Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program

• Published in: PLoS genetics 2020-12, Vol.16 (12), p.e1009252-e1009252
• Main Authors: Srinivasan, Rajalakshmi, Walvekar, Adhish S, Rashida, Zeenat, Seshasayee, Aswin, Laxman, Sunil
• Format: Article
• Language: English
• Subjects: Amino acids; Basic-Leucine Zipper Transcription Factors - genetics; Basic-Leucine Zipper Transcription Factors - metabolism; Biology and Life Sciences; Biosynthesis; Brewer's yeast; Carbon; Cell growth; Cell Proliferation; Control; Funding; Gene expression; Gene Expression Regulation, Fungal; Gene Regulatory Networks; Genetic aspects; Genetic research; Genome, Fungal; Genomes; Growth; Kinases; Mammals; Metabolism; Metabolites; Microbial growth; Observations; Physical Sciences; Physiological aspects; Protein biosynthesis; Proteins; Research and Analysis Methods; Ribosomes - genetics; Ribosomes - metabolism; Roles; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Transcription; Transcription factors; Transcriptional Activation
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1009252

Growth and starvation are considered opposite ends of a spectrum. To sustain growth, cells use coordinated gene expression programs and manage biomolecule supply in order to match the demands of metabolism and translation. Global growth programs complement increased ribosomal biogenesis with sufficient carbon metabolism, amino acid and nucleotide biosynthesis. How these resources are collectively managed is a fundamental question. The role of the Gcn4/ATF4 transcription factor has been best studied in contexts where cells encounter amino acid starvation. However, high Gcn4 activity has been observed in contexts of rapid cell proliferation, and the roles of Gcn4 in such growth contexts are unclear. Here, using a methionine-induced growth program in yeast, we show that Gcn4/ATF4 is the fulcrum that maintains metabolic supply in order to sustain translation outputs. By integrating matched transcriptome and ChIP-Seq analysis, we decipher genome-wide direct and indirect roles for Gcn4 in this growth program. Genes that enable metabolic precursor biosynthesis indispensably require Gcn4; contrastingly ribosomal genes are partly repressed by Gcn4. Gcn4 directly binds promoter-regions and transcribes a subset of metabolic genes, particularly driving lysine and arginine biosynthesis. Gcn4 also globally represses lysine and arginine enriched transcripts, which include genes encoding the translation machinery. The Gcn4 dependent lysine and arginine supply thereby maintains the synthesis of the translation machinery. This is required to maintain translation capacity. Gcn4 consequently enables metabolic-precursor supply to bolster protein synthesis, and drive a growth program. Thus, we illustrate how growth and starvation outcomes are both controlled using the same Gcn4 transcriptional outputs that function in distinct contexts.