A cDNA Cloning of a Novel Alpha-Class Tyrosinase of Pinctada fucata: Its Expression Analysis and Characterization of the Expressed Protein

Comprehensive analysis of differentially expressed mRNA, lncRNA and miRNA, and their ceRNA networks in the regulation of shell color in the Manila clam (Ruditapes philippinarum)

The regulatory mechanism of ceRNA network plays an important role in molecular function and biological processes, however, the molecular mechanism in the shell color of Ruditapes philippinarum has not yet been reported. In this study, we performed transcriptome sequencing on the mantle of R. philippinarum with different shell colors, and screened for mRNA, miRNA, and lncRNA. A total of 61 mRNAs, 3725 lncRNAs and 90 miRNAs were obtained from all the shell color comparison groups (all mRNAs, lncRNAs and miRNAs P < 0.05), and 7 mRNAs, 8 lncRNAs, and 4 miRNAs of the porphyrin pathway and melanin pathway were screened for competitive endogenous RNA (ceRNA) network construction. The results indicate that the ceRNA network composed of mRNA and lncRNA, centered around efu-miR-101, mle-bantam-3p, egr-miR-9-5p, and sma-miR-75p, may play a crucial regulatory role in shell color formation. This study reveals for the first time the mechanism of ceRNA regulatory networks in the shell color of R. philippinarum and providing important reference data for molecular breeding of shell color in R. philippinarum.

Molecular characterization of Pax7 and its role in melanin synthesis in Crassostrea gigas

The paired-box 7 (Pax7) is a transcription factor crucial for skin color polymorphism. However, the mechanism underlying the pigmentation associated with Pax7 in mollusks have yet to be elucidated. In this study, the cDNA sequence of Pax7 in the Pacific oyster Crassostrea gigas (CgPax7) was characterized. Phylogenetically, the identity of deduced amino acid sequence was similar to that of other mollusks and contained 463 amino acids, with conserved features of paired domain (PRD), homeobox domain (HD) and octapeptide. Gene expression analysis revealed that CgPax7 was markedly increased at D-shaped larvae stage and ubiquitously expressed in six examined tissues in adult oyster. The result of whole-mount in situ hybridization (WMISH) showed a restricted pattern of CgPax7 expression on margins of shell valves at D-shaped and umbo larvae stages. Additionally, although CgPax7 silencing had no significant effect on CgMitf expression, it significantly inhibited the expressions of CgPax7, CgTyr, CgTyrp1, CgTyrp2 and CgCdk2, genes involved in Tyr-mediated melanin synthesis. Furthermore, CgPax7 knockdown obviously decreased the tyrosinase activity. Less brown-granules at mantle edge was detected by micrographic examination and melanosomes defect was observed by transmission electron microscopy. It was demonstrated that CgPax7 play a key role in melanin synthesis by regulating Tyr-pathway in C. gigas. These findings indicated the potential framework by which mollusks pigmentation.

Shell Biosynthesis and Pigmentation as Revealed by the Expression of Tyrosinase and Tyrosinase-like Protein Genes in Pacific Oyster (Crassostrea gigas) with Different Shell Colors

The widely recognized color polymorphisms of molluscan shell have been appreciated for hundreds of years by collectors and scientists, while molecular mechanisms underlying shell pigmentation are still poorly understood. Tyrosinase is a key rate-limiting enzyme for the biosynthesis of melanin. Here, we performed an extensive multi-omics data mining and identified two tyrosinase genes, including tyrosinase and tyrosinase-like protein 2 (Tyr and Typ-2 respectively), in the Pacific oyster Crassostrea gigas, and investigated the expression patterns of tyrosinase during adults and embryogenesis in black and white shell color C. gigas. Tissue expression analysis showed that two tyrosinase genes were both specifically expressed in the mantle, and the expression levels of Tyr and Typ-2 in the edge mantle were significantly higher than that in the central mantle. Besides, Tyr and Typ-2 genes were black shell-specific compared with white shell oysters. In situ hybridization showed that strong signals for Tyr were detected in the inner surface of the outer fold, whereas positive signals for Typ-2 were mainly localized in the outer surface of the outer fold. In the embryos and larvae, the high expression of Tyr mRNA was detected in eyed-larvae, while Typ-2 mRNA was mainly expressed at the trochophore and early D-veliger. Furthermore, the tyrosinase activity in the edge mantle was significantly higher than that in the central mantle. These findings indicated that Tyr gene may be involved in shell pigmentation, and Typ-2 is more likely to play critical roles not only in the formation of shell prismatic layer but also in shell pigmentation. In particular, Typ-2 gene was likely to involve in the initial non-calcified shell of trochophores. The work provides valuable information for the molecular mechanism study of shell formation and pigmentation in C. gigas.

