De novo assembly of the sea cucumber Apostichopus japonicus hemocytes transcriptome to identify miRNA targets associated with skin ulceration syndrome

Investigation on the cellular mechanism of Prunetin evidenced through next generation sequencing and bioinformatic approaches against gastric cancer

Gastric cancer is the common type of malignancy positioned at second in mortality rate causing burden worldwide with increasing treatment options. More accurate and reliable diagnostic methods/biomarkers are urgently needed. The application of transcriptomics technologies possesses the high efficiency of identifying key metabolic pathways and functional genes in cancer research. In this study, we performed a transcriptome analysis on Prunetin treated AGS cells. A total of 1,118 differentially expressed (DE) genes on Prunetin treated AGS cancer cells, among which 463 were up-regulated and 655 were down-regulated. Notably, around 40 genes were found to be related with necroptosis, among which 16 genes were found to be in close association with Receptor Interacting Protein Kinase (RIPK) family. Validation of the RIPK genes through GEPIA identified 8 genes (NRP1, MNX1, SSRP1, PRDX2, PLRG1, LGALS4, SNX5 and FXYD3) which are highly expressed in stomach cancer were significantly down-regulated in PRU treated samples. In conclusion, the sequencing data explores the expression of RIPK mediated genes through necroptosis signaling network in treating gastric cancer. The futuristic validations on the 8 genes as candidate biomarkers will offer a treatment approach against gastric cancer using PRU.

IL-17/IL-17 Receptor Pathway-Mediated Inflammatory Response in Apostichopus japonicus Supports the Conserved Functions of Cytokines in Invertebrates

Inflammation participates in host defenses against infectious agents and contributes to the pathophysiology of many diseases. IL-17 is a well-known proinflammatory cytokine that contributes to various aspects of inflammation in vertebrates. However, the functional role of invertebrate IL-17 in inflammatory regulation is not well understood. In this study, we first established an inflammatory model in the Vibrio splendidus-challenged sea cucumber Apostichopus japonicus (Echinodermata). Typical inflammatory symptoms, such as increased coelomocyte infiltration, tissue vacuoles, and tissue fractures, were observed in the V. splendidus-infected and diseased tissue of the body wall. Interestingly, A. japonicus IL-17 (AjIL-17) expression in the body wall and coelomocytes was positively correlated with the development of inflammation. The administration of purified recombinant AjIL-17 protein also directly promoted inflammation in A. japonicus Through genome searches and ZDOCK prediction, a novel IL-17R counterpart containing FNIII and hypothetical TIR domains was identified in the sea cucumber genome. Coimmunoprecipitation, far-Western blotting, and laser confocal microscopy confirmed that AjIL-17R could bind AjIL-17. A subsequent cross-linking assay revealed that the AjIL-17 dimer mediates the inflammatory response by the specific binding of dimeric AjIL-17R upon pathogen infection. Moreover, silencing AjIL-17R significantly attenuated the LPS- or exogenous AjIL-17-mediated inflammatory response. Functional analysis revealed that AjIL-17/AjIL-17R modulated inflammatory responses by promoting A. japonicus TRAF6 ubiquitination and p65 nuclear translocation and evenly mediated coelomocyte proliferation and migration. Taken together, our results provide functional evidence that IL-17 is a conserved cytokine in invertebrates and vertebrates associated with inflammatory regulation via the IL-17-IL-17R-TRAF6 axis.

Epidemiology of a SKin Ulceration Disease (SKUD) in the sea cucumber Holothuria scabra with a review on the SKUDs in Holothuroidea (Echinodermata)

Aquacultivated sea cucumbers often suffer from SKin Ulceration Diseases (SKUDs). SKUDs have been observed in six holothuroid species from nine countries. All SKUDs present a similar symptom-the skin ulceration-and can be induced by bacteria, viruses, or abiotic factors. We here provide an update on SKUDs in holothuroids and analyse the case of the SKUD observed in Holothuria scabra in Madagascar. Field observations revealed a seasonality of the disease (i.e. wintertime maximum peak). Morphological analyses of integument ulcers showed that sea cucumbers react by forming a collagen fibre plug. Metagenomic analyses revealed a higher proportion of Vibrionaceae (Gammaproteobacteria) in ulcers in comparison to the healthy integument of the same individuals. Experimental infection assays were performed with ulcer crude extracts and bacteria isolated from these extracts (e.g. Vibrio parahaemolyticus) but did not significantly induce skin ulceration. Our results suggest that the disease is not induced by a pathogen or, at the very least, that the pathogen is not found within the ulcers as the disease is not transmissible by contact. An initial cause of the SKUD in Madagascar might be the repeated and prolonged exposures to cold temperatures. Opportunistic bacteria could settle in the dermis of ulcerated individuals and promote the ulcer extension. We propose a general nomenclature for SKUDs based on the acronym of the disease, the affected sea cucumber species (e.g. Hs for Holothuria scabra), the concerned region using an ISO code 3166-2 (e.g. MG for Madagascar), the description date (e.g. 20 for the year 2020), and, when known, the inducing agent (first letter of the general taxon, b for bacteria, v for virus in currently known cases; a a if it is an abiotic inducing parameter; nothing if the inducing cause has not been precisely identified). The disease described in this work will be designated under the name SKUD Hs-MG-20.

MiR-210 regulates coelomocyte proliferation through targeting E2F3 in Apostichopus japonicus

MiR-210 plays a crucial role in cell survival, migration, and regeneration in vertebrates. In our previous work, the expression of miR-210 was considerably induced in diseased Apostichopus japonicus with skin ulcer syndrome (SUS). To further explore the mechanism of miR-210 in regulating the SUS, this study identified E2F transcription factor 3 (E2F3), a candidate target of miR-210, from the sea cucumber A. japonicus via RNA-seq and RACE (designated as AjE2F3). A 1992 bp fragment representing the full-length cDNA of AjE2F3 was obtained, which includes an ORF of 1194 bp encoding a polypeptide of 398 amino acids with a molecular weight of 44.43 kDa. Expression profiling analysis suggested that the expression of AjE2F3 decreased while that of miR-210 increased in Vibrio splendidus-challenged sea cucumber coelomocytes. Dual-luciferase reporter assay revealed that miR-210 targeted AjE2F3 via binding to the 3'UTR region from 108 nt to 128 nt. MiR-210 overexpression in cultured coelomocytes repressed AjE2F3 at the mRNA level and reduced cell proliferation in vitro. Consistently, AjE2F3 overexpression significantly promoted coelomocyte proliferation, as assessed by MTT in vitro. Overall, our results indicated that miR-210 can suppress coelomocyte proliferation by targeting AjE2F3 in pathogen-challenged sea cucumbers.

Sedoheptulose kinase bridges the pentose phosphate pathway and immune responses in pathogen-challenged sea cucumber Apostichopus japonicus

The sedoheptulose kinase carbohydrate kinase-like protein (CARKL) is critical for immune cell activation, reactive oxygen species (ROS) production, and cell polarization by restricting flux through the pentose phosphate pathway (PPP). To date, little is known about CARKL in regulating immune responses in marine invertebrates. In this study, we first cloned and characterized the CARKL gene from Apostichopus japonicus (designated as AjCARKL). Time-course analysis revealed that Vibrio splendidus challenge in vivo and lipopolysaccharide stimulation in vitro significantly downregulated AjCARKL mRNA expression. Furthermore, AjCARKL overexpression in cultured coelomocytes not only significantly inhibited the mRNA expression level of the rate-limiting enzyme glucose-6-phosphate dehydrogenase of the PPP but sharply decreased coelomocyte proliferation, ROS production, and phagocytic rate. Additionally, AjCARKL overexpression in mouse peritoneal macrophages (RAW264.7 cells) significantly attenuated the intracellular ROS production and sensitized the M2 phenotype macrophage polarization. These results revealed that AjCARKL serves as a rheostat for cellular metabolism and is required for proper immune response by negatively regulating PPP in pathogen-challenged A. japonicus.

