Dermatopontin, a shell matrix protein gene from pearl oyster Pinctada martensii, participates in nacre formation

Physical Phenomena Governing Mineral Morphogenesis in Molluscan Nacre

Mollusks, as well as many other living organisms, have the ability to shape mineral crystals into unconventional morphologies and to assemble them into complex functional mineral-organic structures, an observation that inspired tremendous research efforts in scientific and technological domains. Despite these, a biochemical toolkit that accounts for the formation of the vast variety of the observed mineral morphologies cannot be identified yet. Herein, phase-field modeling of molluscan nacre formation, an intensively studied biomineralization process, is used to identify key physical parameters that govern mineral morphogenesis. Manipulating such parameters, various nacre properties ranging from the morphology of a single mineral building block to that of the entire nacreous assembly are reproduced. The results support the hypothesis that the control over mineral morphogenesis in mineralized tissues happens via regulating the physico-chemical environment, in which biomineralization occurs: the organic content manipulates the geometric and thermodynamic boundary conditions, which in turn, determine the process of growth and the form of the biomineral phase. The approach developed here has the potential of providing explicit guidelines for the morphogenetic control of synthetically formed composite materials.

miR-10a-3p Participates in Nacre Formation in the Pearl Oyster Pinctada fucata martensii by Targeting NPY

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via the recognition of their target messenger RNAs. MiR-10a-3p plays an important role in the process of ossification. In this study, we obtained the precursor sequence of miR-10a-3p in the pearl oyster Pinctada fucata martensii (Pm-miR-10a-3p) and verified its sequence by miR-RACE technology, and detected its expression level in the mantle tissues of the pearl oyster P. f. martensii. Pm-nAChRsα and Pm-NPY were identified as the potential target genes of Pm-miR-10a-3p. After the over-expression of Pm-miR-10a-3p, the target genes Pm-nAChRsα and Pm-NPY were downregulated, and the nacre microstructure became disordered. The Pm-miR-10a-3p mimic obviously inhibited the luciferase activity of the 3' untranslated region of the Pm-NPY gene. When the interaction site was mutated, the inhibitory effect disappeared. Our results suggested that Pm-miR-10a-3p participates in nacre formation in P. f. martensii by targeting Pm-NPY. This study can expand our understanding of the mechanism of biomineralization in pearl oysters.

Review: Post-translational modifications of marine shell matrix proteins

Shell matrix proteins (SMPs) are key components for the Mollusk shell biomineralization. SMPs function has been hypothesized in several proteins by bioinformatics analysis, and through in vitro crystallization assays. However, studies of the post-translational modifications (PTMs) of SMPs, which contribute to their structure and the function, are limited. This review provides the current status of the SMPs with the most common PTMs described (glycosylation, phosphorylation, and disulfide bond formation) and their role in shell biomineralization. Also, recent studies based on recombinant production of SMPs are discussed. Finally, recommendations for the study of SMPs and their PTMs are provided. The review showed that PTMs are widely distributed in SMPs, and their presence on SMPs may contribute to the modulation of their activity in some SMPs, contributing to the crystal growth formation and differentiation through different mechanisms, however, in a few cases the lack of the PTMs do not alter their inherent function.

Molecular and functional analysis of PmC1qDC in nacre formation of Pinctada fucata martensii

The C1q-domain-containing (C1qDC) proteins are a family of proteins characterized by a globular C1q (gC1q) domain in their C-terminus which hold the potential function in the shell formation as shell matrix proteins. In this study, a C1qDC protein was identified and characterized in pearl oyster (Pinctada fucata martensii) (PmC1qDC) to explore its function in nacre formation. The PmC1qDC-deduced protein sequence carried a typical globular C1q (gC1q) domain that possessed the typical 10-stranded β-sandwich fold with a jelly-roll topology common to all C1qDC family members and shared high homology with other gC1q domains. Homologous analysis of PmC1qDC presented it contained conserved secondary structure and Phe135, Phe155, Tyr166, Phe173, Tyr181, Phe183, and Phe256 amino acid residues. Expression pattern analysis showed that PmC1qDC expressed in all the detected tissues and exhibited a significantly higher expression level in nacre formation-associated tissues. After the shell notching, the expression level of PmC1qDC showed significantly up-regulation after 12 h in the central zone of mantle (MC). PmC1qDC expression significantly decreased in the MC after RNA interference (RNAi). Furthermore, disordered crystals with evident rough surface and irregular crystal tablets were observed in the nacre after RNAi. Results suggested that PmC1qDC affects the shell nacre formation, which is significant to improve the pearl production of pearl oyster.

