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Identification of a quality-control mechanism for mRNA 5′-end capping

Nature volume 467, pages 608–611 (2010)Cite this article

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Abstract

The 7-methylguanosine cap structure at the 5′ end of eukaryotic messenger RNAs is a critical determinant of their stability and translational efficiency1,2,3. It is generally believed that 5′-end capping is a constitutive process that occurs during mRNA maturation and lacks the need for a quality-control mechanism to ensure its fidelity. We recently reported that the yeast Rai1 protein has pyrophosphohydrolase activity towards mRNAs lacking a 5′-end cap4. Here we show that, in vitro as well as in yeast cells, Rai1 possesses a novel decapping endonuclease activity that can also remove the entire cap structure dinucleotide from an mRNA. This activity is targeted preferentially towards mRNAs with unmethylated caps in contrast to the canonical decapping enzyme, Dcp2, which targets mRNAs with a methylated cap. Capped but unmethylated mRNAs generated in yeast cells with a defect in the methyltransferase gene are more stable in a rai1-gene-disrupted background. Moreover, rai1Δ yeast cells with wild-type capping enzymes show significant accumulation of mRNAs with 5′-end capping defects under nutritional stress conditions of glucose starvation or amino acid starvation. These findings provide evidence that 5′-end capping is not a constitutive process that necessarily always proceeds to completion and demonstrates that Rai1 has an essential role in clearing mRNAs with aberrant 5′-end caps. We propose that Rai1 is involved in an as yet uncharacterized quality control process that ensures mRNA 5′-end integrity by an aberrant-cap-mediated mRNA decay mechanism.

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Figure 1: Rai1 preferentially hydrolyses unmethylated capped RNA.
Figure 2: Rai1 preferentially hydrolyses unmethylated 5′-end-capped mRNA in yeast cells.
Figure 3: Rai1 functions to clear mRNAs in cells subjected to glucose starvation or amino acid starvation.
Figure 4: Aberrantly capped mRNA levels increase in cells exposed to nutrient starvation.

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References

  1. Li, Y. & Kiledjian, M. Regulation of mRNA decapping. Wiley Interdiscipl. Rev. RNA 10.1002/wrna.15 (6 May, 2010)

  2. Meyer, S., Temme, C. & Wahle, E. Messenger RNA turnover in eukaryotes: pathways and enzymes. Crit. Rev. Biochem. Mol. Biol. 39, 197–216 (2004)

    CAS  Google Scholar 

  3. Merrick, W. C. Cap-dependent and cap-independent translation in eukaryotic systems. Gene 332, 1–11 (2004)

    CAS  Google Scholar 

  4. Xiang, S. et al. Structure and function of the 5′→3′ exoribonuclease Rat1 and its activating partner Rai1. Nature 458, 784–788 (2009)

    CAS  Google Scholar 

  5. Furuichi, Y. & Shatkin, A. J. Viral and cellular mRNA capping: past and prospects. Adv. Virus Res. 55, 135–184 (2000)

    CAS  Google Scholar 

  6. Shatkin, A. J. Capping of eucaryotic mRNAs. Cell 9, 645–653 (1976)

    CAS  Google Scholar 

  7. Shuman, S. Capping enzyme in eukaryotic mRNA synthesis. Prog. Nucleic Acid Res. Mol. Biol. 50, 101–129 (1995)

    CAS  Google Scholar 

  8. Shuman, S. What messenger RNA capping tells us about eukaryotic evolution. Nature Rev. Mol. Cell Biol. 3, 619–625 (2002)

    CAS  Google Scholar 

  9. Yue, Z. et al. Mammalian capping enzyme complements mutant Saccharomyces cerevisiae lacking mRNA guanylyltransferase and selectively binds the elongating form of RNA polymerase II. Proc. Natl Acad. Sci. USA 94, 12898–12903 (1997)

    CAS  Google Scholar 

  10. Goodfellow, I. G. & Roberts, L. O. Eukaryotic initiation factor 4E. Int. J. Biochem. Cell Biol. 40, 2675–2680 (2008)

    CAS  Google Scholar 

  11. Fischer, P. M. Cap in hand: targeting eIF4E. Cell Cycle 8, 2535–2541 (2009)

    CAS  Google Scholar 

  12. Dunckley, T. & Parker, R. The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif. EMBO J. 18, 5411–5422 (1999)

    CAS  Google Scholar 

  13. Wang, Z., Jiao, X., Carr-Schmid, A. & Kiledjian, M. The hDcp2 protein is a mammalian mRNA decapping enzyme. Proc. Natl Acad. Sci. USA 99, 12663–12668 (2002)

    CAS  Google Scholar 

  14. Lykke-Andersen, J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol. Cell. Biol. 22, 8114–8121 (2002)

    CAS  Google Scholar 

  15. Decker, C. J. & Parker, R. A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev. 7, 1632–1643 (1993)

    CAS  Google Scholar 

  16. Hsu, C. L. & Stevens, A. Yeast cells lacking 5′→3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure. Mol. Cell. Biol. 13, 4826–4835 (1993)

