Letter | Published:

mRNA quality control is bypassed for immediate export of stress-responsive transcripts

Nature volume 540, pages 593596 (22 December 2016) | Download Citation

Abstract

Cells grow well only in a narrow range of physiological conditions. Surviving extreme conditions requires the instantaneous expression of chaperones that help to overcome stressful situations. To ensure the preferential synthesis of these heat-shock proteins, cells inhibit transcription, pre-mRNA processing and nuclear export of non-heat-shock transcripts, while stress-specific mRNAs are exclusively exported and translated1. How cells manage the selective retention of regular transcripts and the simultaneous rapid export of heat-shock mRNAs is largely unknown. In Saccharomyces cerevisiae, the shuttling RNA adaptor proteins Npl3, Gbp2, Hrb1 and Nab2 are loaded co-transcriptionally onto growing pre-mRNAs. For nuclear export, they recruit the export-receptor heterodimer Mex67–Mtr2 (TAP–p15 in humans)2. Here we show that cellular stress induces the dissociation of Mex67 and its adaptor proteins from regular mRNAs to prevent general mRNA export. At the same time, heat-shock mRNAs are rapidly exported in association with Mex67, without the need for adapters. The immediate co-transcriptional loading of Mex67 onto heat-shock mRNAs involves Hsf1, a heat-shock transcription factor that binds to heat-shock-promoter elements in stress-responsive genes. An important difference between the export modes is that adaptor-protein-bound mRNAs undergo quality control, whereas stress-specific transcripts do not. In fact, regular mRNAs are converted into uncontrolled stress-responsive transcripts if expressed under the control of a heat-shock promoter, suggesting that whether an mRNA undergoes quality control is encrypted therein. Under normal conditions, Mex67 adaptor proteins are recruited for RNA surveillance, with only quality-controlled mRNAs allowed to associate with Mex67 and leave the nucleus. Thus, at the cost of error-free mRNA formation, heat-shock mRNAs are exported and translated without delay, allowing cells to survive extreme situations.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

References

  1. 1.

    Stressed out! Effects of environmental stress on mRNA metabolism. FEMS Yeast Res. 6, 160–170 (2006)

  2. 2.

    & Keeping mRNPs in check during assembly and nuclear export. Nat. Rev. Mol. Cell Biol. 12, 377–384 (2011)

  3. 3.

    , , , & The mitogen-activated protein kinase Slt2 regulates nuclear retention of non-heat shock mRNAs during heat shock-induced stress. Mol. Cell. Biol. 30, 5168–5179 (2010)

  4. 4.

    , , & Uncoupling of the hnRNP Npl3p from mRNAs during the stress-induced block in mRNA export. Genes Dev. 13, 1994–2004 (1999)

  5. 5.

    et al. Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress. Cell 162, 1286–1298 (2015)

  6. 6.

    , , & Global analysis of yeast mRNPs. Nat. Struct. Mol. Biol. 20, 127–133 (2013)

  7. 7.

    , & Following temperature stress, export of heat shock mRNA occurs efficiently in cells with mutations in genes normally important for mRNA export. Eukaryot. Cell 6, 505–513 (2007)

  8. 8.

    , & Identification of a novel class of target genes and a novel type of binding sequence of heat shock transcription factor in Saccharomyces cerevisiae. J. Biol. Chem. 280, 11911–11919 (2005)

  9. 9.

    et al. Nuclear export of ribosomal 60S subunits by the general mRNA export receptor Mex67-Mtr2. Mol. Cell 26, 51–62 (2007)

  10. 10.

    et al. A functional module of yeast mediator that governs the dynamic range of heat-shock gene expression. Genetics 172, 2169–2184 (2006)

  11. 11.

    & Mediator recruitment to heat shock genes requires dual Hsf1 activation domains and mediator tail subunits Med15 and Med16. J. Biol. Chem. 288, 12197–12213 (2013)

  12. 12.

    et al. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417, 304–308 (2002)

  13. 13.

    & RNA quality control in eukaryotes. Cell 131, 660–668 (2007)

  14. 14.

    & A nuclear 3′-5′ exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p. Mol. Cell. Biol. 20, 604–616 (2000)

  15. 15.

    et al. Nuclear retention of unspliced mRNAs in yeast is mediated by perinuclear Mlp1. Cell 116, 63–73 (2004)

  16. 16.

    , , & The C-terminal domain of myosin-like protein 1 (Mlp1p) is a docking site for heterogeneous nuclear ribonucleoproteins that are required for mRNA export. Proc. Natl Acad. Sci. USA 100, 1010–1015 (2003)

  17. 17.

    et al. Quality control of spliced mRNAs requires the shuttling SR proteins Gbp2 and Hrb1. Nat. Commun. 5, 3123 (2014)

  18. 18.

    , , & Novel RING finger proteins, Air1p and Air2p, interact with Hmt1p and inhibit the arginine methylation of Npl3p. J. Biol. Chem. 275, 32793–32799 (2000)

  19. 19.

    et al. Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins. Mol. Cell 47, 267–280 (2012)

  20. 20.

    et al. Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition. Mol. Cell 55, 745–757 (2014)

  21. 21.

    , , & 7The yeast mRNA-binding protein Npl3p interacts with the cap-binding complex. J. Biol. Chem. 275, 23718–23724 (2000)

  22. 22.

    & A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell 154, 996–1009 (2013)

  23. 23.

    et al. The nuclear polyA-binding protein Nab2p is essential for mRNA production. Cell Reports 12, 128–139 (2015)

  24. 24.

    & Identification of Gbp2 as a novel poly(A)+ RNA-binding protein involved in the cytoplasmic delivery of messenger RNAs in yeast. EMBO Rep. 4, 278–283 (2003)

  25. 25.

