U-rich tracts enhance 3′ splice site recognition in plant nuclei

Plant Journal

Volumn 10, Issue 4, 1996, Pages 703-711

  Baynton, Clair E ^a   Potthoff, Sara J ^a   McCullough, Andrew J ^a,b   Schuler, Mary A ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBULOSEBISPHOSPHATE CARBOXYLASE; RNA PRECURSOR; URIDINE;

ARTICLE; CELL NUCLEUS; COMPARATIVE STUDY; DNA BASE COMPOSITION; DNA SEQUENCE; EXON; GENETIC TRANSFECTION; GENETICS; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PEA; PLANT; PLANT LEAF; RNA SPLICING; TOBACCO;

BASE COMPOSITION; BASE SEQUENCE; CELL NUCLEUS; CLONING, MOLECULAR; EXONS; MOLECULAR SEQUENCE DATA; MUTATION; PEAS; PLANT LEAVES; PLANTS, TOXIC; RIBULOSE-BISPHOSPHATE CARBOXYLASE; RNA PRECURSORS; RNA SPLICING; SEQUENCE ANALYSIS, DNA; TOBACCO; TRANSFECTION; URIDINE;

MAMMALIA; NICOTIANA TABACUM; PISUM SATIVUM;

EID: 0030268481     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-313x.1996.10040703.x     Document Type: Article

References (67)

