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

Abstract

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 Ca 2+ regulate lysosome transport is not well understood. Here, we identify RNF13 as a key regulator of lysosomal positioning via pH i - and Ca 2+ -dependent degradation of ARL8B. Ca 2+ -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 Ca 2+ -bound ALG-2 and inhibition of ARL8B-mediated anterograde transport. Alkaline pH e elevates pH lys and activates the lysosomal Ca 2+ 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 Ca 2+ signaling and pH dynamics in regulating lysosomal positioning.