Intracellular sphingolipid sorting drives membrane phase separation in the yeast vacuole

Abstract The yeast vacuole membrane can phase separate into ordered and disordered domains, a phenomenon that is required for micro-lipophagy under nutrient limitation. Here we report that sorting of sphingolipids (SLs) into the vacuole membrane controls this process. We first developed a vacuole isolation method to identify lipidome changes during the onset of phase separation in early stationary stage cells. We found that phase separated vacuoles are characterized by increases in lipid raft-forming components not found in the whole cell, including a dramatic change in SL composition. Sorting of both SLs and ergosterol into the vacuole membrane is dependent on Npc2, the yeast homologue of the Niemann-Pick Type C2 lipid transporter. Genetic dissection of SL biosynthesis revealed that the composition of vacuole SLs modulates membrane phase separation and micro-lipophagy under glucose restriction. These results show that lipid trafficking can drive membrane phase separation in vivo and identify SLs as key mediators of this process in yeast.