Molecular cloning and characterisation of scavenger receptor class B in pearl oyster Pinctada fuctada martensii

Transcriptome and exosome proteome analyses provide insights into the mantle exosome involved in nacre color formation of pearl oyster Pinctada fucata martensii

Color polymorphisms in molluscan shells play an important economic in the aquaculture industry. Among bivalves, shell color diversity can reflect properties such as growth rate and tolerance. In pearl oysters, the nacre color of the donor is closely related to the pearl color. Numerous genes and proteins involved in nacre color formation have been identified within the exosomes of the mantle. In this study, we analyzed the carotenoids present in the mantle of gold- and silver-lipped pearl oysters, identifying capsanthin and xanthophyll as crucial pigments contributing to coloration. Transcriptome analysis of the mantle revealed several differentially expressed genes (DEGs) involved in color formation, including ferric-chelate reductase, mantle genes, and larval shell matrix proteins. We also isolated and identified exosomes from the mantles of both gold- and silver-lipped strains of the pearl oyster Pinctada fucata martensii, revealing the extracellular transition mechanism of coloration-related proteins. From these exosomes, we obtained a total of 1223 proteins, with 126 differentially expressed proteins (DEPs) identified. These proteins include those associated with carotenoid metabolism and Fe(III) metabolism, such as apolipoproteins, scavenger receptor proteins, β,β-carotene-15,15'-dioxygenase, ferritin, and ferritin heavy chains. This study may provide a new perspective on the nacre color formation process and the pathways involved in deposition within the pearl oyster P. f. martensii.

Identification of a key gene StAR-like-3 responsible for carotenoids accumulation in the noble scallop Chlamys nobilis

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Significantly higher expression level of StAR-like-3 in intestine and hemocytes in golden scallops than that of brown ones.

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StAR-like-3 protein only existed in intestinal epithelial cells in golden scallops.

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Recombinant StAR-like-3 protein can bind lutein.

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The expression level of StAR-like-3 is significantly positive with the total carotenoids content in hemolymph.

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StAR-like-3 is a key gene responsible for carotenoids accumulation in golden scallops.

Carotenoids play important roles in living organisms. However, animals cannot synthesize carotenoids by themselves, and they must absorb and accumulate carotenoids from their diets in which some key genes are involved. In present study, a gene named StAR-like-3 was characterized in the noble scallop Chlamys nobilis, and its function was identified using golden scallops with higher carotenoids content and brown scallops with less carotenoids content by immunohistochemistry, carotenoid binding assay and RNAi. Results showed that the StAR-like-3 encodes a 54.7 kDa transmembrane protein (named as StAR3) of 481 amino acids containing a MENTAL domain and a START (Steroidogenic acute regulatory protein-related lipid transfer) domain, and its expression level in hemocytes and intestine of golden scallops were significantly higher than those of brown ones. Subsequently, the StAR3 protein was detected in the intestinal epithelial cells of golden scallops, and recombinant StAR3 could bind lutein conjugated to protein G and antibody to form a yellow complex, suggesting it is a carotenoid binding protein involving in carotenoids accumulation in golden scallops. Furthermore, total carotenoids content of hemolymph in golden scallops was significantly decreased when the expression of StAR-like-3 suppressed, suggesting this gene plays an important role in transport of carotenoids. Conclusion, the present results indicated that the StAR-like-3 is a key gene responsible for the carotenoids accumulation in the scallop.

DNA Methylation Analyses Unveil a Regulatory Landscape in the Formation of Nacre Color in Pearl Oyster Pinctada fucata martensii

Pearl color is regulated by genetics, biological pigments, and organic matrices and an important factor that influences the pearl economic value. The epigenetic regulation mechanism underlying pearl pigmentation remains poorly understood. In this study, we collected the mantle pallial (MP) and mantle central (MC) of the golden-lipped strain, and MP of the silver-lipped strain of pearl oyster Pinctada fucata martensii. The whole-genome bisulfite sequencing (WGBS) technology was employed to investigate the possible implication of epigenetic factors regulating nacre color variation. Our results revealed approximately 2.5% of the cytosines in the genome of the P. fucata martensii were methylated, with the CG methylation type was in most abundance. Overall, we identified 12, 621 differentially methylated regions (DMRs) corresponding to 3,471 DMR-associated genes (DMGs) between the two comparison groups. These DMGs were principally enriched into KEGG metabolic pathways including ABC transporters, Terpenoid backbone biosynthesis, and fatty acid degradation. In addition, integrating information about DMGs, DEGs, and function annotation indicated eight genes LDLR, NinaB, RDH, CYP, FADS, fn3, PU-1, KRMP as the candidate genes related to pigmentation of nacre color. A further study proved that the pigment in nacre is violaxanthin. The results of our study provide the support that there is an association between nacre color formation and DNA methylation profiles and will help to reveal the epigenetic regulation of nacre pigmentation formation in pearl oyster P. fucata martensii.

