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

Abstract

How cells manage biomolecule supply to enable constructive metabolism for growth is a fundamental question. Methionine directly activates genomic programs where translation and metabolism are induced. In otherwise amino acid limitations, methionine induced ribosomal biogenesis, carbon metabolism, amino acid and nucleotide biosynthesis. Here, we find that the methionine--induced anabolic program is carbon--source independent, and requires the 'starvation-responsive' transcription factor Gcn4/ATF4. Integrating transcriptome and ChIP--Seq analysis, we decipher direct and indirect, methionine--dependent roles for Gcn4. Methionine--induced genes enabling metabolic precursor biosynthesis critically require Gcn4; contrastingly ribosomal genes are partly repressed by Gcn4. Gcn4 binds promoter--regions and transcribes a subset of metabolic genes, driving amino acid (particularly lysine and arginine) biosynthesis. This sustained lys/arg supply maintains high translation capacity, by allowing the translation of lys/arg enriched transcripts, notably the translation machinery itself. Thus, we discover how Gcn4 enabled metabolic--precursor supply bolsters protein synthesis demand, and drive a methionine--mediated anabolic program.

Methylated PP2A stabilizes Gcn4 to enable a methionine-induced anabolic program

“…Using a strain in which a C-terminal hemagglutinin (HA) tag was inserted at the chromosomal GCN4 locus, we measured steady state levels of Gcn4 protein after a shift from RM to MM. As observed earlier (14,22), Gcn4 levels were high only in cells shifted from robust growth conditions (RM) to methionine supplemented medium (MM+Met), in contrast to cells shifted to medium with no amino acids (MM) ( Figure 1C), or even with all non sulphur amino acids supplemented except tyrosine (MM+nonSAA), as shown earlier (14). This reiterated the above stated paradox; when methionine is abundant, global translation increases, but Gcn4 amounts are strongly induced as well.…”

“…Consequently, Gcn4/ATF4 is annotated as a marker of the cellular amino acid starvation response. Paradoxically, our earlier findings (14,22) are noteworthy because Gcn4 was critical in a context of high growth and proliferation, rather than survival, when methionine alone was supplemented. Therefore, in such a context of increased proliferation, what signaling processes control Gcn4 induction?…”

“…In yeast cells growing in overall amino acid limited conditions, supplementing methionine drives a transcriptional and metabolic growth program (14,22). Methionine transcriptionally and functionally induces rate-limiting reactions in amino acid biosynthesis, leading to enhanced amino acid and nucleotide pools (14).…”

“…While dissecting the anabolic program that methionine controls, we had unexpectedly uncovered a critical role for Gcn4 (14,22). Gcn4 is a transcription factor that has been best studied as an activator of amino acid biosynthetic genes during severe amino acid starvation, to restore intracellular amino acid homeostasis (24)(25)(26)(28)(29)(30).…”

“…The addition of methionine induces the expression of genes involved in translation and ribosomal biogenesis, as well as key metabolic reactions, primarily the pentose-phosphate pathway, glutamine synthesis, and amino acid and nucleotide biosynthesis. In short, addition of methionine switched cells to an anabolic state and enabled efficient assimilation and utilization of available carbon and nitrogen sources, resulting in increased amino acid and nucleotide biosynthesis required for growth (14,22). Surprisingly, in order to sustain the growth program, cells required the activity of what is primarily considered a starvation/survival response factor, Gcn4, to balance metabolism with translation (22).…”