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Mechanism and Control of Pre-mRNA Splicing

  • Andreas N. Kuhn
  • Norbert E. Käufer

Abstract

Most protein-encoding genes in eukaryotes are interrupted by intervening sequences that must be precisely removed to assure correct gene expression. The process by which these intervening sequences, the introns, are excised from a pre-mRNA and the flanking sequences, the exons, are joined to generate a functional mRNA is called pre-mRNA splicing. Pre-mRNA splicing is executed by a large ribonucleoprotein (RNP) machinery, the spliceosome, which consists of five small nuclear RNAs (snRNAs), U1, U2, U4, U5, and U6, and more than 80 proteins (Burge et al. 1999). The spliceosome is a highly dynamic complex, and extensive RNA-RNA and RNA-protein interactions are involved in the recognition of an intron and its removal from the pre-mRNA.

Keywords

Splice Site Spinal Muscular Atrophy Fission Yeast Splice Factor Survival Motor Neuron 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Ajuh P, Sleeman J, Chusainow J, Lamond AI (2001) A direct interaction between the carboxyl-terminal region of CDC5L and the WD40 domain of PLRG1 is essential for pre-mRNA splicing. J Biol Chem 276: 42370–42381PubMedCrossRefGoogle Scholar
  2. Alahari SK, Schmidt H, Käufer NF (1993) The fission yeast prp4 + gene involved in premRNA splicing codes for a predicted serine/threonine kinase and is essential for growth. Nucleic Acids Res 21: 4079–4083PubMedCrossRefGoogle Scholar
  3. Burge CB, Tuschl TH, Sharp PA (1999) Splicing of precursors to mRNAs by the spliceosomes. In: Gesteland RF, Cech TR, Atkins JF (eds) RNA World II. CSH Laboratory Press, Cold Spring Harbor, pp 525–560Google Scholar
  4. Collins CA, Guthrie C (2000) The question remains: is the spliceosome a ribozyme? Nat Struct Biol 10: 850–854Google Scholar
  5. Dellaire G, Makarov EM, Cowger JJ et al. (2002) Mammalian PRP4 kinase copurifies and interacts with components of both the U5 snRNP and the N-CoR deacetylase complexes. Mol Cell Biol 22: 5141–5156PubMedCrossRefGoogle Scholar
  6. Gatermann KB, Hoffmann A, Rosenberg GH, Käufer NF (1989) Introduction of functional artificial introns into the naturally intronless ura4 gene of Schizosaccharomyces pombe. Mol Cell Biol 9: 1526–1535PubMedGoogle Scholar
  7. Gozani O, Potashkin J, Reed R (1998) A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site. Mol Cell Biol 18: 4752–4760PubMedGoogle Scholar
  8. Graveley BR (2000) Sorting out the complexity of SR protein functions. RNA 6: 1197–1211PubMedCrossRefGoogle Scholar
  9. Groß T, Lützelberger M, Weigmann H et al. (1997) Functional analysis of the fission yeast Prp4 protein kinase involved in pre-mRNA splicing and isolation of a putative mammalian homologue. Nucleic Acids Res 25: 1028–1035PubMedCrossRefGoogle Scholar
  10. Groß T, Richert K, Mierke C et al. (1998) Identification and characterization of srpl, a gene of fission yeast encoding a RNA binding domain and a RS domain typical of SR splicing factors. Nucleic Acids Res 26: 505–511PubMedCrossRefGoogle Scholar
  11. Habara Y, Urushiyama S, Tani T, Ohshima Y (1998) The fission yeast prp10 + gene involved in pre-mRNA splicing encodes a homologue of highly conserved splicing factor, SAP155. Nucleic Acids Res 26: 5662–5669PubMedCrossRefGoogle Scholar
  12. Habara Y, Urushiyama S, Shibuya T et al. (2001) Mutation in the prp12 + gene encoding a homolog of SAP130/SF3b130 causes differential inhibition of pre-mRNA splicing and arrest of cell-cycle progression in Schizosaccharomyces pombe. RNA 7: 671–681PubMedCrossRefGoogle Scholar
