TOR inhibition drives accumulation of amino acids through transcriptional activation in algae

Cellular homeostasis is maintained by the balance between energy production and breakdown and is fundamental to all forms of life. The conserved, ancient target of rapamycin (TOR) kinase is a central metabolic regulator in eukaryotes that integrates carbon and nitrogen to maintain homeostasis and promote growth and development through protein synthesis. While TOR regulatory mechanisms of amino acid accumulation are well known in yeast and mammals, they remain unknown in photosynthetic organisms. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler model system for understanding TOR function. Multiomics experiments showed that TOR inhibition leads to an increase in amino acid levels independent of hexokinase-mediated glucose signaling. We observed upregulation of selective amino acid biosynthesis pathways at the transcript and protein levels as potential mechanisms driving the increase in amino acids. Transcriptomics and proteomics experiments identified a basic helix-loop-helix (bHLH) transcription factor with rapid upregulation during TOR inhibition. DAP-seq analysis demonstrated that bHLH can bind directly to the promoters of amino acid biosynthesis genes, potentially regulating their transcription in response to TOR inhibition. We found high conservation of the bHLH-binding motif in the genomes of other green algae and plants, suggesting a conserved regulatory mechanism for amino acid biosynthesis across Viridiplantae. Phosphoproteomics experiments also revealed novel conserved targets that are not currently recognized as part of the TOR pathway. Altogether, our findings elucidate the transcriptional regulation of amino acid metabolism and explain how TOR regulates nitrogen metabolism to support growth and development in photosynthetic organisms. Significance StatementCarbon and nitrogen metabolism play key roles in enhancing plant yield and reducing fertilizer use. Thus, improving nitrogen utilization can significantly boost crop productivity and algal biotechnology. From yeast to plants to mammals, the protein target of rapamycin (TOR) kinase is an essential metabolic regulator. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler system to study conserved mechanisms in TOR signaling. Using a multiomics approach, we showed transcriptional regulation of amino acid accumulation upon TOR inhibition and identified a transcription factor with evolutionarily conserved DNA binding sites in nitrogen metabolism genes. We also discovered novel conserved targets of TOR. Our study demonstrates the role of TOR in regulating nitrogen metabolism to support growth and development in photosynthetic organisms.