Endo-lysosomes are considered acidic Ca2+ stores but direct measurements of luminal Ca2+ within them are limited. Here we report that the Ca2+-sensitive luminescent protein aequorin does not reconstitute with its cofactor at highly acidic pH but that a significant fraction of the probe is functional within a mildly acidic compartment when targeted to the endo-lysosomal system. We leveraged this probe (ELGA) to report Ca2+ dynamics in this compartment. We show that Ca2+ uptake is ATP-dependent and sensitive to blockers of endoplasmic reticulum Ca2+ pumps. We find that the Ca2+ mobilizing messenger IP3 which typically targets the endoplasmic reticulum evokes robust luminal responses in wild type cells, but not in IP3 receptor knock-out cells. Responses were comparable to those evoked by activation of the endo-lysosomal ion channel TRPML1. Stimulation with IP3-forming agonists also mobilized the store in intact cells. Our data reveal a physiologically-relevant, IP3-sensitive store of Ca2+ within the endo-lysosomal system.

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