A human protein required for the second step of pre-mRNA splicing is functionally related to a yeast splicing factor

Genes and Development

Volumn 11, Issue 1, 1997, Pages 139-151

  Horowitz, David S ^a   Krainer, Adrian R ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

Pre mRNA splicing; Prp18; splicing factor; U4 U6 snRNP

Indexed keywords

MESSENGER RNA PRECURSOR; RECOMBINANT PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN;

ARTICLE; CONTROLLED STUDY; HELA CELL; HUMAN; HUMAN CELL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; RNA SPLICING; SEQUENCE HOMOLOGY; SPLICEOSOME; YEAST;

EID: 0031027009     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.11.1.139     Document Type: Article

References (77)

1. 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.
2. Adams, M.D., D.Z. Rudner, and D.C. Rio. 1996. Biochemistry and regulation of pre-messenger-RNA splicing. Curr. Opin. Cell Biol. 8: 331-339.
3. Ansari, A. and B. Schwer. 1995. SLU7 and a novel activity, SSF1, act during the PRP16-dependent step of yeast pre-mRNA splicing. EMBO J. 14: 4001-4009.
4. Ares, M., Jr. and B. Weiser. 1995. Rearrangement of snRNA structure during assembly and function of the spliceosome. Pros. Nucleic Acid Res. Mol. Biol. 50: 131-159.
5. Bach, M., G. Winkelmann, and R. Lührmann. 1989. 20S small nuclear ribonucleoprotein U5 shows a surprisingly complex protein composition. Proc. Natl. Acad. Sci. 86: 6038-6042.
6. Banroques, J. and J.N. Abelson. 1989. PRP4: A protein of the yeast U4/U6 small nuclear ribonucleoprotein particle. Mol. Cell. Biol. 9: 3710-3719.
7. Behrens, S.-E. and R. Lührmann. 1991. Immunoaffinity purification of a [U4/U6.U5] tri-snRNP for human cells. Genes & Dev. 5: 1439-1452.
8. Behrens, S.-E., F. Galisson, P. Legrain, and R. Lührmann. 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. 90: 8229-8233.
9. Bennett, M. and R. Reed. 1993. Correspondence between a mammalian spliceosome component and an essential yeast splicing factor. Science 262: 105-108.
10. Black, D.L. 1995. Finding splice sites within a wilderness of RNA. RNA 1: 763-771.
11. Black, D.L. and A.L. Pinto. 1989. U5 small nuclear ribonucleoprotein: RNA structure analysis and ATP-dependent interaction with U4/U6. Mol. Cell. Biol. 9: 3350-3359.
12. Brosi, R., K. Gröning, S.-E. Behrens, R. Lührmann, and A. Krämer. 1993. Interaction of mammalian splicing factor SF3a with U2 snRNP and relation of its 60-kD subunit to yeast PRP9. Science 262: 102-105.
13. 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.
14. Cooper, M., L.H. Johnston, and J.D. Beggs. 1995. Identification and characterization of Uss1p (Sdb23p): A novel U6 snRNA-associated protein with significant similarity to core proteins of small nuclear ribonucleoproteins. EMBO J. 14: 2066-2075.
15. Couto, J.R., J. Tamm, R. Parker, and C. Guthrie. 1987. A transacting suppressor restores splicing of a yeast intron with a branch point mutation. Genes &. Dev. 1: 445-455.
16. Datta, B. and A.M. Weiner. 1993. The phylogenetically invariant ACAGAGA and AGC sequences of U6 small nuclear RNA are more tolerant of mutation in human cells than in Saccharomyces cerevisiae. Mol. Cell. Biol. 13: 5377-5382.
17. nrb, a nuclear protein with two RNA recognition motifs and extensive homology to human splicing factor PSF and Drosophila NONA/BJ6. Nucleic Acids Res. 21: 4085-4092.
18. 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.
19. Frank, D. and C. Guthrie. 1992. An essential splicing factor, SLU7, mediates 3′ splice site choice in yeast. Genes & Dev. 6: 2112-2124.
20. 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.
21. Garcia-Blanco, M.A., G.J. Anderson, J. Beggs, and P.A. Sharp. 1990. A mammalian protein of 220 kDa binds pre-messenger-RNAs in the spliceosome-A potential homolog of the yeast PRP8 protein. Proc. Natl. Acad. Sci. 87: 3082-3086.
22. Genetics Computer Group. 1994. Program Manual for the Wisconsin Package. Version 8. Genetics Computer Group, Madison, WI.
23. Gozani, O., J.G. Patton, and R. Reed. 1994. A novel set of spliceosome-associated proteins 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.
24. Gozani, O., R. Feld, and R. Reed. 1996. Evidence that sequence-independent binding of highly conserved U2 snRNP proteins upstream of the branch site is required for assembly of spliceosomal complex A. Genes & Dev. 10: 233-243.
