Abstract
The PRP2 gene in Saccharomyces cerevisiae encodes an RNA-dependent ATPase that activates spliceosomes for the first transesterification reaction in pre-mRNA splicing. We have identified a mutation in the elongation methionine tRNA gene EMT1 as a dominant, allele-specific suppressor of the temperature-sensitive prp2-1 mutation. The EMT1-201 mutant suppressed prp2-1 by relieving the splicing block at high temperature. Furthermore, EMT1-201 single mutant cells displayed pre-mRNA splicing and cold-sensitive growth defects at 18 degrees. The mutation in EMT1-201 is located in the anticodon, changing CAT to CAG, which presumably allowed EMT1-201 suppressor tRNA to recognize CUG leucine codons instead of AUG methionine codons. Interestingly, the prp2-1 allele contains a point mutation that changes glycine to aspartate, indicating that EMT1-201 does not act by classical missense suppression. Extra copies of the tRNA(Leu)(UAG) gene rescued the cold sensitivity and in vitro splicing defect of EMT1-201. This study provides the first example in which a mutation in a tRNA gene confers a pre-mRNA processing (prp) phenotype.
Full Text
The Full Text of this article is available as a PDF (323.6 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Arenas J. E., Abelson J. N. Prp43: An RNA helicase-like factor involved in spliceosome disassembly. Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):11798–11802. doi: 10.1073/pnas.94.22.11798. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Arenas J. E., Abelson J. N. The Saccharomyces cerevisiae PRP21 gene product is an integral component of the prespliceosome. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6771–6775. doi: 10.1073/pnas.90.14.6771. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ares M., Jr, Weiser B. Rearrangement of snRNA structure during assembly and function of the spliceosome. Prog Nucleic Acid Res Mol Biol. 1995;50:131–159. doi: 10.1016/s0079-6603(08)60813-2. [DOI] [PubMed] [Google Scholar]
- Aström S. U., von Pawel-Rammingen U., Byström A. S. The yeast initiator tRNAMet can act as an elongator tRNA(Met) in vivo. J Mol Biol. 1993 Sep 5;233(1):43–58. doi: 10.1006/jmbi.1993.1483. [DOI] [PubMed] [Google Scholar]
- Blanton S., Srinivasan A., Rymond B. C. PRP38 encodes a yeast protein required for pre-mRNA splicing and maintenance of stable U6 small nuclear RNA levels. Mol Cell Biol. 1992 Sep;12(9):3939–3947. doi: 10.1128/mcb.12.9.3939. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chapon C., Legrain P. A novel gene, spp91-1, suppresses the splicing defect and the pre-mRNA nuclear export in the prp9-1 mutant. EMBO J. 1992 Sep;11(9):3279–3288. doi: 10.1002/j.1460-2075.1992.tb05406.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng S. C., Abelson J. Spliceosome assembly in yeast. Genes Dev. 1987 Nov;1(9):1014–1027. doi: 10.1101/gad.1.9.1014. [DOI] [PubMed] [Google Scholar]
- Christianson T. W., Sikorski R. S., Dante M., Shero J. H., Hieter P. Multifunctional yeast high-copy-number shuttle vectors. Gene. 1992 Jan 2;110(1):119–122. doi: 10.1016/0378-1119(92)90454-w. [DOI] [PubMed] [Google Scholar]
- Chuang R. Y., Weaver P. L., Liu Z., Chang T. H. Requirement of the DEAD-Box protein ded1p for messenger RNA translation. Science. 1997 Mar 7;275(5305):1468–1471. doi: 10.1126/science.275.5305.1468. [DOI] [PubMed] [Google Scholar]
- Company M., Arenas J., Abelson J. Requirement of the RNA helicase-like protein PRP22 for release of messenger RNA from spliceosomes. Nature. 1991 Feb 7;349(6309):487–493. doi: 10.1038/349487a0. [DOI] [PubMed] [Google Scholar]
- Couto J. R., Tamm J., Parker R., Guthrie C. A trans-acting suppressor restores splicing of a yeast intron with a branch point mutation. Genes Dev. 1987 Jul;1(5):445–455. doi: 10.1101/gad.1.5.445. [DOI] [PubMed] [Google Scholar]
