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.

Frequency-modulated nuclear localization bursts coordinate gene regulation

Abstract

In yeast, the transcription factor Crz1 is dephosphorylated and translocates into the nucleus in response to extracellular calcium. Here we show, using time-lapse microscopy, that Crz1 exhibits short bursts of nuclear localization (typically lasting 2 min) that occur stochastically in individual cells and propagate to the expression of downstream genes. Strikingly, calcium concentration controls the frequency, but not the duration, of localization bursts. Using an analytic model, we also show that this frequency modulation of bursts ensures proportional expression of multiple target genes across a wide dynamic range of expression levels, independent of promoter characteristics. We experimentally confirm this theory with natural and synthetic Crz1 target promoters. Another stress-response transcription factor, Msn2, exhibits similar, but largely uncorrelated, localization bursts under calcium stress suggesting that frequency-modulation regulation of localization bursts may be a general control strategy used by the cell to coordinate multi-gene responses to external signals.

This is a preview of subscription content, access via your institution

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: Crz1 undergoes bursts of nuclear localization in response to calcium.
Figure 2: Calcium modulates the frequency, but not the duration, of Crz1 nuclear localization bursts.
Figure 3: Crz1 localization bursts are partially independent of other cellular processes and affect downstream gene expression.
Figure 4: Frequency- versus amplitude-modulation regulation of two hypothetical target genes, labelled A and B (schematic).
Figure 5: Frequency-modulated bursts coordinate gene expression.

References

  1. Cyert, M. S. Regulation of nuclear localization during signaling. J. Biol. Chem. 276, 20805–20808 (2001)

    Article  CAS  Google Scholar 

  2. Estruch, F. Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. FEMS Microbiol. Rev. 24, 469–486 (2000)

    Article  CAS  Google Scholar 

  3. Kyriakis, J. M. The integration of signaling by multiprotein complexes containing Raf kinases. Biochim. Biophys. Acta 1773, 1238–1247 (2007)

    Article  CAS  Google Scholar 

  4. Stathopoulos-Gerontides, A., Guo, J. J. & Cyert, M. S. Yeast calcineurin regulates nuclear localization of the Crz1p transcription factor through dephosphorylation. Genes Dev. 13, 798–803 (1999)

    Article  CAS  Google Scholar 

  5. Yoshimoto, H. et al. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae . J. Biol. Chem. 277, 31079–31088 (2002)

    Article  CAS  Google Scholar 

  6. Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003)

    Article  ADS  CAS  Google Scholar 

  7. Mettetal, J. T. et al. The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae . Science 319, 482–484 (2008)

    Article  ADS  CAS  Google Scholar 

  8. Hersen, P. et al. Signal processing by the HOG MAP kinase pathway. Proc. Natl Acad. Sci. USA 105, 7165–7170 (2008)

    Article  ADS  CAS  Google Scholar 

  9. Suel, G. M. et al. Tunability and noise dependence in differentiation dynamics. Science 315, 1716–1719 (2007)

    Article  ADS  Google Scholar 

  10. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737–741 (2003)

    Article  ADS  CAS  Google Scholar 

  11. Di Talia, S. et al. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature 448, 947–951 (2007)

    Article  ADS  CAS  Google Scholar 

  12. Fewtrell, C. Ca2+ oscillations in non-excitable cells. Annu. Rev. Physiol. 55, 427–454 (1993)

    Article  CAS  Google Scholar 

  13. Wiesenberger, G. et al. Mg2+ deprivation elicits rapid Ca2+ uptake and activates Ca2+/calcineurin signaling in Saccharomyces cerevisiae . Eukaryot. Cell 6, 592–599 (2007)

    Article  CAS  Google Scholar 

  14. Boustany, L. M. & Cyert, M. S. Calcineurin-dependent regulation of Crz1p nuclear export requires Msn5p and a conserved calcineurin docking site. Genes Dev. 16, 608–619 (2002)