Purification and functional analysis of the shell matrix protein N66 from the shell of the pearl oyster Pteria sterna

Mollusk biomineralization is a process controlled by a complex interplay of proteins, ions and external regulators. In spite of several studies, there is a lack of knowledge of who (molecules involved), how (mechanism) and why (evolution and adaptation) mollusk are designed as we know them. In this study, a shell matrix protein, N66, has been purified and characterized biochemically from the shell of Pteria sterna. Two protein bands with carbohydrates associated were separated with a molecular weight of ~60 and 64 kDa. It has carbonic anhydrase activity and it is able to form crystal polymorphs of calcium carbonate in vitro. The mRNA N66 was obtained from the mantle tissue of Pteria sterna and the deduced amino acid sequence contained a carbonic anhydrase (CA) domain and a Asn/Gly-rich domain (aa243-439). The CA domain contained three His residues acting as zinc ligands and the gate-keeper residues present in all α-CAs (Glu₁₆₆-Thr₅₂₅), being thus similar to the human isoform hCAVII. Also, to test whether the posttranslational modifications present on the native N66 affects the CA activity and its crystallization capability in vitro, a recombinant N66 was overexpressed in Escherichia coli and functionally characterized. Our results show that recombinant N66 has higher CA activity and produce larger size crystals in vitro than the native N66 protein, suggesting that intrinsic properties of the native N66, such as glycosylations and/or phosphorylations, might regulate its activity.

Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions

Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO₃.

Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes

In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and thermal response in Mytilus edulis from the North Sea and M. galloprovincialis from the Mediterranean Sea. The phylogenetic analysis within the genus Mytilus revealed M. californianus and M. coruscus to be genetically more distant from the other taxa: M. trossulus, M. edulis, M. chilensis and M. galloprovincialis. This work represents the first mantle transcriptome comparison between Mytilus taxa and provides contigs putatively involved in biomineralization.

Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions

Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO₃.

Transcriptome analysis of mantle tissues reveals potential biomineralization-related genes in Tectus pyramis Born

The marine mollusk Tectus pyramis is a valuable shellfish primarily distributed in the tropical waters of the South China Sea, as well as in the Indo-Pacific Ocean and areas near the southern portion of the Japanese Peninsula. Despite major economic interest in this mollusk, limited genomic resources are available for this species, which has prevented studies of the molecular mechanism, such as biomineralization. Here, we report the first comprehensive transcript dataset of T. pyramis mantle tissue. From a total of 16,801,141 reads, 173,671 unique transcripts were assembled, which provides new genomic resources for the understanding of biomineralization in T. pyramis. The most abundant unique sequences of the top 30 most highly expressed genes were annotated as shematrin, while other highly expressed genes included glycine-rich protein and shematrin-1. Based on transcriptome annotation and Gene Ontology classification, 130 biomineralization-related genes were found including members of the BMP (bone morphogenetic proteins), calmodulin, perlucin, and shematrin families, as well as mantle genes, nacrein, and MSI60. The results of qPCR showed that 14 of 24 examined genes were highly expressed in the mantle. A phylogenetic tree of BMP, perlucin, shematrin proteins revealed conservation of their structure and functions and indicated that some members participated in biomineralization in T. pyramis. Taken together, the results presented herein will be useful in studies of molecular mechanisms and pathways of biomineralization in T. pyramis, as well as provide new insight into the mechanisms of biomineralization in gastropods.

