Cell cycle-linked vacuolar pH dynamics regulate amino acid homeostasis and cell growth

Amino acid homeostasis is critical for many cellular processes. It is well established that amino acids are compartmentalized using pH gradients generated between organelles and the cytoplasm; however, the dynamics of this partitioning has not been explored. We have developed a highly sensitive pH reporter, and we find that the major amino acid storage compartment in Saccharomyces cerevisiae, the lysosome-like vacuole, alkalinizes prior to cell division and re-acidifies as cells divide. The vacuolar pH dynamics require the uptake of extracellular amino acids and activity of TORC1, the v-ATPase and the cycling of the vacuolar specific lipid, PI3,5P2 which is regulated by the cyclin-dependent kinase, CDK5/Pho85. Vacuolar pH regulation enables amino acid sequestration and mobilization from the organelle, which is important for mitochondrial function, ribosome homeostasis and cell size control. Collectively, our data provide a new paradigm for the use of dynamic pH-dependent amino acid compartmentalization during cell growth/division. duplicate cultures wild-type, atg18∆, fab1∆ and vph1∆ S. cerevisiae cells were grown in synthetic defined media containing dextrose, yeast nitrogen base and amino acids (SDC) to early log-phase. Experiment was repeated on two different days to give 4 samples per cell line.