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Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast

Nature Genetics volume 38, pages 1082–1087 (2006)Cite this article

Abstract

Transcriptional noise is known to be an important cause of cellular heterogeneity and phenotypic variation. The extent to which molecular interaction networks may have evolved to either filter or exploit transcriptional noise is a much debated question. The yeast genetic network regulating galactose metabolism involves two proteins, Gal3p and Gal80p, that feed back positively and negatively, respectively, on GAL gene expression. Using kinetic modeling and experimental validation, we demonstrate that these feedback interactions together are important for (i) controlling the cell-to-cell variability of GAL gene expression and (ii) ensuring that cells rapidly switch to an induced state for galactose uptake.

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Figure 1: Schematic of the GAL network.
Figure 2: Reporter response to galactose induction.
Figure 3: Fluorescence distributions over time for mutant and wild-type cells pre-grown on 2% raffinose and introduced to 0.1% galactose.
Figure 4: Population heterogeneity of reporter expression.
Figure 5: Simulation results showing the steady-state dose-response of four strains: wild-type, mutant (both GAL3 and GAL80 feedback loops disabled), GAL3 feedback loop disabled and GAL80 feedback loop disabled.

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Acknowledgements

We thank D. Hwang for helpful advice on the statistical analysis, H. Kostner for assistance with the QPCR experiments and E. Schweighofer for assistance with the cluster computing infrastructure. This work was supported in part by grants from the US National Institutes of Health (GM076547, GM067228).

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Authors and Affiliations

  1. Institute for Systems Biology, 1441 N 34th Street, Seattle, 98103, Washington, USA

    Stephen A Ramsey, Jennifer J Smith, David Orrell, Marcello Marelli, Timothy W Petersen, Pedro de Atauri, Hamid Bolouri & John D Aitchison

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  1. Stephen A Ramsey
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  2. Jennifer J Smith
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Contributions

S.A.R., J.J.S., D.O., H.B. and J.D.A. designed the study. J.J.S., M.M. and T.W.P. carried out the experimental validation. S.A.R., D.O. and P.A. performed the modeling and simulations. S.A.R., J.J.S., H.B. and J.D.A. wrote the paper.

Corresponding authors

Correspondence to Hamid Bolouri or John D Aitchison.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Control experiments. (PDF 70 kb)

Supplementary Fig. 2

Analytic model of galactose import. (PDF 25 kb)

Supplementary Fig. 3

Simulated distribution of the number of molecules of Gal80p homodimer within the nucleus, for a cell population of wild-type and mutant strains grown on raffinose (noninducing media). (PDF 42 kb)

Supplementary Fig. 4

Steady-state galactose dose-response. (PDF 63 kb)

Supplementary Fig. 5

Simulated growth of wild-type and mutant strains on alternating galactose and raffinose media. (PDF 55 kb)

Supplementary Table 1

Fractional activity level of the reporter at 6 h, for the wild-type and mutant strains on different initial concentrations of galactose. (PDF 10 kb)

Supplementary Table 2

Oligonucleotide primers used in strain construction and in QPCR measurement of GAL3 and GAL80 expression levels. (PDF 18 kb)

Supplementary Note (PDF 105 kb)

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Ramsey, S., Smith, J., Orrell, D. et al. Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet 38, 1082–1087 (2006). https://doi.org/10.1038/ng1869

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