Identification of a gene encoding microphthalmia-associated transcription factor and its association with shell color in the clam Meretrix petechialis

The microphthalmia-associated transcription factor (MITF) is a master regulator of melanocyte development through the direct transcriptional control of related genes, e.g., the phenoloxidase gene. In this study, an MITF gene, MpMITF2, was identified in the clam Meretrix petechialis. The full-length cDNA of MpMITF2 was 2026 bp, and the molecular mass of the predicted protein was 42.6 kDa. A basic helix-loop-helix leucine zipper domain was detected in the deduced protein sequence, which can bind the E-box motif within the promoter of the downstream genes. The mRNA of MpMITF2 was more highly expressed in the mantle compared to the other four tissues. Furthermore, there was a significant difference in the mRNA expression of MpMITF2 among three clam strains with different shell colors. The protein level of MpMITF2 was also different among these strains. These results implied that MpMITF2 was associated with shell color formation in the clam M. petechialis. When the mRNA expression of MpMITF2 was knocked down, the new shell showed discontinuous pigment distribution, suggesting that the reduced expression of MpMITF2 influenced pigment synthesis. A gene encoding phenoloxidase (MpPO) was identified as related to the shell color of the clam and was also a putative downstream gene of MITF. Both the mRNA and protein levels of MpPO decreased significantly at 12 h post-MpMITF-suppression, suggesting that MpMITF2 is required for the expression of MpPO. Our results indicate the close relationships among MpMITF2, MpPO and shell color. This study implicates the role of MITF in shell color formation in the clam M. petechialis.

Candidate genes for shell colour polymorphism in Cepaea nemoralis

The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the foot and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Inspection of the overlap between the differential expression analysis and SNP analysis yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are thought to be involved in production of the shell’s nacreous layer. Comparison with morph-associated Restriction-site Associated DNA (RAD)-tags from a published study yielded eight transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism.

Design strategies and applications of nacre-based biomaterials

The field of tissue engineering and regenerative medicine relies heavily on materials capable of implantation without significant foreign body reactions and with the ability to promote tissue differentiation and regeneration. The field of bone tissue engineering in particular requires materials capable of providing enhanced mechanical properties and promoting osteogenic cell lineage commitment. While bone repair has long relied almost exclusively on inorganic, calcium phosphate ceramics such as hydroxyapatite and their composites or on non-degradable metals, the organically derived shell and pearl nacre generated by mollusks has emerged as a promising alternative. Nacre is a naturally occurring composite material composed of inorganic, calcium carbonate plates connected by a framework of organic molecules. Similar to mammalian bone, the highly organized microstructure of nacre endows the composite with superior mechanical properties while the organic phase contributes to significant bioactivity. Studies, both in vitro and in vivo, have demonstrated nacre's biocompatibility, biodegradability, and osteogenic potential, which are superior to pure inorganic minerals such as hydroxyapatite or non-degradable metals. Nacre can be used directly as a bulk implant or as part of a composite material when combined with polymers or other ceramics. While nacre has demonstrated its effectiveness in multiple cell culture and animal models, it remains a relatively underexplored biomaterial. This review introduces the formation, structure, and characteristics of nacre, and discusses the present and future uses of this biologically-derived material as a novel biomaterial for orthopedic and other tissue engineering applications.

STATEMENT OF SIGNIFICANCE

Mussel derived nacre, a biological composite composed of mineralized calcium carbonate platelets and interplatelet protein components, has recently gained interest as a potential alternative ceramic material in orthopedic biomaterials, combining the integration and mechanical capabilities of calcium phosphates with increased bioactivity derived from proteins and biomolecules; however, there is limited awareness of this material's potential. Herein, we present, to our knowledge, the first comprehensive review of nacre as a biomaterial. Nacre is a highly promising yet overlooked biomaterial for orthopedic tissue engineering with great potential in a wide variety of material systems. It is our hope that publication of this article will lead to increased community awareness of the potential of nacre as a versatile, bioactive ceramic capable of improving bone tissue regeneration and will elicit increased research effort and innovation utilizing nacre.

