Parallel Evolution of Nacre Building Gene Sets in Molluscs

Abstract

The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently and in parallel in at least some groups. To test this proposition and gain insight into the evolution of structural genes that contribute to shell fabrication, we compared genes expressed in nacre (mother-of-pearl) forming cells in the mantle of the bivalve Pinctada maxima and the gastropod Haliotis asinina. Despite both species having highly lustrous nacre, we find extensive differences in these expressed gene sets. Following the removal of housekeeping genes, less than 10% of all gene clusters are shared between these molluscs, with some being conserved biomineralization genes that are also found in deuterostomes. These differences extend to secreted proteins that may localize to the organic shell matrix, with less than 15% of this secretome being shared. Despite these differences, H. asinina and P. maxima both secrete proteins with repetitive low-complexity domains (RLCDs). Pinctada maxima RLCD proteins-for example, the shematrins-are predominated by silk/fibroin-like domains, which are absent from the H. asinina data set. Comparisons of shematrin genes across three species of Pinctada indicate that this gene family has undergone extensive divergent evolution within pearl oysters. We also detect fundamental bivalve-gastropod differences in extracellular matrix proteins involved in mollusc-shell formation. Pinctada maxima expresses a chitin synthase at high levels and several chitin deacetylation genes, whereas only one protein involved in chitin interactions is present in the H. asinina data set, suggesting that the organic matrix on which calcification proceeds differs fundamentally between these species. Large-scale differences in genes expressed in nacre-forming cells of Pinctada and Haliotis are compatible with the hypothesis that gastropod and bivalve nacre is the result of convergent evolution. The expression of novel biomineralizing RLCD proteins in each of these two molluscs and, interestingly, sea urchins suggests that the evolution of such structural proteins has occurred independently multiple times in the Metazoa.

Deep conservation of bivalve nacre proteins highlighted by shell matrix proteomics of the Unionoida Elliptio complanata and Villosa lienosa

“…While recent data suggest a rapid evolution of shell matrix proteins leading to their extreme diversity [20], our work indicates the contrary: a deeply conserved biomineralization toolkit within nacre-bearing bivalves.…”

“…The overall primary structure of shematrins is characterized by a signal peptide, G-G-Y-repeat motif, together with other more variable G-and Y-rich RLCDs and KKKY N-termini [36] that are also observed in this novel unionoid putative member. Shematrin-likes constitute one of the main SMP families, found in both the nacre and prismatic layer of the shell of Pinctada spp., and their corresponding transcripts are highly expressed in the mantle [2,20]. Surprisingly, their homologous sequences are missing from the Transcriptome Shotgun Assembly (TSA) databases of E. complanata and V. lienosa.…”

Mineralization and non-ideality: on nature’s foundry

“…Several of the attached proteins adopt antiparallel β-sheet conformations and consist of repetitive lowcomplexity domains (RLCDs) rich in glycine (Evans 2008;Jackson et al 2010). With similarities to silk fibroin, crowding might have similar effects on these two functional classes originating from distinct sources.…”

The Microstructure of the Cultured Freshwater Pearl

“…In the case of shell formation it is well established that the organic matrix located between the aragonite layer plates or tablets, often referred to as the intertabular matrix, controls the formation of the calcium carbonate crystal polymorphs and dictates when and where they nucleate and stop growing, their expansion and positioning, and adjustments in growth where appropriate. 12,13,18 This is therefore a genetically directed nucleation process rather than a crystallographically directed nucleation process as in epitaxial nucleation and growth of single crystals. For nacre growth in bivalve shells, holes or porous regions exist in the intertubular organic matrix, and nucleation for a given stack of crystals occurs by mineral bridges through the matrix, as recently illustrated for abalone nacre by Meyers et al 9 When the mantle seed is inserted too close to the mother of pearl in the shell surface, the growing pearl in contact with the nacre surface will flatten, altering the pearl curvature as illustrated on comparing two comparable pearl morphologies in Fig.…”

“…The mantle edge secretes the organic framework which controls the formation of the calcium carbonate crystals: their nucleation, growth, polymorphic structure, and even the positioning and elongation of crystal polygons within the concentric layers, and in the surface region which defines pearl quality. [11][12][13] Pearl formation involves a number of biological genes and transcription factors which are part of the organism's DNA-derived modeling software. 14 Unlike natural pearl production, which results by the mollusk's response to an irritant (such as a fine sand grain) which acts as a nucleating agent, cultured freshwater pearls are nucleated by inserting (or seeding) a roughly 3 mm square of mantle tissue (a tissue graft) cut from a suitable donor mussel, initially in 3-mm-wide strips.…”