1. Barta, A., Sommergruber, K., Thompson, D., Hartmuth, K., Matzke, M.A. and Matzke, A.J.M. (1986) The expression of a nopaline synthase-human growth hormone chimeric gene in transformed tobacco and sunflower callus tissue. Plant Mol. Biol. 6, 347-357.
2. Brown, J.W.S. (1986) A catalogue of splice junction and putative branch point sequences from plant introns. Nucl. Acids Res. 14, 9549-9559.
3. Brown, J.W.S., Feix, G. and Frendeway, D. (1986) Accurate in vitro splicing of two pre-mRNA plant introns in a HeLa cell nuclear extract. EMBO J. 5, 2749-2758.
4. Buvoli, M., Cobianchi, F., Biamonti, G. and Riva, S. (1990) Recombinant hnRNP protein A1 and its N-terminal domain show preferential affinity for oligodeoxynucleotides homologous to intron/exon acceptor sites. Nucl Acids Res. 18, 6595-6600.
5. Carle-Urioste, J.C., Ko, C.H., Benito, M.-I. and Walbot, V. (1994) In vivo analysis of intron processing using splicing-dependent reporter gene assays. Plant Mol. Biol. 26, 1785-1795.
6. Csank, C., Taylor, F.M. and Martindale, D.W. (1990) Nuclear pre-mRNA introns: analysis and comparison of intron sequences from Tetrahymena thermophila and other eukaryotes. Nucl. Acids Res. 18, 5133-5141.
7. Fouser, L.A. and Friesen, J.D. (1986) Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear mRNA splicing. Cell, 45, 81-93.
8. Fouser, L.A. and Friesen, J.D. (1987) Effects on mRNA splicing of mutations in the 3′ region of the Saccharomyces cerevisiae actin intron. Mol. Cell. Biol. 7, 225-230.
9. Frendeway, D. and Keller, W. (1985) Stepwise assembly of a pre-mRNA splicing complex requires U-snRNAs and specific intron sequences. Cell, 42, 355-367.
10. Garcia-Blanco, M.A., Jamison, S.F. and Sharp, P.A. (1989) Identification and purification of a 62,000-dalton protein that binds specifically to the polypyrimidine tract of introns. Genes Devel. 3, 1874-1886.
11. Ghetti, A., Pinol-Roma, S., Michael, W.M., Morandi, C. and Dreyfuss, G. (1992) hnRNP I, the polypyrimidine tract-binding protein: distinct nuclear localization and association with hnRNAs. Nucl. Acids Res. 20, 3671-3678.
12. Gil, A., Sharp, P.A., Jamison, S.F. and Garcia-Blanco, M.A. (1991) Characterization of cDNAs encoding the polypyrimidine tract-binding protein. Genes Devel. 5, 1224-1236.
13. Goodall, G.J. and Filipowicz, W. (1989) The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell, 58, 473-483.
14. Goodall, G.J. and Filipowicz, W. (1991) Different effects of intron nucleotide composition and secondary structure on pre-mRNA splicing in monocot and dicot plants. EMBO J. 10, 2635-2644.
15. Goodall, G.J., Kiss, T. and Filipowicz, W. (1991) Nuclear RNA splicing and small nuclear RNAs and their genes in higher plants. In Oxford Surveys of Plant Molecular and Cell Biology, Volume 7 (Miflin, B.J., ed.). Oxford: Oxford University Press, pp. 255-296.
16. Green, M.R. (1991) Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Ann. Rev. Cell Biol. 7, 559-599.
17. Hanley, B.A. and Schuler, M.A. (1988) Plant intron sequences: evidence for distinct groups of introns. Nucl. Acids Res. 16, 7159-7176.
18. Hartmuth, K. and Barta, A. (1986) In vitro processing of a plant pre-mRNA in a HeLa cell nuclear extract. Nucl. Acids Res. 14, 7513-7527.
19. Lesser, C.F. and Guthrie, C. (1993) Mutations in U6 snRNA that alter splice site specificity: Implications for the active site. Science, 262, 1982-1988.
20. Lou, H., McCullough, A.J. and Schuler, M.A. (1993a) 3′ splice site selection in dicot plant nuclei is position-dependent. Mol. Cell. Biol. 13, 4485-4493.
21. Lou, H., McCullough, A.J. and Schuler, M.A. (1993b) Expression of maize Adh1 intron mutants in tobacco nuclei. Plant J. 3, 393-403.
22. Luehrsen, K.R. and Walbot, V. (1994a) Intron creation and polyadenylation in maize are directed by AU-rich RNA. Genes Devel. 8, 1117-1130.
23. Luehrsen, K.R. and Walbot, V. (1994b) Addition of A- and U-rich sequence increases the splicing efficiency of a deleted form of a maize intron. Plant Mol. Biol. 24, 449-463.
24. McCullough, A.J. and Schuler, M.A. (1993) AU-rich intronic elements affect pre-mRNA 5′ splice site selection in Drosophila melanogaster. Mol. Cell. Biol. 13, 7689-7697.
25. McCullough, A.J., Lou, H. and Schuler, M.A. (1991) In vivo analysis of plant pre-mRNA splicing using an autonomously replicating vector. Nucl. Acids Res. 19, 3001-3009.
26. McCullough, A.J., Lou, H. and Schuler, M.A. (1993) Factors affecting authentic 5′ splice site selection in plant nuclei. Mol. Cell. Biol. 13, 1323-1331.
27. Moore, M.J., Query, C.C. and Sharp, P.A. (1993) Splicing of precursors to messenger RNAs bythespliceosome. In The RNA World (Gesteiand, R. and Atkins, J., eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 303-357.
28. Mount, S.M. (1982) A catalogue of splice junctions. Nucl. Acids Res. 10, 459-472.
29. Nelson, K.K. and Green, M.R. (1989) Mammalian U2 snRNP has a sequence specific RNA-binding activity. Genes Devel. 3, 1562-1571.
30. Nelson, K.K. and Green, M.R. (1990) Mechanism for cryptic splice site activation during pre-mRNA splicing. Proc. Natl Acad. Sci. USA, 87, 6253-6257.
31. Newman, A.J. and Norman, C. (1991) Mutations in yeast U5 snRNA alter the specificity of 5′ splice-site cleavage. Cell, 65, 115-123.
32. Newman, A.J. and Norman, C. (1992) U5 snRNA interacts with exon sequences at 5′ and 3′ splice sites. Cell, 68, 743-754.
33. Newman, A.J., Lin, R.-J., Cheng, S.-C. and Abelson, J. (1985) Molecular consequences of specific intron mutations on yeast mRNA splicing in vivo and in vitro. Cell, 42, 335-344.
