Mechanical devices of the spliceosome: Motors, clocks, springs, and things

Cell

Volumn 92, Issue 3, 1998, Pages 315-326

  Staley, Jonathan P ^a   Guthrie, Christine ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; CHEMICAL REACTION; CROSS LINKING; ENZYME SUBSTRATE; ESTERIFICATION; GENE REARRANGEMENT; INTRON; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN SECONDARY STRUCTURE; PROTEIN SYNTHESIS REGULATION; REVIEW; SPLICEOSOME;

EID: 0032489021     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)80925-3     Document Type: Review

References (76)

1. Abel, K., and Jurnak, F. (1996). A complex profile of protein elongation: translating chemical energy into molecular movement. Structure 4, 229-238.
2. Abovich, N., Liao, X.C., and Rosbash, M. (1994). The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition. Genes Dev. 8, 843-854.
3. Ali, J.A., and Lohman, T.M. (1997). Kinetic measurement of the step size of DNA unwinding by Escherichia coli UvrD helicase. Science 275, 377-380.
4. Arenas, J.E., and Abelson, J.N. (1997). Prp43: An RNA helicase-like factor involved in spliceosome disassembly. Proc. Natl. Acad. Sci. USA 94, 11798-11802.
5. Auble, D.T., Wang, D., Post, K.W., and Hahn, S. (1997). Molecular analysis of the SNF2/SWI2 protein family member MOT1, an ATP-driven enzyme that dissociates TATA-binding protein from DNA. Mol. Cell Biol. 17, 4842-4851.
6. Bennet, M., Michaud, S., Kingston, J., and Reed, R. (1992). Protein components specifically associated with prespliceosome and spliceosome complexes. Genes Dev. 6, 1986-2000.
7. Berget, S.M., Moore, C., and Sharp, P.A. (1977). Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc. Natl. Acad. Sci. USA 74, 3171-3175.
8. Berglund, J.A., Chua, K., Abovich, N., Reed, R., and Rosbash, M. (1997). The splicing factor BBP interacts specifically with the pre-mRNA branch point sequence UACUAAC. Cell 89, 781-787.
9. Bourne, H.R. (1995). GTPases: a family of molecular switches and clocks. Philos. Trans. R Soc. Lond. [Biol.] 349, 283-289.
10. Brody, E., and Abelson, J. (1985). The "spliceosome": yeast premessenger RNA associates with a 40S complex in a splicing-dependent reaction. Science 228, 963-967.
11. Burgess, S.M., and Guthrie, C. (1993). Beat the clock: paradigms for NTPases in the maintenance of biological fidelity. Trends Biochem. Sci. 18, 381-384.
12. Bycroft, M., Hubbard, T.J.P., Proctor, M., Freund, S.M.V., and Murzin, A.G. (1997). The solution structure of the S1 RNA-binding domain: a member of an ancient nucleic acid-binding fold. Cell 88, 235-242.
13. Chow, L.T., Gelinas, R.E., Broker, T.R., and Roberts, R.J. (1977). An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12, 1-8.
14. Company, M., Arenas, J., and Abelson, J. (1991). Requirement of the RNA helicase-like protein PRP22 for release of messenger RNA from spliceosomes. Nature 349, 487-493.
15. Fabrizio, P., Laggerbauer, B., Lauber, J., Lane, W.S., and Lührmann, R. (1997). An evolutionarily conserved U5 snRNP-specific protein is a GTP-binding factor closely related to the ribosomal translocase EF-2. EMBO J. 16, 4092-4106.
16. 65 recruits a novel human DEAD box protein required for the U2 snRNP-branch point interaction. Genes Dev. 11, 1864-1872.
17. Fu, X.-D. (1995). The superfamily of arginine/serine-rich splicing factors. RNA 1, 663-680.
18. Fuller-Pace, F.V. (1994). RNA helicases: modulators of RNA structure. Trends Cell Biol. 4, 271-274.
19. Gee, S., Krauss, S.W., Miller, E., Aoyagi, K., Arenas, J., and Conboy, J.G. (1997). Cloning of mDEAH9, a putative RNA helicase and mammalian homolog of Saccharomyces cerevisiae splicing factor Prp43. Proc. Natl. Acad. Sci. USA 94, 11803-11807.
20. Gesteland, R.F., and Atkins, J.F., eds. (1993). The RNA World (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press).
21. Ghetti, A., Company, M., and Abelson, J. (1995). Specificity of Prp24 binding to RNA: a role for Prp24 in the dynamic interaction of U4 and U6 snRNAs. RNA 1, 132-145.
22. Gorbalenya, A.E., and Koonin, E.V. (1993). Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3, 419-429.
23. Herschlag, D. (1995). RNA chaperones and the RNA folding problem. J. Biol. Chem. 270, 20871-20874.
