TORC1 autonomously controls its spatial partitioning via the Rag GTPase tether Tco89

The eukaryotic target of rapamycin complex 1 (TORC1) kinase is a homeostatic regulator of growth, integrating nutritional cues at the endolysosomal compartment. Amino acids activate mammalian TORC1 (mTORC1) through the Rag GTPases that recruit it to lysosomes via a short domain within the mTORC1 subunit Raptor. Intriguingly, this “Raptor claw” domain is absent in Kog1, the Raptor ortholog in yeast. Instead, as we show here, yeast utilizes the fungal-specific Tco89 to tether TORC1 to active Rag GTPases. This interaction enables TORC1 to precisely calibrate the activity of the S6K1-related effector kinase Sch9 in response to amino acid availability. TORC1 stabilizes Tco89 by phosphorylation, and its inactivation causes swift Tco89 proteolysis, provoking a redistribution of TORC1 from the vacuole to signaling endosomes and its spatial separation from Sch9. Thus, TORC1 not only operates in spatially distinct subcellular pools but also controls its own quantitative distribution between these pools to economize energy resources under fluctuating nutrient conditions.