25. Grünert, S. and R.J. Jackson. 1994. The immediate downstream codon strongly influences the efficiency of utilization of eukaryotic translation intiation codons. EMBO J. 13: 3618-3630.
26. Herman, P.K. and S.D. Emr. 1990. Characterization of VPS34, a gene required for vacuolar protein sorting and vacuole segregation in Saccharomyces cerevisiae. Mol. Cell. Biol. 10: 6742-6754.
27. Hodges, P.E., S.P. Jackson, J.D. Brown, and J.D. Beggs. 1995. Extraordinary sequence conservation of the PRP8 splicing factor. Yeast 11: 337-342.
28. Horowitz, D.S. and J. Abelson. 1993a. Stages in the second reaction of pre-mRNA splicing: The final step is ATP independent. Genes & Dev. 7: 320-329.
29. _. 1993b. A U5 small nuclear rihonucleoprotein particle protein involved only in the second step of splicing in Saccharomyces cerevisiae. Mol. Cell. Biol. 13: 2959-2970.
30. Horowitz, D.S. and A.R. Krainer. 1994. Mechanisms for selecting 5′ splice sites in mammalian pre-mRNA splicing. Trends Genet. 10: 100-106.
31. 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. 92: 9687-9691.
32. Konarska, M.M. and P.A. Sharp. 1987. Interactions between small nuclear ribonucleoprotein particles in formation of spliceosomes. Cell 49: 763-774.
33. Krainer, A.R. 1988. Pre-mRNA splicing by complementation with purified human U1, U2, U4/U6 and U5 snRNPs. Nucleic Acids Res. 16: 9415-9429.
34. Krainer, A.R. and T. Maniatis. 1985. Multiple factors including the small ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. Cell 42: 725-736.
35. Krainer, A.R., T. Maniatis, B. Ruskin, and M.R. Green. 1984. Normal and mutant human β-globin pre-mRNAs are faithfully and efficiently spliced in vitro. Cell 36: 993-1005.
36. Krainer, A.R., G.C. Conway, and D. Kozak. 1990. The essential pre-mRNA splicing factor SF2 influences 5′ splice site selection by activating proximal sites. Cell 62: 35-42.
37. Krämer, A. 1996. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu. Rev. Biochem. 65: 367-409.
38. Krämer, A., F. Mulhauser, C. Wersig, K. Gröning, and G. Bilbe. 1995. Mammalian splicing factor SF3a120 represents a new member of the SURP family of proteins and is homologous to the essential splicing factor PRP21p of Saccharomyces cerevisiae. RNA 1: 260-272.
39. Lauber, J., P. Fabrizio, S. Teigelkamp, W.S. Lane, E. Hartmann, and R. Lührmann. 1996. The HeLa 200 kDa US 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.
40. Liao, X.C., J. Tang, and M. Rosbash. 1993. An enhancer screen identifies a gene that encodes the yeast U1 snRNP A protein: Implications for snRNP protein function in pre-mRNA splicing. Genes & Dev. 7: 419-428.
41. Lin, R.-J., A.J. Newman, S.-C. Cheng, and J. Abelson. 1985. Yeast mRNA splicing in vitro. J. Biol. Chem. 260: 14780-14792.
42. Lindsey, L.A., A.J. Crow, and M.A. Garcia-Blanco. 1995. A mammalian activity required for the second step of pre-messenger RNA splicing. J. Biol. Chem. 270: 13415-13421.
43. Lustig, A.J., R.-J. Lin, and J. Abelson. 1986. The yeast RNA gene products are essential for mRNA splicing in vitro. Cell 47: 953-963.
44. Madhani, H. 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 71: 803-817.
45. 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.
46. Michaud, S. and R. Reed. 1993. A functional association between the 5′ and 3′ splice sites is established in the earliest prespliceosome complex (E) in mammals. Genes & Dev. 7: 1008-1020.
47. Newman, A.J. and C. Norman. 1992. U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell 68: 743-754.
48. Noble, S.M. and C. Guthrie. 1996. Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations. Genetics 143: 67-80.
49. Ono, Y., M. Ohno, and Y. Shimura. 1994. Identification of a putative RNA helicase (HRH1), a human homolog of yeast Prp22. Mol. Cell. Biol. 14: 7611-7620.
50. Patton, J.G., E.B. Porro, J. Galceran, P. Tempst, and B. Nadal-Ginard. 1993. Cloning and characterization of PSF, a novel pre-mRNA splicing factor. Genes &. Dev. 7: 393-406.
51. Perkins, K.K., H.M. Furneaux, and J. Hurwitz. 1986. RNA splicing products formed with isolated fractions from HeLa cells are associated with fast-sedimenting complexes. Proc. Natl. Acad. Sci. 83: 887-891.