- Frank D., Patterson B., Guthrie C. Synthetic lethal mutations suggest interactions between U5 small nuclear RNA and four proteins required for the second step of splicing. Mol Cell Biol. 1992 Nov;12(11):5197–5205. doi: 10.1128/mcb.12.11.5197. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fujimura H., Sakuma Y. Simplified isolation of chromosomal and plasmid DNA from yeasts. Biotechniques. 1993 Apr;14(4):538–540. [PubMed] [Google Scholar]
- Guthrie C. Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science. 1991 Jul 12;253(5016):157–163. doi: 10.1126/science.1853200. [DOI] [PubMed] [Google Scholar]
- Happel A. M., Winston F. A mutant tRNA affects delta-mediated transcription in Saccharomyces cerevisiae. Genetics. 1992 Oct;132(2):361–374. doi: 10.1093/genetics/132.2.361. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hartwell L. H. Macromolecule synthesis in temperature-sensitive mutants of yeast. J Bacteriol. 1967 May;93(5):1662–1670. doi: 10.1128/jb.93.5.1662-1670.1967. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hinnebusch A. G. Mechanisms of gene regulation in the general control of amino acid biosynthesis in Saccharomyces cerevisiae. Microbiol Rev. 1988 Jun;52(2):248–273. doi: 10.1128/mr.52.2.248-273.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huffaker T. C., Hoyt M. A., Botstein D. Genetic analysis of the yeast cytoskeleton. Annu Rev Genet. 1987;21:259–284. doi: 10.1146/annurev.ge.21.120187.001355. [DOI] [PubMed] [Google Scholar]
- Jamieson D. J., Rahe B., Pringle J., Beggs J. D. A suppressor of a yeast splicing mutation (prp8-1) encodes a putative ATP-dependent RNA helicase. Nature. 1991 Feb 21;349(6311):715–717. doi: 10.1038/349715a0. [DOI] [PubMed] [Google Scholar]
- Kim S. H., Lin R. J. Pre-mRNA splicing within an assembled yeast spliceosome requires an RNA-dependent ATPase and ATP hydrolysis. Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):888–892. doi: 10.1073/pnas.90.3.888. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kim S. H., Lin R. J. Spliceosome activation by PRP2 ATPase prior to the first transesterification reaction of pre-mRNA splicing. Mol Cell Biol. 1996 Dec;16(12):6810–6819. doi: 10.1128/mcb.16.12.6810. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kim S. H., Smith J., Claude A., Lin R. J. The purified yeast pre-mRNA splicing factor PRP2 is an RNA-dependent NTPase. EMBO J. 1992 Jun;11(6):2319–2326. doi: 10.1002/j.1460-2075.1992.tb05291.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- King D. S., Beggs J. D. Interactions of PRP2 protein with pre-mRNA splicing complexes in Saccharomyces cerevisiae. Nucleic Acids Res. 1990 Nov 25;18(22):6559–6564. doi: 10.1093/nar/18.22.6559. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Krämer A. The structure and function of proteins involved in mammalian pre-mRNA splicing. Annu Rev Biochem. 1996;65:367–409. doi: 10.1146/annurev.bi.65.070196.002055. [DOI] [PubMed] [Google Scholar]
- Laggerbauer B., Achsel T., Lührmann R. The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4188–4192. doi: 10.1073/pnas.95.8.4188. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Last R. L., Maddock J. R., Woolford J. L., Jr Evidence for related functions of the RNA genes of Saccharomyces cerevisiae. Genetics. 1987 Dec;117(4):619–631. doi: 10.1093/genetics/117.4.619. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lauber J., Fabrizio P., Teigelkamp S., Lane W. S., Hartmann E., Luhrmann R. The HeLa 200 kDa U5 snRNP-specific protein and its homologue in Saccharomyces cerevisiae are members of the DEXH-box protein family of putative RNA helicases. EMBO J. 1996 Aug 1;15(15):4001–4015. [PMC free article] [PubMed] [Google Scholar]