4-Hydroxyphenylpyruvate dioxygenase from sea cucumber Apostichopus japonicus negatively regulates reactive oxygen species production

As a wide distribution molecule, 4-hydroxyphenylpyruvate dioxygenase (4-HPPD) catalyzes the second step in the tyrosine catabolism pathway. This process commonly occurs in all aerobic life forms. The broad distribution of these metabolites suggests that they have an important role in many organisms. A portion of the 4-HPPD homology sequence was also identified in Apostichopus japonicus transcriptome. However, the functional roles of A. japonicus 4-HPPD remain unclear. In the current study, a 4-HPPD homolog was cloned from A. japonicus (designated as AjHPPD). The nucleotide sequence analysis showed that the open reading frame of AjHPPD was 1149 bp and encoded a 382-amino-acid residue polyprotein with glyoxalase_4 (residues 20-133) and glyoxalase (residues 180-335) domains. The spatial expression analysis revealed that AjHPPD was ubiquitously expressed in all examined tissues with large-magnitude in the respiratory tree and was minimally expressed in coelomocytes. Compared with a control group, the significant increase in transcription of AjHPPD mRNA in the Vibrio splendidus-challenged sea cucumber was 2.10-fold (p < 0.01) at 48 h and returned to the normal level at 72 and 96 h. Similarly, compared with a control group, the significant increase in the transcription of AjHPPD mRNA was 3.36-fold (p < 0.01) at 24 h after stimulation with 10 mg mL^-1 of LPS. On the one hand, silencing AjHPPD in vitro could inhibit the expression of pentose phosphate pathway (PPP) flux enzyme glucose-6-phosphate dehydrogenase (G6PD) at the mRNA level and prevent the clearance of reactive oxygen species (ROS) in sea cucumbers. On the other hand, interference of AjHPPD by using specific siRNA can result in the significant promotion of coelomocyte apoptosis with a 1.61-fold increase in vitro. AjHPPD negatively regulated ROS levels by modulating tyrosine catabolism on AjG6PD expression and coelomocyte apoptosis in response to pathogen infection.

Molecular cloning and functional characterization of MYC transcription factor in pathogen-challenged Apostichopus japonicus

Myelocytomatosis viral oncogene (MYC), a transcription factor in the MYC family, plays vital roles in vertebrate innate immunity by regulating related immune gene expressions. In this study, we cloned and characterized an MYC gene from sea cucumber Apostichopus japonicus via RNA-seq and RACE approaches (designated as AjMYC). A 2074 bp fragment representing the full-length cDNA of AjMYC was obtained. This gene includes an open reading frame (ORF) of 1296 bp encoding a polypeptide of 432 amino acid residues with the molecular weight of 48.85 kDa and theoretical pI of 7.22. SMART analysis indicated that AjMYC shares an MYC common HLH motif (354-406 aa) at the C-terminal. Spatial expression analysis revealed that AjMYC is constitutively expressed in all detected tissues with peak expression in the tentacle. Vibrio splendidus-challenged sea cucumber could significantly boost the expression of AjMYC transcripts by a 5.58-fold increase in the first stage. Similarly, 2.75- and 3.23-fold increases were detected in LPS-exposed coelomocytes at 1 and 24 h, respectively. In this condition, coelomocyte apoptotic rate increased from 11.98% to 56.23% at 1 h and to 59.08% at 24 h. MYC inhibitor treatment could not only inhibit the expression of AjMYC and Ajcaspase3, but also depress the coelomocyte apoptosis. Furthermore, AjMYC overexpression in EPC cells for 24 h also promoted the cell apoptosis rate from 21.31% to 45.85%. Collectively, all these results suggested that AjMYC is an important immune factor in coelomocyte apoptosis toward pathogen-challenged sea cucumber.

Characterization of a gC1qR homolog from sea cucumber Apostichopus japonicus

gC1qR is a multifunctional and multiligand binding protein that plays important roles in inflammation and infection. In this study, a novel gC1qR homolog called AjgC1qR from the invertebrate sea cucumber Apostichopus japonicus was cloned and characterized. The open reading frame of AjgC1qR encoded 292 amino acid residues with a conserved mitochondrial targeting sequence and MAM33 domain. Multiple sequence alignment and phylogenetic analyses proved that AjgC1qR is a homolog of the gC1qR family. Spatial mRNA transcription in five tissues revealed the ubiquitous expression of AjgC1qR. The highest and lowest levels of expression were found in the tentacle and muscle, respectively, and AjgC1qR expression was remarkably up-regulated in coelomocytes after Vibrio splendidus challenge. Moreover, the recombinant rAjgC1qR protein exhibited high binding activity toward pathogen-associated molecules, such as lipopolysaccharides, peptidoglycan, and mannan. These findings demonstrate that AjgC1qR may play important roles in innate immunity and function as a pathogen recognition receptor.

Cloning and functional analysis of scavenger receptor B gene from the sea cucumber Apostichopus japonicus

Scavenger receptor (SR) class B (SR-B) is a transmembrane protein that belongs to the SR family with a wide range of functions in innate immunity. Here, an SR-B homologue, designated as AjSR-B, was cloned from the sea cucumber Apostichopus japonicus. AjSR-B comprised 2519 nucleotides with a 5'-untranslated region (UTR) of 153 bp, an open reading frame of 1581 bp encoding a 526 amino acid protein, and a 3'-UTR of 785 bp. SMART analysis indicated that AjSR-B has two transmembrane regions and a cluster determinant 36 domain. Multiple alignments and phylogenetic analysis supported that AjSR-B is a novel member of the SR-B protein family. Moreover, AjSR-B was constitutively expressed in all detected tissues, with the highest levels recorded in the intestine. Both were significantly induced in coelomocytes and the intestine after Vibrio splendidus challenge. Functionally, the recombinant rAjSR-B that corresponds to a large extracellular loop can bind pathogen-associated molecular patterns (PAMPs), including lipopolysaccharide (LPS), peptidoglycan, and mannan, with a high binding affinity to LPS. Bacterial agglutination assay showed that rAjSR-B can agglutinate the four tested bacteria (Gram-negative and Gram-positive bacteria) with calcium dependence. However, the agglutination ability for Gram-negative bacteria completely disappeared in the presence of PAMPs but a weak ability to bind Gram-positive bacteria (Micrococcus luteus) was still exhibited, suggesting there might exist a competition between Gram-positive bacteria and PAMPs under same condition. Our current study indicated that AjSR-B is a PAMP that plays important roles in the innate immune process of sea cucumbers.

Acute effects of UVB radiation on the survival, growth, development, and reproduction of Daphniopsis tibetana Sars (Crustacea: Cladocera)

Daphniopsis tibetana Sars lives in elevation, usually with strong solar UV radiation. We speculate that UV may have an effect on the ecology and evolutionary biology of this species. However, the regulatory effect and mechanism of UV on D. tibetana have not been studied previously. Here, our results showed that UVB could act as a positive factor in the relative body lengths, reproductive parameters, and population growth parameters of D. tibetana when UVB radiation is 20-170 mJ cm^-2, compared with the control group. Strikingly, these parameters were highest at 120 mJ cm^-2. To explore the mechanism underlying the UVB irradiation effects, we conducted a transcriptome analysis using the Trinity platform. The results indicated that differentially regulated genes were mostly enriched in lipid transport and lipid localization by Gene Ontology (GO) enrichment analysis of 146 differentially expressed genes (83 upregulated and 63 downregulated). This is the first study of UVB radiation of D. tibetana to reveal genes that may have crucial roles in survival, growth, and reproduction and could be candidates for future functional studies. Additionally, the study could supply a substantial resource for investigating and elucidating lipids that could play important roles in a physiological context.

