A Genomic Screen in Yeast Reveals Novel Aspects of Nonstop MRNA Metabolism

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 2007 Jul 31

PMID 17660569

Citations 47

Authors

Marenda A Wilson

Stacie Meaux

Ambro van Hoof

Affiliations

Soon will be listed here.

Abstract

Nonstop mRNA decay, a specific mRNA surveillance pathway, rapidly degrades transcripts that lack in-frame stop codons. The cytoplasmic exosome, a complex of 3'-5' exoribonucleases involved in RNA degradation and processing events, degrades nonstop transcripts. To further understand how nonstop mRNAs are recognized and degraded, we performed a genomewide screen for nonessential genes that are required for nonstop mRNA decay. We identified 16 genes that affect the expression of two different nonstop reporters. Most of these genes affected the stability of a nonstop mRNA reporter. Additionally, three mutations that affected nonstop gene expression without stabilizing nonstop mRNA levels implicated the proteasome. This finding not only suggested that the proteasome may degrade proteins encoded by nonstop mRNAs, but also supported previous observations that rapid decay of nonstop mRNAs cannot fully explain the lack of the encoded proteins. Further, we show that the proteasome and Ski7p affected expression of nonstop reporter genes independently of each other. In addition, our results implicate inositol 1,3,4,5,6-pentakisphosphate as an inhibitor of nonstop mRNA decay.

Citing Articles

Coupled protein quality control during nonsense-mediated mRNA decay.

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The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome.

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A yeast model for trichohepatoenteric syndrome suggests strong loss of Ski2 function in most causative mutations.

Orlando L, Yim M, Hallmark T, Cotner M, Johnson S, van Hoof A MicroPubl Biol. 2022; 2022.

PMID: 35607352 PMC: 9123431. DOI: 10.17912/micropub.biology.000575.

Regulation of nonsense-mediated mRNA decay in neural development and disease.

Lee P, Yang S, Sun Y, Guo J J Mol Cell Biol. 2021; 13(4):269-281.

PMID: 33783512 PMC: 8339359. DOI: 10.1093/jmcb/mjab022.

The nascent polypeptide in the 60S subunit determines the Rqc2-dependency of ribosomal quality control.

Mizuno M, Ebine S, Shounai O, Nakajima S, Tomomatsu S, Ikeuchi K Nucleic Acids Res. 2021; 49(4):2102-2113.

PMID: 33511411 PMC: 7913769. DOI: 10.1093/nar/gkab005.

References

Tong A, Evangelista M, Parsons A, Xu H, Bader G, Page N . Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 2001; 294(5550):2364-8. DOI: 10.1126/science.1065810. View

Braun M, Costa P, Crisucci E, Arndt K . Identification of Rkr1, a nuclear RING domain protein with functional connections to chromatin modification in Saccharomyces cerevisiae. Mol Cell Biol. 2007; 27(8):2800-11. PMC: 1899926. DOI: 10.1128/MCB.01947-06. View

van Hoof A, Frischmeyer P, Dietz H, Parker R . Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science. 2002; 295(5563):2262-4. DOI: 10.1126/science.1067272. View

Ueda K, Yamamoto Y, Ogawa K, Abo T, Inokuchi H, Aiba H . Bacterial SsrA system plays a role in coping with unwanted translational readthrough caused by suppressor tRNAs. Genes Cells. 2002; 7(5):509-19. DOI: 10.1046/j.1365-2443.2002.00537.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

Muhlrad D, Parker R . Recognition of yeast mRNAs as "nonsense containing" leads to both inhibition of mRNA translation and mRNA degradation: implications for the control of mRNA decapping. Mol Biol Cell. 1999; 10(11):3971-8. PMC: 25692. DOI: 10.1091/mbc.10.11.3971. View

Hughes T, Roberts C, Dai H, Jones A, Meyer M, Slade D . Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet. 2000; 25(3):333-7. DOI: 10.1038/77116. View

Verma R, Chen S, Feldman R, Schieltz D, Yates J, Dohmen J . Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol Biol Cell. 2000; 11(10):3425-39. PMC: 15004. DOI: 10.1091/mbc.11.10.3425. View

Tucker M, Staples R, Chen J, Denis C, Parker R . The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell. 2001; 104(3):377-86. DOI: 10.1016/s0092-8674(01)00225-2. View

10.

Giaever G, Chu A, Ni L, Connelly C, Riles L, Veronneau S . Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002; 418(6896):387-91. DOI: 10.1038/nature00935. View

11.

Steiger M, Carr-Schmid A, Schwartz D, Kiledjian M, Parker R . Analysis of recombinant yeast decapping enzyme. RNA. 2003; 9(2):231-8. PMC: 1370389. DOI: 10.1261/rna.2151403. View

12.

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

13.

Seminara S, Messager S, Chatzidaki E, Thresher R, Acierno Jr J, Shagoury J . The GPR54 gene as a regulator of puberty. N Engl J Med. 2003; 349(17):1614-27. DOI: 10.1056/NEJMoa035322. View

14.

Liu H, Chiang Y, Pan J, Chen J, SALVADORE C, Audino D . Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme. J Biol Chem. 2000; 276(10):7541-8. DOI: 10.1074/jbc.M009112200. View

15.

Araki Y, Takahashi S, Kobayashi T, Kajiho H, Hoshino S, Katada T . Ski7p G protein interacts with the exosome and the Ski complex for 3'-to-5' mRNA decay in yeast. EMBO J. 2001; 20(17):4684-93. PMC: 125587. DOI: 10.1093/emboj/20.17.4684. View

16.

Dunckley T, Parker R . Yeast mRNA decapping enzyme. Methods Enzymol. 2001; 342:226-33. DOI: 10.1016/s0076-6879(01)42547-x. View

17.

Hallier M, Ivanova N, Rametti A, Pavlov M, Ehrenberg M, Felden B . Pre-binding of small protein B to a stalled ribosome triggers trans-translation. J Biol Chem. 2004; 279(25):25978-85. DOI: 10.1074/jbc.M314086200. View

18.

Zaret K, Sherman F . Mutationally altered 3' ends of yeast CYC1 mRNA affect transcript stability and translational efficiency. J Mol Biol. 1984; 177(1):107-35. DOI: 10.1016/0022-2836(84)90060-3. View

19.

Sikorski R, Hieter P . A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989; 122(1):19-27. PMC: 1203683. DOI: 10.1093/genetics/122.1.19. View

20.

Kelleher 3rd R, Flanagan P, Kornberg R . A novel mediator between activator proteins and the RNA polymerase II transcription apparatus. Cell. 1990; 61(7):1209-15. DOI: 10.1016/0092-8674(90)90685-8. View