Identification and Allelic Variants Associated With Cold Tolerance of PmPIAS in Pinctada fucata martensii

The protein inhibitor of activated STAT (PIAS) functions in diverse aspects, including immune response, cell apoptosis, cell differentiation, and proliferation. In the present study, the PIAS in the pearl oyster Pinctada fucata martensii was characterized. The sequence features of PmPIAS were similar to that of other PIAS sequences with PIAS typical domains, including SAP, Pro-Ile-Asn-Ile-Thr (PINIT), RLD domain, AD, and S/T-rich region. Homologous analysis showed that PmPIAS protein sequence showed the conserved primary structure compared with other species. Ribbon representation of PIAS protein sequences also showed a conserved structure among species, and the PINIT domain and RLD domain showed the conserved structure compared with the sequence of Homo sapiens. The expression pattern of PmPIAS in different tissues showed significant high expression in the gonad. PmPIAS also exhibited a significantly higher expression in the 1 and 2 days after cold tolerance stress (17°C) and showed its potential in the cold tolerance. The SNP analysis of the exon region of PmPIAS obtained 18 SNPs, and among them, 11 SNPs showed significance among different genotypes and alleles between cold tolerance selection line and base stock, which showed their potential in the breeding for cold tolerance traits.

Evolutionary and functional analysis of MyD88 genes in pearl oyster Pinctada fucata martensii

Myeloid differentiation factor 88 (MyD88) is an adapter protein that links toll-like receptor and interleukin 1 receptor-mediated signal transduction. In this study, we identified 20 MyD88 genes from eight mollusk genomes and found that MyD88 was expanded in bivalves. This expansion tends to be tandem duplication. Phylogenetic analysis suggested that the tandem duplication of MyD88 was formed before bivalve differentiation. All of the identified MyD88 contained both of death domain (DD) and toll/interleukin-1 receptor (TIR) domain, and 13 mollusks MyD88 have low complexity regions (LCRs), which were not found in the MyD88 from humans and zebrafish. The genomic structure showed that most of the mollusk MyD88 (14 of 19) contained five conserved introns, four of which were found in humans and zebrafish. Furthermore, the cDNA full length of PfmMyD88-2 (one of the two identified MyD88 in Pincatada fucata martensii) was obtained with 1591 bp, including 260 bp of 5'UTR, 257 bp of 3'UTR, and 1077 bp of open reading frame encoding 358 amino acids. Quantitative real-time PCR analysis demonstrated that PfmMyD88-2 mRNA was widely expressed in all detected tissues. The highest expression level was in the gills and followed by hepatopancreas and feet. After lipopolysaccharide stimulation, PfmMyD88-2 expression level increased and reached the highest level at 12 h and then gradually declined to the normal level. Over-expression of PfmMyD88-2 in HEK293T increased the luciferase activity of the pNF-κB-Luc reporter. We also identified that PfmmiR-4047 could regulate the expression of PfmMyD88-2. These results help us elucidate the mechanism underlying mollusk immune response.

Scavenger receptor class B type I (SR-BI) in Ruditapes philippinarum: A versatile receptor with multiple functions

In the present study, a scavenger receptor class B type I (designed as RpSR-BI) was cloned and characterized from manila clam Ruditapes philippinarum. The full-length cDNA of RpSR-BI was of 2000 bp, containing an open reading frame (ORF) of 1515 bp. Multiple alignments and phylogenetic analysis strongly suggested that RpSR-BI was a member of the scavenger receptors family. The mRNA transcript of RpSR-BI was constitutively expressed in all tested tissues, and mainly expressed in hepatopancreas and hemocytes. Generally, Vibrio anguillarum or Micrococcus luteus challenge induced the expression of RpSR-BI transcripts in hemocytes of manila clams. Recombinant protein of RpSR-BI (rRpSR-BI) could bind lipopolysaccharides, peptidoglycan and glucan, but not chitin in vitro. Coinciding with the PAMPs binding assay, a broad agglutination spectrum was displayed by rRpSR-BI including Gram-positive bacteria and Gram-negative bacteria. Moreover, rRpSR-BI could enhance the phagocytosis and chemotaxis of hemocytes. These results showed that RpSR-BI functioned as a pattern recognition receptor (PRR) with distinct recognition spectrum, and also as an opsonin involved in the innate immune response of R. philippinarum.

Molecular cloning, expression pattern of β-carotene 15,15-dioxygenase gene and association analysis with total carotenoid content in pearl oyster Pinctada fucata martensii

β-carotene-15,15-dioxygenase is an enzyme involved in carotenoid metabolism to catalyze oxidative cleavage of β-carotene at its central double bond to two molecules of retinal in intestinal cells of vertebrate. In this study, we cloned and characterized β-carotene-15,15-dioxygenase in pearl oyster Pinctada fucata martensii (PmβCDOX). The full length of PmβCDOX gene was 1802 bp, including 1554 bp of the open reading frame (ORF) that encoded 517 amino acids, a 5'UTR of 134 bp and a 3' UTR of 114 bp. PmβCDOX was expressed at various tissues with highest level in hepatopancreas. Eighteen and fifteen single nucleotide polymorphisms (SNPs) were separately obtained in the exon and promoter of PmβCDOX. Eight SNPs (six SNPs in the exon and two SNPs in the promoter region) were significantly associated to total carotenoid content (TCC) (P < .05). The eight SNPs of significantly associated TCC were divided three haploblocks. Haplotypes CCTT had larger TCC than other haplotypes. The present results suggest that PmβCDOX is involved in carotenoid metabolism in pearl oyster. Our study will be helpful for development gene marker in selective breeding programs for TCC trait of the species.