Divergent immune roles of two fucolectin isoforms in Apostichopus japonicus

The F-type lectin (fucolectin) family represents a new group with innate immunity. In this study, two fucolectin isoforms (designated as AjFTL-1 and AjFTL-2) were identified in sea cucumber (Apostichopus japonicus) through rapid amplification of cDNA ends. Full-length cDNAs of AjFTL-1 and AjFTL-2 measured 2134 and 1286 bp, encoding two secreted proteins comprising 317 and 181 amino acid residues, respectively. The signal peptide, l-fucose binding motif ("HX(26)RXDX(4)R/K") and cation binding sequence motif ("h2DGx") were conserved in AjFTL-1 and AjFTL-2. However, AjFTL-1 contains an additional complement control protein domain. Multiple sequence alignments supported that AjFTL-1 and AjFTL-2 are new members of the F-type lectin family. Tissues distribution analysis indicated that both AjFTL-1 and AjFTL-2 were widely expressed in all tested tissues, featuring differential expression patterns. Vibrio splendidus infection in vivo can significantly upregulate the mRNA transcripts of the two genes, with a larger magnitude observed in AjFTL-1. By contrast, lipopolysaccharide stimulation in vitro can markedly induce the expression level of AjFTL-2 but not that of AjFTL-1. Silencing AjFTL-2 by siRNA can suppress the AjNOS transcript, whereas injection of the recombinant protein of AjFTL-2 can significantly induce AjNOS expression. By contrast, the loss- and gain-of-function of AjFTL-1 caused no effect on the expression of AjNOS. Our present study provides evidence supporting that AjFTL-1 and AjFTL-2 play diverse roles in the innate immune defense of sea cucumbers toward bacterial infection.

Identification and characterization of a novel PRR of fibrinogen-related protein in Apostichopus japonicus

Fibrinogen-related proteins (FREPs) play important roles in innate immunity by recognizing pathogen associated molecular patterns on pathogenic bacteria surfaces via conserved fibrinogen-like domain (FBG). In this paper, the full-length cDNA of Apostichopus japonicus FREP (designated as AjFREP) was cloned combined with rapid amplification of cDNA ends (RACE) and transcriptome sequencing. The full-length cDNA of AjFREP was of 2110 bp with an open reading frame (ORF) of 1659 bp. SMART analysis revealed that the AjFREP contained a typical signal peptide of 19 amino acid residues, a FBG and two unusual epidermal growth factor-like domains (EGFs). Multiple sequence alignments suggested that FBG domain shared a remarkably high structural conservation in polypeptide binding site and Ca²⁺ binding site. Tissue distribution analysis revealed that AjFREP was constitutively expressed in all examined tissues with the largest magnitude in coelomocytes, indicating AjFREP might play an important role in immune defense. The mRNA level of AjFREP in coelomocytes was sharply up-regulated by Vibrio splendidus challenge, and reached its peak expression at 48 h. Knock-down AjFREP by specific siRNA could significantly repress the coelomocyte phagocytosis rate. Meantime, the survival number of V. splendidus in the coelomic fluid was promoted. All these current results indicated that AjFREP might be involved in pathogen clearance through mediating coelomocytes phagocytosis activity.

Understanding microRNAs regulation in heat shock response in the sea cucumber Apostichopus japonicus

The sea cucumber Apostichopus japonicus is a valuable species in China. The extreme high temperature in the summer often results in high mortality. MicroRNAs (miRNAs) play important post-transcriptional regulatory roles in gene expression and can influence heat shock response (HSR) greatly. In this study, we determined the expression profiles of miRNAs under heat stress (HS) in A. japonicus by using high-throughput sequencing technique. Among the differential expression miRNAs, we highlighted 41 differentially expressed miRNAs, many of which were involved in immunity process and disease regulation. Gene ontology and pathway analyses of putative target genes were also carried out. Cell-substrate adherens junction and cell-substrate junction were significantly enriched in GO analysis. Moreover, we made a correlation analysis between remarkable miRNAs and the differentially expressed genes (DEGs) in sea cucumbers under HS. We identified 17 key miRNA-target pairs potentially regulated HSR of sea cucumbers. These results will provide new insights about miRNAs regulation and molecular adaptive mechanisms in sea cucumbers under HS.

Transcriptome sequencing identifies key pathways and genes involved in gastric adenocarcinoma

The present study aimed to investigate the key pathways and genes associated with gastric adenocarcinoma via transcriptome sequencing. Five pairs of gastric adenocarcinoma tissue and normal tumor-adjacent tissue were harvested. After sequencing, raw data were processed and differentially expressed genes (DEGs) between tumor and control groups were screened, followed by functional enrichment analysis and gene clustering analysis. The effect of DEGs on patient prognosis was analyzed on the basis of the survival data from gastric adenocarcinoma patients in The Cancer Genome Atlas database. Several genes were validated through reverse transcription-quantitative polymerase chain reaction. In total, 1,477 upregulated and 282 downregulated DEGs were screened in tumor groups. These genes were segregated into four clusters. Genes in cluster 1 were significantly involved in metabolism of xenobiotics by cytochrome P450, genes in cluster 2 were majorly involved in apoptosis, tight junction formation, and platelet activation, genes in cluster 3 were primarily enriched in the p53 signaling pathway and genes in cluster 4 were significantly enriched in the insulin resistance pathway. Furthermore, 15 DEGs significantly influenced prognosis, including F2R, CTHRC1, and RASGRP3. The expression levels of CYP2B6, MAPK13, CTHRC, RASGRP3 and PYGM were consistent with our analysis results. In conclusion, pathways for metabolism of xenobiotics via cytochrome P450, apoptosis, tight junction formation, platelet activation, and insulin resistance may serve important roles in the progression of gastric adenocarcinoma. Notably, CTHRC1 and RASGRP3 may serve as key prognostic markers.

Identification of MicroRNAs and Their Target Genes Associated with Ovarian Development in Black Tiger Shrimp (Penaeus monodon) Using High-Throughput Sequencing

Plenty of evidence showing that microRNAs (miRNAs) post-transcriptionally regulate gene expression and are involved in a wide range of biological processes. However, the roles of miRNAs in ovarian development process remain largely unknown in shrimp. In the present study, high-throughput sequencing of small RNAs was performed to find specific miRNAs that are involved in ovarian development process in Penaeus monodon. Two small RNA libraries were constructed from undeveloped (UNDEV group) and developed (DEV group) ovarian tissues in P. monodon. In total, 43 differentially expressed miRNAs were identified between the two groups (P ≤ 0.05, |log2 ratio| ≥1), and their expression profiles were validated by qRT-PCR. In order to further clarify the functional roles of these differentially expressed miRNAs during ovarian development process, target gene prediction was performed. In total, 4,102 target genes of 43 miRNAs were predicted, then clustered by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database; only four specific pathways related to ovarian development were obtained (P < 0.05). Dual-luciferase reporter assays and integrated expression analysis were also conducted to further clarify the interaction between the miRNAs and their target mRNAs. This study provides important information about the function of miRNAs involved in ovarian developmental stages in P. monodon.

Evidence for a Saponin Biosynthesis Pathway in the Body Wall of the Commercially Significant Sea Cucumber Holothuria scabra

The sea cucumber (phylum Echinodermata) body wall is the first line of defense and is well known for its production of secondary metabolites; including vitamins and triterpenoid glycoside saponins that have important ecological functions and potential benefits to human health. The genes involved in the various biosynthetic pathways are unknown. To gain insight into these pathways in an echinoderm, we performed a comparative transcriptome analysis and functional annotation of the body wall and the radial nerve of the sea cucumber Holothuria scabra; to define genes associated with body wall metabolic functioning and secondary metabolite biosynthesis. We show that genes related to signal transduction mechanisms were more highly represented in the H. scabra body wall, including genes encoding enzymes involved in energy production. Eight of the core triterpenoid biosynthesis enzymes were found, however, the identity of the saponin specific biosynthetic pathway enzymes remains unknown. We confirm the body wall release of at least three different triterpenoid saponins using solid phase extraction followed by ultra-high-pressure liquid chromatography-quadrupole time of flight-mass spectrometry. The resource we have established will help to guide future research to explore secondary metabolite biosynthesis in the sea cucumber.