Mitf Involved in Innate Immunity by Activating Tyrosinase-Mediated Melanin Synthesis in Pteria penguin

The microphthalmia-associated transcription factor (MITF) is an important transcription factor that plays a key role in melanogenesis, cell proliferation, survival and immune defense in vertebrate. However, its function and function mechanism in bivalve are still rarely known. In this research, first, a Mitf gene was characterized from Pteria penguin (P. penguin). The PpMitf contained an open reading frame of 1,350 bp, encoding a peptide of 449 deduced amino acids with a highly conserved basic helix-loop-helix-leucine zipper (bHLH-LZ) domain. The PpMITF shared 55.7% identity with amino acid sequence of Crassostrea gigas (C. gigas). Tissue distribution analysis revealed that PpMitf was highly expressed in mantle and hemocytes, which were important tissues for color formation and innate immunity. Second, the functions of PpMitf in melanin synthesis and innate immunity were identified. The PpMitf silencing significantly decreased the tyrosinase activity and melanin content, indicating PpMitf involved in melanin synthesis of P. penguin. Meanwhile, the PpMitf silencing clearly down-regulated the expression of PpBcl2 (B cell lymphoma/leukemia-2 gene) and antibacterial activity of hemolymph supernatant, indicating that PpMitf involved in innate immunity of P. penguin. Third, the function mechanism of PpMitf in immunity was analyzed. The promoter sequence analysis of tyrosinase (Tyr) revealed two highly conserved E-box elements, which were specifically recognized by HLH-LZ of MITF. The luciferase activities analysis showed that Mitf could activate the E-box in Tyr promoter through highly conserved bHLH-LZ domain, and demonstrated that PpMitf involved in melanin synthesis and innate immunity by regulating tyrosinase expression. Finally, melanin from P. penguin, the final production of Mitf-Tyr-melanin pathway, was confirmed to have direct antibacterial activity. The results collectively demonstrated that PpMitf played a key role in innate immunity through activating tyrosinase-mediated melanin synthesis in P. penguin.

Integrated proteomic and transcriptomic analysis reveals that polymorphic shell colors vary with melanin synthesis in Bellamya purificata snail

The snail Bellamya purificata is an ecologically and economically important freshwater gastropod species. However, limited genomic resources are available for this snail. In this study, the transcriptome of mantle tissues and proteome of shells of B. purificata with two shell colors (namely light-cyan line (LC) and light-purple line (LP)) were deeply sequenced and characterized. A total of 5.72 million contigs were assembled into 157,015 unigenes, 21,455 (13.66%) of these unigenes were significantly matched to NR, Swiss-Prot, KOG, GO and KEGG database. 1807 differentially expressed genes (DEGs) were identified between the two different shell color lines. These DEGs were significantly enriched in five KEGG pathways including tyrosine metabolism, tryptophan metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, and histidine metabolism, which suggested that the shell color polymorphism in B. purificata was a result of melanin synthesis variation. A total of 1521 proteins were identified in B. purificata here as well. The differentially expressed protein analysis showed that the tyrosinase content in LP was significantly decreased in comparison to LC, which agreed with the transcriptome analysis results. This study provides valuable genomic resources of B. purificata and improves our understanding of molecular mechanisms of biomineralization and shell color polymorphism in snail.