  13. Hannus S, Bühler D, Romano M et al. (2000) The Schizosaccharomyces pombe protein Yab8p and a novel factor, Yiplp, share structural and functional similarity with the spinal muscular atrophy-associated proteins SMN and SIP1. Hum Mol Genet 9: 663–674PubMedCrossRefGoogle Scholar
  14. Hastings ML, Krainer AR (2001) Pre-mRNA splicing in the new millenium. Curr Opin Cell Biol 13: 302–309PubMedCrossRefGoogle Scholar
  15. Johnson TL, Abelson J (2001) Characterization of U4 and U6 interactions with the 5’ splice site using a S. cerevisiae in vitro trans-splicing system. Genes Dev 15: 1957–1970PubMedCrossRefGoogle Scholar
  16. Käufer NF, Potashkin J (2000) Analysis of the splicing machinery in fission yeast: a comparison with budding yeast and mammals. Nucleic Acids Res 28: 3003–3010PubMedCrossRefGoogle Scholar
  17. Kojima T, Zama T, Wada K et al. (2001) Cloning of human PRP4 reveals interaction with Clkl. J Biol Chem 276: 32247–32256PubMedCrossRefGoogle Scholar
  18. Kuhn AN, Brow DA (2000) Suppressors of a cold-sensitive mutation in yeast U4 RNA define five domains in the splicing factor Prp8 that influence spliceosome activation. Genetics 155: 1667–1682PubMedGoogle Scholar
  19. Kuhn AN, Reichl EM, Brow DA (2002) Distinct domains of splicing factor Prp8 mediate different aspects of spliceosome activation. Proc Natl Acad Sci USA 99: 9145–9149PubMedCrossRefGoogle Scholar
  20. Lefebvre S, Burglen L, Reboullet S et al. (1995) Identification and characterization of a spinal muscular atrophy-determining gene. Cell 80: 155–165PubMedCrossRefGoogle Scholar
  21. Lopez PJ, Séraphin B (1999) Genomic-scale quantitative analysis of yeast pre-mRNA splicing: implications for splice-site recognition. RNA 5: 1135–1137PubMedCrossRefGoogle Scholar
  22. Lundgren K, Allan S, Urushiyama S et al. (1996) A connection between pre-mRNA splicing and the cell cycle in fission yeast: cdc28 + is allelic with prp8 + and encodes an RNA-dependent ATPase/helicase. Mol Biol Cell 7: 1083–1094PubMedGoogle Scholar
  23. Lützelberger M, Groß T, Käufer NF (1999) Srp2, an SR protein family member of fission yeast: in vivo characterization of its modular domains. Nucleic Acids Res 27: 2618–2626PubMedCrossRefGoogle Scholar
  24. Madhani HD, Guthrie C (1992) A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell 71: 803–817PubMedCrossRefGoogle Scholar
  25. Makarov EM, Makarova OV, Achsel T, Lührmann R (2000) The human homologue of the yeast splicing factor Prp6p contains multiple TPR elements and is stably associated with the U5 snRNP via protein-protein interactions. J Mol Biol 298: 567–575PubMedCrossRefGoogle Scholar
  26. Maroney PA, Romfo CM, Nilsen TW (2000) Functional recognition of 5’ splice site by U4/ U6.U5 tri-snRNP defines a novel ATP-dependent step in early spliceosome assembly. Mol Cell 6: 317–328PubMedCrossRefGoogle Scholar
  27. Mayeda A, Badolato J, Kobayashi R et al. (1999) Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. EMBO J 18: 4560–4570PubMedCrossRefGoogle Scholar
  28. McDonald WH, Ohi R, Smelkova N et al. (1999) Myb-related fission yeast Cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing. Mol Cell Biol 19: 5352–5362PubMedGoogle Scholar
  29. Meister G, Bühler D, Laggerbauer B et al. (2000) Characterization of a nuclear 20S complex containing the survival of motor neurons (SMN) protein and a specific subset of spliceosomal Sm proteins. Hum Mol Genet 9: 1977–1986PubMedCrossRefGoogle Scholar
