Analysis of mutant phenotypes and splicing defects demonstrates functional collaboration between the large and small subunits of the essential splicing factor U2AF in vivo

Molecular Biology of the Cell

Volumn 16, Issue 2, 2005, Pages 584-596

  Webb, Christopher J ^a   Lakhe Reddy, Sujata ^a   Romfo, Charles M ^a   Wise, Jo Ann ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; PROTEIN SUBUNIT; PROTEIN U2AF; RNA; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; GENE DELETION; GENETIC ANALYSIS; GENETIC DISORDER; IN VIVO STUDY; INTRON; MOLECULAR RECOGNITION; PHENOTYPE; PRIORITY JOURNAL; RNA SPLICING; SCHIZOSACCHAROMYCES POMBE;

ALLELES; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CELL SURVIVAL; CONSERVED SEQUENCE; DIMERIZATION; INTRONS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEAR PROTEINS; PHENOTYPE; PHENYLALANINE; PLASMIDS; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEOPROTEINS; RNA PRECURSORS; RNA SPLICE SITES; RNA SPLICING; SCHIZOSACCHAROMYCES; SEQUENCE HOMOLOGY, AMINO ACID; TEMPERATURE; TRANSFORMATION, GENETIC; TWO-HYBRID SYSTEM TECHNIQUES;

METAZOA; SCHIZOSACCHAROMYCES POMBE;

EID: 12844258048     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E04-09-0768     Document Type: Article

References (64)

