Cloning, characterization and expression analysis of the gene for a putative lipopolysaccharide-induced TNF-alpha factor of the Pacific oyster, Crassostrea gigas

Transcriptome analysis provides new insights into the immune response of Ruditapes philippinarum infected with Vibrio alginolyticus

Manila clam (Ruditapes philippinarum) is a bivalve species with commercial value, but it is easily infected by pathogenic microorganisms in aquaculture, which restricts the shellfish industry. Notably, the impact of Vibrio alginolyticus on clam culture is obvious. In this study, RNA-seq was performed to analyze clam hepatopancreas tissue in 48 h (challenge group, G48h) and 96 h (challenge group, G96h) after infection with V. alginolyticus and 0 h after injection of PBS (control group, C). The results showed that a total of 1670 differentially expressed genes were detected in the G48h vs C group, and 1427 differentially expressed genes were detected in the G96h vs C group. In addition, KEGG analysis showed that DEGs were significantly enriched in pathways such as Lysosome and Mitophagy. Moreover, 15 immune related DEGs were selected for qRT-PCR analysis to verify the accuracy of RNA-seq, and the results showed that the expression level of DEGs was consistent with that of RNA-seq. Therefore, the results obtained in this study provides a preliminary understanding of the immune defense of R. philippinarum and molecular insights for genetic breeding of V. alginolyticus resistance in Manila clam.

Effects of the tumor necrosis factor on hemocyte proliferation and bacterial infection in Chinese mitten crab (Eriocheir sinensis)

Tumor necrosis factor (TNF) is an important cytokine that can regulate a variety of cellular responses by binding tumor necrosis factor receptor (TNFR). We studied whether the TNF of Eriocheir sinensis can regulate hemocyte proliferation. The results showed that the EsTNF and EsTNFR were constitutively expressed in all tested tissues, including the heart, hepatopancreas, muscles, gills, stomachs, intestines, and hemocytes. We found that low levels of EsTNF and EsTNFR transcripts were present in hemocytes. The gene expression levels were significantly increased in the hemocytes after being stimulated by Staphylococcus aureus or Vibrio parahaemolyticus. We also found some genes related to cell proliferation were expressed at a higher level in pulsing rTNF-stimulated hemocytes compared with the control group. We also knocked down the EsTNFR gene with RNAi technology. The results showed that the expression level of these genes related to cell proliferation was significantly down-regulated compared with the control group when the TNF does not bind TNFR. We used Edu technology to repeat the above experiments and the results were similar. Compared with the control group, the hemocytes stimulated by rTNF showed more significant proliferation, and the proliferation rate was significantly down-regulated after knocking down the EsTNFR gene. Therefore, we indicate that TNF binding TNFR can affect the proliferation of E. sinensis hemocytes, which might be manifested by affecting the expression of some proliferation-related genes.

Comparative transcriptomics of two coral holobionts collected during the 2017 El Niño heat wave reveal differential stress response mechanisms

Although coral species exhibit differential susceptibility to stressors, little is known about the underlying molecular mechanisms. Here we compared scleractinian corals Montipora peltiformis and Platygyra carnosa collected during the 2017 El Niño heat wave. Zooxanthellae density and chlorophyll a content declined and increased substantially during and after heat stress event, respective. However, the magnitude of change was larger in M. peltiformis. Transcriptome analysis showed that heat-stressed corals corresponded to metabolic depression and catabolism of amino acids in both hosts which might promote their survival. However, only M. peltiformis has developed the bleached coral phenotype with corresponding strong stress- and immune-related responses in the host and symbiont, and strong suppression of photosynthesis-related genes in the symbiont. Overall, our study reveals differences among species in the homeostatic capacity to prevent the development of the bleached phenotype under environmental stressors, eventually determining their likelihood of survival in the warming ocean.

Molecular identification and functional analysis of a tumor necrosis factor superfamily gene from Chinese mitten crab (Eriocheir sinensis)

Tumor necrosis factor (TNF) is one of the most important cytokines involved in various biological processes in vertebrates and invertebrates. In the present study, a new member of the TNF superfamily (named EsTNFSF) was identified from the Chinese mitten crab (Eriocheir sinensis). The full-length cDNA of EsTNFSF is 2462 bp and encodes a polypeptide with 499 amino acids. The deduced EsTNFSF protein contained a transmembrane region and a conserved extracellular C-terminal TNF domain. Phylogenetic analysis indicated that EsTNFSF was closely related to other TNFSFs from crustaceans. Quantitative real-time PCR analysis showed that EsTNFSF was expressed in all the tissues examined, and the highest expression was found in the hepatopancreas. The mRNA levels of EsTNFSF in hemocytes underwent a time-dependent and variable degree of enhancement after stimulation with lipopolysaccharide, peptidoglycan, Staphylococcus aureus, and Vibrio parahaemolyticus. Functionally, EsTNFSF knockdown by siRNA suppressed the transcriptional levels of c-Jun N-terminal kinase and two antimicrobial peptides, anti-lipopolysaccharide factor and crustin. Furthermore, purified recombinant EsTNFSF protein accelerated the bacterial clearance in vivo and inhibited the growth of V. parahaemolyticus and S. aureus in vitro. The results revealed that EsTNFSF, as an inducible immune response gene, plays a crucial role in the antibacterial immune defense of E. sinensis.

Transcriptome analysis reveals fluid shear stress (FSS) and atherosclerosis pathway as a candidate molecular mechanism of short-term low salinity stress tolerance in abalone

Background

Transcriptome sequencing is an effective tool to reveal the essential genes and pathways underlying countless biotic and abiotic stress adaptation mechanisms. Although severely challenged by diverse environmental conditions, the Pacific abalone Haliotis discus hannai remains a high-value aquaculture mollusk and a Chinese predominantly cultured abalone species. Salinity is one of such environmental factors whose fluctuation could significantly affect the abalone’s cellular and molecular immune responses and result in high mortality and reduced growth rate during prolonged exposure. Meanwhile, hybrids have shown superiority in tolerating diverse environmental stresses over their purebred counterparts and have gained admiration in the Chinese abalone aquaculture industry.

The objective of this study was to investigate the molecular and cellular mechanisms of low salinity adaptation in abalone. Therefore, this study used transcriptome analysis of the gill tissues and flow cytometric analysis of hemolymph of H. discus hannai (DD) and interspecific hybrid H. discus hannai ♀ x H. fulgens ♂ (DF) during low salinity exposure. Also, the survival and growth rate of the species under various salinities were assessed.

Results

The transcriptome data revealed that the differentially expressed genes (DEGs) were significantly enriched on the fluid shear stress and atherosclerosis (FSS) pathway. Meanwhile, the expression profiles of some essential genes involved in this pathway suggest that abalone significantly up-regulated calmodulin-4 (CaM-4) and heat-shock protein90 (HSP90), and significantly down-regulated tumor necrosis factor (TNF), bone morphogenetic protein-4 (BMP-4), and nuclear factor kappa B (NF-kB).

Also, the hybrid DF showed significantly higher and sustained expression of CaM and HSP90, significantly higher phagocytosis, significantly lower hemocyte mortality, and significantly higher survival at low salinity, suggesting a more active molecular and hemocyte-mediated immune response and a more efficient capacity to tolerate low salinity than DD.

Conclusions

Our study argues that the abalone CaM gene might be necessary to maintain ion equilibrium while HSP90 can offset the adverse changes caused by low salinity, thereby preventing damage to gill epithelial cells (ECs).

The data reveal a potential molecular mechanism by which abalone responds to low salinity and confirms that hybridization could be a method for breeding more stress-resilient aquatic species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08611-8.

Host-symbiont transcriptomic changes during natural bleaching and recovery in the leaf coral Pavona decussata

Coral bleaching has become a major threat to coral reefs worldwide, but for most coral species little is known about their resilience to environmental changes. We aimed to understand the gene expressional regulation underlying natural bleaching and recovery in Pavona decussata, a dominant species of scleractinian coral in the northern South China Sea. Analyzing samples collected in 2017 from the field revealed distinct zooxanthellae density, chlorophyll a concentration and transcriptomic signatures corresponding to changes in health conditions of the coral holobiont. In the host, normal-looking tissues of partially bleached colonies were frontloaded with stress responsive genes, as indicated by upregulation of immune defense, response to endoplasmic reticulum, and oxidative stress genes. Bleaching was characterized by upregulation of apoptosis-related genes which could cause a reduction in algal symbionts, and downregulation of genes involved in stress responses and metabolic processes. The transcription factors stat5b and irf1 played key roles in bleaching by regulating immune and apoptosis pathways. Recovery from bleaching was characterized by enrichment of pathways involved in mitosis, DNA replication, and recombination for tissue repairing, as well as restoration of energy and metabolism. In the symbionts, bleaching corresponded to imbalance in photosystems I and II activities which enhanced oxidative stress and limited energy production and nutrient assimilation. Overall, our study revealed distinct gene expressional profiles and regulation in the different phases of the bleaching and recovery process, and provided new insight into the molecular mechanisms underlying the holobiont's resilience that may determine the species' fate in response to global and regional environmental changes.

