott, and M. J. Moore. 2004. The ever-increasing complexities of the exon junction complex. Curr. Opin. Cell Biol. 16:279–284.
   PubMed Web of Science ®Google Scholar
• Valadkhan, S. 2005. snRNAs as the catalysts of pre-mRNA splicing. Curr. Opin. Chem. Biol. 9:603–608.
   PubMedGoogle Scholar
• van Heel, M., and J. Frank. 1981. Use of multivariate statistics in analysing the images of biological macromolecules. Ultramicroscopy 6:187–194.
   PubMed Web of Science ®Google Scholar
• van Heel, M. 1989. Classification of very large electron microscopical image data sets. Optik 82:114–126.
   Web of Science ®Google Scholar
• Wieringa, B., E. Hofer, and C. Weissmann. 1984. A minimal intron length but no specific internal sequence is required for splicing the large rabbit beta-globin intron. Cell 37:915–925.
   PubMed Web of Science ®Google Scholar
• Will, C. L., and R. Lührmann. 2006. Spliceosome structure and function, p. 369-400. In R. F. Gesteland, T. R. Cech, and J. F. Atkins (ed.), The RNA world, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
   Google Scholar
• Zhang, Z., and A. R. Krainer. 2007. Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components. Proc. Natl. Acad. Sci. USA 104:11574–11579.
   PubMed Web of Science ®Google Scholar
• Zhou, Z., L. J. Licklider, S. P. Gygi, and R. Reed. 2002. Comprehensive proteomic analysis of the human spliceosome. Nature 419:182–185.
   PubMed Web of Science ®Google Scholar