Stress-induced metabolite release creates an ecological and evolutionary opportunity for restoring growth regulation

Abstract

Nutrient sensing is a fundamental component of eukaryote survival. In order to convert environmental stimuli to a proper physiological response, many systems like the budding yeast Saccharomyces cerevisiae, rely on tight regulation by complexes such as TOR. Yeast, when starved for natural nutrients such as glucose, repress TOR signaling and undergo a quiescence phenotype. However, when yeasts are made auxotrophic for certain compounds, like the amino acid lysine, this ‘unnatural’ nutrient limitation is not properly regulated: cells continue to waste glucose and rapidly decrease in viability. This differential response in to different types of nutrient limitation (‘natural’ vs ‘unnatural’) suggest differing evolutionary pressures to properly maintain adequate nutrient sensing. To study how cells could adapt to an ‘unnatural’ nutrient limitation, I evolved a lysine auxotroph of S. cerevisiae under lysine limitation. As expected, many strains had gained mutations that increased the affinity for lysine. However, I found that a significant percentage of my clones had become auxotrophic for metabolites (organosulfur and glutamine) that had not been supplied exogenously. The nature of these autotrophies was suggestive the reemergence of TOR-regulated metabolite sensing, as these classes of metabolites have previously been shown to interact with TOR and other similar effectors. To understand how this was possible for the nascent organosulfur auxotrophs, I first used a combination of phenotypic assays and metabolomics to determine that live lysine-requiring cells when limited for lysine release glutathione in a stress-dependent manner. New organosulfur auxotrophs, when supported by this emergent pool of glutathione, were able to rise to high frequencies through a negative frequency dependent fitness benefit compared to organosulfur prototrophs. This adaptive benefit appears to be due to enhanced survival under lysine limitation, mediated through the regaining of TOR signaling, as the removal of a downstream process, autophagy, significantly diminishes the survival phenotype. This study demonstrates the cells can generate their own ecological pressures which may in turn drive the emergence of novel metabolic strategies, a finding with consequences both at the cellular and community level.