Survival, retention rate and immunity of the black shell colored stocks of pearl oyster Pinctada fucata martensii after grafting operation

We have developed a black shell colored selected line observed to have higher survival ability. In this study, to understand its immune capacity, total carotenoid content (TCC) of the black shell colored line (BG) and the control group (CG) were compared. Survival and retention rates, immunity and antioxidant capacity of BG were compared relative to CG at different times after grafting operation. The results showed that BG had significantly larger TCC than CG (P < 0.05). BG had significantly higher survival and retention rates than CG on days 7, 30 and 360 after grafting (P < 0.05). On days 360, BG had significantly larger pearl thickness than CG (P < 0.05). BG exhibited increased ACP, AKP, SOD, CAT, TAOC and LZ activity than the CG on 0 h, 12 h, 1 d, 3 d, 5 d, 7 d and 30 d after grafting. BG had higher expression levels of Fascin, SOD, CDK-7, CDAP-1, IRAK-1, α2m, GST-1, TRAF-3 and Caspase-2 than CG. The results suggested that BG had higher immune competence and pearl production performances, which is promising to improve pearl quality and production.

Immune-related molecular and physiological differences between black-shelled and white-shelled Pacific oysters Crassostrea gigas

The black-and-white traits on shells and mantle edges of the Pacific oyster, Crassostrea gigas, are inheritable and correlated, and black shells (melanin pigmentation) are usually found in the Pacific oysters. Based on differentially expressed genes from RNA-Seq and physiological characteristics, in this study, Black-shelled Pacific oysters (BSO) and White-shelled Pacific oysters (WSO) were selected to determine the molecular differences between oysters with obviously different melanin content. The differences in the process of immune recognition and modulation indicated that BSO may be more sensitive to the immune substances. There might have different modulation mode of apoptosis and phagocytosis between BSO and WSO, and caspase-3 might have played a key role in the apoptotic process of BSO. Different oxidation-related pathways were enriched in both BSO and WSO, suggesting the different response strategies of BSO and WSO to oxidative stress. The physiological evidences showed that, compared with WSO, in BSO, the tyrosinase content, the caspase-3 activity and the suppression of hydroxyl radical increased, and the reactive oxygen species concentration decreased. Therefore, immune-related molecular and physiological differences were found between BSO and WSO.

Relationship of the orange tissue morphotype with shell and pearl colouration in the mollusc Pinctada margaritifera

Molluscs display a vast range of shell colours both between and within species. However, only a few species show colour variation in their soft tissues. In French Polynesia, the pearl oyster Pinctada margaritifera has three tissue morphotypes: the black wild-type and two rare mutations: white albino and orange mantle. Phenotypic transmission is known to occur from these phenotypes when they are used as graft donors for pearl production, leading to multicoloured and white pearls from black and albino mantle grafts, respectively. The present study furthers this knowledge by examining the phenotypic association between the orange mantle tissue morphotype and hard tissues: shells and cultured pearls. Based on a large experimental graft, shell colour quantification and pearl qualification showed that the orange morphotype is associated with light-coloured shells and pearls. Expression analysis of some candidate genes previously identified in the white mantle mutant, tested here on both graft and pearl sac tissues from orange mantle donors, confirmed the involvement of genes associated with shell matrix protein (shem4) and the melanin biosynthesis pathway (zinc). This study provides fundamental information on the mechanism behind mantle tissue colour in P. margaritifera and its association with biomineralisation and pigmentation processes that will be potentially valuable in future selection programs.

Pax3 Gene Regulated Melanin Synthesis by Tyrosinase Pathway in Pteria penguin

The paired-box 3 (Pax3) is a transcription factor and it plays an important part in melanin synthesis. In this study, a new Pax3 gene was identified from Pteria penguin (Röding, 1798) (P. penguin) by RACE-PCR (rapid-amplification of cDNA ends-polymerase chain reaction) and its effect on melanin synthesis was deliberated by RNA interference (RNAi). The cDNA of PpPax3 was 2250 bp long, containing an open reading fragment of 1365 bp encoding 455 amino acids. Amino acid alignment and phylogenetic tree showed PpPax3 shared the highest (69.2%) identity with Pax3 of Mizuhopecten yessoensis. Tissue expression profile showed that PpPax3 had the highest expression in mantle, a nacre-formation related tissue. The PpPax3 silencing significantly inhibited the expression of PpPax3, PpMitf, PpTyr and PpCdk2, genes involved in Tyr-mediated melanin synthesis, but had no effect on PpCreb2 and an increase effect on PpBcl2. Furthermore, the PpPax3 knockdown obviously decreased the tyrosinase activity, the total content of eumelanin and the proportion of PDCA (pyrrole-2,3-dicarboxylic acid) in eumelanin, consistent with influence of tyrosinase (Tyr) knockdown. These data indicated that PpPax3 played an important regulating role in melanin synthesis by Tyr pathway in P. penguin.

Versatile Fungal Polyphenol Oxidase with Chlorophenol Bioremediation Potential: Characterization and Protein Engineering

Polyphenol oxidases (PPOs) have been mostly associated with the undesirable postharvest browning in fruits and vegetables and have implications in human melanogenesis. Nonetheless, they are considered useful biocatalysts in the food, pharmaceutical, and cosmetic industries. The aim of the present work was to characterize a novel PPO and explore its potential as a bioremediation agent. A gene encoding an extracellular tyrosinase-like enzyme was amplified from the genome of Thermothelomyces thermophila and expressed in Pichia pastoris The recombinant enzyme (TtPPO) was purified and biochemically characterized. Its production reached 40 mg/liter, and it appeared to be a glycosylated and N-terminally processed protein. TtPPO showed broad substrate specificity, as it could oxidize 28/30 compounds tested, including polyphenols, substituted phenols, catechols, and methoxyphenols. Its optimum temperature was 65°C, with a half-life of 18.3 h at 50°C, while its optimum pH was 7.5. The homology model of TtPPO was constructed, and site-directed mutagenesis was performed in order to increase its activity on mono- and dichlorophenols (di-CPs). The G292N/Y296V variant of TtPPO 5.3-fold increased activity on 3,5-dichlorophenol (3,5-diCP) compared to the wild type.IMPORTANCE A novel fungal PPO was heterologously expressed and biochemically characterized. Construction of single and double mutants led to the generation of variants with altered specificity against CPs. Through this work, knowledge is gained regarding the effect of mutations on the substrate specificity of PPOs. This work also demonstrates that more potent biocatalysts for the bioremediation of harmful CPs can be developed by applying site-directed mutagenesis.

Identification of a tyrosinase gene and its functional analysis in melanin synthesis of Pteria penguin

Tyrosinase is a key rate-limiting enzyme in melanin synthesis. In this study, a new tyrosinase gene (Tyr) was identified from Pteria penguin and its effect on melanin synthesis was deliberated by RNA interference (RNAi). The cDNA of PpTyr was 1728 bp long, containing a 5'untranslated region (UTR) of 11 bp, a 3'UTR of 295 bp, and an open reading fragment of 1422 bp encoding 473 amino acids. Amino acid alignment showed PpTyr had the highest (50%) identity to tyrosinase-like protein 1 from Pinctada fucata. Phylogenetic tree analysis classified PpTyr into α-subclass of type-3 copper protein. Tissue expression analysis indicated that PpTyr was highly expressed in mantle, a nacre formation related tissue. After PpTyr RNA interference, PpTyr mRNA was significantly inhibited by 71.0% (P < 0.05). For other melanin-related genes, PpCreb2 and PpPax3 expression showed no significant change, but PpBcl2 was obviously increased. By liquid chromatograph-tandem mass spectrometer (LC-MS/MS) analysis, the total content of PDCA (pyrrole-2, 3-dicarboxylic acid) and PTCA (pyrrole-2,3,5-tricarboxylic acid), as main markers for eumelanin, was sharply decreased by 66.6% after PpTyr RNAi (P < 0.05). The percentage of PDCA was also obviously decreased from 20.1% to 13.9%. This indicated that tyrosinase played a key role in melanin synthesis and color formation of P. penguin.