1. Abovich, N., Liao, X., and Rosbash, M. (1994). The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complex and U2 snRNP addition. Genes Dev. 8, 843-854.
2. Alvarez, C. J., Romfo, C. M., VanHoy, R. W., Porter, G. L., and Wise, J. A. (1996). Mutational analysis of U1 function in Schizosaccharomyces pombe: pre-mRNAs differ in the extent and nature of their requirements for this snRNA in vivo. RNA 2, 404-418.
3. Alvarez, C. J., and Wise, J. A. (2001). Activation of a cryptic 6′ splice site by U1 snRNA. RNA 7, 342-350.
4. Banerjee, H., Rahn, A., Gawande, B., Guth, S., Valcarcel, J., and Singh, R. (2004). The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro. RNA 10, 240-253.
5. Beales, M., Flay, N., McKinney, R., Habara, Y., Ohshima, Y., Tani, T., and Potashkin, J. (2000). Mutations in the large subunit of U2AF disrupt pre-mRNA splicing, cell cycle progression and nuclear structure. Yeast 16, 1001-1013.
6. Berglund, J. A., Abovich, N., and Rosbash, M. (1998). The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Genes Dev. 12, 858-867.
7. 50 in the nuclear export of intronless mRNAs. Mol. Cell 34, 775-786.
8. Blumenthal, T., and Steward, K. (1997). RNA processing and gene structure. In: C. elegans II, ed. D. Riddle, T. Blumenthal, B. Meyers, and J. Priess, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 117-145.
9. Burge, C. B., Tuschl, T., and Sharp, P. A. (1999). Splicing of Precursors to mRNAs by the Spliceosome. In: The RNA World, ed. R. Gesteland, T. Cech, and J. Atkins, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 525-560.
10. Caceres, J. F., and Krainer, A. R. (1993). Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains. EMBO J. 12, 4715-4726.
11. Clark, T. A., Sugnet, C. W., and Ares, M., Jr. (2002). Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296, 907-910.
12. Davies, R. C., Calvio, C., Bratt, E., Larsson, S. H., Lamond, A. I., and Hastie, N. D. (1998). WT1 interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes. Genes Dev. 12, 3217-3225.
13. Eckmann, C. R., Kraemer, B., Wickens, M., and Kimble, J. (2002). GLD-3, a bicaudal-C homolog that inhibits FBF to control germline sex determination in C. elegans. Dev. Cell 3, 697-710.
14. Fewell, S. W., and Woolford, J. R. (1999). Ribosomal protein S14 of Saccharomyces cerevisiae regulates its expression by binding to RPS14B pre-mRNA and to 18S rRNA. Mol. Cell. Biol. 19, 826-834.
15. 65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. Genes Dev. 11, 1864-1872.
16. Gozani, O., Potashkin, J., and Reed, R. (1998). A potential role for U2AF-SAP 155 interactions in recruiting U2 snRNP to the branch site. Mol. Cell. Biol. 18, 4752-4760.
17. 35 in AG-dependent pre-mRNA splicing. Mol. Cell. Biol. 21, 7673-7681.
18. Huang, T., Vilardell, J., and Query, C. (2002). Pre-spliceosomal formation in S. pombe requires a stable complex of SF1-U2AF59-U2AF23. EMBO J. 21, 5516-5526.
19. 65). EMBO J. 18, 453-4534.
20. James, P., Halladay, J., and Craig, E. A. (1996). Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144, 1425-1436.
21. Kanaar, R., Roche, S. E., Beall, E. L., Green, M. R., and Rio, D. C. (1993). The conserved pre-mRNA splicing factor U2AF from Drosophila: requirement for viability. Science 262, 569-573.
22. 65 heterodimer. Cell 106, 595-605.
23. Kielkopf, C. L., Lucke, S., and Green, M. R. (2004). U2AF homology motifs: protein recognition in the RRM world. Genes Dev. 18, 1513-1526.
24. Le Goff, X., Utzig, S., and Simanis, V. (1999). Controlling septation in fission yeast: finding the middle, and timing it right. Curr. Genet. 35, 571-584.
25. Mazroui, R., Puoti, A., and Kramer, A. (1999). Splicing factor SF1 from Drosophila and Caenorhabditis: presence of an N-terminal RS domain and requirement for viability. RNA 5, 1615-1631.
26. 35 and the 3′ splice site AG. Nature 402, 838-841.
27. Moore, M. (2000). Intron recognition comes of AGe. Nature 7, 14-16.
28. Mount, S. M., and Salz, H. K. (2000). Pre-messenger RNA processing factors in the Drosophila genome. J. Cell Biol. 150, F37-F44.
29. 35: identification of alternatively spliced U2AF1 mRNAs. J. Biol. Chem. 279, 27039-27049.
30. 65-related splicing activity. RNA 5, 1548-1560.
31. Potashkin, J., Naik, K., and Wentz-Hunter, K. (1993). U2AF homolog required for splicing in vivo. Science 262, 573-575.
32. Reed, R. (1989). The organization of 3′ splice-site sequences in mammalin introns. Genes Dev. 3, 2113-2123.
33. 59 in Schizosaccharomyces pombe: differential sensitivity of introns to mutational inactivation. RNA 5, 49-65.