Divergent roles of three cytochrome c in CTSB-modulating coelomocyte apoptosis in Apostichopus japonicus

Cytochrome c plays crucial roles in apoptosis and the immune response. We previously demonstrated that cathepsin B from Apostichopus japonicus (AjCTSB) induces coelomocyte apoptosis. However, the mechanistic explanation and the regulation of this process have not been investigated. In the present study, we identified three cytochrome c cDNAs from A. japonicus (designated Ajcytc1, Ajcytc-1, and Ajcytc-2) using expressed sequence tag- (EST) and RACE-based approaches. The deduced amino acid sequences of the three cytochrome isoforms contained conserved CXXCH motifs, which are involved in binding heme and maintaining proteolytic activity. Time course expression analysis in vitro and in vivo revealed that the three cytochrome isoforms were induced upon pathogen challenge and LPS exposure. More importantly, AjCTSB knockdown by siRNA dramatically increased mitochondrial membrane potential (ΔΨm) in a time-dependent manner based on JC-1 fluorescent probe staining. AjCTSB knockdown also resulted in decreased expression of these three cytochromes 24 h after siAjCTSB transfection. Functional analysis using isoform-specific siRNAs revealed that Ajcytc-1, but not Ajcytc1 or Ajcytc-2, is involved in coelomocyte apoptosis. Moreover, the transcript level of Ajcaspase-3, an apoptosis executioner, was also consistently down-regulated upon silencing of Ajcytc-1 but not Ajcytc1 or Ajcytc-2. Collectively, these results indicate that Ajcytc1, Ajcytc-1, and Ajcytc-2 play distinct roles in mediating the immune response to bacteria according to AjCTSB expression. Moreover, Ajcytc-1 could be released upon dissipation of the ΔΨm, which could further trigger coelomocyte apoptosis through the activation of Ajcaspase-3.

A novel TNFAIP8 gene mediates l-arginine metabolism in Apostichopus japonicus

Tumor necrosis factor (TNF)-α-induced protein 8 (TNFAIP8) family is a newly identified protein with vital roles in maintaining immune homeostasis. In the current study, we first cloned and characterized a TNFAIP8 gene from the invertebrate sea cucumber Apostichopus japonicus. The gene was designated as AjTNFAIP8. The full-length cDNA of AjTNFAIP8 was 1455 bp long and encoded a matured protein of 201 amino acid residues. Structural analysis indicated that AjTNFAIP8 had a death effector domain (DED)-like domain and composed of six α-helices. Multiple sequence alignment and phylogenetic analysis supported that AjTNFAIP8 is a new member of the TNFAIP8 family. Analysis of basal transcription in five tissues revealed the constitutive expression of AjTNFAIP8 in the detected tissues with highest expression in the respiratory tree and minimum expression in the tentacle. Vibrio splendidus infection and LPS stimulation could significantly downregulate the mRNA expression of AjTNFAIP8. More importantly, the transcription of pro-inflammatory molecule NOS and its production of NO content were significantly increased after AjTNFAIP8 silencing, with the suppression of agmatinase transcript and arginase activity. These results clearly indicated that AjTNFAIP8 is an essential negative regulator in innate immunity. Basic information for further exploration of the functional mechanisms of TNFAIP8 family in other marine invertebrate is provided.

miR-92a regulates coelomocytes apoptosis in sea cucumber Apostichopus japonicus via targeting Aj14-3-3ζ in vivo

miR-92a, a well-documented oncogene, was previously found to be differentially expressed in diseased sea cucumber Apostichopus japonicus by high-throughput sequencing. In this study, we identified Aj14-3-3ζ as a novel target of miR-92a in this species and investigated their regulatory roles in vivo. The negative expression profiles between miR-92a and Aj14-3-3ζ protein were detected in both LPS-exposed primary coelomocytes and Vibrio splendidus-challenged sea cucumbers. Over-expression of miR-92a by injection of miR-92a agomir significantly depressed the mRNA and protein expression of Aj14-3-3ζ and promoted coelomocytes apoptosis with 5.04-fold increase in vivo, which was consistent with those from siRNA-mediated Aj14-3-3ζ knockdown assay. In contrast, miR-92a antagomir significantly elevated the mRNA and protein expression of Aj14-3-3ζ and decreased coelomocytes apoptosis. Taken together, our result confirmed that miR-92a is involved in apoptotic signaling pathway regulation perhaps via targeting Aj14-3-3ζ in sea cucumbers, which will enhance our understanding of miR-92a regulatory roles in sea cucumber pathogenesis.

Microsomal glutathione transferase 1 attenuated ROS-induced lipid peroxidation in Apostichopus japonicus

Microsomal glutathione transferase (mGST) is a membrane bound glutathione transferase in multifunctional detoxification isoenzymes family and also plays crucial roles in innate immunity. In the present study, a novel microsomal GST homology was identified from Apostichopus japonicus (designated as AjmGST1) by RACE approaches. The full-length cDNA of AjmGST1 was of 1296 bp encoded a protein of 169 amino acids residues. Multiple sequence alignment and phylogenetic analysis together supported that AjmGST1 belonged to a new member in invertebrates mGST family. Spatial expression analysis revealed that AjmGST1was ubiquitously expressed in all examined tissues with the larger magnitude in tentacle. Time-course expression of AjmGST1 mRNA in coelomocytes was up-regulated after Vibrio splendidus challenge from 6 h until 72 h with the peak expression in 24 h, compared with that in the control group. Similarly, the induced expression of AjmGST1 expression was also detected in lipopolysaccharide (LPS) exposed primary coelomocytes. The purified recombinant protein of AjmGST1 showed high activity with GST substrate at pH of 7.0 and temperature of 35 °C. Meantime, the recombinant AjmGST1 depressed H₂O₂-induced MDA production both in vivo and in vitro. All of these results indicated that AjmGST1 was an important regulator in elimination of lipid peroxidation under immune response.

Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth

The sea cucumber (Apostichopus japonicus) is an economically important aquaculture species in China. However, the serious individual growth variation often caused financial losses to farmers and the genetic mechanisms are poorly understood. In the present study, the extensively analysis at the transcriptome level for individual growth variation in sea cucumber was carried out. A total of 118946 unigenes were assembled from 255861 transcripts, with N50 of 1700. Of all unigenes, about 23% were identified with at least one significant match to known databases. In all four pair of comparison, 1840 genes were found to be expressed differently. Global hypometabolism was found to be occurred in the slow growing population, based on which the hypothesis was raised that growth retardation in individual growth variation of sea cucumber is one type of dormancy which is used to be against to adverse circumstances. Besides, the pathways such as ECM-receptor interaction and focal adhesion were enriched in the maintenance of cell and tissue structure and communication. Further, 76645 SSRs, 765242 SNPs and 146886 ins-dels were detected in the current study providing an extensive set of data for future studies of genetic mapping and selective breeding. In summary, these results will provides deep insight into the molecular basis of individual growth variation in marine invertebrates, and be valuable for understanding the physiological differences of growth process.

Molecular cloning and functional characterization of theta class glutathione S-transferase from Apostichopus japonicus

Glutathione S-transferases (GSTs) are the superfamily of multifunctional detoxification isoenzymes and play crucial roles in innate immunity. In the present study, a theta class GST homology was identified from A. japonicus (designated as AjGST-θ) by RACE approaches. The full-length cDNA of AjGST-θ was of 1013 bp encoded a cytosolic protein of 231 amino acids residues. Structural analysis revealed that AjGST-θ processed the characteristic N-terminal GSH-binding site (G-site) and the C-terminal hydrophobic substrate binding site (H-site). Multiple sequence alignment and phylogenetic analysis together supported that AjGST-θ belonged to a new member of theta class GST protein subfamily. Spatial expression analysis revealed that AjGST-θ was ubiquitously expressed in all examined tissues with the larger magnitude in intestine. The Vibrio splendidus challenge in vivo and LPS stimulation in vitro could both significantly up-regulate the mRNA expression of AjGST-θ when compared with control group. The recombinant protein was expressed in Escherichia coli and the purified AjGST-θ showed high activity with GST substrate. Meantime, disc diffusion assay showed that recombinant AjGST-θ protein could markedly improve bacterial growth under Cumene hydroperoxide exposure. More importantly, the recombinant AjGST-θ could effectively prevent primary coelomocytes apoptosis after LPS exposure. Our present findings suggested that AjGST-θ might play significantly roles in the modulation of immune response and protect cells from pathogens infection in A. japonicus.

miR-31 Links Lipid Metabolism and Cell Apoptosis in Bacteria-Challenged Apostichopus japonicus via Targeting CTRP9

The biological functions of microRNAs (miRNAs) have been studied in a number of eukaryotic species. Recent studies on vertebrate animals have demonstrated critical roles of miRNA in immune and metabolic activities. However, studies on the functions of miRNA in invertebrates are very limited. Here, we demonstrated that miR-31 from Apostichopus japonicus disrupts the balance of lipid metabolism, thus resulting in cell apoptosis by targeting complement C1q tumor necrosis factor-related protein 9 (AjCTRP9), a novel adipokine with pleiotropic functions in immunity and metabolism. Lipidomic analysis suggested that the intercellular lipid metabolites were markedly altered, and three ceramide (Cer) species synchronously increased in the AjCTRP9-silenced coelomocytes. Moreover, exogenous Cer exposure significantly induced apoptosis in the coelomocytes in vivo, in agreement with findings from miR-31 mimic- or AjCTRP9 small-interfering RNA-transfected coelomocytes. Furthermore, we found that the imbalance in sphingolipid metabolism triggered by the overproduction of Cers ultimately resulted in the activation of the apoptosis initiator caspase-8 and executioner caspase-3. Our findings provide the first direct evidence that miR-31 negatively modulates the expression of AjCTRP9 and disturbance of Cer channels, thus leading to caspase-3- and caspase-8-dependent apoptosis, during the interactions between pathogens and host.

