Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Coordinated control of replication and transcription by a SAPK protects genomic integrity

Abstract

Upon environmental changes or extracellular signals, cells are subjected to marked changes in gene expression 1,2. Dealing with high levels of transcription during replication is critical to prevent collisions between the transcription and replication pathways and avoid recombination events3,4,5. In response to osmostress, hundreds of stress-responsive genes are rapidly induced by the stress-activated protein kinase (SAPK) Hog1 (ref. 6), even during S phase7. Here we show in Saccharomyces cerevisae that a single signalling molecule, Hog1, coordinates both replication and transcription upon osmostress. Hog1 interacts with and phosphorylates Mrc1, a component of the replication complex8,9,10,11. Phosphorylation occurs at different sites to those targeted by Mec1 upon DNA damage8,9. Mrc1 phosphorylation by Hog1 delays early and late origin firing by preventing Cdc45 loading, as well as slowing down replication-complex progression. Regulation of Mrc1 by Hog1 is completely independent of Mec1 and Rad53. Cells carrying a non-phosphorylatable allele of MRC1 (mrc13A ) do not delay replication upon stress and show a marked increase in transcription-associated recombination, genomic instability and Rad52 foci. In contrast, mrc13A induces Rad53 and survival in the presence of hydroxyurea or methyl methanesulphonate. Therefore, Hog1 and Mrc1 define a novel S-phase checkpoint independent of the DNA-damage checkpoint that permits eukaryotic cells to prevent conflicts between DNA replication and transcription, which would otherwise lead to genomic instability when both phenomena are temporally coincident.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Mrc1 is a Hog1 target.
Figure 2: mrc1 3A bypasses the osmostress-induced S phase delay.
Figure 3: Hog1 delays replication by inhibiting fork progression and origin firing.
Figure 4: Hog1–Mrc1 checkpoint prevents genomic instability upon osmostress.

References

  1. López-Maury, L., Marguerat, S. & Bahler, J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nature Rev. Genet. 9, 583–593 (2008)

    Article  Google Scholar 

  2. de Nadal, E., Ammerer, G. & Posas, F. Controlling gene expression in response to stress. Nature Rev. Genet. 12, 833–845 (2011)

    CAS  Article  Google Scholar 

  3. Prado, F. & Aguilera, A. Impairment of replication fork progression mediates RNA polII transcription-associated recombination. EMBO J. 24, 1267–1276 (2005)

    CAS  Article  Google Scholar 

  4. Pomerantz, R. T. & O’Donnell, M. Direct restart of a replication fork stalled by a head-on RNA polymerase. Science 327, 590–592 (2010)

    ADS  CAS  Article  Google Scholar 

  5. Muers, M. Mutation: the perils of transcription. Nature Rev. Genet. 12, 156 (2011)

    CAS  Article  Google Scholar 

  6. de Nadal, E. & Posas, F. Multilayered control of gene expression by stress-activated protein kinases. EMBO J. 29, 4–13 (2010)

    CAS  Article  Google Scholar 

  7. Yaakov, G. et al. The stress-activated protein kinase Hog1 mediates S phase delay in response to osmostress. Mol. Biol. Cell 20, 3572–3582 (2009)

    CAS  Article  Google Scholar 

  8. Alcasabas, A. A. et al. Mrc1 transduces signals of DNA replication stress to activate Rad53. Nature Cell Biol. 3, 958–965 (2001)

    CAS  Article  Google Scholar 

  9. Osborn, A. J. & Elledge, S. J. Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53. Genes Dev. 17, 1755–1767 (2003)

    CAS  Article  Google Scholar 

  10. Katou, Y. et al. S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature 424, 1078–1083 (2003)

    ADS  CAS  Article  Google Scholar 

  11. Tourrière, H. et al. Mrc1 and Tof1 promote replication fork progression and recovery independently of Rad53. Mol. Cell 19, 699–706 (2005)

    Article  Google Scholar 

  12. Weake, V. M. & Workman, J. L. Inducible gene expression: diverse regulatory mechanisms. Nature Rev. Genet. 11, 426–437 (2010)

    CAS  Article  Google Scholar 

  13. Chen, R. E. & Thorner, J. Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae . Biochim. Biophys. Acta 1773, 1311–1340 (2007)

    CAS  Article  Google Scholar 

  14. Hohmann, S. Osmotic stress signaling and osmoadaptation in yeasts. Microbiol. Mol. Biol. Rev. 66, 300–372 (2002)

    CAS  Article  Google Scholar 

  15. Escoté, X. et al. Hog1 mediates cell-cycle arrest in G1 phase by the dual targeting of Sic1. Nature Cell Biol. 6, 997–1002 (2004)

