The Diversity of Shell Matrix Proteins: Genome-Wide Investigation of the Pearl Oyster, Pinctada fucata

Abstract

In molluscs, shell matrix proteins are associated with biomineralization, a biologically controlled process that involves nucleation and growth of calcium carbonate crystals. Identification and characterization of shell matrix proteins are important for better understanding of the adaptive radiation of a large variety of molluscs. We searched the draft genome sequence of the pearl oyster Pinctada fucata and annotated 30 different kinds of shell matrix proteins. Of these, we could identified Perlucin, ependymin-related protein and SPARC as common genes shared by bivalves and gastropods; however, most gastropod shell matrix proteins were not found in the P. fucata genome. Glycinerich proteins were conserved in the genus Pinctada. Another important finding with regard to these annotated genes was that numerous shell matrix proteins are encoded by more than one gene; e.g., three ACCBP-like proteins, three CaLPs, five chitin synthase-like proteins, two N16 proteins (pearlins), 10 N19 proteins, two nacreins, four Pifs, nine shematrins, two prismalin-14 proteins, and 21 tyrosinases. This diversity of shell matrix proteins may be implicated in the morphological diversity of mollusc shells. The annotated genes reported here can be searched in P. fucata gene models version 1.1 and genome assembly version 1.0 ( http://marinegenomics.oist.jp/pinctada_fucata ). These genes should provide a useful resource for studies of the genetic basis of biomineralization and evaluation of the role of shell matrix proteins as an evolutionary toolkit among the molluscs.

Identification of conserved proteins from diverse shell matrix proteome in Crassostrea gigas: characterization of genetic bases regulating shell formation

“…Nacrein-related proteins have been found in some congeneric species ( P. maxima and P. margaritifera ) and also one gastropod, Turbo marmoratus 39. They have a similar primary structure as nacrein in P. fucata 11. No nacrein-related genes could be identified using BLASTp search with E-value < E-21 and score > 100.…”

“…Many studies have been focused on the SMPs and genes expressed in the mantle, leading to the identification and characterization of several specific shell proteins11. Recently, high-throughput transcriptomics and proteomics analyses have been successively used to characterize shell matrix proteomes (SMPEs) in Haliotis asinina 8, Pinctada margaritifera 12, Pinctada maxima 12, Crassostrea gigas 13, Lottia gigantea 14, Cepaea nemoralis 6, Mytilus coruscus 15, Pinctada.…”

Top-Down Proteomics and Farm Animal and Aquatic Sciences

“…Gene expansion constitutes a unique evolutionary adaptation of bivalves to a sessile lifestyle in the intertidal zone [77,78]. Among the genes present in bivalves with high sequence and structural polymorphisms are the immune and stress response proteins, such as C1q domain-containing proteins and heat shock protein 70 kDa [77,79].…”

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

“…Here it was activated in EFA-deficient pediveligers and only in healthy juveniles. Additionally, MERP1 is a conserved protein with biomineralization properties in bivalves (Miyamoto et al, 2013). In addition, the collagen triple helix repeat containing 1 (CTHRC1) is associated with injuries and promotes cell migration (Pyagay et al, 2005) and the mannose-binding protein (MBL) with lectin properties can neutralize aggressors and promotes cell adhesion (Drickamer, 1992).…”