  30. Meister G, Bühler D, Pillai R et al. (2001) A multiprotein complex mediates the ATP-dependent assembly of spliceosomal U snRNPs. Nat Cell Biol 3: 945–949PubMedCrossRefGoogle Scholar
  31. Mermoud JE, Cohen P, Lamond AI (1992) Ser/Thr-specific protein phosphatases are required for both catalytic steps of pre-mRNA splicing. Nucleic Acids Res 20: 5263–5269PubMedCrossRefGoogle Scholar
  32. Mount SM, Salz HK (2000) Pre-messenger RNA processing factors in the Drosophila genome. J Cell Biol 150: F37–44PubMedCrossRefGoogle Scholar
  33. Murray MV, Kobayashi R, Krainer AR (1999) The type 2C Ser/Thr phosphatase PP2Cg is a pre-mRNA splicing factor. Genes Dev 13: 87–97PubMedCrossRefGoogle Scholar
  34. Nilsen TW (2002) The spliceosome: no assembly required? Mol Cell 9: 8–9PubMedCrossRefGoogle Scholar
  35. Ohi MD, Gould KL (2002) Characterization of interactions among the Ceflp-Prpl9p-associated splicing complex. RNA 8: 798–815PubMedCrossRefGoogle Scholar
  36. Ohi R, McCollum D, Hirani B et al. (1994) The Schizosaccharomyces pombe cdc5 + gene encodes an essential protein with homology to c-Myb. EMBO J 13: 471–483PubMedGoogle Scholar
  37. Ohi MD, Link AJ, Ren L et al. (2002) Proteomics analysis reveals stable multiprotein cornplexes in both fission and budding yeasts containing Myb-related Cdc5p/Ceflp, novel pre-mRNA splicing factors, and snRNAs. Mol Cell Biol 22: 2011–2024PubMedCrossRefGoogle Scholar
  38. Owen N, Doe CL, Mellor J, Davies KE (2000) Characterization of the Schizosaccharomyces pombe orthologue of the human survival motor neuron (SMN) protein. Hum Mol Genet 9: 675–684PubMedCrossRefGoogle Scholar
  39. Paushkin S, Charroux B, Abel L et al. (2000) The survival motor neuron protein of Schizosacharomyces pombe. Conservation of survival motor neuron interaction domains in divergent organisms. J Biol Chem 275: 23841–23846PubMedCrossRefGoogle Scholar
  40. Potashkin J, Li R, Frendewey D (1989) Pre-mRNA splicing mutants of Schizosaccharomyces pombe. EMBO J 8: 551–559PubMedGoogle Scholar
  41. Potashkin J, Naik K, Wentz-Hunter K (1993) U2AF homolog required for splicing in vivo. Science 262: 573–575PubMedCrossRefGoogle Scholar
  42. Potashkin J, Kim D, Fons M et al. (1998) Cell-division-cycle defects associated with fission yeast pre-mRNA splicing mutants. Curr Genet 34: 153–163PubMedCrossRefGoogle Scholar
  43. Prabhala G, Rosenberg GH, Käufer NF (1992) Architectural features of pre-mRNA introns in the fission yeast Schizosaccharomyces pombe. Yeast 8: 171–182PubMedCrossRefGoogle Scholar
  44. Romfo CM, Alvarez CJ, van Heeckeren WJ et al. (2000) Evidence for splice site pairing via intron definition in Schizosaccharomyces pombe. Mol Cell Biol 20: 7955–7970PubMedCrossRefGoogle Scholar
  45. Rosenberg GH, Alahari SK, Käufer NF (1991) prp4 from Schizosaccharomyces pombe, a mutant deficient in pre-mRNA splicing isolated using genes containing artificial introns. Mol Gen Genet 226: 305–309Google Scholar
  46. Schmidt H, Richert K, Drakas RA, Käufer NF (1999) spp42, identified as a classical suppressor of prp4–73, which encodes a kinase involved in pre-mRNA splicing in fission yeast, is a homologue of the splicing factor Prp8p. Genetics 153: 1183–1191Google Scholar
  47. Schwelnus W, Richert K, Opitz F et al. (2001) Fission yeast Prp4p kinase regulates premRNA splicing by phosphorylating a non-SR-splicing factor. EMBO Rep 2: 35–41PubMedCrossRefGoogle Scholar
