A novel ferritin subunit involved in shell formation from the pearl oyster (Pinctada fucata)

Glycogen and zinc-enriched ferritin as bioavailable nanoparticulate nutrients released from gastrointestinal digestion of pacific oyster (Crassostrea gigas)

Oyster is a low-carbon animal food enriched with protein, glycogen, and trace minerals. Nano-nutrients are increasingly perceived as an unignorable part of foods. Here, simulated gastrointestinal digestion released a considerable amount of nanoparticulate nutrients from raw and cooked oysters. They were identified as glycogen monomers with size of 20-40 nm and their aggregates, as well as 6 nm-sized bare cores of ferritin containing iron and zinc (4:1, w/w). FITC-labeling and flow cytometry unveiled the efficient uptake of oyster glycogen by polarized Caco-2 cells via macropinocytosis and receptor-mediated endocytosis. Calcein-fluorescence-quenching assay revealed divalent-metal-transporter-1- and macropinocytosis-mediated enterocyte iron absorption from oyster ferritin. Zinquin-fluorescence flow cytometry and ex-vivo mouse ileal loop experiments demonstrated the ready intestinal zinc absorption from oyster ferritin via macropinocytosis, as well as the good resistance of oyster ferritin to phytate's inhibition on zinc absorption. Overall, our results offer a new insight into the digestive and chemical properties of oysters.

Search for new biomarkers of tolerance to Perkinsus olseni parasite infection in Ruditapes decussatus clams

The grooved carpet shell (Ruditapes decussatus) is a clam species with high economic and social importance in several European and Mediterranean countries. Production of this species suffered a decline caused by biotic (parasite infection) and abiotic factors (environmental factors, stress, poor management methods and intensive culture of the introduced species Ruditapes philippinarum). The protozoan parasite Perkinsus olseni is also responsible for the decline of production, being nowadays one of the major issues for clam culture. Molecular biomarkers that might represent tolerance of R. decussatus to P. olseni have already been uncovered, shedding light in a possible production improvement by selecting those clams with a strongest immune response. In the present study, new tolerance biomarkers to P. olseni infection in R. decussatus were identified. The haemolymph proteomic profiles of naturally non/low-infected (tolerant) and highly-infected (susceptible) clams by the parasite across several heavy affected areas of Europe were characterized through a shotgun proteomics approach. Also, the mechanisms that might be involved in the responses against the disease in chronic infections were explored. Proteins related to energy restoration and balance, metabolic regulation, energy accumulation, ROS production, lysosomal activity, amino acid synthesis, proteolytic activity, iron regulation, iron withholding, and immune response modulation were significantly regulated in susceptible clams. In the tolerant group, proteins related to phagocytosis regulation, control of cell growth and proliferation, gonadal maturation, regulation of apoptosis, growth modulation, response to oxidative stress, iron regulation, shell development and metabolic regulation were significantly expressed. In summary, the protein expression profile of tolerant individuals suggests that an efficient pathogen elimination mechanism coupled to a better metabolic regulation leads to a tolerance to the parasite infection by limiting the spread through the tissues.

Molecular basis of ocean acidification sensitivity and adaptation in Mytilus galloprovincialis

Predicting the potential for species adaption to climate change is challenged by the need to identify the physiological mechanisms that underpin species vulnerability. Here, we investigated the sensitivity to ocean acidification in marine mussels during early development, and specifically the trochophore stage. Using RNA and DNA sequencing and in situ RNA hybridization, we identified developmental processes associated with abnormal development and rapid adaptation to low pH. Trochophores exposed to low pH seawater exhibited 43 differentially expressed genes. Gene annotation and in situ hybridization of differentially expressed genes point to pH sensitivity of (1) shell field development and (2) cellular stress response. Five genes within these two processes exhibited shifts in allele frequencies indicative of a potential for rapid adaptation. This case study contributes direct evidence that protecting species’ existing genetic diversity is a critical management action to facilitate species resilience to climate change.

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Marine mussel larval development and genetic adaptation in low pH seawater

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RNA and DNA responses reveal impacts on shell field development and cell stress

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Five genes exhibited both physiological sensitivity and long-term adaptive potential

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Conserving standing genetic variation could bolster resilience to global change

RNA Interference Analysis Reveals the Positive Regulatory Role of Ferritin in Testis Development in the Oriental River Prawn, Macrobrachium nipponense

Ferritin plays an essential role in organismic and cellular iron homeostasis in Macrobrachium nipponense. In this study, we aimed to investigate the role of ferritin in the sexual development of male M. nipponense. According to the qPCR analysis of different tissues and developmental stages, ferritin exhibited high expression levels in the testis and androgenic gland, from post-larval developmental stage 5 (PL5) to PL15, indicating that it may be involved in gonad differentiation and development, especially in male sexual development. In situ hybridization and qPCR analysis in various reproductive cycles of the testis indicated that ferritin may play an essential role in spermatogonia development in M. nipponense. RNAi analysis revealed that ferritin positively affected mRNA expression of the insulin-like androgenic gland (Mn-IAG) and the secretion of testosterone, and thus positively affected testis development in M. nipponense. This study highlighted the functions of ferritin in the sexual development of male M. nipponense and provided important information for the establishment of a technique to regulate the process of testis development in M. nipponense.

De novo assembly transcriptome analysis reveals the genes associated with body color formation in the freshwater ornamental shrimps Neocaridina denticulate sinensis

The body color of Neocaridina denticulate sinensis is a compelling phenotypic trait, in which a cascade of carotenoid metabolic processes plays an important role. The study was conducted to compare the transcriptome of cephalothoraxes among three pigmentation phenotypes (red, blue, and chocolate) of N. denticulate sinensis. The purpose of this study was to explore the candidate genes associated with different colors of N. denticulate sinensis. Nine cDNA libraries in three groups were constructed from the cephalothoraxes of shrimps. After assembly, 75022 unigenes were obtained in total with an average length of 1026 bp and N50 length of 1876 bp. There were 45977, 25284, 23605, 21913 unigenes annotated in the Nr, Swissprot, KOG, and KEGG databases, respectively. Differential expression analysis revealed that there were 829, 554, and 3194 differentially expressed genes (DEGs) in RD vs BL, RD vs CH, and BL vs CH, respectively. These DEGs may play roles in the absorption, transport, and metabolism of carotenoids. We also emphasized that electron transfer across the inner mitochondrial membrane (IMM) was a key process in pigment metabolism. In addition, a total of 6328 simple sequence repeats (SSRs) were also detected in N. denticulate sinensis. The results laid a solid foundation for further research on the molecular mechanism of integument pigmentation in the crustacean and contributed to developing more attractive aquatic animals.