24. Hertel, K.J., Lynch, K.W., and Maniatis, T. (1997). Common themes in the function of transcription and splicing enhancers. Curr. Opin. Cell Biol. 9, 350-357.
25. Kadonaga, J.T. (1998). Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell 92, 307-313.
26. Kim, S.-H., and Lin, R.-J. (1996). Spliceosome activation by PRP2 ATPase prior to the first transesterification reaction of pre-mRNA splicing. Mol. Cell Biol. 16, 6810-6819.
27. Kim, S.-H., Smith, J., Claude, A., and Lin, R.-J. (1992). The purified yeast pre-mRNA splicing factor PRP2is an RNA-dependent NTPase. EMBO J. 11, 2319-2326.
28. Korolev, S., Hsieh, J., Gauss, G.H., Lohman, T.M., and Waksman, G. (1997a). Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90, 635-647.
29. Korolev, S., Yao, N., Lohman, T.M., Weber, P.C., and Waksman, G. (1997b). Comparisons between the structures of HCV and Rep helicases reveal structural similarities between SF1 and SF2 superfamilies of helicases. Protein Sci., in press.
30. Laggerbauer, B., Achsel, T., and Lührmann, R. (1998). The human 200kD DEXH-box U5 snRNP protein unwinds U4/U6 RNA duplices in vitro. Proc. Natl. Acad. Sci. USA, in press.
31. Lauber, J., Fabrizio, P., Teigelkamp, S., Lane, W.S., Hartmann, E., and Lührmann, R. (1996). The HeLa 200 kDa U5 snRNP-specific protein and its homologue in Saccharomyces cerevisiae are members of the DEXH-box protein family of putative RNA helicases. EMBO J. 15, 4001-4015.
32. Lin, J., and Rossi, J.J. (1996). Identification and characterization of yeast mutants that overcome an experimentally introduced block to splicing at the 3′ splice site. RNA 2, 835-848.
33. Lohman, T.M., and Bjornson, K.P. (1996). Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65, 169-214.
34. Lorsch, J.R., and Herschlag, D. (1998). The DEAD box protein elF-4A. 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide. Biochemistry, in press.
35. Marians, K.J. (1997). Helicase structures: a new twist on DNA unwinding. Structure 5, 1129-1134.
36. Matlack, K.E.S., Mothes, W., and Rapoport, T.A. (1998). Protein translocation: tunnel vision. Cell 92, 381-390.
37. Michel, F., and Ferat, J.-L. (1995). Structure and activities of group II introns. Annu. Rev. Biochem. 64, 435-461.
38. Moore, M.J., Query, C.C., and Sharp, P.A. (1993). Splicing of precursors to mRNA by the spliceosome. In The RNA World, R.F. Gesteland and J.F. Atkins, eds. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 303-357.
39. Mount, S.M., Pettersson, I., Hinterberger, M., Karmas, A., and Steitz, J.A. (1983). The U1 small nuclear RNA-protein complex selectively binds a 5′ splice site in vitro. Cell 33, 509-518.
40. Newman, A.J. (1997). The role of U5 snRNP in pre-mRNA splicing. EMBO J. 16, 5797-5800.
41. Nilsen, T.W. (1998). RNA-RNA interactions in nuclear pre-mRNA splicing. In RNA Structure and Function, R. Simons and M. Grunberg-Manago, eds. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 279-307.
42. Noble, S.M. (1995). The BRR genes encode novel factors involved in RNA processing. PhD thesis, University of California, San Francisco, California.
43. Noble, S.M., and Guthrie, C. (1996). Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations. Genetics 143, 67-80.
44. O'Day, C.L., Dalbadie-McFarland, G., and Abelson, J. (1996). The Saccharomyces cerevisiae Prp5 protein has RNA-dependent ATPase activity with specificity for U2 small nuclear RNA. J. Biol. Chem. 271, 33261-33267.
45. Ohno, M., and Shimura, Y. (1996). A human RNA helicase-like protein, HRH1, facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. Genes Dev. 10, 997-1007.
46. Ohno, M., Fornerod, M., and Mattaj, I.W. (1998). Nucleocytoplasmic transport: the last 200 nanometers. Cell 92, 327-336.
47. Ono, Y.,Ohno, M., and Shimura, Y. (1994). Identification of a putative RNA helicase (HRH1), a human homolog of yeast Prp22. Mol. Cell Biol. 14, 7611-7620.
48. Raghunathan, P.L. (1997). Antagonistic control of RNA basepairing in the spliceosome cycle. PhD thesis, University of California, San Francisco, California.
49. Raghunathan, P.L., and Guthrie, C. (1998). A spliceosomal recycling factor that reanneals U4 and U6 snRNPs. Science, in press.
50. Rodnina, M.V., Pape, T., Fricke, R., and Wintermeyer, W. (1995). Elongation factor Tu, a GTPase triggered by codon recognition on the ribosome: mechanism and GTP consumption. Biochem. Cell Biol. 73, 1221-1227.
