A Single SR-like Protein, Npl3, Promotes Pre-mRNA Splicing in Budding Yeast

Molecular Cell - Tập 32 - Trang 727-734 - 2008
Tracy L. Kress1, Nevan J. Krogan2, Christine Guthrie1
1Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143, USA
2Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA

Tài liệu tham khảo

Abovich, 1994, The yeast MUD2 protein: an interaction with PRP11 defines a bridge between commitment complexes and U2 snRNP addition, Genes Dev., 8, 843, 10.1101/gad.8.7.843 Arenas, 1997, Prp43: An RNA helicase-like factor involved in spliceosome disassembly, Proc. Natl. Acad. Sci. USA, 94, 11798, 10.1073/pnas.94.22.11798 Bartels, 2002, The ribosomal translocase homologue Snu114p is involved in unwinding U4/U6 RNA during activation of the spliceosome, EMBO Rep., 3, 875, 10.1093/embo-reports/kvf172 Berglund, 1997, The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC, Cell, 89, 781, 10.1016/S0092-8674(00)80261-5 Blencowe, 1999, SR-related proteins and the processing of messenger RNA precursors, Biochem. Cell Biol., 77, 277, 10.1139/o99-048 Bourgeois, 2004, Broad specificity of SR (serine/arginine) proteins in the regulation of alternative splicing of pre-messenger RNA, Prog. Nucleic Acid Res. Mol. Biol., 78, 37, 10.1016/S0079-6603(04)78002-2 Bucheli, 2005, Npl3 is an antagonist of mRNA 3′ end formation by RNA polymerase II, EMBO J., 24, 2150, 10.1038/sj.emboj.7600687 Bucheli, 2007, Polyadenylation site choice in yeast is affected by competition between Npl3 and polyadenylation factor CFI, RNA, 13, 1756, 10.1261/rna.607207 Burckin, 2005, Exploring functional relationships between components of the gene expression machinery, Nat. Struct. Mol. Biol., 12, 175, 10.1038/nsmb891 Caspary, 1998, The yeast U2A′/U2B complex is required for pre-spliceosome formation, EMBO J., 17, 6348, 10.1093/emboj/17.21.6348 Collins, 2007, Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map, Nature, 446, 806, 10.1038/nature05649 Collins, 2006, A strategy for extracting and analyzing large-scale quantitative epistatic interaction data, Genome Biol., 7, R63, 10.1186/gb-2006-7-7-r63 Das, 2007, SR proteins function in coupling RNAP II transcription to pre-mRNA splicing, Mol. Cell, 26, 867, 10.1016/j.molcel.2007.05.036 Davis, 2000, Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast, Nucleic Acids Res., 28, 1700, 10.1093/nar/28.8.1700 de Hoon, 2004, Open source clustering software, Bioinformatics, 20, 1453, 10.1093/bioinformatics/bth078 Deka, 2008, Structure of the yeast SR protein Npl3 and Interaction with mRNA 3′-end processing signals, J. Mol. Biol., 375, 136, 10.1016/j.jmb.2007.09.029 Dermody, 2008, Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation, PLoS ONE, 3, e3273, 10.1371/journal.pone.0003273 Engebrecht, 1991, Meiosis-specific RNA splicing in yeast, Cell, 66, 1257, 10.1016/0092-8674(91)90047-3 Gavin, 2002, Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, 415, 141, 10.1038/415141a Gilbert, 2001, Phosphorylation by Sky1p promotes Npl3p shuttling and mRNA dissociation, RNA, 7, 302, 10.1017/S1355838201002369 Gornemann, 2005, Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex, Mol. Cell, 19, 53, 10.1016/j.molcel.2005.05.007 Gottschalk, 1998, A comprehensive biochemical and genetic analysis of the yeast U1 snRNP reveals five novel proteins, RNA, 4, 374 Hacker, 2004, Differential export requirements for shuttling serine/arginine-type mRNA-binding proteins, J. Biol. Chem., 279, 5049, 10.1074/jbc.C300522200 He, 1995, Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen, Genes Dev., 9, 437, 10.1101/gad.9.4.437 Henry, 1996, Potential RNA binding proteins in Saccharomyces cerevisiae identified as suppressors of temperature-sensitive mutations in NPL3, Genetics, 142, 103, 10.1093/genetics/142.1.103 Hertel, 2005, RS domains contact the pre-mRNA throughout spliceosome assembly, Trends Biochem. Sci., 30, 115, 10.1016/j.tibs.2005.01.002 Huang, 2003, SR splicing factors serve as adapter proteins for TAP-dependent mRNA export, Mol. Cell, 11, 837, 10.1016/S1097-2765(03)00089-3 Huang, 2001, Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA, Mol. Cell, 7, 899, 10.1016/S1097-2765(01)00233-7 Huh, 2003, Global analysis of protein localization in budding yeast, Nature, 425, 686, 10.1038/nature02026 Jurica, 2003, Pre-mRNA splicing: awash in a sea of proteins, Mol. Cell, 12, 5, 10.1016/S1097-2765(03)00270-3 Kadowaki, 1994, Isolation and characterization of Saccharomyces cerevisiae mRNA transport-defective (mtr) mutants, J. Cell Biol., 126, 649, 10.1083/jcb.126.3.649 Kim Guisbert, 2005, Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles, RNA, 11, 383, 10.1261/rna.7234205 Kotovic, 2003, Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast, Mol. Cell. Biol., 23, 