Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast

Starvation for amino acids induces Gcn4p, a transcriptional activator of am ino acid biosynthetic genes in Saccharomyces cerevisiae. In an effort to id entify all genes regulated by Gcn4p during amino acid starvation, we perfor med cDNA microarray analysis. Data from 21 pairs of hybridization experimen ts using two different strains derived from S288c revealed that more than 1 ,000 genes were induced, and a similar number were repressed, by a factor o f 2 or more in response to histidine starvation imposed by 3-aminotriazole (3AT). Profiling of a gcn4 Delta strain and a constitutively induced mutant showed that Gcn4p is required for the full induction by 3AT of at least 53 9 genes, termed Gcn4p targets. Genes in every amino acid biosynthetic pathw ay except cysteine and genes encoding amino acid precursors, vitamin biosyn thetic enzymes, peroxisomal components, mitochondrial carrier proteins, and autophagy proteins were all identified as Gcn4p targets. Unexpectedly, gen es involved in amino acid biosynthesis represent only a quarter of the Gcn4 p target genes. Gcn4p also activates genes involved in glycogen homeostasis , and mutant analysis showed that Gcn4p suppresses glycogen levels in amino acid-starved cells. Numerous genes encoding protein kinases and transcript ion factors were identified as targets, suggesting that Gcn4p is a master r egulator of gene expression. Interestingly, expression profiles for 3AT and the alkylating agent methyl methanesulfonate (MMS) overlapped extensively, and MMS induced GCN4 translation. Thus, the broad transcriptional response evoked by Gcn4p is produced by diverse stress conditions. Finally, profili ng of a gcn4 Delta mutant uncovered an alternative induction pathway operat ing at many Gcn4p target genes in histidine-starved cells.