The Metabolostasis System Regulates the Aggregation and Toxicity of Essential Metabolites

Although metabolites are essential across all branches of life, it has been recently reported that they can form cytotoxic aggregates that resemble those formed by proteins in misfolding diseases. The phenomenon of metabolite aggregation suggests the existence of a metabolite homeostasis (metabolostasis) system capable of maintaining metabolites within a concentration range optimal for cellular function. To investigate this system, using Saccharomyces cerevisiae as a model organism, we identified the critical upper limits of metabolite consumption, beyond which metabolostasis is disrupted, leading to toxicity and growth inhibition. By enforcing a metabolite intake near the upper limits, we monitored the changes at the metabolome, transcriptome, and proteome levels, enabling us to map the metabolostasis system. Among the most affected pathways, we identified oxidative phosphorylation and intracellular membrane trafficking, particularly within the vacuole, which emerges as a containment and detoxification hub for potentially toxic metabolites. Near the upper limits of metabolite consumption, we observed the formation of amyloid-like metabolite aggregates, suggesting that the cytotoxicity is, at least in part, related to the conformational state of the metabolites and, in turn, the physicochemical properties that determine their solubility. Our findings characterize metabolostasis as the cellular system that maintains metabolites within their safe concentration limits and prevents their aberrant accumulation into cytotoxic aggregates. Overall design: In this study, we investigate the metabolostasis system by performing a comprehensive analysis of the cellular responses associated with acute metabolostasis imbalance. Using Saccharomyces cerevisiae as a model system, we report a dose-dependent toxicity of many of the twenty coding amino acids and assess their upper limit for consumption. Our findings demonstrate that overfeeding many of these essential metabolites induces toxicity and growth inhibition, accompanied by significant accumulation of the same metabolites and broad disruptions to the amino acid pool. We further characterize the effects of metabolite overfeeding on transcriptomic and proteomic levels, revealing extensive changes in gene expression, impacting up to a half of the coding genes. We then report that growth inhibition is associated with the formation of amyloid-like aggregates, suggesting a potential mechanism for the observed toxicity.

尽管代谢物在所有生命分支中均发挥必需作用，但近期有研究报道，它们可形成类似错误折叠疾病中蛋白质所形成的细胞毒性聚集体。代谢物聚集现象提示，存在一套代谢物稳态（metabolostasis）系统，能够将代谢物维持在适合细胞功能的浓度范围内。为探究该系统，本研究以酿酒酵母（Saccharomyces cerevisiae）作为模式生物，确定了代谢物消耗的临界上限——超过该上限时，代谢物稳态将被破坏，进而引发毒性与生长抑制。通过使代谢物摄入接近该临界上限，我们监测了代谢组（metabolome）、转录组（transcriptome）与蛋白质组（proteome）水平的变化，得以绘制代谢物稳态系统图谱。在受影响最为显著的通路中，我们发现氧化磷酸化与细胞内膜运输通路，尤其是液泡（vacuole）相关通路——液泡成为了潜在毒性代谢物的隔离与解毒枢纽。在代谢物消耗接近临界上限时，我们观察到淀粉样蛋白样（amyloid-like）代谢物聚集体的形成，这提示细胞毒性至少部分与代谢物的构象状态相关，进而与决定其溶解度的物理化学性质有关。本研究将代谢物稳态定义为一类细胞系统，其功能为将代谢物维持在安全浓度范围之内，并阻止其异常积累形成细胞毒性聚集体。

研究整体设计：本研究通过全面分析急性代谢物稳态失衡相关的细胞应答，探究代谢物稳态系统。以酿酒酵母为模式系统，我们发现20种编码氨基酸中的多数呈现剂量依赖性毒性，并评估了它们的消耗上限。研究结果表明，过量饲喂这些必需代谢物会引发毒性与生长抑制，伴随对应代谢物的显著积累以及氨基酸库的广泛紊乱。我们进一步表征了代谢物过量饲喂对转录组与蛋白质组水平的影响，揭示了基因表达的广泛变化，影响多达半数的编码基因。随后我们发现，生长抑制与淀粉样蛋白样聚集体的形成相关，这为观察到的毒性提供了潜在的作用机制。