52. Petersen-Bjørn, S., A. Soltyk, J.D. Beggs, and J.D. Friesen. 1989. PRP4 (RNA4) from Saccharomyces cerevisiae: Its gene product is associated with the U4/U6 small nuclear ribonucleoprotein particle. Mol. Cell. Biol. 9: 3698-3709.
53. Petty, K.J. 1993. Metal-chelate affinity chromatography. In Current protocols in molecular biology. John Wiley & Sons, New York, NY.
54. Pinto, A.L. and J.A. Steitz. 1989. The mammalian analogue of the yeast PRP8 splicing protein is present in the U4/5/6 small ribonucleoprotein particle and the spliceosome. Proc. Natl. Acad. Sci. 86: 8742-8746.
55. Polycarpou-Schwarz, M., S.I. Gunderson, S. Kandels-Lewis, B. Séraphin, and I.W. Mattaj. 1996. Drosophila SNF/D25 combines the functions of the two snRNP proteins U1A and U2B" that are encoded separately in human, potato, and yeast. RNA 2: 11-23.
56. Reed, R. and T. Maniatis. 1986. A role for exon sequences and splice-site proximity in splice-site selection. Cell 46: 681-690.
57. Rio, D.C. 1988. Accurate and efficient pre-mRNA splicing in Drosophila cell-free extracts. Proc. Natl. Acad. Sci. 85: 2904-2908.
58. Rymond, B.C., L.A. Rokeach, and S.A. Hoch. 1993. Human snRNP polypeptide D1 promotes pre-mRNA splicing in yeast and defines nonessential yeast Smd1p sequences. Nucleic Acids Res. 21: 3501-3505.
59. Schmitt, P., R. Gattoni, P. Keohavong, and J. Stévenin. 1987. Alternative splicing of E1A transcripts of adenovirus requires appropriate ionic conditions in vitro. Cell 50: 31-39.
60. Schwer, B. and C. Guthrie. 1991. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature 349: 494-499.
61. _. 1992. A conformational rearrangement in the spliceosome is dependent on PRP16 and ATP hydrolysis. EMBO J. 11: 5033-5039.
62. Shannon, K.W. and C. Guthrie. 1991, Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA-binding motifs. Genes &. Dev. 5: 773-785.
63. Shuster, E.O. and C. Guthrie. 1990, Human U2 can function in pre-mRNA splicing in yeast. Nature 345: 270-273.
64. Smith, C.W.J. and B. Nadal-Ginard. 1989. Mutually exclusive splicing of α-tropomyosin exons enforced by an unusual lariat branch point location: Implications for constitutive splicing. Cell 56: 749-758.
65. Smith, V. and B.G. Barrell. 1991. Cloning of a yeast U1 snRNP 70K protein homologue: Functional conservation of an RNA-binding domain between humans and yeast. EMBO J. 10: 2627-2634.
66. Teigelkamp, S., E. Whittaker, and J.D. Beggs. 1995. Interaction of the yeast splicing factor PRP8 with substrate RNA during both steps of splicing. Nucleic Acids Res. 23: 320-326.
67. Tsukahara, T., C. Casciato, and D.M. Helfman. 1994. Alternative splicing of β-tropomyosin pre-mRNA: Multiple cis-elements can contribute to the use of the 5′- and 3′-splice sites of the nonmuscle/smooth muscle exon 6. Nucleic Acids, Res. 22: 2318-2325.
68. Umen, J.G. and C. Guthrie. 1995a. A novel role for a U5 snRNP protein in 3′ splice site selection. Genes &. Dev. 9: 855-868.
69. _. 1995b. 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.
70. _. 1995c. The second catalytic step of pre-mRNA splicing. RNA 1: 869-885.
71. Vijayraghavan, U. and J. Abelson. 1990. PRP18, a protein required for the second reaction in pre-mRNA splicing. Mol. Cell. Biol. 10: 324-332.
72. Vijayraghavan, U., M. Company, and J. Abelson. 1989. Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes & Dev. 3: 1206-1216.
73. Wells, S.E., M. Neville, M. Haynes, J. Wang, H. Igel, and M. Ares, Jr. 1996. CUS1, a suppressor of cold-sensitive U2 snRNA mutations, is a novel yeast splicing factor homologous to human SAP 145. Genes & Dev. 10: 220-232.
74. Whittaker, E., M. Lossky, and J.D. Beggs. 1990. Affinity purification of spliceosomes reveals that the precursor RNA processing protein PRP8, a protein in the U5 small nuclear ribonucleoprotein particle, is a component of yeast spliceosomes. Proc. Natl. Acad. Sci. 87: 2216-2219.
75. Will, C.L. and R. Lührmann. 1997. snRNP structure and function. In Eukaryotic mRNA processing (ed. A. R. Krainer), IRL Press, Oxford. (In press.)
76. 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. 91: 903-907.
77. Xu, D., S. Nouraini, D. Field, S.J. Tang, and J.D. Friesen. 1996. An RNA-dependent ATPase associated with U2/U6 snRNAs in pre-mRNA splicing. Nature 381: 709-713.