Transcriptome analysis of the freshwater pearl mussel (Cristaria plicata) mantle unravels genes involved in the formation of shell and pearl

Cristaria plicata, a bivalve widespread in Eastern Asia fresh water, is utilized as the freshwater pearl mussel in China. With a high economic value in pearl production, it is also an ideal object used for the studies on biomineralization in freshwater. In the research, we performed a large-scale sequencing of Cristaria plicata mantle transcriptome using Illumina HiSeq™ 2500, obtaining 98,501 unigenes with 67,817,724 bases. 22.28 and 16.64% of the unigenes were annotated in the NR and Swiss-Prot databases, respectively. Most of the annotated unigenes were homologous with proteins of Crassostrea gigas (47.4%) and some were similar to proteins of Aplysia californica (16.7%). Here, we identified 109 homologous unigenes of 15 decided shell matrix proteins, including nacrein, Pif, perlucin, tyrosinase (Tyr), PfN44, PUSP1, chitinase, shell matrix protein, MSI80, fibronectin type III, AmOxCo, perlwapin, BMSP, PfCHS1 and CaLP. Two other mantle transcriptomes of Pinctada margaritifera and Pinctada fucata were also analyzed to perform a biomineralization protein comparison of the three molluscan transcriptomes. All the three compared mollusks shared four proteins, including nacrein, Pif, Tyr and PfCHS1. It was also discovered that Cristaria plicata shared more biomineralization proteins with Pinctada fucata than that with Pinctada margaritifera. Our study explored a whole draft of mantle transcriptome of freshwater mussel and unraveled genes involved in the formation of shell and pearl, making it possible to identify massive novel biomineralization proteins in mollusks.

Molecular characterization of an inhibitor of NF-κB in the scallop Argopecten purpuratus: First insights into its role on antimicrobial peptide regulation in a mollusk

Inhibitors of nuclear factor kappa B (IκBs) are major control components of the Rel/NF-κB signaling pathway, a key regulator in the modulation of the expression of immune-related genes in vertebrates and invertebrates. The activation of the Rel/NF-κB signaling pathway depends largely in the degradation of IκB proteins and thus, IκBs are a main target for the identification of genes whose expression is controlled by Rel/NF-κB pathway. In order to identify such regulation in bivalve mollusks, the cDNA sequence encoding an IκB protein was characterized in the scallop Argopecten purpuratus, ApIκB. The cDNA sequence of ApIκB is comprised of 1480 nucleotides with a 1086 bp open reading frame encoding for 362 amino acids. Bioinformatics analysis showed that ApIκB displays the conserved features of IκB proteins. The deduced amino acid sequence consists of a 39.7 kDa protein, which has an N-terminal degradation motif, six ankyrin repeats and a C-terminal phosphorylation site motif. Phylogenetic analysis revealed a high degree of identity between ApIκB and other IκBs from mollusks, but also to arthropod cactus proteins and vertebrate IκBs. Tissue expression analysis indicated that ApIκB is expressed in all examined tissues and it is upregulated in circulating hemocytes from scallops challenged with the pathogenic Gram-negative bacterium Vibrio splendidus. After inhibiting ApIκB gene expression using the RNA interference technology, the gene expression of the antimicrobial peptide big defensin was upregulated in hemocytes from non-challenged scallops. Results suggest that ApIκB may control the expression of antimicrobial effectors such as big defensin via a putative Rel/NF-κB signaling pathway. This first evidence will help to deepen the knowledge of the Rel/NF-κB conserved pathway in scallops.

PfSMAD4 plays a role in biomineralization and can transduce bone morphogenetic protein-2 signals in the pearl oyster Pinctada fucata

Background

Mollusca is the second largest phylum in nature. The shell of molluscs is a remarkable example of a natural composite biomaterial. Biomineralization and how it affects mollusks is a popular research topic. The BMP-2 signaling pathway plays a canonical role in biomineralization. SMAD4 is an intracellular transmitter in the BMP signaling pathway in mammals, and some genomic data show SMAD4’s involvment in BMP signaling in invertbrates, but whether SMAD4 plays a conservative role in pearl oyster, Pinctada fucata, still need to be tested.

Results

In this study, we identified a SMAD4 gene (hereafter designated PfSMAD4) in pearl oyster Pinctada fucata. Bioinformatics analysis of PfSMAD4 showed high identity with its orthologs. PfSMAD4 was located in the cytoplasm in immunofluorescence assays and analyses of PfSMAD4 mRNA in tissues and developmental stages showed high expression in ovaries and D-shaped larvae. An RNA interference experiment, performed by PfSMAD4 double-stranded RNA (dsRNA) injection, demonstrated inhibition not only of nacre growth but also organic sheet formation with a decrease in PfSMAD4 expression. A knockdown experiment using PfBMP2 dsRNA showed decreased PfBMP2 and PfSMAD4 mRNA and irregular crystallization of the nacreous layer using scanning electron microscopy. In co-transfection experiments, PfBMP2-transactivated reporter constructs contained PfSMAD4 promoter sequences.

