Cells adapt to extracellular acidic pH through TM9SF3-mediated PI(4,5)P2 flop

The plasma membrane (PM), a physical barrier separating cells from their environment, responds to fluctuating extracellular environment through receptor-mediated signaling. While these pathways have been extensively studied, the role of PM lipids remains poorly understood. Here, we show that phosphatidylinositol 4,5-bisphosphate (PIP2), a multifunctional phospholipid, translocates from the inner to the outer leaflet of the PM in response to extracellular acidification. A genome-wide screening identifies Transmembrane 9 superfamily 3 (TM9SF3) as a critical regulator for PIP2 translocation. During zebrafish gastrulation, when intracellular pH increases and extracellular interstitial fluid pH decreases, mutant anterior axial mesoderm lacking Tm9sf3 exhibits disorganized collective cell migration due to impaired PIP2-dependent cytoskeletal organization. Our results demonstrate that TM9SF3 mediates the PIP2 translocation when cells encounter a low pH for adapting the cells to their environment. Given that “pH-dependent PIP2 translocation” is evolutionarily conserved, cells may broadly employ lipid topology as a strategy to respond to extracellular stimuli.