The Atlas of the Shell Proteome in Oysters Reveals the Potential Roles of the Cytoskeleton and Extracellular Matrix in Biomineralization

Shell matrix proteins (SMPs) are fundamental biological macromolecules for mollusk shell formation, yet fewer than 400 SMPs in mollusks have been previously identified, hindering our understanding of how mollusks construct and maintain their shells. Here, we identified 1689 SMPs in the Pacific oyster Crassostrea gigas using three different mass spectrometry techniques, representing a significant methodological advancement in shell proteomics, enabling a 6.52-fold increase in SMP identification compared to previous studies. Gene ontology and domain annotation revealed cytoskeletal proteins (with cofilin ADF, tubulin, and myosin head domains) and extracellular matrix (ECM)-related proteins (with carbonic anhydrase, chitin-binding, von Willebrand type A, and EGF domains) as the key functional SMPs involved in biomineralization. Furthermore, developmental transcriptomics highlighted that microtubule- and microfilament-related SMPs were enriched in larvae and adults, respectively, potentially reflecting differences in cytoskeletal regulation associated with larval aragonitic and adult calcitic shells. Transcriptomic analyses revealed that acidifying stress significantly downregulated the expression of genes encoding collagen and stress-fiber-related proteins, while activating the BMP signaling pathway in oysters. These transcriptional changes suggest a potential impairment in ECM and cytoskeletal maintenance. Our findings indicate the potential roles of the cytoskeleton and ECM proteins in biomineralization and emphasize the complexity of biological controls on shell formation in oysters. Furthermore, the proteomic strategy combining three distinct technologies can be applied to other mollusks and provide deeper insights into their evolutionary trajectories under future environmental changes.