Conclusions

Our results suggest that PfSMAD4 plays a role in biomineralization and can transduce BMP signals in P. fucata. Our data provides important clues about the molecular mechanisms that regulate biomineralization in pearl oyster.

Mantle Branch-Specific RNA Sequences of Moon Scallop Amusium pleuronectes to Identify Shell Color-Associated Genes

Amusium pleuronectes (Linnaeus) that secretes red- and white-colored valves in two branches of mantle tissues is an excellent model for shell color research. High-throughput transcriptome sequencing and profiling were applied in this project to reveal the detailed molecular mechanism of this phenotype differentiation. In this study, 50,796,780 and 54,361,178 clean reads were generated from the left branch (secreting red valve, RS) and right branch (secreting white valve, WS) using the Illumina Hiseq 2000 platform. De novo assembly generated 149,375 and 176,652 unigenes with an average length of 764 bp and 698 bp in RS and WS, respectively. Kyoto encyclopedia of genes and genomes (KEGG) metabolic pathway analysis indicated that the differentially expressed genes were involved in 228 signaling pathways, and 43 genes were significantly enriched (P<0.01). Nineteen of 20 differentially expressed vitellogenin genes showed significantly high expression in RS, which suggested that they probably played a crucial role in organic pigment assembly and transportation of the shell. Moreover, 687 crystal formation-related (or biomineralization-related) genes were detected in A. pleuronectes, among which 144 genes exhibited significant difference between the two branches. Those genes could be classified into shell matrix framework participants, crystal nucleation and growth-related elements, upstream regulation factors, Ca level regulators, and other classifications. We also identified putative SNP and SSR markers from these samples which provided the markers for genetic diversity analysis, genetic linkage, QTL analysis. These results provide insight into the complexity of shell color differentiation in A. pleuronectes so as valuable resources for further research.

A Novel Matrix Protein Hic31 from the Prismatic Layer of Hyriopsis Cumingii Displays a Collagen-Like Structure

In this study, we clone and characterize a novel matrix protein, hic31, from the mantle of Hyriopsis cumingii. The amino acid composition of hic31 consists of a high proportion of Glycine residues (26.67%). Tissue expression detection by RT-PCR indicates that hic31 is expressed specifically at the mantle edge. In situ hybridization results reveals strong signals from the dorsal epithelial cells of the outer fold at the mantle edge, and weak signals from inner epithelial cells of the same fold, indicating that hic31 is a prismatic-layer matrix protein. Although BLASTP results identify no shared homology with other shell-matrix proteins or any other known proteins, the hic31 tertiary structure is similar to that of collagen I, alpha 1 and alpha 2. It has been well proved that collagen forms the basic organic frameworks in way of collagen fibrils and minerals present within or outside of these fibrils. Therefore, hic31 might be a framework-matrix protein involved in the prismatic-layer biomineralization. Besides, the gene expression of hic31 increase in the early stages of pearl sac development, indicating that hic31 may play important roles in biomineralization of the pearl prismatic layer.

Transcription factor CgMTF-1 regulates CgZnT1 and CgMT expression in Pacific oyster (Crassostrea gigas) under zinc stress

