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Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock

Abstract

Recent advances in measuring gene expression at the single-cell level have highlighted the stochastic nature of messenger RNA and protein synthesis1,2,3. Stochastic gene expression creates a source of variability in the abundance of cellular components, even among isogenic cells exposed to an identical environment. Recent integrated experimental and modelling studies4,5,6,7,8,9,10,11,12,13 have shed light on the molecular sources of this variability. However, many of these studies focus on systems that have reached a steady state and therefore do not address a large class of dynamic phenomena including oscillatory gene expression. Here we develop a general protocol for analysing and predicting stochastic gene expression in systems that never reach steady states. We use this framework to analyse experimentally stochastic expression of genes driven by the Synechococcus elongatus circadian clock. We find that, although the average expression at two points in the circadian cycle separated by 12 hours is identical, the variability at these two time points can be different. We show that this is a general feature of out-of-steady-state systems. We demonstrate how intrinsic noise sources, owing to random births and deaths of mRNAs and proteins, or extrinsic noise sources, which introduce fluctuations in rate constants, affect the cell-to-cell variability. To distinguish experimentally between these sources, we measured how the correlation between expression fluctuations of two identical genes is modulated during the circadian cycle. This quantitative framework is generally applicable to any out-of-steady-state system and will be necessary for understanding the fidelity of dynamic cellular systems.

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Figure 1: Monitoring circadian oscillations in single S. elongatus PCC7942 cells using fluorescence microscopy.
Figure 2: Circadian oscillations in single cells.
Figure 3: A dynamic analysis of stochastic gene expression reveals noise loops.
Figure 4: Cell to cell variability in single- and double-copy-number constructs.

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References

  1. 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  PubMed  Google Scholar 

  2. 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  PubMed  Google Scholar 

  3. 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  PubMed  Google Scholar 

  4. Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D. & van Oudenaarden, A. Regulation of noise in the expression of a single gene. Nature Genet. 31, 69–73 (2002)

    Article  CAS  PubMed  Google Scholar 

  5. Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. Stochastic gene expression in a single cell. Science 297, 1183–1186 (2002)

    Article  ADS  CAS  PubMed  Google Scholar 

  6. Blake, W. J., Kaern, M., Cantor, C. R. & Collins, J. J. Noise in eukaryotic gene expression. Nature 422, 633–637 (2003)

    Article  ADS  CAS  PubMed  Google Scholar 

  7. Raser, J. M. & O’Shea, E. K. Control of stochasticity in eukaryotic gene expression. Science 304, 1811–1814 (2004)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  8. Paulsson, J. Summing up the noise in gene networks. Nature 427, 415–418 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  9. 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  PubMed  Google Scholar 

  10. 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  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  ADS  CAS  PubMed  Google Scholar 

  13. Geva-Zatorsky, N. et al. Oscillations and variability in the p53 system. Mol. Syst. Biol. 2, 0033 (2006)

    Article  PubMed  Google Scholar 

  14. Kondo, T. et al. Circadian rhythms in prokaryotes: luciferase as a reporter of circadian gene expression in cyanobacteria. Proc. Natl Acad. Sci. USA 90, 5672–5676 (1993)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  15. Liu, Y., Golden, S. S., Kondo, T., Ishiura, M. & Johnson, C. H. Bacterial luciferase as a reporter of circadian gene expression in cyanobacteria. J. Bacteriol. 177, 2080–2086 (1995)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Mihalcescu, I., Hsing, W. & Leibler, S. Resilient circadian oscillator revealed in individual cyanobacteria. Nature 430, 81–85 (2004)

    Article  ADS  CAS  PubMed  Google Scholar 

  17. Andersen, J. B. et al. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64, 2240–2246 (1998)

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Andersson, C. R. et al. Application of bioluminescence to the study of circadian rhythms in cyanobacteria. Methods Enzymol. 305, 527–542 (2000)

    Article  CAS  PubMed  Google Scholar 

  19. Xu, Y., Mori, T. & Johnson, C. H. Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC. EMBO J. 22, 2117–2126 (2003)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Thattai, M. & van Oudenaarden, A. Intrinsic noise in gene regulatory networks. Proc. Natl Acad. Sci. USA 98, 8614–8619 (2001)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  21. Swain, P. S., Elowitz, M. B. & Siggia, E. D. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl Acad. Sci. USA 99, 12795–12800 (2002)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  22. Kepler, T. B. & Elston, T. C. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys. J. 81, 3116–3136 (2001)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  23. Becskei, A., Kaufmann, B. B. & van Oudenaarden, A. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nature Genet. 37, 937–944 (2005)

    Article  CAS  PubMed  Google Scholar 

  24. Volfson, D. et al. Origins of extrinsic variability in eukaryotic gene expression. Nature 439, 861–864 (2006)

    Article  ADS  CAS  PubMed  Google Scholar 

  25. Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S. & Elowitz, M. B. Gene regulation at the single-cell level. Science 307, 1962–1965 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Pedraza, J. M. & van Oudenaarden, A. Noise propagation in gene networks. Science 307, 1965–1969 (2005)

    Article  ADS  CAS  PubMed  Google Scholar 

  27. Johnson, C. H. Global orchestration of gene expression by the biological clock of cyanobacteria. Genome Biol. 5, 217 (2004)

    Article  PubMed  PubMed Central  Google Scholar 

  28. Smith, R. M. & Williams, S. B. Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus. Proc. Natl Acad. Sci. USA 103, 8564–8569 (2006)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Vilar, J. M., Kueh, H. Y., Barkai, N. & Leibler, S. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl Acad. Sci. USA 99, 5988–5992 (2002)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  30. Gonze, D., Halloy, J. & Goldbeter, A. Robustness of circadian rhythms with respect to molecular noise. Proc. Natl Acad. Sci. USA 99, 673–678 (2002)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank S. S. Golden and J. L. Ditty for assistance with the initial phase of this work and their gifts of plasmids and strains. We acknowledge I. Lipchin and M. J. T. O’Kelly for assistance with data collection, cloning and bioluminescence measurements. We acknowledge A. Tolonen, S. W. Chisholm, M. Thattai, H. Lim, J. C. Gore and A. Raj for discussions and suggestions. This work was performed in part at the MIT Laser Biomedical Research Center. This work was supported by NSF and NIH grants.

Author Contributions J.R.C. and P.L. performed the experiments. J.M.P. developed the model. J.R.C., .J.M.P. and A.v.O. designed the experiments, interpreted the results and wrote the paper.

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Correspondence to Alexander van Oudenaarden.

Supplementary information

Supplementary Information

This file contains Supplementary experimental and modeling Methods and Materials with Supplementary Figures S1-S2. (PDF 585 kb)

Supplementary Movie 1

This file contains Supplementary Movie 1 demonstrating circadian oscillations in single S. elongatus PCC7942 cells. This file was modified on 31 January 2008 because of the technical difficulties with the file format. (AVI 3601 kb)

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Chabot, J., Pedraza, J., Luitel, P. et al. Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature 450, 1249–1252 (2007). https://doi.org/10.1038/nature06395

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