A novel ferritin subunit gene from Asian green mussel, Perna viridis (Linnaeus, 1758)

Iron sequestration through ferritin forms a major part of innate immune response in molluscs and detailed understanding of ferritin gene and its functions can be directly applied in infection and disease management studies. Accordingly, identification and detailed molecular characterization of a ferritin subunit gene from a commercially significant marine mussel Perna viridis was targeted. Molecular screening using degenerate primers in total mantle RNA resulted in the amplification of a novel ferritin gene fragment having <87% identity to the reported ferritin gene sequences. Rapid amplification of cDNA ends-PCR was followed to generate complete cDNA sequence of P.viridis ferritin (PvFer). The complete cDNA was found to be 798 bp, containing an open reading frame of 522 bp, 5' untranslated region (UTR) of 112 bp and 3' UTR of 165 bp. The 5' UTR and 3' UTR were shown to contain an iron response element (IRE) and a polyadenylation signal (767AATAAA772) with poly (A) tail, respectively. Prediction of stem loop structure revealed that, PvFer-IRE can be folded into a typical secondary stem loop structure, having 5-CAGUGA-3' loop, proximal stem of five paired bases followed by a bulged cysteine, and six nucleotide bottom stem, indicating that expression of PvFer is regulated by iron at the translational level. ORF was found to encode 175 amino acid protein with calculated molecular mass of 19.97 kDa and isoelectric point of 4.97. Examination for signal peptide and phylogenetic analysis confirmed that PvFer belonged to cytosolic ferritins of molluscs. Conserved domain analysis showed that PvFer contained both ferroxidase diiron center and ferrihydrite nucleation center, analogous to ferritin M subunit of bony fishes and amphibians. However, amino acid sequence and glycosylation site showed more homology to vertebrate ferritin H subunits. Predicted 3D models of PvFer resembled the typical spatial features of ferritin proteins. The study forms the first comprehensive identification of a ferritin subunit gene in a true/common mussel (Order: Mytilida). Further, the detailed molecular phylogeny conducted through the present study revealed certain thought provoking insights on ferritin genes of the phylum Mollusca.

The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity

BACKGROUND

Venoms are deadly weapons to subdue prey or deter predators that have evolved independently in many animal lineages. The genomes of venomous animals are essential to understand the evolutionary mechanisms involved in the origin and diversification of venoms.

RESULTS

Here, we report the chromosome-level genome of the venomous Mediterranean cone snail, Lautoconus ventricosus (Caenogastropoda: Conidae). The total size of the assembly is 3.59 Gb; it has high contiguity (N50 = 93.53 Mb) and 86.6 Mb of the genome assembled into the 35 largest scaffolds or pseudochromosomes. On the basis of venom gland transcriptomes, we annotated 262 complete genes encoding conotoxin precursors, hormones, and other venom-related proteins. These genes were scattered in the different pseudochromosomes and located within repetitive regions. The genes encoding conotoxin precursors were normally structured into 3 exons, which did not necessarily coincide with the 3 structural domains of the corresponding proteins. Additionally, we found evidence in the L. ventricosus genome for a past whole-genome duplication event by means of conserved gene synteny with the Pomacea canaliculata genome, the only one available at the chromosome level within Caenogastropoda. The whole-genome duplication event was further confirmed by the presence of a duplicated hox gene cluster. Key genes for gastropod biology including those encoding proteins related to development, shell formation, and sex were located in the genome.

CONCLUSIONS

The new high-quality L. ventricosus genome should become a reference for assembling and analyzing new gastropod genomes and will contribute to future evolutionary genomic studies among venomous animals.

RNAi-mediated silencing of ferritin genes in the brown planthopper Nilaparvata lugens affects survival, growth and female fecundity

BACKGROUND

The brown planthopper (BPH), Nilaparvata lugens, is the most destructive rice insect pest. To exploit potential target genes for applications in transgenic rice to control this sap-sucking insect pest, three ferritin genes were functionally characterized in this study.

RESULTS

In this study, three ferritin genes, that is, ferritin 1 Heavy Chain (NlFer1), ferritin 2 Light Chain (NlFer2) and soma ferritin (Nlsoma-Fer), were identified from BPH. Tissue-specific analyses showed that all three genes were highly expressed in the gut. Although double-stranded RNA injection-mediated RNA inference (RNAi) of Nlsoma-Fer expression resulted in only < 14% mortality in BPH, knockdown of NlFer1 or NlFer2 led to retarded growth and 100% mortality in young nymphs, and downregulation of NlFer1 and NlFer2 in newly emerged female adults caused undeveloped ovaries and severely inhibited oocyte growth, resulting in extremely low fecundity and a zero hatching rate. Knockdown of NlFer1 and NlFer2 caused similar phenotypes in BPH, indicating that they function together, as in many other animals. The results demonstrated that NlFer1 and NlFer2 were essential for BPH development and reproduction. BPHs showed high sensitivity to both dsNlFer1 and dsNlFer2, and injection of only 0.625 ng dsNlFer1 per BPH resulted in 100% mortality. Additionally, the effectiveness of feeding dsNlFer1 and dsNlFer2 to BPH nymphs was further proven.

CONCLUSION

NlFer1 and NlFer2 are essential for BPH development and reproduction, and the insect is highly sensitive to their depletion, suggesting that the two gut-highly-expressed genes are promising candidates for application in RNAi-based control of this destructive pest.

Proteome of larval metamorphosis induced by epinephrine in the Fujian oyster Crassostrea angulata

Background

The Fujian oyster Crassostrea angulata is an economically important species that has typical settlement and metamorphosis stages. The development of the oyster involves complex morphological and physiological changes, the molecular mechanisms of which are as yet unclear.

Results

In this study, changes in proteins were investigated during larval settlement and metamorphosis of Crassostrea angulata using epinephrine induction. Protein abundance and identity were characterized using label-free quantitative proteomics, tandem mass spectrometry (MS/ MS), and Mascot methods. The results showed that more than 50% (764 out of 1471) of the quantified proteins were characterized as differentially expressed. Notably, more than two-thirds of the differentially expressed proteins were down-regulated in epinephrine-induced larvae. The results showed that “metabolic process” was closely related to the development of settlement and metamorphosis; 5 × 10^− 4 M epinephrine induced direct metamorphosis of larvae and was non-toxic. Calmodulin and MAPK pathways were involved in the regulation of settlement of the oyster. Expression levels of immune-related proteins increased during metamorphosis. Hepatic lectin-like proteins, cadherins, calmodulin, calreticulin, and cytoskeletal proteins were involved in metamorphosis. The nervous system may be remodeled in larval metamorphosis induced by epinephrine. Expression levels of proteins that were enriched in the epinephrine signaling pathway may reflect the developmental stage of the larvae, that may reflect whether or not larvae were directly involved in metamorphosis when the larvae were treated with epinephrine.

Conclusion

The study provides insight into proteins that function in energy metabolism, immune responses, settlement and metamorphosis, and shell formation in C. angulata. The results contribute valuable information for further research on larval settlement and metamorphosis.