34. Romfo, C. M., and Wise, J. A. (1997). Both the polypyrimidine tract and the 3′ splice site function prior to the first step of splicing in fission yeast. Nucleic Acids Res. 25, 4658-4665.
35. Rudner, D., Breger, K., Kanaar, R., Adams, M., and Rio, D. (1998a). RNA binding activity of heterodimeric splicing factor U2AF: at least one RS domain is required for high-affinity binding. Mol. Cell. Biol. 18, 4004-4011.
36. Rudner, D. Z., Breger, K. S., and Rio, D. (1998b). Molecular genetic analysis of the heterodimeric splicing factor U2AF: the RS domain on either the large or small Drosophila subunit is dispensable in vivo. Genes Dev. 12, 1010-1021.
37. Rudner, D., Kanaar, R., Breger, K., and Rio, D. (1998c). Interaction between subunits of heterodimeric splicing factor U2AF is essential in vivo. Mol. Cell. Biol. 18, 1765-1773.
38. Rudner, D., Kanaar, K., Breger, S., and Rio, D. (1996). Mutations in the small subunit of the Drosophila U2AF splicing factor cause lethality and developmental defects. Proc. Natl. Acad. Sci. USA 93, 10333-10337.
39. Ruskin, B., Zamore, P. D., and Green, M. R. (1988). A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly. Cell 52, 207-219.
40. Selenko, P., Gregorovic, G., Sprangers, R., Stier, G., Rhani, Z., Kramer, A., and Sattler, M. (2003). Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Mol. Cell 11, 965-976.
41. SenGupta, D. J., Zhang, B., Kraemer, B., Pochart, P. Fields, S., and Wickens, M. (1996). A three-hybrid system to detect RNA-protein interactions in vivo. Proc. Natl. Acad. Sci. USA 93, 8496-8501.
42. Singh, R., Valcarcel, J., and Green, M. R. (1995). Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science 268, 1173-1176.
43. 35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA. Nature 388, 397-400.
44. Tupler, R., Perini, G., and Green, M.R. (2001). Expressing the human genome. Nature 409, 832-833.
45. Uruyishiyama, S., Tani, T., and Ohshima, Y. (1996). Isolation of novel pre-mRNA splicing mutants of Schizosaccharomyces pombe. Mol. Gen. Genet. 253, 118-127.
46. 65 to couple 3′-end processing and splicing. Genes Dev. 14, 403-413.
47. 65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA. Science 273, 1706-1709.
48. Wang, X., Bruderer, S., Rafi, Z., Xue, J., Milburn, P. J., Kramer, A., and Robinson, P. J. (1999). Phosphorylation of splicing factor SF1 on Ser20 by cGMP-dependent protein kinase regulates spliceosome assembly. EMBO J. 18, 4549-4559.
49. Webb, C. J., and Wise, J. A. (2004). The splicing factor U2AF small subunit is functionally conserved between fission yeast and humans. Mol. Cell. Biol. 24, 4229-4240.
50. Wentz-Hunter, K., and Potashkin, J. (1996). The small subunit of the splicing factor U2AF is conserved in fission yeast. Nucleic Acids Res. 24, 1849-1854.
51. Wood, V. et al. (2002). The genome sequence of Schizosaccharomyces pombe. Nature 415, 871-880.
52. 35. Nature 402, 832-835.
53. Zamore, P. D., and Green, M. R. (1991). Biochemical characterization of U2 snRNP auxiliary factor: an essential pre-mRNA splicing factor with a novel intranuclear distribution. EMBO J. 10, 207-214.
54. Zamore, P. D., and Green, M. R. (1989). Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor. Proc. Natl. Acad. Sci. USA 86, 9243-9247.
55. Zamore, P., Patton, J., and Green, M. (1992). Cloning and domain structure of the mammalian splicing factor U2AF. Nature 355, 609-614.
56. Zhang, M., Zamore, P. D., Carmo-Fonseca, M., Lamond, A. I., and Green, M. R. (1992). Cloning and intracellular localization of the U2 small nuclear ribonucleoprotein auxiliary factor small subunit. Proc. Natl. Acad. Sci. USA 89, 8769-8773.
57. Zhang, M. Q., and Marr, T. G. (1994). Fission yeast gene stucture and recognition. Nucleic Acids Res. 22, 1750-1759.
58. Zhang, W. J., and Wu, J. Y. (1996). Functional properties of p54, a novel SR protein active in constitutive and alternative splicing. Mol. Cell. Biol. 16, 5400-5408.
59. Zhang, W. J., and Wu, J. Y. (1998). Sip1, a novel RS domain-containing protein essential for pre-mRNA splicing. Mol. Cell. Biol. 18, 676-684.
60. Zhuang, Y., and Weiner, A. M. (1986). A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation. Cell 46, 827-835.
61. 65: an alternatively spliced RNA containing a novel exon. Mol. Cell. Biol. 17, 946-953.
62. 35 is encoded by an essential gene clustered in an operon with RRM/cyclophilin in Coenorhabditis elegans. RNA 5, 487-494.
63. Zorio, D., and Blumenthal, T. (1999b). Both subunits of U2AF recognize the 3′ splice site in Caenorhabditis elegans. Nature 402, 835-838.
64. 35 mediates critical protein-protein interactions in constitutive and enhancer-dependent splicing. Genes Dev. 10, 1356-1368.