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Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system

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Systems and Synthetic Biology

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Abstract

Cellular signaling is key for organisms to survive immediate stresses from fluctuating environments as well as relaying important information about external stimuli. Effective mechanisms have evolved to ensure appropriate responses for an optimal adaptation process. For them to be functional despite the noise that occurs in biochemical transmission, the cell needs to be able to infer reliably what was sensed in the first place. For example Saccharomyces cerevisiae are able to adjust their response to osmotic shock depending on the severity of the shock and initiate responses that lead to near perfect adaptation of the cell. We investigate the Sln1–Ypd1–Ssk1-phosphorelay as a module in the high-osmolarity glycerol pathway by incorporating a stochastic model. Within this framework, we can imitate the noisy perception of the cell and interpret the phosphorelay as an information transmitting channel in the sense of C.E. Shannon’s “Information Theory”. We refer to the channel capacity as a measure to quantify and investigate the transmission properties of this system, enabling us to draw conclusions on viable parameter sets for modeling the system.

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Notes

  1. This is believed to happen between dimerized Sln1 molecules as kind of an exchange instead of intra-molecular (Qin et al. 2000).

  2. Numbers taken from “http://www.yeastgenome.org/”.

  3. In our model, this enabled us to choose the shuttling rate \(k_3\) in a non restrictive but computationally more efficient manner.

  4. The related Boltzmann entropy as used in statistical physics for example sets \(K=k_{B}\) (the Boltzmann constant) and employs the natural logarithm \(\log _{e}.\)

  5. Note that this is symmetric by definition.

  6. “Fidelity” in this sense refers to a measure on how accurate the signaling can reproduce the input signal.

  7. This input being a percentage of the auto-phosphorylation rate \(k_1\) of Sln1, depending on the stress level.

  8. In the extreme case with 1 bit.

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Acknowledgments

This work has been funded by the DFG (Deutsche Forschungsgemeinschaft, GRK 1772 “Computational Systems Biology”).

Conflict of interest

The authors declare that they have no conflict of interest.

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Correspondence to Edda Klipp.

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Uschner, F., Klipp, E. Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system. Syst Synth Biol 8, 297–306 (2014). https://doi.org/10.1007/s11693-014-9146-6

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  • DOI: https://doi.org/10.1007/s11693-014-9146-6

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