    Article  CAS  Google Scholar 

  15. Roy, J. et al. A conserved docking site modulates substrate affinity for calcineurin, signaling output, and in vivo function. Mol. Cell 25, 889–901 (2007)

    Article  CAS  Google Scholar 

  16. Breuder, T. et al. Calcineurin is essential in cyclosporin A- and FK506-sensitive yeast strains. Proc. Natl Acad. Sci. USA 91, 5372–5376 (1994)

    Article  ADS  CAS  Google Scholar 

  17. Jacquet, M. et al. Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae . J. Cell Biol. 161, 497–505 (2003)

    Article  CAS  Google Scholar 

  18. Garmendia-Torres, C., Goldbeter, A. & Jacquet, M. Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation. Curr. Biol. 17, 1044–1049 (2007)

    Article  CAS  Google Scholar 

  19. Medvedik, O. et al. MSN2 and MSN4 Link calorie restriction and tor to sirtuin-mediated lifespan extension in Saccharomyces cerevisiae . PLoS Biol. 5, e261 (2007)

    Article  Google Scholar 

  20. Stathopoulos, A. M. & Cyert, M. S. Calcineurin acts through the CRZ1/TCN1-encoded transcription factor to regulate gene expression in yeast. Genes Dev. 11, 3432–3444 (1997)

    Article  CAS  Google Scholar 

  21. Golding, I. et al. Real-time kinetics of gene activity in individual bacteria. Cell 123, 1025–1036 (2005)

    Article  CAS  Google Scholar 

  22. Raj, A. et al. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006)

    Article  Google Scholar 

  23. Rodriguez, A. J. et al. Visualization of mRNA translation in living cells. J. Cell Biol. 175, 67–76 (2006)

    Article  CAS  Google Scholar 

  24. Elowitz, M. B. et al. Stochastic gene expression in a single cell. Science 297, 1183–1186 (2002)

    Article  ADS  CAS  Google Scholar 

  25. Bar-Even, A. et al. Noise in protein expression scales with natural protein abundance. Nature Genet. 38, 636–643 (2006)

    Article  CAS  Google Scholar 

  26. Cai, L., Friedman, N. & Xie, X. S. Stochastic protein expression in individual cells at the single molecule level. Nature 440, 358–362 (2006)

    Article  ADS  CAS  Google Scholar 

  27. Friedman, N., Cai, L. & Xie, X. S. Linking stochastic dynamics to population distribution: an analytical framework of gene expression. Phys. Rev. Lett. 97, 168302-1–168302-4 (2006)

    Article  ADS  Google Scholar 

  28. Kaern, M., Elston, T. C., Blake, W. J. & Collins, J. J. Stochasticity in gene expression: from theories to phenotypes. Nature Rev. Genet. 6, 451–464 (2005)

    Article  CAS  Google Scholar 

  29. Kaufmann, B. B. & van Oudenaarden, A. Stochastic gene expression: from single molecules to the proteome. Curr. Opin. Genet. Dev. 17, 107–112 (2007)

    Article  CAS  Google Scholar 

  30. Maheshri, N. & O’Shea, E. K. Living with noisy genes: how cells function reliably with inherent variability in gene expression. Annu. Rev. Biophys. Biomol. Struct. 36, 413–434 (2007)

    Article  CAS  Google Scholar 

  31. Newman, J. R. et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441, 840–846 (2006)

    Article  ADS  CAS  Google Scholar 

  32. Ozbudak, E. M. et al. Regulation of noise in the expression of a single gene. Nature Genet. 31, 69–73 (2002)

    Article  CAS  Google Scholar 

  33. Sigal, A. et al. Variability and memory of protein levels in human cells. Nature 444, 643–646 (2006)

    Article  ADS  CAS  Google Scholar 

  34. Yu, J. et al. Probing gene expression in live cells, one protein molecule at a time. Science 311, 1600–1603 (2006)

    Article  ADS  CAS  Google Scholar 

  35. Rosenfeld, N. et al. Gene regulation at the single-cell level. Science 307, 1962–1965 (2005)

    Article  ADS  CAS  Google Scholar 

  36. Matheos, D. P. et al. Tcn1p/Crz1p, a calcineurin-dependent transcription factor that differentially regulates gene expression in Saccharomyces cerevisiae . Genes Dev. 11, 3445–3458 (1997)