Transcriptome sequencing combined with bioinformatics predicts potential genes and pathways associated with bupivacaine-induced apoptosis

This study aimed to explore the potential genes and pathways associated with bupivacaine-induced apoptosis. Human neuroblastoma cell line SH-SY5Y was used in this study. The effect of bupivacaine on cell viability of SH-SY5Y was detected by Cell Counting Kit-8. Transcriptome sequencing was performed for SH-SY5Y cells that were treated and untreated with bupivacaine based on the HiSeq 4000 sequencing platform. The sequencing results were analyzed using bioinformatics methods, including differentially expressed genes (DEGs) identification, functional enrichment analysis, protein-protein interaction (PPI) network analysis and module analysis. The cell viability of SH-SY5Y cells decreased significantly after bupivacaine treatment (p < .01). Based on the HiSeq 4000 sequencing platform, we obtained a global overview of the transcriptome of SH-SY5Y treated with/without bupivacaine. Bioinformatics analysis identified 335 up-regulated and 294 down-regulated DEGs in bupivacaine group. They were significantly enriched in cell cycle-associated functions and pathways and cAMP signaling pathway. In the PPI network, proliferating cell nuclear antigen (PCNA), v-Akt murine thymoma viral oncogene homolog 3 (AKT3), cyclin-dependent kinase inhibitor 1A (CDKN1A) and cell division cycle 6 (CDC6) had high topology scores. Module analysis obtained two sub-network modules (cluster 1 and cluster 2). PCNA, CDC6, CDKN1A and AKT3 may play important roles in bupivacaine-induced apoptosis. Additionally, bupivacaine may also induce apoptosis via pathways of cell cycle and cAMP signaling pathway.

miR-137 modulates coelomocyte apoptosis by targeting 14-3-3ζ in the sea cucumber Apostichopus japonicus

MicroRNAs (miRNAs) have emerged as key regulators in the host immune response and play a pivotal role in host-pathogen interactions by suppressing the transcriptional and post-transcriptional expression of target genes. miR-137, a well-documented tumor repressor, was previously found by high-throughput sequencing to be differentially expressed in diseased specimens of the sea cucumber Apostichopus japonicus. In this study, we identified 14-3-3ζ protein (Aj14-3-3ζ) as a novel target of miR-137 using isobaric tags for relative and absolute quantification (iTRAQ) and transcriptome screening. Expression analysis indicated that consistently depressed expression profiles of miR-137 and Aj14-3-3ζ were detected in both LPS-exposed primary coelomocytes and Vibrio splendidus-challenged sea cucumbers, suggesting a positive regulatory interaction. Consistently, miR-137 overexpression or inhibition in vitro and in vivo showed no effect on Aj14-3-3ζ mRNA levels, but the concentration of Aj14-3-3ζ protein was induced or repressed, respectively. Moreover, siRNA-mediated Aj14-3-3ζ knockdown in vivo decreased both mRNA and protein expression levels of Aj14-3-3ζ and significantly promoted coelomocyte apoptosis as assessed by flow cytometry, consistent with miR-137 inhibition. Overall, these results enhance our understanding of miR-137 regulatory roles in sea cucumber pathogenesis.

Molecular cloning and functional characterization of cathepsin B from the sea cucumber Apostichopus japonicus

Cathepsin B (CTSB), a member of lysosomal cysteine protease, is involved in multiple levels of physiological and biological processes, and also plays crucial roles in host immune defense against pathogen infection in vertebrates. However, the function of CTSB within the innate immune system of invertebrates, particularly in marine echinoderms, has been poorly documented. In this study, the immune function of CTSB in Apostichopus japonicus (designated as AjCTSB), a commercially important and disease vulnerable aquaculture specie, was investigated by integrated molecular and protein approaches. A 2153 bp cDNA representing the full-length of AjCTSB was cloned via overlapping ESTs and RACE fragments. AjCTSB contained an open reading frame of 999 bp encoding a secreted protein of 332 amino acid residues with a predicted molecular mass of 36.8 kDa. The deduced amino acid of AjCTSB shared a typical activity center containing three conserved amino acid residues (Cys¹⁰⁸, His²⁷⁷ and Asn²⁹⁷). Phylogenetic tree analysis also supported that AjCTSB was a new member of CTSB family with clustering firstly with invertebrate CTSBs. Quantitative real time PCR analysis revealed that AjCTSB was ubiquitously expressed in all examined tissues with the highest levels in intestine. The Vibrio splendidus challenged sea cucumber and LPS-exposed coelomocytes could both significantly boost the expression of AjCTSB. Moreover, the purified recombinant AjCTSB exhibited dose-dependent CTSB activities at the concentration ranged from 0 to 0.24 μg μL^-1. Further functional analysis indicated that coelomocytes apoptosis was significantly inhibited by 0.16-fold in vivo and the apoptosis execution Ajcaspase 3 was extremely reduced in Apostichopus japonicus coelomocytes treated with specific AjCTSB siRNA. Collectively, all these results suggested that AjCTSB was an important immune factor and might be served as apoptosis enhancers in pathogen challenged sea cucumber.

miR210 modulates respiratory burst in Apostichopus japonicus coelomocytes via targeting Toll-like receptor

Immune responses of species in Echinodermata remains mysterious due to the lack of efforts made in the study of host defense mechanism in these species. More researches start focusing on this ancient immune system with the recognition the economic values of several species in this phylum, especially sea cucumbers. Here, we reported a study in the innate immunity of a sea cucumber species (Apostichopus japonicus) in response to infection of Vibrio splendidus. A novel differential expressed miRNA (miR-210) from the diseased sea cucumber coelomocytes was identified in our study. This miRNA molecule modulates Toll-like receptor gene (AjToll) expression via binding 3'UTR region from 906 nt to 930 nt. Upon the challenge of V. splendidus, coelomocytes in A. japonicas demonstrated a upregulation of AjToll but a downregulation of miR-210. Transfection of miR-210 agomirs in coelomocytes significantly depressed the expression of AjToll in cells. As a result of AjToll expression inhibition by miR-210, the AjToll downstream molecules involved in reactive oxygen species (ROS) were also altered in vivo. This ROS pathway alternation was consistent with that caused by knockdown of AjToll through small inference RNA (siRNA). Taken together, the results of this study demonstrated a novel immune regulatory pathway via miRN-210 in A. japonica, which provides basic knowledge in exploring innate immunity of Echinodermata, and also can be reference in disease control in sea cucumber culture industry.

