Reconstructing The S. Cerevisiae Growth Control Network In Stress Conditions

Abstract

To thrive when conditions are favorable and survive when they are stressful, cells must carefully regulate their growth rate and stress response programs. This requires rapid, coordinated regulation of many genes in response to information about the levels of numerous nutrients and stress conditions. We are beginning to understand how, in eukaryotes, the TORC1 and PKA pathways regulate growth in nutrient rich conditions. However, how cells tune growth and stress responses in suboptimal conditions is largely unknown. To address this, we ran screens to begin reconstructing the growth regulation network in stress conditions. We found many novel regulators, including signaling proteins, components of the vacuolar ATPase, transcription factors, and components of the endomembrane system. In order to place these regulators in the TORC1 pathway, we performed follow up experiments on over 300 of these regulators using the TORC1 inhibitor rapamycin. We were able to place many new components in the TORC1 pathway, including 59 genes that act downstream of TORC1. We were particularly interested in the discovery that Vip1, a conserved inositol pyrophosphate kinase, was necessary for the shutdown of hundreds of growth genes in stress and starvation conditions. In subsequent experiments, we learned that the inositol pyrophosphate second messengers (including 1-PP-IP5, 5-PP-IP4, and 5-PP-IP5) are critical regulators of cell growth and the general stress response, acting in parallel to the TORC1 pathway to control the activity of the class I HDAC Rpd3L. Taken together, this work reveals many new regulators of cell growth and shows how delineation of one such regulator uncovered a global role for a little known family of second messengers.