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. 2004 Jan;166(1):53–65. doi: 10.1534/genetics.166.1.53

The yeast splicing factor Prp40p contains functional leucine-rich nuclear export signals that are essential for splicing.

Mark W Murphy 1, Brian L Olson 1, Paul G Siliciano 1
PMCID: PMC1470677  PMID: 15020406

Abstract

To investigate the function of the essential U1 snRNP protein Prp40p, we performed a synthetic lethal screen in Saccharomyces cerevisiae. Using an allele of PRP40 that deletes 47 internal residues and causes only a slight growth defect, we identified aphenotypic mutations in three distinct complementation groups that conferred synthetic lethality. The synthetic phenotypes caused by these mutations were suppressed by wild-type copies of CRM1 (XPO1), YNL187w, and SME1, respectively. The strains whose synthetic phenotypes were suppressed by CRM1 contained no mutations in the CRM1 coding sequence or promoter. This indicates that overexpression of CRM1 confers dosage suppression of the synthetic lethality. Interestingly, PRP40 and YNL187w encode proteins with putative leucine-rich nuclear export signal (NES) sequences that fit the consensus sequence recognized by Crm1p. One of Prp40p's two NESs lies within the internal deletion. We demonstrate here that the NES sequences of Prp40p are functional for nuclear export in a leptomycin B-sensitive manner. Furthermore, mutation of these NES sequences confers temperature-sensitive growth and a pre-mRNA splicing defect. Although we do not expect that yeast snRNPs undergo compartmentalized biogenesis like their metazoan counterparts, our results suggest that Prp40p and Ynl187wp contain redundant NESs that aid in an important, Crm1p-mediated nuclear export event.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Abovich N., Rosbash M. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell. 1997 May 2;89(3):403–412. doi: 10.1016/s0092-8674(00)80221-4. [DOI] [PubMed] [Google Scholar]
  2. Adachi Y., Yanagida M. Higher order chromosome structure is affected by cold-sensitive mutations in a Schizosaccharomyces pombe gene crm1+ which encodes a 115-kD protein preferentially localized in the nucleus and its periphery. J Cell Biol. 1989 Apr;108(4):1195–1207. doi: 10.1083/jcb.108.4.1195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bass B. L. Double-stranded RNA binding proteins and their substrates. Nucleic Acids Symp Ser. 1995;(33):13–15. [PubMed] [Google Scholar]
  4. Bogerd H. P., Fridell R. A., Benson R. E., Hua J., Cullen B. R. Protein sequence requirements for function of the human T-cell leukemia virus type 1 Rex nuclear export signal delineated by a novel in vivo randomization-selection assay. Mol Cell Biol. 1996 Aug;16(8):4207–4214. doi: 10.1128/mcb.16.8.4207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bordonné R., Tarassov I. The yeast SME1 gene encodes the homologue of the human E core protein. Gene. 1996 Oct 17;176(1-2):111–117. doi: 10.1016/0378-1119(96)00230-2. [DOI] [PubMed] [Google Scholar]
  6. Bracken A. P., Bond U. Reassembly and protection of small nuclear ribonucleoprotein particles by heat shock proteins in yeast cells. RNA. 1999 Dec;5(12):1586–1596. doi: 10.1017/s1355838299991203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brownawell Amy M., Macara Ian G. Exportin-5, a novel karyopherin, mediates nuclear export of double-stranded RNA binding proteins. J Cell Biol. 2002 Jan 3;156(1):53–64. doi: 10.1083/jcb.200110082. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Domdey H., Apostol B., Lin R. J., Newman A., Brody E., Abelson J. Lariat structures are in vivo intermediates in yeast pre-mRNA splicing. Cell. 1984 Dec;39(3 Pt 2):611–621. doi: 10.1016/0092-8674(84)90468-9. [DOI] [PubMed] [Google Scholar]
  9. Fischer U., Huber J., Boelens W. C., Mattaj I. W., Lührmann R. The HIV-1 Rev activation domain is a nuclear export signal that accesses an export pathway used by specific cellular RNAs. Cell. 1995 Aug 11;82(3):475–483. doi: 10.1016/0092-8674(95)90436-0. [DOI] [PubMed] [Google Scholar]
  10. Fornerod M., Ohno M., Yoshida M., Mattaj I. W. CRM1 is an export receptor for leucine-rich nuclear export signals. Cell. 1997 Sep 19;90(6):1051–1060. doi: 10.1016/s0092-8674(00)80371-2. [DOI] [PubMed] [Google Scholar]
