Correlative Soft X-ray Tomography and Transcriptomics Unveil How Calcium Alleviates Uranyl Cytotoxicity

Abstract Uranium contamination poses increasing environmental and health risks, yet the subcellular mechanisms underlying its toxicity and the protective effects of coexisting ions remain poorly understood. Here, by integrating cryo-SXT, transcriptomics, and physiological assays, we systematically decipher the multichannel protective mechanisms of calcium (Ca2+) against uranyl (UO22+) toxicity in Candida utilis, which act through metabolic reprogramming and biomineralization. Exposure to UO22+ alone induces pronounced lipotoxicity, characterized by the accumulation of free fatty acids (FFA), expansion of lipid droplets (LDs), and upregulation of genes involved in triacylglycerol synthesis. In contrast, Ca2+ pretreatment effectively mitigates these lipotoxic effects by redirecting lipid flux to fatty acid β-oxidation. Concurrently, UO22+ triggers mitochondrial membrane potential (MMP) loss, mitochondrial fragmentation, cristae disorganization, and downregulation of genes essential for cristae architecture and the electron transport chain (ETC). Such cellular disorders can be reversed by Ca2+, which restores reticular mitochondrial networks and cristae integrity. Furthermore, UO22+ enlarges the contact area between mitochondria and LDs, as well as between mitochondria and the nucleus, whereas Ca2+ pretreatment restores these contacts to near-normal levels. Notably, Ca2+ induces the accumulation of polyphosphate (polyP) within vacuoles and its subsequent mobilization to the cell wall, where it coprecipitates with UO22+ and Ca2+ to form stable extracellular calcium–uranium-phosphate nanoclusters. Collectively, this cross-scale imaging-omics strategy provides a mechanistic blueprint for cation-enhanced uranium tolerance and biomineralization, while also offering a transferable methodological framework for environmental toxicology.