Plant serine/arginine-rich proteins and their role in pre-mRNA splicing

Trends in Plant Science

Volumn 9, Issue 11, 2004, Pages 541-547

  Reddy, Anireddy S N ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; MESSENGER RNA; PLANT RNA; SERINE; VEGETABLE PROTEIN;

ALTERNATIVE RNA SPLICING; CHEMISTRY; GENE EXPRESSION REGULATION; METABOLISM; PHYSIOLOGY; REVIEW; RNA SPLICING;

ALTERNATIVE SPLICING; ARGININE; GENE EXPRESSION REGULATION, PLANT; PLANT PROTEINS; RNA SPLICING; RNA, MESSENGER; RNA, PLANT; SERINE;

ANIMALIA; EMBRYOPHYTA; EUKARYOTA;

EID: 6944222929     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2004.09.007     Document Type: Review

References (80)

1. L.T. Chow An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA Cell 12 1977 1 8
2. S.M. Berget Spliced segments at the 5′ terminus of adenovirus 2 late mRNA Proc. Natl. Acad. Sci. U. S. A. 74 1977 3171 3175
3. H. Le Hir The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions EMBO J. 19 2000 6860 6869
4. V.L. Reichert 5′ exon interactions within the human spliceosome establish a framework for exon junction complex structure and assembly Genes Dev. 16 2002 2778 2791
5. T. Maniatis, and R. Reed An extensive network of coupling among gene expression machines Nature 416 2002 499 506
6. D. Brett Alternative splicing and genome complexity Nat. Genet. 30 2002 29 30
7. J.M. Johnson Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays Science 302 2003 2141 2144
8. B.J. Haas Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Nucleic Acids Res. 31 2003 5654 5666
9. A.S.N. Reddy Nuclear pre-mRNA splicing in plants CRC Crit. Rev. Plant Sci. 20 2001 523 572
10. T. Jordan Alternative splicing of transcripts encoding Toll-like plant resistance proteins - what's the functional relevance to innate immunity? Trends Plant Sci. 7 2002 392 398
11. S.P. Dinesh-Kumar, and B.J. Baker Alternatively spliced N resistance gene transcripts: their possible role in tobacco mosaic virus resistance Proc. Natl. Acad. Sci. U. S. A. 97 2000 1908 1913
12. X.C. Zhang, and W. Gassmann RPS4-mediated disease resistance requires the combined presence of RPS4 transcripts with full-length and truncated open reading frames Plant Cell 15 2003 2333 2342
13. R. Macknight Functional significance of the alternative transcript processing of the Arabidopsis floral promoter FCA Plant Cell 14 2002 877 888
14. V. Quesada Autoregulation of FCA pre-mRNA processing controls Arabidopsis flowering time EMBO J. 22 2003 3142 3152
15. C.B. Burge Splicing of precursors to mRNAs by the spliceosomes R.F. Gesteland The RNA World 1999 Cold Spring Harbor Laboratory Press 525 560
16. G.C. Shukla, and R.A. Padgett Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants RNA 5 1999 525 538
17. W. Zhu, and V. Brendel Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome Nucleic Acids Res. 31 2003 4561 4572
18. J. Rappsilber Large-scale proteomic analysis of the human spliceosome Genome Res. 12 2002 1231 1245
19. Z. Zhou Comprehensive proteomic analysis of the human spliceosome Nature 419 2002 182 185
20. M. Rosbash, and B. Séraphin Who's on first? The U1 snRNP-5′ splice site interaction and splicing Trends Biochem. Sci. 16 1991 187 190
21. C.L. Will, and R. Luhrmann Protein functions in pre-mRNA splicing Curr. Opin. Cell Biol. 9 1997 320 328
22. J.L. Manley, and R. Tacke SR proteins and splicing control Genes Dev. 10 1996 1569 1579
23. M. Golovkin, and A.S.N. Reddy Structure and expression of a plant U1 snRNP 70K gene: alternative splicing of U1 snRNP 70K pre-mRNAs produces two different transcripts Plant Cell 8 1996 1421 1435
24. G.G. Simpson Molecular characterization of spliceosomal proteins U1A and U2B″ from higher plants EMBO J. 14 1995 4540 4550
