RNF13 mediates pH- and Ca²⁺-dependent regulation of lysosomal positioning

Environmental factors such as extracellular pH (pH_e) and nutrition status affect lysosomal localization and autophagy, but how pH_e, intracellular pH (pH_i), and Ca²⁺ regulate lysosome transport is not well understood. Here, we identify RNF13 as a key regulator of lysosomal positioning via pH_i- and Ca²⁺-dependent degradation of ARL8B. Ca²⁺-activated apoptosis-linked gene 2 (ALG-2) promotes retrograde lysosomal transport while increasing pH_i and decreasing lysosomal pH (pH_lys). Elevated pH_i deprotonates RNF13 at His332, enabling its interaction with Ca²⁺-bound ALG-2 and inhibition of ARL8B-mediated anterograde transport. Alkaline pH_e elevates pH_lys and activates the lysosomal Ca²⁺ channel TRPML3, enhancing RNF13 activity and driving lysosomes toward a perinuclear position. Thus, starvation or alkaline pH_e induces ALG-2 activation and pH_i elevation, facilitating RNF13-mediated ARL8B degradation. In contrast, acidic pH_i suppresses RNF13, keeping ARL8B levels high even when ALG-2 is active. These findings reveal a coordinated mechanism involving Ca²⁺ signaling and pH dynamics in regulating lysosomal positioning.