Graphical abstract

In situ experiment to evaluate biochemical responses in the freshwater mussel Diplodon chilensis under anthropogenic eutrophication conditions

An in-situ experiment was performed to study metabolic responses of the freshwater mussel Diplodon chilensis to water contaminated by leachates from an open dump and cattle activity, in order to analyze both the effects of those contaminants on aquatic environments and the potential use of a native bivalve to evaluate the effects of anthropic influence and eutrophication. Bivalves from a reference site were cage-transplanted to a control site (site A) and to a temporal water pond (site B) over 30 and 60 periods. Water quality analyses revealed that the site B was affected by anthropogenic influence. Mussel's hemocytes from site B showed 50% lower reactive oxygen species production and 130% higher lysosomal membrane stability in the site B mussels. In addition, no oxidative stress was evident in gills, despite the elevated copper and iron concentrations recorded in the site B water samples (Cu_B = 0.3350 ± 0.0636 mg. L^-1vs. Cu_A = 0.0045 ± 0.0007 mg. L^-1; Fe_B = 3.8650 ± 0.4031 mg. L^-1vs. Fe_A = 0.0365 ± 0.0049 mg. L^-1). In contrast, the adductor muscle accumulated more Fe (~10-20-fold) than the gills and showed signs of oxidative stress, e.g. superoxide dismutase activity and TBARS levels were increased by 10% were 34%, respectively, in the site B compared with the site A after 60 days of exposure. Additionally, the adductor muscle showed signs of anaerobic metabolism activation. Cu is accumulated in gills from both sites' individuals, at 60 days, in concordance with the increase in the activity of the cu-containing enzyme cytochrome-c-oxidase. There was a reduction in the overall condition and digestive gland index in bivalves exposed at site B, associated with diminished levels of lipid and protein contents. Metal-pollution and eutrophication affects D. chilensis metabolism and is associated to tissue-specific exposure, anaerobic metabolism and general energetic condition depletion.

Trivalent Iron Is Responsible for the Yellow Color Development in the Nacre of Akoya Pearl Oyster Shells

The gold and cream colors of cultured Akoya pearls, as well as natural yellow nacre of pearl oyster shells, are thought to arise from intrinsic yellow pigments. While the isolation of the yellow pigments has been attempted using a large amount of gold pearls, the substance concerned is still unknown. We report here on the purification and characterization of yellow pigments from the nacre of Akoya pearl oyster shells. Two yellow components, YC1 and YC2, were isolated from the HCl-methanol (HCl-MeOH) extract from nacreous organic matrices obtained by decalcification of the shells with ethylenediaminetetraacetic acid (EDTA). Energy-dispersive X-ray and infrared spectroscopy analyses suggested that YC1 and YC2 precipitated under basic conditions are composed of Fe-containing inorganic and polyamide-containing organic compounds, respectively. YC1 solubilized under acidic conditions exhibited positive reactions to KSCN and K₄[Fe(CN)₆] reagents, showing the same ultraviolet-visible absorption spectrum as those of Fe(III)-containing compounds. In addition, X-ray absorption fine structure analysis supported the compound in the form of Fe(III). The total amount of Fe was approximately 2.6 times higher in the yellow than white nacre, and most Fe was fractionated into the EDTA-decalcifying and HCl-MeOH extracts. These results suggest that Fe(III) coordinated to EDTA-soluble and insoluble matrix compounds are mainly associated with yellow color development not only in the Akoya pearl oyster shells but also in the cultured Akoya pearls.

Crystallographic characterization of ferritin from Sinonovacula constricta

Ferritins are ubiquitous iron-binding proteins that are mainly related to iron storage, detoxification and innate immunity. Here, we present the crystal structure of a marine invertebrate ferritin from Sinonovacula constricta at a resolution of 1.98 Å. The S. constricta ferritin (ScFer) possessed some structural similarities with vertebrate ferritins, and they shared a well-conserved architecture composed of five α-helical bundles that assembled into a cage-like structure with 24-subunits. The structure of ScFer also showed iron binding sites in the 3-fold channel, ferroxidase center, and putative nucleation sites. Further, electrostatic potential calculations suggested that the electrostatic gradient of the 3-fold channel could provide a guidance mechanism for iron entering the ferritin cavity.

Effect on macrophage proliferation of a novel polysaccharide from Lactarius deliciosus (L. ex Fr.) Gray

The fundamental mechanisms underlying the preventional and therapeutic effects of polysaccharides from fungi, including the immunostimulatory, antiviral and antitumor effects, are considered to occur through the modulation and stimulation of the macrophage and complement system. LDG-A, a novel polysaccharide from Lactarius deliciosus (L. ex Fr.) Gray exhibits marked antitumor activities in vivo. However, the underlying molecular mechanism of the antitumor activities of LDG-A remains unclear. In the present study, cell cycle analysis was performed in macrophages and B cells, and the transcriptomes of macrophages in the control group and LDG-A group were sequenced using Illumina sequencing technology to analyze the differentially expressed genes (DEGs), and elucidate the molecular mechanisms underlying the immunomodulatory and antitumor activities of LDG-A. The cell cycle analysis results indicated that LDG-A was able to promote the proliferation of B cells by promoting cell cycle progression in S phase and G2/M phase and eliminating cell cycle arrest in G0/G1, and promote the proliferation of macrophages by promoting cell cycle progression in G0/G1 phase and eliminating cell cycle arrest in G2/M phase. Of the total number of genes (8,140), ~77.00% were expressed [reads per kilobase per million reads (RPKM) ≥1] and 1,352 genes were highly expressed (RPKM >60) in the LDG-A group. Of 775 unigenes which were identified as DEGs, 469 were downregulated and 306 genes were upregulated. A protein chip method was also used to determine the cytokines secreted by macrophages. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and GO enrichment analysis indicated that the Janus kinase/signal transducer and activator of transcription, mitogen-activated protein kinase, chemokine, vascular endothelial growth factor and transforming growth factor β signaling pathways are markedly enriched for DEGs.

A novel basic matrix protein of Pinctada fucata, PNU9, functions as inhibitor during crystallization of aragonite

The injection of dsRNA of PNU9 could lead to the overgrowth of nacreous lamellas and the matrix membrane.

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.

Cloning and molecular characterization of two ferritins from red abalone Haliotis rufescens and their expressions in response to bacterial challenge at juvenile and adult life stages

Ferritins are ubiquitous proteins with a pivotal role in iron storage and homeostasis, and in host defense responses during infection by pathogens in several organisms, including mollusks. In this study, we characterized two ferritin homologues in the red abalone Haliotis rufescens, a species of economic importance for Chile, USA and Mexico. Two ferritin subunits (Hrfer1 and Hrfer2) were cloned. Hrfer1 cDNA is an 807 bp clone containing a 516 bp open reading frame (ORF) that corresponds to a novel ferritin subunit in H. rufescens. Hrfer2 cDNA is an 868 bp clone containing a 516 bp ORF that corresponds to a previously reported ferritin subunit, but in this study 5'- and 3'-UTR sequences were additionally found. We detected a putative Iron Responsive Element (IRE) in the 5'-UTR sequence, suggesting a posttranscriptional regulation of Hrfer2 translation by iron. The deduced protein sequences of both cDNAs possessed the motifs and domains required in functional ferritin subunits. Expression patterns of both ferritins in different tissues, during different developmental stages, and in response to bacterial (Vibrio splendidus) exposure were examined. Both Hrfer1 and Hrfer2 are most expressed in digestive gland and gonad. Hrfer1 mRNA levels increased about 34-fold along with larval developmental process, attaining the highest level in the creeping post-larvae. Exogenous feeding is initiated at the creeping larva stage; thus, the increase of Hrfer1 may suggest and immunity-related role upon exposure to bacteria. Highest Hrfer2 expression levels were detected at trochophore stage; which may be related with early shell formation. Upon challenge with, the bacteria an early mild induction of Hrfer2 (2 h post-challenge), followed by a stronger induction of Hrfer1 at 15 h post-challenge, was observed in haemocytes from adult abalones. While maximal upregulation of both genes in the whole individual occurred at 24 h post-challenge, in juveniles. A significant increase in ferritin protein levels from 6 h to 24 h post-challenge was also detected. Our results suggest an involvement of Hrfer1 and Hrfer2, and of ferritin proteins in the immune response of H. rufescens to bacterial infection.

Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs

The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam Venerupis philippinarum introduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium, Vibrio tapetis, which is also pathogenic to fish. Here we report the first assembly of the complete genome of V. tapetis CECT4600^T, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan- and core genomes and to identify putative virulence factors. The V. tapetis core genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I restriction modification system, GGDEF domain proteins, several conjugative plasmids, and a Type IV secretion system. Future research on the coevolutionary arms race between V. tapetis virulence factors and host resistance mechanisms will improve our understanding of how pathogenicity develops in this emerging pathogen.

Proteomic analysis of trochophore and veliger larvae development in the small abalone Haliotis diversicolor

Background

Haliotis diversicolor is commercially important species. The trochophore and veliger are distinct larval stages in gastropod development. Their development involves complex morphological and physiological changes. We studied protein changes during the embryonic development of H. diversicolor using two dimensional electrophoresis (2-DE) and label-free methods, tandem mass spectrometry (MS/ MS), and Mascot for protein identification.

Results

A total of 150 2-DE gel spots were identified. Protein spots showed upregulation of 15 proteins and downregulation of 28 proteins as H. diversicolor developed from trochophore to veliger larvae. Trochophore and veliger larvae were compared using a label-free quantitative proteomic approach. A total of 526 proteins were identified from both samples, and 104 proteins were differentially expressed (> 1.5 fold). Compared with trochophore larvae, veliger larvae had 55 proteins upregulated and 49 proteins downregulated. These differentially expressed proteins were involved in shell formation, energy metabolism, cellular and stress response processes, protein synthesis and folding, cell cycle, and cell fate determination. Compared with the 5 protein (fructose-bisphosphate aldolase, 14–3-3ε, profilin, actin-depolymerizing factor (ADF)/cofilin) and calreticulin) expression patterns, the mRNA expression exhibited similar patterns except gene of fructose-bisphosphate aldolase.

Conclusion

Our results provide insight into novel aspects of protein function in shell formation, torsion, and nervous system development, and muscle system differentiation in H. diversicolor larvae. “Quality control” proteins were identified to be involved in abalone larval development.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4203-7) contains supplementary material, which is available to authorized users.

Identification and Differential Expression of Biomineralization Genes in the Mantle of Pearl Oyster Pinctada fucata

A series of proteins are involved in shell formation of the pearl oyster Pinctada fucata, but the involved mechanisms and the relative expression levels of these proteins have not been elucidated. In this study, we sequenced and characterized the transcriptome of P. fucata mantle tissue. A total of 100,679 unique transcripts were assembled, 43687 Unigenes were annotated, and 48654 CDSs were determined. Of these, GO annotated 16353 Unigenes, COG defined 11585 unigenes into 25 categories, and KEGG sorted 25053 unigenes into 258 pathways. In total, 67 biomineralization-related genes were identified, of which 23 genes were newly described in P. fucata. These genes included ones that expressed shell matrix proteins, regulatory factors, and uncharacterized genes. Differential expression of these 67 genes and 9 other biomineralization-related genes was confirmed using qPCR. Of the 8 nacreous layer-related genes, MSI60 (774.00) was expressed at a much higher level than the others. KRMP2-4 and MSI31 were the most highly expressed of the 13 prismatic layer-related genes and KRMP2 was expressed at nearly 10000 times of the level of the 18S gene. For genes related to both layers, shematrin 2 (3977.84), nacrein (2404.75), PFMG 10 (2113.93), and PFMG 4 (1015.89) were highly expressed, and ferritin-like protein (877.54) and PFMG 8 (516.48) were highly expressed among the 16 undefined genes. The expression levels of regulation factors were generally low, and the highest level was 324.09 (EF-hand) and the lowest occurred in the BMP and wnt families. The expression levels of the prismatic matrix proteins were much higher than those of nacreous ones, consistent with a thicker prismatic layer. MSI60 and nacrein are likely the main components of the nacreous layer, and KRMP2-4, MSI31, shematrin 2, and PFMG 10 gene products are the main components of the prismatic layer. This is the first report of transient expression levels of a large number of biomineralization-related genes at the same time in mantle tissue of P. fucata. These findings provide a novel perspective to understand the molecular mechanisms of shell formation and will be beneficial to genetic improvement of P. fucata for the production of high-quality pearls as well.

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.

Identification and characterization of a ferritin gene involved in the immune defense response of scallop Chlamys farreri

Scallop Chlamys farreri is an important aquaculture species in northern China. However, its mass mortality caused by several pathogens can result in great economic loss and negative impacts to the sustainable development of the scallop industry. Thus, improving the overall understanding of immune response mechanisms involved in host-pathogen interactions is necessary. Ferritins are conserved molecules in organisms that are involved in diverse biological processes, such as mediating host-pathogen responses. In this study, we report a novel ferritin gene from C. farreri (denoted as CfFER). The full length of CfFER is 848 bp and contains a 5'-UTR of 113 bp, a 3'-UTR of 219 bp, and a complete open reading frame (ORF) of 516 bp. The ORF encodes a polypeptide of 171 amino acid residues with a molecular weight of approximately 19.95 kDa and an isoelectric point of 5.07. The CfFER protein exhibited typical ferritin structures, namely, a ferroxidase diiron center, a ferrihydrite nucleation center, and an iron-binding response signature. Phylogenetic analysis revealed that CfFER was closely related to other mollusk ferritin proteins. Expression of CfFER in different tissues was analyzed by quantitative real-time PCR, and results showed that CfFER was ubiquitously expressed in all examined tissues. The highest and lowest expression levels of CfFER were measured in the muscle and hemocyte, respectively. The relative mRNA expression of CfFER in response to bacterial (Vibrio anguillarum) and viral (acute viral necrobiotic virus) challenges sharply increased by ca. 5-fold about12 h post-infection (hpi) and then normalized at 48 hpi. Western blot analysis with polyclonal antibodies generated from the recombinant product of CfFER also demonstrated the presence of ferritin protein in hemocytes. These findings strongly suggest that CfFER is involved in the immune response of C. farreri and protection against pathogen challenge.