- Liao X. C., Tang J., Rosbash M. An enhancer screen identifies a gene that encodes the yeast U1 snRNP A protein: implications for snRNP protein function in pre-mRNA splicing. Genes Dev. 1993 Mar;7(3):419–428. doi: 10.1101/gad.7.3.419. [DOI] [PubMed] [Google Scholar]
- Lin J., Rossi J. J. Identification and characterization of yeast mutants that overcome an experimentally introduced block to splicing at the 3' splice site. RNA. 1996 Aug;2(8):835–848. [PMC free article] [PubMed] [Google Scholar]
- Lin R. J., Lustig A. J., Abelson J. Splicing of yeast nuclear pre-mRNA in vitro requires a functional 40S spliceosome and several extrinsic factors. Genes Dev. 1987 Mar;1(1):7–18. doi: 10.1101/gad.1.1.7. [DOI] [PubMed] [Google Scholar]
- Lund E., Dahlberg J. E. Proofreading and aminoacylation of tRNAs before export from the nucleus. Science. 1998 Dec 11;282(5396):2082–2085. doi: 10.1126/science.282.5396.2082. [DOI] [PubMed] [Google Scholar]
- Lustig A. J., Lin R. J., Abelson J. The yeast RNA gene products are essential for mRNA splicing in vitro. Cell. 1986 Dec 26;47(6):953–963. doi: 10.1016/0092-8674(86)90810-x. [DOI] [PubMed] [Google Scholar]
- Maddock J. R., Roy J., Woolford J. L., Jr Six novel genes necessary for pre-mRNA splicing in Saccharomyces cerevisiae. Nucleic Acids Res. 1996 Mar 15;24(6):1037–1044. doi: 10.1093/nar/24.6.1037. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maddock J. R., Weidenhammer E. M., Adams C. C., Lunz R. L., Woolford J. L., Jr Extragenic suppressors of Saccharomyces cerevisiae prp4 mutations identify a negative regulator of PRP genes. Genetics. 1994 Mar;136(3):833–847. doi: 10.1093/genetics/136.3.833. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Noble S. M., Guthrie C. Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations. Genetics. 1996 May;143(1):67–80. doi: 10.1093/genetics/143.1.67. [DOI] [PMC free article] [PubMed] [Google Scholar]
- O'Day C. L., Dalbadie-McFarland G., Abelson J. The Saccharomyces cerevisiae Prp5 protein has RNA-dependent ATPase activity with specificity for U2 small nuclear RNA. J Biol Chem. 1996 Dec 27;271(52):33261–33267. doi: 10.1074/jbc.271.52.33261. [DOI] [PubMed] [Google Scholar]
- Orr-Weaver T. L., Szostak J. W., Rothstein R. J. Yeast transformation: a model system for the study of recombination. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6354–6358. doi: 10.1073/pnas.78.10.6354. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pearson N. J., Thorburn P. C., Haber J. E. A suppressor of temperature-sensitive rna mutations that affect mRNA metabolism in Saccharomyces cerevisiae. Mol Cell Biol. 1982 May;2(5):571–577. doi: 10.1128/mcb.2.5.571. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Percudani R., Pavesi A., Ottonello S. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J Mol Biol. 1997 May 2;268(2):322–330. doi: 10.1006/jmbi.1997.0942. [DOI] [PubMed] [Google Scholar]
- Plumpton M., McGarvey M., Beggs J. D. A dominant negative mutation in the conserved RNA helicase motif 'SAT' causes splicing factor PRP2 to stall in spliceosomes. EMBO J. 1994 Feb 15;13(4):879–887. doi: 10.1002/j.1460-2075.1994.tb06331.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roy J., Kim K., Maddock J. R., Anthony J. G., Woolford J. L., Jr The final stages of spliceosome maturation require Spp2p that can interact with the DEAH box protein Prp2p and promote step 1 of splicing. RNA. 1995 Jun;1(4):375–390. [PMC free article] [PubMed] [Google Scholar]
- Ruby S. W., Abelson J. Pre-mRNA splicing in yeast. Trends Genet. 1991 Mar;7(3):79–85. doi: 10.1016/0168-9525(91)90276-V. [DOI] [PubMed] [Google Scholar]