Oysters accumulate zinc at high tissue concentrations, and the metal response element (MRE)-binding transcription factor (MTF) functions as the cellular zinc sensor that coordinates the expression of genes involved in zinc efflux and storage, as well as those that protect against metal toxicity. In this study, we cloned MTF-1 in oysters and examined its regulation mechanism for its classic target genes, including MTs and ZnT1 under zinc exposure conditions. We cloned CgMTF-1 and determined the subcellular locations of its protein product in HEK293 cells. CgMTF-1 has a 2826bp open reading frame that encodes a predicted polypeptide with 707 amino acid residues, showing six well-conserved zinc finger domains that are required for metal binding. In HEK293 cell lines, CgMTF-1 primarily localizes in the cell nucleus under unstressed conditions and nuclear translocation was not critical for the activation of this gene. We searched for CgMTF-1-regulated genes in oysters using RNA interference. Decreased expression levels of CgMT1, CgMT4, and CgZnT1 were observed after CgMTF-1 interference (>70% inhibition) under zinc exposure, indicating the critical role of CgMTF-1 in the regulation of these genes. We searched for a direct regulation mechanism involving CgMTF-1 for CgMT1, CgMT4, and CgZnT1 in vitro. EMSA experiments indicated that CgMTF-1 can bind with the MREs found in the CgZnT1, CgMT1 and CgMT4 promoter regions. Additionally, luciferase reporter gene experiments indicated that CgMTF-1 could activate the CgMT1, CgMT4, and CgZnT1 promoters. Overall, our results suggest that CgMTF-1 directly coordinates the regulation of CgMTs and CgZnT1 expression and plays important roles in protecting oysters under zinc exposure conditions. To our knowledge, this is the first study to elucidate the function of MTF-1 in marine bivalves and provides new insights into the mechanisms of zinc accumulation and tolerance in mollusks.

Differential gene expression analysis of benzo(a)pyrene toxicity in the clam, Ruditapes philippinarum

Polycyclic aromatic hydrocarbons (PAHs) are known for their carcinogenic, teratogenic and mutagenic properties. Benzo(a)pyrene (BaP) possesses the greatest carcinogenic potential among the various PAHs. In this study, digital gene expression (DGE) was performed to investigate the digestive gland transcriptome profile of the clam Ruditapes philippinarum exposed to BaP. A total of 10,508,312 and 11,414,297 clean reads were generated respectively, from control and BaP exposure DGE libraries. One hundred and forty-five differentially expressed genes were detected after comparing two libraries with 58 up-regulated and 87 down-regulated genes. GO annotation and KEGG pathway analyses were performed on all genes to understand their biological functions and processes. The results showed that numerous enriched differentially expressed genes are related to growth and development, antioxidant metabolism, apoptosis and detoxification metabolism. Quantitative real-time PCR was performed to verify the expressed genes of DGE. Our results provide evidences that RNA-seq is a powerful tool for toxicology and capable of generating novel and valuable information at the transcriptome level for characterizing deleterious effects caused by BaP.

Shell extracts from the marine bivalve Pecten maximus regulate the synthesis of extracellular matrix in primary cultured human skin fibroblasts

Mollusc shells are composed of more than 95% calcium carbonate and less than 5% of an organic matrix consisting mostly of proteins, glycoproteins and polysaccharides. Previous studies have elucidated the biological activities of the shell matrices from bivalve molluscs on skin, especially on the expression of the extracellular matrix components of fibroblasts. In this work, we have investigated the potential biological activities of shell matrix components extracted from the shell of the scallop Pecten maximus on human fibroblasts in primary culture. Firstly, we demonstrated that shell matrix components had different effects on general cellular activities. Secondly, we have shown that the shell matrix components stimulate the synthesis of type I and III collagens, as well as that of sulphated GAGs. The increased expression of type I collagen is likely mediated by the recruitment of transactivating factors (Sp1, Sp3 and human c-Krox) in the −112/−61 bp COL1A1 promoter region. Finally, contrarily to what was obtained in previous works, we demonstrated that the scallop shell extracts have only a small effect on cell migration during in vitro wound tests and have no effect on cell proliferation. Thus, our research emphasizes the potential use of shell matrix of Pecten maximus for dermo-cosmetic applications.