Structure elucidation, proliferation effect on macrophage and its mechanism of a new heteropolysaccharide from Lactarius deliciosus Gray

A new heteropolysaccharide was isolated from the fruiting bodies of Lactarius deliciosus Gray which had a molecular weight of 16kDa and was mainly composed of the galactose and glucose. Structural elucidation results indicated that Lactarius deliciosus Gray polysaccharide (LDG-B) had a backbone of (1,6)-linked d-galactose and (1, 2, 6)-linked d-galactose which branches were mainly composed of 4-linked d-glucose and 6-linked d-galactose residue. Cell cycle test results showed that LDG-B could promote the proliferation of B cells and macrophage cells by affecting G0/G1 phase, S phases and G2/M phases. The analysis of transcriptomes sequence of macrophages showed a total of 1839 genes were identified as DEGs, and approximately 708 genes were up-regulated, whereas 1131 genes were down-regulated in LDG-B group. KEGG pathway enrichment analysis showed that the MAPK, JAK-STAT and NF-κB signaling pathways are significantly enriched for DEGs in LDG-B group. Analysis of transcriptome resources enabled us to examine gene expression profiles, verify differential gene expression, and select candidate signaling pathways as the mechanisms of the immunomodulatory activity of LDG-B.

Identification and involvement of ferritin in the response to pathogen challenge in the abalone, Haliotis diversicolor

Accumulating data has demonstrated that ferritin plays an important role in host defense responses against infection by pathogens in many organisms. In this study, ultracentrifugation was used to isolate ferritin from abalone, Haliotis diversicolor, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis revealed that this ferritin consisted of two subunits (designated as HdFer1 and HdFer2). There are no disulfide bonds between the HdFer1 and HdFer2 subunits; however, these subunits co-assemble to form heteropolymers. A novel ferritin subunit (HdFer2) was cloned from H. diversicolor by 5' and 3' RACE (rapid amplification of cDNA ends) approach. The full-length HdFer2 cDNA sequence consists of 878 bp with an open reading frame of 513 bp that encodes a protein that is 170 amino acids in length. Quantitative real-time PCR analysis revealed that HdFer1 and HdFer2 were transcribed in various tissues, such as the mantle, gill and hepatopancreas, with the highest levels of expression in the hepatopancreas. Following a challenge with the pathogen, Vibrio harveyi, the expression of HdFer1 and HdFer2 were markedly induced at different times. This study has identified a novel ferritin subunit in H. diversicolor which will contribute to further exploration of the role of ferritin in mollusk innate immune defense against invading pathogens.

Seasonal proliferation rates and the capacity to express genes involved in cell cycling and maintenance in response to seasonal and experimental food shortage in Laternula elliptica from King George Island

Melting of coastal glaciers at the West Antarctic Peninsula (WAP) causes shorter winter sea ice duration, intensified ice scouring, sediment erosion and surface freshening in summer, which alters coastal productivity and feeding conditions for the benthos. The soft shell clam Laternula elliptica is a fast growing and abundant filter feeder in coastal Antarctica and a key element for bentho-pelagic carbon recycling. Our aim was to assess the cellular growth and maintenance capacity of small and large clams during natural winter food shortage (seasonal sampling) and in response to experimental starvation exposure. We measured tissue specific proliferation rates, the expression of cell cycling genes, and the iron binding protein Le-ferritin in freshly collected specimens in spring (Nov 2008) and at the end of summer (March 2009). For the experimental approach, we focused on 14 cell cycling and metabolic genes using the same animal size groups. Mantle tissue of young bivalves was the only tissue showing accelerated proliferation in summer (1.7% of cells dividing per day in March) compared to 0.4% dividing cells in animals collected in November. In mantle, siphon and adductor muscle proliferation rates were higher in younger compared to older individuals. At transcript level, Le-cyclin D was upregulated in digestive gland of older animals collected in spring (Nov) compared to March indicating initiation of cell proliferation. Likewise, during experimental starvation Le-cyclin D expression increased in large clam digestive gland, whereas Le-cyclin D and the autophagic factor beclin1 decreased in digestive gland of smaller starved clams. The paper corroborates earlier findings of size and age dependent differences in the metabolic response and gene expression patterns in L. elliptica under energetic deprivation. Age structure of shallow water populations can potentially change due to differences in cellular response between young and old animals as environmental stress levels increase.

Ferritin has an important immune function in the ark shell Scapharca broughtonii

Ferritin, the principle cytosolic iron storage protein in the majority of living organisms, has important roles during immune process in invertebrates. Detailed information about ferritin in the ark shell Scapharca broughtonii, however, has been very limited. In this study, full-length ferritin (termed SbFer) was cloned by the rapid amplication of cDNA ends (RACE) method based upon the sequence from the transcriptome library. The cDNA contained a 182 bp 5'-untranslated region, a 519 bp open reading frame encoding a polypeptide of 172 amino acids, a 229 bp 3'-untranslated region, and three introns (902, 373 and 402 bp) embedded in four exons. There was an iron response element (IRE) in the 5'-untranslated region. The deduced amino acid sequence of SbFer possessed many characteristics of vertebrate H type ferritin, shared 63%-91% identity with mollusks and greater identity with vertebrate H type ferritin compared to the L type. The SbFer gene expression pattern examined by quantitative real-time PCR showed ferritin mRNA was expressed in all ark shell tissues examined. The highest levels of expression were found in hemocytes with decreasing levels of expression in foot, mantle, gill, adductor muscle and hepatopancreas. A challenge with Vibrio anguillarum resulted in time-dependent significant upregulation of SbFer mRNA, indicating SbFer participated actively in the bacterial defense process. Further analysis of the antibacterial activity indicated recombinant SbFer could function as an immune antibacterial agent to both Gram-positive and Gram-negative bacteria. Taken together, these results suggested strongly that ferritin of the ark shell is involved in immune defense against microbial infection and it is a constitutive and inducible acute-phase protein.

Comparative analysis of macrophage transcriptomes reveals a key mechanism of the immunomodulatory activity of Tricholoma matsutake polysaccharide

In the present study, we performed a proliferation assay, phagocytosis assay and cell cycle analysis of macrophages and sequenced the transcriptomes of control group macrophages and TMP-A group macrophages using Illumina sequencing technology to identify differentially expressed genes (DEGs) and determine the molecular mechanisms associated with differences in the immunomodulatory activity of TMP-A in macrophages. The results showed that TMP-A exhibits strong proliferation activity and phagocytosis activity in RAW264.7 cells in vitro and could also promote the proliferation of macrophage cells by abolishing cell-cycle arrest in the G0/G1 phase and promoting the cell cycle in the G2/M phase, which may induce cell division. A total of 12,616,096 and 11,798,839 bp paired-end reads were obtained for the control group and TMP-A group, respectively, and they corresponded to a total size of 12.5 G bp and 11.7 G bp, respectively, after the low-quality reads and adapter sequences were removed. Approximately 79.8% of the total number of genes (10,191) were expressed (RPKM ≥1), and more than 1,372 genes were highly expressed (RPKM >60) in the TMP-A group. A total of 1,043 unigenes were identified as DEGs, and approximately 486 genes were upregulated, whereas 557 genes were down-regulated, which might have contributed to the proliferation activity and phagocytosis activity of TMP-A in the RAW264.7 cells in vitro. A Gene Ontology (GO) enrichment analysis generated 13,042 assignments to cellular components, 13,094 assignments to biological processes, and 13,135 assignments to molecular functions. A KEGG pathway enrichment analysis showed that the MAPK and NF-κB signaling pathways are significantly enriched for DEGs between the two cell groups. Based on the experimental data, we believe that the significant antitumor activities of TMP-A in vivo involve the MAPK and NF-κB signaling pathways because the two signaling pathways intersect.

Microarray: a global analysis of biomineralization-related gene expression profiles during larval development in the pearl oyster, Pinctada fucata

BACKGROUND

The molluscan Pinctada fucata is an important pearl-culturing organism to study biomineralization mechanisms. Several biomineralization-related genes play important roles regulating shell formation, but most previous work has focused only on their functions in adult oysters. Few studies have investigated biomineralization during larval development, when the shell is initially constructed and formed until the juvenile stage in dissoconch shells. Here, we report, for the first time, a global gene analysis during larval development of P. fucata based on a microarray and reveal the relationships between biomineralization-related genes and the shell formation process.

RESULTS

Based on the P. fucata mantle transcriptome, 58,940 probes (60 nt), representing 58,623 transcripts, were synthesized. The gene expression profiles of the fertilized egg, trochophore, D-shaped, and umbonal stage larvae, as well as juveniles were analyzed by microarray performance. The expression patterns of the biomineralization-related genes changed corresponding to their regulatory function during shell formation. Matrix proteins chitin synthase and PFMG2 were highly expressed at the D-shaped stage, whereas PFMG6, PFMG8 and PfN23 were significantly up-regulated at the umbonal stage, indicating different roles regulating the formation of either periostracum, Prodissoconch I or Prodissoconch II shells. However, the majority of matrix proteins were expressed at high levels at the juvenile stage, and the shells comprised both an aragonitic nacreous layer and a calcitic prismatic layer as adults. We also identified five new genes that were significantly up-regulated in juveniles. These genes were expressed particularly in the mantle and coded for secreted proteins with tandem-arranged repeat units, as most matrix proteins. RNAi knockdown resulted in disrupted nacreous and prismatic shell layers, indicating their potential roles in shell formation.

CONCLUSIONS

Our results add a global perspective on larval expression patterns of P. fucata genes and propose a mechanism of how biomineralization-related genes regulate the larval shell formation process. These results increase knowledge about biomineralization-related genes and highlight new aspects of shell formation mechanisms.

Preparation and representation of recombinant Mn-ferritin flower-like spherical aggregates from marine invertebrates

Ferritin has important functions in the transition and storage of toxic metal ions, but its regulation and function in many invertebrate species are still largely unknown. In our previous work, the cDNA sequence of Sinonovacula constricta, Apostichopus japonicas and Acaudina leucoprocta were constructed and efficiently expressed in E. Coli BL21 under IPTG induction. In this follow-up study, the recombinant ferritins were exposed to heavy metal manganese. The manganese concentration levels in three recombinant ferritins were greater than horse spleen ferritin (HSF). Compared with HSF, the amount of manganese enrichment in the three recombinant ferritins was 1.75-fold, 3.25-fold and 2.42-fold increases in ScFER, AjFER, and AlFER, respectively. After phosphate stimulation, the concentration of manganese increased and was higher than the ordinary dialysis control groups. The ScFER was four times its baseline value. The AjFER and AlFER were 1.4- and 8-fold higher, respectively. The AlFER sample stimulated by phosphate was 22-fold that of HSF. The morphologies of the resulting Mn-Ferritin from different marine invertebrates were characterized with scanning electron microscopy. Surface morphologies were lamella flower-like and are consistent with changes in surface morphologies of the standard Mn-HSF. Invertebrate recombinant ferritin and HSF both can uptake manganese. We found that the structure of A. leucoproctarecombinant Mn-Ferritin aggregate changed over time. The surface formed lamella flower-like aggregate, but gradually merged to create a relatively uniform plate-like phase of aggregate spherically and fused without clear boundaries.

Identification and expression of antioxidant and immune defense genes in the surf clam Mesodesma donacium challenged with Vibrio anguillarum

The immune system in marine invertebrates is mediated through cellular and humoral components, which act together to address the action of potential pathogenic microorganisms. In bivalve mollusks biomolecules implicated in oxidative stress and recognition of pathogens have been involved in the innate immune response. To better understand the molecular basis of the immune response of surf clam Mesodesma donacium, qPCR approaches were used to identify genes related to its immune response against Vibrio anguillarum infection. Genes related to oxidative stress response and recognition of pathogens like superoxide dismutase (MdSOD), catalase (MdCAT), ferritin (MdFER) and filamin (MdFLMN) were identified from 454-pyrosequencing cDNA library of M. donacium and were evaluated in mantle, adductor muscle and gills. The results for transcripts expression indicated that MdSOD, MdFLMN and MdFER were primarily expressed in the muscle, while MdCAT was more expressed in gills. Challenge experiments with the pathogen V. anguillarum had showed that levels of transcript expression for MdSOD, MdCAT, MdFER, and MdFLMN were positively regulated by pathogen, following a time-dependent expression pattern with significant statistical differences between control and challenge group responses (p<0.05). These results suggest that superoxide dismutase, catalase, ferritin and filamin, could be contributing to the innate immune response of M. donacium against the pathogen V. anguillarum.

Identification and functional characterization of a novel ferritin subunit from the tropical sea cucumber, Stichopus monotuberculatus

Ferritin is one of the major non-harm iron storage proteins that found in most cell types of animals, plants and microorganisms. In this study, a ferritin subunit named StmFer was identified from the sea cucumber (Stichopus monotuberculatus) and characterized functionally. The full-length cDNA of StmFer is 1184 bp in size with a 5'-untranslated region (UTR) of 131 bp, a 3'-UTR of 531 bp and an open reading frame of 522 bp that encoding a protein of 173 amino acids with a deduced molecular weight of 19.95 kDa. StmFer possesses both the ferroxidase center of vertebrate ferritin heavy subunit and iron nucleation sites of vertebrate ferritin light subunit. For the gene structure, StmFer contains only three exons separated by two introns. Higher levels of mRNA expression were noticed in intestine and coelomocyte of S. monotuberculatus by northern blot analysis. In in vitro experiments performed in coelomocytes, transcriptional expression of StmFer showed the strongest response to polyriboinosinic polyribocytidylic acid [Poly (I:C)] (9.08 fold up-regulation), followed by lipopolysaccharides (LPS), ferrous chloride (FeCl2) and inactivated bacteria (Vibrio alginolyticus) (7.84, 7.41 and 4.90 fold up-regulation, respectively) after 3 h post-challenge. In addition, the anti-oxidation activity and iron binding capacity of recombinant ferritin protein were demonstrated in this study. As a whole, our study suggested that the ferritin from sea cucumber may play critical roles not only in the cellular and organismic iron homeostasis, but also in the innate immune defense.

