Mitochondria transported by Kinesin 3 prevent localized calcium spiking to inhibit caspase-dependent specialized cell death

Polarized cells (such as neurons), defined by distinct compartments are, like many cell types, subject to developmental elimination, as in neurite pruning. The molecular mechanism behind specialized elimination remains a largely open question. We previously introduced the “tri-partite” embryonic cell death program Compartmentalized Cell Elimination (CCE) in the scaffolding tail-spike epithelial cell and sex-specific CEM neurons of C. elegans . CCE is stereotyped and ordered, with three distinct programs eliminating three cell compartments, and bearing morphological hallmarks reminiscent of neurite pruning. Here we report first, that, prior to CCE onset, mitochondria undergo UNC-116/Kinesin 1-dependent irreversible retrograde transport; and second, that the caspase protease CED-3 promotes the completion of the proximal nicking event of CCE by helping inhibit the kinesin 3 homolog UNC-104. While known canonically to carry only synaptic vesicles, UNC-104/Kinesin 3, in the CCE context, and in the absence of CED-3/Caspase, can transport mitochondria anterogradely to the severing site. We observe both caspase activity and Ca ²⁺ spiking at this site prior to nicking. Mitochondria appear to protect against nicking in the absence of CED-3 via their MCU-1 uniporter-dependent Ca ²⁺ uptake capacity. Our study sheds light on the molecular machinery of specialized cell elimination and pruning, highlighting involvement of region-specific Ca ²⁺ signaling, an anti-death function of mitochondria via local Ca ²⁺ uptake, mitochondrial transport as a regulatory strategy, with UNC-116/kinesin 1-mediated retrograde transport important for cell elimination priming and UNC-104/kinesin 3 in a previously undescribed role as a non-canonical anterograde mitochondrial motor.