25. M. Golovkin, and A.S.N. Reddy Expression of U1snRNP 70K antisense transcript using APETALA3 promoter suppresses the development of petals and stamens Plant Physiol. 132 2003 1884 1891
26. Z.J. Lorkovic Pre-mRNA splicing in higher plants Trends Plant Sci. 5 2000 160 167
27. W.W.S. Brown, and C.G. Simpson Splice site selection in plant pre-mRNA splicing Annu. Rev. Plant Physiol. Plant Mol. Biol. 49 1998 77 95
28. M.A. Schuler Plant pre-mRNA splicing J. Bailey-Serres D.R. Gallie A Look Beyond Transcription: Mechanisms Determining mRNA Stability and Translation in Plants 1998 American Society of Plant Physiologists 1 19
29. W. Zhu Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping Plant Physiol. 132 2003 469 484
30. K.R. Luehrsen Nuclear pre-mRNA processing in higher plants Prog. Nucleic Acids Res. Mol. Biol. 47 1994 149 193
31. D. Lewandowska Determinants of plant U12-dependent intron splicing efficiency Plant Cell 16 2004 1340 1352
32. M.H. Lambermon UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation EMBO J. 19 2000 1638 1649
33. J.C. Carle-Urioste A combinatorial role for exon, intron and splice site sequences in splicing in maize Plant J. 11 1997 1253 1263
34. M.J. Latijnhouwers Test of the combinatorial model of intron recognition in a native maize gene Plant Mol. Biol. 41 1999 637 644
35. A.J. McCullough, and M.A. Schuler Intronic and exonic sequences modulate 5′ splice site selection in plant nuclei Nucleic Acids Res. 25 1997 1071 1077
36. K. Yoshimura Identification of a cis element for tissue-specific alternative splicing of chloroplast ascorbate peroxidase pre-mRNA in higher plants J. Biol. Chem. 277 2002 40623 40632
37. B.R. Graveley Sorting out the complexity of SR protein functions RNA 6 2000 1197 1211
38. Sanford, J.R. et al. (2003) Multiple roles of the SR protein family in splicing regulation. In Regulation of Alternative Splicing (Vol. 31) (Jeanteur, P., ed.), pp. 33-58, Springer
39. A.M. Zahler SR proteins: a conserved family of pre-mRNA splicing factors Genes Dev. 6 1992 837 847
40. Y. Huang, and J.A. Steitz Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA Mol. Cell 7 2001 899 905
41. R. Lemaire Stability of a PKCI-1-related mRNA is controlled by the splicing factor ASF/SF2: a novel function for SR proteins Genes Dev. 16 2002 594 607
42. J.R. Sanford A novel role for shuttling SR proteins in mRNA translation Genes Dev. 18 2004 755 768
43. R. Tacke, and J.L. Manley Determinants of SR protein specificity Curr. Opin. Cell Biol. 11 1999 358 362
44. Z.J. Lorkovic, and A. Barta Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana Nucleic Acids Res. 30 2002 623 635
45. M. Kalyna, and A. Barta A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions? Biochem. Soc. Trans. 32 2004 561 564
46. S. Lopato Pre-mRNA splicing in plants: characterization of Ser/Arg splicing factors Proc. Natl. Acad. Sci. U. S. A. 93 1996 3074 3079
47. S. Lopato A novel family of plant splicing factors with a Zn knuckle motif: examination of RNA binding and splicing activities Plant Mol. Biol. 39 1999 761 773
48. M. Kalyna Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development Mol. Biol. Cell 14 2003 3565 3577
49. G. Lazar Identification of a plant serine-arginine-rich protein similar to the mammalian splicing factor SF2/ASF Proc. Natl. Acad. Sci. U. S. A. 92 1995 7672 7676
50. G. Lazar, and H.M. Goodman The Arabidopsis splicing factor SR1 is regulated by alternative splicing Plant Mol. Biol. 42 2000 571 581
51. Y. Fang Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis Mol. Biol. Cell 15 2004 2664 2673
52. M. Golovkin, and A.S.N. Reddy The plant U1 small nuclear ribonucleoprotein particle 70K protein interacts with two novel serine/arginine-rich proteins Plant Cell 10 1998 1637 1648
53. M. Golovkin, and A.S.N. Reddy An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein J. Biol. Chem. 274 1999 36428 36438
54. S. Lopato Characterization of a novel arginine/serine-rich splicing factor in Arabidopsis Plant Cell 8 1996 2255 2264
55. S. Lopato atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes Genes Dev. 13 1999 987 1001
56. T. Misteli RNA splicing: what has phosphorylation got to do with it? Curr. Biol. 9 1999 R198 R200
57. S.H. Shiu, and A.B. Bleecker Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis Plant Physiol. 132 2003 530 543
58. S. Savaldi-Goldstein The ethylene-inducible PK12 kinase mediates the phosphorylation of SR splicing factors Plant J. 21 2000 91 96
59. S. Savaldi-Goldstein Alternative splicing modulation by a LAMMER kinase impinges on developmental and transcriptome expression Plant Cell 15 2003 926 938
60. A.I. Lamond, and D.L. Spector Nuclear speckles: a model for nuclear organelles Nat. Rev. Mol. Cell Biol. 4 2003 605 612
61. K. Boudonck Coiled body numbers in the Arabidopsis root epidermis are regulated by cell type, developmental stage and cell cycle parameters J. Cell Sci. 111 1998 3687 3694
62. T. Misteli The dynamics of a pre-mRNA splicing factor in living cells Nature 387 1997 523 527
63. G.S. Ali Nuclear localization and in vivo dynamics of a plant-specific serine/arginine-rich protein Plant J. 36 2003 883 893
64. S. Docquier Nuclear bodies and compartmentalization of pre-mRNA splicing factors in higher plants Chromosoma 112 2004 255 266
65. Z.J. Lorkovic Use of fluorescent protein tags to study nuclear organization of the spliceosomal machinery in transiently transformed living plant cells Mol. Biol. Cell 15 2004 3233 3243
66. R.D. Phair, and T. Misteli High mobility of proteins in the mammalian cell nucleus Nature 404 2000 604 609
67. S. Lopato Network of interactions of a novel plant-specific Arg/Ser-rich protein, atRSZ33, with atSC35-like splicing factors J. Biol. Chem. 277 2002 39989 39998
68. Z.J. Lorkovic Interactions of Arabidopsis RS domain containing cyclophilins with SR proteins and U1 and U11 snRNP-specific proteins suggest their involvement in pre-mRNA splicing J. Biol. Chem. 279 2004 33890 33898
69. J.Y. Wu, and T. Maniatis Specific interactions between proteins implicated in splice site selection and regulated alternative splicing Cell 75 1993 1061 1070
70. C. Shin Dephosphorylated SRp38 acts as a splicing repressor in response to heat shock Nature 427 2004 553 558
71. D. Longman Functional characterization of SR and SR-related genes in Caenorhabditis elegans EMBO J. 19 2000 1625 1637
72. A.C. Gavin, and G. Superti-Furga Protein complexes and proteome organization from yeast to man Curr. Opin. Chem. Biol. 7 2003 21 27
73. E.M. Makarov Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome Science 298 2002 2205 2208
74. C. Turek, and L. Gold Systemic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249 1990 505 510
75. D. Schneider Selection of high affinity RNA ligands to the bacteriophage R17 coat protein J. Mol. Biol. 228 1992 862 869
76. B.S. Singer Libraries for genomic SELEX Nucleic Acids Res. 25 1997 781 786
77. S. Kim Specific SR protein-dependent splicing substrates identified through genomic SELEX Nucleic Acids Res. 31 2003 1955 1961
78. T.A. Clark Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays Science 296 2002 907 910
79. K. Yamada Empirical analysis of transcriptional activity in the Arabidopsis genome Science 302 2003 842 846
80. Reddy, A.S.N. et al. Arabidopsis U1 snRNP 70K protein and its interacting proteins: nuclear localization and in vivo dynamics of a novel plant-specific serine/arginine-rich protein. In The Nuclear Envelope (Evans, D. and Bryant, J., eds), BIOS Scientific Publisher (in press)