The involvement of CgCaspase-8-2 in regulating the expressions of cytokines, antibacterial peptide and autophagy-related genes in oysters

Caspase-8 has been reported to be involved not only in apoptosis, but also in many other important immune response processes, such as inflammation and autophagy. In the present study, the open reading frame of CgCaspase-8-2 was cloned from the Pacific oyster Crassostrea gigas, which was of 2160 bp encoding 737 amino acids. There were two death effector domains (DEDs) and a cysteine aspartase cysteine structural (CASc) domain in the deduced amino acid sequences of CgCaspase-8-2. The mRNA expressions of CgCaspase-8-2 in haemocytes and gills all increased significantly after Vibrio splendidus stimulation at 3 h, 6 h, and 24 h. The cleaved CgCaspase-8-2 protein was observed in haemocytes at 3 h after V. splendidus stimulation and the expression of CgCaspase-8-2 protein was relatively higher in granulocytes, compared with that in agranulocytes. In CgCaspase-8-2-RNAi oysters, the mRNA expressions of CgIL17s (CgIL17-1, -2, -3, -4, -6), CgTNF, CgIFNLP and CgBigDef1 all decreased significantly at 12 h after V. splendidus stimulation. Meanwhile, the mRNA expressions of CgATG5 and CgBeclin1 decreased significantly at 12 h after V. splendidus stimulation, while CgBcl2 increased significantly. These results indicated that CgCaspase-8-2 was involved in not only the regulation of cytokine and antibacterial peptide production, but also autophagy-related gene expressions.

RNA-seq analyses of Marine Medaka (Oryzias melastigma) reveals salinity responsive transcriptomes in the gills and livers

Increasing salinity levels in marine and estuarine ecosystems greatly influence developmental, physiological and molecular activities of inhabiting fauna. Marine medaka (Oryzias melastigma), a euryhaline research model, has extraordinary abilities to survive in a wide range of aquatic salinity. To elucidate how marine medaka copes with salinity differences, the responses of Oryzias melastigma after being transferred to different salt concentrations [0 practical salinity units (psu), 15 psu, 30 psu (control), 45 psu] were studied at developmental, histochemical and transcriptome levels in the gill and liver tissues. A greater number of gills differentially expressed genes (DEG) under 0 psu (609) than 15 psu (157) and 45 psu (312), indicating transcriptomic adjustments in gills were more sensitive to the extreme hypotonic environment. A greater number of livers DEGs were observed in 45 psu (1,664) than 0 psu (87) and L15 psu (512), suggesting that liver was more susceptible to hypertonic environment. Further functional analyses of DEGs showed that gills have a more immediate response, mainly in adjusting ion balance, immune and signal transduction. In contrast, DEGs in livers were involved in protein synthesis and processing. We also identified common DEGs in both gill and liver and found they were mostly involved in osmotic regulation of amino sugar and nucleotide sugar metabolism and steroid biosynthesis. Additionally, salinity stresses showed no significant effects on most developmental and histochemical parameters except increased heartbeat with increasing salinity and decreased glycogen after transferred from stable conditions (30 psu) to other salinity environments. These findings suggested that salinity-stress induced changes in gene expressions could reduce the effects on developmental and histochemical parameters. Overall, this study provides a useful resource for understanding the molecular mechanisms of fish responses to salinity stresses.

A Gut-Specific LITAF-Like Gene in Antheraea pernyi (Lepidoptera: Saturniidae) Involved in the Immune Response to Three Pathogens

Antheraea pernyi (Guérin-Méneville 1855) is an important resource for silk, food, and biohealth products; however, exogenous pathogens largely affect the commercial application potential of this species. Since the gut is a key organ for the digestion and absorption of nutrients as well as for immune defense, we used comparative transcriptome analysis to screen for a gut-specific molecular tool for further functional research in A. pernyi. In total, 3,331 differentially expressed genes (DEGs) were identified in the gut compared with all other pooled tissues of A. pernyi, including 1,463 upregulated genes in the gut. Among these, we further focused on a lipopolysaccharide-induced tumor necrosis factor-α factor (LITAF) gene because of its high gut-specific expression and the presence of a highly conserved SIMPLE-like domain, which is related to the immune response to pathogenic infections in many species. The cDNA sequence of ApLITAF was 447-bp long and contained a 243-bp open reading frame encoding an 80-amino acid protein. Immune challenge assays indicated that ApLITAF expression was significantly upregulated in the gut of A. pernyi naturally infected with nucleopolyhedrovirus (NPV) or fed leaves infected with the gram-negative bacterium Escherichia coli (Migula 1895) and the gram-positive bacterium Bacillus subtilis (Ehrenberg 1835). Cell transfection showed that ApLITAF localized to the lysosome. Collectively, these results suggested that ApLITAF played a role in the immune response of A. pernyi and could facilitate the future research and breeding application in this species.

The role of Smad1/5 in mantle immunity of the pearl oyster Pinctada fucata martensii

The Smad protein family is an important medium for transducing BMP-Smads signals, and which have been proved that their important role in regulating shell biomineralization in Pinctada fucata martensii in our previous study. The members of TGF-β superfamily were involved in innate immunity in vertebrates and invertebrates, and Smad regulatory networks construct a balanced immune system. However, little is known about the role of Smad1/5 in immunity in P. f. martensii. The present study shows that the tissue distribution and the expression profiles of Smad1/5 at developmental stages suggested its wide distribution and crucial role in development at embryonic stages other than larval stage; the increased expression of bone morphogenetic proteins 2 (BMP2), Smad4, Smad1/5 and MSX mRNAs at mantle tissue after LPS and Poly (I:C) challenged implied the potential immune role of Smad1/5 and BMP2-Smad signals to defense against bacterial and virus infections; the reduced expression of immune gene nuclear factor kappa-B (NF-κB), matrix metalloproteinase (MMP), interleukin 17 (IL-17), CuZn-superoxide dismutase (CuZn-SOD), tissue inhibitors of metalloproteinase (TIMP) and lipopolysaccharide-induced TNF-α factor (LITAF) mRNA following knockdown of Smad1/5 indicated that Smad1/5 can regulate their expression via BMP2-Smads pathway in the immunity process; the up-regulated expression of Smad1/5 and BMP2-Smad signals genes, and immune genes during wound healing indicated that Smad1/5 and BMP2-Smad signals genes may be involved in wound healing collaborated with immune genes via a different and complex Smads signaling pathway. These results indicated Smad1/5 could regulate innate immunity via BMP2-Smads signal pathway, and which provided new insights into the relationship between BMP2-Smads signal pathway and mantle immunity.

Phylogenetic analysis of the caspase family in bivalves: implications for programmed cell death, immune response and development

BACKGROUND

Apoptosis is an important process for an organism's innate immune system to respond to pathogens, while also allowing for cell differentiation and other essential life functions. Caspases are one of the key protease enzymes involved in the apoptotic process, however there is currently a very limited understanding of bivalve caspase diversity and function.

RESULTS

In this work, we investigated the presence of caspase homologues using a combination of bioinformatics and phylogenetic analyses. We blasted the Crassostrea gigas genome for caspase homologues and identified 35 potential homologues in the addition to the already cloned 23 bivalve caspases. As such, we present information about the phylogenetic relationship of all identified bivalve caspases in relation to their homology to well-established vertebrate and invertebrate caspases. Our results reveal unexpected novelty and complexity in the bivalve caspase family. Notably, we were unable to identify direct homologues to the initiator caspase-9, a key-caspase in the vertebrate apoptotic pathway, inflammatory caspases (caspase-1, - 4 or - 5) or executioner caspases-3, - 6, - 7. We also explored the fact that bivalves appear to possess several unique homologues to the initiator caspase groups - 2 and - 8. Large expansions of caspase-3 like homologues (caspase-3A-C), caspase-3/7 group and caspase-3/7-like homologues were also identified, suggesting unusual roles of caspases with direct implications for our understanding of immune response in relation to common bivalve diseases. Furthermore, we assessed the gene expression of two initiator (Cg2A, Cg8B) and four executioner caspases (Cg3A, Cg3B, Cg3C, Cg3/7) in C. gigas late-larval development and during metamorphosis, indicating that caspase expression varies across the different developmental stages.