51. Roy, J., Kim, K., Maddock, J.R., Anthony, J.G., and Woolford, J.L., Jr. (1995). The final stages of spliceosome maturation require Spp2p that can interact with the DEAH box protein Prp2p and promote step 1 of splicing. RNA 1, 375-390.
52. Saldanha, R., Mohr, G., Belfort, M., and Lambowitz, A.M. (1993). Group I and group II introns. FASEB J. 7, 15-24.
53. Schwer, B., and Guthrie, C. (1991). PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 349, 494-499.
54. Schwer, B., and Guthrie, C. (1992). A conformational rearrangement in the spliceosome is dependent on PRP16 and ATP hydrolysis. EMBO J. 11, 5033-5039.
55. Shamoo, Y., Abdul-Manan, N., and Williams, K.R. (1995). Multiple RNA binding domains (RBDs) just don't add up. Nucleic Acids Res. 23, 725-728.
56. Shamoo, Y., Krueger, U., Rice, L.M., Williams, K.R., and Steitz, T.A. (1997). Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 Å resolution. Nat. Struct. Biol. 4, 215-222.
57. Sontheimer, E.J., Sun, S., and Piccirilli, J.A. (1997). Metal ion catalysis during splicing of premessenger RNA. Nature 388, 801-805.
58. Sprang, S.R. (1997). G protein mechanisms: insights from structural analysis. Annu. Rev. Biochem. 66, 639-678.
59. Steitz, T.A., and Steitz, J.A. (1993). A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA 90, 6498-6502.
60. Strauss, E.J., and Guthrie, C. (1994). PRP28, a "DEAD-box" protein, is required for the first step of mRNA splicing in vitro. Nucleic Acids Res. 22, 3187-3193.
61. Subramanya, H.S., Bird, L.E., Brannigan, J.A., and Wigley, D.B. (1996). Crystal structure of a DExx box DNA helicase. Nature 384, 379-383.
62. Tarn, W.-Y., and Steitz, J.A. (1997). Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge. Trends Biochem. Sci. 22, 132-137.
63. Teigelkamp, S., Mundt, C., Achsel, T., Will, C.L., and Lührmann, R. (1997). The human U5 snRNP-specific 100-kD protein is an RS domain-containing, putative RNA helicase with significant homology to the yeast splicing factor Prp28p. RNA 3, 1313-1326.
64. Umen, J.G., and Guthrie, C. (1995). The second catalytic step of pre-mRNA splicing. RNA 1, 869-885.
65. Utans, U., Behrens, S.-E., Lührmann, R., Kole, R., and Krämer, A. (1992). A splicing factor that is inactivated during in vivo heat shock is functionally equivalent to the [U4/U6-U5] triple snRNP-specific proteins. Genes Dev. 6, 631-641.
66. 65 RS region with pre-mRNA of (sic) branch point and promotion (sic) base pairing with U2 snRNA. Science 273, 1706-1709.
67. Wang, J., and Manley, J.L. (1997). Regulation of pre-mRNA splicing in metazoa. Curr. Opin. Genet. Dev. 7, 205-211.
68. Wiest, D.K., O'Day, C.L., and Abelson, J. (1996). In vitro studies of the Prp9-Prp11-Prp21 complex indicate a pathway for U2 small nuclear ribonucleoprotein activation. J. Biol. Chem. 271, 33268-33276.
69. Will, C.L., and Lührmann, R. (1997). Protein functions in pre-mRNA splicing. Curr. Opin. Cell Biol. 9, 320-328.
70. Wilson, K.S., and Noller, H.F. (1998). Molecular movement inside the translational engine. Cell 92, 337-349.
71. Xu, D., Nouraini, S., Field, D., Tang, S.-J., and Friesen, J.D. (1996). An RNA-dependent ATPase associated with U2/U6 snRNAs in pre-mRNA splicing. Nature 381, 709-713.
72. Xu, R.-M., Jokhan, L., Cheng, X., Mayeda, A., and Krainer, A.R. (1997). Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs. Structure 5, 559-570.
73. Yao, N., Hesson, T., Cable, M., Hong, Z., Kwong, A.D., Le, H.V., and Weber, P.C. (1997). Structure of the hepatitis C virus RNA helicase domain. Nat. Struct. Biol. 4, 463-467.
74. Yean, S.-L., and Lin, R.-J. (1991). U4 small nuclear RNA dissociates from a yeast spliceosome and does not participate in the subsequent splicing reaction. Mol. Cell Biol. 11, 5571-5577.
75. Yean, S.-L., and Lin, R.-J. (1996). Analysis of small nuclear RNAs in a precatalytic spliceosome. Gene Expr. 5, 301-313.
76. Zavanelli, M.I., Britton, J.S., Igel, A.H., and Ares, M., Jr. (1994). Mutations in an essential U2 small nuclear RNA structure cause cold-sensitive U2 small nuclear ribonucleoprotein function by favoring competing alternative U2 RNA structures. Mol. Cell Biol. 14, 1689-1697.