    Article  CAS  Google Scholar 

  37. Armstrong, E. H. A method of reducing disturbances in radio signaling by a system of frequency modulation. Proc. Inst. Radio Eng. 24, 689–740 (1936)

    Google Scholar 

  38. Song, G. B., Buck, N. V. & Agrawal, B. N. Spacecraft vibration reduction using pulse-width pulse-frequency modulated input shaper. J. Guid. Control Dyn. 22, 433–440 (1999)

    Article  ADS  Google Scholar 

  39. Adrian, E. D. & Zotterman, Y. The impulses produced by sensory nerve-endings: Part II. The response of a single end-organ. J. Physiol. (Lond.) 61, 151–171 (1926)

    Article  CAS  Google Scholar 

  40. Sarpeshkar, R. Analog versus digital: extrapolating from electronics to neurobiology. Neural Comput. 10, 1601–1638 (1998)

    Article  CAS  Google Scholar 

  41. Dolmetsch, R. E., Xu, K. & Lewis, R. S. Calcium oscillations increase the efficiency and specificity of gene expression. Nature 392, 933–936 (1998)

    Article  ADS  CAS  Google Scholar 

  42. Geva-Zatorsky, N. et al. Oscillations and variability in the p53 system. Mol. Syst. Biol. 2, 2006.0033 (2006)

    Article  Google Scholar 

  43. Nelson, D. E. et al. Oscillations in NF-κB signaling control the dynamics of gene expression. Science 306, 704–708 (2004)

    Article  ADS  CAS  Google Scholar 

  44. Friedman, N. et al. Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. PLoS Biol. 3, e238 (2005)

    Article  Google Scholar 

  45. Sheff, M. A. & Thorn, K. S. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae . Yeast 21, 661–670 (2004)

    Article  CAS  Google Scholar 

  46. Gietz, R. D. & Woods, R. A. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 350, 87–96 (2002)

    Article  CAS  Google Scholar 

  47. Sherman, F. Getting started with yeast. Methods Enzymol. 350, 3–41 (2002)

    Article  CAS  Google Scholar 

  48. Nachman, I., Regev, A. & Ramanathan, S. Dissecting timing variability in yeast meiosis. Cell 131, 544–556 (2007)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Cyert for the CDRE and Crz1 mutant plasmids, K. Cunningham for the Crz1 overexpression plasmid pLE66, J. Stadler for the pGW845 FRET plasmid, S. Ramanathan for image analysis code, and K. Thorn, C.-L. Guo and L. LeBon for technical assistance. We thank U. Alon, M. Carlson, M. Cyert, H. Garcia, R. Kishony, G. Lahav, J.-G. Ojalvo, I. Riedel-Kruse, B. Shraiman, G. Süel, members of the laboratory, and especially N. Friedman for discussions. L.C. is supported by the Beckman Fellows Program at Caltech. This work was supported by National Institutes of Health grants R01GM079771 and P50 GM068763 for National Centers of Systems Biology, and the Packard Foundation.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Michael B. Elowitz.

Supplementary information

Supplementary Information

This file contains Supplementary Materials, Supplementary Figures S1-S18 and Supplementary References (PDF 1019 kb)

Supplementary Movie

This file contains a time-lapse fluorescence movie of Crz1-GFP cells with 150 mM Ca2+ added at the beginning of the movie. (MOV 5739 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Cai, L., Dalal, C. & Elowitz, M. Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455, 485–490 (2008). https://doi.org/10.1038/nature07292

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature07292

This article is cited by

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