CONCLUSION

Our analysis provides the first overview of caspases across different bivalve species with essential new insights into caspase diversity, knowledge that can be used for further investigations into immune response to pathogens or regulation of developmental processes.

Estrogen receptor regulates immune defense by suppressing NF-κB signaling in the Crassostrea hongkongensis

The crosstalk between the estrogen receptor (ER) and NF-κB signalling pathways has merged in vertebrates and plays a key role in the control of genes involved in inflammation, cell proliferation and apoptosis. However, such crosstalk between the endocrine and immune systems needs to be explored in lower invertebrates. In this study, we identified a 2856-bp homologue of the estrogen receptor from Hong Kong oyster (ChER), containing a 5' untranslated region (UTR) of 234 bp, a 3' UTR of 387 bp, and an open reading frame (ORF) of 2235 bp. We observed that overexpression of ChER suppressed ChRel-dependent NF-kappaB (NF-κB) activation in the HEK293T (human embryonic kidney 293T) cell line, and depletion of ChER in vivo resulted in upregulation of two NF-κB-responsive marker genes, namely, TNF-α and IL-17, which confirmed its potential role in controlling NF-κB signalling. Furthermore, an EMSA (electrophoretic mobility shift assay) showed that ChER could negatively regulate the binding of ChRel to NF-κB probe-responsive elements. Serial domain requirement analysis showed that both region C (DNA-binding domain) and region E (ligand-binding domain) of ChER were essential for mediating the crosstalk underlying ChER-dependent NF-κB suppression. In conclusion, we demonstrate for the first time the negative regulatory role of the ER in NF-κB signalling in oysters, strongly indicating the presence of complex crosstalk between the endocrine and immune systems in lower marine molluscs.

A novel Adiponectin receptor (AdipoR) involved in regulating cytokines production and apoptosis of haemocytes in oyster Crassostrea gigas

Adiponectin receptors (AdipoRs) comprise a seven-transmembrane domain-containing protein family, which specifically recognize adiponectin (APN) and play critical roles in the immunological and physiological processes in vertebrates. In the present study, a novel AdipoR is identified from oyster Crassostrea gigas (designated as CgAdipoR). The full-length cDNA of CgAdipoR is of 1209 bp encoding a polypeptide of 343 amino acids. There is an N-terminal domain, a Hly III domain, and a C-terminal domain in CgAdipoR. After the transfection of CgAdipoR, the level of intracellular Ca²⁺ into HEK293T cells increases significantly (1.36-fold, p < 0.05) after APN incubation. The mRNA transcripts of CgAdipoR are widely distributed in all the tested tissues, with the highest expression level in haemocytes (3.20-fold of that in hepatopancreas, p < 0.05). After lipopolysaccharide (LPS), Vibrio splendidus and polyinosinic-polycytidylic acid (poly (I:C)) stimulations, the mRNA expression of CgAdipoR in haemocytes is significantly up-regulated and reached the highest level at 24 h (15.07-fold, p < 0.01), 6 h (4.39-fold, p < 0.01) and 24 h (5.62-fold, p < 0.01) compared to control group, respectively. After CgAdipoR is interfered by specific CgAdipoR-dsRNA, the expression level of interleukins (CgIL17-1, CgIL17-2, CgIL17-3 and CgIL17-5) in haemocytes decreases significantly (p < 0.01) at 24 h post LPS stimulation, while the expression level of CgTNF-1 increases significantly (1.68-fold, p < 0.01), compared to that in the dsEGFP group. In CgAdipoR dsRNA-injected oysters, the mRNA expressions of anti-apoptotic B-cell lymphoma-2 (Bcl-2) in haemocytes significantly decreases at 24 h after LPS challenge, which is (0.58-fold, p < 0.05) of that in dsEGFP-injected oysters, while the apoptotic rate of haemocytes is significantly up-regulated (1.93-fold of that in dsEGFP group, p < 0.05). These results collectively suggest that CgAdipoR plays an important role in the immune response of oysters by regulating the expressions of inflammatory cytokines and haemocyte apoptosis.

A novel programmed cell death protein 4 negatively regulates CgIL17-5 expression in hemocytes of oyster Pacific oyster (Crassostrea gigas)

The programmed cell death protein 4 (PDCD4) is a newly defined transcriptional and translational inhibitor, which plays a key role in regulating the synthesis of inflammatory cytokines in vertebrates species. In the present study, the full-length cDNA of PDCD4 from oyster Crassostrea gigas (designed as CgPDCD4) was identified to explore its possible involvement in immune response. The open reading frame of pdcd4 gene was of 1344 bp encoding a polypeptide of 447 amino acids with two conserved MA-3 domains. The deduced amino acid sequence of CgPDCD4 shared 60.18% similarity with PDCD4 from Mizuhopecten yessoensis. The mRNA transcripts of CgPDCD4 could be detected in all the tested tissues with a higher expression level in adductor muscle and hemocytes. The mRNA expression of CgPDCD4 in hemocytes was significantly down-regulated at 3 h and 6 h (0.61-fold and 0.42-fold of that in PBS group, p < 0.01, respectively) after LPS stimulation. In hemocytes, CgPDCD4 protein was found to be mainly located in the cytoplasm. After the mRNA expression of CgPDCD4 in hemocytes was knocked down (0.40-fold of that in EGFP-RNAi group) by CgPDCD4 dsRNA (dsCgPDCD4) injection, the CgIL17-5 transcripts were up-regulated (20.11-fold of that in PBS group, p < 0.01) post LPS stimulation, which was significantly higher than that in dsEGFP-injected oysters (7.06-fold of that in PBS group, p < 0.01). Meanwhile, the nuclear translocation of CgRel (homologue of Rel/NF-κB) was significantly enhanced (about 1.36-fold of that in PBS group, p < 0.01), but it was similar as that in EGFP-RNAi group (about 1.52-fold of that in PBS group, p < 0.01) after LPS stimulation. All the results suggested that CgPDCD4 in oysters played the same role as PDCD4 of vertebrates in negatively regulating the production of interleukin in immune response, but the underpinning signal pathway was not conserved during evolution.

The effects of glyphosate and AMPA on the mediterranean mussel Mytilus galloprovincialis and its microbiota

Glyphosate, the most widely used herbicide worldwide, targets the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme in the shikimate pathway found in plants and some microorganisms. While the potential for glyphosate to induce a broad range of biological effects in exposed organisms has been demonstrated, the global molecular mechanisms of toxicity and potential effects in bacterial symbionts remain unclear, in particular for ecologically important marine species such as bivalve molluscs. Here, the effects of glyphosate (GLY), its degradation product aminomethylphosphonic acid (AMPA), and a mixture of both (MIX) on the mussel M. galloprovincialis were assessed in a controlled experiment. For the first time, next generation sequencing (RNA-seq and 16S rRNA amplicon sequencing) was used to evaluate such effects at the molecular level in both the host and its respective microbiota. The results suggest that the variable capacity of bacterial species to proliferate in the presence of these compounds and the impairment of host physiological homeostasis due to AMPA and GLY toxicity may cause significant perturbations to the digestive gland microbiota, as well as elicit the spread of potential opportunistic pathogens such as Vibrio spp.. The consequent host-immune system activation identified at the molecular and cellular level could be aimed at controlling changes occurring in the composition of symbiotic microbial communities. Overall, our data raise further concerns about the potential adverse effects of glyphosate and AMPA in marine species, suggesting that both the effects of direct toxicity and the ensuing changes occurring in the host-microbial community must be taken into consideration to determine the overall ecotoxicological hazard of these compounds.

Functional characterization of a putative lipopolysaccharide-induced TNF-alpha factor (LITAF) from blood clam Tegillarca granosa in innate immunity

Lipopolysaccharide-induced TNF-alpha factor (LITAF), as a transcription factor, activates the transcription of TNF and other cytokines in inflammatory response upon lipopolysaccharide (LPS) stimulation. In the present study, we cloned and identified the full-length cDNA of LITAF homolog from blood clam Tegillarca granosa for the first time. The full-length cDNA of TgLITAF was 1801 bp encoding a polypeptide of 147 amino acids with an estimated molecular mass of 16.13 kDa. TgLITAF contained a zf-LITAF-like zinc ribbon domain at the C-terminal of the protein and the TgLITAF domain showed 48-74% amino acid sequence identity with other known LITAFs from other species. Subcellular localization study showed that TgLITAF was mainly expressed in the nucleus. qRT-PCR analysis showed that the TgLITAF transcription expressed constitutively in all the examined tissues with the highest expression level in the gills. After LPS or V. alginolyticus treatment, expression of TgLITAF in hemocytes was both up-regulated significantly at 3-6 h. Furthermore, in vitro study indicated that overexpression of TgLITAF in HeLa cells resulted in the activation of TNFα, p53, and influenced the expression levels of apoptotic-related genes Bax, Bcl-2, Caspase-3, Caspase-6, and Caspase-7. The proliferation of HeLa cells was inhibited by overexpression of TgLITAF. Apoptotic fluorescence assay further revealed that TgLITAF participated in the apoptotic process of HeLa cells. Western blotting analysis showed that overexpression of TgLITAF increased endogenous level of cleaved Caspase-7. Taken together, these results revealed that TgLITAF participates in the innate immune response to the pathogen invasion in blood clams and induces apoptosis in HeLa cells.