5768, 10.1128/MCB.23.16.5768-5779.2003 Lacadie, 2005, Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5′ss base pairing in yeast, Mol. Cell, 19, 65, 10.1016/j.molcel.2005.05.006 Lee, 1996, A protein that shuttles between the nucleus and the cytoplasm is an important mediator of RNA export, Genes Dev., 10, 1233, 10.1101/gad.10.10.1233 Lei, 2002, Intron status and 3′-end formation control cotranscriptional export of mRNA, Genes Dev., 16, 2761, 10.1101/gad.1032902 Lei, 2001, Messenger RNAs are recruited for nuclear export during transcription, Genes Dev., 15, 1771, 10.1101/gad.892401 Leu, 1999, Splicing of the meiosis-specific HOP2 transcript utilizes a unique 5′ splice site, Mol. Cell. Biol., 19, 7933, 10.1128/MCB.19.12.7933 Lukasiewicz, 2007, Structurally unique yeast and mammalian serine-arginine protein kinases catalyze evolutionarily conserved phosphorylation reactions, J. Biol. Chem., 282, 23036, 10.1074/jbc.M611305200 Pan, 2006, A DNA integrity network in the yeast Saccharomyces cerevisiae, Cell, 124, 1069, 10.1016/j.cell.2005.12.036 Pleiss, 2007, Rapid, trascript-specific changes in splicing in response to environmental stress, Mol. Cell, 27, 928, 10.1016/j.molcel.2007.07.018 Pleiss, 2007, Transcript Specificity in Yeast pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components, PLoS Biol., 5, e90, 10.1371/journal.pbio.0050090 Rain, 1997, In vivo commitment to splicing in yeast involves the nucleotide upstream from the branch site conserved sequence and the Mud2 protein, EMBO J., 16, 1759, 10.1093/emboj/16.7.1759 Rollenhagen, 2007, Following temperature stress, export of heat shock mRNA occurs efficiently in cells with mutations in genes normally important for mRNA export, Eukaryot. Cell, 6, 505, 10.1128/EC.00317-06 Sanders, 2002, Proteomics of the eukaryotic transcription machinery: identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry, Mol. Cell. Biol., 22, 4723, 10.1128/MCB.22.13.4723-4738.2002 Sawa, 1991, Requirement of protein factors and ATP for the disassembly of the spliceosome after mRNA splicing reaction, Nucleic Acids Res., 19, 6819, 10.1093/nar/19.24.6819 Sayani, 2008, Widespread impact of nonsense-mediated mRNA decay on the yeast intronome, Mol. Cell, 31, 360, 10.1016/j.molcel.2008.07.005 Schuldiner, 2005, Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile, Cell, 123, 507, 10.1016/j.cell.2005.08.031 Shen, 2006, RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humans, Genes Dev., 20, 1755, 10.1101/gad.1422106 Siebel, 1996, The essential yeast RNA binding protein Np13p is methylated, Proc. Natl. Acad. Sci. USA, 93, 13641, 10.1073/pnas.93.24.13641 Siebel, 1999, Conservation in budding yeast of a kinase specific for SR splicing factors, Proc. Natl. Acad. Sci. USA, 96, 5440, 10.1073/pnas.96.10.5440 Singleton, 1995, A yeast protein that bidirectionally affects nucleocytoplasmic transport, J. Cell Sci., 108, 265, 10.1242/jcs.108.1.265 Spingola, 2000, A yeast intronic splicing enhancer and Nam8p are required for Mer1p-activated splicing, Mol. Cell, 6, 329, 10.1016/S1097-2765(00)00033-2 Stevens, 2001, Biochemical and genetic analyses of the U5, U6, and U4/U6 x U5 small nuclear ribonucleoproteins from Saccharomyces cerevisiae, RNA, 7, 1543 Strahl-Bolsinger, 1997, SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast, Genes Dev., 11, 83, 10.1101/gad.11.1.83 Tardiff, 2006, A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional, Mol. Cell, 24, 917, 10.1016/j.molcel.2006.12.002 Tardiff, 2007, Protein characterization of Saccharomyces cerevisiae RNA polymerase II after in vivo cross-linking, Proc. Natl. Acad. Sci. USA, 104, 19948, 10.1073/pnas.0710179104 Tong, 2004, Global mapping of the yeast genetic interaction network, Science, 303, 808, 10.1126/science.1091317 Wilmes, 2008, A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing, Mol. Cell, 32, 735, 10.1016/j.molcel.2008.11.012 Windgassen, 2003, Identification of Gbp2 as a novel poly(A)+ RNA-binding protein involved in the cytoplasmic delivery of messenger RNAs in yeast, EMBO Rep., 4, 278, 10.1038/sj.embor.embor763 Windgassen, 2004, Yeast shuttling SR proteins Npl3p, Gbp2p, and Hrb1p are part of the translating mRNPs, and Npl3p can function as a translational repressor, Mol. Cell. Biol., 24, 10479, 10.1128/MCB.24.23.10479-10491.2004 Wong, 2007, Yeast cap binding complex impedes recruitment of cleavage factor IA to weak termination sites, Mol. Cell. Biol., 27, 6520, 10.1128/MCB.00733-07 Yan, 1998, CUS2, a yeast homolog of human Tat-SF1, rescues function of misfolded U2 through an unusual RNA recognition motif, Mol. Cell. Biol., 18, 5000, 10.1128/MCB.18.9.5000 Yu, 2004, Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors, Genes Dev., 18, 2024, 10.1101/gad.1223204