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

Mol Cell Biol. 2001 Jul;21(13):4347-68. doi: 10.1128/MCB.21.13.4347-4368.2001.


Starvation for amino acids induces Gcn4p, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. In an effort to identify all genes regulated by Gcn4p during amino acid starvation, we performed cDNA microarray analysis. Data from 21 pairs of hybridization experiments 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 of 2 or more in response to histidine starvation imposed by 3-aminotriazole (3AT). Profiling of a gcn4Delta strain and a constitutively induced mutant showed that Gcn4p is required for the full induction by 3AT of at least 539 genes, termed Gcn4p targets. Genes in every amino acid biosynthetic pathway except cysteine and genes encoding amino acid precursors, vitamin biosynthetic enzymes, peroxisomal components, mitochondrial carrier proteins, and autophagy proteins were all identified as Gcn4p targets. Unexpectedly, genes involved in amino acid biosynthesis represent only a quarter of the Gcn4p 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 transcription factors were identified as targets, suggesting that Gcn4p is a master regulator 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, profiling of a gcn4Delta mutant uncovered an alternative induction pathway operating at many Gcn4p target genes in histidine-starved cells.

MeSH terms

  • Amino Acids / biosynthesis*
  • Amino Acids / genetics
  • Amitrole / pharmacology
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Fungal Proteins / genetics
  • Fungal Proteins / metabolism*
  • Gene Expression Profiling*
  • Gene Expression Regulation, Fungal / genetics*
  • Genes, Reporter / genetics
  • Glycogen / metabolism
  • Methyl Methanesulfonate / pharmacology
  • Mitochondria / genetics
  • Mitochondria / metabolism
  • Models, Theoretical
  • Mutagens / pharmacology
  • Oligonucleotide Array Sequence Analysis
  • Peroxisomes / genetics
  • Peroxisomes / metabolism
  • Promoter Regions, Genetic / genetics
  • Protein Kinases / genetics
  • Protein Kinases / metabolism*
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / physiology
  • Saccharomyces cerevisiae Proteins*
  • Trans-Activators / genetics
  • Trans-Activators / metabolism


  • Amino Acids
  • DNA-Binding Proteins
  • Fungal Proteins
  • Mutagens
  • Recombinant Fusion Proteins
  • Saccharomyces cerevisiae Proteins
  • Trans-Activators
  • Glycogen
  • Methyl Methanesulfonate
  • Protein Kinases
  • Amitrole