P38 is involved in immune response by regulating inflammatory cytokine expressions in the Pacific oyster Crassostrea gigas

P38 mitogen-activated protein kinases are serine/threonine protein kinases reportedly involved in the innate immunity of vertebrates and invertebrates. In the present study, a P38 homolog (CgP38) was characterized from the Pacific oyster Crassostrea gigas. The full-length cDNA of CgP38 was of 1515 bp containing a 1101 bp open reading frame. A serine/threonine protein kinase (S_TKc) domain with a conserved Thr-Gly-Tyr motif and an ATRW substrate-binding site was found in the deduced amino acid sequence of CgP38. CgP38 shared a close evolutionary relationship with ChP38 from the Hong Kong oyster Crassostrea hongkongensis. The transcript levels of CgP38 in hemocytes increased significantly from 12 h to 48 h after lipopolysaccharide (LPS) stimulation and from 12 h to 24 h after Vibrio splendidus stimulation. The phosphorylation level of CgP38 in oyster hemocytes increased significantly at 2 h after LPS stimulation. CgP38 positively regulated the expression of interleukins, such as CgIL17-1, CgIL17-2, CgIL17-3, CgIL17-4 and CgIL17-6, and tumor necrosis factor CgTNF after LPS or V. splendidus stimulation. These results suggested that CgP38 participated in oyster immune response by regulating the expressions of inflammatory cytokines.

A novel JNK is involved in immune response by regulating IL expression in oyster Crassostrea gigas

The c-Jun N-terminal kinase (JNK) is a member of mitogen-activated protein kinases (MAPK) highly conserved from yeast to mammals and participates in regulating many physiological and pathological processes. In the present study, a novel JNK was identified from oyster Crassostrea gigas (designated as CgJNK) and its biological functions were investigated in response against lipopolysaccharide (LPS) stimulation. The CgJNK consists of 415 amino acids, which includes a serine/threonine protein kinase (S_TKc) domain with a conserved Thr-Pro-Tyr (TPY) motif. Phylogenetic analysis revealed that CgJNK shared high similarity with other members of the JNK subfamily. CgJNK mRNA was detected in all the tested tissues and CgJNK mRNA expression levels in hemocytes were significantly up-regulated from 6 to 72 h after LPS stimulation and reached the highest level (16.1-fold, p < 0.01) at 24 h. The phosphorylation level of CgJNK in C. gigas hemocytes was increased at 2 h after LPS stimulation. The subcellular localization of CgJNK phosphorylation in hemocytes was analyzed after LPS stimulation, and CgJNK phosphorylation could be detected in both cytoplasm and nucleus of oyster hemocytes at 2 h post LPS stimulation. Additionally, the interleukins (CgILs) were detected in hemocytes of CgJNK-knockdown oysters. CgIL17-1, CgIL17-2, CgIL17-4 and CgIL17-6 transcripts were decreased significantly in CgJNK-knockdown oysters at 24 h post LPS stimulation. In summary, these results suggested that CgJNK played an important role in the immune response of oysters by regulating IL expression.

Differentially expressed immune-related genes in hemocytes of the pearl oyster Pinctada fucata against allograft identified by transcriptome analysis

The pearl oyster Pinctada fucata is commonly cultured for marine pearls in China. To culture pearls, a mantle piece from a donor pearl oyster is grafted with a nucleus into a receptor. This transplanted mantle piece may be rejected by the immune system of the recipient oyster, thus reducing the success of transplantation. However, there have been limited studies about the oyster's immune defense against allograft. In this study, hemocyte transcriptome analysis was performed to detect the immune responses to allograft in P. fucata at 0 h and 48 h after a transplant. The sequencing reaction produced 92.5 million reads that were mapped against the reference genome sequences of P. fucata. The Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify all immune-related differentially expressed genes (DEGs). Compared with patterns at 0 h, a total of 798 DEGs were identified, including 410 up-regulated and 388 down-regulated genes at 48 h. The expression levels of interleukin receptor and toll-like receptor in hemocytes were increased significantly 48 h post-transplant, indicating that the oyster immune response was induced. Finally, altered levels of 18 randomly selected immune-related DEGs were confirmed by quantitative real-time PCR (qRT-PCR). Our results provide the basis for further analysis of the immune rejection of allotransplantation.

Transcriptomic analysis of Crassostrea sikamea × Crassostrea angulata hybrids in response to low salinity stress

Hybrid oysters often show heterosis in growth rate, weight, survival and adaptability to extremes of salinity. Oysters have also been used as model organisms to study the evolution of host-defense system. To gain comprehensive knowledge about various physiological processes in hybrid oysters under low salinity stress, we performed transcriptomic analysis of gill tissue of Crassostrea sikamea ♀ × Crassostrea angulata♂ hybrid using the deep-sequencing platform Illumina HiSeq. We exploited the high-throughput technique to delineate differentially expressed genes (DEGs) in oysters maintained in hypotonic conditions. A total of 199,391 high quality unigenes, with average length of 644 bp, were generated. Of these 35 and 31 genes showed up- and down-regulation, respectively. Functional categorization and pathway analysis of these DEGs revealed enrichment for immune mechanism, apoptosis, energy metabolism and osmoregulation under low salinity stress. The expression patterns of 41 DEGs in hybrids and their parental species were further analyzed by quantitative real-time PCR (qRT-PCR). This study will serve as a platform for subsequent gene expression analysis regarding environmental stress. Our findings will also provide valuable information about gene expression to better understand the immune mechanism, apoptosis, energy metabolism and osmoregulation in hybrid oysters under low salinity stress.

Cgi-miR-92d indirectly regulates TNF expression by targeting CDS region of lipopolysaccharide-induced TNF-α factor 3 (CgLITAF3) in oyster Crassostrea gigas

Tumor necrosis factor alpha (TNF-α) mediated inflammatory response plays indispensable roles in organisms defending against the invaded bacteria, during which microRNAs have been found crucial by controlling multiple TNF-α-related genes. In the present study, cgi-miR-92d was annotated as a member of miR-17-92 family and could target the CDS region of lipopolysaccharide (LPS)-induced TNF-α factor (CgLITAF3) in oyster Crassostrea gigas. It was observed that cgi-miR-92d could be vigorously modulated by Vibrio splendidus or LPS stimulation while CgLITAF3 altered oppositely. Two putative binding sites of cgi-miR-92d were then found at CDS region of CgLITAF3. The interaction between cgi-miR-92d and CgLITAF3 was subsequently verified both in vitro and in vivo. As a result, a significant decrease of cellular luminescence was observed in CgLITAF3 luciferase reporter assay when cgi-miR-92d was overexpressed. The luminescent decrease was then recuperated when cgi-miR-92d inhibitor was co-transfected with miRNA mimics. Besides, CgLITAF3 transcripts were significantly down-regulated when cgi-miR-92d was overexpressed in vivo during V. splendidus challenge. Gain-of-function assay of CgLITAF3 was then conducted in HEK293T cells to verify its function. Consequently, a significant increase of TNF-α was observed during the assay. At the meantime, CgTNF was also down-regulated in gain-of-function assay of cgi-miR-92 in vivo, which was a member of TNF superfamily in oysters which could be robustly induced after pathogen stimulation. Together, these results verify the interaction between CgLITAF3 and cgi-miR-92d, which might dedicate crucially in the repaid activation of CgTNF expression during inflammatory response of oysters.

