Nucleic Acids Research, 1993, Vol. 21, No. 25 5803-5816
© 1993
SURVEY AND SUMMARY |
Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors
Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor NY 11724-2208, USA
To whom correspondence should be addressed
Received July 30, 1993. Revised October 27, 1993. Accepted October 27, 1993.
We present a systematic analysis of sequence motifs found in metazoan protein factors involved in constitutive pre-mRNA splicing and in alternative splicing regulation. Using profile analysis we constructed a database enriched in protein sequences containing one or more presumptive copies of the RNArecognition motif (RRM). We provide an accurate alignment of RRMs and structure-based criteria for identifying new RRMs, including many that lack the prototype RNP-1 submotif. We present a comprehensive table of 125 sequences containing 252 RRMs, including 22 previously unreported RRMs in 17 proteins. The presence of a putative RRM in these proteins, which are implicated in a variety of cellular processes, strongly suggests that their function involves binding to RNA. Unreported homologies in the RRM-enriched database to the metazoan SR family of splicing factors are described for an Arg-rich human nuclear protein and two yeast proteins (S. pombe mei2 and S. cerevisiae Npl3). We have rigorously tested the phylogenetic relationships of a large sample of RRMs. This analysis indicates that the RRM is an ancient conserved region (ACR) that has diversified by duplication of genes and intragenic domains. Statistical analyses and classification of repeated Arg-Ser (RS)and RGG domains in various protein splicing factors are presented.
+Balliol College, Oxford, OX1 3BJ, UK
New England Biolabs, Beverly, MA 01915, USA
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X. Chen, A. M. Quinn, and S. L. Wolin Ro ribonucleoproteins contribute to the resistance of Deinococcus radiodurans to ultraviolet irradiation Genes & Dev., April 1, 2000; 14(7): 777 - 782. [Abstract] [Full Text]
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J.P. Venables, D.J. Elliott, O.V. Makarova, E.M. Makarov, H.J. Cooke, and I.C. Eperon RBMY, a probable human spermatogenesis factor, and other hnRNP G proteins interact with Tra2{beta} and affect splicing Hum. Mol. Genet., March 22, 2000; 9(5): 685 - 694. [Abstract] [Full Text] [PDF]
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J. Zhou, K. Hidaka, and B. Futcher The Est1 Subunit of Yeast Telomerase Binds the Tlc1 Telomerase RNA Mol. Cell. Biol., March 15, 2000; 20(6): 1947 - 1955. [Abstract] [Full Text]
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M.-C. Lai, R.-I. Lin, S.-Y. Huang, C.-W. Tsai, and W.-Y. Tarn A Human Importin-beta Family Protein, Transportin-SR2, Interacts with the Phosphorylated RS Domain of SR Proteins J. Biol. Chem., March 10, 2000; 275(11): 7950 - 7957. [Abstract] [Full Text] [PDF]
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A. E. McBride, V. H. Weiss, H. K. Kim, J. M. Hogle, and P. A. Silver Analysis of the Yeast Arginine Methyltransferase Hmt1p/Rmt1p and Its in Vivo Function. COFACTOR BINDING AND SUBSTRATE INTERACTIONS J. Biol. Chem., February 4, 2000; 275(5): 3128 - 3136. [Abstract] [Full Text] [PDF]
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C Pazman, C. Mayes, M Fanto, S. Haynes, and M Mlodzik Rasputin, the Drosophila homologue of the RasGAP SH3 binding protein, functions in ras- and Rho-mediated signaling Development, January 4, 2000; 127(8): 1715 - 1725. [Abstract] [PDF]
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R. Perriman and M. Ares Jr. ATP can be dispensable for prespliceosome formation in yeast Genes & Dev., January 1, 2000; 14(1): 97 - 107. [Abstract] [Full Text]
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E. Welin Henriksson, M. Wahren-Herlenius, I. Lundberg, E. Mellquist, and I. Pettersson Key residues revealed in a major conformational epitope of the U1-70K protein PNAS, December 7, 1999; 96(25): 14487 - 14492. [Abstract] [Full Text] [PDF]