34. Padgett, R.A., Konarska, M.M., Aebi, M., Hornig, H., Weissmann, C. and Sharp, P.A. (1985) Nonconsensus branch-site sequences in the in vitro splicing of transcripts of mutant rabbit β-globin genes. Proc. Natl Acad. Sci. USA, 82, 8349-8353.
35. Padgett, R.A., Grabowski, P.J., Konarska, M.M., Seiler, S. and Sharp, P.A. (1986) Splicing of messenger RNA precursors. Ann. Rev. Biochem. 55, 1119-1150.
36. Parker, R. and Guthrie, C. (1985) A point mutation in the conserved hexanucleotide at a yeast 5′ splice junction uncouples recognition, cleavage, and ligation. Cell, 41, 107-118.
37. Parker, R., Siliciano, P.G. and Guthrie, C. (1987) Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. Cell, 49, 229-239.
38. Patterson, B. and Guthrie, C. (1991) A U-rich tract enhances usage of an alternative 3′ splice site in yeast. Cell, 64, 181-187.
39. Patton, J.G., Mayer, S.A., Tempst, P. and Nadal-Ginard, B. (1991) Characterization and molecular cloning of polypyrimidine tract-binding protein: a component of a complex necessary for pre-mRNA splicing. Genes Devel. 5, 1237-1251.
40. Pautot, V., Brzezinski, R. and Tepfer, M. (1989) Expression of a mouse metallothionein gene in transgenic plant tissues. Gene, 77, 133-140.
41. Reed, R. (1989) The organization of 3′ splice-site sequences in mammalian introns. Genes Devel. 3, 2113-2123.
42. Reed, R. and Maniatis, T. (1985) Intron sequences involved in lariat formation during pre-mRNA splicing. Cell, 41, 95-105.
43. Reich, C.I., VanHoy, R.W., Porter, G.L. and Wise, J.A. (1992) Mutations at the 3′ splice site can be suppressed by compensatory base changes in U1 snRNA in fission yeast. Cell, 69, 1159-1169.
44. Roscigno, R.F., Weiner, M. and Garcia-Blanco, M.A. (1993) A mutational analysis of the polypyrimidine tract of introns: effects of sequence differences in pyrimidine tracts on splicing. J. Biol. Chem. 268, 11 222-11 229.
45. Ruis, B.L, Kivens, W.J. and Siliciano, P.G. (1994) The interaction between the first and last intron nucleotides in the second step of pre-mRNA splicing is independent of other conserved intron nucleotides. Nucl. Acids Res. 22, 5190-5195.
46. Ruskin, B. and Green, M.R. (1985) Role of the 3′ splice site consensus sequence in mammalian pre-mRNA splicing. Nature, 317, 732-734.
47. Ruskin, B., Greene, J.M. and Green, M.R. (1985) Cryptic branch point activation allows accurate in vitro splicing of human β-globin intron mutants. Cell, 41, 833-844.
48. 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.
49. Rymond, B.C. and Rosbash, M. (1992) Yeast pre-mRNA splicing. In The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression. (Jones, E.W., Pringle, J.R. and Broach, J.R., eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 143-193.
50. Sawa, H. and Abelson, J. (1992) Evidence for a base-pairing interaction between U6 small nuclear RNA and the 5′ splice site during the splicing reaction in yeast. Proc. Natl Acad. Sci. USA, 89, 11 269-11 273.
51. Sharp, P.A. (1994) Split genes and RNA splicing. Cell, 77, 805-815.
52. Siliciano, P.G. and Guthrie, C. (1988) 5′ splice site selection in yeast: genetic alterations in base pairing with U1 reveal additional requirements. Genes Devel. 2, 1258-1267.
53. Simpson, G.G. and Brown, J.W.S. (1993) Efficient splicing of an AU-rich antisense intron sequence. Plant Mol. Biol. 21, 205-211.
54. Smith, C.W.J., Porro, E.B., Patton, J.G. and Nadal-Ginard, B. (1989) Scanning from an independently specified branch point defines the 3′ splice site of mammalian introns. Nature, 342, 243-247.
55. Sontheimer, E.J. and Steitz, J.A. (1993) The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science, 262, 1989-1996.
56. Sun, J.-S. and Manley, J.L. (1995) A novel U2-U6 snRNA structure is necessary for mammalian mRNA splicing. Genes Devel. 9, 843-854.
57. Swanson, M.S. and Dreyfuss, G. (1988) RNA binding specificity of hnRNP proteins: a subset bind to the 3′ end of introns. EMBO J. 7, 3519-3529.
58. Tazi, J., Alibert, C., Temsamani, J., Reveilland, I., Cathala, G., Brunel, C. and Jeanteau, P. (1986) A protein that specifically recognizes the 3′ splice site of mammalian pre-mRNA introns is associated with a small nuclear ribonucleoprotein. Cell, 45, 755-766.
59. Umen, J.G. and Guthrie, C. (1995) A novel role for a U5 snRNP protein in 3′ splice site selection. Genes Devel. 9, 855-868.
60. Vallette, F., Mege, E., Reiss, A. and Adesnik, M. (1989) Construction of mutant and chimeric genes using the polymerase chain reaction. Nuel. Acids Res. 17, 723-733.
61. Van Santen, V. and Spritz, R. (1987) Splicing of plant pre-mRNAs in animal systems and vice versa. Gene, 56, 253-265.
62. Vijayraghavan, U., Parker, R., Tamm, J., Iimura, Y., Rossi, J., Abelson, J. and Guthrie, C. (1986) Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of thespliceosome. EMBO J. 5, 1683-1695.
63. Wassarman, D.A. and Steitz, J.A. (1992) Interactions of small nuclear RNA's with precursor messenger RNA during in vitro splicing. Science, 257, 1918-1925.
64. Wiebauer, K., Herrero, J.-J. and Filipowicz, W. (1988) Nuclear pre-mRNA processing in plants: Distinct modes of 3′-splice site selection in plants and animals. Mol. Cell. Biol. 8, 2042-2051.
65. Wu, J. and Manley, J.L. (1989) Mammalian pre-mRNA branch site selection by U2 snRNP involves base pairing. Genes Devel. 3, 1553-1561.
66. Zhuang, Y. and Weiner, A.M. (1986) A compensatory base change in U1 snRNA suppresses a 5′ splice site mutation. Cell, 46, 827-835.
67. Zhuang, Y. and Weiner, A.M. (1989) A compensatory base change in human U2 snRNA can suppress a branch site mutation. Genes Devel. 3, 1545-1552.