Prp43p is a DEAH-box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis

Overview

Journal Mol Cell Biol

Specialty Cell Biology

Date 2005 Dec 31

PMID 16382144

Citations 75

Authors

D Joshua Combs

Roland J Nagel

Manuel Ares Jr

Scott W Stevens

Affiliations

Soon will be listed here.

Abstract

The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified Prp43p-associated material includes the expected spliceosomal components; however, we also identify several preribosomal complexes that are specifically purified with Prp43p. Conditional prp43 mutant alleles confer a 35S pre-rRNA processing defect, with subsequent depletion of 27S and 20S precursors. Upon a shift to a nonpermissive temperature, both large and small-ribosomal-subunit proteins accumulate in the nucleolus of prp43 mutants. Pulse-chase analysis demonstrates delayed kinetics of 35S, 27S, and 20S pre-rRNA processing with turnover of these intermediates. Microarray analysis of pre-mRNA splicing defects in prp43 mutants shows a very mild effect, similar to that of nonessential pre-mRNA splicing factors. Prp43p is the first DEXH/D-box protein shown to function in both RNA polymerase I and polymerase II transcript metabolism. Its essential function is in its newly characterized role in ribosome biogenesis of both ribosomal subunits, positioning Prp43p to regulate both pre-mRNA splicing and ribosome biogenesis.

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References

Strasser K, Hurt E . Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p. Nature. 2001; 413(6856):648-52. DOI: 10.1038/35098113. View

Kallstrom G, Hedges J, Johnson A . The putative GTPases Nog1p and Lsg1p are required for 60S ribosomal subunit biogenesis and are localized to the nucleus and cytoplasm, respectively. Mol Cell Biol. 2003; 23(12):4344-55. PMC: 156149. DOI: 10.1128/MCB.23.12.4344-4355.2003. View

Chapman K, Boeke J . Isolation and characterization of the gene encoding yeast debranching enzyme. Cell. 1991; 65(3):483-92. DOI: 10.1016/0092-8674(91)90466-c. View

Fromont-Racine M, Senger B, Saveanu C, Fasiolo F . Ribosome assembly in eukaryotes. Gene. 2003; 313:17-42. DOI: 10.1016/s0378-1119(03)00629-2. View

Jensen T, Boulay J, Rosbash M, Libri D . The DECD box putative ATPase Sub2p is an early mRNA export factor. Curr Biol. 2001; 11(21):1711-5. DOI: 10.1016/s0960-9822(01)00529-2. View

Hartmuth K, Urlaub H, Vornlocher H, Will C, Gentzel M, Wilm M . Protein composition of human prespliceosomes isolated by a tobramycin affinity-selection method. Proc Natl Acad Sci U S A. 2002; 99(26):16719-24. PMC: 139210. DOI: 10.1073/pnas.262483899. View

Tanner N, Linder P . DExD/H box RNA helicases: from generic motors to specific dissociation functions. Mol Cell. 2001; 8(2):251-62. DOI: 10.1016/s1097-2765(01)00329-x. View

Gietz R, Woods R . Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 2002; 350:87-96. DOI: 10.1016/s0076-6879(02)50957-5. View

Leeds N, Small E, Hiley S, Hughes T, Staley J . The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis. Mol Cell Biol. 2005; 26(2):513-22. PMC: 1346897. DOI: 10.1128/MCB.26.2.513-522.2006. View

10.

Svitkin Y, Pause A, Haghighat A, Pyronnet S, Witherell G, Belsham G . The requirement for eukaryotic initiation factor 4A (elF4A) in translation is in direct proportion to the degree of mRNA 5' secondary structure. RNA. 2001; 7(3):382-94. PMC: 1370095. DOI: 10.1017/s135583820100108x. View

11.

Company M, Arenas J, Abelson J . Requirement of the RNA helicase-like protein PRP22 for release of messenger RNA from spliceosomes. Nature. 1991; 349(6309):487-93. DOI: 10.1038/349487a0. View

12.

Martin A, Schneider S, Schwer B . Prp43 is an essential RNA-dependent ATPase required for release of lariat-intron from the spliceosome. J Biol Chem. 2002; 277(20):17743-50. DOI: 10.1074/jbc.M200762200. View

13.

Huh W, Falvo J, Gerke L, Carroll A, Howson R, Weissman J . Global analysis of protein localization in budding yeast. Nature. 2003; 425(6959):686-91. DOI: 10.1038/nature02026. View

14.

Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L . miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev. 2002; 16(6):720-8. PMC: 155365. DOI: 10.1101/gad.974702. View

15.

Fraser A, Marcotte E . A probabilistic view of gene function. Nat Genet. 2004; 36(6):559-64. DOI: 10.1038/ng1370. View

16.

Kistler A, Guthrie C . Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for sub2, an essential spliceosomal ATPase. Genes Dev. 2001; 15(1):42-9. PMC: 312603. DOI: 10.1101/gad.851301. View

17.

Stevens S, Barta I, Ge H, Moore R, Young M, Lee T . Biochemical and genetic analyses of the U5, U6, and U4/U6 x U5 small nuclear ribonucleoproteins from Saccharomyces cerevisiae. RNA. 2001; 7(11):1543-53. PMC: 1370197. View

18.

Fairman M, Maroney P, Wang W, Bowers H, Gollnick P, Nilsen T . Protein displacement by DExH/D "RNA helicases" without duplex unwinding. Science. 2004; 304(5671):730-4. DOI: 10.1126/science.1095596. View

19.

Gadal O, Strauss D, Kessl J, Trumpower B, Tollervey D, Hurt E . Nuclear export of 60s ribosomal subunits depends on Xpo1p and requires a nuclear export sequence-containing factor, Nmd3p, that associates with the large subunit protein Rpl10p. Mol Cell Biol. 2001; 21(10):3405-15. PMC: 100262. DOI: 10.1128/MCB.21.10.3405-3415.2001. View

20.

Puig O, Caspary F, Rigaut G, Rutz B, Bouveret E, Wilm M . The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods. 2001; 24(3):218-29. DOI: 10.1006/meth.2001.1183. View