The complexity of apoptotic cell death in mollusks: An update

Apoptosis is a type of programmed cell death that produces changes in cell morphology and in biochemical intracellular processes without inflammatory reactions. The components of the apoptotic pathways are conserved throughout evolution. Caspases are key molecules involved in the transduction of the death signal and are responsible for many of the biochemical and morphological changes associated with apoptosis. Nowadays, It is known that caspases are activated through two major apoptotic pathways (the extrinsic or death receptor pathway and the intrinsic or mitochondrial pathway), but there are also evidences of at least other alternative pathway (the perforin/granzyme pathway). Apoptosis in mollusks seems to be similar in complexity to apoptosis in vertebrates but also has unique features maybe related to their recurrent exposure to environmental changes, pollutants, pathogens and also related to the sedentary nature of some stages in the life cycle of mollusks bivalves and gastropods. As in other animals, apoptotic process is involved in the maintenance of tissue homeostasis and also constitutes an important immune response that can be triggered by a variety of stimuli, including cytokines, hormones, toxic insults, viruses, and protozoan parasites. The main goal of this work is to present the current knowledge of the molecular mechanisms of apoptosis in mollusks and to highlight those steps that need further study.

Functional analysis of Pacific oyster (Crassostrea gigas) β-thymosin: Focus on antimicrobial activity

An antimicrobial peptide, ∼5 kDa in size, was isolated and purified in its active form from the mantle of the Pacific oyster Crassostrea gigas by C18 reversed-phase high-performance liquid chromatography. Matrix-assisted laser desorption ionisation time-of-flight analysis revealed 4656.4 Da of the purified and unreduced peptide. A comparison of the N-terminal amino acid sequence of oyster antimicrobial peptide with deduced amino acid sequences in our local expressed sequence tag (EST) database of C. gigas (unpublished data) revealed that the oyster antimicrobial peptide sequence entirely matched the deduced amino acid sequence of an EST clone (HM-8_A04), which was highly homologous with the β-thymosin of other species. The cDNA possessed a 126-bp open reading frame that encoded a protein of 41 amino acids. To confirm the antimicrobial activity of C. gigas β-thymosin, we overexpressed a recombinant β-thymosin (rcgTβ) using a pET22 expression plasmid in an Escherichia coli system. The antimicrobial activity of rcgTβ was evaluated and demonstrated using a bacterial growth inhibition test in both liquid and solid cultures.

Characterization of two regulators of the TNF-α signaling pathway in Apostichopus japonicus: LPS-induced TNF-α factor and baculoviral inhibitor of apoptosis repeat-containing 2

The TNF-α signaling cascade is involved in the regulation of a variety of biological processes, including cell proliferation, differentiation, apoptosis and the immune response in vertebrates. Here, two regulatory genes, lipopolysaccharide-induced tumor necrosis factor α factor (LITAF) and baculoviral inhibitor of apoptosis repeat-containing 2 (BIRC2), were identified in coelomocytes from the sea cucumber Apostichopus japonicus by RNA-seq and RACE (denoted as AjLITAF and AjBIRC2, respectively). The full-length cDNA of AjLITAF was 1417 bp, with a 5' untranslated region (UTR) of 189 bp, a 3' UTR of 637 bp with one cytokine RNA instability motif (ATTTA) and an open reading frame (ORF) of 591 bp encoding a polypeptide of 196 amino acid residues and a predicted molecular weight of 22.1 kDa. The partial AjBIRC2 cDNA was 2324 bp with a 5' UTR of 145 bp, a 3' UTR of 469 bp and a complete ORF of 1710 bp encoding a polypeptide of 569 amino acid residues. Analysis of the deduced amino acid sequences revealed that both genes shared a remarkably high degree of structural conservation with their mammalian orthologs, including a highly conserved LITAF domain in AjLITAF and three types of BIR domains in AjBIRC2. Spatial expression analysis revealed that AjLITAF and AjBIRC2 were expressed at a slightly lower level in the intestine and tentacle tissues compared with the other four tissues examined. After challenging the sea cucumbers with Vibrio splendidus, the expression levels of AjLITAF and AjBIRC2 in coelomocytes were increased by 2.65-fold at 6 h and 1.76-fold at 24 h compared with the control group. In primary cultured coelomocytes, a significant increase in the expression of AjLITAF and AjBIRC2 was detected after 6 h of exposure to 1 µg mL(-1) LPS. Together, these results suggest that AjLITAF and AjBIRC2 might be involved in the sea cucumber immune response during the course of a pathogenic infection or exposure to pathogen-associated molecular pattern (PAMP) molecules.

De novo transcriptome sequencing of the Octopus vulgaris hemocytes using Illumina RNA-Seq technology: response to the infection by the gastrointestinal parasite Aggregata octopiana

Background

Octopus vulgaris is a highly valuable species of great commercial interest and excellent candidate for aquaculture diversification; however, the octopus’ well-being is impaired by pathogens, of which the gastrointestinal coccidian parasite Aggregata octopiana is one of the most important. The knowledge of the molecular mechanisms of the immune response in cephalopods, especially in octopus is scarce. The transcriptome of the hemocytes of O. vulgaris was de novo sequenced using the high-throughput paired-end Illumina technology to identify genes involved in immune defense and to understand the molecular basis of octopus tolerance/resistance to coccidiosis.

Results

A bi-directional mRNA library was constructed from hemocytes of two groups of octopus according to the infection by A. octopiana, sick octopus, suffering coccidiosis, and healthy octopus, and reads were de novo assembled together. The differential expression of transcripts was analysed using the general assembly as a reference for mapping the reads from each condition. After sequencing, a total of 75,571,280 high quality reads were obtained from the sick octopus group and 74,731,646 from the healthy group. The general transcriptome of the O. vulgaris hemocytes was assembled in 254,506 contigs. A total of 48,225 contigs were successfully identified, and 538 transcripts exhibited differential expression between groups of infection. The general transcriptome revealed genes involved in pathways like NF-kB, TLR and Complement. Differential expression of TLR-2, PGRP, C1q and PRDX genes due to infection was validated using RT-qPCR. In sick octopuses, only TLR-2 was up-regulated in hemocytes, but all of them were up-regulated in caecum and gills.

Conclusion

The transcriptome reported here de novo establishes the first molecular clues to understand how the octopus immune system works and interacts with a highly pathogenic coccidian. The data provided here will contribute to identification of biomarkers for octopus resistance against pathogens, which could improve octopus farming in the near future.

Genomic organization and promoter analysis of a transcriptional repressor gene from Fenneropenaeus chinensis

In this study, we cloned and sequenced genomic sequences from a Fenneropenaeus chinensis transcriptional repressor gene, FcTR. The FcTR gene is 2,671 bp in length and has four exons and three introns. The 873 bp promoter contains several transcription factor binding sites, including a TATA box and a cyclic AMP-responsive element. Promoter deletion analysis using a luciferase reporter gene identified regulatory elements. Challenge with white spot syndrome virus increased expression from the promoter-deletion constructs. These results suggest that FcTR might play an important role in the shrimp immune response.

The immunomodulation of a novel tumor necrosis factor (CgTNF-1) in oyster Crassostrea gigas

Tumor necrosis factor (TNF) is one of the most important cytokines involved in many processes in both vertebrate and invertebrate. In the present study, a new tumor necrosis factor with a typical TNF domain was identified in oyster Crassostrea gigas (designated CgTNF-1). CgTNF-1 shared low sequence identity and similarity with the TNF superfamily members from other vertebrate and invertebrate. After LPS stimulation, the mRNA expression of CgTNF-1 in haemocytes increased significantly and peaked at 12h (1.39±0.12, P<0.05) post treatment, and the expression of CgTNF-1 protein in haemolymph also increased obviously during 6-12h. When the oyster haemocytes were incubated with rCgTNF-1, its apoptosis and phagocytosis rate were both effectively induced and peaked at 12h post the treatment of rCgTNF-1 with the concentration of 100ngmL(-1) (23.3±3%, P<0.01), 50ngmL(-1) (5.3±0.6%, P<0.05) and 10ngmL(-1) (6.7±1.2%, P<0.05), respectively. After the co-stimulation of LPS and rCgTNF-1, the apoptosis and phagocytosis rate of oyster haemocytes, and the activities of PO and lysozyme in the haemolymph all increased significantly, and reached the peak at 12h (apoptosis rate 26.7±1.5%, P<0.01), 12h (phagocytosis rate 8.3±0.6%, P<0.01), 6h (PO 1.11±0.01Umg prot(-1), P<0.01) and 12h (lysozyme 168.9±8.3Umg prot(-1), P<0.05), respectively, which were significantly higher than that in the LPS group. Furthermore, the anti-bacteria activity in the LPS+TNF group was significantly higher than that in the LPS group during 6-12h. All the results collectively indicated that CgTNF-1 was involved in the oyster immunity and played a crucial role in the modulation of immune response including apoptosis and phagocytosis of haemocytes, and regulation of anti-bacterial activity as well as the activation of immune relevant enzymes.