    Article  Google Scholar 

  16. Clotet, J. et al. Phosphorylation of Hsl1 by Hog1 leads to a G2 arrest essential for cell survival at high osmolarity. EMBO J. 25, 2338–2346 (2006)

    CAS  Article  Google Scholar 

  17. Clotet, J. & Posas, F. Control of cell cycle in response to osmostress: lessons from yeast. Methods Enzymol. 428, 63–76 (2007)

    CAS  Article  Google Scholar 

  18. Wurgler-Murphy, S. M. et al. Regulation of the Saccharomyces cerevisiae HOG1 mitogen-activated protein kinase by the PTP2 and PTP3 protein tyrosine phosphatases. Mol. Cell. Biol. 17, 1289–1297 (1997)

    CAS  Article  Google Scholar 

  19. Shirayama, M. et al. APC(Cdc20) promotes exit from mitosis by destroying the anaphase inhibitor Pds1 and cyclin Clb5. Nature 402, 203–207 (1999)

    ADS  CAS  Article  Google Scholar 

  20. Jacobson, M. D. et al. Testing cyclin specificity in the exit from mitosis. Mol. Cell. Biol. 20, 4483–4493 (2000)

    CAS  Article  Google Scholar 

  21. Aparicio, O. M., Weinstein, D. M. & Bell, S. P. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 91, 59–69 (1997)

    CAS  Article  Google Scholar 

  22. Lou, H. et al. Mrc1 and DNA polymerase ε function together in linking DNA replication and the S phase checkpoint. Mol. Cell 32, 106–117 (2008)

    CAS  Article  Google Scholar 

  23. Aguilera, A. The connection between transcription and genomic instability. EMBO J. 21, 195–201 (2002)

    CAS  Article  Google Scholar 

  24. Aguilera, A. mRNA processing and genomic instability. Nature Struct. Mol. Biol. 12, 737–738 (2005)

    CAS  Article  Google Scholar 

  25. García-Rubio, M. et al. Different physiological relevance of yeast THO/TREX subunits in gene expression and genome integrity. Mol. Genet. Genomics 279, 123–132 (2008)

    Article  Google Scholar 

  26. Gonzalez-Barrera, S., Garcia-Rubio, M. & Aguilera, A. Transcription and double-strand breaks induce similar mitotic recombination events in Saccharomyces cerevisiae . Genetics 162, 603–614 (2002)

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Lisby, M., Mortensen, U. H. & Rothstein, R. Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre. Nature Cell Biol. 5, 572–577 (2003)

    CAS  Article  Google Scholar 

  28. Nadal, E., Casadome, L. & Posas, F. Targeting the MEF2-like transcription factor Smp1 by the stress-activated Hog1 mitogen-activated protein kinase. Mol. Cell. Biol. 23, 229–237 (2003)

    Article  Google Scholar 

  29. Spencer, F. et al. Mitotic chromosome transmission fidelity mutants in Saccharomyces cerevisiae . Genetics 124, 237–249 (1990)

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Bousset, K. & Diffley, J. F. The Cdc7 protein kinase is required for origin firing during S phase. Genes Dev. 12, 480–490 (1998)

    CAS  Article  Google Scholar 

  31. Moriel-Carretero, M. & Aguilera, A. A postincision-deficient TFIIH causes replication fork breakage and uncovers alternative Rad51- or Pol32-mediated restart mechanisms. Mol. Cell 37, 690–701 (2010)

    CAS  Article  Google Scholar 

  32. Bianco, J. N. et al. Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing. Methods 57, 149–157 (2012)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank L. Subirana, S. Ovejas and A. Fernandez for technical support. This work was supported by grants from the Spanish Government (BIO2009-07762 and BFU2012-33503 to F.P., BFU2011-26722 to E.d.N., BFU2010-16372 to A.A., and Consolider Ingenio 2010 programme CSD2007-0015 to F.P. and A.A.) and FP7 UNICELLSYS grant (no. 201142) and the Fundación Marcelino Botín to F.P. F.P. and E.d.N. are recipients of an ICREA Acadèmia (Generalitat de Catalunya).

Author information

Authors and Affiliations

Authors

Contributions

A.D. conducted most of the experiments. I.F.-A., S.B. and M.G.-R. worked on the analysis of replication. G.Y. initiated the studies. A.D., E.d.N., A.A., G.Y. and F.P. did the experimental designs. A.D., A.A., E.d.N. and F.P. wrote the paper.

Corresponding author

Correspondence to Francesc Posas.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-15. (PDF 1067 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Duch, A., Felipe-Abrio, I., Barroso, S. et al. Coordinated control of replication and transcription by a SAPK protects genomic integrity. Nature 493, 116–119 (2013). https://doi.org/10.1038/nature11675

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11675

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.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing