Phylogenetic comparisons reveal mosaic histories of larval and adult shell matrix protein deployment in pteriomorph bivalves.

Molluscan shells are organo-mineral composites, in which the dominant calcium carbonate is intimately associated with an organic matrix comprised mainly of proteins and polysaccharides. However, whether the various shell matrix proteins (SMPs) date to the origin of hard skeletons in the Cambrian, or whether they represent later deployment through adaptive evolution, is still debated. In order to address this issue and to better understand the origins and evolution of biomineralization, phylogenetic analyses have been performed on the three SMP families, Von Willebrand factor type A (VWA) and chitin-binding domain-containing protein (VWA-CB dcp), chitobiase, and carbonic anhydrase (CA), which exist in both larval and adult shell proteomes in the bivalves, Crassostrea gigas and Pinctada fucata. In VWA-CB dcp and chitobiase, paralogs for larval and adult SMPs evolved before the divergence of these species. CA-SMPs have been taken as evidence for ancient origins of SMPs by their presumed indispensable function in biomineralization and ubiquitous distribution in molluscs. However, our results indicate gene duplications that gave rise to separate deployments as larval and adult CA-SMPs occurred independently in each lineage after their divergence, which is considerably more recent than hitherto assumed, supporting the "recent heritage and fast evolution" scenario for SMP evolution.

Molecular identification of an insulin growth factor binding protein (IGFBP) and its potential role in an insulin-like peptide system of the pearl oyster, Pinctada fucata.

Insulin-like growth factors (IGFs) play critical roles in regulating metabolism, growth, and reproduction in invertebrates. IGF binding proteins (IGFBPs) serve as major regulators of IGF activity and regulate endocrine system. In the present study, the full-length cDNA of an igfbp was identified from the pearl oyster, Pinctada fucata, using expressed sequence tag (EST) sequence. The 1124bp Pfigfbp cDNA contains a 465bp open reading frame (ORF) encoding a putative protein of 154 amino acids, a 5'-untranslated region (UTR) of 238bp, and a 3'-UTR of 394bp (not including polyA+). Multiple sequence alignment of the deduced IB domain sequences revealed that twelve conserved Cys and ILP binding site in PfIGFBP were well aligned with human IGFBPs1-7, Mizuhopecten yessoensis IGFBP5 and Eriocheir sinensis IGFBP7. Gene expression analysis indicated that Pfigfbp mRNA was expressed in all the tissues and developmental stages examined, with a higher level in the foot than in other tissues and a higher level in the polar body stage and 32-cell stage than in the other stages. Pfigfbp and PfILP (insulin-like peptide) mRNA levels significantly increased in the digestive gland after feeding, while levels were dramatically reduced during a week of food deprivation and increased upon refeeding. In vitro experiments indicated that Pfigfbp mRNA expression in mantle cells was affected by insulin/IGFs (IGF-I, IGF-II). Our data suggests that Pfigfbp may be involved in endocrine signaling in P. fucata via the regulation of insulin-like peptide signaling.

A novel toll-like receptor from the pearl oyster Pinctada fucata martensii is induced in response to stress.

Graft rejection due to immune incompatibility is a common occurrence in pearl culture, which often cause death to the host oyster. To improve cultured pearl production, host mortality and bead rejection rates must be reduced. Toll-like receptor 4 (TLR4) plays an important role in innate immunity, and may be related to allograft rejection. Here, we cloned the TLR4 cDNA from the pearl oyster Pinctada fucata martensii (PmTLR4). PmTLR4 cDNA was 3138bp, including a 2625bp open reading frame encoding 874 amino acids. The predicted PmTLR4 protein was structurally typical of the TLR family. PmTLR4 had relatively high sequence similarity and identity to the TLR4 of the Cyclina sinensis (48.1% and 27.6%, respectively). Multiple alignment of TLR4 sequences across species indicated that the Toll/interleukin-1 (IL-1) receptor domain was conserved among species. PmTLR4 mRNA was expressed in all tissues tested, with the most abundant mRNA expression in hepatopancreas and gill in P. fucata martensii. After being stressed by either lipopolysaccharide (LPS) exposure or the nucleus insertion operation, PmTLR4 mRNA expression increased significantly in the hemocytes as compared to controls. Peak level of PmTLR4 mRNA was observed 6h after the LPS injection, and 2d after the nucleus insertion operation. These data suggest that PmTLR4 may play a vital role in the induction of innate immunity and is therefore associated with allograft immunity in the pearl oyster P. fucata martensii.

The receptor genes PfBMPR1B and PfBAMBI are involved in regulating shell biomineralization in the pearl oyster Pinctada fucata.

Mounting evidence suggests that TGFß/BMP signaling pathway is most likely involved in shell biomineralization in molluscs, but the function of pathway receptors is poorly studied. Here, we cloned and identified two homologous BMP receptor genes, PfBMPR1B and PfBAMBI, from the pearl oyster Pinctada fucata. Real-time quantitative PCR and in situ hybridization revealed that these genes were expressed in mantle edge and pallial, specifically located at the outer epithelia. Knockdown of PfBMPR1B by RNA interference (RNAi) significantly decreased the expression levels of matrix protein (MP) genes and induced the abnormal ultrastructure of prismatic and nacreous layers. Conversely, knockdown of PfBAMBI significantly increased the expression levels of a portion of MP genes and induced the overgrowth of nacreous layer crystals. In the RNAi and shell notching experiments, MP gene expressions were competitively regulated by PfBMPR1B and PfBAMBI. In addition, the receptor inhibitor LDN193189 reduced the expression levels of MP genes in mantle primary cells and larvae, and induced abnormal D-shaped shell formation during larval development. Collectively, these results clearly show that PfBMPR1B and PfBAMBI are involved in regulating shell biomineralization in P. fucata. Our study therefore provides the direct evidence that BMP receptors participate in mollusc biomineralization.

Identification and Characterization of the Lysine-Rich Matrix Protein Family in Pinctada fucata: Indicative of Roles in Shell Formation.

Mantle can secret matrix proteins playing key roles in regulating the process of shell formation. The genes encoding lysine-rich matrix proteins (KRMPs) are one of the most highly expressed matrix genes in pearl oysters. However, the expression pattern of KRMPs is limited and the functions of them still remain unknown. In this study, we isolated and identified six new members of lysine-rich matrix proteins, rich in lysine, glycine and tyrosine, and all of them are basic matrix proteins. Combined with four members of the KRMPs previously reported, all these proteins can be divided into three subclasses according to the results of phylogenetic analyses: KRMP1-3 belong to subclass KPI, KRMP4-5 belong to KPII, and KRMP6-10 belong to KPIII. Three subcategories of lysine-rich matrix proteins are highly expressed in the D-phase, the larvae and adult mantle. Lysine-rich matrix proteins are involved in the shell repairing process and associated with the formation of the shell and pearl. What's more, they can cause abnormal shell growth after RNA interference. In detail, KPI subgroup was critical for the beginning formation of the prismatic layer; both KPII and KPIII subgroups participated in the formation of prismatic layer and nacreous layer. Compared with different temperatures and salinity stimulation treatments, the influence of changes in pH on KRMPs gene expression was the greatest. Recombinant KRMP7 significantly inhibited CaCO3 precipitation, changed the morphology of calcite, and inhibited the growth of aragonite in vitro. Our results are beneficial to understand the functions of the KRMP genes during shell formation.

[Identication of pearl powder and conch powder from different origins by differential scanning calorimetry].

The paper is aimed to establish a methods for identication of pearl powder and conch powder from different origins. Hermetic aluminum pan was used to encapsulate samples. The optimal testing conditions were: heating rate 10 degrees C x min(-1), sample weight 3 mg and nitrogen gas flow rate 40 mL x min(-1). The enthalpy values of pearl powder and conch powder was obvious different. Identication of pearl powder and conch powder by DSC is a practical method for its accuracy, convenience and practificality.

Molecular cloning and expression analysis of a pearl oyster (Pinctada martensii) heat shock protein 90 (HSP90).

Heat shock protein 90 (HSP90) is an important molecular chaperone required for proper folding of cellular proteins, and thus, it plays an essential role in protecting cells from damage during stress. In this study, an HSP90 cDNA designated PmHSP90 was cloned from the mantle tissue of the pearl oyster Pinctada martensii using reverse transcription polymerase chain reaction (RT-PCR) coupled with the rapid amplification of cDNA ends (RACE) approach. PmHSP90 cDNA was 2584 bp in length, including an open reading frame of 2160 bp, which encodes a polypeptide of 719 amino acid residues, with predicted molecular mass and isoelectric point of 83.0 kDa and 4.87, respectively. Multiple-sequence alignment indicated that HSP90 is highly conserved among species, and PmHSP90 showed 89% sequence identity to Crassostrea gigas HSP90. Five conserved amino acid blocks defined as HSP90 protein family signatures were also observed in PmHSP90, indicating that PmHSP90 may be a cytosolic member of the HSP90 family. Expression levels of PmHSP90 were detected in various tissues of P. martensii and in hemocytes under three different stress conditions using quantitative real-time PCR (qPCR). The results demonstrate that PmHSP90 mRNA is constitutively expressed in all the tested tissues and may be involved in the immune response against thermal stress, lipopolysaccharide stimulation, and nucleus insertion operations. Studies on PmHSP90 are a valuable source to further explore the immune system in pearl oysters during the production of pearls, and may enhance our knowledge of molluscan innate immunity.

Efficacy of calcein and Coomassie Blue dyeing of shell growing-edges and micro growth-bands: ageing juvenile of Pinctada mazatlanica (Pterioida: Pteriidae).

Age validation is the first step to determine shellfish species age determination. This information is vital for different inferential models used in marine ecosystem management activities. In spite that various validation techniques are used for marking carbon calcium structures, the calcein marking technique for oysters had never been used for age validation in Pinctada mazatlanica. Thus the objectives of this study included: the evaluation of calcein to mark a shell growing-edge, and the efficacy of Coomassie Blue staining on posterior shell growth, to produce visible micro growth-bands that would enable age validation of juvenile mother-of-pearl oysters. Oysters were collected and cultivated at The Perlas del Cortez S. de R. L. MI. pearl-farming operation, in Pichilingue, La Paz Bay, Baja California Sur, Mexico; a total of 36 oysters (shell height 11.5-36.4 mm) were injected with calcein (0.125 g/L), and another 50 oysters (shell height 14.8-42.7 mm) were submersed in calcein (0.4 and 0.7 g/L). Shell slices of calcein-marked oysters were posteriourly stained with Coomassie Blue R-25 for micro growth-band recognition. Our results showed that Calcein marking only worked by submersion and produced a concise bright lime-green florescent band along the growing-edge with clear boundaries for both concentrations. However, marks resulted better at the lower calcein concentration (0.4 g/L) with more "perfect" and "good" marks on the growing-edge (p = 0.0012). Commassie Blue staining technique was successful, and allowed to conclude that one micro growth-band was laid down per day, similar to other oyster species. Mean 15-d increment of shell growth height was slightly greater at the lower calcein concentration (= 0.735 mm) than at the higher one (= 0.577 mm) (not significant difference, p = 0.198). Calcein marking of shell growing-edges and Commassie Blue staining of posterior shell growth, as a method for age validation is recommended for shellfish shell growth-band counts. This will allow back-dating for estimation of very precise colonization dates, both spatially and temporally in future work.

Efficacy of calcein and Coomassie Blue dyeing of shell growing-edges and micro growth-bands: Ageing juvenile of Pinctada mazatlanica (Pterioida: Pteriidae) / Eficiencia de la tinción de bandas de crecimiento con calceina y azul de coomassie, para estimar la edad de jóvenes de Pinctada mazatlanica (Pterioida: Pteriidae)

Age validation is the first step to determine shellfish species age determination. This information is vital for different inferential models used in marine ecosystem management activities. In spite that various validation techniques are used for marking carbon calcium structures, the calcein marking technique for oysters had never been used for age validation in Pinctada mazatlanica. Thus the objectives of this study included: the evaluation of calcein to mark a shell growing-edge, and the efficacy of Coomassie Blue staining on posterior shell growth, to produce visible micro growth-bands that would enable age validation of juvenile mother-of- pearl oysters. Oysters were collected and cultivated at The Perlas del Cortez S. de R. L. MI. pearl-farming opera tion, in Pichilingue, La Paz Bay, Baja California Sur, Mexico; a total of 36 oysters (shell height 11.5-36.4mm) were injected with calcein (0.125g/L), and another 50 oysters (shell height 14.8-42.7mm) were submersed in calcein (0.4 and 0.7g/L). Shell slices of calcein-marked oysters were posteriourly stained with Coomassie Blue R-25 for micro growth-band recognition. Our results showed that Calcein marking only worked by submersion and produced a concise bright lime-green florescent band along the growing-edge with clear boundaries for both concentrations. However, marks resulted better at the lower calcein concentration (0.4g/L) with more “perfect” and “good” marks on the growing-edge (p=0.0012). Commassie Blue staining technique was successful, and allowed to conclude that one micro growth-band was laid down per day, similar to other oyster species. Mean 15-d increment of shell growth height was slightly greater at the lower calcein concentration ( =0.735mm) than at the higher one ( =0.577mm) (not significant difference, p=0.198). Calcein marking of shell growing- edges and Commassie Blue staining of posterior shell growth, as a method for age validation is recommended for shellfish shell growth-band counts. This will allow back-dating for estimation of very precise colonization dates, both spatially and temporally in future work.

La validación de la edad es el primer paso para determinar las edades de las especies de moluscos, esta información es de vital importancia para los diferentes modelos de inferencia utilizados en actividades de gestión de los ecosistemas marinos. Diversas técnicas de valida- ción se utilizan para marcar estructuras de carbonato de calcio, aunque la técnica de marcado de calceína en ostras nunca se había utilizado para la validación de la edad de P. mazatlanica. Los objetivos de este estudio fueron: evaluar la calceína como marcador interno de la concha y la eficiencia del azul de Coomassie en la tinción de la matriz proteica de la concha, para facilitar la observación y conteo de micro bandas de crecimiento que permiten validar la edad de las ostras juveniles de madre perla. Las ostras fue- ron recolectadas en la costa de la empresa Perlas del Cortez S. de RL MI., en Pichilingue en Bahía de La Paz, Baja California Sur, México. Se inyectaron 36 ostras (altura de concha 11.5-36.4mm) (0.125g/L de calceína) y otras 50 ostras (altura de la concha 14.8-42.7mm) se sumergieron (0.4 y 0.7g/L de calceína). Secciones de la concha marcadas con calceína fueron teñidos con azul de Coomassie R-25 para el reconocimiento de las micro bandas de crecimiento. El marcado con calceína fue exitoso por inmersión y produjo una banda fluorescente de color verde lima brillante con- cisa a lo largo del crecimiento interno de la concha. Sin embargo, las marcas fueron mejores a una concentración de calceína inferior (0.4g/L), con mayor cantidad de marcas “buenas” y “perfectas” (p=0.0012). La técnica de tinción con azul de Commassie también fue exitosa. Se detectó un crecimiento diario por micro banda, similar a lo encontrado en otras especies de ostras. La diferencia del crecimiento medio en relación a la altura de la concha en un lapso de 15 días, fue ligeramente mayor con una concentración de calceína inferior ( =0.735mm) que con la de mayor concentración ( =0.577mm), pero no significativamente (p=0.198). El marcado de conchas con calceína y tinción de matrices proteicas con azul de Coomassie posterior a su crecimiento, es recomendando como un método para la validación de la edad facilitando el conteo de micro bandas de crecimiento internas de la concha. Además, permitirá estimar edades con el fin de predecir fechas de colonización y ubicación de bancos naturales.

DNA fingerprinting of pearls to determine their origins.

We report the first successful extraction of oyster DNA from a pearl and use it to identify the source oyster species for the three major pearl-producing oyster species Pinctada margaritifera, P. maxima and P. radiata. Both mitochondrial and nuclear gene fragments could be PCR-amplified and sequenced. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay in the internal transcribed spacer (ITS) region was developed and used to identify 18 pearls of unknown origin. A micro-drilling technique was developed to obtain small amounts of DNA while maintaining the commercial value of the pearls. This DNA fingerprinting method could be used to document the source of historic pearls and will provide more transparency for traders and consumers within the pearl industry.

Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology.

The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ~1150-Mb genome at ~40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry.

cDNA cloning and mRNA expression of a tandem-repeat galectin (PoGal2) from the pearl oyster, Pinctada fucata.

Galectins can recognize and specifically bind to ß-galactoside residues, playing crucial roles in innate immune responses of vertebrates and invertebrates. We cloned the cDNA of a tandem-repeat galectin from the pearl oyster Pinctada fucata (designated as PoGal2). PoGal2 cDNA is 1347 bp long and consists of a 5'-untranslated region (UTR) of 3 bp, a 3'-UTR of 297 bp with one cytokine RNA instability motif (ATTTA), and an open reading frame of 1047 bp, encoding a polypeptide of 349 amino acids, with an estimated molecular mass of 38.1 kDa and a theoretical isoelectric point of 8.5. PoGal2 contains two carbohydrate recognition domains (CRDs); both have the conserved carbohydrate-binding motifs H-NPR and WG-EE. PoGal2 shares 50.6 and 50.9% identity with those of abalone (Haliotis discus) and the Manila clam (Venerupis philippinarum), respectively. Phylogenetic analysis revealed that the tandem-repeat galectins formed two clades for the different species. Molluscan tandem-repeat galectins were clustered into a single clade, and nematode tandem-repeat galectins were clustered into another single clade. In both clades, CRD-N and CRD-C were divided into different groups. PoGal2 mRNA was constitutively expressed in all tissues analyzed, and the expression level of PoGal2 mRNA was found to be significantly up-regulated in digestive glands, gills and hemocytes after Vibrio alginolyticus stimulation/infection. Expression profile analysis showed that the expression level of PoGal2 mRNA was significantly up-regulated at 8, 12 and 24 h after V. alginolyticus infection. These results suggest that PoGal2 is a constitutive and inducible acute-phase protein involved in the innate immune response of pearl oysters.

A macrophage migration inhibitory factor like oxidoreductase from pearl oyster Pinctada fucata involved in innate immune responses.

Macrophage migration inhibitory factor (MIF) is an important cytokine and plays a crucial role as a pivotal regulator of innate immunity. In this study, a MIF cDNA was identified and characterized from the pearl oyster Pinctada fucata (designated as PoMIF). The full-length of PoMIF was 1544 bp and consisted of a 5'-untranslated region (UTR) of 45 bp, a 3'-UTR of 1139 bp with a polyadenylation signal (AATAAA) at 12 nucleotides upstream of the poly (A) tail. The open reading frame (ORF) of PoMIF was 360 bp which encoded a polypeptide of 120 amino acids with an estimated molecular mass of 13.3 kDa and a predicted pI of 6.1. SMART analysis showed that PoMIF contained the catalytic-sites P² and K³³ for tautomerase activity, a motif C57GSV6° for oxidoreductase activity and a MIF family signature D55PCGSVEVYSIGALG69. Homology analysis revealed that the PoMIF shared 40.3-65.5% similarity and 26.9-45.0% identity to other known MIF sequences. PoMIF mRNA was constitutively expressed in seven selected tissues of healthy pearl oysters, with the highest expression level in digestive gland. Eight hours after P. fucata was injected with Vibrio alginolyticus, the expression of PoMIF mRNA was significantly up-regulated in digestive gland, gills, hemocytes and intestine. The cDNA fragment encoding mature protein of PoMIF was subcloned to expression vector pRSET and transformed into Escherichia coli BL21 (DE3). The recombinant PoMIF (rPoMIF) was expressed and purified under optimized conditions. Function analysis showed that rPoMIF had oxidoreductase activity and could utilize dithiothreitol (DTT) as reductant to reduce insulin.

F-type lectin involved in defense against bacterial infection in the pearl oyster (Pinctada martensii).

In invertebrates and vertebrates, carbohydrate-binding proteins (lectins) play an important role in innate immunity against microbial invasion. In the present study, we report the cloning of an F-type lectin (designated as PmF-lectin) from pearl oyster (Pinctada martensii) using a combination of expression sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) PCR. The full-length cDNA of PmF-lectin contains an open reading frame (ORF) of 579 bp coding for192 amino acids. The deduced polypeptide possesses six conserved residues of the F-lectin family critical for the formation of disulfide bonds (Cys4³-Cys¹4³, Cys75-Cys76 and Cys¹°²-Cys¹¹9). Reverse transcription PCR (RT-PCR) and real-time quantitative PCR (qRT-PCR) analyses in adult tissues showed that the PmF-lectin mRNA was abundantly expressed in haemocytes and gill, moderately expressed in the mantle, and rarely expressed in other tissues tested. After challenge with Vibrio alginolyticus, expression of PmF-lectin mRNA in haemocytes was dramatically up-regulated, reaching the highest level (13-fold higher than that of the control group) at 3 h post challenge, and then dropped gradually. These results suggest that PmF-lectin is a member of the F-lectin family and is involved in the innate immune response in pearl oyster.

A multidomain galectin involved in innate immune response of pearl oyster Pinctada fucata.

Galectins could specifically bind to ß-galactoside residues and play crucial roles in innate immune responses of vertebrates and invertebrates. In this study, the cDNA of a galectin with multiple carbohydrate-recognition domains (CRDs) was cloned from pearl oyster Pinctada fucata (designated as PoGal). PoGal cDNA was 2138bp long and consisted of a 5'-untranslated region (UTR) of 120bp, a 3'-UTR of 350bp with two cytokine RNA instability motifs (ATTTA), and an open reading frame (ORF) of 1668bp encoding a polypeptide of 555 amino acids with an estimated molecular mass of 63.4kDa and a theoretical isoelectric point of 4.8. PoGal contained four CRDs, each CRD of PoGal all had the conserved carbohydrate-binding motifs H-NPR and WG-ER. PoGal shared 43.7% and 62.9% identity to those of bay scallop and eastern oyster, respectively, which were only two galectins with four CRDs. The phylogenetic analysis revealed that all galectins with four CRDs formed a single clade. PoGal mRNA was constitutively expressed in all detected tissues, and the expression level of PoGal mRNA was significantly up-regulated in digestive gland, mantle, haemocyte, gonad and intestine after Vibrio alginolyticus stimulation. The expression profile analysis showed that the expression level of PoGal mRNA was significantly up-regulated at 4, 8 and 12h after V. alginolyticus stimulation. These results suggested that PoGal was a constitutive and inducible acute-phase protein that perhaps involved in innate immune response of pearl oyster.

Molecular phylogeny of pearl oysters and their relatives (Mollusca, Bivalvia, Pterioidea).

BACKGROUND: The superfamily Pterioidea is a morphologically and ecologically diverse lineage of epifaunal marine bivalves distributed throughout the tropical and subtropical continental shelf regions. This group includes commercially important pearl culture species and model organisms used for medical studies of biomineralization. Recent morphological treatment of selected pterioideans and molecular phylogenetic analyses of higher-level relationships in Bivalvia have challenged the traditional view that pterioidean families are monophyletic. This issue is examined here in light of molecular data sets composed of DNA sequences for nuclear and mitochondrial loci, and a published character data set of anatomical and shell morphological characters. RESULTS: The present study is the first comprehensive species-level analysis of the Pterioidea to produce a well-resolved, robust phylogenetic hypothesis for nearly all extant taxa. The data were analyzed for potential biases due to taxon and character sampling, and idiosyncracies of different molecular evolutionary processes. The congruence and contribution of different partitions were quantified, and the sensitivity of clade stability to alignment parameters was explored. CONCLUSIONS: Four primary conclusions were reached: (1) the results strongly supported the monophyly of the Pterioidea; (2) none of the previously defined families (except for the monotypic Pulvinitidae) were monophyletic; (3) the arrangement of the genera was novel and unanticipated, however strongly supported and robust to changes in alignment parameters; and (4) optimizing key morphological characters onto topologies derived from the analysis of molecular data revealed many instances of homoplasy and uncovered synapomorphies for major nodes. Additionally, a complete species-level sampling of the genus Pinctada provided further insights into the on-going controversy regarding the taxonomic identity of major pearl culture species.

Molecular characterization and expression analysis of cathepsin L1 cysteine protease from pearl oyster Pinctada fucata.

Cathepsin L is one of the crucial enzyme superfamilies and involved in the immune responses. In this study, a cDNA encoding cathepsin L cysteine protease was identified and characterized from pearl oyster Pinctada fucata (designated as poCL1). The poCL1 cDNA was 1160 bp long and consisted of a 5'-untranslated region (UTR) of 15 bp, a 3'-UTR of 149 bp with a polyadenylation signal (AATAAA) at 11 nucleotides upstream of the poly(A) tail, and an open reading frame (ORF) of 996 bp encoding a polypeptide of 331 amino acids, which contained a typical signal peptide sequence (Met(1)-Ala(16)), a prodomain (Thr(17)-Asp(113)), and a mature domain (Leu(114)-Val(331)). The preproprotein contained the oxyanion hole (Gln), the active triad formed by Cys, His and Asn, and the conserved ERFNIN, GNFD motifs, which is characteristic for cathepsin L proteases. Homology analysis revealed that the poCL1 shared 62.5-72.5% similarity and 42.9-56.0% identity to other known cathepsin L sequences. The phylogenetic tree showed that the poCL1 clustered with the invertebrate cathepsin L cysteine proteases and was closely related to Stichopus japonicus CL, Strongylocentrotus salar CL1 and Radix peregra CL. The mRNA expression of the poCL1 in blank group and bacterial challenge group could be detected in all studied tissues with the higher level in digestive gland. The expression level of poCL1 mRNA was significantly up-regulated at 4 h and 8 h, and then significantly down-regulated at 12 h and 24 h in digestive gland after Vibrio alginolyticus stimulation. These results provided important information for further exploring the roles of pearl oyster cathepsin L in the immune responses.

Molecular characterization and expression analysis of a putative LPS-induced TNF-alpha factor (LITAF) from pearl oyster Pinctada fucata.

The lipopolysaccharide-induced TNF-alpha factor (LITAF) is a novel transcription factor, which plays an important role in regulating the expression of TNF-alpha and various inflammatory cytokines in response to LPS stimulation and forms a dependent signaling pathway separated from NF-kappaB. Herein, we described the identification and characterization of pearl oyster Pinctada fucata LPS-induced TNF-alpha factor gene (designated as poLITAF). The poLITAF cDNA was 932 bp long and consisted of a 5'-untranslated region (UTR) of 45 bp, a 3'-UTR of 497 bp with two cytokine RNA instability motifs (ATTTA), and an open reading frame (ORF) of 390 bp encoding a polypeptide of 129 amino acids with an estimated molecular mass of 13.5 kDa and a theoretical isoelectric point of 8.36. A LITAF domain at C-terminal was identified in the poLITAF using SMART analysis, which contained two conserved CXXC motifs. Homology analysis of the deduced amino acid sequence of the poLITAF with other known LITAF sequences by MatGAT software revealed that the poLITAF shared 44.2-67.4% similarity and 35.4-50.0% identity to the other known LITAF sequences. The expression level of poLITAF mRNA was the highest in digestive gland and gill, moderate in adductor muscle, gonad, intestine and mantle, the lowest in haemocytes. The poLITAF mRNA expression was significantly up-regulated at 24 h in gill and at 12 h in digestive gland after LPS stimulation respectively. These results suggested that the poLITAF was a constitutive and inducible acute-phase protein that perhaps involved in the innate immune response of pearl oyster.

Molecular cloning, characterization and expression analysis of a clip-domain serine protease from pearl oyster Pinctada fucata.

The clip-domain serine proteases (SPs) are the essential components of extracellular signaling cascade in various biological processes, especially in embryonic development and the innate immune responses of invertebrate. Herein, we described the isolation and characterization of pearl oyster Pinctada fucata clip-domain SP gene (designated as poSP). The poSP cDNA was 1080 bp long and consisted of a 5'-untranslated region (UTR) of 13 bp, a 3'-UTR of 68 bp with a polyadenylation signal (AATAAA) at 22 nucleotides upstream of the poly(A) tail, and an open reading frame (ORF) of 999 bp encoding a polypeptide of 332 amino acids with an estimated molecular mass of 36.5 kDa and a theoretical isoelectric point of 7.3. A clip-domain and a trypsin-like serine protease domain were identified in the poSP using SMART analysis. Homology analysis of the deduced amino acid sequence of the poSP with other known SP sequences by MatGAT software revealed that the poSP shared 47.0-68.4% similarity to the other known SP sequences. The poSP mRNA was expressed in haemocytes, gonad, digestive gland and mantle, but not expressed in adductor muscle and gill. The poSP mRNA was up-regulated and increased nearly double-fold after LPS or Vibrio alginolyticus stimulation, respectively. These results suggested that the poSP was an inducible acute-phase protein that perhaps involved in the innate immune response of pearl oyster.

Cloning and expression of heat shock protein 70 gene in the haemocytes of pearl oyster (Pinctada fucata, Gould 1850) responding to bacterial challenge.

The cDNA of pearl oyster Pinctada fucata Hsp70 (designated PFHsp70) was cloned by EST and rapid amplification of cDNA ends (RACE) techniques. The full length of PFHsp70 cDNA was 2376 bp, consisting of a 5'-terminal untranslated region (UTR) of 89 bp, a 3' terminal UTR of 328 bp, and an open reading frame (ORF) of 1959 bp encoding a polypeptide of 652 amino acids with a theoretical molecular weight of 71.42 kDa and an estimated isoelectric point of 5.18. BLAST analysis revealed that the PFHsp70 gene shared high similarity with other Hsp70 genes. PFHsp70 contained all the three classical Hsp70 family signatures. The results indicated that the PFHsp70 was a member of the heat shock protein 70 family. Fluorescent real-time quantitative RT-PCR was used to examine the expression of PFHsp70 gene in haemocytes of P. fucata after the challenge of bacteria Vibrio alginolyticus. There was a clear time-dependent expression pattern of PFHsp70 after bacterial challenge, and the mRNA expression reached a maximum level at 4 h post-challenge, which returned to control level after 32 h. The up-regulated mRNA expression of PFHsp70 in P. fucata after bacterial challenge indicates that the Hsp70 gene is inducible and involved in immune response.