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J. Gordon, T. K. Sengupta, C. A. Phillips, S. M. O'Malley, K. R. Williams, and E. K. Spicer Identification of the RNA Binding Domain of T4 RegA Protein by Structure-based Mutagenesis J. Biol. Chem., November 5, 1999; 274(45): 32265 - 32273. [Abstract] [Full Text] [PDF]
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S. G. Sobel and S. L. Wolin Two Yeast La Motif-containing Proteins Are RNA-binding Proteins that Associate with Polyribosomes Mol. Biol. Cell, November 1, 1999; 10(11): 3849 - 3862. [Abstract] [Full Text]
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A. G. Davies, C. A. Spike, J. E. Shaw, and R. K. Herman Functional Overlap Between the mec-8 Gene and Five sym Genes in Caenorhabditis elegans Genetics, September 1, 1999; 153(1): 117 - 134. [Abstract] [Full Text]
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M. Piron, T. Delaunay, J. Grosclaude, and D. Poncet Identification of the RNA-Binding, Dimerization, and eIF4GI-Binding Domains of Rotavirus Nonstructural Protein NSP3 J. Virol., July 1, 1999; 73(7): 5411 - 5421. [Abstract] [Full Text]
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K. Boudonck, L. Dolan, and P. J. Shaw The Movement of Coiled Bodies Visualized in Living Plant Cells by the Green Fluorescent Protein Mol. Biol. Cell, July 1, 1999; 10(7): 2297 - 2307. [Abstract] [Full Text]
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L. A. Hanakahi, H. Sun, and N. Maizels High Affinity Interactions of Nucleolin with G-G-paired rDNA J. Biol. Chem., May 28, 1999; 274(22): 15908 - 15912. [Abstract] [Full Text] [PDF]
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C. W. Siebel, L. Feng, C. Guthrie, and X.-D. Fu Conservation in budding yeast of a kinase specific for SR splicing factors PNAS, May 11, 1999; 96(10): 5440 - 5445. [Abstract] [Full Text] [PDF]
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J. Ding, M. K. Hayashi, Y. Zhang, L. Manche, A. R. Krainer, and R.-M. Xu Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA Genes & Dev., May 1, 1999; 13(9): 1102 - 1115. [Abstract] [Full Text]
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S. M. Crowder, R. Kanaar, D. C. Rio, and T. Alber Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal PNAS, April 27, 1999; 96(9): 4892 - 4897. [Abstract] [Full Text] [PDF]
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S. Lopato, M. Kalyna, S. Dorner, R. Kobayashi, A. R. Krainer, and A. Barta atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes Genes & Dev., April 15, 1999; 13(8): 987 - 1001. [Abstract] [Full Text]
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L. Perrin, P. Romby, P. Laurenti, H. Berenger, S. Kallenbach, H.-M. Bourbon, and J. Pradel The Drosophila Modifier of Variegation modulo Gene Product Binds Specific RNA Sequences at the Nucleolus and Interacts with DNA and Chromatin in a Phosphorylation-dependent Manner J. Biol. Chem., March 5, 1999; 274(10): 6315 - 6323. [Abstract] [Full Text] [PDF]
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A. Mayeda, G. R. Screaton, S. D. Chandler, X.-D. Fu, and A. R. Krainer Substrate Specificities of SR Proteins in Constitutive Splicing Are Determined by Their RNA Recognition Motifs and Composite Pre-mRNA Exonic Elements Mol. Cell. Biol., March 1, 1999; 19(3): 1853 - 1863. [Abstract] [Full Text] [PDF]
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F Weighardt, F Cobianchi, L Cartegni, I Chiodi, A Villa, S Riva, and G Biamonti A novel hnRNP protein (HAP/SAF-B) enters a subset of hnRNP complexes and relocates in nuclear granules in response to heat shock J. Cell Sci., January 5, 1999; 112(10): 1465 - 1476. [Abstract] [PDF]
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