  11. Fornerod M., van Deursen J., van Baal S., Reynolds A., Davis D., Murti K. G., Fransen J., Grosveld G. The human homologue of yeast CRM1 is in a dynamic subcomplex with CAN/Nup214 and a novel nuclear pore component Nup88. EMBO J. 1997 Feb 17;16(4):807–816. doi: 10.1093/emboj/16.4.807. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fortes P., Bilbao-Cortés D., Fornerod M., Rigaut G., Raymond W., Séraphin B., Mattaj I. W. Luc7p, a novel yeast U1 snRNP protein with a role in 5' splice site recognition. Genes Dev. 1999 Sep 15;13(18):2425–2438. doi: 10.1101/gad.13.18.2425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Frank D., Guthrie C. An essential splicing factor, SLU7, mediates 3' splice site choice in yeast. Genes Dev. 1992 Nov;6(11):2112–2124. doi: 10.1101/gad.6.11.2112. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. Fromont-Racine M., Rain J. C., Legrain P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat Genet. 1997 Jul;16(3):277–282. doi: 10.1038/ng0797-277. [DOI] [PubMed] [Google Scholar]
  16. Gavin Anne-Claude, Bösche Markus, Krause Roland, Grandi Paola, Marzioch Martina, Bauer Andreas, Schultz Jörg, Rick Jens M., Michon Anne-Marie, Cruciat Cristina-Maria. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002 Jan 10;415(6868):141–147. doi: 10.1038/415141a. [DOI] [PubMed] [Google Scholar]
  17. Giaever Guri, Chu Angela M., Ni Li, Connelly Carla, Riles Linda, Véronneau Steeve, Dow Sally, Lucau-Danila Ankuta, Anderson Keith, André Bruno. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002 Jul 25;418(6896):387–391. doi: 10.1038/nature00935. [DOI] [PubMed] [Google Scholar]
  18. Gottschalk A., Kastner B., Lührmann R., Fabrizio P. The yeast U5 snRNP coisolated with the U1 snRNP has an unexpected protein composition and includes the splicing factor Aar2p. RNA. 2001 Nov;7(11):1554–1565. [PMC free article] [PubMed] [Google Scholar]
  19. Gottschalk A., Tang J., Puig O., Salgado J., Neubauer G., Colot H. V., Mann M., Séraphin B., Rosbash M., Lührmann R. A comprehensive biochemical and genetic analysis of the yeast U1 snRNP reveals five novel proteins. RNA. 1998 Apr;4(4):374–393. [PMC free article] [PubMed] [Google Scholar]
  20. Hamm J., Mattaj I. W. Monomethylated cap structures facilitate RNA export from the nucleus. Cell. 1990 Oct 5;63(1):109–118. doi: 10.1016/0092-8674(90)90292-m. [DOI] [PubMed] [Google Scholar]
  21. Huber J., Cronshagen U., Kadokura M., Marshallsay C., Wada T., Sekine M., Lührmann R. Snurportin1, an m3G-cap-specific nuclear import receptor with a novel domain structure. EMBO J. 1998 Jul 15;17(14):4114–4126. doi: 10.1093/emboj/17.14.4114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kaffman A., Rank N. M., O'Neill E. M., Huang L. S., O'Shea E. K. The receptor Msn5 exports the phosphorylated transcription factor Pho4 out of the nucleus. Nature. 1998 Dec 3;396(6710):482–486. doi: 10.1038/24898. [DOI] [PubMed] [Google Scholar]
  23. Kao H. Y., Siliciano P. G. Identification of Prp40, a novel essential yeast splicing factor associated with the U1 small nuclear ribonucleoprotein particle. Mol Cell Biol. 1996 Mar;16(3):960–967. doi: 10.1128/mcb.16.3.960. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Komeili A., O'Shea E. K. New perspectives on nuclear transport. Annu Rev Genet. 2001;35:341–364. doi: 10.1146/annurev.genet.35.102401.090720. [DOI] [PubMed] [Google Scholar]
  25. Kudo N., Wolff B., Sekimoto T., Schreiner E. P., Yoneda Y., Yanagida M., Horinouchi S., Yoshida M. Leptomycin B inhibition of signal-mediated nuclear export by direct binding to CRM1. Exp Cell Res. 1998 Aug 1;242(2):540–547. doi: 10.1006/excr.1998.4136. [DOI] [PubMed] [Google Scholar]
  26. Kuersten S., Ohno M., Mattaj I. W. Nucleocytoplasmic transport: Ran, beta and beyond. Trends Cell Biol. 2001 Dec;11(12):497–503. doi: 10.1016/s0962-8924(01)02144-4. [DOI] [PubMed] [Google Scholar]
  27. Lührmann R., Kastner B., Bach M. Structure of spliceosomal snRNPs and their role in pre-mRNA splicing. Biochim Biophys Acta. 1990 Nov 30;1087(3):265–292. doi: 10.1016/0167-4781(90)90001-i. [DOI] [PubMed] [Google Scholar]
  28. Mattaj I. W. Cap trimethylation of U snRNA is cytoplasmic and dependent on U snRNP protein binding. Cell. 1986 Sep 12;46(6):905–911. doi: 10.1016/0092-8674(86)90072-3. [DOI] [PubMed] [Google Scholar]
  29. McLean M. R., Rymond B. C. Yeast pre-mRNA splicing requires a pair of U1 snRNP-associated tetratricopeptide repeat proteins. Mol Cell Biol. 1998 Jan;18(1):353–360. doi: 10.1128/mcb.18.1.353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Mouaikel John, Verheggen Céline, Bertrand Edouard, Tazi Jamal, Bordonné Rémy. Hypermethylation of the cap structure of both yeast snRNAs and snoRNAs requires a conserved methyltransferase that is localized to the nucleolus. Mol Cell. 2002 Apr;9(4):891–901. doi: 10.1016/s1097-2765(02)00484-7. [DOI] [PubMed] [Google Scholar]
