Mechanism of metabolic control: Target of rapamycin signaling links nitrogen quality to the activity of the Rtg1 and Rtg3 transcription factors

De novo biosynthesis of amino acids uses intermediates provided by the TCA cycle that must be replenished by anaplerotic reactions to maintain the res piratory competency of the cell. Genome-wide expression analyses in Sacchav omyces ceuevisiae reveal that many of the genes involved in these reactions are repressed in the presence of the preferred nitrogen sources glutamine or glutamate. Expression of these genes in media containing urea or ammonia as a sole nitrogen source requires the heterodimeric bZip transcription fa ctors Rtg1 and Rtg3 and correlates with a redistribution of the Rtg1p/Rtg3 complex from a predominantly cytoplasmic to a predominantly nuclear locatio n. Nuclear import of the complex requires the cytoplasmic protein Rtg2, a p reviously identified up-stream regulator of Rtg1 and Rtg3, whereas export r equires the importin-beta -family member Msn5. Remarkably, nuclear accumula tion of Rtg1/Rtg3, as well as expression of their target genes, is induced by addition of rapamycin, a specific inhibitor of the target of rapamycin ( TOR) kinases. We demonstrate further that Rtg3 is a phosphoprotein and that its phosphorylation state changes after rapamycin treatment. Taken togethe r, these results demonstrate that target of rapamycin signaling regulates s pecific anaplerotic reactions by coupling nitrogen quality to the activity and subcellular localization of distinct transcription factors.