Asymmetric distribution of mitochondrial Ca ²⁺ regulators specifies compartment-specific mitochondrial function and neuronal development

Neuronal polarization is essential for functional compartmentalization, enabling dendritic synaptic integration and axonal action potential generation. While structural differences in mitochondria across compartments have been identified, their functional distinctions remain unclear. Here, we uncovered compartment-specific mitochondrial Ca ²⁺ dynamics and their molecular determinants. In axonal mitochondria, Ca ²⁺ uptake through MCU occurs independently of ER-stored Ca ²⁺ release, with faster matrix Ca ²⁺ clearance than dendritic mitochondria, where Ca ²⁺ uptake predominantly originates from ER Ca ²⁺ . The ER-independent mitochondrial Ca ²⁺ uptake in axonal mitochondria is mediated by enriched MCU-regulating proteins, MICU1 and MICU2, while higher NCLX expression facilitates rapid Ca ²⁺ clearance. Moreover, NCLX knockdown, which functionally mimics a mental retardation-associated mutation, caused more significant axonal branching defects compared to dendrites in vivo, aligning with its enrichment in axons. These findings highlight fundamental Ca ²⁺ -modulating features and developmental importance of neuronal mitochondria in a compartment-specific manner and reveal the key underlying molecular mechanisms.