Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins

TLDR

Rapamycin blocks Tor1p/Tor2p, triggering nutrient‑deprivation responses via translational arrest, while poor nitrogen quality activates the Ure2p/Gln3p‑controlled nitrogen‑discrimination pathway. The study measured the immediate transcriptional response of yeast to rapamycin to probe the direct effects of Tor proteins on nutrient‑sensitive signaling pathways. The authors used genome‑wide transcriptional profiling and biochemical assays to delineate Tor‑regulated pathways in rapamycin‑treated yeast. Tor proteins directly regulate glucose activation, nitrogen discrimination, and diauxic‑shift pathways (glycolysis and citric‑acid cycle), but not general amino‑acid control, nitrogen starvation, or sporulation pathways, and rapamycin‑induced Tor inhibition increases Ure2p mobility.

Abstract

The immunosuppressant rapamycin inhibits Tor1p and Tor2p (target of rapamycin proteins), ultimately resulting in cellular responses characteristic of nutrient deprivation through a mechanism involving translational arrest. We measured the immediate transcriptional response of yeast grown in rich media and treated with rapamycin to investigate the direct effects of Tor proteins on nutrient-sensitive signaling pathways. The results suggest that Tor proteins directly modulate the glucose activation and nitrogen discrimination pathways and the pathways that respond to the diauxic shift (including glycolysis and the citric acid cycle). Tor proteins do not directly modulate the general amino acid control, nitrogen starvation, or sporulation (in diploid cells) pathways. Poor nitrogen quality activates the nitrogen discrimination pathway, which is controlled by the complex of the transcriptional repressor Ure2p and activator Gln3p. Inhibiting Tor proteins with rapamycin increases the electrophoretic mobility of Ure2p. The work presented here illustrates the coordinated use of genome-based and biochemical approaches to delineate a cellular pathway modulated by the protein target of a small molecule.