Dimensionality and the Stress/Growth Axis of Gene Expression in S. cerevisiae
To thrive in different circumstances cells tightly regulate and tune gene expression to optimize their protein complement to the environment. Understanding and manipulating this regulation is an apparently intractable goal as even budding yeast has more than 6000 genes. Even from the perspective of the organism, achieving precise control over the expression of every gene would amount to an enormous and perhaps impossible burden. Instead organisms regulate genes in large groups, activating suites of genes required for stress resistance or growth on alternative carbon sources. In this work we show that by measuring gene expression in single cells in high throughput using yeast genetics and the GFP library it is possible to define expression `regulons' which describe the functional arrangement of the budding yeast exome. From this analysis we focused on one particular axis of gene expression which regulates the transition from growth to stress resistance and is regulated by the Protein Kinase A (PKA) pathway. We show that the PKA and two of the transcription factors it regulates, Msn2/4, respond in a graded manner to a range of stresses and that demonstrate that this graded response is due to negative feedback regulation in the PKA network and unsaturated non-cooperative association of Msn2/4 with its target promoters. These features allows for co-linear activation of target genes, maintaining stoichiometry within the Msn2/4-responsive program across a wide range of conditions. In addition, we find that under different environmental conditions PKA shows distinct dynamic behaviors at the single cell level ranging from steady state activation to pseudo-oscillatory regimes. We observe that Msn2 faithfully follows these dynamics, whereas other PKA regulated transcription factors do not, suggesting a mechanism by which the PKA regulatory circuit may specifically activate subsets of regulated genes in response to different conditions.