ELife assessment: Inositol pyrophosphate dynamics reveals control of the yeast PHO starvation program through 1,5-IP8 and the SPX domain of Pho81

Abstract

Eukaryotic cells control cytosolic inorganic phosphate to balance its role as essential macronutrient with its negative bioenergetic impacts. Phosphate homeostasis depends on a conserved signaling pathway including inositol pyrophosphates (PP-IPs) and SPX receptor domains. Since cells synthesize various PP-IPs and SPX domains bind them promiscuously, it is unclear whether a specific PP-IP regulates SPX domains in vivo, or whether multiple PP-IPs act as a pool. In contrast to previous models, which postulated that phosphate starvation is signaled by increased 1-IP7 production, we now show that the levels of all detectable PP-IPs of yeast, 1-IP7, 5-IP7 and 1,5-IP8, strongly decline upon phosphate starvation. Among these, specifically the decline of 1,5-IP8 triggers the transcriptional phosphate starvation response, the PHO pathway. 1,5-IP8 inactivates the cyclin-dependent kinase inhibitor Pho81 through its SPX domain. This stimulates the cyclin-dependent kinase Pho85/Pho80 to phosphorylate the transcription factor Pho4 and repress the PHO pathway. Combining our results with observations from other systems we propose a unified model where 1,5-IP8 signals cytosolic phosphate abundance to SPX proteins in fungi, plants, and mammals. Its absence triggers starvation responses.Cytosolic Pi is of prime importance for cellular bioenergetics because Pi influences free energy of nucleotide hydrolysis and the metabolite fluxes through glycolysis and oxidative phosphorylation. Eukaryotic cells signal Pi via SPX domains binding critical ligands, inositol pyrophosphates (IP7, IP8), which control Pi homeostasis through a network of target proteins that import, export, store or detoxify Pi. Studies with different systems failed to yield a coherent model on this regulation.We performed the first time-resolved profiling of the full isomer spectrum of inositol pyrophosphates and dissected the isomer that is relevant to intracellular Pi signaling. Our results support a unified model of Pi signaling across all eukaryotic kingdoms, which is in accord with the fundamental importance of Pi management for metabolism.