AbstractAccurate delivery of cargo over long distances through axonal transport requires precise spatiotemporal regulation. Here we discover that Zn2+, either released from lysosomes through TRPML1 or influx via depolarization, inhibits axonal transport. Zn2+-mediated inhibition is neither selective for cargo nor for cell type because elevated Zn2+ (IC50 ≈ 5 nM) reduces both lysosomal and mitochondrial motility in primary rat hippocampal neurons and HeLa cells. We further reveal that Zn2+ directly binds to microtubules and inhibits movement of kinesin motors. Loss of TRPML1 function, which causes Mucolipidosis Type IV (MLIV) disease, impairs lysosomal Zn2+ release, disrupts Zn2+-mediated regulation of axonal transport, and increases overall organellar motility. In addition, MLIV patient mutations in TRPML1 have decreased Zn2+ permeability, which parallels disease severity. Our results reveal that Zn2+ acts as a critical signal to locally pause axonal transport by directly blocking the progression of motor proteins on microtubules.Significance StatementDisruptions in proper axonal transport have been linked to neurodevelopmental and neurodegenerative diseases. Here we discover that activation of the lysosomal channel TRPML1 arrests lysosomal trafficking. Such lysosome self-regulation mechanism is mediated via TRPML1-mediated Zn2+, not Ca2+. We further reveal that Zn2+ acts as a critical brake signal to pause axonal transport locally by directly decorating microtubules and blocking the movement of motor proteins. Dysfunction of TRPML1, the genetic cause of Mucolipidosis type IV (MLIV), blocks lysosomal Zn2+ release, causing loss of fine-tuning of lysosomal motility. Overall, this study implicates the importance of Zn2+ signals and axonal transport in the pathology of MLIV and reveals new signaling roles for Zn2+ in regulating cell processes involved with microtubule-based transport.