Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae

Abstract

Little is known about pre-mRNA splicing in Dictyostelium discoideum although its genome has been completely sequenced. Our analysis suggests that pre-mRNA splicing plays an important role in D. discoideum gene expression as two thirds of its genes contain at least one intron. Ongoing curation of the genome to date has revealed 40 genes in D. discoideum with clear evidence of alternative splicing, supporting the existence of alternative splicing in this unicellular organism. We identified 160 candidate U2-type spliceosomal proteins and related factors in D. discoideum based on 264 known human genes involved in splicing. Spliceosomal small ribonucleoproteins (snRNPs), PRP19 complex proteins and late-acting proteins are highly conserved in D. discoideum and throughout the metazoa. In non-snRNP and hnRNP families, D. discoideum orthologs are closer to those in A. thaliana, D. melanogaster and H. sapiens than to their counterparts in S. cerevisiae. Several splicing regulators, including SR proteins and CUG-binding proteins, were found in D. discoideum, but not in yeast. Our comprehensive catalog of spliceosomal proteins provides useful information for future studies of splicing in D.βdiscoideum where the efficient genetic and biochemical manipulation will also further our general understanding of pre-mRNA splicing.

Keywords

pre-mRNA splicing / spliceosomal genes / Dictyostelium discoideum / comparative genomics / splicing regulators