Identification and expression analysis of lipopolysaccharide-induced TNF-alpha factor gene in Chinese mitten crab Eriocheir sinensis

Lipopolysaccharide-induced TNF-alpha factor (LITAF) is an important transcription factor in transcriptional regulation of TNF-alpha and other cytokines. Here we identified a full-length LITAF homolog cDNA, termed EsLITAF, that contains a 71 bp 5'-untranslated sequence, an open reading frame consisting of 381 bp, and a 208 bp 3'-untranslated sequence in Chinese mitten crab (Eriocheir sinensis), an economically important freshwater crustacean species in China. EsLITAF protein possesses a conserved C-terminal LITAF-like domain with two CXXC motifs and is comprised of 126 amino acids with a theoretical molecular mass of 13.1 kDa and an isoelectric point of 6.36. Blast search against GenBank database revealed that EsLITAF protein shared the highest sequence identity (84%) with the counterpart of Pacific white shrimp (Litopenaeus vannamei). EsLITAF mRNA transcript expresses ubiquitously in all examined tissues with the highest expression in hepatopancreas and lowest expression in haemocytes. Furthermore, EsLITAF mRNA expression could be significantly and rapidly induced in haemocytes by LPS and Poly(I:C) stimulations in vitro. Moreover, EsLITAF gene expression was up-regulated in haemocytes, gill and hepatopancreas after Edwardsiella tarda and Vibrio anguillarum challenges. Taken together, we have identified and characterized a new crustacean LITAF homolog from the Chinese mitten crab.

Transcriptional profiles of Rel/NF-κB, inhibitor of NF-κB (IκB), and lipopolysaccharide-induced TNF-α factor (LITAF) in the lipopolysaccharide (LPS) and two Vibrio sp.-exposed intertidal copepod, Tigriopus japonicus

The immune system and the role of immunity-related genes have rarely been studied in copepods, even though copepods have a primitive immune response system and also have a potential in pathogen transport higher trophic levels. In this study, we firstly cloned and characterized three core immune genes such as nuclear factor κB (NF-κB), inhibitor of NF-κB (IκB), and lipopolysaccharide-induced TNF-α factor (LITAF) genes in the intertidal copepod Tigriopus japonicus. Several in silico analyses based on conserved domains, motifs, and phylogenetic relationships were supporting their annotations. To investigate the immune-related role of three genes, we exposed lipopolysaccharide (LPS) and two Vibrio sp. to T. japonicus. After exposure of different concentrations of LPS and two Vibrio sp., transcripts of TJ-IκB and TJ-LITAF genes were significantly elevated during the time course in a dose-dependent manner, while TJ-NF-κB transcripts were not significantly changed during exposure. These findings demonstrated that the copepod T. japonicus has a conserved immunity against infection.

Molecular cloning and expression analysis of two lipopolysaccharide-induced TNF-α factors (LITAFs) from rock bream, Oplegnathus fasciatus

Lipopolysaccharide (LPS)-induced tumor necrosis factor (TNF)-α factor (LITAF) plays an important role controlling the expression of TNF-α and the other cytokine genes in the presence of LPS. However, two LITAF homologues have not been characterized in fish. In this study, we cloned two distinct LITAF (RbLITAF1 and RbLITAF2) cDNAs from rock bream (Oplegnathus fasciatus) and characterized their expression profiles after infection with Edwardsiella tarda, Streptococcus iniae or red seabream iridovirus (RSIV). The coding regions of RbLITAF1 and RbLITAF2 cDNAs were 492 bp and 417 bp, encoding 153 and 138 amino acid residues, respectively. The genes consisted of a LITAF domain. RbLITAF1 was highly expressed in the spleen and heart of healthy rock bream, whereas RbLITAF2 was highly expressed in the gill, intestine and stomach. In spleen, the gene expression of RbLITAF1 and RbLITAF2 were increased until 5 days post-infection (dpi), and then decreased at 7 dpi. In kidney, E. tarda and RSIV infection led to induction of the RbLITAF1 gene at 1 dpi, RbLITAF2 gene was down-regulated after pathogen infection. These results suggest that RbLITAFs may be involved in the LITAF-mediated immune response and regulate systemic immune responses against pathogen infection.

Characterization of LPS-induced TNFα factor (LITAF) from orange-spotted grouper, Epinephelus coioides

Lipopolysaccharide-induced TNFα factor (LITAF) is an important transcription factor that mediates cell apoptosis and inflammatory response. In the present study, we cloned and characterized a LITAF gene from orange-spotted grouper (Epinephelus coioides) (Ec-LITAF). Ec-LITAF encoded a predicted 142 amino acid protein which shared 74% identity to sablefish (Anoplopoma fimbria) LITAF homolog. Multiple amino acid alignment showed that Ec-LITAF contained a typical LITAF domain with two CXXC motifs. Phylogenetic analysis indicated that Ec-LITAF was closely related to that of sablefish. Ec-LITAF mRNA was widely expressed in different tissues and its expression level in spleen was up-regulated after Singapore grouper iridovirus (SGIV) infection. Subcellular localization analysis revealed that the distribution of Ec-LITAF showed diffuse and aggregated patterns in cytoplasm. Interestingly, the distribution of Ec-LITAF overlayed with a viral LITAF homolog (vLITAF) encoded by SGIV. Overexpression of Ec-LITAF in vitro up-regulated the expression of tumor necrosis factors (TNF1 and TNF2) and TNF receptors (TNFR1 and TNFR2), and the expression of itself initiated apoptosis in fish cells. In addition, overexpression of Ec-LITAF not only accelerated SGIV infection induced CPE and cell death, but also increased viral gene transcription. Taken together, our data suggested that Ec-LITAF might play crucial roles during SGIV replication.

Identification of a LPS-induced TNF-α factor (LITAF) from mollusk Solen grandis and its expression pattern towards PAMPs stimulation

Lipopolysaccharide-induced TNF-α factor (LITAF) is one of the most important transcription factors mediating TNF-α transcription. In the present study, a LITAF gene (designated as SgLITAF) was identified from razor clams Solen grandis. The full-length cDNA of SgLITAF was of 1476 bp, encoding a polypeptide of 130 amino acids showed high similarity to other known LITAFs. SgLITAF encoded a LITAF domain and the Zn(2+)-binding motifs in the domain were well conserved. The mRNA transcripts of SgLITAF were detected in all tested tissues of healthy razor clams, including mantle, gill, gonad, hemocytes, muscle and hepatopancreas, and with the highest expression level in hepatopancreas. The expression level of SgLITAF in hemocytes was significantly up-regulated (P < 0.01) after razor clams were stimulated by LPS or β-1, 3-glucan, but no obvious fluctuation of SgLITAF mRNA expression was observed after PGN stimulation. All the results indicated that there might be a LITAF-regulated TNF-α signaling pathway existing in S. grandis, which involved in the immune response not only against gram-negative bacteria but also towards fungi.

cgMolluscidin, a novel dibasic residue repeat rich antimicrobial peptide, purified from the gill of the Pacific oyster, Crassostrea gigas

A 5.5 kDa antimicrobial peptide consisting of 55 amino acids, cgMolluscidin, was purified from the acidified gill extract of the Pacific oyster, Crassostrea gigas, by ion-exchange and C18 reversed-phase high performance liquid chromatography. By comparing the N-terminal amino acid sequences and the molecular weight of this peptide with those of other known antimicrobial peptides, it has been revealed that this peptide had no homology with any known peptides. cgMolluscidin showed potent antimicrobial activity against both Gram-positive bacteria, including Bacillus subtilis, Micrococcus luteus, and Staphylococcus aureus (minimal effective concentrations [MECs]; 1.3-31.3 μg/mL), and Gram-negative bacteria, including Escherichia coli, Salmonella enterica, and Vibrio parahaemolyticus ([MECs]; 0.4-2.3 μg/mL), without hemolytic activity. However, cgMolluscidin did not show any significant activity against Candida albicans. The deduced amino acid sequence of the cgMolluscidin showed no hit in public protein databases, while the nucleotide sequence had a 99% homology (E value = 0) with only the unknown ESTs sequenced by C. gigas EST project. Tissue distribution of the cgMolluscidin mRNA suggests that it is constitutively expressed as a mature form in a non-tissue-specific manner. The cgMolluscidin mRNA expression level was significantly up-regulated at 12 h (2.8-fold) post injection with Vibrio sp. This peptide is highly basic and contains several dibasic residue repeats including Lysine-Lysine or Lysine-Arginine in the sequence, but may not form an ordered structure. These results suggest that cgMolluscidin might be an oyster-specific novel antimicrobial peptide.