Identification of two secreted ferritin subunits involved in immune defense of Yesso scallop Patinopecten yessoensis

As an important iron storage protein, ferritin plays a crucial role in the iron-withholding defense system. In this study, two secreted ferritin subunits (PyFerS1 and PyFerS2) were identified from the Yesso scallop, Patinopecten yessoensis. The complete DNA sequences of the two ferritins are 7101 and 5359 bp, consisting of seven and five exons, respectively. The full-length cDNAs of PyFerS1 and PyFerS2 are 960 and 956 bp in length, encoding 228 and 220 amino acids, respectively. They have typical ferritin structures, with four long α-helices, one short α-helix and an L-loop. Signal peptides were found at the N-terminus of both ferritins, and phylogenetic analysis showed that they both clustered with secreted mollusc ferritins. PyFerS1 possesses all seven conserved residues of the ferroxidase center, whereas PyFerS2 only has two. Real-time PCR analysis indicated high expression level of PyFerS2 in the D-shaped larvae, and PyFerS1 in both D-shaped larvae and fertilized eggs. In adult scallops, PyFerS1 was only detected in the hepatopancreas, whereas PyFerS2 was detected in both hepatopancreas and mantle. After the scallops were challenged by iron ion or bacteria Vibrio anguillarum, the expression of both PyFerS1 and PyFerS2 was significantly elevated, suggesting they may play a role in scallop innate immune defense. For the first time, secreted ferritins were cloned and comprehensively characterized in bivalve molluscs. It will assist in better understanding of the role of secreted ferritins in bivalve innate immunity.

Differential response of two ferritin subunit genes (VpFer1 and VpFer2) from Venerupis philippinarum following pathogen and heavy metals challenge

As a principal extracellular iron storage molecule, ferritin plays an important role in the iron-withholding strategy of innate immunity and detoxification system. In this study, we cloned and characterized another ferritin from Venerupis philippinarum (designated as VpFer2), in addition to one previously reported (VpFer1). VpFer2 possessed all the conserved features critical for the fundamental structure and function of ferritin H subunit. VpFer1 and VpFer2 mRNA were both found to be most abundantly expressed in hepatopancreas. Vibrio challenge could significantly up-regulate the mRNA expression of VpFers, and VpFer2 showed more sensitive to Vibrio anguillarum infection. For heavy metals exposure, the expression level of VpFer1 was significantly induced by Cd at 48 h, but kept relatively constant after exposure to Cu. With regards to VpFer2, the expression level dropped significantly at 24 h, then began to increase to the peak value at 48 h under Cd exposure, while Cu exposure constantly depressed the expression level of VpFer2 throughout the time course. Similarly, VpFer2 seemed to be more sensitive to heavy metals exposure than VpFer1 as its mRNA level changed by higher magnitudes. All these results suggested that VpFers may be important proteins involved in host immune defense and heavy metals detoxification. The diverse expression patterns of VpFers demonstrated that VpFer2 was an early and sensitive responder to environmental stress in V. philippinarum.

Concholepas concholepas Ferritin H-like subunit (CcFer): Molecular characterization and single nucleotide polymorphism associated to innate immune response

Ferritin has been identified as the principal protein of iron storage and iron detoxification, playing a pivotal role for the cellular homeostasis in living organisms. However, recent studies in marine invertebrates have suggested its association with innate immune system. In the present study, one Ferritin subunit was identified from the gastropod Concholepas concholepas (CcFer), which was fully characterized by Rapid Amplification of cDNA Ends technique. Simultaneously, a challenge test was performed to evaluate the immune response against Vibrio anguillarum. The full length of cDNA Ccfer was 1030 bp, containing 513 bp of open reading frame that encodes to 170 amino acid peptide, which was similar to the Ferritin H subunit described in vertebrates. Untranslated Regions (UTRs) were identified with a 5'UTR of 244 bp that contains iron responsive element (IRE), and a 3'UTR of 273 bp. The predicted molecular mass of deduced amino acid of CcFer was 19.66 kDa and isoelectric point of 4.92. Gene transcription analysis revealed that CcFer increases against infections with V. anguillarum, showing a peak expression at 6 h post-infection. Moreover, a single nucleotide polymorphism was detected at -64 downstream 5'UTR sequence (SNP-64). Quantitative real time analysis showed that homozygous mutant allele (TT) was significantly associated with higher expression levels of the challenged group compared to wild (CC) and heterozygous (CT) variants. Our findings suggest that CcFer is associated to innate immune response in C. concholepas and that the presence of SNPs may involve differential transcriptional expression of CcFer.

Differential effects of metal contamination on the transcript expression of immune- and stress-response genes in the Sydney Rock oyster, Saccostrea glomerata

Environmental contamination by metals is a serious threat to the biological sustainability of coastal ecosystems. Our current understanding of the potential biological effects of metals in these ecosystems is limited. This study tested the transcriptional expression of immune- and stress-response genes in Sydney Rock oysters (Saccostrea glomerata). Oysters were exposed to four metals (cadmium, copper, lead and zinc) commonly associated with anthropogenic pollution in coastal waterways. Seven target genes (superoxide dismutase, ferritin, ficolin, defensin, HSP70, HSP90 and metallothionein) were selected. Quantitative (real-time) PCR analyses of the transcript expression of these genes showed that each of the different metals elicited unique transcriptional profiles. Significant changes in transcription were found for 18 of the 28 combinations tested (4 metals × 7 genes). Of these, 16 reflected down-regulation of gene transcription. HSP90 was the only gene significantly up-regulated by metal contamination (cadmium and zinc only), while defensin expression was significantly down-regulated by exposure to all four metals. This inhibition could have a significant negative effect on the oyster immune system, promoting susceptibility to opportunistic infections and disease.

Identification and characterization of four ferritin subunits involved in immune defense of the Yesso scallop (Patinopecten yessoensis)

As a primary iron storage protein, ferritin plays a vital role in iron homeostasis and innate immunity. In this study, four ferritin subunits (PyFer1, PyFer2, PyFer3, and PyFer4) were cloned from the Yesso scallop, Patinopecten yessoensis, by rapid amplification of cDNA ends (RACE) following in silico transcriptome analysis. The full-length cDNAs of the four ferritins are 895, 920, 891, and 1400 bp in length, respectively, and each contains a putative iron response element (IRE) in its 5' UTR. Meanwhile, multiple A+U-destabilizing elements (TATT or ATTTA) are present in the 3' UTRs of PyFer2 and PyFer4. The open reading frames of the four ferritins are 522, 516, 516, and 519 bp, encoding 173, 171, 171, and 172 amino acids, respectively. These proteins have typical ferritin structures, with four long α-helices, one short α-helix and an L-loop. All of the predicted proteins possess both the ferroxidase center of mammalian H ferritins (E25, Y32, E59, E60, H63, E105, and Q139) and the iron nucleation site of mammalian L ferritins (H116, D129, and E132), and the recombinant proteins possess apparent ferroxidase activity. Quantitative real-time PCR analysis revealed that the expression of the four PyFers was significantly elevated at the D-shaped stage and was relatively high in the adult mantle and hepatopancreas. Furthermore, the four PyFers were significantly up-regulated by iron or bacterial challenge, and all four purified recombinant PyFers were able to inhibit the growth of the scallop pathogen Vibrio anguillarum. These results suggest that these PyFers are likely to play important roles in many fundamental biological processes in P. yessoensis, including immune defense, iron homeostasis, and shell development.