References

[1] Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J Mol Biol 215, 403–410 .2231712
[2] Aspegren, A., Hinas, A., Larsson, P., Larsson, A., and S?derbom, F. (2004). Novel non-coding RNAs in Dictyostelium discoideum and their expression during development. Nucleic Acids Res 32, 4646–4656 .15333696
[3] Bain, G., Grant, C.E., and Tsang, A. (1991). Isolation and characterization of cDNA clones encoding polypeptides related to a Dictyostelium discoideum cyclic AMP binding protein. J Gen Microbiol 137, 501–508 .1851802
[4] Baldauf, S.L., Roger, A.J., Wenk-Siefert, I., and Doolittle, W.F. (2000). A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972–977 .11062127
[5] Barbosa-Morais, N.L., Carmo-Fonseca, M., and Aparício, S. (2006). Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. Genome Res 16, 66–77 .16344558
[6] Bessonov, S., Anokhina, M., Will, C.L., Urlaub, H., and Lührmann, R. (2008). Isolation of an active step I spliceosome and composition of its RNP core. Nature 452, 846–850 .18322460
[7] Black, D.L. (2003). Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72, 291–336 .12626338
[8] Blencowe, B.J. (2000). Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem Sci 25, 106–110 .10694877
[9] Calarco, J.A., Zhen, M., and Blencowe, B.J. (2011). Networking in a global world: Establishing functional connections between neural splicing regulators and their target transcripts. RNA 17, 775–791 .11967553
[10] Cartegni, L., Chew, S.L., and Krainer, A.R. (2002). Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 3, 285–298 .11967553
[11] Chisholm, R.L., Gaudet, P., Just, E.M., Pilcher, K.E., Fey, P., Merchant, S.N., and Kibbe, W.A. (2006). dictyBase, the model organism database for Dictyostelium discoideum. Nucleic Acids Res 34, D423–D427 .16381903
[12] Collins, L., and Penny, D. (2005). Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol 22, 1053–1066 .15659557
[13] Cordin, O., Banroques, J., Tanner, N.K., and Linder, P. (2006). The DEAD-box protein family of RNA helicases. Gene 367, 17–37 .16337753
[14] Crosby, M.A., Goodman, J.L., Strelets, V.B., Zhang, P., and Gelbart, W.M., and the FlyBase Consortium. (2007). FlyBase: genomes by the dozen. Nucleic Acids Res 35, D486–D491 .17099233
[15] Ebralidze, A., Wang, Y., Petkova, V., Ebralidse, K., and Junghans, R.P. (2004). RNA leaching of transcription factors disrupts transcription in myotonic dystrophy. Science 303, 383–387 .14657503
[16] Eichinger, L., Pachebat, J.A., Gl?ckner, G., Rajandream, M.A., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., (2005). The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43–57 .15875012
[17] Escalante, R., Moreno, N., and Sastre, L. (2003). Dictyostelium discoideum developmentally regulated genes whose expression is dependent on MADS box transcription factor SrfA. Eukaryot Cell 2, 1327–1335 .14665466
[18] Fushimi, K., Ray, P., Kar, A., Wang, L., Sutherland, L.C., and Wu, J.Y., (2008). Up-regulation of the proapoptotic caspase 2 splicing isoform by a candidate tumor suppressor, RBM 5. Proc Natl Acad Sci USA .14665466
[19] Grant, C.E., and Tsang, A. (1990). Cloning and characterization of cDNAs encoding a novel cyclic AMP-binding protein in Dictyostelium discoideum. Gene 96, 213–218 .2176639
[20] Greenwood, M., and Tsang, A. (1991). Sequence and expression of annexin VII of Dictyostelium discoideum. Biochim Biophys Acta 1088, 429–432 .1826615
[21] Hartmuth, K., Urlaub, H., Vornlocher, H.-P., Will, C.L., Gentzel, M., Wilm, M., and Lührmann, R. (2002). Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method. Proc Natl Acad Sci U S A 99, 16719–16724 .12477934
[22] Hinas, A., Larsson, P., Avesson, L., Kirsebom, L.A., Virtanen, A., and S?derbom, F. (2006). Identification of the major spliceosomal RNAs in Dictyostelium discoideum reveals developmentally regulated U2 variants and polyadenylated snRNAs. Eukaryot Cell 5, 924–934 .16757740
[23] Hoskins, A.A., Friedman, L.J., Gallagher, S.S., Crauford, D.J., Anderson, E.G., Wombacher, R., Ramirez, N., Cornish, V.W., Gelles, J., and Moore, M.J. (2011). Ordered and dynamic assembly of single spliceosomes. Science 331, 1289–1289 .14671308
[24] Kanadia, R.N., Johnstone, K.A., Mankodi, A., Lungu, C., Thornton, C.A., Esson, D., Timmers, A.M., Hauswirth, W.W., and Swanson, M.S. (2003). A muscleblind knockout model for myotonic dystrophy. Science 302, 1978–1980 .14671308
[25] Kar, A., Fushimi, K., Zhou, X., Ray, P., Shi, C., Chen, X., Liu, Z., Chen, S., and Wu., J.Y., (2011). RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5′ splice site. Mol Cell Biol 31, 1812–1821 .14671308
[26] Ladd, A.N., Charlet, N., and Cooper, T.A. (2001). The CELF family of RNA binding proteins is implicated in cell-specific and developmentally regulated alternative splicing. Mol Cell Biol 21, 1285–1296 .11158314
[27] Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 .17846036
[28] Lejeune, F., and Maquat, L.E. (2005). Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr Opin Cell Biol 17, 309–315 .15901502
[29] Lin, S., and Fu, X.D. (2007). SR proteins and related factors in alternative splicing. Adv Exp Med Biol 623, 107–122 .18380343
[30] Matlin, A.J., and Moore, M.J. (2007). Spliceosome assembly and composition. Adv Exp Med Biol 623, 14–35 .18380338
[31] Moore, M.J., and Silver, P.A., (2008). Global analysis of mRNA splicing. RNA 14, 197–203 .18380338
[32] Mordes, D., Luo, X., Kar, A., Kuo, D., Xu, L., Fushimi, K., Yu, G., Sternberg, P. Jr, and Wu, J.Y. (2006). Pre-mRNA splicing and retinitis pigmentosa. Mol Vis 12, 1259–1271 .17110909
[33] Nilsen, T.W., and Graveley, B.R. (2010). Expansion of the eukaryotic proteome bu alternative splicing. Nature 28, 463 457–463 .18380338
[34] Pacione, L.R., Szego, M.J., Ikeda, S., Nishina, P.M., and McInnes, R.R. (2003). Progress toward understanding the genetic and biochemical mechanisms of inherited photoreceptor degenerations. Annu Rev Neurosci 26, 657–700 .14527271
[35] Page, R.D. (2002). Visualizing phylogenetic trees using TreeView. Curr Protoc Bioinformatics, Chapter 6, Unit 6 2.
[36] Patel, A.A., and Steitz, J.A. (2003). Splicing double: insights from the second spliceosome. Nat Rev Mol Cell Biol 4, 960–970 .14685174
[37] Ramani, A.K., Calarco, J.A., Pan, Q., Mavandadi, S., Wang, Y., Nelson, A.C., Lee, L.J., Morris, Q., Blencowe, B.J., Zhen, M., and Fraser, A.G., (2011). Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res 21, 342–348 .14671308
[38] Ronquist, F., and Huelsenbeck, J.P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 .12912839
[39] Sanford, J.R., Ellis, J., and Cáceres, J.F. (2005). Multiple roles of arginine/serine-rich splicing factors in RNA processing. Biochem Soc Trans 33, 443–446 .15916537
[40] Staley, J.P., and Guthrie, C. (1998). Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell 92, 315–326 .9476892
[41] Tange, T.O., Nott, A., and Moore, M.J. (2004). The ever-increasing complexities of the exon junction complex. Curr Opin Cell Biol 16, 279–284 .15145352
[42] Wang, G.S., and Cooper, T.A. (2007). Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 8, 749–761 .17726481
[43] Will, C.L., and Lührmann, R. (2005). Splicing of a rare class of introns by the U12-dependent spliceosome. Biol Chem 386, 713–724 .16201866
[44] Wu, J.Y., Havlioglu, N., and Yuan, L. (2004). Alternatively spliced genes. In: Encyclopedia of Molecular Cell Biology and Molecular Medicine . Vol 1, 2nd ed. Meyers RA, ed. New York: Wiley-VCH.
[45] Wu, J.Y., Kar, A., Kuo, B., and Havlioglu, N. (2006). SR_p54 (SFRS11), a regulator for tau exon 10 alternative splicing identified by an expression Cloning strategy. Mol Cell Biol 26, 6739–6747 .14527271
[46] Zhou, Z., Licklider, L.J., Gygi, S.P., and Reed, R. (2002). Comprehensive proteomic analysis of the human spliceosome. Nature 419, 182–185 .12226669