非典型磷酸甘油酸脫氫酶調控溶酶體的生合成

Abstract

磷酸甘油酸脫氫酶（PHGDH）在傳統上被視為一種參與絲胺酸（serine）新生合成的代謝酵素，且已有研究指出其透過典型與非典型功能參與癌症調控。在本研究中，我們發現PHGDH具有一項先前未被揭示的非典型功能，即在不依賴其代謝活性的情況下，參與溶酶體（lysosome）生合成的調控。當PHGDH被剔除時，轉錄因子EB（TFEB）與轉錄因子E3（TFE3）發生核移位（nuclear translocation），進而促使溶酶體與自噬相關基因表現上升、蛋白質表現量增加，並導致溶酶體體積膨大。這些變化無法透過補充絲胺酸逆轉，卻可由失去酵素活性的PHGDH突變體所挽救，進一步支持此作用為一種與代謝功能無關的非典型機制。此外，PHGDH的剔除亦會降低mTOR活性，顯示在正常情況下，PHGDH可能透過維持mTOR訊號傳導，使TFEB與TFE3滯留於細胞質中。為進一步釐清其功能機制，我們進行蛋白質結構域的鑑定，並透過結構域剔除實驗發現，SUB2與REG結構域對於PHGDH調控溶酶體生合成至關重要。缺失任一結構域皆會損害PHGDH的溶酶體定位能力，並導致TFEB與TFE3進入細胞核，以及溶酶體膨大等表徵。本研究揭示了PHGDH在溶酶體生合成中的一項新穎且非典型的功能，該功能獨立於其代謝活性，拓展了我們對PHGDH生理角色的理解。

Phosphoglycerate dehydrogenase (PHGDH) is traditionally known for its metabolic role in de novo serine biosynthesis and has been implicated in cancer regulation through both canonical and non-canonical functions. In this study, we identify a novel role of PHGDH in regulating lysosome biogenesis independently of its metabolic activity. PHGDH depletion induces nuclear translocation of the transcription factors TFEB and TFE3, resulting in elevated expression of lysosome- and autophagy-related genes, increased protein levels, and lysosomal enlargement. These changes are not reversed by serine supplementation and are rescued by catalytically inactive PHGDH mutants, supporting a non-metabolic mechanism. Additionally, PHGDH depletion reduces mTOR activity, suggesting that PHGDH may sustain mTOR signaling to retain TFEB and TEF3 in the cytoplasm under normal conditions. Further analysis using domain-deletion mutants reveals that the SUB2 and REG domains are critical for PHGDH’s function in lysosome biogenesis. Specifically, loss of either domain impairs PHDGH’s lysosomal localization and its ability to prevent TFEB and TFE3 nuclear translocation and lysosomal enlargement. These findings uncover a previously unrecognized role for PHGDH in the regulation of lysosome biogenesis independent of its canonical metabolic function.