Characteristics and expression patterns of the lipopolysaccharide-induced TNF-α factor (LITAF) gene family in the Pacific oyster, Crassostrea gigas

Lipopolysaccharide-induced tumor necrosis factor-alpha factor (LITAF) is a novel transcription factor responsible for lipopolysaccharide (LPS)-induced transcription of tumor necrosis factor-alpha. Here, we identified and characterized five new LITAF genes in a mollusk, Crassostrea gigas. The complete cDNA sequences of these newly-cloned CgLITAFs each contain one small ORF encoding putative proteins ranging from 67 to 132 amino acids in length. Each CgLITAF, except LITAF2, includes a conserved domain with two motifs, (H)XCXXC and CXXC; LITAF2 lacks the N-terminal CXXC motif. Phylogenetic analysis shows that the six CgLITAFs members (including a previously reported one) cluster into two different mollusk LITAF branches, implying an ancient origin of two LITAF genes that later diversified. CgLITAF members show distinct gene expression patterns with higher expression in digestive gland, gill, and mantle. Except for LITAF4 and LITAF6, CgLITAF expressions can be induced selectively and to various degrees by different Pathogen-Associated Molecular Patterns (PAMPs). Our results strongly demonstrated that the CgLITAF gene family has diversified in function such that each gene plays a distinct and non-redundant role in host defense of C. gigas.

[Cloning and expression analysis of lipopolysaccharide-induced TNF-a(LITAF) of Japanese scallop (Mizuhopecten yessoensis)]

The lipopolysaccharide-induced TNF-alpha factor (LITAF) is an inflammatory cytokine, which plays an important role in innate immunity system. Based on the expressed sequence tag (EST) of Japanese scallop (Mizuhopecten yessoensis), the cDNA of LITAF gene was amplified using rapid amplification of cDNA ends (RACE) approach. Results showed that the full-length cDNA of LITAF is 1 551 bp consisting of a 5' untranslated region (UTR) of 76 bp, a 3' UTR of 1 001 bp, and an open reading frame (ORF) of 474 bp encoding a polypeptide of 157 amino acids, and there is a conserved LITAF domain in amino acid sequences. The estimated molecular mass is 16.99 kDa and the theoretical isoelectric point is 6.24. The total length of LITAF is 3 698 bp, which includes three exons and two introns. Real-time quantitative PCR was carried out to measure LITAF mRNA expression in adult tissues and monitor mRNA expression patterns during embryonic development after bacteria (Vibrio anguillarum) challenged. The expression level of LITAF mRNA was detected in all the adult tissues with the highest in the kidneys. The trochophore owns the highest expression level of LITAF in embryonic development. LITAF expression showed significant difference(P<0.01)between the control and bacteria challenged specimens at 36 h. These results suggest that the LITAF should be a member of the LITAF family that perhaps involved in the innate immune response of Japanese scallop.

Purification and antimicrobial function of ubiquitin isolated from the gill of Pacific oyster, Crassostrea gigas

An antimicrobial polypeptide was purified from an acidified gill extract of Pacific oyster (Crassostrea gigas) by C(18) reversed-phase HPLC. The purified polypeptide had a molecular weight of 8471Da containing 74 amino acid residues. Comparison of the obtained N-terminal sequences with those of others revealed that it was identical to ubiquitin reported from other species and named cgUbiquitin. cgUbiquitin showed broad potent antimicrobial activity against Gram-positive and -negative bacteria including Streptococcus iniae and Vibrio parahemolyticus (minimal effective concentrations, 7.8 and 9.8μg/mL), respectively, without hemolytic activity. The cgUbiquitin cDNA was identified from an expressed sequence tag (EST) library of oyster gill as a precursor form, encoding ubiquitin consisting of 76 amino acids fused to ribosomal protein of S27. Although the cgUbiquitin precursor mRNA was expressed at the intermediate level in the gill, the mRNA was significantly up-regulated at 48h post injection with Vibrio sp. Analysis of the cgUbiquitin C-terminus by carboxypeptidase B treatment and comparison of the retention times revealed that cgUbiquitin lacks the terminal Gly-Gly doublet and ends in an C-terminal Arg residue which might be related to antimicrobial activity. Study of the kinetics of killing and membrane permeabilization showed that this peptide was not membrane permeable and acted through a bacteriostatic process. According to the homology modeling, this peptide is composed of three secondary structural motifs including three α-helices and four β-strands separated by 7 loops regions. Our results indicate that cgUbiquitin might be related to the innate immune defenses in the Pacific oyster and this is the first report for antimicrobial function of ubiquitin isolated from any oyster species.

Identification and characterization of a putative lipopolysaccharide-induced TNF-α factor (LITAF) gene from Amphioxus (Branchiostoma belcheri): an insight into the innate immunity of Amphioxus and the evolution of LITAF

Innate immunity defenses against infectious agent in all multicultural organisms. TNF-α is an important cytokine that can be stimulated by Lipopolysaccharide (LPS) to regulate the innate immunity. The lipopolysaccharide-induced TNF-α factor (LITAF) functions as a transcription factor for regulating the expression of TNF-α as well as various inflammatory cytokines in response to LPS stimulation. The physiological significance of LITAF gene in the innate immunity of various animals has recently been reported. However, no LITAF gene has yet been identified in amphioxus, which is the best available stand-in for the proximate invertebrate ancestor of the vertebrates. In this study, we identified and characterized an amphioxus LITAF gene (designated as AmphiLITAF). First, we identified the AmphiLITAF from the amphioxus and found that AmphiLITAF gene with ~1.6 kb in length has a 827bp cDNA transcription product which encodes a putative protein with 127 amino acids containing conserved LITAF-domain, and the deduced amino acid of AmphiLITAF shared 37-60% similarity with the LITAFs from other species; second, we uncovered the spatial distribution of the LITAF in different tissues, the expression level of AmphiLITAF mRNA was the highest in hepatic cecum and intestine, moderate in muscles, gills and gonad, and the lowest in notochord. Our findings provide an insight into the innate immune response in the amphioxus and the evolution of the LITAF family.

Transcriptomics of in vitro immune-stimulated hemocytes from the Manila clam Ruditapes philippinarum using high-throughput sequencing

Background

The Manila clam (Ruditapes philippinarum) is a worldwide cultured bivalve species with important commercial value. Diseases affecting this species can result in large economic losses. Because knowledge of the molecular mechanisms of the immune response in bivalves, especially clams, is scarce and fragmentary, we sequenced RNA from immune-stimulated R. philippinarum hemocytes by 454-pyrosequencing to identify genes involved in their immune defense against infectious diseases.

Methodology and Principal Findings

High-throughput deep sequencing of R. philippinarum using 454 pyrosequencing technology yielded 974,976 high-quality reads with an average read length of 250 bp. The reads were assembled into 51,265 contigs and the 44.7% of the translated nucleotide sequences into protein were annotated successfully. The 35 most frequently found contigs included a large number of immune-related genes, and a more detailed analysis showed the presence of putative members of several immune pathways and processes like the apoptosis, the toll like signaling pathway and the complement cascade. We have found sequences from molecules never described in bivalves before, especially in the complement pathway where almost all the components are present.

Conclusions

This study represents the first transcriptome analysis using 454-pyrosequencing conducted on R. philippinarum focused on its immune system. Our results will provide a rich source of data to discover and identify new genes, which will serve as a basis for microarray construction and the study of gene expression as well as for the identification of genetic markers. The discovery of new immune sequences was very productive and resulted in a large variety of contigs that may play a role in the defense mechanisms of Ruditapes philippinarum.

MIF from mussel: coding sequence, phylogeny, polymorphism, 3D model and regulation of expression

Three macrophage migration inhibitory factor (MIF)-related sequences were identified from a Mytilus galloprovincialis EST library. The consensus sequence included a 5'-UTR of 32 nucleotides, the complete ORF of 345 nucleotides, and a 3'-UTR of 349 nucleotides. As for other MIFs, M. galloprovincialis ORF does not include any signal or C-terminus extensions. The translated sequence of 115 amino acids possesses a molecular mass of 12,681.4, a pI of 6.27 and a stability index of 21.48. Its 3D structure resembles human MIF except for one shorter α-helix. Although evolutionary separated from ticks and vertebrates, Mg-MIF appeared to be closely related to Pinctada fucata and Haliotis, but not to Chlamys farreri and Biomphalaria glabrata. Numerous mutation points were observed within the Mg-MIF ORF, defining 11 amino acid variants within the mussels from Palavas-France and 14 amino acid variants within the mussels from Palermo-Italy. The 2 major variants from Palavas were identical to 2 of the 4 major variants from Palermo. In all the 18 Mg-MIF variants, residues involved in tautomerase and in oxidoreductase activities were conserved. Generally, one mussel expressed 2 Mg-MIF amino acid sequences but with different frequencies of occurrence. Mg-MIF is constitutively expressed principally in hemocytes and in the mantle. In contrast to other animal models, Mg-MIF expression was always down regulated following challenge by bacteria and fungi, confirming previous data obtained with microarray. Down regulation started as soon as 1 h and Mg-MIF expression returned to background 9-48 h after the challenge. Exception was regarding the yeast, Candidaalbicans, down-regulation between 9 and 72 h, suggesting yeast and bacteria-filamentous fungi trigger different mechanisms of elimination.

Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis

The marine mussel Mytilus edulis and its closely related sister species are distributed world-wide and play an important role in coastal ecology and economy. The diversification in different species and their hybrids, broad ecological distribution, as well as the filter feeding mode of life has made this genus an attractive model to investigate physiological and molecular adaptations and responses to various biotic and abiotic environmental factors. In the present study we investigated the immune system of Mytilus, which may contribute to the ecological plasticity of this species. We generated a large Mytilus transcriptome database from different tissues of immune challenged and stress treated individuals from the Baltic Sea using 454 pyrosequencing. Phylogenetic comparison of orthologous groups of 23 species demonstrated the basal position of lophotrochozoans within protostomes. The investigation of immune related transcripts revealed a complex repertoire of innate recognition receptors and downstream pathway members including transcripts for 27 toll-like receptors and 524 C1q domain containing transcripts. NOD-like receptors on the other hand were absent. We also found evidence for sophisticated TNF, autophagy and apoptosis systems as well as for cytokines. Gill tissue and hemocytes showed highest expression of putative immune related contigs and are promising tissues for further functional studies. Our results partly contrast with findings of a less complex immune repertoire in ecdysozoan and other lophotrochozoan protostomes. We show that bivalves are interesting candidates to investigate the evolution of the immune system from basal metazoans to deuterostomes and protostomes and provide a basis for future molecular work directed to immune system functioning in Mytilus.

LPS-induced TNFα factor (LITAF) in the snail Cipangopaludina chinensis: gene cloning and its apoptotic effect on NCI-H446 cells

LPS-induced TNFα factor (LITAF) is a transcription factor mediating TNF-α expression under LPS stimulation, and playing important roles in immune responses. In the present study, partial cDNA sequence of a LITAF (designated CcLITAF) gene was cloned and identified from snail Cipangopaludina chinensis. It contains an open reading frame of 348 nucleotides encoding a predicted protein of 115 amino acids, with a conserved LITAF domain at C-terminal, and shares a similarity ranging from 34% to 96% with other LITAF from oyster to mammals. CcLITAF mRNA ubiquitously expressed in all analyzed tissues. Interestingly, cLITAF could induce apoptosis in human tumor cell line, NCI-H446 cells, and caspase 3 play key roles in CcLITAF-mediated apoptosis. Present studies provide new insight into the biological function of CcLITAF.

Molecular cloning, characterization and expression analysis of the tumor necrosis factor (TNF) superfamily gene, TNF receptor superfamily gene and lipopolysaccharide-induced TNF-α factor (LITAF) gene from Litopenaeus vannamei

In vertebrates, the tumor necrosis factor (TNF)-receptor (TNFR) system participates in diverse physiological and pathological events, such as inflammation and protective immune responses to microbial infections. There are few reports about the role of the invertebrate TNF-TNFR system in immune responses. Here, we isolated and characterized the TNF superfamily (LvTNFSF) gene, TNFR superfamily (LvTNFRSF) gene and lipopolysaccharide-induced TNF-α factor (LvLITAF) gene from Litopenaeus vannamei. LvTNFSF consists of 472 amino acids with a conserved C-terminal TNF domain and has 89.8% identity with the Marsupenaeus japonicus TNF superfamily gene. LvTNFRSF consists of 296 amino acids with a conserved TNFR domain and has 18.0% identity with Chlamys farreri TNFR, 14.6% identity with Drosophila melanogaster Wengen and 14.6% identity with Homo sapiens TNFR1. LvLITAF consists of 124 amino acids with the LITAF domain and shows 62.6% identity with D. melanogaster LITAF and 32.3% identity with H. sapiens LITAF. The promoter region of LvTNFSF was cloned and used to construct a luciferase reporter. In Drosophila S2 cells, the promoter of LvTNFSF can be activated by LvLITAF, L. vannamei NF-κB family proteins (LvRelish and LvDorsal) and LvSTAT. Unlike its mammalian counterparts, LvTNFRSF could not activate the NF-κB pathway in Drosophila S2 cells. Using real-time quantitative PCR, we obtained expression profiles of LvTNFSF, LvTNFRSF and LvLITAF in the gill, intestine and hepatopancreas of L. vannamei after challenge with Gram-negative Vibrio alginolyticus, Gram-positive Staphylococcus aureus, the fungus Candida albicans and white spot syndrome virus (WSSV). Taken together, our results reveal that LvTNFSF, LvTNFRSF and LvLITAF may be involved in shrimp immune responses to pathogenic infections.

Whole transcriptome profiling of successful immune response to Vibrio infections in the oyster Crassostrea gigas by digital gene expression analysis

The cultivated Pacific oyster Crassostrea gigas has suffered for decades large scale summer mortality phenomenon resulting from the interaction between the environment parameters, the oyster physiological and/or genetic status and the presence of pathogenic microorganisms including Vibrio species. To obtain a general picture of the molecular mechanisms implicated in C. gigas immune responsiveness to circumvent Vibrio infections, we have developed the first deep sequencing study of the transcriptome of hemocytes, the immunocompetent cells. Using Digital Gene Expression (DGE), we generated a transcript catalog of up-regulated genes from oysters surviving infection with virulent Vibrio strains (Vibrio splendidus LGP32 and V. aestuarianus LPi 02/41) compared to an avirulent one, V. tasmaniensis LMG 20012(T). For that an original experimental infection protocol was developed in which only animals that were able to survive infections were considered for the DGE approach. We report the identification of cellular and immune functions that characterize the oyster capability to survive pathogenic Vibrio infections. Functional annotations highlight genes related to signal transduction of immune response, cell adhesion and communication as well as cellular processes and defence mechanisms of phagocytosis, actin cytosqueleton reorganization, cell trafficking and autophagy, but also antioxidant and anti-apoptotic reactions. In addition, quantitative PCR analysis reveals the first identification of pathogen-specific signatures in oyster gene regulation, which opens the way for in depth molecular studies of oyster-pathogen interaction and pathogenesis. This work is a prerequisite for the identification of those physiological traits controlling oyster capacity to survive a Vibrio infection and, subsequently, for a better understanding of the phenomenon of summer mortality.

Identification and expression of a putative LPS-induced TNF-α factor from Asiatic hard clam Meretrix meretrix

LPS-induced TNF-α (LITAF) is a novel transcriptional factor that mediates the expression of inflammatory cytokines in LPS-induced processes. In the present study, the full-length cDNA encoding LITAF (designated as Mm-LITAF) was identified from Asiatic hard clam, Meretrix meretrix, by expressed sequence tag and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of Mm-LITAF was 1653 bp, consisting of a 5' untranslated region (UTR) of 91 bp, a 3'UTR of 1166 bp with one cytokine RNA instability motif (ATTTA) and one polyadenylation signal (AATAAA), and an open reading frame (ORF) of 396 bp encoding a polypeptide of 131 amino acids with a theoretical isoelectric point of 7.49, and predicted molecular weight of 14.47 kDa. The deduced amino acid of Mm-LITAF shared 29-63% similarity with the LITAFs from other species, indicating that Mm-LITAF should be a member of the LITAF family. Two highly conserved CXXC motifs forming a compact Zn(2+)-binding structure were also identified in Mm-LITAF. A quantitative reverse transcriptase real-time PCR (qRT-PCR) assay was developed to assess the expression of Mm-LITAF mRNA in different tissues, and the temporal expression of Mm-LITAF in clams challenged with Vibrio anguillarum. The mRNA transcript of Mm-LITAF could be detected in all the examined tissues with the highest expression level in the gill. Mm-LITAF expression was up-regulated significantly at 16 h in the gill and at 8 h in haemocytes after bacterial challenge, respectively. These results suggest that the Mm-LITAF is a constitutive and inducible acute-phase protein that perhaps involved in the innate immune response of hard clam.