Tissue inhibitor of metalloproteinase gene from pearl oyster Pinctada martensii participates in nacre formation

Tissue inhibitors of metalloproteinases (TIMPs) are nature inhibitors of matrix metalloproteinases and play a vital role in the regulation of extracellular matrix turnover, tissue remodeling and bone formation. In this study, the molecular characterization of TIMP and its potential function in nacre formation was described in pearl oyster Pinctada martensii. The cDNA of TIMP gene in P. martensii (Pm-TIMP) was 901 bp long, containing a 5' untranslated region (UTR) of 51 bp, a 3' UTR of 169 bp, and an open reading fragment (ORF) of 681 bp encoding 226 amino acids with an estimated molecular mass of 23.37 kDa and a theoretical isoelectric point of 5.42; The predicted amino acid sequence had a signal peptide, 13 cysteine residues, a N-terminal domain and a C-terminal domain, similar to that from other species. Amino acid multiple alignment showed Pm-TIMP had the highest (41%) identity to that from Crassostrea gigas. Tissue expression analysis indicated Pm-TIMP was highly expressed in nacre formation related-tissues, including mantle and pearl sac. After decreasing Pm-TIMP gene expression by RNA interference (RNAi) technology in the mantle pallium, the inner nacreous layer of the shells showed a disordered growth. These results indicated that the obtained Pm-TIMP in this study participated in nacre formation.

Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis

BACKGROUND

With a diversity of pigmented shell morphotypes governed by Mendelian patterns of inheritance, the common grove snail, Cepaea nemoralis, has served as a model for evolutionary biologists and population geneticists for decades. Surprisingly, the molecular mechanisms by which C. nemoralis generates this pigmented shelled diversity, and the degree of evolutionary conservation present between molluscan shell-forming proteomes, remain unknown.

RESULTS

Here, using next generation sequencing and high throughput proteomics, we identify and characterize the major proteinaceous components of the C. nemoralis shell, the first shell-proteome for a pulmonate mollusc. The recent availability of several marine molluscan shell-proteomes, and the dataset we report here, allow us to identify 59 evolutionarily conserved and novel shell-forming proteins. While the C. nemoralis dataset is dominated by proteins that share little to no similarity with proteins in public databases, almost half of it shares similarity with proteins present in other molluscan shells. In addition, we could not find any indication that a protein (or class of proteins) is directly associated with shell pigmentation in C. nemoralis. This is in contrast to the only other partially characterized molluscan-shell pigmentation mechanism employed by the tropical abalone Haliotis asinina.

CONCLUSIONS

The unique pulmonate shell-forming proteome that we report here reveals an abundance of both mollusc-specific and pulmonate-specific proteins, suggesting that novel coding sequences, and/or the extensive divergence of these sequences from ancestral sequences, supported the innovation of new shell types within the Conchifera. In addition, we report here the first evidence that molluscs use independently evolved mechanisms to pigment their shells. This proteome provides a solid foundation from which further studies aimed at the functional characterization of these shell-forming proteins can be conducted.

Identification and characterization of microRNAs in pearl oyster Pinctada martensii by Solexa deep sequencing

MicroRNAs (miRNAs) are short-nucleotide RNA molecules that function as negative regulators of gene expression in various organisms. However, miRNAs of Pinctada martensii have not been reported yet. P. martensii is one of the main species cultured for marine pearl production in China and Japan. In order to obtain the repertoire of miRNAs in P. martensii, we constructed and sequenced small RNA libraries prepared from P. martensii by Solexa deep sequencing technology and got a total of 27,479,838 reads representing 3,176,630 distinct sequences. After removing tRNAs, rRNAs, snRNAs, and snoRNAs, 10,596,306 miRNA reads representing 18,050 distinct miRNA reads were obtained. Based on sequence similarity and hairpin structure prediction, 258 P. martensii miRNAs (pm-miRNA) were identified. Among these pm-miRNAs, 205 were conserved across the species, whereas 53 were specific for P. martensii. The 3' end sequence of U6 snRNA was obtained from P. martensii by 3' rapid amplification of cDNA end PCR reaction and sequence-directed cloning. Eight conserved pm-miRNAs and two novel pm-miRNAs were validated by stem-loop quantitative real-time PCR with U6 snRNA as an internal reference gene. pm-miRNAs and the reported biomineralization-related genes were subjected to target analysis by using target prediction tools. Some of the pm-miRNAs, such as miR-2305 and miR-0046, were predicted to participate in biomineralization by regulating the biomineralization-related genes. Thus, this study demonstrated a large-scale characterization of pm-miRNAs and their potential function in biomineralization, providing a foundation to understand shell formation.