HcTyr and HcTyp-1 of Hyriopsis cumingii, novel tyrosinase and tyrosinase-related protein genes involved in nacre color formation

Tyrosinase is an important enzyme that is involved in biological processes such as pigmentation, wound healing, sclerotization of the cuticles, oxygen transport and innate immunity. As nacre color has an effect on pearl color, we studied the effect of tyrosinase on nacre color in Hyriopsis cumingii (an important freshwater pearl-producing mussel) by cloning novel tyrosinase protein and tyrosinase-related protein genes (HcTyr and HcTyp-1 respectively) from the mantle. The predicted amino acid sequences of HcTyr and HcTyp-1 contain conserved domains, and HcTyp-1 contains an additional chitin-binding domain. Two different types of mussels, purple shelled and white shelled, were used to investigate the role of tyrosinase in shell color. HcTyr and HcTyp-1 mRNAs were mainly expressed in the mantle, but the expression of HcTyr was higher in the purple mussel than in the white mussel while the expression of HcTyp-1 was higher in the white mussel. Strong and specific mRNA signals for HcTyp-1 were detected in the dorsal epithelial cells of the mantle pallial and some signals were detected in the epithelial cells of the periostracal groove, so HcTyp-1 may be involved in periostracum and nacreous layer formation. Strong and specific mRNA signals were also detected in the dorsal epithelial cells of the mantle pallial, so HcTyr may be involved in nacre formation. Further, the tyrosinase activity of the mantle in the purple mussel was higher than that in the white mussel. These findings indicate that HcTyr and HcTyp-1 may be involved in the formation of nacre color in H. cumingii.

Characterisation of the mantle transcriptome and biomineralisation genes in the blunt-gaper clam, Mya truncata

Members of the Myidae family are ecologically and economically important, but there is currently very little molecular data on these species. The present study sequenced and assembled the mantle transcriptome of Mya truncata from the North West coast of Scotland and identified candidate biomineralisation genes. RNA-Seq reads were assembled to create 20,106 contigs in a de novo transciptome, 18.81% of which were assigned putative functions using BLAST sequence similarity searching (cuttoff E-value 1E-10). The most highly expressed genes were compared to the Antarctic clam (Laternula elliptica) and showed that many of the dominant biological functions (muscle contraction, energy production, biomineralisation) in the mantle were conserved. There were however, differences in the constitutive expression of heat shock proteins, which were possibly due to the M. truncata sampling location being at a relatively low latitude, and hence relatively warm, in terms of the global distribution of the species. Phylogenetic analyses of the Tyrosinase proteins from M. truncata showed a gene expansion which was absent in L. elliptica. The tissue distribution expression patterns of putative biomineralisation genes were investigated using quantitative PCR, all genes showed a mantle specific expression pattern supporting their hypothesised role in shell secretion. The present study provides some preliminary insights into how clams from different environments - temperate versus polar - build their shells. In addition, the transcriptome data provides a valuable resource for future comparative studies investigating biomineralisation.

Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera

Population genomic investigations on highly dispersive marine organisms typically require thousands of genome-wide SNP loci to resolve fine-scale population structure and detect signatures of selection. This information is important for species conservation efforts and stock management in both wild and captive populations, as well as genome mapping and genome wide association studies. Double digest Restriction site-Associated DNA Sequencing (ddRADseq) is a recent tool for delivering genome wide SNPs for non-model organisms. However, its application to marine invertebrate taxa has been limited, particularly given the complex and highly repetitive nature of many of these organisms' genomes. This study develops and evaluates an optimised ddRADseq technique together with associated analyses for generating genome-wide SNP data, and performs population genomic analyses to inform aquaculture and fishery management of a marine bivalve, the black-lip pearl oyster Pinctada margaritifera. A total of 5243 high-quality genome-wide SNP markers were detected, and used to assess population structure, genome diversity, detect Fst outliers and perform association testing in 156 individuals belonging to three wild and one hatchery produced populations from the Fiji Islands. Shallow but significant population structure was revealed among all wild populations (average pairwise Fst=0.046) when visualised with DAPC and an individual network analysis (NetView P), with clear evidence of a genetic bottleneck in the hatchery population (NeLD=6.1), compared to wild populations (NeLD>192.5). Fst outlier detection revealed 42-62 highly differentiated SNPs (p<0.02), while case-control association discovered up to 152 SNPs (p<0.001). Both analyses were able to successfully differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species. BLAST searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating their biological relevance. This study has produced highly informative SNP and population genomic data in P. margaritifera, and using the same approach promises to be of substantial value to a range of other non-model, broadcast-spawning or marine invertebrate taxa.