Proteolytic control of mitochondrial calcium transport by intermembrane-space proteases

The mitochondrial intermembrane space (IMS) is a critical regulatory interface for mitochondrial calcium (mCa2+) flux. Positioned between the outer and inner mitochondrial membranes, the IMS links cytosolic Ca2+ signal to regulated Ca2+ uptake into the matrix. This positioning allows the IMS to influence mCa2+ transport and Ca2+-dependent mitochondrial metabolism. mCa2+ homeostasis is governed mainly by the mitochondrial calcium uniporter complex (mtCU), which mediates mCa2+ uptake, and the Na+/Ca2+ exchanger NCLX, which drives mCa2+ efflux. However, whether IMS regulatory events, particularly proteolytic remodeling by IMS proteases, control this transport machinery remains unclear. Using complementary knockout and overexpression approaches targeting ten IMS proteases (NLN, ATP23, IMMP1L, IMMP2L, YME1L1, OMA1, LACTB2, PARL, and HTRA2), we identified protease-specific remodeling of mtCU components and NCLX abundance. Transcriptomic and proteomic analyses showed that these changes arise largely from protease-specific control of transporter stability rather than transcriptional regulation alone. Proximity-labeling proteomics further revealed spatial associations between IMS proteases and mCa2+ transport components. Functionally, perturbing IMS proteases altered mCa2+ flux and reduced mCa2+ retention capacity, indicating impaired buffering against Ca2+ overload. Together, these findings identify IMS proteases as a proteostatic regulatory network controlling mCa2+ transport and establish a mechanistic link between mitochondrial proteostasis and Ca2+ homeostasis.