mTORC1/AMPK responses define a core gene set for developmental cell fate switching

The kinases mTORC1 and AMPK are at the nexus of nutrient responses and control of cellular growth. However, responses to nutrient loss are complex and affect multiple transcriptional pathways. We are interested in the mTORC1-directed regulation of transcription networks that specifically regulate developmental decisions. Dictyostelium grow logarithmically as single cells in nutrient-rich media, but, upon nutrient withdrawal, growth ceases and cells enter a program for multi-cellular development. Within 30 minutes of starvation, >4,000 genes show significant (p<0.05) changes in gene expression patterns. However, we hypothesize that not all these gene changes are required for development and that many expression changes reflect stress response to a media shift supplementary to nutrient loss, apart from developmental effects. We, thus, sought ways to promote development in the absence of nutrient loss, to better focus on developmentally essential gene sets. Since kinases mTORC1 and AMPK function as nutrient and energy sensors, we first examined their relative activities in Dictyostelium during phases of rapid growth and starvation-induced development. We found that these kinases exhibited reciprocal patterns of activation under various conditions. With this knowledge, we identified rich media conditions that permitted rapid cell growth, but a growth/development switch upon the directed and reciprocal inactivation/activation of mTORC1/AMPK. Examination of gene expression under conditions of development in nutrient-rich media indicated that changes in expression of most starvation-regulated genes were not required for development. Our data suggest that the up-regulation of ~300 genes defines essential early signaling pathways for developmental induction, integrating cAMP/PKA circuitries and including many unclassified genes. We compared Dictyostelium discoideum gene expression by deep RNA-seq under conditions of stavation and rapamycin-induced development in nutrient-rich media and identify an extensive gene network involved in developmental signal transduction that is upregulated by both starvation and rapamycin and separate downregulated gene classes involved in protein synthesis and in DNA replication and cell division.