Identification of reference genes for qRT-PCR analysis in Yesso scallop Patinopecten yessoensis

BACKGROUND

Bivalves comprise around 30,000 extant species and have received much attention for their importance in ecosystems, aquaculture and evolutionary studies. Despite the increasing application of real-time quantitative reverse transcription PCR (qRT-PCR) in gene expression studies on bivalve species, little research has been conducted on reference gene selection which is critical for reliable and accurate qRT-PCR analysis. For scallops, systematic evaluation of reference genes that can be used among tissues or embryo/larva stages is lacking, and β-actin (ACT) is most frequently used as qRT-PCR reference gene without validation.

RESULTS

In this study, 12 commonly used candidate reference genes were selected from the transcriptome data of Yesso scallop (Patinopectenyessoensis) for suitable qRT-PCR reference genes identification. The expression of these genes in 36 tissue samples and 15 embryo/larva samples under normal physiological conditions was examined by qRT-PCR, and their expression stabilities were evaluated using three statistic algorithms, geNorm, NormFinder, and comparative ∆Ct method. Similar results were obtained by the three approaches for the most and the least stably expressed genes. Final comprehensive ranking for the 12 genes combing the results from the three programs showed that, for different tissues, DEAD-box RNA helicase (HELI), ubiquitin (UBQ), and 60S ribosomal protein L16 (RPL16) were the optimal reference genes combination, while for different embryo/larva stages, gene set containing Cytochrome B (CB), Cytochrome C (CC), Histone H3.3 (His3.3), and Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were recommended for qRT-PCR normalization. ACT was among the least stable genes for both adult tissues and embryos/larvae.

CONCLUSIONS

This work constitutes the first systematic analysis on reference genes selection for qRT-PCR normalization in scallop under normal conditions. The suitable reference genes we recommended will be useful for the identification of genes related to biological processes in Yesso scallop, and also in the reference gene selection for other scallop or bivalve species.

Effects of RNA interference-mediated knock-down of hypoxia-inducible factor-α on respiratory burst activity of the Pacific oyster Crassostrea gigas hemocytes

In mammals, hypoxia-inducible factor-1 α (HIF-1α) is known to play important roles not only in oxygen homeostasis but also in innate immune responses. In this study, to assess the functional role of HIF-α in respiratory burst activity of Crassostrea gigas hemocytes, oysters were injected with HIF-α- or green fluorescent protein (GFP)-targeted-long double-stranded RNAs (dsRNAs), and at 1, 3, and 7 days post-injection, knock-down of C. gigas HIF-α expression and production of reactive oxygen species (ROS) were analyzed. Expression of HIF-α in mantle, gill, and hemocytes of C. gigas was clearly down-regulated by injection of the HIF-α-targeted-long dsRNA, but was not inhibited by the GFP-targeted-long dsRNA, indicating that HIF-α expression was suppressed through sequence-specific and systemic RNA interference (RNAi). Respiratory burst activity of hemocytes was significantly increased by administration of GFP-targeted-long dsRNA. However, knock-down of HIF-α expression led to significant decrease of chemiluminescence (CL) response of C. gigas hemocytes at 3 and 7 days post-administration of HIF-α-targeted-long dsRNA, indicating the critical role of HIF-α in activation of respiratory burst activity of oyster hemocytes.

Exploring RNAi as a therapeutic strategy for controlling disease in aquaculture

Aquatic animal diseases are one of the most significant constraints to the development and management of aquaculture worldwide. As a result, measures to combat diseases of fish and shellfish have assumed a high priority in many aquaculture-producing countries. RNA interference (RNAi), a natural mechanism for post-transcriptional silencing of homologous genes by double-stranded RNA (dsRNA), has emerged as a powerful tool not only to investigate the function of specific genes, but also to suppress infection or replication of many pathogens that cause severe economic losses in aquaculture. However, despite the enormous potential as a novel therapeutical approach, many obstacles must still be overcome before RNAi therapy finds practical application in aquaculture, largely due to the potential for off-target effects and the difficulties in providing safe and effective delivery of RNAi molecules in vivo. In the present review, we discuss the current knowledge of RNAi as an experimental tool, as well as the concerns and challenges ahead for the application of such technology to combat infectious disease of farmed aquatic animals.