Molecular properties and immune defense of two ferritin subunits from freshwater pearl mussel, Hyriopsis schlegelii

Ferritin is a conserved iron-binding protein involved in cellular iron metabolism and host defense. In the present study, two distinct cDNAs for ferritins in the freshwater pearl mussel Hyriopsis schlegelii were identified (designated as HsFer-1 and HsFer-2) by SMART RACE approach and expressed sequence tag (EST) analysis. The full-length cDNAs of HsFer-1 and HsFer-2 were of 760 and 877 bp, respectively. Both of the two cDNAs contained an open reading frame (ORF) of 522 bp encoding for 174 amino acid residues. Sequence characterization and homology alignment indicated that HsFer-1 and HsFer-2 had higher similarity to H-type subunit of vertebrate ferritins than L-type subunit. Analysis of the HsFer-1 and HsFer-2 untranslated regions (UTR) showed that both of them had an iron response element (IRE) in the 5'-UTR, which was considered to be the binding site for iron regulatory protein (IRP). Quantitative real-time PCR (qPCR) assays were employed to examine the mRNA expression profiles. Under normal physiological conditions, the expression level of both HsFer-1 and HsFer-2 mRNA were the highest in hepatopancreas, moderate in gonad, axe foot, intestine, kidney, heart, gill, adductor muscle and mantle, the lowest in hemocytes. After stimulation with bacteria Aeromonas hydrophila, HsFer-1 mRNA experienced a different degree of increase in the tissues of hepatopancreas, gonad and hemocytes, the peak level was 2.47-fold, 9.59-fold and 1.37-fold, respectively. Comparatively, HsFer-2 showed up-regulation in gonad but down-regulation in hepatopancreas and hemocytes. Varying expression patterns indicate that two types of ferritins in H. schlegelii might play different roles in response to bacterial challenge. Further bacteriostatic analysis showed that both the purified recombinant ferritins inhibited the growth of A. hydrophila to a certain degree. Collectively, our results suggest that HsFer-1 and HsFer-2 are likely to be functional proteins involved in immune defense against bacterial infection.

The mining of pearl formation genes in pearl oyster Pinctada fucata by cDNA suppression subtractive hybridization

Recent researches revealed the regional preference of biomineralization gene transcription in the pearl oyster Pinctada fucata: it transcribed mainly the genes responsible for nacre secretion in mantle pallial, whereas the ones regulating calcite shells expressed in mantle edge. This study took use of this character and constructed the forward and reverse suppression subtractive hybridization (SSH) cDNA libraries. A total of 669 cDNA clones were sequenced and 360 expressed sequence tags (ESTs) greater than 100 bp were generated. Functional annotation associated 95 ESTs with specific functions, and 79 among them were identified from P. fucata at the first time. In the forward SSH cDNA library, it recognized mass amount of nacre protein genes, biomineralization genes dominantly expressed in the mantle pallial, calcium-ion-binding genes, and other biomineralization-related genes important for pearl formation. Real-time PCR showed that all the examined genes were distributed in oyster mantle tissues with a consistence to the SSH design. The detection of their RNA transcripts in pearl sac confirmed that the identified genes were certainly involved in pearl formation. Therefore, the data from this work will initiate a new round of pearl formation gene study and shed new insights into molluscan biomineralization.

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.

Transcriptomic analysis of the clam Meretrix meretrix on different larval stages

The clam Meretrix meretrix (Mollusca: Bivalvia) is an important commercial species in China. The deficiency of genomic and transcriptomic data is becoming the bottleneck of further researches on its complex and unique developmental processes. To improve this situation, in this study, a large-scale RNA sequencing was conducted on M. meretrix on larval stages. In particular, mRNAs of trochophore, D-veliger, pediveliger, and postlarva were purified, reverse transcribed, and sequenced through 454 sequencing technology. A total of 704,671 reads were obtained and assembled into 124,737 unique sequences (35,205 contigs and 89,532 singletons). Further analysis showed that 118,075 (94.66%) of these sequences were low-expression-level transcripts. Fifteen thousand two hundred fifteen (12.20%) of the unique sequences were annotated by searching against Uniprot Protein Knowledgebase, while the others (109,522, 87.80%) were left as novel sequences. Gene ontology analysis of the annotated sequences showed that most of them were assigned to certain gene ontology terms. By analyzing the depth of each unique sequence, a preliminary quantification analysis was conducted. An amount of sequences that showed a dramatic transcript discrepancy among the four larval stages were screened, which were related to development, growth, shell formation, and immune responses etc. As the first attempt on large-scale RNA sequencing of marine bivalve larvae, this work would enrich the knowledge of larval development of marine bivalves and provide fundamental support for further researches.

Three ferritin subunits involved in immune defense from bay scallop Argopecten irradians

Ferritin is a ubiquitous protein that plays an important role in iron storage and iron-withholding strategy of innate immunity. In this study, three genes encoding different ferritin subunits were cloned from bay scallop Argopecten irradians (AiFer1, AiFer2 and AiFer3) by rapid amplification of cDNA ends (RACE) approaches based on the known ESTs. The open reading frames of the three ferritins are of 516 bp, 522 bp and 519 bp, encoding 171,173 and 172 amino acids, respectively. All the AiFers contain a putative Iron Regulatory Element (IRE) in their 5'-untranslated regions. The deduced amino acid sequences of AiFers possess both the ferroxidase center of mammalian H ferritin and the iron nucleation site of mammalian L ferritin. Gene structure study revealed two distinct structured genes encoding a ferritin subunit (AiFer3). Quantitative real-time PCR analysis indicated the significant up-regulation of AiFers in hemocytes after challenged with Listonella anguillarum, though the magnitudes of AiFer1 and AiFer2 were much higher than that of AiFer3. Taken together, these results suggest that AiFers are likely to play roles in both iron storage and innate immune defense against microbial infections.

Isolation and gene expression of yellow grouper ferritin heavy chain subunit after lipopolysaccharide treatment

Ferritin is a ubiquitous and conserved iron storage protein that plays a central role in iron metabolism. The ferritin heavy chain subunit (FerH) homolog was isolated from yellow grouper (Epinephelus awoara) spleen using suppression subtractive hybridization and RACE-PCR. The nucleotide sequence of FerH full-length cDNA was 1173 bp and contained an open reading frame of 534 bp, encoding a putative protein of 177 amino acids. The encoded protein shows 78-94% identity with homologs. Based on phylogenetic analysis, yellow grouper FerH is highly conserved throughout evolution and is closer to European seabass than to other species. RT-PCR analysis demonstrated that FerH was widely expressed in various healthy tissues and significantly up-regulated in liver, spleen, and anterior kidney by lipopolysaccharide. The results suggest that yellow grouper FerH may play a role in immune response.

Molecular characterization and tissue distribution of ferritin M in kelp grouper, Epinephelus bruneus

This study, reports the identification and analysis of ferritin M chain, from kelp grouper, Epinephelus bruneus (EbFerM); it comprises 1004 base pair (bp), including 528bp open reading frame (ORF) which encodes 176 amino acid (aa) residues; the calculated molecular weight is 20kDa. The 5'-untranslated region (UTR) possesses 476bp proceeded by a putative Iron Regulatory Element (IRE). Pair wise alignments showed that EbFerM shared 94% identity with that of Larimichthys crocea and Sciaenops. It is expressed in abundance in liver, spleen, and kidney when challenged with Vibrio anguillarum, lipopolysaccharide (LPS), or poly I:C.