RNA-seq analysis revealed ROS-mediated related genes involved in cadmium detoxification in the razor clam Sinonovacula constricta

The razor clam Sinonovacula constricta is a eukaryotic benthic intertidal bivalve species that is tolerant to different heavy metals, such as cadmium ion (Cd(2+)). However, the mechanism by which S. constricta responds to Cd(2+)-induced stress remains unclear. In this study, eight transcriptome libraries were constructed and sequenced using razor clams exposed to Cd(2+) for 12 and 48 h. A total of 18,330 unigenes with an average length of 500 bp were annotated. Among these 18,330 unigenes, 582 and 649 displayed differential expression profiles at 12 and 48 h in the gill, respectively. The corresponding differential unigenes in the hepatopancreas were 1056 and 382. Gene Ontology annotation revealed that these unigenes were highly pronounced in metabolic process, cellular process, binding, and catalytic activity. Notably, ROS production-related genes, such as heat shock proteins 32, metallothionein, and glutathione, were synchronously enriched in all experimental samples with induced expression profiles, which was also validated by qPCR. Our results highlighted the relation between immune regulation and Cd(2+)-induced stress in razor clam and provided new insights into the molecular mechanisms of heavy toxicology.

Long Non-Coding RNAs (lncRNAs) of Sea Cucumber: Large-Scale Prediction, Expression Profiling, Non-Coding Network Construction, and lncRNA-microRNA-Gene Interaction Analysis of lncRNAs in Apostichopus japonicus and Holothuria glaberrima During LPS Challenge and Radial Organ Complex Regeneration

Long non-coding RNA (lncRNA) structurally resembles mRNA but cannot be translated into protein. Although the systematic identification and characterization of lncRNAs have been increasingly reported in model species, information concerning non-model species is still lacking. Here, we report the first systematic identification and characterization of lncRNAs in two sea cucumber species: (1) Apostichopus japonicus during lipopolysaccharide (LPS) challenge and in heathy tissues and (2) Holothuria glaberrima during radial organ complex regeneration, using RNA-seq datasets and bioinformatics analysis. We identified A. japonicus and H. glaberrima lncRNAs that were differentially expressed during LPS challenge and radial organ complex regeneration, respectively. Notably, the predicted lncRNA-microRNA-gene trinities revealed that, in addition to targeting protein-coding transcripts, miRNAs might also target lncRNAs, thereby participating in a potential novel layer of regulatory interactions among non-coding RNA classes in echinoderms. Furthermore, the constructed coding-non-coding network implied the potential involvement of lncRNA-gene interactions during the regulation of several important genes (e.g., Toll-like receptor 1 [TLR1] and transglutaminase-1 [TGM1]) in response to LPS challenge and radial organ complex regeneration in sea cucumbers. Overall, this pioneer systematic identification, annotation, and characterization of lncRNAs in echinoderm pave the way for similar studies and future genetic, genomic, and evolutionary research in non-model species.

Molecular cloning and characterization of four caspases members in Apostichopus japonicus

The caspase family representing aspartate-specific cysteine proteases have been demonstrated to possess key roles in apoptosis and immune response. We previously demonstrated that LPS challenged Apostichopus japonicus coelomocyte could significantly induced apoptosis in vitro. However, apoptosis related molecules were scarcely investigated in this economic species. In the present work, we cloned and characterized four members caspase family from A. japonicus (designated as Ajcaspase-2, Ajcaspase-3, Ajcaspase-6, and Ajcaspase-8, respectively) by RACE. Multiple sequence alignment and structural analysis revealed that all Ajcaspases contained the conservative CASC domain at C terminal, in which some unique features for each Ajcaspase made them different from each other. These specific domains together with phylogenetic analysis supported that all these four identified proteins belonged to novel members of apoptotic signaling pathway in sea cucumber. Tissue distribution analysis revealed that four Ajcaspase genes were constitutively expressed in all examined tissues. The expression of Ajcaspase-2 was tightly correlated with that of Ajcaspase-8 in each detected tissues. Ajcaspase-3 and Ajcaspase-6 transcripts were both highly expressed in immune tissue of coelomocytes. Furthermore, the Vibrio splendidus challenged sea cucumber coelomocytes could significantly up-regulate the mRNA expressions of four genes. The expression levels of Ajcaspase-2 and Ajcaspase-8 were relative earlier than those of Ajcaspase-6 and Ajcaspase-3, respectively, which could be inferred that Ajcapase-2 might directly modulate Ajcaspase-6, and Ajcaspase-8 initiate the expression of Ajcaspase-3. The induce expressions differed among each Ajcaspase depending upon their roles such as initiator or effector caspase. All our results demonstrated that four Ajcaspases present diversified functions in apoptotic cascade signaling pathway of sea cucumber under immune response.

NF-κB/Rel, not STAT5, regulates nitric oxide synthase transcription in Apostichopus japonicus

Nitric oxide (NO) is an important signaling molecular in the immune system of all vertebrates and invertebrates for pathologic and physiologic process, and it is largely produced by inducible nitric oxide synthase (iNOS). To uncover key mechanisms regulating NOS expression in sea cucumber Apostichopus japonicus, we amplified a fragment of the NOS promoter by genome walking approach and characterized putative transcription factor binding motifs using luciferase assay. Transient transfection of EPC cells using 5'-deletion constructs linked to luciferase reporter revealed that the region -614/+39 contributed importantly to expression of the AjNOS gene, and the -614 bp of the 5'-flanking region of the AjNOS gene responded well to LPS. Analysis of the functional promoter region revealed the presence of two potential NF-κB (-375 bp to -366 bp, -76 bp to -67 bp) and three STAT binding sites (-284 bp to -276 bp, -95 bp to 87 bp, -81 bp to -73 bp). When luciferase reporter vector and expression vector co-transfected revealed that NF-κB/Rel, but not STAT5, activate the AjNOS promoter fragment. Furthermore, two truncated reporter vectors co-transfected with vector expressing NF-κB/Rel revealed that the first NF-κB binding site (-375 bp to -366 bp) was essential for the ability of this promoter to induce AjNOS transcription. In addition, blocking the AjRel by SN50 (NF-κB inhibitory peptide) depressed the AjNOS expression and NO production both in vivo and in vitro, respectively, revealing that AjRel might directly modulate AjNOS. All our findings confirmed that NF-κB dependent mechanisms regulating expression of AjNOS and suggested a means of linking NO production to the immune response.

RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus

Background

Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression.

Results

RNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson’s correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches.

Conclusions

Dynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important in clarifying the molecular mechanisms associated with the development of SUS in sea cucumber.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2810-3) contains supplementary material, which is available to authorized users.

The first description of complete invertebrate arginine metabolism pathways implies dose-dependent pathogen regulation in Apostichopus japonicus

In this study, three typical members representative of different arginine metabolic pathways were firstly identified from Apostichopus japonicus, including nitric oxide synthase (NOS), arginase, and agmatinase. Spatial expression analysis revealed that the AjNOS transcript presented negative expression patterns relative to those of Ajarginase or Ajagmatinase in most detected tissues. Furthermore, Vibrio splendidus-challenged coelomocytes and intestine, and LPS-exposed primary coelomocytes could significantly induce AjNOS expression, followed by obviously inhibited Arginase and AjAgmatinase transcripts at the most detected time points. Silencing the three members with two specific siRNAs in vivo and in vitro collectively indicated that AjNOS not only compete with Ajarginase but also with Ajagmatinase in arginine metabolism. Interestingly, Ajarginase and Ajagmatinase displayed cooperative expression profiles in arginine utilization. More importantly, live pathogens of V. splendidus and Vibrio parahaemolyticus co-incubated with primary cells also induced NO production and suppressed arginase activity in a time-dependent at an appropriate multiplicity of infection (MOI) of 10, without non-pathogen Escherichia coli. When increasing the pathogen dose (MOI = 100), arginase activity was significantly elevated, and NO production was depressed, with a larger magnitude in V. splendidus co-incubation. The present study expands our understanding of the connection between arginine's metabolic and immune responses in non-model invertebrates.

