Novel insights into conserved biomineralization mechanisms revealed from a cold-water scleractinian coral skeletal proteome

Abstract Stony corals exhibit striking morphological plasticity across diverse environments and trophic strategies, raising fundamental questions about the conservation of their biomineralization machinery. Here, we characterize the skeletal organic matrix proteome (SOM) of the cosmopolitan cold-water, asymbiotic coral Desmophyllum pertusum and compare it with published skeletal proteomes from a facultatively photosymbiotic temperate coral and an obligately photosymbiotic subtropical coral. Despite pronounced differences in habitat, symbiotic status, and skeletal micro-density, we observe convergence on a conserved “biomineralization toolkit” spanning these taxa. Comparative proteomics and AI-based structural predictions reveal that this toolkit integrates acidic matrix proteins, carbonic anhydrases, adhesion and structural proteins, and signaling components with multiple export pathways, including classical secretion, vesicle-mediated trafficking, and cytoskeleton-associated transport. Newly predicted protein architectures expand the diversity of acidic proteins, suggesting roles not only in stabilizing amorphous calcium carbonate but also in proton buffering within intracellular and extracellular calcifying compartments. Together, these findings redefine coral biomineralization as a dynamic, coordinated network of cellular pathways rather than a static assemblage of matrix components. By establishing D. pertusum as a symbiont-free model system, this work provides a mechanistic framework for dissecting coral calcification across environments and for assessing the resilience of this conserved machinery to ongoing ocean change. Teaser Corals share a conserved, dynamic, and coordinated biomineralization toolkit across diverse trophic modes and environments.