  48. Shimoseki M, Shimoda C (2001) The 5’ terminal region of the Schizosaccharomyces pombe mesi mRNA is crucial for its meiosis-specific splicing. Mol Genet Genomics 265: 673–682PubMedCrossRefGoogle Scholar
  49. Smith CW, Valcârcel J (2000) Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem Sci 25: 381–388PubMedCrossRefGoogle Scholar
  50. Sontheimer EJ, Sun S, Piccirilli JA (1997) Metal ion catalysis during splicing of premessenger RNA. Nature 388: 801–805PubMedCrossRefGoogle Scholar
  51. Spector DL (1996) Nuclear organization and gene expression. Exp Cell Res 229: 189–197PubMedCrossRefGoogle Scholar
  52. Spingola M, Grate L, Haussler D, Ares Jr M (1999) Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 5: 221–234PubMedCrossRefGoogle Scholar
  53. Staley JP, Guthrie C (1998) Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92: 315–326PubMedCrossRefGoogle Scholar
  54. Stevens SW, Ryan DE, Ge HY et al. (2002) Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol Cell 9: 31–44PubMedCrossRefGoogle Scholar
  55. Takeuchi M, Yanagida M (1993) A mitotic role for a novel fission yeast protein kinase dskl with cell cycle stage dependent phosphorylation and localization. Mol Biol Cell 4: 247260Google Scholar
  56. Tang Z, Yanagida M, Lin RJ (1998) Fission yeast mitotic regulator Dskl is an SR protein-specific kinase. J Biol Chem 273: 5963–5969PubMedCrossRefGoogle Scholar
  57. Tang Z, Kuo T, Shen J, Lin RJ (2000) Biochemical and genetic conservation of fission yeast Dskl and human SR protein-specific kinase 1. Mol Cell Biol 20: 816–824PubMedCrossRefGoogle Scholar
  58. Tang Z, Käufer NF, Lin RJ (2002) Interactions between two fission yeast SR-related proteins and their modulation by phosphorylation. Biochem J, Immediate Publication, doi:  10.1042/BJ20021133 Google Scholar
  59. Tsai WY, Chow YT, Chen HR et al. (1999) Ceflp is a component of the Prpl9p-associated complex and essential for pre-mRNA splicing. J Biol Chem 274: 9455–9462PubMedCrossRefGoogle Scholar
  60. Umen JG, Guthrie C (1995) The second catalytic step of pre-mRNA splicing. RNA 1: 869–885PubMedGoogle Scholar
  61. Urushiyama S, Tani T, Ohshima Y (1996) Isolation of novel pre-mRNA splicing mutants of Schizosaccharomyces pombe. Mol Gen Genet 253: 118–127PubMedCrossRefGoogle Scholar
  62. Urushiyama S, Tani T, Ohshima Y (1997) The prp1+ gene required for pre-mRNA splicing in Schizosaccharomyces pombe encodes â protein that contains TPR motifs and is similar to Prp6p of budding yeast. Genetics 147: 101–115PubMedGoogle Scholar
  63. Valadkhan S, Manley JL (2001) Splicing-related catalysis by protein-free snRNAs. Nature 413: 701–707PubMedCrossRefGoogle Scholar
  64. van Nues RW, Beggs JD (2001) Functional contacts with a range of splicing proteins suggest a central role for Brr2p in the dynamic control of the order of events in spliceosomes of Saccharomyces cerevisiae. Genetics 157: 1451–1467PubMedGoogle Scholar
  65. Wang C, Chua K, Seghezzi W et al. (1998) Phosphorylation of spliceosomal protein SAP 155 coupled with splicing catalysis. Genes Dev 12: 1409–1014PubMedCrossRefGoogle Scholar
  66. Will CL, Lührmann R (2001) Spliceosomal UsnRNP biogenesis, structure and function. Curr Opin Cell Biol 13: 290–301PubMedCrossRefGoogle Scholar
  67. Yean SL, Wuenschell G, Termini J, Lin RJ (2000) Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome. Nature 408: 881–884PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Andreas N. Kuhn
  • Norbert E. Käufer

There are no affiliations available

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