The shellome of the crocus clam Tridacna crocea emphasizes essential components of mollusc shell biomineralization

Molluscan shells are among the most fascinating research objects because
of their diverse morphologies and textures. The formation of these
delicate biomineralized structures is a matrix-mediated process. A
question that arises is what are the essential components required to
build these exoskeletons. In order to understand the molecular mechanisms
of molluscan shell formation, it is crucial to identify organic
macromolecules in different shells from diverse taxa. In the case of
bivalves, however, taxon sampling in previous shell proteomics studies are
biased and focus exclusively on representatives of the class Pteriomorphia
such as pearl oysters, edible oysters and mussels. In this study, we have
characterized the shell organic matrix from the crocus clam, Tridacna
crocea, (Heterodonta) using various biochemical techniques, including
SDS-PAGE, FT-IR, monosaccharide analysis, and enzyme-linked lectin assay
(ELLA). Furthermore, we have identified a number of shell matrix proteins
(SMPs) using a comprehensive proteomics approach combined to RNA-seq. The
biochemical studies confirmed the presence of proteins, polysaccharides,
and sulphates in the T. crocea shell organic matrix. Proteomics analysis
revealed that the majority of the T. crocea SMPs are novel and dissimilar
to known SMPs identified from the other bivalve species. Meanwhile, the
SMP repertoire of the crocus clam also includes proteins with conserved
functional domains such as chitin-binding domain, VWA domain, and protease
inhibitor domain. We also identified BMSP (Blue Mussel Shell Protein,
originally reported from Mytilus), which is widely distributed among
molluscan shell matrix proteins. Tridacna SMPs also include low-complexity
regions or LCRs that are absent in the other molluscan genomes, indicating
that these genes may have evolved in specific lineage. These results
highlight the diversity of the organic molecules - in particular proteins
- that are essential for molluscan shell formation.