- Schwer B., Gross C. H. Prp22, a DExH-box RNA helicase, plays two distinct roles in yeast pre-mRNA splicing. EMBO J. 1998 Apr 1;17(7):2086–2094. doi: 10.1093/emboj/17.7.2086. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schwer B., Guthrie C. PRP16 is an RNA-dependent ATPase that interacts transiently with the spliceosome. Nature. 1991 Feb 7;349(6309):494–499. doi: 10.1038/349494a0. [DOI] [PubMed] [Google Scholar]
- Senger B., Despons L., Walter P., Fasiolo F. The anticodon triplet is not sufficient to confer methionine acceptance to a transfer RNA. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10768–10771. doi: 10.1073/pnas.89.22.10768. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Seraphin B., Rosbash M. Identification of functional U1 snRNA-pre-mRNA complexes committed to spliceosome assembly and splicing. Cell. 1989 Oct 20;59(2):349–358. doi: 10.1016/0092-8674(89)90296-1. [DOI] [PubMed] [Google Scholar]
- Sharp P. A. Split genes and RNA splicing. Cell. 1994 Jun 17;77(6):805–815. doi: 10.1016/0092-8674(94)90130-9. [DOI] [PubMed] [Google Scholar]
- Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staley J. P., Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. 1998 Feb 6;92(3):315–326. doi: 10.1016/s0092-8674(00)80925-3. [DOI] [PubMed] [Google Scholar]
- Strauss E. J., Guthrie C. A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family. Genes Dev. 1991 Apr;5(4):629–641. doi: 10.1101/gad.5.4.629. [DOI] [PubMed] [Google Scholar]
- Tu J., Carlson M. REG1 binds to protein phosphatase type 1 and regulates glucose repression in Saccharomyces cerevisiae. EMBO J. 1995 Dec 1;14(23):5939–5946. doi: 10.1002/j.1460-2075.1995.tb00282.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tung K. S., Norbeck L. L., Nolan S. L., Atkinson N. S., Hopper A. K. SRN1, a yeast gene involved in RNA processing, is identical to HEX2/REG1, a negative regulator in glucose repression. Mol Cell Biol. 1992 Jun;12(6):2673–2680. doi: 10.1128/mcb.12.6.2673. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vijayraghavan U., Company M., Abelson J. Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae. Genes Dev. 1989 Aug;3(8):1206–1216. doi: 10.1101/gad.3.8.1206. [DOI] [PubMed] [Google Scholar]
- Wagner J. D., Jankowsky E., Company M., Pyle A. M., Abelson J. N. The DEAH-box protein PRP22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes. EMBO J. 1998 May 15;17(10):2926–2937. doi: 10.1093/emboj/17.10.2926. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang Y., Wagner J. D., Guthrie C. The DEAH-box splicing factor Prp16 unwinds RNA duplexes in vitro. Curr Biol. 1998 Apr 9;8(8):441–451. doi: 10.1016/s0960-9822(98)70178-2. [DOI] [PubMed] [Google Scholar]
- Warner J. R., Gorenstein C. Yeast has a true stringent response. Nature. 1978 Sep 28;275(5678):338–339. doi: 10.1038/275338a0. [DOI] [PubMed] [Google Scholar]
- Wells S. E., Neville M., Haynes M., Wang J., Igel H., Ares M., Jr CUS1, a suppressor of cold-sensitive U2 snRNA mutations, is a novel yeast splicing factor homologous to human SAP 145. Genes Dev. 1996 Jan 15;10(2):220–232. doi: 10.1101/gad.10.2.220. [DOI] [PubMed] [Google Scholar]
- Will C. L., Lührmann R. Protein functions in pre-mRNA splicing. Curr Opin Cell Biol. 1997 Jun;9(3):320–328. doi: 10.1016/s0955-0674(97)80003-8. [DOI] [PubMed] [Google Scholar]
- Xu D., Field D. J., Tang S. J., Moris A., Bobechko B. P., Friesen J. D. Synthetic lethality of yeast slt mutations with U2 small nuclear RNA mutations suggests functional interactions between U2 and U5 snRNPs that are important for both steps of pre-mRNA splicing. Mol Cell Biol. 1998 Apr;18(4):2055–2066. doi: 10.1128/mcb.18.4.2055. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Xu D., Nouraini S., Field D., Tang S. J., Friesen J. D. An RNA-dependent ATPase associated with U2/U6 snRNAs in pre-mRNA splicing. Nature. 1996 Jun 20;381(6584):709–713. doi: 10.1038/381709a0. [DOI] [PubMed] [Google Scholar]