Identification and characterization of miR-31 potential targets by RNA-seq

In our previous work, miR-31 displayed differential significant expression in Apostichopus japonicus sea cucumber with skin ulcer syndrome and modulated coelomocytes ROS production by targeting p105. To identify other promising targets ofmiR-31, 4 transcriptome libraries of coelomocytes, as well as 2 control libraries, were constructed frommiR-31 mimics (31 M) or AMO-miR-31 (31I) and injected into a sea cucumber at 12 and 24 h. A total of207,977 unigenes with an average length of 363 bp were assembled, in which17,204 distinct sequences (8.27% of the unigenes) were successfully matched with annotated protein sequences. Fragments per kilobase of transcript per million fragments mapped analysis indicated that 1325 unigenes displayed up-regulated expression profiles in the 31I-12 group and were depressed in the 31M - 12 group compared with the control group. A total of 1470 unigenes showed down-regulated expressions in 31I-12 and were induced in 31 M-12. Similarly, 2079 and 2098 unigenes were detected at 24 h post-injection. Among these unigenes, 36 unigenes (depressed expression in the 31 M group and induced in the 31I group) showed consistent expression patterns at 2 examined time points and were considered promising targets of miR-31. qPCR analysis confirmed that all 4 unigenes showed opposite expression profiles to miR-31 in cultured coelomocytes. Our present work provided a fast and feasible method of identifying miR-31 targets by transcriptome analysis. The results of this study would enhance our present understanding ofmiR-31 function insea cucumber immune regulation.

Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus

Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber.

High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response

Increasing evidence suggests that microRNAs post-transcriptionally regulate gene expression and are involved in responses to biotic and abiotic stress. However, the role of miRNAs involved in osmotic plasticity remains largely unknown in marine bivalves. In the present study, we performed low salinity challenge with two Crassostrea species (C. gigas and C. hongkongensis), and conducted high-throughput sequencing of four small RNA libraries constructed from the gill tissues. A total of 202 and 87 miRNAs were identified from C. gigas and C. hongkongensis, respectively. Six miRNAs in C. gigas and two in C. hongkongensis were differentially expressed in response to osmotic stress. The expression profiles of these eight miRNAs were validated by qRT-PCR. Based on GO enrichment and KEGG pathway analysis, genes associated with microtubule-based process and cellular component movement were enriched in both species. In addition, five miRNA-mRNA interaction pairs that showed opposite expression patterns were identified in the C. hongkongensis, Differential expression analysis identified the miRNAs that play important regulatory roles in response to low salinity stress, providing insights into molecular mechanisms that are essential for salinity tolerance in marine bivalves.

The Roles of Two miRNAs in Regulating the Immune Response of Sea Cucumber

MicroRNAs (miRNAs) have emerged as key regulators in many pathological processes by suppressing the transcriptional and post-transcriptional expression of target genes. MiR-2008 was previously found to be significantly up-regulated in diseased sea cucumber Apostichopus japonicus by high-through sequencing, whereas the reads of miR-137, a well-documented tumor repressor, displayed no significant change. In the present study, we found that miR-137 expression was slightly attenuated and miR-2008 was significantly enhanced after Vibrio splendidus infection or Lipopolysaccharides application. Further target screening and dual-luciferase reporter assay revealed that the two important miRNAs shared a common target gene of betaine-homocysteine S-methyltransferase (AjBHMT), which exhibited noncorrelated messenger RNA and protein expression patterns after bacterial challenge. In order to fully understand their regulatory mechanisms, we conducted the functional experiments in vitro and in vivo. The overexpression of miR-137 in sea cucumber or primary coelomocytes significantly decreased, whereas the inhibition of miR-137 increased the mRNA and protein expression levels of AjBHMT. In contrast, miR-2008 overexpression and inhibition showed no effect on AjBHMT mRNA levels, but the concentration of AjBHMT protein displayed significant changes both in vitro and in vivo. Consistently, the homocysteine (Hcy) contents were also accordingly altered in the aberrant expression analysis of both miRNAs, consistent with the results of the AjBHMT silencing assay in vitro and in vivo. More importantly, small interfering RNA mediated AjBHMT knockdown and Hcy exposure analyses both significantly increased reactive oxygen species (ROS) production and decreased the number of surviving invasive pathogen in sea cucumber coelomocytes. Taken together, these findings confirmed the differential roles of sea cucumber miR-137 and miR-2008 in regulating the common target AjBHMT to promote ROS production and the clearance of pathogenic microorganisms through Hcy accumulation.

Cloning and characterization of two lipopolysaccharide-binding protein/bactericidal permeability-increasing protein (LBP/BPI) genes from the sea cucumber Apostichopus japonicus with diversified function in modulating ROS production

Lipopolysaccharide-binding protein and bactericidal permeability-increasing protein (LBP/BPI) play crucial role in modulating cellular signals in response to Gram-negative bacteria infection. In the present study, two isoforms of LBP/BPI genes (designated as AjLBP/BPI1 and AjLBP/BPI2, respectively) were cloned from the sea cucumber Apostichopus japonicus by RACE approach. The full-length cDNAs of AjLBP/BPI1 and AjLBP/BPI2 were of 1479 and 1455 bp and encoded two secreted proteins of 492 and 484 amino acid residues, respectively. Signal peptide, two BPI/LBP/CETP and one central domain were totally conserved in the deduced amino acid of AjLBP/BPI1 and AjLBP/BPI2. Phylogentic analysis further supported that AjLBP/BPI1 and AjLBP/BPI2 belonged to new members of invertebrates LBP/BPI family. Spatial expression analysis revealed that both AjLBP/BPI1 and AjLBP/BPI2 were ubiquitously expressed in all examined tissues with the larger magnitude in AjLBP/BPI1. The Vibrio splenfidus challenge and LPS stimulation could significantly up-regulate the mRNA expression of both AjLBP/BPI1 and AjLBP/BPI2, with the increase of AjLBP/BPI2 expression occurred earlier than that of AjLBP/BPI1. More importantly, we found that LPS induced ROS production was markedly depressed after AjLBP/BPI1 knock-down, but there was no significant change by AjLBP/BPI2 silencing. Consistently, the expression level of unclassified AjToll, not AjTLR3, was tightly correlated with that of AjLBP/BPI1. Silencing the AjToll also depressed the ROS production in the cultured coelomocytes. All these results indicated that AjLBP/BPI1 and AjLBP/BPI2 probably played distinct roles in bacterial mediating immune response in sea cucumber, and AjLBP/BPI1 depressed coelomocytes ROS production via modulating AjToll cascade.

MiR-31 modulates coelomocytes ROS production via targeting p105 in Vibrio splendidus challenged sea cucumber Apostichopus japonicus in vitro and in vivo

MiR-31 is a critical regulator of gene expression in many pathogenic processes in vertebrates. In this study, we identified p105 as a novel target of miR-31 in Apostichopus japonicus and investigated their regulatory roles in vitro and in vivo. The negative expression profiles between miR-31 and Ajp105 were detected in both LPS-exposed primary coelomocytes and Vibrio splendidus-challenged sea cucumber. Co-infection miR-31 mimics significantly depressed the expression of Ajp105 and increased ROS production in vitro. In contrast, miR-31 inhibitor significantly elevated the expression of Ajp105 and decreased ROS level. Consistently, miR-31 over-expression or Ajp105 silencing in vivo both greatly promoted ROS accumulation. Taken together, our findings confirmed that miR-31 could modulate respiratory burst via targeting Ajp105 during sea cucumber pathological development.

miRNA-133 augments coelomocyte phagocytosis in bacteria-challenged Apostichopus japonicus via targeting the TLR component of IRAK-1 in vitro and in vivo

In this study, we explored the potential roles of miRNA-133 in regulating TLR pathways in the sea cucumber Apostichopus japonicus. Target screening of RNA-Seq data successfully identified interleukin-1 receptor-associated kinase (AjIRAK−1) as a putative target of miR-133. This result was further validated by negative expression profiles in Vibrio splendidus-challenged coelomocytes and lipopolysaccharide (LPS)-exposed cell cultures. HEK-293T cells transfected with a dual-luciferase reporter fused to the 3′UTR of wild-type or mutant AjIRAK-1 exhibited a 52.9% reduction in luciferase activity (p < 0.01) compared to controls. Co-infection with a miR-133 mimics or a specific siRNA targeting AjIRAK-1 significantly repressed the mRNA and protein expression levels of AjIRAK-1 and its downstream molecules, such as AjTRAF6 and Ajp105, in primary coelomocytes. In contrast, a miR-133 inhibitor significantly increased the expression of these TLR pathway members. The injection of miR-133 agomir or AjIRAK-1 siRNA into sea cucumbers not only decreased the expression of AjIRAK-1 and its downstream molecules but also significantly increased V. splendidus coelomocyte phagocytosis. All of the present data provide direct evidence that miR-133 is involved in TLR cascade modulation through AjIRAK-1 targeting to promote V. splendidus coelomocyte phagocytosis in these non-model invertebrates.

Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus

Molecular chaperones of 78 kDa glucose-regulated protein (GRP78) and protein disulfide isomerase (PDI) are involved in protein folding and assembly in the endoplasmic reticulum (ER). Increasing evidences also suggest that these two molecules play an important role in immune response. In the present study, we cloned and characterized GRP78 and PDI genes from Apostichopus japonicus by RNA-seq and RACE approaches (designated as AjGRP78 and AjPDI, respectively). The AjGRP78 cDNA was of 2355bp including an open reading frame (ORF) of 2013 bp encoding a protein of 670 amino acids with three heat shock protein 70 (HSP70) family signatures. AjGRP78 contained a 23-amino acid signal peptide at the N-terminus and a HDEL motif at the C-terminus, which supported the location of the protein in the ER. The full length cDNA of AjPDI was of 1893 bp with a 5' untranslated region (UTR) of 153 bp, a 3' UTR of 228 bp and an ORF of 1512 bp encoding a protein of 503 amino acids. A 17-amino acid signal peptide, two thioredoxin domains with two active sites of CGHC, and KDEL retention signal were totally conserved in the deduced amino acid of AjPDI. Phylogenic analysis and multiple alignments have shown that both genes shared remarkably higher degree of structural conservation and sequence identities with other counterparts from invertebrates and vertebrates, further supporting that the two proteins were novel members of molecular chaperone family. Spatial expression analysis revealed that AjGRP78 mRNA transcripts were dominantly expressed in the tentacle, while AjPDI mRNA levels were abundant in the muscle, intestine and respiratory trees. For Vibrio splendidus challenged sea cucumber, the peak expression of AjGRP78 and AjPDI mRNAs in coelomocytes were detected at 24h with 1.73-fold increase and at 6h with 1.83-fold increase compared with the control group, respectively. Similarly, a significant increase in the relative mRNA levels of AjGRP78 and AjPDI was also identified in 1 μg mL(-1) LPS exposed primary cultured coelomocytes. These results collectively suggested that AjGRP78 and AjPDI were ER chaperones of A. japonicus, of which expression is induced upon bacterial infection.

Identification and characterization of a novel Foxo transcription factors in Apostichopus japonicus

The forkhead box O (Foxo) transcription factors are involved in multiple signaling pathways and play key roles in immunoregulation in vertebrates. In the present study, we firstly identified a novel Foxo gene in Apostichopus japonicus coelomocytes using transcriptome sequencing and RACE approaches (denoted as AjFoxo). The full-length cDNA of AjFoxo was of 2248 bp with a 5' untranslated region (UTR) of 177 bp, a 3' UTR of 367 bp and an ORF of 1704 bp encoding a polypeptide of 567 amino acid residues. The highly conserved forkhead domain was also identified in AjFoxo with remarkably higher degree of structural conservation. AjFoxo transcripts could be detected in all examined tissues with predominant expression in the coelomocytes and muscle, and slightly weak in the tissues of tentacle, intestine and respiratory trees. Concerning the time-course expression of AjFoxo in coelomocytes, the relative expression of AjFoxo was dramatically decreased to 0.44-fold at 48 h compared with that in the control group after Vibrio splendidus challenge, which was consistent with that of AjIκB. RNA interference of AjFoxo in primary coelomocytes also significantly depressed the relative expression of AjIκB with a 0.37-fold decrease compared with control group. Taken together, these results indicated that AjFoxo was a novel immune regulator and might be involved in the processes of anti-bacteria response in sea cucumber through activating the transcription of AjIκB.

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 assembly of the grass carp Ctenopharyngodon idella transcriptome to identify miRNA targets associated with motile aeromonad septicemia

Background

De novo transcriptome sequencing is a robust method of predicting miRNA target genes, especially for organisms without reference genomes. Differentially expressed miRNAs had been identified previously in kidney samples collected from susceptible and resistant grass carp (Ctenopharyngodon idella) affected by Aeromonas hydrophila. Target identification for these differentially expressed miRNAs poses a major challenge in this non-model organism.

Results

Two cDNA libraries constructed from mRNAs of susceptible and resistant C. idella were sequenced by Illumina Hiseq 2000 technology. A total of more than 100 million reads were generated and de novo assembled into 199,593 transcripts which were further extensively annotated by comparing their sequences to different protein databases. Biochemical pathways were predicted from these transcript sequences. A BLASTx analysis against a non-redundant protein database revealed that 61,373 unigenes coded for 28,311 annotated proteins. Two cDNA libraries from susceptible and resistant samples showed that 721 unigenes were expressed at significantly different levels; 475 were significantly up-regulated and 246 were significantly down-regulated in the SG samples compared to the RG samples. The computational prediction of miRNA targets from these differentially expressed genes identified 188 unigenes as the targets of 5 conserved and 4 putative novel miRNA families.

Conclusion

This study demonstrates the feasibility of identifying miRNA targets by transcriptome analysis. The transcriptome assembly data represent a substantial increase in the genomic resources available for C. idella and will provide insights into the gene expression profile analysis and the miRNA function annotations in further studies.

iTRAQ-based proteomics reveals novel members involved in pathogen challenge in sea cucumber Apostichopus japonicus

Skin ulceration syndrome (SUS) is considered to be a major constraint for the stable development of Apostichopus japonicus culture industries. In this study, we investigated protein changes in the coelomocytes of A. japonicus challenged by Vibrio splendidus using isobaric tags for relative and absolute quantification (iTRAQ) over a 96 h time course. Consequently, 228 differentially expressed proteins were identified in two iTRAQs. A comparison of the protein expression profiles among different time points detected 125 proteins primarily involved in response to endogenous stimuli at 24 h. At 48 h, the number of differentially expressed proteins decreased to 67, with their primary function being oxidation reduction. At the end of pathogen infection, proteins responsive to amino acid stimuli and some metabolic processes were classified as the predominant group. Fifteen proteins were differentially expressed at all time points, among which eight proteins related to pathologies in higher animals were shown to be down-regulated after V. splendidus infection: paxillin, fascin-2, aggrecan, ololfactomedin-1, nesprin-3, a disintegrin-like and metallopeptidase with thrombospondin type 1 motif (Adamts7), C-type lectin domain family 4 (Clec4g) and n-myc downstream regulated gene 1 (Ndrg1). To gain more insight into two SUS-related miRNA (miR-31 and miR-2008) targets at the protein level, all 129 down-regulated proteins were further analyzed in combination with RNA-seq. Twelve and eight proteins were identified as putative targets for miR-31 and miR-2008, respectively, in which six proteins (5 for miR-31 and 1 for miR-2008) displayed higher possibilities to be regulated at the level of translation. Overall, the present work enhances our understanding of the process of V. splendidus-challenged sea cucumber and provides a new method for screening miRNAs targets at the translation level.

Proteomic identification of differentially expressed proteins in sea cucumber Apostichopus japonicus coelomocytes after Vibrio splendidus infection

Skin ulceration syndrome (SUS) was the main limitation in the development of Apostichopus japonicus culture industries. To better understand how Vibrio splendidus modulates SUS outbreak, the immune response of A. japonicus coelomocytes after the pathogen challenge were investigated through comparative proteomics approach, and differentially expressed proteins were screened and characterized in the present study. A total of 40 protein spots representing 30 entries were identified at 24, 72 and 96 h post-infection. Of these proteins, 32 were up-regulated and 8 were down-regulated in the V. splendidus challenged samples compared to those of control. These differentially expressed proteins were mainly classified into four categories by GO analysis, in which approximate 33% of proteins showed to be related to immunity response. The mRNA expression levels of 6 differentially expressed proteins were further validated by qRT-PCR. Similar protein-mRNA-level expression patterns were detected in genes of phospholipase (spot 4), G protein (spot 20), annexin (spot 30) and filamin (spot 31). Whilst the levels of ficolin (spot 12) and calumenin (spot 14) transcripts were not corresponded with those of their translation products. These data provide a new insight to understand the molecular immune mechanism of sea cucumber responsive towards pathogen infection.