Many cells growing in high glucose repress mitochondrial respiration, as observed in the Crabtree and Warburg effects. A parsimonious biochemical explanation for this phenomenon is missing. Using a Saccharomyces cerevisiae screen, we identified the conserved deubiquitinase Ubp3 (Usp10), as necessary for proper mitochondrial repression. Ubp3 mutants have increased mitochondrial activity despite abundant glucose, with downregulated glycolytic enzymes, rewired glucose metabolism, and increased trehalose. Utilizing ∆ubp3 cells, along with orthogonal approaches, we find that the Crabtree effect is driven mechanistically by controling mitochondrial access of inorganic phosphate (Pi), as determined by glycolytic flux. High glycolytic flux consumes free Pi, limiting available Pi for entry into the mitochondria. Cytosolic Pi-dependent mitochondrial Pi entry is necessary and sufficient to derepress mitochondria, driving synchronous requirements to sustain mitochondrial activity. Restricting Pi entry to the mitochondria prevents mitochondrial derepression. Collectively, we propose a biochemical basis of mitochondrial repression in high-glucose based on intracellular Pi budgeting.

Cells require disparate amounts of distinct amino acids, which themselves have discrete biosynthetic costs. However, it remains unclear if and how cells respond differently to their scarcity. To explore this, we re-organized amino acids into distinct groups based on their metabolic origins. Subsequently, using yeast we assessed responses to transient disruptions in amino acid supply, and uncover diverse restoration responses for distinct amino acids. Cells hierarchically prioritize restoring glutamate-, sulfur-, pentose-phosphate- and pyruvate-derived amino acids. Particularly, the strongest response is to the glutamate-derived amino acid arginine. We find that the extent and priority of the restoration response is determined by the composite demand for an amino acid, coupled with low individual biosynthetic costs of that amino acid. We propose that cells employ a conserved strategy guided by the law of demand, to prioritize amino acids restoration upon transient limitation.