    , , , & Quality control of mRNA 3′-end processing is linked to the nuclear exosome. Nature 413, 538–542 (2001)

  26. 26.

    , , , & Localization of nuclear retained mRNAs in Saccharomyces cerevisiae. RNA 9, 1049–1057 (2003)

  27. 27.

    & Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature 514, 117–121 (2014)

  28. 28.

    , & Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 11, 53–55 (1995)

  29. 29.

    , & A conditional allele of the novel repeat-containing yeast nucleoporin RAT7/NUP159 causes both rapid cessation of mRNA export and reversible clustering of nuclear pore complexes. J. Cell Biol. 129, 939–955 (1995)

  30. 30.

    et al. Arginine methylation facilitates the nuclear export of hnRNP proteins. Genes Dev. 12, 679–691 (1998)

  31. 31.

    , & Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export. J. Cell Biol. 150, 695–706 (2000)

  32. 32.

    et al. Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J. 16, 3256–3271 (1997)

  33. 33.

    et al. Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol. Cell 8, 517–529 (2001)

  34. 34.

    , , & The mRNA export factor Npl3 mediates the nuclear export of large ribosomal subunits. EMBO Rep. 12, 1024–1031 (2011). 10.1038/embor.2011.155

  35. 35.

    et al. Monosome formation during translation initiation requires the serine/arginine-rich protein Npl3. Mol. Cell. Biol. 33, 4811–4823 (2013). 10.1128/MCB.00873-13

  36. 36.

    , , & Domain analysis of the Saccharomyces cerevisiae heterogeneous nuclear ribonucleoprotein, Nab2p. Dissecting the requirements for Nab2p-facilitated poly(A) RNA export. J. Biol. Chem. 278, 6731–6740 (2003)

  37. 37.

    , & A member of the Ran-binding protein family, Yrb2p, is involved in nuclear protein export. Proc. Natl Acad. Sci. USA 95, 7427–7432 (1998)

  38. 38.

    & A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122, 19–27 (1989)

  39. 39.

    , , , & Multifunctional yeast high-copy-number shuttle vectors. Gene 110, 119–122 (1992)

  40. 40.

    , & A protein that shuttles between the nucleus and the cytoplasm is an important mediator of RNA export. Genes Dev. 10, 1233–1246 (1996)

  41. 41.

    & Differential export requirements for shuttling serine/arginine-type mRNA-binding proteins. J. Biol. Chem. 279, 5049–5052 (2004)

  42. 42.

    et al. Nuclear mRNA export requires complex formation between Mex67p and Mtr2p at the nuclear pores. Mol. Cell. Biol. 18, 6826–6838 (1998)

  43. 43.

    , & A putative ubiquitin ligase required for efficient mRNA export differentially affects hnRNP transport. Curr. Biol. 10, 687–696 (2000)

  44. 44.

    , & Phosphorylation by Sky1p promotes Npl3p shuttling and mRNA dissociation. RNA 7, 302–313 (2001)

  45. 45.

    , , & The yeast hnRNP-Like proteins Yra1p and Yra2p participate in mRNA export through interaction with Mex67p. Mol. Cell. Biol. 21, 4219–4232 (2001)

  46. 46.

    et al. A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 154, 557–571 (2000)

  47. 47.

    , & Proteins connecting the nuclear pore complex with the nuclear interior. J. Cell Biol. 144, 839–855 (1999)

  48. 48.

    , , , & Role of Mex67-Mtr2 in the nuclear export of 40S pre-ribosomes. PLoS Genet. 8, e1002915 (2012)

Download references

Acknowledgements

We thank H. Bastians for advice, L. Oldehaver for technical assistance, W. Kramer for discussion and R. Lill, P. A. Silver, C. Dargemont and E. Hurt for providing plasmids, strains or antibodies. This work was funded by grants from the Deutsche Forschungsgemeinschaft and the SFB860 to H.K.

Author information

Author notes

    • Gesa Zander
    • , Alexandra Hackmann
    •  & Lysann Bender

    These authors contributed equally to this work

Affiliations

  1. Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August Universität Göttingen, Göttingen, Germany

    • Gesa Zander
    • , Alexandra Hackmann
    • , Lysann Bender
    • , Daniel Becker
    •  & Heike Krebber
  2. Transkriptomanalyselabor, Institut für Entwicklungsbiochemie, Georg-August Universität Göttingen, Göttingen, Germany

    • Thomas Lingner
    •  & Gabriela Salinas

Authors

  1. Search for Gesa Zander in:

  2. Search for Alexandra Hackmann in:

  3. Search for Lysann Bender in:

  4. Search for Daniel Becker in:

  5. Search for Thomas Lingner in:

  6. Search for Gabriela Salinas in:

  7. Search for Heike Krebber in:

Contributions

Experiments were designed and data interpreted by all authors; experiments were performed by G.Z. (Figs 1b, c, 2d, e, 3c, 4b–d), A.H. (Figs 1c, 3a, b, 4a), L.B. (Figs 1a, 2a–c) D.B. (Fig. 1c) and T.L. and G.S. (Fig. 1c). The manuscript was written by H.K.; all authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Heike Krebber.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Methods for RIP-Microarray experiments and Supplementary Tables for Microarray.

  2. 2.

    Supplementary Information

    This file contains Supplementary Methods for RNA-Seq experiments and Supplementary Tables for RNA-sequencing.

  3. 3.

    Supplementary Information

    This file contains uncropped gel source data with size marker indications and Supplementary Figures 1-4.

Excel files

  1. 1.

    Supplementary Data

    This file contains raw data of the Microarray with functional groups for each gene, genes sorted for binding >0,5 log2 fold change for Mex67 and Npl3 at 42°C and 25°C and raw data for the total dissociation of mRNAs at 42°C.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature20572

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.