  31. Myslinski E., Ségault V., Branlant C. An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science. 1990 Mar 9;247(4947):1213–1216. doi: 10.1126/science.1690452. [DOI] [PubMed] [Google Scholar]
  32. Neubauer G., Gottschalk A., Fabrizio P., Séraphin B., Lührmann R., Mann M. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc Natl Acad Sci U S A. 1997 Jan 21;94(2):385–390. doi: 10.1073/pnas.94.2.385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Neville M., Rosbash M. The NES-Crm1p export pathway is not a major mRNA export route in Saccharomyces cerevisiae. EMBO J. 1999 Jul 1;18(13):3746–3756. doi: 10.1093/emboj/18.13.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Neville M., Stutz F., Lee L., Davis L. I., Rosbash M. The importin-beta family member Crm1p bridges the interaction between Rev and the nuclear pore complex during nuclear export. Curr Biol. 1997 Oct 1;7(10):767–775. doi: 10.1016/s0960-9822(06)00335-6. [DOI] [PubMed] [Google Scholar]
  35. Nishi K., Yoshida M., Fujiwara D., Nishikawa M., Horinouchi S., Beppu T. Leptomycin B targets a regulatory cascade of crm1, a fission yeast nuclear protein, involved in control of higher order chromosome structure and gene expression. J Biol Chem. 1994 Mar 4;269(9):6320–6324. [PubMed] [Google Scholar]
  36. Ohno M., Segref A., Bachi A., Wilm M., Mattaj I. W. PHAX, a mediator of U snRNA nuclear export whose activity is regulated by phosphorylation. Cell. 2000 Apr 14;101(2):187–198. doi: 10.1016/S0092-8674(00)80829-6. [DOI] [PubMed] [Google Scholar]
  37. Ossareh-Nazari B., Gwizdek C., Dargemont C. Protein export from the nucleus. Traffic. 2001 Oct;2(10):684–689. doi: 10.1034/j.1600-0854.2001.21002.x. [DOI] [PubMed] [Google Scholar]
  38. Parker R., Simmons T., Shuster E. O., Siliciano P. G., Guthrie C. Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable sextuple mutant. Mol Cell Biol. 1988 Aug;8(8):3150–3159. doi: 10.1128/mcb.8.8.3150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Rudolf Paul, Bartelme Amanda, Center for Insulin-Dependent Diabetes Access' Blue Ribbon Panel A strategic action plan for achieving uncompromising "treat to target" in individuals with insulin-dependent diabetes: a report by the Center for Insulin-Dependent Diabetes Access' Blue Ribbon Panel. Diabetes Technol Ther. 2005 Oct;7(5):755–767. doi: 10.1089/dia.2005.7.755. [DOI] [PubMed] [Google Scholar]
  40. St Johnston D., Brown N. H., Gall J. G., Jantsch M. A conserved double-stranded RNA-binding domain. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10979–10983. doi: 10.1073/pnas.89.22.10979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Stade K., Ford C. S., Guthrie C., Weis K. Exportin 1 (Crm1p) is an essential nuclear export factor. Cell. 1997 Sep 19;90(6):1041–1050. doi: 10.1016/s0092-8674(00)80370-0. [DOI] [PubMed] [Google Scholar]
  42. Stevens Scott W., Ryan Daniel E., Ge Helen Y., Moore Roger E., Young Mary K., Lee Terry D., Abelson John. Composition and functional characterization of the yeast spliceosomal penta-snRNP. Mol Cell. 2002 Jan;9(1):31–44. doi: 10.1016/s1097-2765(02)00436-7. [DOI] [PubMed] [Google Scholar]
  43. Stutz F., Rosbash M. Nuclear RNA export. Genes Dev. 1998 Nov 1;12(21):3303–3319. doi: 10.1101/gad.12.21.3303. [DOI] [PubMed] [Google Scholar]
  44. Wen W., Meinkoth J. L., Tsien R. Y., Taylor S. S. Identification of a signal for rapid export of proteins from the nucleus. Cell. 1995 Aug 11;82(3):463–473. doi: 10.1016/0092-8674(95)90435-2. [DOI] [PubMed] [Google Scholar]
  45. Will C. L., Lührmann R. Spliceosomal UsnRNP biogenesis, structure and function. Curr Opin Cell Biol. 2001 Jun;13(3):290–301. doi: 10.1016/s0955-0674(00)00211-8. [DOI] [PubMed] [Google Scholar]
  46. Yoshida K., Blobel G. The karyopherin Kap142p/Msn5p mediates nuclear import and nuclear export of different cargo proteins. J Cell Biol. 2001 Feb 19;152(4):729–740. doi: 10.1083/jcb.152.4.729. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Zhang D., Abovich N., Rosbash M. A biochemical function for the Sm complex. Mol Cell. 2001 Feb;7(2):319–329. doi: 10.1016/s1097-2765(01)00180-0. [DOI] [PubMed] [Google Scholar]

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