    CAS  Google Scholar 

  17. Schwer, B., Saha, N., Mao, X., Chen, H. W. & Shuman, S. Structure–function analysis of yeast mRNA cap methyltransferase and high-copy suppression of conditional mutants by AdoMet synthase and the ubiquitin conjugating enzyme Cdc34p. Genetics 155, 1561–1576 (2000)

    CAS  Google Scholar 

  18. Hilgers, V., Teixeira, D. & Parker, R. Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae . RNA 12, 1835–1845 (2006)

    CAS  Google Scholar 

  19. Wen, Y. & Shatkin, A. J. Cap methyltransferase selective binding and methylation of GpppG-RNA are stimulated by importin-α. Genes Dev. 14, 2944–2949 (2000)

    CAS  Google Scholar 

  20. Cowling, V. H. & Cole, M. D. The Myc transactivation domain promotes global phosphorylation of the RNA polymerase II carboxy-terminal domain independently of direct DNA binding. Mol. Cell. Biol. 27, 2059–2073 (2007)

    CAS  Google Scholar 

  21. Jimeno-González, S., Haaning, L. L., Malagon, F. & Jensen, T. H. The yeast 5′-3′ exonuclease Rat1p functions during transcription elongation by RNA polymerase II. Mol. Cell 37, 580–587 (2010)

    Google Scholar 

  22. Otsuka, Y., Kedersha, N. L. & Schoenberg, D. R. Identification of a cytoplasmic complex that adds a cap onto 5′-monophosphate RNA. Mol. Cell. Biol. 29, 2155–2167 (2009)

    CAS  Google Scholar 

  23. Piccirillo, C., Khanna, R. & Kiledjian, M. Functional characterization of the mammalian mRNA decapping enzyme hDcp2. RNA 9, 1138–1147 (2003)

    CAS  Google Scholar 

  24. Gasch, A. P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241–4257 (2000)

    CAS  Google Scholar 

  25. Natarajan, K. et al. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol. Cell. Biol. 21, 4347–4368 (2001)

    CAS  Google Scholar 

  26. Köhrer, K. & Domdey, H. Preparation of high molecular weight RNA. Methods Enzymol. 194, 398–405 (1991)

    Google Scholar 

  27. He, F. & Jacobson, A. Upf1p, Nmd2p, and Upf3p regulate the decapping and exonucleolytic degradation of both nonsense-containing mRNAs and wild-type mRNAs. Mol. Cell. Biol. 21, 1515–1530 (2001)

    CAS  Google Scholar 

  28. Liu, H. & Kiledjian, M. Scavenger decapping activity facilitates 5′ to 3′ mRNA decay. Mol. Cell. Biol. 25, 9764–9772 (2005)

    CAS  Google Scholar 

  29. Jiao, X. et al. Modulation of neuritogenesis by a protein implicated in X-linked mental retardation. J. Neurosci. 29, 12419–12427 (2009)

    CAS  Google Scholar 

  30. Herrick, D., Parker, R. & Jacobson, A. Identification and comparison of stable and unstable mRNAs in Saccharomyces cerevisiae . Mol. Cell. Biol. 10, 2269–2284 (1990)

    CAS  Google Scholar 

  31. Wang, Z. & Kiledjian, M. Functional link between the mammalian exosome and mRNA decapping. Cell 107, 751–762 (2001)

    CAS  Google Scholar 

  32. Wang, Z., Day, N., Trifillis, P. & Kiledjian, M. An mRNA stability complex functions with poly(A)-binding protein to stabilize mRNA in vitro . Mol. Cell. Biol. 19, 4552–4560 (1999)

    CAS  Google Scholar 

  33. Liu, H., Rodgers, N. D., Jiao, X. & Kiledjian, M. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J. 21, 4699–4708 (2002)

    CAS  Google Scholar 

  34. Amin-ul Mannan, M., Sharma, S. & Ganesan, K. Total RNA isolation from recalcitrant yeast cells. Anal. Biochem. 389, 77–79 (2009)

    CAS  Google Scholar 

  35. Zhang, S., Williams, C. J., Wormington, M., Stevens, A. & Peltz, S. W. Monitoring mRNA decapping activity. Methods 17, 46–51 (1999)

    Google Scholar 

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Acknowledgements

We thank B. Schwer for the abd1-5 yeast strain and A. Shatkin for discussions. This research was supported by grants from the National Institutes of Health (NIH) to L.T. (GM077175) and M.K. (GM67005).

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Authors and Affiliations

  1. Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, 08854, New Jersey, USA

    Xinfu Jiao, ChanSeok Oh, Charles E. Martin & Megerditch Kiledjian

  2. Department of Biological Sciences, Columbia University, New York, 10027, New York, USA

    Song Xiang & Liang Tong

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  1. Xinfu Jiao
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Contributions

X.J. and M.K. conceived the project, analysed the data and wrote the manuscript. X.J. carried out the experiments. S.X. and L.T. provided the recombinant proteins. C.O. and C.E.M. generated the yeast mutant strains. All authors discussed the results and commented on the manuscript.

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Correspondence to Megerditch Kiledjian.

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The authors declare no competing financial interests.

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Jiao, X., Xiang, S., Oh, C. et al. Identification of a quality-control mechanism for mRNA 5′-end capping. Nature 467, 608–611 (2010). https://doi.org/10.1038/nature09338

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