Computational and experimental dissection of the response of Saccharomyces cerevisiae to inorganic phosphate starvation

Cells grow in complex and dynamic environments. In order to survive, cells must be able to adapt by bring in the proper amounts of nutrients regardless of their extracellular level and form. The response of the budding yeast Saccharomyces cerevisiae to inorganic phosphate starvation serves as a model system for studying this process. I used experimental in vitro data to simulate the rate at which Pho80-Pho85, the central kinase of the phosphate response, phosphorylates Pho4, the transcription factor which controls all phosphate responsive genes. This allowed me to form a testable model about the regulation of Pho4 by Pho80-Pho85 in vivo. The model predicted that three different phosphorylated forms of Pho4 should exist in vivo: a completely phosphorylated form, a completely unphosphorylated form, and a form where the predominate phosphorylation is on only one of the five potential phosphorylation sites. I predicted that changes in the levels of external phosphate concentrations should control which of these three forms of Pho4 would exist in vivo . I experimentally tested this model and found that in fact yeast have three distinct responses to different levels of phosphate in their environment. These three states correlate with the three different predicted phosphorylated forms of Pho4. Comparison of the phosphate response to other homeostatic responses led to a broad but simple model for the core homeostatic network. The model of this core homeostatic network predicts that homeostatic systems respond like damped harmonic oscillators with the ability to respond to any change in environment or intracellular needs without changing the steady-state level of nutrients. This model is robust but evolvable and provides an explanation for many of the additional features of the phosphate response such as an intracellular buffer and low affinity receptors. In total this combined approach of computational and experimental approaches has increased our understanding of the physiology of the response to phosphate starvation.